NCBI Conserved Domain Search

Conserved domains on [gi|890799132|ref|NP_001297531|]

View

tripartite motif-containing 5 [Mus musculus]

Protein Classification

Graphical summary

Zoom to residue level

show extra options »

Show site features Horizontal zoom: ×

List of domain hits

Name

Accession

Description

Interval

E-value

SPRY_PRY_TRIM5

cd15822

PRY/SPRY domain in tripartite motif-binding protein 5 (TRIM5), also known as RING finger ...

289-493

2.72e-122

PRY/SPRY domain in tripartite motif-binding protein 5 (TRIM5), also known as RING finger protein 88 (RNF88); This domain, consisting of the distinct N-terminal PRY subdomain followed by the SPRY subdomain, is found at the C-terminus of TRIM5 which is also known as RING finger protein 88 (RNF88) or TRIM5alpha (TRIM5a), an antiretroviral restriction factor and a retrovirus capsid sensor in immune signaling. TRIM5 domain is composed of RING/B-box/coiled-coil core and also known as RBCC protein. It blocks retrovirus infection soon after the virion core enters the cell cytoplasm by recognizing the capsid protein lattice that encases the viral genomic RNA; the SPRY domain provides the capsid recognition motif that dictates specificity to retroviral restriction. TRIM5a, an E3 ubiquitin ligase, promotes innate immune signaling by activating the TAK1 kinase complex by cooperating with the heterodimeric E2, UBC13/UEV1A. It also stimulates NFkB and AP-1 signaling, and the transcription of inflammatory cytokines and chemokines, and amplifies these activities upon retroviral infection. Interaction of its PRY-SPRY or cyclophilin domains with the retroviral capsid lattice stimulates the formation of a complementary lattice by TRIM5, with greatly increased TRIM5 E3 activity, and host cell signal transduction.

Pssm-ID: 293994 Cd Length: 200 Bit Score: 355.77 E-value: 2.72e-122

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 890799132 289 QEVTEAQRYWVQVTLVQNNHPNIAITDDKRQVRYEDHQASNLiHECENSHEGVLGHPAIQSGKHYWEVDVSGKGAWVLGL 368
Cdd:cd15822    2 NELTDVQRYWVHVTLDPSNNKNIVISEDRRQVRYVRKQQRYN-SNGNNEDYGVLGSPSITSGKHYWEVDVSKKRAWILGV 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 890799132 369 SDGSYLFCPIFHSNAERNRlfcrGIKNDSHYQPKYGFWVIGLWKKSVYNAFEECPFtGKPSVLTLSLMVPPCRVGVFLDY 448
Cdd:cd15822   81 CGGKYPNSTLKDFNKQGKN----NQKQCSNYQPKYGYWVIGLQNKSEYNAFEDSSS-SDPLILTLSLTVPPCRVGVFLDY 155

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*
gi 890799132 449 AAGTLSFYNISNNGTLIYRFCTASFPDRVFPYFNPTGSSEPMTIC 493
Cdd:cd15822  156 EAGTVSFFNVTNHGFLIYKFSSCSFSQEVFPYFNPMKCPVPMTLC 200

RING_Ubox super family

cl17238

RING finger (Really Interesting New Gene) domain and U-box domain superfamily; The RING finger ...

8-78

4.31e-29

RING finger (Really Interesting New Gene) domain and U-box domain superfamily; The RING finger is a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc. It is defined by the "cross-brace" motif that chelates zinc atoms by eight amino acid residues, typically Cys or His, arranged in a characteristic spacing. Canonical RING motifs have been categorized into two major subclasses, RING-HC (C3HC4-type) and RING-H2 (C3H2C3-type), according to their Cys/His content. There are also many variants of RING fingers: some have different Cys/His patterns while some lack a single Cys or His residue at typical Zn ligand positions (the fourth or eighth zinc ligand is prevalently exchanged for an Asp, which can indeed chelate Zn in a RING finger as well). C4C4-, C3HC3D-, C2H2C4-, and C3HC5-type RING fingers are closely related to RING-HC fingers. In contrast, C4HC3- (RING-CH alias RINGv), C3H3C2-, C3H2C2D-, C3DHC3-, and C4HC2H-type RING fingers are more closely related to RING-H2 fingers. However, not all RING finger-containing proteins display regular RING finger features, and the RING finger family has turned out to be multifarious. The degenerate RING fingers of the Siz/PIAS RING (SP-RING) family proteins and sporulation protein RMD5, are characterized by lacking the second, fifth, and sixth Zn2+ ion-coordinating residues. They bind only one Zn2+ ion. On the other hand, the RING fingers of the human APC11 and RBX1 proteins can bind a third Zn atom since they harbor four additional Zn ligands. U-box is a modified form of the RING finger domain that lacks metal chelating Cys and His residues. It resembles the cross-brace RING structure consisting of three beta-sheets and a single alpha-helix, which would be stabilized by salt bridges instead of chelated metal ions. U-box proteins are widely distributed among eukaryotic organisms and show a higher prevalence in plants than in other organisms. RING finger/U-box-containing proteins are a group of diverse proteins with a variety of cellular functions, including oncogenesis, development, viral replication, signal transduction, the cell cycle and apoptosis. Many of them are ubiquitin-protein ligases (E3s) that serve as scaffolds for binding to ubiquitin-conjugating enzymes (E2s, also referred to as ubiquitin carrier proteins or UBCs) in close proximity to substrate proteins, which enable efficient transfer of ubiquitin from E2 to the substrates.

The actual alignment was detected with superfamily member cd16591:

Pssm-ID: 473075 [Multi-domain] Cd Length: 72 Bit Score: 109.07 E-value: 4.31e-29

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 890799132   8 NLKEEVTCPVCLNLMVKPVSADCGHTFCQGCITLYFESIKCDKEMFSCPVCRLSYQSSNLRPNLHVANIVE 78
Cdd:cd16591    2 NIKEEVTCPICLELLTEPLSLDCGHSFCQACITANHKESVNQEGESSCPVCRTSYQPENLRPNRHLANIVE 72

Bbox2_TRIM5-like

cd19761

B-box-type 2 zinc finger found in tripartite motif-containing proteins, TRIM5, TRIM6, TRIM22, ...

96-133

2.78e-16

B-box-type 2 zinc finger found in tripartite motif-containing proteins, TRIM5, TRIM6, TRIM22, TRIM34, TRIM38 and similar proteins; The family includes TRIM5, TRIM6, TRIM22, TRIM34, and TRIM38, all of which belong to the C-IV subclass of the TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a RING finger, Bbox2, and a coiled coil region, as well as a B30.2/SPRY (SplA and ryanodine receptor) domain positioned C-terminal to the RBCC domain. The type 2 B-box (Bbox2) zinc finger is characterized by a CHC3H2 zinc-binding consensus motif. TRIM5, also termed RING finger protein 88 (RNF88), is a capsid-specific restriction factor that prevents infection from non-host-adapted retroviruses in a species-specific manner by binding to and destabilizing the retroviral capsid lattice before reverse transcription is completed. Its retroviral restriction activity correlates with the ability to activate TAK1-dependent innate immune signaling. TRIM5 also acts as a pattern recognition receptor that activates innate immune signaling in response to the retroviral capsid lattice. Moreover, TRIM5 plays a role in regulating autophagy through activation of autophagy regulator BECN1 by causing its dissociation from its inhibitors BCL2 and TAB2. It also plays a role in autophagy by acting as a selective autophagy receptor which recognizes and targets HIV-1 capsid protein p24 for autophagic destruction. TRIM6, also termed RING finger protein 89 (RNF89), is an E3-ubiquitin ligase that cooperates with the E2-ubiquitin conjugase UbE2K to catalyze the synthesis of unanchored K48-linked polyubiquitin chains, and further stimulates the interferon-I kappa B kinase epsilon (IKKepsilon) kinase-mediated antiviral response. It also regulates the transcriptional activity of Myc during the maintenance of embryonic stem (ES) cell pluripotency, and may act as a novel regulator for Myc-mediated transcription in ES cells. TRIM22, also termed 50 kDa-stimulated trans-acting factor (Staf-50), or RING finger protein 94 (RNF94), is an E3 ubiquitin-protein ligase that plays an integral role in the host innate immune response to viruses. It has been shown to inhibit the replication of a number of viruses, including HIV-1, hepatitis B, and influenza A. TRIM22 acts as a suppressor of basal HIV-1 long terminal repeat (LTR)-driven transcription by preventing transcription factor specificity protein 1 (Sp1) binding to the HIV-1 promoter. It also controls FoxO4 activity and cell survival by directing Toll-like receptor 3 (TLR3)-stimulated cells toward type I interferon (IFN) type I gene induction or apoptosis. Moreover, TRIM22 can activate the noncanonical nuclear factor-kappaB (NF-kappaB) pathway by activating I kappa B kinase alpha (IKKalpha). It also regulates nucleotide binding oligomerization domain containing 2 (NOD2)-dependent activation of interferon-beta signaling and nuclear factor-kappaB. TRIM34, also termed interferon-responsive finger protein 1, or RING finger protein 21 (RNF21), may function as an antiviral protein that contributes to the defense against retroviral infections. TRIM38, also known as RING finger protein 15 (RNF15) or zinc finger protein RoRet, is an E3 ubiquitin-protein ligase that promotes K63- and K48-linked ubiquitination of cellular proteins and also catalyzes self-ubiquitination. It negatively regulates tumor necrosis factor alpha (TNF-alpha) and interleukin-1beta-triggered nuclear factor-kappaB (NF-kappaB) activation by mediating lysosomal-dependent degradation of transforming growth factor beta (TGFbeta)-activated kinase 1 (TAK1)-binding protein (TAB)2/3, two critical components of the TAK1 kinase complex. It also inhibits TLR3/4-mediated activation of NF-kappaB and interferon regulatory factor 3 (IRF3) by mediating ubiquitin-proteasomal degradation of TNF receptor-associated factor 6 (Traf6) and NAK-associated protein 1 (Nap1), respectively. Moreover, TRIM38 negatively regulates TLR3-mediated interferon beta (IFN-beta) signaling by targeting ubiquitin-proteasomal degradation of TIR domain-containing adaptor inducing IFN-beta (TRIF). It functions as a valid target for autoantibodies in primary Sjogren's Syndrome.

Pssm-ID: 380819 [Multi-domain] Cd Length: 40 Bit Score: 72.53 E-value: 2.78e-16

                         10        20        30
                 ....*....|....*....|....*....|....*...
gi 890799132  96 CARHGEKLQLFCRKDMMAICWLCERSQEHRGHKTALIE 133
Cdd:cd19761    3 CEHHGEKLLLFCQEDGKVICWLCERSQEHRGHHTFLLE 40

SMC_N super family

cl47134

RecF/RecN/SMC N terminal domain; This domain is found at the N terminus of SMC proteins. The ...

117-239

2.84e-05

RecF/RecN/SMC N terminal domain; This domain is found at the N terminus of SMC proteins. The SMC (structural maintenance of chromosomes) superfamily proteins have ATP-binding domains at the N- and C-termini, and two extended coiled-coil domains separated by a hinge in the middle. The eukaryotic SMC proteins form two kind of heterodimers: the SMC1/SMC3 and the SMC2/SMC4 types. These heterodimers constitute an essential part of higher order complexes, which are involved in chromatin and DNA dynamics. This family also includes the RecF and RecN proteins that are involved in DNA metabolism and recombination.

The actual alignment was detected with superfamily member TIGR02169:

Pssm-ID: 481474 [Multi-domain] Cd Length: 1164 Bit Score: 46.98 E-value: 2.84e-05

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 890799132   117 LCERSQEHRGHKTALIEEVArEYKEQLQVVLQRLMADKKEFENWKDELQKDRTYWEnQIQKDVENVQSEFKRMRDiidse 196
Cdd:TIGR02169  341 LEREIEEERKRRDKLTEEYA-ELKEELEDLRAELEEVDKEFAETRDELKDYREKLE-KLKREINELKRELDRLQE----- 413

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|...
gi 890799132   197 eknELQKLRQEKEDILNNLAESESEHAQQSKLLEDFISDVEHQ 239
Cdd:TIGR02169  414 ---ELQRLSEELADLNAAIAGIEAKINELEEEKEDKALEIKKQ 453

Name

Accession

Description

Interval

E-value

SPRY_PRY_TRIM5

cd15822

PRY/SPRY domain in tripartite motif-binding protein 5 (TRIM5), also known as RING finger ...

289-493

2.72e-122

Pssm-ID: 293994 Cd Length: 200 Bit Score: 355.77 E-value: 2.72e-122

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 890799132 289 QEVTEAQRYWVQVTLVQNNHPNIAITDDKRQVRYEDHQASNLiHECENSHEGVLGHPAIQSGKHYWEVDVSGKGAWVLGL 368
Cdd:cd15822    2 NELTDVQRYWVHVTLDPSNNKNIVISEDRRQVRYVRKQQRYN-SNGNNEDYGVLGSPSITSGKHYWEVDVSKKRAWILGV 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 890799132 369 SDGSYLFCPIFHSNAERNRlfcrGIKNDSHYQPKYGFWVIGLWKKSVYNAFEECPFtGKPSVLTLSLMVPPCRVGVFLDY 448
Cdd:cd15822   81 CGGKYPNSTLKDFNKQGKN----NQKQCSNYQPKYGYWVIGLQNKSEYNAFEDSSS-SDPLILTLSLTVPPCRVGVFLDY 155

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*
gi 890799132 449 AAGTLSFYNISNNGTLIYRFCTASFPDRVFPYFNPTGSSEPMTIC 493
Cdd:cd15822  156 EAGTVSFFNVTNHGFLIYKFSSCSFSQEVFPYFNPMKCPVPMTLC 200

RING-HC_TRIM5-like_C-IV

cd16591

RING finger, HC subclass, found in tripartite motif-containing proteins TRIM5, TRIM6, TRIM22, ...

8-78

4.31e-29

RING finger, HC subclass, found in tripartite motif-containing proteins TRIM5, TRIM6, TRIM22, TRIM34 and similar proteins; TRIM5, TRIM6, TRIM22, and TRIM34, four closely related tripartite motif-containing proteins, belong to the C-IV subclass of the TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a C3HC4-type RING-HC finger, Bbox1 and Bbox2, and a coiled coil region, as well as a B30.2/SPRY (SplA and ryanodine receptor) domain positioned C-terminal to the RBCC domain. TRIM5, also known as RING finger protein 88 (RNF88), is a capsid-specific restriction factor that prevents infection from non-host-adapted retroviruses in a species-specific manner by binding to and destabilizing the retroviral capsid lattice before reverse transcription is completed. Its retroviral restriction activity correlates with the ability to activate TAK1-dependent innate immune signaling. TRIM5 also acts as a pattern recognition receptor that activates innate immune signaling in response to the retroviral capsid lattice. Moreover, TRIM5 plays a role in regulating autophagy through activation of autophagy regulator BECN1 by causing its dissociation from its inhibitors BCL2 and TAB2. It also plays a role in autophagy by acting as a selective autophagy receptor which recognizes and targets HIV-1 capsid protein p24 for autophagic destruction. TRIM6, also known as RING finger protein 89 (RNF89), is an E3-ubiquitin ligase that cooperates with the E2-ubiquitin conjugase UbE2K to catalyze the synthesis of unanchored K48-linked polyubiquitin chains, and further stimulates the interferon-I kappa B kinase epsilon (IKKepsilon) kinase-mediated antiviral response. It also regulates the transcriptional activity of Myc during the maintenance of embryonic stem (ES) cell pluripotency, and may act as a novel regulator for Myc-mediated transcription in ES cells. TRIM22, also known as 50 kDa-stimulated trans-acting factor (Staf-50) or RING finger protein 94 (RNF94), is an E3 ubiquitin-protein ligase that plays an integral role in the host innate immune response to viruses. It has been shown to inhibit the replication of a number of viruses, including HIV-1, hepatitis B, and influenza A. TRIM22 acts as a suppressor of basal HIV-1 long terminal repeat (LTR)-driven transcription by preventing the transcription factor specificity protein 1 (Sp1) binding to the HIV-1 promoter. It also controls FoxO4 activity and cell survival by directing Toll-like receptor 3 (TLR3)-stimulated cells toward type I interferon (IFN) type I gene induction or apoptosis. Moreover, TRIM22 can activate the noncanonical nuclear factor-kappaB (NF-kappaB) pathway by activating I kappa B kinase alpha (IKKalpha). It also regulates nucleotide binding oligomerization domain containing 2 (NOD2)-dependent activation of interferon-beta signaling and nuclear factor-kappaB. TRIM34, also known as interferon-responsive finger protein 1 or RING finger protein 21 (RNF21), may function as antiviral protein that contribute to the defense against retroviral infections.

Pssm-ID: 438253 [Multi-domain] Cd Length: 72 Bit Score: 109.07 E-value: 4.31e-29

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 890799132   8 NLKEEVTCPVCLNLMVKPVSADCGHTFCQGCITLYFESIKCDKEMFSCPVCRLSYQSSNLRPNLHVANIVE 78
Cdd:cd16591    2 NIKEEVTCPICLELLTEPLSLDCGHSFCQACITANHKESVNQEGESSCPVCRTSYQPENLRPNRHLANIVE 72

SPRY

smart00449

Domain in SPla and the RYanodine Receptor; Domain of unknown function. Distant homologues are ...

349-493

5.23e-22

Domain in SPla and the RYanodine Receptor; Domain of unknown function. Distant homologues are domains in butyrophilin/marenostrin/pyrin homologues.

Pssm-ID: 214669 Cd Length: 122 Bit Score: 91.20 E-value: 5.23e-22

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 890799132   349 SGKHYWEVDVSGKGAWVLGLSDGSYlfcpifhsnaerNRLFCRGIKNDShyqpkyGFWVIGLWKKSVYNAFEECPFtgkp 428
Cdd:smart00449   1 SGRHYFEVEIGDGGHWRVGVATKSV------------PRGYFALLGEDK------GSWGYDGDGGKKYHNSTGPEY---- 58

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 890799132   429 svlTLSLMVPPCRVGVFLDYAAGTLSFYnisNNGT--LIYRFCTASFPDRVFPYFNPTGS-SEPMTIC 493
Cdd:smart00449  59 ---GLPLQEPGDVIGCFLDLEAGTISFY---KNGKylHGLAFFDVKFSGPLYPAFSLGSGnSVRLNFG 120

SPRY

pfam00622

SPRY domain; SPRY Domain is named from SPla and the RYanodine Receptor and it is found in many ...

351-481

2.10e-19

SPRY domain; SPRY Domain is named from SPla and the RYanodine Receptor and it is found in many eukaryotic proteins with a wide range of functions. It is a protein-interaction module involved in many important signalling pathways like RNA processing, regulation of histone H3 methylation, innate immunity or embryonic development. It can be divided into 11 subfamilies based on amino acid sequence similarity or the presence of additional protein domains. The greater SPRY family is divided into the SPRY/B30.2 (which contains a PRY extension at the N-terminal) and SPRY-only sub-families which are preceded by a subdomain that is structurally similar to the PRY region. SPRY/B30.2 structures revealed a bent beta-sandwich fold comprised of two beta-sheets. Distant homologs are domains in butyrophilin/ marenostrin/pyrin.

Pssm-ID: 459877 Cd Length: 121 Bit Score: 83.93 E-value: 2.10e-19

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 890799132  351 KHYWEVDVSG--KGAWVLGLSdgsylfcpifhsnaernRLFCRGiKNDSHYQPKYGFWVIGLWKKSVYNAFEEcPFTGKP 428
Cdd:pfam00622   1 RHYFEVEIFGqdGGGWRVGWA-----------------TKSVPR-KGERFLGDESGSWGYDGWTGKKYWASTS-PLTGLP 61

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|...
gi 890799132  429 svltlsLMVPPCRVGVFLDYAAGTLSFYNisNNGTLIYRFCTASFPDRVFPYF 481
Cdd:pfam00622  62 ------LFEPGDVIGCFLDYEAGTISFTK--NGKSLGYAFRDVPFAGPLFPAV 106

Bbox2_TRIM5-like

cd19761

B-box-type 2 zinc finger found in tripartite motif-containing proteins, TRIM5, TRIM6, TRIM22, ...

96-133

2.78e-16

Pssm-ID: 380819 [Multi-domain] Cd Length: 40 Bit Score: 72.53 E-value: 2.78e-16

                         10        20        30
                 ....*....|....*....|....*....|....*...
gi 890799132  96 CARHGEKLQLFCRKDMMAICWLCERSQEHRGHKTALIE 133
Cdd:cd19761    3 CEHHGEKLLLFCQEDGKVICWLCERSQEHRGHHTFLLE 40

zf-C3HC4_4

pfam15227

zinc finger of C3HC4-type, RING; This is a family of primate-specific Ret finger protein-like ...

15-58

3.49e-10

zinc finger of C3HC4-type, RING; This is a family of primate-specific Ret finger protein-like (RFPL) zinc-fingers of the C3HC4 type. Ret finger protein-like proteins are primate-specific target genes of Pax6, a key transcription factor for pancreas, eye and neocortex development. This domain is likely to be DNA-binding. This zinc-finger domain together with the RDM domain, pfam11002, forms a large zinc-finger structure of the RING/U-Box superfamily. RING-containing proteins are known to exert an E3 ubiquitin protein ligase activity with the zinc-finger structure being mandatory for binding to the E2 ubiquitin-conjugating enzyme.

Pssm-ID: 464570 [Multi-domain] Cd Length: 42 Bit Score: 55.13 E-value: 3.49e-10

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 890799132   15 CPVCLNLMVKPVSADCGHTFCQGCITLYFEsiKCDKEMFSCPVC 58
Cdd:pfam15227   1 CPICLDYLEKPVSIECGHSFCLSCINSLQK--EPDGESLLCPQC 42

rad18

TIGR00599

DNA repair protein rad18; All proteins in this family for which functions are known are ...

6-86

1.97e-09

DNA repair protein rad18; All proteins in this family for which functions are known are involved in nucleotide excision repair.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]

Pssm-ID: 273165 [Multi-domain] Cd Length: 397 Bit Score: 59.63 E-value: 1.97e-09

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 890799132    6 MKNLKEEVTCPVCLNLMVKPVSADCGHTFCQGCITlyfesiKCDKEMFSCPVCRLSYQSSNLRPNLHVANIVERLKEFKP 85
Cdd:TIGR00599  20 LYPLDTSLRCHICKDFFDVPVLTSCSHTFCSLCIR------RCLSNQPKCPLCRAEDQESKLRSNWLVSEIVESFKNLRP 93


                  .
gi 890799132   86 S 86
Cdd:TIGR00599  94 S 94

BBOX

smart00336

B-Box-type zinc finger;

96-132

2.34e-08

B-Box-type zinc finger;

Pssm-ID: 197662 [Multi-domain] Cd Length: 42 Bit Score: 50.03 E-value: 2.34e-08

                           10        20        30
                   ....*....|....*....|....*....|....*...
gi 890799132    96 CARHG-EKLQLFCRKDMMAICWLCERSqEHRGHKTALI 132
Cdd:smart00336   6 CDSHGdEPAEFFCEECGALLCRTCDEA-EHRGHTVVLL 42

RAD18

COG5432

RING-finger-containing E3 ubiquitin ligase [Signal transduction mechanisms];

6-112

3.96e-08

RING-finger-containing E3 ubiquitin ligase [Signal transduction mechanisms];

Pssm-ID: 227719 [Multi-domain] Cd Length: 391 Bit Score: 55.48 E-value: 3.96e-08

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 890799132   6 MKNLKEEVTCPVCLNLMVKPVSADCGHTFCQGCITLYFesikcdKEMFSCPVCRLSYQSSNLRPNLHVANIVERLKEFKP 85
Cdd:COG5432   19 LKGLDSMLRCRICDCRISIPCETTCGHTFCSLCIRRHL------GTQPFCPVCREDPCESRLRGSSGSREINESHARNRD 92

                         90       100
                 ....*....|....*....|....*..
gi 890799132  86 SPEEEQKVFNCARHGEKLQLFCRKDMM 112
Cdd:COG5432   93 LLRKVLESLCRLPRPIKEERPCRWETV 119

RING

smart00184

Ring finger; E3 ubiquitin-protein ligase activity is intrinsic to the RING domain of c-Cbl and ...

15-58

1.01e-07

Ring finger; E3 ubiquitin-protein ligase activity is intrinsic to the RING domain of c-Cbl and is likely to be a general function of this domain; Various RING fingers exhibit binding activity towards E2 ubiquitin-conjugating enzymes (Ubc' s)

Pssm-ID: 214546 [Multi-domain] Cd Length: 40 Bit Score: 48.27 E-value: 1.01e-07

                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*
gi 890799132    15 CPVCLNLMVK-PVSADCGHTFCQGCITLYFESikcdkEMFSCPVC 58
Cdd:smart00184   1 CPICLEEYLKdPVILPCGHTFCRSCIRKWLES-----GNNTCPIC 40

SMC_prok_A

TIGR02169

chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of ...

117-239

2.84e-05

chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]

Pssm-ID: 274009 [Multi-domain] Cd Length: 1164 Bit Score: 46.98 E-value: 2.84e-05

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 890799132   117 LCERSQEHRGHKTALIEEVArEYKEQLQVVLQRLMADKKEFENWKDELQKDRTYWEnQIQKDVENVQSEFKRMRDiidse 196
Cdd:TIGR02169  341 LEREIEEERKRRDKLTEEYA-ELKEELEDLRAELEEVDKEFAETRDELKDYREKLE-KLKREINELKRELDRLQE----- 413

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|...
gi 890799132   197 eknELQKLRQEKEDILNNLAESESEHAQQSKLLEDFISDVEHQ 239
Cdd:TIGR02169  414 ---ELQRLSEELADLNAAIAGIEAKINELEEEKEDKALEIKKQ 453

PTZ00121

MAEBL; Provisional

79-246

1.40e-04

MAEBL; Provisional

Pssm-ID: 173412 [Multi-domain] Cd Length: 2084 Bit Score: 44.75 E-value: 1.40e-04

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 890799132   79 RLKEFKPSPEEEQKVFNCAR--HGEKlqlfcRKDMMAICWLCERSQEHRGHKTALIEEVAREYKEQLQVVLQRLMADKKE 156
Cdd:PTZ00121 1731 KAEEAKKEAEEDKKKAEEAKkdEEEK-----KKIAHLKKEEEKKAEEIRKEKEAVIEEELDEEDEKRRMEVDKKIKDIFD 1805

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 890799132  157 -FENWKDELQKDRTYwenqIQKDVENVQSEFKRMRDIIDS--EEKNELQKLRQEKEDILNNLAESESEHAQQSKLLEDFI 233
Cdd:PTZ00121 1806 nFANIIEGGKEGNLV----INDSKEMEDSAIKEVADSKNMqlEEADAFEKHKFNKNNENGEDGNKEADFNKEKDLKEDDE 1881

                         170
                  ....*....|....*...
gi 890799132  234 SDVEH-----QLQCSDIE 246
Cdd:PTZ00121 1882 EEIEEadeieKIDKDDIE 1899

zf-B_box

pfam00643

B-box zinc finger;

91-132

3.40e-04

B-box zinc finger;

Pssm-ID: 459886 [Multi-domain] Cd Length: 42 Bit Score: 38.22 E-value: 3.40e-04

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 890799132   91 QKVFNCARHG-EKLQLFCRKDMMAICWLCERSqEHRGHKTALI 132
Cdd:pfam00643   1 SKERLCPEHEeEPLTLYCNDCQELLCEECSVG-EHRGHTVVPL 42

COG1340

Uncharacterized coiled-coil protein, contains DUF342 domain [Function unknown];

119-228

1.29e-03

Uncharacterized coiled-coil protein, contains DUF342 domain [Function unknown];

Pssm-ID: 440951 [Multi-domain] Cd Length: 297 Bit Score: 40.66 E-value: 1.29e-03

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 890799132 119 ERSQEHRGHKTALIEEVaREYKEQLQVVLQRLMADKKEFENWKDELQKDRT--YWENQIQKDVEnvQSEFKRM------- 189
Cdd:COG1340   57 EEAQELREKRDELNEKV-KELKEERDELNEKLNELREELDELRKELAELNKagGSIDKLRKEIE--RLEWRQQtevlspe 133

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*.
gi 890799132 190 --RDIID-----SEEKNELQKLRQEKEDILNNLAESESEHAQQSKL 228
Cdd:COG1340  134 eeKELVEkikelEKELEKAKKALEKNEKLKELRAELKELRKEAEEI 179

OmpH

smart00935

Outer membrane protein (OmpH-like); This family includes outer membrane proteins such as OmpH ...

132-219

2.14e-03

Outer membrane protein (OmpH-like); This family includes outer membrane proteins such as OmpH among others. Skp (OmpH) has been characterized as a molecular chaperone that interacts with unfolded proteins as they emerge in the periplasm from the Sec translocation machinery.

Pssm-ID: 214922 [Multi-domain] Cd Length: 140 Bit Score: 38.33 E-value: 2.14e-03

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 890799132   132 IEEVAREYKEQLQVVLQRLMADKKEFENWKDEL-QKDRTYWENQIQKDVENVQSEFKRMRDIIDSEEKNELQKLRQEKED 210
Cdd:smart00935  23 LEKEFKKRQAELEKLEKELQKLKEKLQKDAATLsEAAREKKEKELQKKVQEFQRKQQKLQQDLQKRQQEELQKILDKINK 102


                   ....*....
gi 890799132   211 ILNNLAESE 219
Cdd:smart00935 103 AIKEVAKKK 111

ClyA_Cry6Aa-like

cd22656

Bacillus thuringiensis crystal 6Aa (Cry6Aa) toxin, and similar proteins; This model includes ...

138-260

3.65e-03

Bacillus thuringiensis crystal 6Aa (Cry6Aa) toxin, and similar proteins; This model includes pesticidal Cry6Aa toxin from Bacillus thuringiensis, one of the many parasporal crystal (Cry) toxins produced during the sporulation phase of growth. Many of these proteins are toxic to numerous insect species and have been effectively used as proteinaceous insecticides to directly kill insect pests; some have been used to control insect growth on transgenic agricultural plants. Cry6Aa exists as a protoxin, which is activated by cleavage using trypsin. Structure studies for Cry6Aa support a mechanism of action by pore formation, similar to cytolysin A (ClyA)-type alpha pore-forming toxins (alpha-PFTs) such as HblB, and bioassay and mutation studies show that Cry6Aa is an active pore-forming toxin. Cry6Aa shows atypical features compared to other members of alpha-PFTs, including internal repeat sequences and small loop regions within major alpha helices.

Pssm-ID: 439154 [Multi-domain] Cd Length: 309 Bit Score: 39.28 E-value: 3.65e-03

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 890799132 138 EYKEQLQVVLQRLMADKKEFENWKDELQKDRTYWENQIQKDVENVQSEFKRMRDIIDSE----EKNELQKLRQEKEDILN 213
Cdd:cd22656  114 EAKKTIKALLDDLLKEAKKYQDKAAKVVDKLTDFENQTEKDQTALETLEKALKDLLTDEggaiARKEIKDLQKELEKLNE 193

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*....
gi 890799132 214 NLAEsesehAQQSKL--LEDFISDVEHQLQcsDIEILQGVENIIKRSLT 260
Cdd:cd22656  194 EYAA-----KLKAKIdeLKALIADDEAKLA--AALRLIADLTAADTDLD 235

Name

Accession

Description

Interval

E-value

SPRY_PRY_TRIM5

cd15822

PRY/SPRY domain in tripartite motif-binding protein 5 (TRIM5), also known as RING finger ...

289-493

2.72e-122

Pssm-ID: 293994 Cd Length: 200 Bit Score: 355.77 E-value: 2.72e-122

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 890799132 289 QEVTEAQRYWVQVTLVQNNHPNIAITDDKRQVRYEDHQASNLiHECENSHEGVLGHPAIQSGKHYWEVDVSGKGAWVLGL 368
Cdd:cd15822    2 NELTDVQRYWVHVTLDPSNNKNIVISEDRRQVRYVRKQQRYN-SNGNNEDYGVLGSPSITSGKHYWEVDVSKKRAWILGV 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 890799132 369 SDGSYLFCPIFHSNAERNRlfcrGIKNDSHYQPKYGFWVIGLWKKSVYNAFEECPFtGKPSVLTLSLMVPPCRVGVFLDY 448
Cdd:cd15822   81 CGGKYPNSTLKDFNKQGKN----NQKQCSNYQPKYGYWVIGLQNKSEYNAFEDSSS-SDPLILTLSLTVPPCRVGVFLDY 155

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*
gi 890799132 449 AAGTLSFYNISNNGTLIYRFCTASFPDRVFPYFNPTGSSEPMTIC 493
Cdd:cd15822  156 EAGTVSFFNVTNHGFLIYKFSSCSFSQEVFPYFNPMKCPVPMTLC 200

SPRY_PRY_TRIM5_6_22_34

cd15810

PRY/SPRY domain of tripartite motif-binding protein 5, 6, 22 and 34 (TRIM5, TRIM6, TRIM22 and ...

301-493

1.75e-67

PRY/SPRY domain of tripartite motif-binding protein 5, 6, 22 and 34 (TRIM5, TRIM6, TRIM22 and TRIM34); This domain, consisting of the distinct N-terminal PRY subdomain followed by the SPRY subdomain, is found at the C-terminus of very close paralogs, TRIM5, TRIM6, TRIM22 and TRIM34. These domains are composed of RING/B-box/coiled-coil core and are also known as RBCC proteins. They form a locus of four closely related TRIM genes within an olfactory receptor-rich region on chromosome 11 of the human genome. Genetic analysis of this locus indicates that these four genes have evolved by gene duplication from a common ancestral gene. All genes in the TRIM6/TRIM34/TRIM5/TRIM22 locus are type I interferon inducible, with TRIM5 and TRIM22 possessing antiviral properties. TRIM5 promotes innate immune signaling by activating the TAK1 kinase complex by cooperating with the heterodimeric E2, UBC13/UEV1A. It also stimulates NFkB and AP-1 signaling, and the transcription of inflammatory cytokines and chemokines, amplifying these activities upon retroviral infection. Interaction of its PRY-SPRY or cyclophilin domains with the retroviral capsid lattice stimulates the formation of a complementary lattice by TRIM5, with greatly increased TRIM5 E3 activity, and host cell signal transduction. TRIM6 is selectively expressed in embryonic stem (ES) cells and interacts with the proto-oncogene product Myc, maintaining the pluripotency of the ES cells. TRIM6, together with E2 Ubiquitin conjugase (UbE2K) and K48-linked poly-Ub chains, is critical for the IkappaB kinase epsilon (IKKepsilon) branch of type I interferon (IFN-I) signaling pathway and subsequent establishment of a protective antiviral response. TRIM22 plays an integral role in the host innate immune response to viruses; it has been shown to inhibit the replication of a number of viruses, including HIV-1, hepatitis B, and influenza A. Altered TRIM22 expression has also been associated with multiple sclerosis, cancer, and autoimmune disease. While the PRY-SPRY domain of TRIM5a provides specificity and the capsid recognition motif to retroviral restriction, TRIM34 binds HIV-1 capsid but does not restrict HIV-1 infection.

Pssm-ID: 293982 [Multi-domain] Cd Length: 189 Bit Score: 215.04 E-value: 1.75e-67

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 890799132 301 VTLVQNN-HPNIAITDDKRQVRYEDHQASNLIHECENSHEGVLGHPAIQSGKHYWEVDVSGKGAWVLGLSDGSylfcpIF 379
Cdd:cd15810    2 VTLNPVNiSLNIVISEDQRQVRIVPPQTSGQALTNNNYDFGVLGSQYFSSGKHYWEVDVSKKSAWILGVCSHK-----RS 76

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 890799132 380 HSNAERNRLFCRGIKNDSHYQPKYGFWVIGLWKKSVYNAFEECPfTGKPSVLTLSLMVPPCRVGVFLDYAAGTLSFYNIS 459
Cdd:cd15810   77 DAMTKSNANQINHQNVYSRYQPQYGYWVIGLQNESEYNAFEDSS-SFNPHVLTLSVTVPPHRVGVFLDYEAGTVSFFNVT 155

                        170       180       190
                 ....*....|....*....|....*....|....
gi 890799132 460 NNGTLIYRFCTASFPDRVFPYFNPTGSSEPMTIC 493
Cdd:cd15810  156 NHGSLIYKFSKCCFSTTVCPYFNPWNCPVPMTLC 189

SPRY_PRY_TRIM22

cd15824

PRY/SPRY domain in tripartite motif-containing protein 22 (TRIM22), also known as RING finger ...

297-495

1.34e-61

PRY/SPRY domain in tripartite motif-containing protein 22 (TRIM22), also known as RING finger protein 94 (RNF94) or Stimulated trans-acting factor of 50 kDa (STAF50); This domain, consisting of the distinct N-terminal PRY subdomain followed by the SPRY subdomain, is found at the C-terminus of TRIM22, also known as RING finger protein 94 (RNF94) or STAF50 (Stimulated trans-acting factor of 50 kDa). TRIM6 domain is composed of RING/B-box/coiled-coil core and also known as RBCC protein. TRIM22 is an interferon-induced protein, predominantly expressed in peripheral blood leukocytes, in lymphoid tissue such as spleen and thymus, and in the ovary.TRIM22 plays an integral role in the host innate immune response to viruses; it has been shown to inhibit the replication of a number of viruses, including HIV-1, hepatitis B, and influenza A. TRIM22 inhibits influenza A virus (IAV) infection by targeting the viral nucleoprotein for degradation; it represents a novel restriction factor up-regulated upon IAV infection that curtails its replicative capacity in epithelial cells. Altered TRIM22 expression has also been associated with multiple sclerosis, cancer, and autoimmune disease. A large number of high-risk non-synonymous (ns)SNPs have been identified in the highly polymorphic TRIM22 gene, most of which are located in the SPRY domain and could possibly alter critical regions of the SPRY structural and functional residues, including several sites that undergo post-translational modification. TRIM22 is a direct p53 target gene and inhibits the clonogenic growth of leukemic cells. Its expression in Wilms tumors is negatively associated with disease relapse. It is greatly under-expressed in breast cancer cells as compared to non-malignant cell lines; p53 dysfunction may be one of the mechanisms for its down-regulation.

Pssm-ID: 293996 [Multi-domain] Cd Length: 198 Bit Score: 200.07 E-value: 1.34e-61

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 890799132 297 YWVQVTLVQNNHP-NIAITDDKRQVRYEDHQASNLIHECENSHEGVLGHPAIQSGKHYWEVDVSGKGAWVLGL------- 368
Cdd:cd15824    1 YWVDVMLNPVNAVsNVVVSADQRQVTVVHICMFRNSNPCDFSAFDVLGCQYFSSGKYYWEVDVSGKIAWILGVyskrnnl 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 890799132 369 -SDGSYLFcpIFHSNAERNRLFCRgikndshYQPKYGFWVIGLWKKSVYNAFEEcPFTGKPSVLTLSLMVPPCRVGVFLD 447
Cdd:cd15824   81 nKRKSSGF--AFDPNVNHPNVYSR-------YRPQNGYWVIGLQNESEYNAFED-SSSSDPKVLTLSMAVPPHRVGVFLD 150

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*...
gi 890799132 448 YAAGTLSFYNISNNGTLIYRFCTASFPDRVFPYFNPTGSSEPMTICWP 495
Cdd:cd15824  151 YEAGTVSFFNVTNHGSLIYKFSKCCFSQPVYPYFNPWNCPAPMTLCPP 198

SPRY_PRY_TRIM34

cd15825

PRY/SPRY domain in tripartite motif-containing protein 34 (TRIM34), also known as RING finger ...

298-493

2.14e-55

PRY/SPRY domain in tripartite motif-containing protein 34 (TRIM34), also known as RING finger protein 21 (RNF21) or interferon-responsive finger protein (IFP1); This domain, consisting of the distinct N-terminal PRY subdomain followed by the SPRY subdomain, is found at the C-terminus of TRIM34, also known as RING finger protein 21 (RNF21) or interferon-responsive finger protein (IFP1). TRIM34 domain is composed of RING/B-box/coiled-coil core and also known as RBCC protein. The TRIM21 cDNA possesses at least three kinds of isoforms, due to alternative splicing, of which only the long and medium forms contain the SPRY domain. It is an interferon-induced protein, predominantly expressed in the testis, kidney, and ovary. The SPRY domain provides the capsid recognition motif that dictates specificity to retroviral restriction. While the PRY-SPRY domain provides specificity and the capsid recognition motif to retroviral restriction, TRIM34 binds HIV-1 capsid but does not restrict HIV-1 infection.

Pssm-ID: 293997 Cd Length: 185 Bit Score: 183.50 E-value: 2.14e-55

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 890799132 298 WVQVTLVQNN-HPNIAITDDKRQVRyedhQASNLIHECENSheGVLGHPAIQSGKHYWEVDVSGKGAWVLGLsdgsylFC 376
Cdd:cd15825    1 WVDFTLNPVNlNLNLVLSEDQRQVT----SVPIWPFKCYNY--GILGSQYFSSGKHYWEVDVSKKTAWILGV------YC 68

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 890799132 377 PIFHSNAERNRLFCRGIKNDSHYQPKYGFWVIGLWKKSVYNAFEECPfTGKPSVLTLSLMVPPCRVGVFLDYAAGTLSFY 456
Cdd:cd15825   69 RKRSRTFKYVRQGKNHPNVYSRYRPQYGYWVIGLQNKSEYYAFEDSS-TSDPKVLTLSVATPPHRVGVFLDYEAGTVSFF 147

                        170       180       190
                 ....*....|....*....|....*....|....*..
gi 890799132 457 NISNNGTLIYRFCTASFPDRVFPYFNPTGSSEPMTIC 493
Cdd:cd15825  148 NVTNHGSLIYKFSKCCFSQPVYPYFNPWNCPAPMTLC 184

SPRY_PRY_C-I_1

cd13733

PRY/SPRY domain in tripartite motif-containing (TRIM) proteins, including TRIM5, TRIM6, TRIM7, ...

301-493

7.03e-49

PRY/SPRY domain in tripartite motif-containing (TRIM) proteins, including TRIM5, TRIM6, TRIM7, TRIM10, TRIM11, TRIM17, TRIM20, TRIM21, TRIM27, TRIM35, TRIM38, TRIM41, TRIM50, TRIM58, TRIM60, TRIM62, TRIM69, TRIM72, NF7 and bloodthirsty; This domain, consisting of the distinct N-terminal PRY subdomain followed by the SPRY subdomain, is found at the C-terminus of several Class IV TRIM proteins, including TRIM7, TRIM35, TRIM41, TRIM50, TRIM62, TRIM69, TRIM72, TRIM protein NF7 and bloodthirsty (bty). TRIM7 interacts with glycogenin and stimulates its self-glucosylating activity via its SPRY domain. TRIM35 may play a role as a tumor suppressor and is implicated in the cell death mechanism. TRIM41 is localized to speckles in the cytoplasm and nucleus, and functions as an E3 ligase that catalyzes the ubiquitin-mediated degradation of protein kinase C. TRIM50, an E3 ubiquitin ligase, is deleted in Williams-Beuren (WBS) syndrome, a multi-system neurodevelopmental disorder caused by the deletion of contiguous genes at chromosome region 7q11.23. TRIM62 is involved in the morphogenesis of the mammary gland; loss of TRIM62 gene expression in breast is associated with increased risk of recurrence in early-onset breast cancer. TRIM69 is a novel testis E3 ubiquitin ligase that may function to ubiquitinate its particular substrates during spermatogenesis. In humans, TRIM69 localizes in the cytoplasm and nucleus, and requires an intact RING finger domain to function. TRIM protein NF7, which also contains a chromodomain (CHD) at the N-terminus and an RFP (Ret finger protein)-like domain at the C-terminus, is required for its association with transcriptional units of RNA polymerase II which is mediated by a trimeric B box. In Xenopus oocyte, xNF7 has been identified as a nuclear microtubule-associated protein (MAP) whose microtubule-bundling activity, but not E3-ligase activity, contributes to microtubule organization and spindle integrity. Bloodthirsty (bty) is a novel gene identified in zebrafish and has been shown to likely play a role in in regulation of the terminal steps of erythropoiesis. TRIM72 has been shown to perform a critical function in membrane repair following acute muscle injury by nucleating the assembly of the repair machinery at injury sites. The PRY-SPRY domain in these TRIM families is suggested to serve as the target binding site.

Pssm-ID: 293968 [Multi-domain] Cd Length: 174 Bit Score: 165.73 E-value: 7.03e-49

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 890799132 301 VTL-VQNNHPNIAITDDKRQVRYEDhQASNLIHECE--NSHEGVLGHPAIQSGKHYWEVDVSGKGAWVLGLSDGSYlfcp 377
Cdd:cd13733    2 VTLdPDTAHPNLILSEDLKSVRYGD-KRQNLPDNPErfDTCVCVLGSEGFSSGRHYWEVEVGGKTDWDLGVARESV---- 76

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 890799132 378 ifhsnaerNRlfcrgiKNDSHYQPKYGFWVIGLWKKSVYNAFEEcpftgkPSVLtLSLMVPPCRVGVFLDYAAGTLSFYN 457
Cdd:cd13733   77 --------NR------KGKITLSPENGYWTVGLRNGNEYKALTS------PSTP-LSLREKPQKVGVFLDYEEGQVSFYN 135

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|.
gi 890799132 458 IsNNGTLIYRFcTASFPDRVFPYFNP-----TGSSEPMTIC 493
Cdd:cd13733  136 V-DDGSHIYTF-TDCFTEKLYPYFSPclndgGKNSAPLIIC 174

SPRY_PRY_TRIM6

cd15823

PRY/SPRY domain in tripartite motif-binding protein 6 (TRIM6), also known as RING finger ...

297-495

9.64e-46

PRY/SPRY domain in tripartite motif-binding protein 6 (TRIM6), also known as RING finger protein 89 (RNF89); This domain, consisting of the distinct N-terminal PRY subdomain followed by the SPRY subdomain, is found at the C-terminus of TRIM6, also known as RING finger protein 89 (RNF89). TRIM6 domain is composed of RING/B-box/coiled-coil core and also known as RBCC protein. It is selectively expressed in embryonic stem (ES) cells and interacts with the proto-oncogene product Myc, maintaining the pluripotency of the ES cells. TRIM6, together with E2 Ubiquitin conjugase (UbE2K) and K48-linked poly-Ub chains, is critical for the IkappaB kinase epsilon (IKKepsilon) branch of type I interferon (IFN-I) signaling pathway and subsequent establishment of a protective antiviral response.

Pssm-ID: 293995 Cd Length: 188 Bit Score: 158.10 E-value: 9.64e-46

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 890799132 297 YWVQVTLvqNNHP---NIAITDDKRQVRYEDHQASNLIHECENSHEGVLGHPAIQSGKHYWEVDVSGKGAWVLGLSDGSY 373
Cdd:cd15823    1 YWVDVTL--NPHTanlNLVLSKNRRQVRFVGAKLSGPSYLEEHYDCSVLGSQHFSSGKHYWEVDVTKKTAWILGVCSHSL 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 890799132 374 LFCPIFHSNAERNRLFCRgikndshYQPKYGFWVIGLWKKSVYNAFEEcpftGKPSVLtLSLMVPPCRVGVFLDYAAGTL 453
Cdd:cd15823   79 GPTFSFNQYAQNHNAYSR-------YQPQSGYWVIGLQHNHEYRAYED----SSTSLL-LSMTVPPRRVGVFLDYEAGTV 146

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|..
gi 890799132 454 SFYNISNNGTLIYRFCTASFPDRVFPYFNPTGSSEPMTICWP 495
Cdd:cd15823  147 SFYNVTNHGFPIYTFSKYYFPTTLCPYFNPCNCVVPMTLRRP 188

SPRY_PRY_TRIM21

cd12900

PRY/SPRY domain in tripartite motif-binding protein 21 (TRIM21) also known as 52kD ...

297-493

8.74e-39

PRY/SPRY domain in tripartite motif-binding protein 21 (TRIM21) also known as 52kD Ribonucleoprotein Autoantigen (Ro52); This domain, consisting of the distinct N-terminal PRY subdomain followed by the SPRY subdomain, is found at the C-terminus of TRIM21, which is also known as Sjogren Syndrome Antigen A (SSA), SSA1, 52kD Ribonucleoprotein Autoantigen (Ro52, Ro/SSA, SS-A/Ro) or RING finger protein 81 (RNF81). TRIM21 domains are composed of RING/B-box/coiled-coil core and also known as RBCC proteins. As an E3 ligase, TRIM21 mediates target specificity in ubiquitination; it regulates type 1 interferon and proinflammatory cytokines via ubiquitination of interferon regulatory factors (IRFs). It is up-regulated at the site of autoimmune inflammation, such as cutaneous lupus lesions, indicating a central role in the tissue destructive inflammatory process. It interacts with auto-antigens in patients with Sjogren syndrome and systemic lupus erythematosus, a chronic systemic autoimmune disease characterized by the presence of autoantibodies against the protein component of the human intracellular ribonucleoprotein-RNA complexes and more specifically TRIM21, Ro60/TROVE2 and La/SSB proteins. It binds the Fc part of IgG molecules via its PRY-SPRY domain with unexpectedly high affinity.

Pssm-ID: 293957 Cd Length: 180 Bit Score: 139.25 E-value: 8.74e-39

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 890799132 297 YWVQVTLVQNN-HPNIAITDDKRQVRYED-HQASNLIHECENSHEGVLGHPAIQSGKHYWEVDVSGKGAWVLGLsdgsyl 374
Cdd:cd12900    1 HMVHITLDPDTaNPWLILSKDRRQVRLGDtHQNVPENEERFDNYPMVLGAQRFNSGKHYWEVDVTGKEAWDLGV------ 74

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 890799132 375 fcpifhsnaernrlfCR-GIKNDSHY--QPKYGFWVIGLWKKSvYNAfEECPFTgkpsvlTLSLMVPPCRVGVFLDYAAG 451
Cdd:cd12900   75 ---------------CRdSVRRKGQFllSPENGFWTIWLWNKK-YEA-GTSPQT------TLHLQVPPCQVGIFLDYEAG 131

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*..
gi 890799132 452 TLSFYNISNNGTLIYRFCTASFPDRVFPYFNP-----TGSSEPMTIC 493
Cdd:cd12900  132 VVSFYNITDHGSLIYTFSECAFTGPLRPFFNPgfndsGGNAAPLTLC 178

SPRY_PRY_TRIM20

cd15813

PRY/SPRY domain in tripartite motif-binding protein 20 (TRIM20), also known as pyrin; This ...

293-493

2.07e-32

PRY/SPRY domain in tripartite motif-binding protein 20 (TRIM20), also known as pyrin; This domain, consisting of the distinct N-terminal PRY subdomain followed by the SPRY subdomain, is found at the C-terminus of TRIM20, which is also known as pyrin or marenostrin. Unlike TRIM domains that are composed of RING/B-box/coiled-coil core, the N-terminal RING domain in TRIM20 is exchanged by a PYRIN domain (PYD), a prime mediator of protein interactions necessary for apoptosis, inflammation and innate immune signaling pathway, and it also harbors a C-terminal B30.2 domain. Mutations in pyrin (TRIM20) are associated with familial Mediterranean fever (FMF), a recessively hereditary periodic fever syndrome, characterized by episodes of inflammation and fever. These mutations cluster in the C-terminal B30.2 domain and therefore it is assumed that pyrin plays a role in the innate immune system by possibly effecting caspase-1-dependent IL-1beta maturation.

Pssm-ID: 293985 Cd Length: 184 Bit Score: 122.17 E-value: 2.07e-32

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 890799132 293 EAQRYWVQVTL-VQNNHPNIAITDDKRQVRY---EDHQASNLihECENSHEGVLGHPAIQSGKHYWEVDVSGKGAWVLGL 368
Cdd:cd15813    3 AAQAHAVNVTLdPETAHPNLIFSDDLKSVRLgnkWDRLPDNP--ERFDSCIIVLGSPSFTSGRHYWEVEVGDKTGWILGV 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 890799132 369 SDGSylfcpifhsnaernrlFCRgiKNDSHYQPKYGFWVIGLWKKSVYNAfEECPFTgkpsvlTLSLMVPPCRVGVFLDY 448
Cdd:cd15813   81 CKAS----------------VSR--KGSMTLSPENGYWVVMMTKRNEYQA-STSPPT------RLWLREPPRRVGIFLDY 135

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|
gi 890799132 449 AAGTLSFYNISNNgTLIYRFCTASFPDRVFPYFNPTGSS-----EPMTIC 493
Cdd:cd15813  136 EAGDISFYNVTAK-SHIYTFTSFSSSGPLQPIFSPGTHDggknmDPLTIC 184

SPRY_PRY_TRIM35

cd12893

PRY/SPRY domain in tripartite motif-containing protein 35 (TRIM35); This PRY/SPRY domain is ...

301-493

2.89e-29

PRY/SPRY domain in tripartite motif-containing protein 35 (TRIM35); This PRY/SPRY domain is found at the C-terminus of the overall domain architecture of tripartite motif 35, TRIM35 (also known as hemopoietic lineage switch protein), which includes a RING finger domain (RING) and a B-box motif (BBOX). TRIM35 may play a role as a tumor suppressor and is implicated in the cell death mechanism.

Pssm-ID: 293950 [Multi-domain] Cd Length: 171 Bit Score: 113.11 E-value: 2.89e-29

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 890799132 301 VTLVQNN-HPNIAITDDKRQVRY-EDHQASNLIHECENSHEGVLGHPAIQSGKHYWEVDVSGKGAWVLGLSDGSylfcpi 378
Cdd:cd12893    2 VTLDPNTaHPWLSLSEDLTSVRYsSEKQQLPDNPERFDPYPCVLGSEGFTSGKHSWDVEVGDNTSWMLGVAKES------ 75

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 890799132 379 fhsnAERNRLFcrgikndsHYQPKYGFWVIGLWKKsVYNAfeecpFTGKPSVLTLSLMVPPCRVGVFLDYAAGTLSFYNI 458
Cdd:cd12893   76 ----VQRKGKF--------TLSPESGFWTIGFSEG-KYSA-----RTSPEPRTPLRVKQKPQRIRVQLDWDRGKVSFSDP 137

                        170       180       190
                 ....*....|....*....|....*....|....*
gi 890799132 459 SNNgTLIYRFcTASFPDRVFPYFNPTGSSEPMTIC 493
Cdd:cd12893  138 DTN-THIHTF-THTFTERVFPYFYTGCKSEPLRIL 170

RING-HC_TRIM5-like_C-IV

cd16591

RING finger, HC subclass, found in tripartite motif-containing proteins TRIM5, TRIM6, TRIM22, ...

8-78

4.31e-29

Pssm-ID: 438253 [Multi-domain] Cd Length: 72 Bit Score: 109.07 E-value: 4.31e-29

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 890799132   8 NLKEEVTCPVCLNLMVKPVSADCGHTFCQGCITLYFESIKCDKEMFSCPVCRLSYQSSNLRPNLHVANIVE 78
Cdd:cd16591    2 NIKEEVTCPICLELLTEPLSLDCGHSFCQACITANHKESVNQEGESSCPVCRTSYQPENLRPNRHLANIVE 72

SPRY_PRY_BTN1_2

cd15819

butyrophilin subfamily member A1 and A2 (BTN1A and BTN2A); This domain, consisting of the ...

299-493

2.08e-28

butyrophilin subfamily member A1 and A2 (BTN1A and BTN2A); This domain, consisting of the distinct N-terminal PRY subdomain followed by the SPRY subdomain, is found at the C-terminus of butyrophilin family 1A and 2A (BTN1A and BTN2A). BTNs belong to receptor glycoproteins of immunoglobulin (Ig) superfamily, characterized by the presence of extracellular Ig-like domains (IgV and/or IgC). BTN1A plays a role in the secretion, formation and stabilization of milk fat globules. The B30.2 domain of BTN1A1 binds the enzyme xanthine oxidoreductase (XOR) in order to participate in milk fat globule secretion; this interaction may lead to the production of reactive oxygen species, which have immunomodulatory and antimicrobial functions. Duplication events have led to three paralogs of BTN2A in primates: BTN2A1, BTN2A2, and BTN2A3. In humans, only BTN2A1 has been functionally characterized; it has been detected on epithelial cells and leukocytes, and identified as a novel ligand of dendritic cell-specific ICAM-3 grabbing nonintegrin (DCSIGN), a C-type lectin receptor that acts as an internalization receptor for HIV-1, HCV, and other pathogens. BTN2A2 mRNA has been shown to be expressed in circulating human immune cells.

Pssm-ID: 293991 [Multi-domain] Cd Length: 172 Bit Score: 110.78 E-value: 2.08e-28

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 890799132 299 VQVTLVQNN-HPNIAITDDKRQVRYEDHQasnliHECENSHEG------VLGHPAIQSGKHYWEVDVSGKGAWVLGlsdg 371
Cdd:cd15819    2 VNVTLDPDTaHPALILSEDGRSVTWGETR-----QDLPENPERfdslpcVLGQEGFTSGRHYWEVEVGDRTSWDLG---- 72

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 890799132 372 sylfcpIFHSNAERnrlfcrgiKNDSHYQPKYGFWVIGLWKKSvYNAfeecpftgkpsvLT-----LSLMVPPCRVGVFL 446
Cdd:cd15819   73 ------VCRDNVMR--------KGRVTLSPENGFWAIRLYGNE-YWA------------LTspetpLTLKEPPRRVGIFL 125

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*....
gi 890799132 447 DYAAGTLSFYNIsNNGTLIYRFCTASFPDRVFPYFNpTGSSE--PMTIC 493
Cdd:cd15819  126 DYEAGDVSFYNM-TDGSHIYTFPQTAFSGPLRPFFR-LWSSDsgPLTIC 172

SPRY_PRY_RFPL

cd15821

Ret finger protein-like (RFPL), includes RFP1, 2, 3, 4; This domain, consisting of the ...

296-493

7.14e-28

Ret finger protein-like (RFPL), includes RFP1, 2, 3, 4; This domain, consisting of the distinct N-terminal PRY subdomain followed by the SPRY subdomain, is found at the C-terminus of RFPL protein family, which includes RFPL1, RFPL2, RFPL3 and RFPL4. In humans, RFPL transcripts can be detected at the onset of neurogenesis in differentiating human embryonic stem cells, and in the developing human neocortex. The human RFPL1, 2, 3 genes have a role in neocortex development. RFPL1 is a primate-specific target gene of Pax6, a key transcription factor for pancreas, eye and neocortex development; human RFPL1 decreases cell number through its RFPL-defining motif (RDM) and SPRY domains. The RFPL4 (also known as RFPL4A) gene encodes a putative E3 ubiquitin-protein ligase expressed in adult germ cells and interacts with oocyte proteins of the ubiquitin-proteasome degradation pathway.

Pssm-ID: 293993 [Multi-domain] Cd Length: 178 Bit Score: 109.32 E-value: 7.14e-28

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 890799132 296 RYWVQVTL-VQNNHPNIAITDDKRQVRY-EDHQASNLIHECENSHEGVLGHPAIQSGKHYWEVDVSGKGAWVLGLSDGSY 373
Cdd:cd15821    1 KFQVDMTLdVDTANNYLIISEDLRSVRCgCFRQNRKELAERFDDALCVLGSPRFTSGRHYWEVDVGTSTEWDLGVCRESV 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 890799132 374 lfcpifhsnaerNRlfcrgiKNDSHYQPKYGFWVIGLWKKSVYNAFEEcPFTGkpsvltlsLMVPPC--RVGVFLDYAAG 451
Cdd:cd15821   81 ------------NR------QGPIELSPEHGFWTVSLRDGSVFFASTV-PLTV--------LWVNPRlhRVGIFLDMEMG 133

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*.
gi 890799132 452 TLSFYNISnNGTLIYRFCTASFPDRVFPYF---NPTGSSE-PMTIC 493
Cdd:cd15821  134 TISFYDVS-DGSHIFTFTKISAEEPLRPFFapaNPYGDDQgVLSIC 178

SPRY_PRY_TRIM60_75

cd15817

PRY/SPRY domain of tripartite motif-binding protein 60 and 75 (TRIM60 and TRIM75); This domain, ...

308-493

7.76e-27

PRY/SPRY domain of tripartite motif-binding protein 60 and 75 (TRIM60 and TRIM75); This domain, consisting of the distinct N-terminal PRY subdomain followed by the SPRY subdomain, is found at the C-terminus of TRIM60 and TRIM75, both composed of RING/B-box/coiled-coil core and also known as RBCC proteins. TRIM60 domain is also known as RING finger protein 33 (RNF33) or 129 (RNF129). Based on its expression profile, RNF33 likely plays an important role in the spermatogenesis process, the development of the pre-implantation embryo, and in testicular functions; Rnf33 is temporally transcribed in the unfertilized egg and the pre-implantation embryo, and is permanently silenced before the blastocyst stage. Mice experiments have shown that RNF33 associates with the cytoplasmic motor proteins, kinesin-2 family members 3A (KIF3A) and 3B (KIF3B), suggesting possible contribution to cargo movement along the microtubule in the expressed sites. TRIM75, also known as Gm794, has a single site of positive selection in its RING domain associated with E3 ubiquitin ligase activity. It has not been detectably expressed experimentally due to their constant turnover by the proteasome, and therefore not been characterized.

Pssm-ID: 293989 [Multi-domain] Cd Length: 168 Bit Score: 106.09 E-value: 7.76e-27

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 890799132 308 HPNIAITDDKRQVRYEDHQASNLIHECE-NSHEGVLGHPAIQSGKHYWEVDVSGKGAWVLGLSDGSylfcpiFHSNAERN 386
Cdd:cd15817   10 HPNLIVSEDRKAVRYRRMKPNCPYDPRRfTVYPAVLGSEGFDSGRHFWEVEVGGKGEWILGVCKDS------LPRNAQDP 83

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 890799132 387 RlfcrgikndshyQPKYGFWVIGLWkKSVYNAFEecpftgkPSVLTLSLMVPPCRVGVFLDYAAGTLSFYNIsNNGTLIY 466
Cdd:cd15817   84 P------------SPLGGCWQIGRY-MSGYVASG-------PKTTQLLPVVKPSRIGIFLDYELGEVSFYNM-NDRSHLY 142

                        170       180
                 ....*....|....*....|....*..
gi 890799132 467 RFcTASFPDRVFPYFNPTGSSEPMTIC 493
Cdd:cd15817  143 TF-TDTFTGKLIPYFYVGPDSEPLTIC 168

SPRY_PRY_BTN3

cd15820

PRY/SPRY domain of butyrophilin 3 (BTN3), includes BTN3A1, BTN3A2, BTN3A3 as well as BTN-like ...

308-493

9.83e-27

PRY/SPRY domain of butyrophilin 3 (BTN3), includes BTN3A1, BTN3A2, BTN3A3 as well as BTN-like 3 (BTNL3); BTN3A also known as CD277; This domain, consisting of the distinct N-terminal PRY subdomain followed by the SPRY subdomain, is found at the C-terminus of butyrophilin family 3A (BTN3A); duplication events have led to three paralogs in primates: BTN3A1, BTN3A2, and BTN3A3. BTNs belong to receptor glycoproteins of immunoglobulin (Ig) superfamily, characterized by the presence of extracellular Ig-like domains (IgV and/or IgC). BTN3 transcripts are ubiquitously present in all immune cells (T cells, B cells, NK cells, monocytes, dendritic cells, and hematopoietic precursors) with different expression levels; BTN3A1 and BTN3A2 are expressed mainly by CD4+ and CD8+ T cells, BTN3A2 is the major form expressed in NK cells, and BTN3A3 is poorly expressed in these immune cells. The PRY/SPRY domain of the BTN3A1 isoform mediates phosphoantigen (pAg)-induced activation by binding directly to the pAg.

Pssm-ID: 293992 [Multi-domain] Cd Length: 176 Bit Score: 106.36 E-value: 9.83e-27

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 890799132 308 HPNIAITDDKRQVRYED-HQASNLIHECENSHEGVLGHPAIQSGKHYWEVDVSGKGAWVLGLsdgsylfCpifHSNAERn 386
Cdd:cd15820   14 NPILLISEDQRSLQWADePQNLPDNPKRFDWHYCVLGCKSFTSGRHFWEVEVGDRKEWYVGV-------C---RENVER- 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 890799132 387 rlfcrgiKNDSHYQPKYGFWVIGLWKKSVYNAFEEcPFTgkpsvlTLSLMVPPCRVGVFLDYAAGTLSFYNiSNNGTLIY 466
Cdd:cd15820   83 -------KLWVKMAPENGFWTIGLSDGNDYQALTD-PRT------KLTIANPPQRVGVFLDYETGEVSFYN-AMDGSHIY 147

                        170       180
                 ....*....|....*....|....*...
gi 890799132 467 RFCTASFPDRVFPYFNPTGS-SEPMTIC 493
Cdd:cd15820  148 TFPHTSFSGPLYPVFRLLSWdPTALTIC 175

SPRY_PRY_TRIM60

cd15828

PRY/SPRY domain of tripartite motif-binding protein 60 (TRIM60) also known as RING finger ...

295-493

4.27e-26

PRY/SPRY domain of tripartite motif-binding protein 60 (TRIM60) also known as RING finger protein 33 (RNF33); This domain, consisting of the distinct N-terminal PRY subdomain followed by the SPRY subdomain, is found at the C-terminus of TRIM60, which is also known as RING finger protein 33 (RNF33) or 129 (RNF129). TRIM60 domains are composed of RING/B-box/coiled-coil core and also known as RBCC proteins. Based on its expression profile, RNF33 likely plays an important role in the spermatogenesis process, the development of the pre-implantation embryo, and in testicular functions; Rnf33 is temporally transcribed in the unfertilized egg and the pre-implantation embryo, and is permanently silenced before the blastocyst stage. Mice experiments have shown that RNF33 associates with the cytoplasmic motor proteins, kinesin-2 family members 3A (KIF3A) and 3B (KIF3B), suggesting possible contribution to cargo movement along the microtubule in the expressed sites.

Pssm-ID: 294000 [Multi-domain] Cd Length: 180 Bit Score: 104.68 E-value: 4.27e-26

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 890799132 295 QRYWVQVTLVQNN-HPNIAITDDKRQVRYEDHQasnlIHECENSHE-----GVLGHPAIQSGKHYWEVDVSGKGAWVLGL 368
Cdd:cd15828    6 KRFQVDVTLDPETaHPQLTVSEDRKSVLYGEMK----QNVCYNPRRfylcpAVLGSEGFHSGRQYWEVEVGDKPEWTLGV 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 890799132 369 SDGSYLfcpifhsnaeRNRlfcrgiKNDSHYQPkyGFWVIGLWKKSVYNAFeecpftgKPSVLTLSLMVPPCRVGVFLDY 448
Cdd:cd15828   82 CQDCLP----------RNW------SNQPSVQD--GLWAIGRYSESNYVAL-------GPKKIQLLPKVRPSKIGIFLDY 136

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*
gi 890799132 449 AAGTLSFYNIsNNGTLIYRFcTASFPDRVFPYFNPTGSSEPMTIC 493
Cdd:cd15828  137 ELGEVSFYNM-NDRSLLYTF-SDSFTGTLWPYFYTGTDSEPLKIC 179

SPRY_PRY_TRIM39

cd13745

PRY/SPRY domain in tripartite motif-binding protein 39 (TRIM39) and TRIM39-like; This domain, ...

299-494

4.78e-26

PRY/SPRY domain in tripartite motif-binding protein 39 (TRIM39) and TRIM39-like; This domain, consisting of the distinct N-terminal PRY subdomain followed by the SPRY subdomain, is found at the C-terminus of pyrin, several tripartite motif-containing proteins (TRIMs), including E3 ubiquitin-protein ligase (TRIM21), RET finger protein (RFP)/tripartite motif protein 27 (TRIM27), as well as butyrophilin (Btns) and butyrophilin-like (Btnl) family members, with the exception of Btnl2. Btn and Btnl family members are novel regulators of immune responses, with many of the genes located within the MHC. They are implicated in T-cell inhibition and modulation of epithelial cell-T cell interactions. TRIM21 (also known as RO52, SSA1 or RNF81) is a major autoantigen in autoimmune diseases such as rheumatoid arthritis, systemic lupus erythematosus, and Sjorgen's syndrome. TRIM27 (also known as Ret finger protein, RFP or RNF76) negatively regulates CD4 T-cells by ubiquitinating and inhibiting the class II phosphatidylinositol 3 kinase C2beta (PI3K-C2beta), a kinase critical for KCa3.1 channel activation. The PRY/SPRY domain of Pyrin, which is mutated in familial Mediterranean fever patients, interacts with inflammasome components and inhibits proIL-1beta processing.

Pssm-ID: 293979 [Multi-domain] Cd Length: 177 Bit Score: 104.24 E-value: 4.78e-26

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 890799132 299 VQVTLVQNN-HPNIAITDDKRQVRYEDHQaSNLIHECE--NSHEGVLGHPAIQSGKHYWEVDVSGKGAWVLGLsdgsylf 375
Cdd:cd13745    3 VDVTLDPDTaHPNLVLSEDRKSVRHGDTR-QDLPDNPErfDTYPCVLGAEGFTGGRHYWEVEVGDKTEWTLGV------- 74

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 890799132 376 cpifhsnaernrlfCR---GIKNDSHYQPKYGFWVIGLWKKsVYNAFEeCPFTgkpsvlTLSLMVPPCRVGVFLDYAAGT 452
Cdd:cd13745   75 --------------CResvSRKGEVTLSPENGYWTVWLRDG-KYEALT-SPPT------PLPVSVRPSRVGIFLDYEAGE 132

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*...
gi 890799132 453 LSFYNIsNNGTLIYRFcTASFPDRVFPYFNPtGSSE------PMTICW 494
Cdd:cd13745  133 VSFYNV-TDRSHLFTF-TDTFSGTLRPYFYP-GLNAggknaaPLIICP 177

SPRY_PRY_TRIM69

cd15818

PRY/SPRY domain in tripartite motif-binding protein 69 (TRIM69), also known as RING finger ...

308-492

1.60e-25

PRY/SPRY domain in tripartite motif-binding protein 69 (TRIM69), also known as RING finger protein 36 (RNF36); This domain, consisting of the distinct N-terminal PRY subdomain followed by the SPRY subdomain, is found at the C-terminus of TRIM69, which is also known as RING finger protein 36 (RNF36) or testis-specific ring finger (Trif). TRIM69 domains are composed of RING/B-box/coiled-coil core and also known as RBCC proteins. It is a novel testis E3 ubiquitin ligase that may function to ubiquitinate its particular substrates during spermatogenesis. In humans, TRIM69 localizes in the cytoplasm and nucleus, and requires an intact RING finger domain to function. The mouse ortholog of this gene is specifically expressed in germ cells at the round spermatid stages during spermatogenesis and, when overexpressed, induces apoptosis. TRIM69 has been shown to be a novel regulator of mitotic spindle assembly in tumor cells; it associates with spindle poles and promotes centrosomal clustering, and is therefore essential for formation of a bipolar spindle.

Pssm-ID: 293990 [Multi-domain] Cd Length: 187 Bit Score: 103.34 E-value: 1.60e-25

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 890799132 308 HPNIAITDDKRQVRYED-HQASNLIHECENSHEGVLGHPAIQSGKHYWEVDVSGKGAWVLGLSDGSYlfcpifhsnaerN 386
Cdd:cd15818   23 HPNLILSEDLTCVWHGDtKQMLPDNPERFDSSVAVLGSEGFTSGKHYWEVEVAKKTKWTLGVVRESI------------N 90

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 890799132 387 RlfcrgiKNDSHYQPKYGFWVIGLWKKSVYNAFEECPFtgkpsvlTLSLMVPPCRVGVFLDYAAGTLSFYNiSNNGTLIY 466
Cdd:cd15818   91 R------KGNCPLSPEDGFWLLRLRNQNELKALDVPSF-------SLTLTSNLNKVGIYLDYEGGQVSFYN-ANTMSHIY 156

                        170       180       190
                 ....*....|....*....|....*....|.
gi 890799132 467 RFCTaSFPDRVFPYF----NPTG-SSEPMTI 492
Cdd:cd15818  157 TFSD-TFTEKIYPYFcpclNDSGeNKEPLKI 186

SPRY_PRY_TRIM11

cd15811

PRY/SPRY domain of tripartite motif-binding protein 11 (TRIM11), also known as RING finger ...

308-493

6.85e-25

PRY/SPRY domain of tripartite motif-binding protein 11 (TRIM11), also known as RING finger protein 92 (RNF92); This domain, consisting of the distinct N-terminal PRY subdomain followed by the SPRY subdomain, is found at the C-terminus of TRIM11, also known as RING finger protein 92 (RNF92) or BIA1. TRIM11 domains are composed of RING/B-box/coiled-coil core and also known as RBCC proteins. It localizes to the nucleus and the cytoplasm; it is overexpressed in high-grade gliomas and promotes proliferation, invasion, migration and glial tumor growth. TRIM11 increases expression of dopamine beta-hydroxylase gene by interacting with the homeodomain transcription factor, PHOX2B, via the B30.2/SPRY domain, thus playing a potential role in the specification of noradrenergic (NA) neuron phenotype. It has also been shown that TRIM11 plays a critical role in the clearance of mutant PHOX2B, which causes congenital central hypoventilation syndrome, via the proteasome. TRIM11 binds a key component of the activator-mediated cofactor complex (ARC105), and destabilizes it, through the ubiquitin-proteasome system; ARC105 mediates chromatin-directed transcription activation and is a key regulatory factor for transforming growth factor beta (TGFbeta) signaling.

Pssm-ID: 293983 [Multi-domain] Cd Length: 169 Bit Score: 100.80 E-value: 6.85e-25

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 890799132 308 HPNIAITDDKRQVRYEDhQASNLIHECENSHEG--VLGHPAIQSGKHYWEVDVSGKGAWVLGLsdgsylfCpifHSNAER 385
Cdd:cd15811   10 NPELVLSEDRRSVRRGD-LRQALPDSPERFDPGpcVLGRERFTSGRHYWEVEVGDRTSWALGV-------C---KENVNR 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 890799132 386 nrlfcrgiKNDSHYQPKYGFWVIGLWkkSVYNAFEECPFTgkpsvltlSLMVPPCRVGVFLDYAAGTLSFYNiSNNGTLI 465
Cdd:cd15811   79 --------KEKGELSAGNGFWILVFL--GNYYSSERRTFA--------PLRDPPRRVGIFLDYEAGHLSFYS-ATDGSLL 139

                        170       180
                 ....*....|....*....|....*....
gi 890799132 466 YRFCTASFPDRVFPYFNPTGSSE-PMTIC 493
Cdd:cd15811  140 FIFPETPFSGTLRPLFSPLSSSPtPMTIC 168

SPRY_PRY_TRIM75

cd15829

PRY/SPRY domain of tripartite motif-binding protein 75 (TRIM75); This domain, consisting of ...

288-493

1.41e-24

PRY/SPRY domain of tripartite motif-binding protein 75 (TRIM75); This domain, consisting of the distinct N-terminal PRY subdomain followed by the SPRY subdomain, is found at the C-terminus of TRIM75, also known as Gm794. TRIM75 domains are composed of RING/B-box/coiled-coil core and also known as RBCC proteins. TRIM75 has a single site of positive selection in its RING domain associated with E3 ubiquitin ligase activity. It has not been detectably expressed experimentally due to their constant turnover by the proteasome, and therefore not been characterized.

Pssm-ID: 294001 Cd Length: 187 Bit Score: 100.44 E-value: 1.41e-24

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 890799132 288 LQEVteAQRYWVQVTL-VQNNHPNIAITDDKRQVRYEDHQASNLIHECE-NSHEGVLGHPAIQSGKHYWEVDVSGKGAWV 365
Cdd:cd15829   10 LQKI--IKKFRVDVTLdPETAHPNLLVSEDKKCVTFTKKKQRVPDSPKRfTVNPVVLGFPGFHSGRHFWEVEVGDKPEWA 87

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 890799132 366 LGLsdgsylfCPIFHSNAERNRLfcrgikndshyQPKYGFWVIgLWKKSVYNAfeecpfTGkPSVLTLSLMVPPCRVGVF 445
Cdd:cd15829   88 VGV-------CKDSLSTKARRPP-----------SGQQGCWRI-QLQGGDYDA------PG-AVPPPLLLEVKPRGIGVF 141

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*...
gi 890799132 446 LDYAAGTLSFYNIsNNGTLIYRFcTASFPDRVFPYFNPTGSSEPMTIC 493
Cdd:cd15829  142 LDYELGEISFYNM-PEKSHIHTF-TDTFSGPLRPYFYVGPDSKPLRIC 187

SPRY_PRY_TRIM38

cd15815

PRY/SPRY domain of tripartite motif-binding protein 38 (TRIM38), also known as Ring finger ...

296-481

2.48e-24

PRY/SPRY domain of tripartite motif-binding protein 38 (TRIM38), also known as Ring finger protein 15 (RNF15); This domain, consisting of the distinct N-terminal PRY subdomain followed by the SPRY subdomain, is found at the C-terminus of TRIM38, which is also known as RING finger protein 15 (RNF15) or RORET. TRIM38 domains are composed of RING/B-box/coiled-coil core and also known as RBCC proteins. TRIM38 has been shown to act as a suppressor in TOLL-like receptor (TLR)-mediated interferon (IFN)-beta induction by promoting degradation of TRAF6 and NAP1 through the ubiquitin-proteasome system. Another study has shown that TRIM38 may act as a novel negative regulator for TLR3-mediated IFN-beta signaling by targeting TRIF for degradation. TRIM38 has been identified as a critical negative regulator in TNFalpha- and IL-1beta-triggered activation of NF-kappaB and MAP Kinases (MAPKs); it causes degradation of two essential cellular components, TGFbeta-associated kinase 1 (TAK1)-associating chaperones 2 and 3 (TAB2/3). The degradation is promoted through a lysosomal-dependent pathway, which requires the C-terminal PRY-SPRY of TRIM38. Enterovirus 71 infection induces degradation of TRIM38, suggesting that TRIM38 may play a role in viral infections.

Pssm-ID: 293987 [Multi-domain] Cd Length: 182 Bit Score: 99.73 E-value: 2.48e-24

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 890799132 296 RYWVQVTLVQNN-HPNIAITDDKRQVRY----EDHQASN---LIHECenshegVLGHPAIQSGKHYWEVDVSGKGAWVLG 367
Cdd:cd15815   10 RHQVSVTLDPDTaHPELTLSKDQRQVTYgrcqENLDASPkrfTVLPC------VLGCEGFTSGRHYFEVDVGEGTGWDVG 83

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 890799132 368 LsdgsylfCpifHSNAERNrlfcrgikNDSHYQPKYGFWVIGLWKKSVYNAFEeCPFTgkpsvlTLSLMVPPCRVGVFLD 447
Cdd:cd15815   84 V-------C---LENVQRG--------FGMKQEPEFGFWTIRLCEEDGYVALT-SPPT------PLPLREKPLVVGVFLD 138

                        170       180       190
                 ....*....|....*....|....*....|....
gi 890799132 448 YAAGTLSFYNISnNGTLIYRFCTASFPDRVFPYF 481
Cdd:cd15815  139 YEAGLVSFYNMT-TGSHIFTFPKASFSDTLRPYF 171

SPRY_PRY_TRIM27

cd15814

PRY/SPRY domain in tripartite motif-containing protein 27 (TRIM27), also known as RING finger ...

299-493

5.09e-24

PRY/SPRY domain in tripartite motif-containing protein 27 (TRIM27), also known as RING finger protein 76 (RNF76); This domain, consisting of the distinct N-terminal PRY subdomain followed by the SPRY subdomain, is found at the C-terminus of TRIM27, also known as RING finger protein 76 (RNF76) or RET finger protein (RFP). TRIM27 domain is composed of RING/B-box/coiled-coil core and also known as RBCC proteins. It is highly expressed in the spleen, thymus and in cells of the hematopoietic compartment. TRIM27 exhibits either nuclear or cytosolic localization depending on the cell type. TRIM27 negatively regulates nucleotide-binding oligomerization domain containing 2 (NOD2)-mediated signaling by proteasomal degradation of NOD2, suggesting that TRIM27 could be a new target for therapeutic intervention in NOD2-associated diseases such as Crohn's. High expression of TRIM27 is observed in several human cancers, including breast and endometrial cancer, where elevated TRIM27 expression predicts poor prognosis. Also, TRIM27 forms an oncogenic fusion protein with Ret proto-oncogene. It is involved in different stages of spermatogenesis and its significant expression in male germ cells and seminomas, suggests that TRIM27 may be associated with the regulation of testicular germ cell proliferation and histological-type of germ cell tumors. TRIM27 could also be a predictive marker for chemoresistance in ovarian cancer patients. In the neurotoxin model of Parkinson's disease (PD), deficiency of TRIM27 decreases apoptosis and protects dopaminergic neurons, making TRIM27 an effective potential target during the treatment of PD.

Pssm-ID: 293986 [Multi-domain] Cd Length: 177 Bit Score: 98.61 E-value: 5.09e-24

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 890799132 299 VQVTLVQNN-HPNIAITDDKRQVRYEDHQaSNLIHECE--NSHEGVLGHPAIQSGKHYWEVDVSGKGAWVLGLSDGSylf 375
Cdd:cd15814    2 VDVTLDPDTaYPSLILSDNLRQVRYSYLQ-QDLPDNPErfNLFPCVLGSPCFIAGRHYWEVEVGDKAKWTIGVCEDS--- 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 890799132 376 cpifhsnaernrlFCRgiKNDSHYQPKYGFWVIGLWKKSVYNAFEEcPFTGKPsvltlsLMVPPCRVGVFLDYAAGTLSF 455
Cdd:cd15814   78 -------------VCR--KGGVTSAPQNGFWAVSLWYGKEYWALTS-PMTALP------LRTPLQRVGIFLDYDAGEVSF 135

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|..
gi 890799132 456 YNISNNgTLIYRFCTASFPDRVFPYFNPT----GSSEPMTIC 493
Cdd:cd15814  136 YNVTER-CHTFTFSHATFCGPVRPYFSLSysggKSAAPLIIC 176

SPRY_PRY

cd12874

PRY/SPRY domain, also known as B30.2; This domain contains residues in the N-terminus that ...

308-493

6.00e-24

PRY/SPRY domain, also known as B30.2; This domain contains residues in the N-terminus that form a distinct PRY domain structure such that the B30.2 domain consists of PRY and SPRY subdomains. B30.2 domains comprise the C-terminus of three protein families: BTNs (receptor glycoproteins of immunoglobulin superfamily); several TRIM proteins (composed of RING/B-box/coiled-coil core); Stonutoxin (secreted poisonous protein of the stonefish Synanceia horrida). While SPRY domains are evolutionarily ancient, B30.2 domains are a more recent adaptation where the SPRY/PRY combination is a possible component of immune defense. Among the TRIM proteins, also known as the N-terminal RING finger/B-box/coiled coil (RBCC) family, only Classes I and II contain the B30.2 domain that has evolved under positive selection. Class I TRIM proteins include multiple members involved in antiviral immunity at various levels of interferon signaling cascade. Among the 75 human TRIMs, roughly half enhance immune response, which they do at multiple levels in signaling pathways. The PRY-SPRY domain in these TRIM families is suggested to serve as the target binding site.

Pssm-ID: 293934 [Multi-domain] Cd Length: 168 Bit Score: 98.15 E-value: 6.00e-24

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 890799132 308 HPNIAITDDKRQVRYeDHQASNLIHECENSHEG--VLGHPAIQSGKHYWEVDVSGKGAWVLGLSDGSYlfcpifhsnaer 385
Cdd:cd12874    9 HLNLILSDDLRSVRV-GDISQHPPEPPPRFFECwqVLGSQSFSSGRHYWEVDVQDDSSWYVGVTYKSL------------ 75

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 890799132 386 NRLfcrgiKNDSHYQPKYGFWVIGlWKKSVYNAFEEcpftGKPSVLtlsLMVPPCRVGVFLDYAAGTLSFYNISNNGTLI 465
Cdd:cd12874   76 PRK-----GKMSNLGRNNGSWCLE-WRENEFSAWHN----NPETRL---PVTPPRRLGVFLDCDGGSLSFYGVTDGVQLL 142

                        170       180
                 ....*....|....*....|....*...
gi 890799132 466 YRFcTASFPDRVFPYFNPtGSSEPMTIC 493
Cdd:cd12874  143 YTF-KAKFTEPLYPAFWL-GEGSTLSIC 168

SPRY_PRY_TRIM7_like

cd12888

PRY/SPRY domain in tripartite motif-binding protein 7 (TRIM7)-like, including TRIM7, TRIM10, ...

308-481

3.76e-23

PRY/SPRY domain in tripartite motif-binding protein 7 (TRIM7)-like, including TRIM7, TRIM10, TRIM15, TRIM26, TRIM39, TRIM41; This domain, consisting of the distinct N-terminal PRY subdomain followed by the SPRY subdomain, is found at the C-terminus of several tripartite motif-containing (TRIM) proteins, including TRIM7 (also referred to as glycogenin-interacting protein, RING finger protein 90 or RNF90), TRIM10, TRIM15, TRIM26, TRIM39 and TRIM41. TRIM7 or GNIP interacts with glycogenin and stimulates its self-glucosylating activity via its SPRY domain. TRIM10 (also known as hematopoietic RING finger 1 (HERF1) or TRIM10/HERF1) plays a key role in definitive erythroid development; downregulation of the Spi-1/PU.1 oncogene induces the expression of TRIM10/HERF1, a key factor required for terminal erythroid cell differentiation and survival. Antiviral activity of TRIM15 is dependent on the ability of its B-box to interact with the MLV Gag precursor protein; downregulation of TRIM15, along with TRIM11, enhances virus release suggesting that these proteins contribute to the endogenous restriction of retroviruses in cells. Tripartite motif-containing 26 (TRIM26) function is as yet unknown; however, since it is localized in the human histocompatibility complex (MHC) class I region, TRIM26 may play a role in immune response although studies show no association between TRIM26 polymorphisms and the risk of aspirin-exacerbated respiratory disease. TRIM39 is a MOAP-1 (Modulator of Apoptosis)-binding protein that stabilizes MOAP-1 through inhibition of its poly-ubiquitination process. TRIM41 (also known as RING finger-interacting protein with C kinase or RINCK) functions as an E3 ligase that catalyzes the ubiquitin-mediated degradation of protein kinase C.

Pssm-ID: 293946 [Multi-domain] Cd Length: 169 Bit Score: 96.09 E-value: 3.76e-23

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 890799132 308 HPNIAITDDKRQVRYED-HQASNLIHECENSHEGVLGHPAIQSGKHYWEVDVSGKGAWVLGLSDGSylfcpifhsnAERn 386
Cdd:cd12888   10 HPRLVLSEDRKSVRWGDtRQDLPDNPERFDTWPCVLGCEGFTSGRHYWEVEVGDGGGWAVGVARES----------VRR- 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 890799132 387 rlfcrgiKNDSHYQPKYGFWVIGLWKKSvYNAFeecpfTGKPSVLTLSLmvPPCRVGVFLDYAAGTLSFYNiSNNGTLIY 466
Cdd:cd12888   79 -------KGEISFSPEEGIWAVGQWGGQ-YWAL-----TSPETPLPLSE--VPRRIRVYLDYEGGQVAFFD-ADNEAPIF 142

                        170
                 ....*....|....*.
gi 890799132 467 RFCTASFP-DRVFPYF 481
Cdd:cd12888  143 TFPPASFAgERIFPWF 158

SPRY_PRY_A33L

cd12905

zinc-binding protein A33-like; This domain, consisting of the distinct N-terminal PRY ...

308-493

8.46e-23

zinc-binding protein A33-like; This domain, consisting of the distinct N-terminal PRY subdomain followed by the SPRY subdomain, is found at the C-terminus of TRIM69 and TRIM proteins NF7 and bloodthirsty (bty). TRIM69 is a novel testis E3 ubiquitin ligase that may function to ubiquitinate its particular substrates during spermatogenesis. In humans, TRIM69 localizes in the cytoplasm and nucleus, and requires an intact RING finger domain to function. TRIM protein NF7, which also contains a chromodomain (CHD) at the N-terminus and an RFP (Ret finger protein)-like domain at the C-terminus, is required for its association with transcriptional units of RNA polymerase II which is mediated by a trimeric B box. In Xenopus oocyte, xNF7 has been identified as a nuclear microtubule-associated protein (MAP) whose microtubule-bundling activity, but not E3-ligase activity, contributes to microtubule organization and spindle integrity. Bloodthirsty (bty) is a novel gene identified in zebrafish and has been shown to likely play a role in in regulation of the terminal steps of erythropoiesis.

Pssm-ID: 293962 [Multi-domain] Cd Length: 178 Bit Score: 95.17 E-value: 8.46e-23

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 890799132 308 HPNIAITDDKRQVRYEDHQ-----ASNLIHECENshegVLGHPAIQSGKHYWEVDVSGKGAWVLGLSDGSYlfcpifhSN 382
Cdd:cd12905   14 HPSLILSRDLTAVTESDEMqpyprSPKRFLQCVN----VLASQGFQSGRHYWEVWVGSKTKWDLGVASESV-------DR 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 890799132 383 AERNRLfCrgikndshyqPKYGFWVIGLWKKSVYNAFEEcPFTgkpsvlTLSLMVPPCRVGVFLDYAAGTLSFYNiSNNG 462
Cdd:cd12905   83 QARVKL-C----------PENGYWTLRLRNGDEYWAGTQ-PWT------RLRVTSRPQRIGVFLDCEERKVSFYN-ADDM 143

                        170       180       190
                 ....*....|....*....|....*....|....*.
gi 890799132 463 TLIYRFCTASfPDRVFPYFNPTGS-----SEPMTIC 493
Cdd:cd12905  144 SLLYSFHQGP-RGKVFPFFSTCFSddgqnAEPMRLL 178

SPRY

smart00449

Domain in SPla and the RYanodine Receptor; Domain of unknown function. Distant homologues are ...

349-493

5.23e-22

Domain in SPla and the RYanodine Receptor; Domain of unknown function. Distant homologues are domains in butyrophilin/marenostrin/pyrin homologues.

Pssm-ID: 214669 Cd Length: 122 Bit Score: 91.20 E-value: 5.23e-22

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 890799132   349 SGKHYWEVDVSGKGAWVLGLSDGSYlfcpifhsnaerNRLFCRGIKNDShyqpkyGFWVIGLWKKSVYNAFEECPFtgkp 428
Cdd:smart00449   1 SGRHYFEVEIGDGGHWRVGVATKSV------------PRGYFALLGEDK------GSWGYDGDGGKKYHNSTGPEY---- 58

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 890799132   429 svlTLSLMVPPCRVGVFLDYAAGTLSFYnisNNGT--LIYRFCTASFPDRVFPYFNPTGS-SEPMTIC 493
Cdd:smart00449  59 ---GLPLQEPGDVIGCFLDLEAGTISFY---KNGKylHGLAFFDVKFSGPLYPAFSLGSGnSVRLNFG 120

SPRY_PRY_TRIM50

cd13743

PRY/SPRY domain in tripartite motif-binding protein 50 (TRIM50); This domain, consisting of ...

341-496

1.69e-20

PRY/SPRY domain in tripartite motif-binding protein 50 (TRIM50); This domain, consisting of the distinct N-terminal PRY subdomain followed by the SPRY subdomain, is found at the C-terminus of TRIM50. TRIM50, an E3 ubiquitin ligase, is deleted in Williams-Beuren (WBS) syndrome, a multi-system neurodevelopmental disorder caused by the deletion of contiguous genes at chromosome region 7q11.23. It is specifically expressed in gastric parietal cells and may play an essential role in tubulovesicular dynamics. It also interacts with and increases the level of p62, a multifunctional adaptor protein that is implicated in various cellular processes such as the autophagy clearance of polyubiquitinated protein aggregates.

Pssm-ID: 293977 Cd Length: 189 Bit Score: 89.09 E-value: 1.69e-20

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 890799132 341 VLGHPAIQSGKHYWEVDVSGKGAWVLGLSDGSylfcpifhsNAERNRLfcrgIKNdshyqPKYGFWVIGLWKKSVYNAFE 420
Cdd:cd13743   56 VLASRGFSSGKHYWEVVVGSKSKWRLGLIKGT---------TSRKGKL----NKS-----PENGVWLIGLKEGRVYEAFA 117

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 890799132 421 eCPftgkpsVLTLSLMVPPCRVGVFLDYAAGTLSFYNISNNGTL--IYRFcTASFPDRVFPYFNptgssepmtICWPD 496
Cdd:cd13743  118 -NP------RVPLPLSTRPQRIGVFLDYEKGELTFYNADSPDELvpIYTF-QAEFQGKLYPLLD---------VCWHE 178

SPRY

pfam00622

SPRY domain; SPRY Domain is named from SPla and the RYanodine Receptor and it is found in many ...

351-481

2.10e-19

Pssm-ID: 459877 Cd Length: 121 Bit Score: 83.93 E-value: 2.10e-19

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 890799132  351 KHYWEVDVSG--KGAWVLGLSdgsylfcpifhsnaernRLFCRGiKNDSHYQPKYGFWVIGLWKKSVYNAFEEcPFTGKP 428
Cdd:pfam00622   1 RHYFEVEIFGqdGGGWRVGWA-----------------TKSVPR-KGERFLGDESGSWGYDGWTGKKYWASTS-PLTGLP 61

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|...
gi 890799132  429 svltlsLMVPPCRVGVFLDYAAGTLSFYNisNNGTLIYRFCTASFPDRVFPYF 481
Cdd:pfam00622  62 ------LFEPGDVIGCFLDYEAGTISFTK--NGKSLGYAFRDVPFAGPLFPAV 106

RING-HC_TRIM21_C-IV

cd16596

RING finger, HC subclass, found in tripartite motif-containing protein TRIM21 and similar ...

6-82

2.11e-19

RING finger, HC subclass, found in tripartite motif-containing protein TRIM21 and similar proteins; TRIM21, also known as 52 kDa Ro protein, 52 kDa ribonucleoprotein autoantigen Ro/SS-A, Ro(SS-A), RING finger protein 81 (RNF81), or Sjoegren syndrome type A antigen (SS-A), is a ubiquitously expressed E3 ubiquitin-protein ligase and a high affinity antibody receptor uniquely expressed in the cytosol of mammalian cells. As a cytosolic Fc receptor, TRIM21 binds the Fc of virus-associated antibodies and targets the complex in the cytosol for proteasomal degradation in a process known as antibody-dependent intracellular neutralization (ADIN), and provides an intracellular immune response to protect host defense against pathogen infection. It shows remarkably broad isotype specificity as it does not only bind IgG, but also IgM and IgA. Moreover, TRIM21 promotes the cytosolic DNA sensor cGAS and the cytosolic RNA sensor RIG-I sensing of viral genomes during infection by antibody-opsonized virus. It stimulates inflammatory signaling and activates innate transcription factors, such as nuclear factor-kappaB (NF-kappaB). TRIM21 also plays an essential role in p62-regulated redox homeostasis, suggesting it may be a viable target for treating pathological conditions resulting from oxidative damage. Furthermore, TRIM21 may have implications for various autoimmune diseases associated with uncontrolled antiviral signaling through the regulation of Nmi-IFI35 complex-mediated inhibition of innate antiviral response. TRIM21 belongs to the C-IV subclass of the TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a C3HC4-type RING-HC finger, Bbox1 and Bbox2, and a coiled coil region, as well as a B30.2/SPRY (SplA and ryanodine receptor) domain positioned C-terminal to the RBCC domain.

Pssm-ID: 438258 [Multi-domain] Cd Length: 77 Bit Score: 82.25 E-value: 2.11e-19

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 890799132   6 MKNLKEEVTCPVCLNLMVKPVSADCGHTFCQGCItlyFESIKCDKEmfSCPVCRLSYQSSNLRPNLHVANIVERLKE 82
Cdd:cd16596    3 LTMMWEEVTCPICLDPFVEPVSIECGHSFCQECI---SQVGKGGGS--VCPVCRQRFLLKNLRPNRQLANMVNNLKE 74

SPRY_PRY_TRIM72

cd13742

PRY/SPRY domain in tripartite motif-binding protein 72 (TRIM72); This domain, consisting of ...

308-493

3.88e-19

PRY/SPRY domain in tripartite motif-binding protein 72 (TRIM72); This domain, consisting of the distinct N-terminal PRY subdomain followed by the SPRY subdomain, is found at the C-terminus of TRIM72. Muscle-specific TRIM72 (also known as Mitsugumin 53 or MG53) has been shown to perform a critical function in membrane repair following acute muscle injury by nucleating the assembly of the repair machinery at injury sites. It is expressed specifically in skeletal muscle and heart, and tethered to the plasma membrane and cytoplasmic vesicles via its interaction with phosphatidylserine. TRIM72 interacts with dysferlin, a sarcolemmal protein whose deficiency causes Miyoshi myopathy (MM) and limb girdle muscular dystrophy type 2B (LGMD2B); this coordination plays an important role in the repair of sarcolemma damage.

Pssm-ID: 293976 [Multi-domain] Cd Length: 192 Bit Score: 85.30 E-value: 3.88e-19

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 890799132 308 HPNIAITDDKRQVRYEDHQASNLIHECE--NSHEGVLGHPAIQSGKHYWEVDVSGKGAWVLGLsdgsylfcpifhSNAER 385
Cdd:cd13742   22 HPYLVVSSDGKRVECADQKQAVSSDDPNrfDKANCVVSHQSFSEGEHYWEVIVGDKPRWALGV------------ISAEA 89

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 890799132 386 NRlfcrgiKNDSHYQPKYGFWVIGLWKKSVYNAFEEcpfTGKPSVLTLSlmVPPCRVGVFLDYAAGTLSFYNISNNGTLI 465
Cdd:cd13742   90 GR------KGRLHALPSNGFWLLGCKEGKVYEAHVE---HKEPRALRVE--GRPTRIGVYLSFSDGVLSFYDASDEDNLV 158

                        170       180       190
                 ....*....|....*....|....*....|....
gi 890799132 466 YRFC-TASFPDRVFPYFNPT-----GSSEPMTIC 493
Cdd:cd13742  159 QLFAfHERFPGPLYPFFDVCwhdkgKNSQPLKIF 192

RING-HC_TRIM25_C-IV

cd16597

RING finger, HC subclass, found in tripartite motif-containing protein TRIM25 and similar ...

9-79

5.22e-18

RING finger, HC subclass, found in tripartite motif-containing protein TRIM25 and similar proteins; TRIM25, also known as estrogen-responsive finger protein (EFP), RING finger protein 147 (RNF147), or RING-type E3 ubiquitin transferase, is an E3 ubiquitin/ISG15 ligase that is induced by estrogen and is therefore particularly abundant in placenta and uterus. TRIM25 regulates various cellular processes through E3 ubiquitin ligase activity, transferring ubiquitin and ISG15 to target proteins. It mediates K63-linked polyubiquitination of retinoic acid inducible gene I (RIG-I) that is crucial for downstream antiviral interferon signaling. It is also required for melanoma differentiation-associated gene 5 (MDA5) and mitochondrial antiviral signaling (MAVS, also known as IPS-1, VISA, Cardiff) mediated activation of nuclear factor-kappaB (NF-kappaB) and interferon production. Upon UV irradiation, TRIM25 interacts with mono-ubiquitinated PCNA and promotes its ISG15 modification (ISGylation), suggesting a crucial role in termination of error-prone translesion DNA synthesis. TRIM25 also functions as a novel regulator of p53 and Mdm2. It enhances p53 and Mdm2 abundance by inhibiting their ubiquitination and degradation in 26S proteasomes. Meanwhile, it inhibits p53's transcriptional activity and dampens the response to DNA damage, and is essential for medaka development and this dependence is rescued by silencing of p53. Moreover, TRIM25 is involved in the host cellular innate immune response against retroviral infection. It interferes with the late stage of feline leukemia virus (FeLV) replication. Furthermore, TRIM25 acts as an oncogene in gastric cancer. Its blockade by RNA interference inhibits migration and invasion of gastric cancer cells through transforming growth factor-beta (TGF-beta) signaling, suggesting it presents a novel target for the detection and treatment of gastric cancer. In addition, TRIM25 acts as an RNA-specific activator for Lin28a/TuT4-mediated uridylation. TRIM25 belongs to the C-IV subclass of TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a C3HC4-type RING-HC finger, Bbox1 and Bbox2, and a coiled coil region, as well as a B30.2/SPRY (SplA and ryanodine receptor) domain positioned C-terminal to the RBCC domain.

Pssm-ID: 438259 [Multi-domain] Cd Length: 71 Bit Score: 78.12 E-value: 5.22e-18

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 890799132   9 LKEEVTCPVCLNLMVKPVSADCGHTFCQGCITLYFESikCDKEMFSCPVCRLSYQSS-NLRPNLHVANIVER 79
Cdd:cd16597    2 LEEELTCSICLELFKDPVTLPCGHNFCGVCIEKTWDS--QHGSEYSCPQCRATFPRRpELHKNTVLRNIVEQ 71

SPRY_PRY_TRIM50_72

cd12897

PRY/SPRY domain in tripartite motif-binding (TRIM) proteins TRIM50 and TRIM72; This domain, ...

341-496

1.04e-17

PRY/SPRY domain in tripartite motif-binding (TRIM) proteins TRIM50 and TRIM72; This domain, consisting of the distinct N-terminal PRY subdomain followed by the SPRY subdomain, is found at the C-terminus of several TRIM proteins, including TRIM72 and TRIM50. TRIM72 (also known as MG53) has been shown to perform a critical function in membrane repair following acute muscle injury by nucleating the assembly of the repair machinery at injury sites. It is expressed specifically in skeletal muscle and heart, and tethered to the plasma membrane and cytoplasmic vesicles via its interaction with phosphatidylserine. TRIM50, an E3 ubiquitin ligase, is deleted in Williams-Beuren (WBS) syndrome, a multi-system neurodevelopmental disorder caused by the deletion of contiguous genes at chromosome region 7q11.23.

Pssm-ID: 293954 Cd Length: 191 Bit Score: 81.12 E-value: 1.04e-17

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 890799132 341 VLGHPAIQSGKHYWEVDVSGKGAWVLGLsdgsylfcpIFHSNAERNRLfcrgikndsHYQPKYGFWVIGLWKKSVYNAFe 420
Cdd:cd12897   56 VVASQGFSEGEHYWEVVVGDKPRWALGV---------IKGTASRKGKL---------HASPSHGVWLIGLKEGKVYEAH- 116

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 890799132 421 ECPFTGKPsvltlsLMVP--PCRVGVFLDYAAGTLSFYNIS--NNGTLIYRFcTASFPDRVFPYFNptgssepmtICWPD 496
Cdd:cd12897  117 GEPKEPRP------LRVAgrPHRIGVYLSFEDGVLSFFDASdpDDLRTLYTF-QERFQGKLYPFFD---------VCWHD 180

SPRY_PRY_TRIM41

cd13741

PRY/SPRY domain in tripartite motif-binding protein 41 (TRIM41); This domain, consisting of ...

308-493

3.58e-17

PRY/SPRY domain in tripartite motif-binding protein 41 (TRIM41); This domain, consisting of the distinct N-terminal PRY subdomain followed by the SPRY subdomain, is found at the C-terminus of tripartite motif-containing protein 41 (TRIM41). TRIM41 (also known as RING finger-interacting protein with C kinase or RINCK) is localized to speckles in the cytoplasm and nucleus, and functions as an E3 ligase that catalyzes the ubiquitin-mediated degradation of protein kinase C.

Pssm-ID: 240499 [Multi-domain] Cd Length: 199 Bit Score: 79.81 E-value: 3.58e-17

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 890799132 308 HPNIAITDDKRQVRYEDHQASNLIHECE-NSHEGVLGHPAIQSGKHYWEVDVSGKGAWVLGLSDGS--------YLFCPI 378
Cdd:cd13741   10 HPALLLSPDRRGVRLAERRQEVPEHPKRfSADCCVLGAQGFRSGRHYWEVEVGGRRGWAVGAARESthhkekvgSGGSSV 89

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 890799132 379 FHSNAERNRLFCRGIKNDSHYQP--KYGFWVIGLWKKSvYNAFEECPFTgkpsvlTLSLMVPPCRVGVFLDYAAGTLSFY 456
Cdd:cd13741   90 SSGDASSSRHHHRRRRLHLPQQPllQREVWCVGTNGKR-YQAQSSTEQT------LLSPSEKPRRFGVYLDYEAGRLGFY 162

                        170       180       190
                 ....*....|....*....|....*....|....*..
gi 890799132 457 NiSNNGTLIYRFCTASFPDRVFPYFNPTGSSEPMTIC 493
Cdd:cd13741  163 N-AETLAHVHTFSAAFLGERVFPFFRVLSKGTRIKLC 198

SPRY_PRY_C-I_2

cd12891

PRY/SPRY domain in tripartite motif-containing (TRIM) proteins, including TRIM14-like, ...

308-481

4.00e-17

PRY/SPRY domain in tripartite motif-containing (TRIM) proteins, including TRIM14-like, TRIM16-like, TRIM25-like, TRIM47-like, TRIM65 and RNF135, and stonustoxin; This domain, consisting of the distinct N-terminal PRY subdomain followed by the SPRY subdomain, is found at the C-terminus of several Class I TRIM proteins, including TRIM14, TRIM16 and TRIM25, TRIM47 as well as RING finger protein RNF135 and stonustoxin, a secreted poisonous protein of the stonefish Synanceja horrida. TRIM16 (also known as estrogen-responsive B box protein or EBBP) has E3 ubiquitin ligase activity. It is a regulator of keratinocyte differentiation and a tumor suppressor in retinoid-sensitive neuroblastoma. TRIM25 (also called Efp) ubiquitinates the N terminus of the viral RNA receptor retinoic acid-inducible gene-I (RIG-I) in response to viral infection, leading to activation of the RIG-I signaling pathway, thus resulting in type I interferon production to limit viral replication. It has been shown that the influenza A virus targets TRIM25 and disables its antiviral function. TRIM47, also known as GOA (Gene overexpressed in astrocytoma protein) or RNF100 (RING finger protein 100), is highly expressed in kidney tubular cells, but low expressed in most tissue. It is overexpressed in astrocytoma tumor cells and plays an important role in the process of dedifferentiation that is associated with astrocytoma tumorigenesis. RNF135 ubiquitinates RIG-I (retinoic acid-inducible gene-I) to promote interferon-beta induction during the early phase of viral infection. Stonustoxin (STNX) is a hypotensive and lethal protein factor that also possesses other biological activities such as species-specific hemolysis (due to its ability to form pores in the cell membrane) and platelet aggregation, edema-induction, and endothelium-dependent vasorelaxation (mediated by the nitric oxide pathway and activation of potassium channels). The PRY-SPRY domain in these TRIM families is suggested to serve as the target binding site.

Pssm-ID: 293949 [Multi-domain] Cd Length: 167 Bit Score: 78.83 E-value: 4.00e-17

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 890799132 308 HPNIAITDDKRQVRYEDHQASNLIHECENSHEGVLGHPAIQSGKHYWEVDVSGKGAWVLGLSdgsylfcpifhsnaernr 387
Cdd:cd12891    9 HNNLALSGDLKTVTCSSENQHYPDSPERFTHSQVLSTQSFSSGRHYWEVEVSESGGWSVGVA------------------ 70

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 890799132 388 lfCRGIK---NDSH--YQPK-YGFWVIGLwKKSVYNAFEECPFtgkPSvltlslmVPPCRVGVFLDYAAGTLSFYNISNN 461
Cdd:cd12891   71 --YPSIErkgDESRigRNDKsWCLEWQDK-SFSAWHNNEETPL---PS-------VSSRRLGVYLDYEAGRLSFYELSDP 137

                        170       180
                 ....*....|....*....|
gi 890799132 462 GTLIYRFcTASFPDRVFPYF 481
Cdd:cd12891  138 IRHLHTF-TATFTEPLHPAF 156

SPRY_PRY_TRIM58

cd15816

PRY/SPRY domain in tripartite motif-binding protein 58 (TRIM58), also known as BIA2; This ...

308-481

7.68e-17

PRY/SPRY domain in tripartite motif-binding protein 58 (TRIM58), also known as BIA2; This domain, consisting of the distinct N-terminal PRY subdomain followed by the SPRY subdomain, is found at the C-terminus of TRIM58, also known as BIA2. TRIM58 domains are composed of RING/B-box/coiled-coil core and also known as RBCC proteins.It is implicated by genome-wide association studies (GWAS) to regulate erythrocyte traits, including cell size and number. Trim58 facilitates erythroblast enucleation by inducing proteolytic degradation of the microtubule motor dynein.

Pssm-ID: 293988 [Multi-domain] Cd Length: 168 Bit Score: 77.91 E-value: 7.68e-17

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 890799132 308 HPNIAITDDKRQVryedhQASNLIHECENSHEG------VLGHPAIQSGKHYWEVDVSGKGAWVLGLSDGSylfcpifhs 381
Cdd:cd15816   10 HPSLLLTADLRSV-----QDGELWRDVPGNPERfdtwpcVLGLQSFSSGRHYWEVAVGEKAEWGLGVCQDS--------- 75

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 890799132 382 nAERnrlfcrgiKNDSHYQPKYGFWVIGLWKKSVYNAFeecpftGKPSVLTLSLMVPPcRVGVFLDYAAGTLSFYNISnN 461
Cdd:cd15816   76 -APR--------KGETTPSPENGVWAVWLLKGNEYMVL------ASPSVPLLQLRRPR-RVGVFLDYEAGEISFYNVT-A 138

                        170       180
                 ....*....|....*....|
gi 890799132 462 GTLIYRFcTASFPDRVFPYF 481
Cdd:cd15816  139 GSHIYTF-RQLFSGILRPYF 157

Bbox2_TRIM5-like

cd19761

B-box-type 2 zinc finger found in tripartite motif-containing proteins, TRIM5, TRIM6, TRIM22, ...

96-133

2.78e-16

Pssm-ID: 380819 [Multi-domain] Cd Length: 40 Bit Score: 72.53 E-value: 2.78e-16

                         10        20        30
                 ....*....|....*....|....*....|....*...
gi 890799132  96 CARHGEKLQLFCRKDMMAICWLCERSQEHRGHKTALIE 133
Cdd:cd19761    3 CEHHGEKLLLFCQEDGKVICWLCERSQEHRGHHTFLLE 40

RING-HC_TRIM26_C-IV

cd16598

RING finger, HC subclass, found in tripartite motif-containing protein 26 (TRIM26) and similar ...

9-70

2.95e-16

RING finger, HC subclass, found in tripartite motif-containing protein 26 (TRIM26) and similar proteins; TRIM26, also known as acid finger protein (AFP), RING finger protein 95 (RNF95), or zinc finger protein 173 (ZNF173), is an E3 ubiquitin-protein ligase that negatively regulates interferon-beta production and antiviral response through polyubiquitination and degradation of nuclear transcription factor IRF3. It functions as an important regulator for RNA virus-triggered innate immune response by bridging TBK1 to NEMO (NF-kappaB essential modulator, also known as IKKgamma) and mediating TBK1 activation. It also acts as a novel tumor suppressor of hepatocellular carcinoma by regulating cancer cell proliferation, colony forming ability, migration, and invasion. TRIM26 belongs the C-IV subclass of the TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a C3HC4-type RING-HC finger, a B-box, and two coiled coil domains, as well as a B30.2/SPRY (SplA and ryanodine receptor) domain positioned C-terminal to the RBCC domain.

Pssm-ID: 438260 [Multi-domain] Cd Length: 64 Bit Score: 72.89 E-value: 2.95e-16

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 890799132   9 LKEEVTCPVCLNLMVKPVSADCGHTFCQGCITLYFEsIKCDKEMFSCPVCRLSYQSSNLRPN 70
Cdd:cd16598    1 LEEEVTCSICLDYLRDPVTIDCGHNFCRSCITDYCP-ISGGHERPVCPLCRKPFKKENIRPN 61

SPRY_PRY_TRIM62

cd13744

PRY/SPRY domain in tripartite motif-binding protein 62 (TRIM62); This domain, consisting of ...

341-486

3.15e-16

PRY/SPRY domain in tripartite motif-binding protein 62 (TRIM62); This domain, consisting of the distinct N-terminal PRY subdomain followed by the SPRY subdomain, is found at the C-terminus of TRIM62. It is also called DEAR1 ductal epithelium (associated RING chromosome 1) and is involved in the morphogenesis of the mammary gland; loss of TRIM62 gene expression in breast is associated with increased risk of recurrence in early-onset breast cancer and thus, making TRIM62 a predictive biomarker. Non-small cell lung cancer lesions show a step-wise loss of TRIM62 levels during disease progression, indicating that it may play a role in the evolution of lung cancer. Decreased levels of TRIM62 also represent an independent adverse prognostic factor in AML.

Pssm-ID: 293978 Cd Length: 188 Bit Score: 76.96 E-value: 3.15e-16

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 890799132 341 VLGHPAIQSGKHYWEVDVSGKGAWVLGLSdgsylfcpifHSNAERnrlfcrgiKNDSHYQPKYGFWVIGLWKKSVYNAFE 420
Cdd:cd13744   57 VLGSEGFSGGVHYWEVVVSEKTQWMIGLA----------HEAVSR--------KGSIQIQPGRGFYCIVMHDGNQYSACT 118

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 890799132 421 EcPFTgkpsvlTLSLMVPPCRVGVFLDYAAGTLSFYNiSNNGTLIYRFcTASFPDRVFPYFNPTGS 486
Cdd:cd13744  119 E-PWT------RLNVKSKLEKVGVYLDYDKGLLIFYN-ADDMSWLYTF-REKFPGKLCSYFSPGQS 175

RING-HC_TRIM7-like_C-IV

cd16594

RING finger, HC subclass, found in tripartite motif-containing proteins, TRIM7, TRIM11 and ...

8-71

5.51e-16

RING finger, HC subclass, found in tripartite motif-containing proteins, TRIM7, TRIM11 and TRIM27, and similar proteins; TRIM7, TRIM11 and TRIM27, closely related tripartite motif-containing proteins, belong to the C-IV subclass of the TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a C3HC4-type RING-HC finger, Bbox2, and a coiled coil region, as well as a SPRY/B30.2 domain positioned C-terminal to the RBCC domain. TRIM7, also known as glycogenin-interacting protein (GNIP) or RING finger protein 90 (RNF90), is an E3 ubiquitin-protein ligase that mediates c-Jun/AP-1 activation by Ras signalling. Its phosphorylation and activation by MSK1 in response to direct activation by the Ras-Raf-MEK-ERK pathway can stimulate TRIM7 E3 ubiquitin ligase activity in mediating Lys63-linked ubiquitination of the AP-1 coactivator RACO-1, leading to RACO-1 protein stabilization. Moreover, TRIM7 binds and activates glycogenin, the self-glucosylating initiator of glycogen biosynthesis. TRIM11, also known as protein BIA1, or RING finger protein 92 (RNF92), is an E3 ubiquitin-protein ligase involved in the development of the central nervous system. It is overexpressed in high-grade gliomas and promotes proliferation, invasion, migration and glial tumor growth. TRIM11 acts as a potential therapeutic target for congenital central hypoventilation syndrome (CCHS) by mediating the degradation of CCHS-associated polyalanine-expanded Phox2b. TRIM11 modulates the function of neurogenic transcription factor Pax6 through the ubiquitin-proteosome system, and thus plays an essential role for Pax6-dependent neurogenesis. It also binds to and destabilizes a key component of the activator-mediated cofactor complex (ARC105), humanin, a neuroprotective peptide against Alzheimer's disease-relevant insults, and further regulates ARC105 function in transforming growth factor beta (TGFbeta) signaling. Moreover, TRIM11 negatively regulates retinoic acid-inducible gene-I (RIG-I)-mediated interferon-beta (IFNbeta) production and antiviral activity by targeting TANK-binding kinase-1 (TBK1). It may contribute to the endogenous restriction of retroviruses in cells. It enhances N-tropic murine leukemia virus (N-MLV) entry by interfering with Ref1 restriction. It also suppresses the early steps of human immunodeficiency virus HIV-1 transduction, resulting in decreased reverse transcripts. TRIM27, also known as RING finger protein 76 (RNF76), RET finger protein (RFP), or zinc finger protein RFP, is a nuclear E3 ubiquitin-protein ligase that is highly expressed in testis and in various tumor cell lines. Expression of TRIM27 is associated with prognosis of colon and endometrial cancers. TRIM27 was first identified as a fusion partner of the RET receptor tyrosine kinase. It functions as a transcriptional repressor and associates with several proteins involved in transcriptional activity, such as enhancer of polycomb 1 (Epc1), a member of the Polycomb group proteins, and Mi-2beta, a main component of the nucleosome remodeling and deacetylase (NuRD) complex, and the cell cycle regulator retinoblastoma protein (RB1). It also interacts with HDAC1, leading to downregulation of thioredoxin binding protein 2 (TBP-2), which inhibits the function of thioredoxin. Moreover, TRIM27 mediates Pax7-induced ubiquitination of MyoD in skeletal muscle atrophy. In addition, it inhibits muscle differentiation by modulating serum response factor (SRF) and Epc1. TRIM27 promotes a non-canonical polyubiquitination of PTEN, a lipid phosphatase that catalyzes PtdIns(3,4,5)P3 (PIP3) to PtdIns(4,5)P2 (PIP2). It is an IKKepsilon-interacting protein that regulates IkappaB kinase (IKK) function and negatively regulates signaling involved in the antiviral response and inflammation. TRIM27 also forms a protein complex with MBD4 or MBD2 or MBD3, and thus plays an important role in the enhancement of transcriptional repression through MBD proteins in tumorigenesis, spermatogenesis, and embryogenesis. It is a component of an estrogen receptor 1 (ESR1) regulatory complex that is involved in estrogen receptor-mediated transcription in MCF-7 cells.

Pssm-ID: 438256 [Multi-domain] Cd Length: 61 Bit Score: 71.95 E-value: 5.51e-16

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 890799132   8 NLKEEVTCPVCLNLMVKPVSADCGHTFCQGCITlyfesiKC---DKEMFSCPVCRLSYQSSNLRPNL 71
Cdd:cd16594    1 SLQEELTCPICLDYFTDPVTLDCGHSFCRACIA------RCweePETSASCPQCRETCPQRNLRPNR 61

RING-HC_TRIM38_C-IV

cd16600

RING finger, HC subclass, found in tripartite motif-containing protein 38 (TRIM38) and similar ...

9-59

2.02e-15

RING finger, HC subclass, found in tripartite motif-containing protein 38 (TRIM38) and similar proteins; TRIM38, also known as RING finger protein 15 (RNF15) or zinc finger protein RoRet, is an E3 ubiquitin-protein ligase that promotes K63- and K48-linked ubiquitination of cellular proteins and also catalyzes self-ubiquitination. It negatively regulates Tumor necrosis factor alpha (TNF-alpha)- and interleukin-1beta-triggered Nuclear factor-kappaB (NF-kappaB) activation by mediating lysosomal-dependent degradation of transforming growth factor beta (TGFbeta)-activated kinase 1 (TAK1)-binding protein (TAB)2/3, two critical components of the TAK1 kinase complex. It also inhibits TLR3/4-mediated activation of NF-kappaB and interferon regulatory factor 3 (IRF3) by mediating ubiquitin-proteasomal degradation of TNF receptor-associated factor 6 (Traf6) and NAK-associated protein 1 (Nap1), respectively. Moreover, TRIM38 negatively regulates TLR3-mediated interferon beta (IFN-beta) signaling by targeting ubiquitin-proteasomal degradation of TIR domain-containing adaptor inducing IFN-beta (TRIF). It functions as a valid target for autoantibodies in primary Sjogren's Syndrome. TRIM38 belongs the C-IV subclass of the TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a C3HC4-type RING-HC finger, a B-box, and two coiled coil domains, as well as a B30.2/SPRY (SplA and ryanodine receptor) domain positioned C-terminal to the RBCC domain.

Pssm-ID: 438262 [Multi-domain] Cd Length: 58 Bit Score: 70.57 E-value: 2.02e-15

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 890799132   9 LKEEVTCPVCLNLMVKPVSADCGHTFCQGCITLYFESIKCDK---EMFSCPVCR 59
Cdd:cd16600    2 MREEATCSICLQLMTEPVSINCGHSYCKRCIVSFLENQSQLEpglETFSCPQCR 55

SPRY_PRY_TRIM17

cd15812

PRY/SPRY domain of tripartite motif-binding protein 17 (TRIM17), also known as testis RING ...

316-481

2.57e-15

PRY/SPRY domain of tripartite motif-binding protein 17 (TRIM17), also known as testis RING finger protein (terf); This domain, consisting of the distinct N-terminal PRY subdomain followed by the SPRY subdomain, is found at the C-terminus of TRIM17, also known as RING finger protein 16 (RNF16) or testis RING finger protein (terf). TRIM17 domain is composed of RING/B-box/coiled-coil core and also known as RBCC protein, expressed almost exclusively in the testis. It exhibits E3 ligase activity, causing protein degradation of ZW10 interacting protein (ZWINT), a known component of the kinetochore complex required for the mitotic spindle checkpoint, and negatively regulates proliferation of breast cancer cells. TRIM17 undergoes ubiquitination in COS7 fibroblast-like cells but is inhibited and stabilized by TRIM44.

Pssm-ID: 293984 [Multi-domain] Cd Length: 176 Bit Score: 73.77 E-value: 2.57e-15

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 890799132 316 DKRQVRYedhqASNLIHECENSHEGVLGHP------AIQSGKHYWEV--DVSGKGAWVLGLsdgsylfCpifHSNAERnr 387
Cdd:cd15812   17 ESRQRRY----LSTPPDGTPCSKDRFLAYPcavgqeTFSSGRHYWEVgmNLTGDALWALGV-------C---RDNVSR-- 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 890799132 388 lfcrgiKNDSHYQPKYGFWVIGLWKKSVYNAfeecPFTGKPSVltlSLMVPPCRVGVFLDYAAGTLSFYNIsNNGTLIYR 467
Cdd:cd15812   81 ------KDRVPKSPENGFWVVQLSKGKKYLS----AMSALTPV---TLTEPPSHMGIFLDFEAGEVSFYSV-NDGSHLHT 146

                        170
                 ....*....|....
gi 890799132 468 FCTASFPDRVFPYF 481
Cdd:cd15812  147 YSQAAFPGPLQPFF 160

SPRY_PRY_TRIM15

cd15826

PRY/SPRY domain in tripartite motif-binding protein 15 (TRIM15); This domain, consisting of ...

301-481

9.84e-15

PRY/SPRY domain in tripartite motif-binding protein 15 (TRIM15); This domain, consisting of the distinct N-terminal PRY subdomain followed by the SPRY subdomain, is found at the C-terminus of tripartite motif-containing protein 15 (TRIM15), also referred to as RING finger protein 93 (RNF93) or Zinc finger protein B7 or 178 (ZNFB7 or ZNF178). TRIM15 domains are composed of RING/B-box/coiled-coil core and also known as RBCC proteins. The PRY and SPRY/B30.2 domains can function as immune defense components and in pathogen sensing. TRIM15 has been shown to regulate inflammatory and innate immune signaling, in addition to displaying antiviral activities. Down-regulation of TRIM15, as well as TRIM11, enhances virus release, suggesting that these proteins contribute to the endogenous restriction of retroviruses in cells. TRIM15 is also a regulatory component of focal adhesion turnover and cell migration.

Pssm-ID: 293998 [Multi-domain] Cd Length: 170 Bit Score: 72.21 E-value: 9.84e-15

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 890799132 301 VTL-VQNNHPNIAITDDKRQVRYEDHQASNLIH----ECEnshEGVLGHPAIQSGKHYWEVDVSgkgawvlgLSDGSYLF 375
Cdd:cd15826    2 VTLdPQTASGSLVLSEDRKSVRYTRQKQNLPDSplrfDGL---PAVLGSPGFSSGRHRWQVEVQ--------LGDGGGCT 70

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 890799132 376 CPIFHSNAERnrlfcrgiKNDSHYQPKYGFWVIGLwkksvynAFEECPFTGKPSVlTLSLMVPPCRVGVFLDYAAGTLSF 455
Cdd:cd15826   71 VGVAGESVRR--------KGEMGLSAEDGVWAVIL-------SHQQCWASTSPGT-DLPLSEIPRRVGVALDYEAGTVTL 134

                        170       180
                 ....*....|....*....|....*.
gi 890799132 456 YNiSNNGTLIYRFcTASFPDRVFPYF 481
Cdd:cd15826  135 TN-AETQEPIFTF-TASFSGKVFPFF 158

SPRY_PRY_C-II

cd13734

PRY/SPRY domain in tripartite motif-containing proteins 1, 9, 18, 36, 46, 67,76 (TRIM1, TRIM9, ...

308-481

9.92e-15

PRY/SPRY domain in tripartite motif-containing proteins 1, 9, 18, 36, 46, 67,76 (TRIM1, TRIM9, TRIM18, TRIM36, TRIM46, TRIM67, TRIM76); This domain, consisting of the distinct N-terminal PRY subdomain followed by the SPRY subdomain, is found at the C-terminus of several Class I TRIM proteins, including TRIM1, TRIM9, TRIM18, TRIM36, TRIM46, TRIM67 and TRIM76. TRIM1 (also known as MID2) and its close homolog, TRIM18 (also known as MID1), both contain a B30.2-like domain at their C-terminus and a single fibronectin type III (FN3) motif between it and their N-terminal RBCC domain. Their coiled-coil motifs mediate both homo- and heterodimerization, a prerequisite for association of the rapamycin-sensitive PP2A regulatory subunit Alpha 4 with microtubules. Mutations in TRIM18 have shown to cause Opitz syndrome, a disorder causing congenital anomalies such as cleft lip and palate as well as heart defects. TRIM9 is expressed mainly in the cerebral cortex, and functions as an E3 ubiquitin ligase. Its immunoreactivity is severely decreased in affected brain areas in Parkinson's disease and dementia with Lewy bodies, possibly playing an important role in the regulation of neuronal function and participating in pathological process of Lewy body disease through its ligase. TRIM36 interacts with centromere protein-H, one of the kinetochore proteins and possibly associates with chromosome segregation; an excess of TRIM36 may cause chromosomal instability. TRIM46 has not yet been characterized. TRIM67 negatively regulates Ras activity via degradation of 80K-H, leading to neural differentiation, including neuritogenesis. TRIM76 (also known as cardiomyopathy-associated protein 5 or CMYA5) is a muscle-specific member of the TRIM superfamily, but lacks the RING domain. It is possibly involved in protein kinase A signaling as well as vesicular trafficking. It has also been implicated in Duchenne muscular dystrophy and cardiac disease. The PRY-SPRY domain in these TRIM families is suggested to serve as the target binding site.

Pssm-ID: 293969 [Multi-domain] Cd Length: 166 Bit Score: 71.93 E-value: 9.92e-15

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 890799132 308 HPNIAITDDKRQVRYEDHQASNLIHECENSHEG---VLGHPAIQSGKHYWEVDVSGKGAWVLGLSDGSylfcpifhsnAE 384
Cdd:cd13734    9 HRKLRLSNDNLTVEYDPEGSKDQAAVLPRRFTGspaVLGDVAISSGRHYWEVSVSRSTSYRVGVAYKS----------AP 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 890799132 385 RNRlfCRGIKNDShyqpkygfWVIglwkkSVYNafEECPFTGKPSVLTLSLMVPPCRVGVFLDYAAGTLSFYNiSNNGTL 464
Cdd:cd13734   79 RDE--DLGKNSTS--------WCL-----SRDN--NRYTARHDGKVVDLRVTGHPARIGVLLDYDNGTLSFYD-AESKQH 140

                        170
                 ....*....|....*..
gi 890799132 465 IYRFCTaSFPDRVFPYF 481
Cdd:cd13734  141 LYTFHV-DFEGPVCPAF 156

RING-HC_TRIM17_C-IV

cd16595

RING finger, HC subclass, found in tripartite motif-containing protein TRIM17 and similar ...

8-70

5.07e-14

RING finger, HC subclass, found in tripartite motif-containing protein TRIM17 and similar proteins; TRIM17, also known as RING finger protein 16 (RNF16) or testis RING finger protein (Terf), is a crucial E3 ubiquitin ligase that is necessary and sufficient for neuronal apoptosis and contributes to Mcl-1 ubiquitination in cerebellar granule neurons (CGNs). It interacts in a SUMO-dependent manner with nuclear factor of activated T cell NFATc3 transcription factor, and thus inhibits the activity of NFATc3 by preventing its nuclear localization. In contrast, it binds to and inhibits NFATc4 transcription factor in a SUMO-independent manner. Moreover, TRIM17 stimulates degradation of kinetochore protein ZW10 interacting protein (ZWINT), a known component of the kinetochore complex required for the mitotic spindle checkpoint, and negatively regulates cell proliferation. TRIM17 belongs to the C-IV subclass of the TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a C3HC4-type RING-HC finger, Bbox1 and Bbox2, and a coiled coil region, as well as a B30.2/SPRY (SplA and ryanodine receptor) domain positioned C-terminal to the RBCC domain.

Pssm-ID: 438257 [Multi-domain] Cd Length: 70 Bit Score: 66.94 E-value: 5.07e-14

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 890799132   8 NLKEEVTCPVCLNLMVKPVSADCGHTFCQGCITLYFESIKCDKEM------FSCPVCRLSYQSSNLRPN 70
Cdd:cd16595    1 RLQEEATCSICLDYFTDPVMTTCGHNFCRACIQLSWEKARGKKGRrkqkgsFPCPECREMSPQRNLRPN 69

SPRY_PRY_SNTX

cd16040

Stonustoxin subunit alpha or SNTX subunit alpha; This domain, consisting of the distinct ...

293-470

2.20e-13

Stonustoxin subunit alpha or SNTX subunit alpha; This domain, consisting of the distinct N-terminal PRY subdomain followed by the SPRY subdomain, is found at the C-terminus of Stonustoxin alpha proteins. Stonustoxin (SNTX) is a multifunctional lethal protein isolated from venom elaborated by the stonefish. It comprises two subunits, termed alpha and beta. SNTX elicits an array of biological responses, particularly a potent hypotension and respiratory difficulties.

Pssm-ID: 294002 [Multi-domain] Cd Length: 180 Bit Score: 68.28 E-value: 2.20e-13

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 890799132 293 EAQRYWVQVTLVQNN-HPNIAITDDKRQVRYEDHQASNLIHE----------CEnshEGVlghpaiqSGKHYWEVDVSGK 361
Cdd:cd16040    3 EFLKYACQLTLDPNTaHRNLSLSEGNRKVTRVKEEQPYPDHPerfdywpqvlCR---EGL-------SGRCYWEVEWSGG 72

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 890799132 362 GAWV---------LGLSDGSylfcpIFHSNAERNRLFCrgikndshYQPKYGFWviglwkksvYNAfEECPFTGKPSvlt 432
Cdd:cd16040   73 GVDIavaykgisrKGDGDDS-----RFGYNDKSWSLEC--------SPSGYSFW---------HNN-KKTEISVPSS--- 126

                        170       180       190
                 ....*....|....*....|....*....|....*...
gi 890799132 433 lslmvPPCRVGVFLDYAAGTLSFYNISNNGTLIYRFCT 470
Cdd:cd16040  127 -----SSSRVGVYLDHSAGTLSFYSVSDTMTLLHTVQT 159

RING-HC_TRIM69_C-IV

cd16611

RING finger, HC subclass, found in tripartite motif-containing protein 69 (TRIM69) and similar ...

9-70

3.25e-13

RING finger, HC subclass, found in tripartite motif-containing protein 69 (TRIM69) and similar proteins; TRIM69, also known as RFP-like domain-containing protein trimless or RING finger protein 36 (RNF36), is a testis E3 ubiquitin-protein ligase that plays a specific role in apoptosis and may also play an important role in germ cell homeostasis during spermatogenesis. TRIM69 belongs to the C-IV subclass of the TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a C3HC4-type RING-HC finger, Bbox1 and Bbox2, and a coiled coil region, as well as a B30.2/SPRY (SplA and ryanodine receptor) domain positioned C-terminal to the RBCC domain.

Pssm-ID: 438273 [Multi-domain] Cd Length: 59 Bit Score: 64.39 E-value: 3.25e-13

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 890799132   9 LKEEVTCPVCLNLMVKPVSADCGHTFCQGCITLYFESIKCDKemfSCPVCRLSYQSSNLRPN 70
Cdd:cd16611    1 LTEELHCPLCLDFFRDPVMLSCGHNFCQSCITGFWELQAEDT---TCPECRELCQYRNLTPN 59

RING-HC_TRIM41-like_C-IV

cd16602

RING finger, HC subclass, found in tripartite motif-containing proteins TRIM41, TRIM52 and ...

10-70

1.07e-12

RING finger, HC subclass, found in tripartite motif-containing proteins TRIM41, TRIM52 and similar proteins; TRIM41 and TRIM52, two closely related tripartite motif-containing proteins, have dramatically expanded RING domains compared with the rest of the TRIM family proteins. TRIM41 belongs to the C-IV subclass of the TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a C3HC4-type RING-HC finger, Bbox1 and Bbox2, and a coiled coil region, as well as a B30.2/SPRY (SplA and ryanodine receptor) domain positioned C-terminal to the RBCC domain. In contrast, TRIM52 lacks the putative viral recognition SPRY/B30.2 domain, and thus has been classified to the C-V subclass of the TRIM family that contains only RBCC domains. TRIM41, also known as RING finger-interacting protein with C kinase (RINCK), is an E3 ubiquitin-protein ligase that promotes the ubiquitination of protein kinase C (PKC) isozymes in cells. It specifically recognizes the C1 domain of PKC isozymes. It controls the amplitude of PKC signaling by controlling the amount of PKC in the cell. TRIM52, also known as RING finger protein 102 (RNF102), is encoded by a novel, noncanonical antiviral TRIM52 gene in primate genomes with unique specificity determined by the rapidly evolving RING domain.

Pssm-ID: 438264 [Multi-domain] Cd Length: 53 Bit Score: 62.64 E-value: 1.07e-12

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 890799132  10 KEEVTCPVCLNLMVKPVSADCGHTFCQGCITLYFEsikcdkemFSCPVCRLSYQSSNLRPN 70
Cdd:cd16602    1 QEEAVCAICLDYFKDPVSIGCGHNFCRVCVTQLWG--------FTCPQCRKSFPRRSFRPN 53

SPRY_PRY_TRIM4

cd15809

PRY/SPRY domain in tripartite motif-binding protein 4 (TRIM4), also known as RING finger ...

341-481

1.36e-12

PRY/SPRY domain in tripartite motif-binding protein 4 (TRIM4), also known as RING finger protein 87 (RNF87); This domain, consisting of the distinct N-terminal PRY subdomain followed by the SPRY subdomain, is found at the C-terminus of TRIM4 which is also known as RING finger protein 87 (RNF87). TRIM4 domain is composed of RING/B-box/coiled-coil core and also known as RBCC protein. It is a positive regulator of RIG-I-mediated interferon (IFN) induction. It regulates virus-induced IFN induction and cellular antiviral innate immunity by targeting RIG-I for K63-linked poly-ubiquitination. Over-expression of TRIM4 enhances virus-triggered activation of transcription factors IRF3 and NF-kappaB, as well as IFN-beta induction. Expression of TRIM4 differs significantly in Huntington's Disease (HD) neural cells when compared with wild-type controls, possibly impacting down-regulation of the Huntingtin (HTT) gene, which is involved in the regulation of diverse cellular activities that are impaired in Huntington's Disease (HD) cells.

Pssm-ID: 293981 Cd Length: 191 Bit Score: 66.39 E-value: 1.36e-12

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 890799132 341 VLGHPAIQSGKHYWEVDVSGKGAWVLGLsdgsylfcpifhsnaernrlfCR----GIKNDSHYQPKYGFWVIGlWKKSVY 416
Cdd:cd15809   66 VLGKNVFTSGKHYWEVENRDSLEIAVGV---------------------CRedvmGITDGSEMSPHVGIWAIC-WSSAGY 123

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 890799132 417 NafeecPFTGKPSVLTlSLMVPPCRVGVFLDYAAGTLSFYNiSNNGTLIYRFcTASFPDRVFPYF 481
Cdd:cd15809  124 R-----PLTSSPVSPT-KQEPALHRVGVFLDHGAGEVSFYS-AVDGVHLHTF-SCPLVSRLRPFF 180

RING-HC_BRCA1

cd16498

RING finger, HC subclass, found in breast cancer type 1 susceptibility protein (BRCA1) and ...

8-82

1.45e-12

RING finger, HC subclass, found in breast cancer type 1 susceptibility protein (BRCA1) and similar proteins; BRCA1, also known as RING finger protein 53 (RNF53), is a RING finger protein encoded by the tumor suppressor gene BRCA1 that regulates all DNA double-strand break (DSB) repair pathways. BRCA1 is frequently mutated in patients with hereditary breast and ovarian cancer (HBOC). Its mutation is also associated with an increased risk of pancreatic, stomach, laryngeal, fallopian tube, and prostate cancer. It plays an important role in the DNA damage response signaling and has been implicated in various cellular processes such as cell cycle regulation, transcriptional regulation, chromatin remodeling, DNA DSBs, and apoptosis. BRCA1 contains an N-terminal C3HC4-type RING-HC finger, and two BRCT (BRCA1 C-terminus domain) repeats at the C-terminus.

Pssm-ID: 438161 [Multi-domain] Cd Length: 94 Bit Score: 63.47 E-value: 1.45e-12

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 890799132   8 NLKEEVTCPVCLNLMVKPVSADCGHTFCQGCITLYFESIKcdKEMFsCPVCRLSYQSSNLRPNLHVANIVERLKE 82
Cdd:cd16498   12 AMQKNLECPICLELLKEPVSTKCDHQFCRFCILKLLQKKK--KPAP-CPLCKKSVTKRSLQESTRFKQLVEAVKK 83

RING-HC_TRIM58_C-IV

cd16606

RING finger, HC subclass, found in tripartite motif-containing protein TRIM58 and similar ...

11-59

5.61e-12

RING finger, HC subclass, found in tripartite motif-containing protein TRIM58 and similar proteins; TRIM58, also known as protein BIA2, is an erythroid E3 ubiquitin-protein ligase induced during late erythropoiesis. It binds and ubiquitinates the intermediate chain of the microtubule motor dynein (DYNC1LI1/DYNC1LI2), stimulating the degradation of the dynein holoprotein complex. It may participate in the erythroblast enucleation process through regulation of nuclear polarization. TRIM58 belongs to the C-IV subclass of TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a C3HC4-type RING-HC finger, Bbox1 and Bbox2, and a coiled coil region, as well as a B30.2/SPRY (SplA and ryanodine receptor) domain positioned C-terminal to the RBCC domain.

Pssm-ID: 438268 [Multi-domain] Cd Length: 53 Bit Score: 60.64 E-value: 5.61e-12

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|
gi 890799132  11 EEVTCPVCLNLMVKPVSADCGHTFCQGCITLYFESIKCDKE-MFSCPVCR 59
Cdd:cd16606    1 EEARCPVCLDFLQEPVSVDCGHSFCLRCISEFCEKSDSAQGgVYACPQCR 50

RING-HC_TRIM4_C-IV

cd16590

RING finger, HC subclass, found in tripartite motif-containing protein TRIM4 and similar ...

7-70

7.92e-12

RING finger, HC subclass, found in tripartite motif-containing protein TRIM4 and similar proteins; TRIM4 belongs to the C-IV subclass of the TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a C3HC4-type RING-HC finger, Bbox2, and a coiled coil region, as well as a SPRY/B30.2 domain positioned C-terminal to the RBCC domain. TRIM4, also known as RING finger protein 87 (RNF87), is a cytoplasmic E3 ubiquitin-protein ligase that has recently evolved and is present only in higher mammals. It transiently interacts with mitochondria, induces mitochondrial aggregation and sensitizes the cells to hydrogen peroxide (H2O2) induced death. Its interaction with peroxiredoxin 1 (PRX1) is critical for the regulation of H2O2 induced cell death. Moreover, TRIM4 functions as a positive regulator of RIG-I-mediated type I interferon induction. It regulates the K63-linked ubiquitination of RIG-1 and assembly of antiviral signaling complex at the mitochondria.

Pssm-ID: 438252 [Multi-domain] Cd Length: 61 Bit Score: 60.43 E-value: 7.92e-12

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 890799132   7 KNLKEEVTCPVCLNLMVKPVSADCGHTFCQGCITLYFESikcDKEMFSCPVCRLSYQSSNLRPN 70
Cdd:cd16590    1 EDIQEELTCPICLDYFQDPVSIECGHNFCRGCLHRNWAP---GGGPFPCPECRHPSAPAALRPN 61

SPRY_PRY_TRIM14

cd13738

PRY/SPRY domain of tripartite motif-binding protein 14 (TRIM14); This is a TRIM14 domain ...

308-481

1.12e-11

PRY/SPRY domain of tripartite motif-binding protein 14 (TRIM14); This is a TRIM14 domain family contains residues in the N-terminus that form a distinct PRY domain structure such that the B30.2 domain consists of PRY and SPRY subdomains. TRIM14 domains have yet to be characterized. These B30.2 domains are a more recent adaptation where the SPRY/PRY combination is a possible component of immune defense. It belongs to Class IV TRIM protein family which has members involved in antiviral immunity at various levels of interferon signaling cascade.

Pssm-ID: 293973 [Multi-domain] Cd Length: 173 Bit Score: 63.27 E-value: 1.12e-11

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 890799132 308 HPNIAITDDKRQVRYEDHQASNLIHECE-NSHEGVLGHPAIQSGKHYWEVDV--SGKGAWVlGLSDGSYLFcpifHSNAE 384
Cdd:cd13738    9 HPRLRLSDDRLTVSCGWLGTLGLCPPQRfDKLWQVLSRDSFFSGRHYWEVDLqeAGAGWWV-GAAYPSIGR----KGDSE 83

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 890799132 385 RNRLfcrGIKNDSHYQPKYGFwviglwkksVYNAFEECPFTgkpsvlTLSLMVPPCRVGVFLDYAAGTLSFYNISNNGTL 464
Cdd:cd13738   84 AARL---GWNRQSWCLKRYDL---------EYWAFHDGQRS------RLRPEDDPDRLGVFLDYEAGILSFYDVTGGMTH 145

                        170
                 ....*....|....*..
gi 890799132 465 IYRFCtASFPDRVFPYF 481
Cdd:cd13738  146 LHTFR-ATFQEPLYPAL 161

RING-HC_TRIM65_C-IV

cd16609

RING finger, HC subclass, found in tripartite motif-containing protein TRIM65 and similar ...

11-62

1.16e-11

RING finger, HC subclass, found in tripartite motif-containing protein TRIM65 and similar proteins; TRIM65 is an E3 ubiquitin-protein ligase that interacts with the innate immune receptor MDA5, enhancing its ability to stimulate interferon-beta signaling. It functions as a potential oncogenic protein that negatively regulates p53 through ubiquitination, providing insight into the development of novel approaches targeting TRIM65 for non-small cell lung carcinoma (NSCLC) treatment, and also overcoming chemotherapy resistance. Moreover, TRIM65 negatively regulates microRNA-driven suppression of mRNA translation by targeting TNRC6 proteins for ubiquitination and degradation. TRIM65 belongs to the C-IV subclass of the TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a C3HC4-type RING-HC finger, Bbox1 and Bbox2, and a coiled coil region, as well as a B30.2/SPRY (SplA and ryanodine receptor) domain positioned C-terminal to the RBCC domain.

Pssm-ID: 438271 [Multi-domain] Cd Length: 58 Bit Score: 59.69 E-value: 1.16e-11

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 890799132  11 EEVTCPVCLNLMVKPVSADCGHTFCQGCITLYFEsiKCDKEMFSCPVCRLSY 62
Cdd:cd16609    2 EELTCSICLGLYQDPVTLPCQHSFCRACIEDHWR--QKDEGSFSCPECRAPF 51

Bbox2_TRIM68_C-IV

cd19795

B-box-type 2 zinc finger found in tripartite motif-containing protein 68 (TRIM68) and similar ...

96-136

1.74e-11

B-box-type 2 zinc finger found in tripartite motif-containing protein 68 (TRIM68) and similar proteins; TRIM68, also known as RING finger protein 137 (RNF137) or SSA protein SS-56 (SS-56), is an E3 ubiquitin-protein ligase that negatively regulates Toll-like receptor (TLR)- and RIG-I-like receptor (RLR)-driven type I interferon production by degrading TRK fused gene (TFG), a novel driver of IFN-beta downstream of anti-viral detection systems. It also functions as a cofactor for androgen receptor-mediated transcription by regulating ligand-dependent transcription of androgen receptor in prostate cancer cells. Moreover, TRIM68 is a cellular target of autoantibody responses in Sjogren's syndrome (SS), as well as systemic lupus erythematosus (SLE). It is also an auto-antigen for T cells in SS and SLE. TRIM68 belongs the C-IV subclass of TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a RING finger, Bbox2, and two coiled coil domains, as well as a B30.2/SPRY (SplA and ryanodine receptor) domain positioned C-terminal to the RBCC domain. The type 2 B-box (Bbox2) zinc finger is characterized by a CHC3H2 zinc-binding consensus motif.

Pssm-ID: 380853 [Multi-domain] Cd Length: 44 Bit Score: 59.00 E-value: 1.74e-11

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|.
gi 890799132  96 CARHGEKLQLFCRKDMMAICWLCERSQEHRGHKTALIEEVA 136
Cdd:cd19795    4 CERHKEKLNLFCEEDQELLCVVCEQSPEHKAHTVVPVEEAA 44

RING-HC_TRIM35_C-IV

cd16599

RING finger, HC subclass, found in tripartite motif-containing protein 35 (TRIM35) and similar ...

9-78

1.98e-11

RING finger, HC subclass, found in tripartite motif-containing protein 35 (TRIM35) and similar proteins; TRIM35, also known as hemopoietic lineage switch protein 5 (HLS5), is a putative hepatocellular carcinoma (HCC) suppressor that inhibits phosphorylation of pyruvate kinase isoform M2 (PKM2), which is involved in aerobic glycolysis of cancer cells and further suppresses the Warburg effect and tumorigenicity in HCC. It also negatively regulates Toll-like receptor 7 (TLR7)- and TLR9-mediated type I interferon production by suppressing the stability of interferon regulatory factor 7 (IRF7). Moreover, TRIM35 regulates erythroid differentiation by modulating globin transcription factor 1 (GATA-1) activity. TRIM35 belongs to the C-IV subclass of the TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a C3HC4-type RING-HC finger, Bbox1 and Bbox2, and a coiled coil region, as well as a B30.2/SPRY (SplA and ryanodine receptor) domain positioned C-terminal to the RBCC domain.

Pssm-ID: 438261 [Multi-domain] Cd Length: 66 Bit Score: 59.40 E-value: 1.98e-11

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 890799132   9 LKEEVTCPVCLNLMVKPVSADCGHTFCQGCITLYFEsiKCDKEmfSCPVCRLSYQSSNLRPNLHVANIVE 78
Cdd:cd16599    1 FKEELLCPICYEPFREAVTLRCGHNFCKGCVSRSWE--RQPRA--PCPVCKEASSSDDLRTNHTLNNLVE 66

RING-HC_RNF39

cd16592

RING finger, HC subclass, found in RING finger protein 39 (RNF39) and similar proteins; RNF39, ...

9-61

3.96e-11

RING finger, HC subclass, found in RING finger protein 39 (RNF39) and similar proteins; RNF39, also called protein HZFw, may play a role in prolonged long term-potentiation (LTP) maintenance. It is involved in the etiology of Behcet's disease (BD). It may also be involved in HIV-1 replication. RNF39 acts as an E3 ubiquitin ligase that inhibits retinoic acid-inducible gene-I (RIG-I)-like receptor (RLR) pathways by mediating K48-linked ubiquitination and proteasomal degradation of DDX3X (DEAD-box RNA helicase 3, X-linked). RNF39 contains a typical C3HC4-type RING-HC finger.

Pssm-ID: 438254 [Multi-domain] Cd Length: 58 Bit Score: 58.23 E-value: 3.96e-11

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 890799132   9 LKEEVTCPVCLNLMVKPVSADCGHTFCQGCITLYFESIK---CDKEMFSCPVCRLS 61
Cdd:cd16592    1 LQEETTCPICLGYFKDPVILDCEHSFCRACIARHWGQEAmegNGAEGVFCPQCGEP 56

Bbox2_TRIM7-like

cd19762

B-box-type 2 zinc finger found in tripartite motif-containing proteins TRIM7, TRIM27 and ...

96-136

9.06e-11

B-box-type 2 zinc finger found in tripartite motif-containing proteins TRIM7, TRIM27 and similar proteins; The family includes TRIM7 and TRIM27, both of which belong to the C-IV subclass of TRIM (tripartite motif) family of proteins that are defined by an N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a RING finger, Bbox2, and a coiled coil region, as well as a B30.2/SPRY (SplA and ryanodine receptor) domain positioned C-terminal to the RBCC domain. The type 2 B-box (Bbox2) zinc finger is characterized by a CHC3H2 zinc-binding consensus motif. TRIM7, also known as glycogenin-interacting protein (GNIP) or RING finger protein 90 (RNF90), is an E3 ubiquitin-protein ligase that mediates c-Jun/AP-1 activation by Ras signalling. Its phosphorylation and activation by MSK1 in response to direct activation by the Ras-Raf-MEK-ERK pathway can stimulate TRIM7 E3 ubiquitin ligase activity in mediating Lys63-linked ubiquitination of the AP-1 coactivator RACO-1, leading to RACO-1 protein stabilization. Moreover, TRIM7 binds and activates glycogenin, the self-glucosylating initiator of glycogen biosynthesis. TRIM27, also termed RING finger protein 76 (RNF76), or RET finger protein (RFP), or zinc finger protein RFP, is a nuclear E3 ubiquitin-protein ligase that is highly expressed in testis and in various tumor cell lines. Expression of TRIM27 is associated with prognosis of colon and endometrial cancers. TRIM27 was first identified as a fusion partner of the RET receptor tyrosine kinase. It functions as a transcriptional repressor and associates with several proteins involved in transcriptional activity, such as enhancer of polycomb 1 (Epc1), a member of the Polycomb group proteins, and Mi-2beta, a main component of the nucleosome remodeling and deacetylase (NuRD) complex, and the cell cycle regulator retinoblastoma protein (RB1). It also interacts with HDAC1, leading to downregulation of thioredoxin binding protein 2 (TBP-2), which inhibits the function of thioredoxin. Moreover, TRIM27 mediates Pax7-induced ubiquitination of MyoD in skeletal muscle atrophy. It also inhibits muscle differentiation by modulating serum response factor (SRF) and Epc1. Furthermore, TRIM27 promotes non-canonical polyubiquitination of PTEN, a lipid phosphatase that catalyzes PtdIns(3,4,5)P3 (PIP3) to PtdIns(4,5)P2 (PIP2). It is an IKKepsilon-interacting protein that regulates IkappaB kinase (IKK) function and negatively regulates signaling involved in the antiviral response and inflammation. In addition, TRIM27 forms a protein complex with MBD4 or MBD2 or MBD3, and thus plays an important role in the enhancement of transcriptional repression through MBD proteins in tumorigenesis, spermatogenesis, and embryogenesis. It is also a component of an estrogen receptor 1 (ESR1) regulatory complex, and is involved in estrogen receptor-mediated transcription in MCF-7 cells. Meanwhile, TRIM27 interacts with the hinge region of chromosome 3 protein (SMC3), a component of the multimeric cohesin complex that holds sister chromatids together and prevents their premature separation during mitosis.

Pssm-ID: 380820 [Multi-domain] Cd Length: 44 Bit Score: 56.94 E-value: 9.06e-11

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|.
gi 890799132  96 CARHGEKLQLFCRKDMMAICWLCERSQEHRGHKTALIEEVA 136
Cdd:cd19762    3 CEKHQEPLKLFCKEDKRPICVVCDRSREHRHHTVLPVEEAA 43

Bbox2_TRIM39-like

cd19780

B-box-type 2 zinc finger found in tripartite motif-containing proteins TRIM39, TRIM58 and ...

96-134

1.07e-10

B-box-type 2 zinc finger found in tripartite motif-containing proteins TRIM39, TRIM58 and similar proteins; The family includes TRIM39 and TRIM58, both of which belong to the C-IV subclass of TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a RING finger, Bbox2, and a coiled coil region, as well as a SPRY/B30.2 domain positioned C-terminal to the RBCC domain. The type 2 B-box (Bbox2) zinc finger is characterized by a CHC3H2 zinc-binding consensus motif. TRIM39, also termed RING finger protein 23 (RNF23), or testis-abundant finger protein, is an E3 ubiquitin-protein ligase that plays a role in controlling DNA damage-induced apoptosis through inhibition of the anaphase promoting complex (APC/C), a multiprotein ubiquitin ligase that controls multiple cell cycle regulators, including cyclins, geminin, and others. TRIM39 also functions as a regulator of several key processes in the proliferative cycle. It directly regulates p53 stability and modulates cell cycle progression and DNA damage responses via stabilization of p21. TRIM39 also negatively regulates the nuclear factor kappaB (NFkappaB)-mediated signaling pathway through stabilization of Cactin, an inhibitor of NFkappaB- and Toll-like receptor (TLR)-mediated transcription, which is induced by inflammatory stimulants such as tumor necrosis factor alpha (TNFalpha). TRIM39 is a MOAP-1-binding protein that can promote apoptosis signaling through stabilization of MOAP-1 via the inhibition of its poly-ubiquitination process. TRIM58, also known as protein BIA2, is an erythroid E3 ubiquitin-protein ligase induced during late erythropoiesis. It binds and ubiquitinates the intermediate chain of the microtubule motor dynein (DYNC1LI1/DYNC1LI2), stimulating the degradation of the dynein holoprotein complex. It may participate in the erythroblast enucleation process through regulation of nuclear polarization.

Pssm-ID: 380838 [Multi-domain] Cd Length: 44 Bit Score: 56.70 E-value: 1.07e-10

                         10        20        30
                 ....*....|....*....|....*....|....*....
gi 890799132  96 CARHGEKLQLFCRKDMMAICWLCERSQEHRGHKTALIEE 134
Cdd:cd19780    5 CARHREALSLFCEEDQEAVCLVCEISHDHRAHTLVPLQD 43

RING-HC_TRIM10_C-IV

cd16593

RING finger, HC subclass, found in tripartite motif-containing protein 10 (TRIM10) and similar ...

8-66

1.36e-10

RING finger, HC subclass, found in tripartite motif-containing protein 10 (TRIM10) and similar proteins; TRIM10, also known as B30-RING finger protein (RFB30), RING finger protein 9 (RNF9), or hematopoietic RING finger 1 (HERF1), is a novel hematopoiesis-specific RING finger protein required for terminal differentiation of erythroid cells. TRIM10 belongs to the C-IV subclass of the TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a C3HC4-type RING-HC finger, Bbox1 and Bbox2, and a coiled coil region, as well as a B30.2/SPRY (SplA and ryanodine receptor) domain positioned C-terminal to the RBCC domain.

Pssm-ID: 438255 [Multi-domain] Cd Length: 61 Bit Score: 56.84 E-value: 1.36e-10

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 890799132   8 NLKEEVTCPVCLNLMVKPVSADCGHTFCQGCITLYFESIKCDKEM-FSCPVCRLSYQSSN 66
Cdd:cd16593    1 SLADEVNCPICQGTLREPVTIDCGHNFCRACLTRYCEIPGPDLEEpPTCPLCKEPFRPGE 60

SPRY_PRY_RNF135

cd12902

PRY/SPRY domain in RING finger protein RNF135; This domain, consisting of the distinct ...

308-481

2.13e-10

PRY/SPRY domain in RING finger protein RNF135; This domain, consisting of the distinct N-terminal PRY subdomain followed by the SPRY subdomain, is found at the C-terminus of the RING finger protein RNF135 (also known as Riplet/RNF135), which ubiquitinates RIG-I (retinoic acid-inducible gene-I) to promote interferon-beta induction during the early phase of viral infection. Normally, RIG-I is activated by TRIM25 in response to viral infection, leading to activation of the RIG-I signaling pathway, thus resulting in type I interferon production to limit viral replication. However, RNF135, consisting of an N-terminal RING finger domain, C-terminal SPRY and PRY motifs and showing sequence similarity to TRIM25, acts as an alternative factor that promotes RIG-I activation independent of TRIM25.

Pssm-ID: 293959 [Multi-domain] Cd Length: 168 Bit Score: 59.45 E-value: 2.13e-10

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 890799132 308 HPNIAITDDKRQVRYEDHQASNLIHECENSHEGVLGHPAIQSGKHYWEVDVSGKGAWVLGLSDGSylfcpifhsnAERNR 387
Cdd:cd12902    9 SCSLEVSEDSRKVTVSHGPQAYAWSPDRFSISQVLCSQAFSSGQHYWEVDTRQCSHWAVGVASWE----------MSRDQ 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 890799132 388 LFCRgiKNDShyqpkygfWVI---GLWKKSVYNAFEECPF-TGKPSVltlslmvppcrVGVFLDYAAGTLSFYNISNNGT 463
Cdd:cd12902   79 MLGR--TMDS--------WCIewkGTGQLSAWHMNKETVLgSDKPRV-----------VGIWLDLEEGKLAFYSVANQER 137

                        170
                 ....*....|....*...
gi 890799132 464 LIYRfCTASFPDRVFPYF 481
Cdd:cd12902  138 LLHE-CEVSASSPLHPAF 154

RING-HC_TRIM31_C-V

cd16582

RING finger, HC subclass, found in tripartite motif-containing protein 31 (TRIM31) and similar ...

12-58

3.02e-10

RING finger, HC subclass, found in tripartite motif-containing protein 31 (TRIM31) and similar proteins; TRIM31 is an E3 ubiquitin-protein ligase that primarily localizes to the cytoplasm, but is also associated with the mitochondria. It can negatively regulate cell proliferation and may be a potential biomarker of gastric cancer as it is overexpressed from the early stage of gastric carcinogenesis. TRIM31 is downregulated in non-small cell lung cancer and serves as a potential tumor suppressor. It interacts with p52 (Shc) and inhibits Src-induced anchorage-independent growth. TRIM31 belongs to the C-V subclass of the TRIM (tripartite motif) family of proteins that are defined by an N-terminal RBCC (RING, Bbox, and coiled coil) domain, including three consecutive zinc-binding domains, a C3HC4-type RING-HC finger, Bbox1 and Bbox2, and a coiled coil region, as well as an uncharacterized region positioned C-terminal to the RBCC domain.

Pssm-ID: 438244 [Multi-domain] Cd Length: 44 Bit Score: 55.22 E-value: 3.02e-10

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
gi 890799132  12 EVTCPVCLNLMVKPVSADCGHTFCQGCITlyfESIKCDKEMFSCPVC 58
Cdd:cd16582    1 EVICPICLDILQKPVTIDCGHNFCLQCIT---QIGETSCGFFKCPLC 44

RING-HC_TRIM43-like_C-IV

cd16603

RING finger, HC subclass, found in tripartite motif-containing proteins TRIM43, TRIM48, TRIM49, ...

12-70

3.25e-10

RING finger, HC subclass, found in tripartite motif-containing proteins TRIM43, TRIM48, TRIM49, TRIM51, TRIM64 and similar proteins; The family includes a group of closely related uncharacterized tripartite motif-containing proteins, TRIM43, TRIM43B, TRIM48/RNF101, TRIM49/RNF18, TRIM49B, TRIM49C/TRIM49L2, TRIM49D/TRIM49L, TRIM51/SPRYD5, TRIM64, TRIM64B, and TRIM64C, whose biological function remain unclear. TRIM49, also known as testis-specific RING-finger protein, has moderate similarity with SS-A/Ro52 antigen, suggesting it may be one of the target proteins of autoantibodies in the sera of patients with these autoimmune disorders. All family members belong to the C-IV subclass of the TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains as well as a SPRY/B30.2 domain positioned C-terminal to the RBCC domain. In RBCC region, they all have a C3HC4-type RING-HC finger.

Pssm-ID: 438265 [Multi-domain] Cd Length: 59 Bit Score: 55.57 E-value: 3.25e-10

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 890799132  12 EVTCPVCLNLMVKPVSADCGHTFCQGCITLYFESIKCdkeMFSCPVCRLSYQSSNLRPN 70
Cdd:cd16603    4 ELTCPICMNYFIDPVTIDCGHSFCRPCLYLNWQDIPF---LAQCPECRKTTEQRNLKTN 59

zf-C3HC4_4

pfam15227

zinc finger of C3HC4-type, RING; This is a family of primate-specific Ret finger protein-like ...

15-58

3.49e-10

Pssm-ID: 464570 [Multi-domain] Cd Length: 42 Bit Score: 55.13 E-value: 3.49e-10

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 890799132   15 CPVCLNLMVKPVSADCGHTFCQGCITLYFEsiKCDKEMFSCPVC 58
Cdd:pfam15227   1 CPICLDYLEKPVSIECGHSFCLSCINSLQK--EPDGESLLCPQC 42

RING-HC_TRIM40-C-V

cd16583

RING finger, HC subclass, found in tripartite motif-containing protein 40 (TRIM40) and similar ...

11-59

4.21e-10

RING finger, HC subclass, found in tripartite motif-containing protein 40 (TRIM40) and similar proteins; TRIM40, also known as probable E3 NEDD8-protein ligase or RING finger protein 35 (RNF35), is highly expressed in the gastrointestinal tract including the stomach, small intestine, and large intestine. It enhances neddylation of inhibitor of nuclear factor kappaB kinase subunit gamma (IKKgamma), inhibits the activity of nuclear factor-kappaB (NF-kappaB)-mediated transcription, and thus prevents inflammation-associated carcinogenesis in the gastrointestinal tract. TRIM40 belongs to the C-V subclass of the TRIM (tripartite motif) family of proteins that are defined by an N-terminal RBCC (RING, Bbox, and coiled coil) domain, including three consecutive zinc-binding domains, a C3HC4-type RING-HC finger, Bbox1 and Bbox2, and a coiled coil region, as well as an uncharacterized region positioned C-terminal to the RBCC domain.

Pssm-ID: 438245 [Multi-domain] Cd Length: 63 Bit Score: 55.61 E-value: 4.21e-10

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*....
gi 890799132  11 EEVTCPVCLNLMVKPVSADCGHTFCQGCITLYFESIKCDKEmFSCPVCR 59
Cdd:cd16583    4 EEGVCPICQEPLKEAVSTDCGHLFCRMCLTQHAKKASASGV-FSCPVCR 51

RING-HC_AtBARD1-like

cd23146

RING finger, HC subclass, found in Arabidopsis thaliana BRCA1-associated RING domain protein 1 ...

12-68

7.92e-10

RING finger, HC subclass, found in Arabidopsis thaliana BRCA1-associated RING domain protein 1 (AtBARD1) and similar proteins; AtBARD1, also called protein REPRESSOR OF WUSCHEL 1, binds specifically to H3K4me3 regions of target gene (e.g. WUS and WOX5) promoters to repress their transcription via chromatin remodeling. It is required for the shoot apical meristem (SAM) organization and maintenance, by confining WUS expression to the organizing center, and for the quiescent center (QC) development in the root apical meristem (RAM), by repressing WOX5 expression in the root proximal meristem. AtBARD1 plays a role in DNA repair and in cell-cycle control. It is required for the repair of DNA double-strand breaks (DSBs), both natural and induced by genotoxic stress, by homologous recombination (HR). AtBARD1 contains a typical C3HC4-type RING-HC finger.

Pssm-ID: 438508 [Multi-domain] Cd Length: 54 Bit Score: 54.40 E-value: 7.92e-10

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 890799132  12 EVTCPVCLNLMVKPVSADCGHTFCQGCITlyfesiKCDKEMFSCPVCRLSYQSSNLR 68
Cdd:cd23146    4 ELKCPICLKLLNRPVLLPCDHIFCSSCIT------DSTKVGSDCPVCKLPYHSQDLR 54

RING-HC_TRIM47-like_C-IV

cd16604

RING finger, HC subclass, found in tripartite motif-containing protein 47 (TRIM47) and similar ...

15-59

9.47e-10

RING finger, HC subclass, found in tripartite motif-containing protein 47 (TRIM47) and similar proteins; TRIM47, also known as gene overexpressed in astrocytoma protein (GOA) or RING finger protein 100 (RNF100), belongs to the C-IV subclass of the TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a C3HC4-type RING-HC finger, a B-box, and two coiled coil domains, as well as a B30.2/SPRY (SplA and ryanodine receptor) domain positioned C-terminal to the RBCC domain. It plays an important role in the process of dedifferentiation that is associated with astrocytoma tumorigenesis. This subfamily also includes RING finger protein 135 (RNF135). RNF135, also known as RIG-I E3 ubiquitin ligase (REUL) or Riplet, is a widely expressed E3 ubiquitin-protein ligase that consists of an N-terminal C3HC4-type RING-HC finger and C-terminal B30.2/SPRY and PRY motifs, but lacks the B-box and coiled-coil domains that are also typically present in TRIM proteins. RNF135 serves as a specific retinoic acid-inducible gene-I (RIG-I)-interacting protein that ubiquitinates RIG-I and specifically stimulates RIG-I-mediated innate antiviral activity to produce antiviral type-I interferon (IFN) during the early phase of viral infection. It also has been identified as a bio-marker and therapy target of glioblastoma. It associates with the ERK signal transduction pathway and plays a role in glioblastoma cell proliferation, migration and cell cycle.

Pssm-ID: 438266 [Multi-domain] Cd Length: 49 Bit Score: 53.96 E-value: 9.47e-10

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*
gi 890799132  15 CPVCLNLMVKPVSADCGHTFCQGCITLYFESIKCDKemFSCPVCR 59
Cdd:cd16604    3 CPICLDLLKDPVTLPCGHSFCMGCLGALWGAGRGGR--ASCPLCR 45

RING-HC_TRIM77_C-IV

cd16543

RING finger, HC subclass, found in tripartite motif-containing protein 77 (TRIM77) and similar ...

11-69

1.05e-09

RING finger, HC subclass, found in tripartite motif-containing protein 77 (TRIM77) and similar proteins; TRIM77 belongs to the C-IV subclass of the TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including two consecutive zinc-binding domains, a C3HC4-type RING-HC finger and Bbox2, as well as a SPRY/B30.2 domain positioned C-terminal to the RBCC domain.

Pssm-ID: 438205 [Multi-domain] Cd Length: 54 Bit Score: 53.93 E-value: 1.05e-09

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 890799132  11 EEVTCPVCLNLMVKPVSADCGHTFCQGCITLYFESikcDKEMFSCPVCRlsyQSSNLRP 69
Cdd:cd16543    2 DQLTCSICLDLLKDPVTIPCGHSFCMNCITLLWDR---KQGVPSCPQCR---ESFPPRP 54

RING-HC_TRIM39_C-IV

cd16601

RING finger, HC subclass, found in tripartite motif-containing protein 39 (TRIM39) and similar ...

12-58

1.08e-09

RING finger, HC subclass, found in tripartite motif-containing protein 39 (TRIM39) and similar proteins; TRIM39, also known as RING finger protein 23 (RNF23) or testis-abundant finger protein, is an E3 ubiquitin-protein ligase that plays a role in controlling DNA damage-induced apoptosis through inhibition of the anaphase promoting complex (APC/C), a multiprotein ubiquitin ligase that controls multiple cell cycle regulators, including cyclins, geminin, and others. TRIM39 also functions as a regulator of several key processes in the proliferative cycle. It directly regulates p53 stability. It modulates cell cycle progression and DNA damage responses via stabilizing p21. Moreover, TRIM39 negatively regulates the nuclear factor kappaB (NFkappaB)-mediated signaling pathway through stabilization of Cactin, an inhibitor of NFkappaB- and Toll-like receptor (TLR)-mediated transcription, which is induced by inflammatory stimulants such as tumor necrosis factor alpha. Furthermore, TRIM39 is a MOAP-1-binding protein that can promote apoptosis signaling through stabilization of MOAP-1 via the inhibition of its poly-ubiquitination process. TRIM39 belongs to the C-IV subclass of the TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a C3HC4-type RING-HC finger, Bbox1 and Bbox2, and a coiled coil region, as well as a B30.2/SPRY (SplA and ryanodine receptor) domain positioned C-terminal to the RBCC domain.

Pssm-ID: 438263 [Multi-domain] Cd Length: 44 Bit Score: 53.64 E-value: 1.08e-09

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
gi 890799132  12 EVTCPVCLNLMVKPVSADCGHTFCQGCITLYFESIKCDkemFSCPVC 58
Cdd:cd16601    1 EASCSLCKEYLKDPVIIECGHNFCRACITRFWEELDGD---FPCPQC 44

RING-HC_TRIM72_C-IV

cd16612

RING finger, HC subclass, found in tripartite motif-containing protein 72 (TRIM72) and similar ...

9-59

1.17e-09

RING finger, HC subclass, found in tripartite motif-containing protein 72 (TRIM72) and similar proteins; TRIM72, also known as Mitsugumin-53 (MG53), is a muscle-specific protein that plays a central role in cell membrane repair by nucleating the assembly of the repair machinery at muscle injury sites. It is required in repair of alveolar epithelial cells under plasma membrane stress failure. It interacts with dysferlin to regulate sarcolemmal repair. Upregulation of TRIM72 develops obesity, systemic insulin resistance, dyslipidemia, and hyperglycemia, as well as induces diabetic cardiomyopathy through transcriptional activation of the peroxisome proliferation-activated receptor alpha (PPAR-alpha) signaling pathway. Compensation for the absence of AKT signaling by ERK signaling during TRIM72 overexpression leads to pathological hypertrophy. Moreover, TRIM72 functions as a novel negative feedback regulator of myogenesis by targeting insulin receptor substrate-1 (IRS-1). It is transcriptionally activated by the synergism of myogenin (MyoD) and myocyte enhancer factor 2 (MEF2). TRIM72 belongs to the C-IV subclass of the TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a C3HC4-type RING-HC finger, Bbox1 and Bbox2, and a coiled coil region, as well as a B30.2/SPRY (SplA and ryanodine receptor) domain positioned C-terminal to the RBCC domain.

Pssm-ID: 438274 [Multi-domain] Cd Length: 60 Bit Score: 53.97 E-value: 1.17e-09

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 890799132   9 LKEEVTCPVCLNLMVKPVSADCGHTFCQGCITLYfeSIKCDKEMFSCPVCR 59
Cdd:cd16612    1 MHQDLSCPLCLKLFQSPVTTECGHTFCQDCLSRV--PKEEDGGSTSCPTCQ 49

RING-HC_TRIM68_C-IV

cd16610

RING finger, HC subclass, found in tripartite motif-containing protein 68 (TRIM68) and similar ...

12-59

1.19e-09

RING finger, HC subclass, found in tripartite motif-containing protein 68 (TRIM68) and similar proteins; TRIM68, also known as RING finger protein 137 (RNF137) or SSA protein SS-56 (SS-56), is an E3 ubiquitin-protein ligase that negatively regulates Toll-like receptor (TLR)- and RIG-I-like receptor (RLR)-driven type I interferon production by degrading TRK fused gene (TFG), a novel driver of IFN-beta downstream of anti-viral detection systems. It also functions as a cofactor for androgen receptor-mediated transcription by regulating ligand-dependent transcription of androgen receptor in prostate cancer cells. Moreover, TRIM68 is a cellular target of autoantibody responses in Sjogre's syndrome (SS), as well as systemic lupus erythematosus (SLE). It is also an auto-antigen for T cells in SS and SLE. TRIM68 belongs the C-IV subclass of the TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a C3HC4-type RING-HC finger, a B-box, and two coiled coil domains, as well as a B30.2/SPRY (SplA and ryanodine receptor) domain positioned C-terminal to the RBCC domain.

Pssm-ID: 438272 [Multi-domain] Cd Length: 49 Bit Score: 53.75 E-value: 1.19e-09

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*....
gi 890799132  12 EVTCPVCLNLMVKPVSADCGHTFCQGCIT-LYFESIKCDKEMFSCPVCR 59
Cdd:cd16610    1 EVACPICMTFLREPVSIDCGHSFCHSCLSgLWEVPGESQNWGYTCPLCR 49

Bbox2_TRIM11_C-IV

cd19766

B-box-type 2 zinc finger found in tripartite motif-containing protein 11 (TRIM11) and similar ...

96-136

1.67e-09

B-box-type 2 zinc finger found in tripartite motif-containing protein 11 (TRIM11) and similar proteins; TRIM11, also known as protein BIA1, or RING finger protein 92 (RNF92), is an E3 ubiquitin-protein ligase involved in the development of the central nervous system. It is overexpressed in high-grade gliomas and promotes proliferation, invasion, migration and glial tumor growth. TRIM11 acts as a potential therapeutic target for congenital central hypoventilation syndrome (CCHS) through mediating the degradation of CCHS-associated polyalanine-expanded Phox2b. Trim11 modulates the function of neurogenic transcription factor Pax6 through the ubiquitin-proteosome system, and thus plays an essential role for Pax6-dependent neurogenesis. It also binds to and destabilizes a key component of the activator-mediated cofactor complex (ARC105), humanin, a neuroprotective peptide against Alzheimer's disease-relevant insults, and further regulates ARC105 function in transforming growth factor beta (TGFbeta) signaling. Moreover, TRIM11 negatively regulates retinoic acid-inducible gene-I (RIG-I)-mediated interferon-beta (IFNbeta) production and antiviral activity by targeting TANK-binding kinase-1 (TBK1). It may contribute to the endogenous restriction of retroviruses in cells. It enhances N-tropic murine leukemia virus (N-MLV) entry by interfering with Ref1 restriction. It also suppresses the early steps of human immunodeficiency virus HIV-1 transduction, resulting in decreased reverse transcripts. TRIM11 belongs to the C-IV subclass of TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a RING finger, Bbox2, and a coiled coil region, as well as a SPRY/B30.2 domain positioned C-terminal to the RBCC domain. The type 2 B-box (Bbox2) zinc finger is characterized by a CHC3H2 zinc-binding consensus motif.

Pssm-ID: 380824 [Multi-domain] Cd Length: 44 Bit Score: 53.29 E-value: 1.67e-09

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|.
gi 890799132  96 CARHGEKLQLFCRKDMMAICWLCERSQEHRGHKTALIEEVA 136
Cdd:cd19766    3 CGKHREPLKLFCKDHEALLCVVCERSREHWGHRVVPAEEAA 43

rad18

TIGR00599

DNA repair protein rad18; All proteins in this family for which functions are known are ...

6-86

1.97e-09

Pssm-ID: 273165 [Multi-domain] Cd Length: 397 Bit Score: 59.63 E-value: 1.97e-09

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 890799132    6 MKNLKEEVTCPVCLNLMVKPVSADCGHTFCQGCITlyfesiKCDKEMFSCPVCRLSYQSSNLRPNLHVANIVERLKEFKP 85
Cdd:TIGR00599  20 LYPLDTSLRCHICKDFFDVPVLTSCSHTFCSLCIR------RCLSNQPKCPLCRAEDQESKLRSNWLVSEIVESFKNLRP 93


                  .
gi 890799132   86 S 86
Cdd:TIGR00599  94 S 94

RING-HC_RNF168

cd16550

RING finger, HC subclass, found in RING finger protein 168 (RNF168) and similar proteins; ...

13-60

2.62e-09

RING finger, HC subclass, found in RING finger protein 168 (RNF168) and similar proteins; RNF168 is an E3 ubiquitin-protein ligase that promotes noncanonical K27 ubiquitination to signal DNA damage. It, together with RNF8, functions as a DNA damage response (DDR) factor that promotes a series of ubiquitylation events on substrates, such as H2A and H2AX with H2AK13/15 ubiquitylation, facilitates recruitment of repair factors p53-binding protein 1 (53BP1) or the RAP80-BRCA1 complex to sites of double-strand breaks (DSBs), and inhibits homologous recombination (HR) in cells deficient in the tumor suppressor BRCA1. RNF168 also promotes H2A neddylation, which antagonizes ubiquitylation of H2A and regulates DNA damage repair. Moreover, RNF168 forms a functional complex with RAD6A or RAD6B during the DNA damage response. RNF168 contains an N-terminal C3HC4-type RING-HC finger that catalyzes H2A-K15ub and interacts with H2A, and two MIU (motif interacting with ubiquitin) domains responsible for the interaction with K63 linked poly-ubiquitin.

Pssm-ID: 438212 [Multi-domain] Cd Length: 48 Bit Score: 52.76 E-value: 2.62e-09

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*...
gi 890799132  13 VTCPVCLNLMVKPVSADCGHTFCQGCITLYFEsikcdKEMFSCPVCRL 60
Cdd:cd16550    1 CLCPICLEILVEPVTLPCNHTLCMPCFQSTVE-----KASLCCPLCRL 43

RING-HC

cd16449

HC subclass of RING (RING-HC) finger and its variants; The RING finger is a specialized type ...

14-58

3.04e-09

HC subclass of RING (RING-HC) finger and its variants; The RING finger is a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc. It is defined by the "cross-brace" motif that chelates zinc atoms by eight amino acid residues, typically Cys or His, arranged in a characteristic spacing. Canonical RING motifs have been categorized into two major subclasses, RING-HC (C3HC4-type) and RING-H2 (C3H2C3-type), according to their Cys/His content. There are also many variants of RING fingers. Some have a different Cys/His pattern. Some lack a single Cys or His residue at typical Zn ligand positions, especially, the fourth or eighth zinc ligand is prevalently exchanged for an Asp, which can chelate Zn in a RING finger as well. This family corresponds to the HC subclass of RING (RING-HC) fingers that are characterized by containing C3HC4-type canonical RING-HC fingers or noncanonical RING-HC finger variants, including C4C4-, C3HC3D-, C2H2C4-, and C3HC5-type modified RING-HC fingers. The canonical RING-HC finger has been defined as C-X2-C-X(9-39)-C-X(1-3)-H-X(2-3)-C-X2-C-X(4-48)-C-X2-C. It binds two Zn ions in a unique "cross-brace" arrangement, which distinguishes it from tandem zinc fingers and other similar motifs. RING-HC fingers can be found in a group of diverse proteins with a variety of cellular functions, including oncogenesis, development, viral replication, signal transduction, the cell cycle, and apoptosis. Many of them are ubiquitin-protein ligases (E3s) that serve as scaffolds for binding to ubiquitin-conjugating enzymes (E2s, also referred to as ubiquitin carrier proteins or UBCs) in close proximity to substrate proteins, which enables efficient transfer of ubiquitin from E2 to the substrates.

Pssm-ID: 438113 [Multi-domain] Cd Length: 41 Bit Score: 52.49 E-value: 3.04e-09

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*
gi 890799132  14 TCPVCLNLMVKPVSADCGHTFCQGCITLYFESIKcdkemFSCPVC 58
Cdd:cd16449    2 ECPICLERLKDPVLLPCGHVFCRECIRRLLESGS-----IKCPIC 41

RING-HC_AtBRCA1-like

cd23147

RING finger, HC subclass, found in Arabidopsis thaliana protein BREAST CANCER SUSCEPTIBILITY 1 ...

9-68

3.58e-09

RING finger, HC subclass, found in Arabidopsis thaliana protein BREAST CANCER SUSCEPTIBILITY 1 homolog (AtBRCA1) and similar proteins; AtBRCA1 plays a role in DNA repair and in cell-cycle control. It is required for the repair of DNA double-strand breaks (DSBs), both natural and induced by genotoxic stress, by homologous recombination (HR). AtBRCA1 contains a typical C3HC4-type RING-HC finger.

Pssm-ID: 438509 [Multi-domain] Cd Length: 54 Bit Score: 52.47 E-value: 3.58e-09

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 890799132   9 LKEEVTCPVCLNLMVKPVSADCGHTFCQGCITlyfESIKCDKemfSCPVCRLSYQSSNLR 68
Cdd:cd23147    1 LGKELKCPICLSLFKSAANLSCNHCFCAGCIG---ESLKLSA---ICPVCKIPATRRDTR 54

SPRY_PRY_TRIM16

cd12890

PRY/SPRY domain in tripartite motif-containing protein 16 (TRIM16); This domain, consisting of ...

341-481

3.72e-09

PRY/SPRY domain in tripartite motif-containing protein 16 (TRIM16); This domain, consisting of the distinct N-terminal PRY subdomain followed by the SPRY subdomain, is found at the C-terminus of TRIM16 and TRIM-like proteins. TRIM16 (also known as estrogen-responsive B box protein or EBBP) does not possess a RING domain like the other TRIM proteins, but contains two B-box domains and can heterodimerize with other TRIM proteins such as TRIM24, Promyelocytic leukemia (PML) protein and Midline-1 (MID1 or TRIM18). It is a regulator of keratinocyte differentiation and a tumor suppressor in retinoid-sensitive neuroblastoma. It has been shown that loss of TRIM16 expression plays an important role in the development of cutaneous squamous cell carcinoma (SCC) and is a determinant of retinoid sensitivity. TRIM16 also has E3 ubiquitin ligase activity.

Pssm-ID: 293948 Cd Length: 182 Bit Score: 56.32 E-value: 3.72e-09

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 890799132 341 VLGHPAIQSGKHYWEVDVSGKGAWVlGLSDGSylfcpIFHSNAERNRlfCRGIKNDShyqpkygfWVIGlWKKSVYNAFE 420
Cdd:cd12890   54 VLSQQSLYLGRYYFEVEISGEGTYV-GLTYKS-----IDRKGSESNS--CISGNNFS--------WCLQ-WNGKEFSAWH 116

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 890799132 421 EcpftGKPSVLTLSlmvPPCRVGVFLDYAAGTLSFYNISNNG-TLIYRFcTASFPDRVFPYF 481
Cdd:cd12890  117 S----DVETPLKKG---PFTRLGIYLDYPGGTLSFYGVEDDGmTLLHKF-QCKFTEPLYPAF 170

Bbox2_TRIM21_C-IV

cd19772

B-box-type 2 zinc finger found in tripartite motif-containing protein 21 (TRIM21) and similar ...

96-133

4.08e-09

B-box-type 2 zinc finger found in tripartite motif-containing protein 21 (TRIM21) and similar proteins; TRIM21, also known as 52 kDa Ro protein, 52 kDa ribonucleoprotein autoantigen Ro/SS-A, Ro(SS-A), RING finger protein 81 (RNF81), or Sjoegren's syndrome type A antigen (SS-A), is a ubiquitously expressed E3 ubiquitin-protein ligase and a high affinity antibody receptor uniquely expressed in the cytosol of mammalian cells. As a cytosolic Fc receptor, TRIM21 binds the Fc of virus-associated antibodies and targets the complex in the cytosol for proteasomal degradation in a process known as antibody-dependent intracellular neutralization (ADIN), and provides an intracellular immune response to protect host defense against pathogen infection. It shows remarkably broad isotype specificity as it does not only bind IgG, but also IgM and IgA. Moreover, TRIM21 promotes the cytosolic DNA sensor cGAS and the cytosolic RNA sensor RIG-I sensing of viral genomes during infection by antibody-opsonized virus. It stimulates inflammatory signaling and activates innate transcription factors, such as nuclear factor-kappaB (NF-kappaB). TRIM21 also plays an essential role in p62-regulated redox homeostasis, suggesting a viable target for treating pathological conditions resulting from oxidative damage. Furthermore, TRIM21 may have implications for various autoimmune diseases associated uncontrolled antiviral signaling through the regulation of Nmi-IFI35 complex-mediated inhibition of innate antiviral response. TRIM21 belongs to the C-IV subclass of TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a RING finger, Bbox2, and a coiled coil region, as well as a B30.2/SPRY (SplA and ryanodine receptor) domain positioned C-terminal to the RBCC domain. The type 2 B-box (Bbox2) zinc finger is characterized by a CHC3H2 zinc-binding consensus motif.

Pssm-ID: 380830 [Multi-domain] Cd Length: 40 Bit Score: 52.11 E-value: 4.08e-09

                         10        20        30
                 ....*....|....*....|....*....|....*...
gi 890799132  96 CARHGEKLQLFCRKDMMAICWLCERSQEHRGHKTALIE 133
Cdd:cd19772    3 CAVHGERLHLFCEEDQKALCLVCAQSQKHRDHAMVPIE 40

RING-HC_MmTRIM43-like

cd23133

RING finger, HC subclass, found in Mus musculus tripartite motif-containing protein 43 (TRIM43) ...

10-59

5.79e-09

RING finger, HC subclass, found in Mus musculus tripartite motif-containing protein 43 (TRIM43) and similar propteins; This subfamily includes TRIM43A, TRIM43B and TRIM43C, which are expressed specifically in mouse preimplantation embryos. They contain a typical C3HC4-type RING-HC finger.

Pssm-ID: 438495 [Multi-domain] Cd Length: 57 Bit Score: 52.22 E-value: 5.79e-09

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|
gi 890799132  10 KEEVTCPVCLNLMVKPVSADCGHTFCQGCITLYFESIKCDKEmfsCPVCR 59
Cdd:cd23133    1 EETLTCSICQGIFMNPVYLRCGHKFCEACLLLFQEDIKFPAY---CPMCR 47

Bbox2_TRIM16-like

cd19769

B-box-type 2 zinc finger found in tripartite motif-containing proteins, TRIM16, TRIM29, ...

96-140

8.13e-09

B-box-type 2 zinc finger found in tripartite motif-containing proteins, TRIM16, TRIM29, TRIM47 and similar proteins; This family includes a group of tripartite motif-containing proteins, such as TRIM16, TRIM29 and TRIM47. TRIM16, also termed estrogen-responsive B box protein (EBBP), is a regulator that may play a role in the regulation of keratinocyte differentiation. It may also act as a tumor suppressor through affecting cell proliferation and migration or tumorigenicity in carcinogenesis. TRIM29, also termed ataxia telangiectasia group D-associated protein (ATDC), plays a crucial role in the regulation of macrophage activation in response to viral or bacterial infections within the respiratory tract. TRIM47, also known as gene overexpressed in astrocytoma protein (GOA) or RING finger protein 100 (RNF100), plays an important role in the process of dedifferentiation that is associated with astrocytoma tumorigenesis. TRIM16 and TRIM29 belong to an unclassified TRIM (tripartite motif) family of proteins that do not have RING fingers and thus lack the characteristic tripartite (RING (R), B-box, and coiled coil (CC)) RBCC motif. TRIM47 belongs to the C-IV subclass of TRIM family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a RING finger, Bbox1 and Bbox2, and two coiled coil domains, as well as a B30.2/SPRY (SplA and ryanodine receptor) domain positioned C-terminal to the RBCC domain. The type 2 B-box (Bbox2) zinc finger is characterized by a CHC3H2 zinc-binding consensus motif.

Pssm-ID: 380827 [Multi-domain] Cd Length: 46 Bit Score: 51.17 E-value: 8.13e-09

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*
gi 890799132  96 CARHGEKLQLFCRKDMMAICWLCeRSQEHRGHKTALIEEVAREYK 140
Cdd:cd19769    3 CPIHKKPLELFCRTDQMCICELC-AKEEHRGHDVVTVEEEREKKE 46

RING-HC_RNF170

cd16553

RING finger, HC subclass, found in RING finger protein 170 (RNF170) and similar proteins; ...

14-59

9.66e-09

RING finger, HC subclass, found in RING finger protein 170 (RNF170) and similar proteins; RNF170, also known as putative LAG1-interacting protein, is an endoplasmic reticulum (ER) membrane-bound E3 ubiquitin-protein ligase that mediates ubiquitination-dependent degradation of type-I inositol 1,4,5-trisphosphate (IP3) receptors (ITPR1) via the endoplasmic-reticulum-associated protein degradation (ERAD) pathway. A point mutation (arginine to cysteine at position 199) in the RNF170 gene is linked with autosomal-dominant sensory ataxia (ADSA), a disease characterized by neurodegeneration in the posterior columns of the spinal cord. RNF170 contains a C3HC4-type RING-HC finger.

Pssm-ID: 438215 [Multi-domain] Cd Length: 57 Bit Score: 51.52 E-value: 9.66e-09

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*.
gi 890799132  14 TCPVCLNLMVKPVSADCGHTFCQGCITLYFESIKCDKEMfSCPVCR 59
Cdd:cd16553    3 ECPICLQDARFPVETNCGHLFCGPCIITYWRHGSWLGAV-SCPVCR 47

RING-HC_TRIM8_C-V

cd16580

RING finger, HC subclass, found in tripartite motif-containing protein 8 (TRIM8) and similar ...

9-70

1.21e-08

RING finger, HC subclass, found in tripartite motif-containing protein 8 (TRIM8) and similar proteins; TRIM8, also known as glioblastoma-expressed RING finger protein (GERP) or RING finger protein 27 (RNF27), is a probable E3 ubiquitin-protein ligase that may promote proteasomal degradation of suppressor of cytokine signaling 1 (SOCS1) and further regulate interferon-gamma signaling. It functions as a new p53 modulator that stabilizes p53 impairing its association with MDM2 and inducing the reduction of cell proliferation. TRIM8 deficit dramatically impairs p53 stabilization and activation in response to chemotherapeutic drugs. TRIM8 also modulates tumor necrosis factor-alpha (TNFalpha) and interleukin-1beta (IL-1beta)-triggered nuclear factor-kappaB (NF- kappa B) activation by targeting transforming growth factor beta (TGFbeta) activated kinase 1 (TAK1) for K63-linked polyubiquitination. Moreover, TRIM8 modulates translocation of phosphorylated STAT3 into the nucleus through interaction with Hsp90beta and consequently regulates transcription of Nanog in embryonic stem cells. It also interacts with protein inhibitor of activated STAT3 (PIAS3), which inhibits IL-6-dependent activation of STAT3. TRIM8 belongs to the C-V subclass of the TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a C3HC4-type RING-HC finger, Bbox1 and Bbox2, and a coiled coil domain, as well as an uncharacterized region positioned C-terminal to the RBCC domain. The coiled coil domain is required for homodimerization and the region immediately C-terminal to the RING motif is sufficient to mediate the interaction with SOCS1.

Pssm-ID: 438242 [Multi-domain] Cd Length: 67 Bit Score: 51.43 E-value: 1.21e-08

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 890799132   9 LKEEVTCPVCLNLMVKPVSADCGHTFCQGCITlyfESIKCDKEMFSCPVCRLSY-QSSNLRPN 70
Cdd:cd16580    8 FEEELICPICLHVFVEPVQLPCKHNFCRGCIG---EAWAKDAGLVRCPECNQAYnQKPSLEKN 67

Bbox2_TRIM4-like

cd19760

B-box-type 2 zinc finger found in tripartite motif-containing proteins, TRIM4, TRIM17, TRIM41, ...

96-128

1.91e-08

B-box-type 2 zinc finger found in tripartite motif-containing proteins, TRIM4, TRIM17, TRIM41, TRIM52 and similar proteins; This family includes a group of tripartite motif-containing proteins, including TRIM4, TRIM17, TRIM41 and TRIM52. TRIM4, also known as RING finger protein 87 (RNF87), is a cytoplasmic E3 ubiquitin-protein ligase that recently evolved and is present only in higher mammals. It transiently interacts with mitochondria, induces mitochondrial aggregation and sensitizes the cells to hydrogen peroxide (H2O2) induced death. Its interaction with peroxiredoxin 1 (PRX1) is critical for the regulation of H2O2 induced cell death. Moreover, TRIM4 functions as a positive regulator of RIG-I-mediated type I interferon induction. It regulates the K63-linked ubiquitination of RIG-1 and assembly of antiviral signaling complex at mitochondria. TRIM17, also known as RING finger protein 16 (RNF16) or testis RING finger protein (Terf), is a crucial E3 ubiquitin ligase that is necessary and sufficient for neuronal apoptosis and contributes to Mcl-1 ubiquitination in cerebellar granule neurons (CGNs). It interacts in a SUMO-dependent manner with nuclear factor of activated T cell NFATc3 transcription factor, and thus inhibits the activity of NFATc3 by preventing its nuclear localization. In contrast, it binds to and inhibits NFATc4 transcription factor in a SUMO-independent manner. Moreover, TRIM17 stimulates degradation of kinetochore protein ZW10 interacting protein (ZWINT), a known component of the kinetochore complex required for mitotic spindle checkpoint, and negatively regulates cell proliferation. TRIM41, also known as RING finger-interacting protein with C kinase (RINCK), is an E3 ubiquitin-protein ligase that promotes the ubiquitination of protein kinase C (PKC) isozymes in cells. It specifically recognizes the C1 domain of PKC isozymes. It controls the amplitude of PKC signaling by controlling the amount of PKC in the cell. TRIM52, also known as RING finger protein 102 (RNF102), is encoded by a novel, noncanonical antiviral TRIM52 gene in primate genomes with unique specificity determined by the rapidly evolving RING domain. TRIM4, TRIM17 and TRIM41 belong to the C-IV subclass of TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a RING finger, Bbox2, and a coiled coil region, as well as a B30.2/SPRY (SplA and ryanodine receptor) domain positioned C-terminal to the RBCC domain. In contrast, TRIM52 lacks the putative viral recognition SPRY/B30.2 domain, and thus has been classified to the C-V subclass of TRIM family that contains only RBCC domains. The type 2 B-box (Bbox2) zinc finger is characterized by a CHC3H2 zinc-binding consensus motif.

Pssm-ID: 380818 [Multi-domain] Cd Length: 39 Bit Score: 49.94 E-value: 1.91e-08

                         10        20        30
                 ....*....|....*....|....*....|...
gi 890799132  96 CARHGEKLQLFCRKDMMAICWLCERSQEHRGHK 128
Cdd:cd19760    3 CEKHQEPLKLFCEEDEALICVICRESRAHRAHT 35

BBOX

smart00336

B-Box-type zinc finger;

96-132

2.34e-08

B-Box-type zinc finger;

Pssm-ID: 197662 [Multi-domain] Cd Length: 42 Bit Score: 50.03 E-value: 2.34e-08

                           10        20        30
                   ....*....|....*....|....*....|....*...
gi 890799132    96 CARHG-EKLQLFCRKDMMAICWLCERSqEHRGHKTALI 132
Cdd:smart00336   6 CDSHGdEPAEFFCEECGALLCRTCDEA-EHRGHTVVLL 42

RING-HC_HLTF

cd16509

RING finger, HC subclass, found in helicase-like transcription factor (HLTF) and similar ...

15-67

3.55e-08

RING finger, HC subclass, found in helicase-like transcription factor (HLTF) and similar proteins; HLTF, also known as DNA-binding protein/plasminogen activator inhibitor 1 regulator, HIP116, RING finger protein 80, SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 3, or sucrose nonfermenting protein 2-like 3, is a yeast RAD5 homolog found in mammals. It has both E3 ubiquitin ligase and DNA helicase activities, and plays a pivotal role in the template-switching pathway of DNA damage tolerance. It is involved in Lys-63-linked poly-ubiquitination of proliferating cell nuclear antigen (PCNA) at Lys-164 and in the regulation of DNA damage tolerance. It shows double-stranded DNA translocase activity with 3'-5' polarity, thereby facilitating regression of the replication fork. HLTF contains an N-terminal HIRAN (HIP116 and RAD5 N-terminal) domain, a SWI/SNF helicase domain that is divided into N- and C-terminal parts by an insertion of a C3HC4-type RING-HC finger involved in the poly-ubiquitination of PCNA.

Pssm-ID: 438172 [Multi-domain] Cd Length: 53 Bit Score: 49.61 E-value: 3.55e-08

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 890799132  15 CPVCLNLMVKPVSADCGHTFCQGCITlyfESIKCDKEmfSCPVCRLSYQSSNL 67
Cdd:cd16509    6 CAICLDSLTNPVITPCAHVFCRRCIC---EVIQREKA--KCPMCRAPLSASDL 53

RAD18

COG5432

RING-finger-containing E3 ubiquitin ligase [Signal transduction mechanisms];

6-112

3.96e-08

RING-finger-containing E3 ubiquitin ligase [Signal transduction mechanisms];

Pssm-ID: 227719 [Multi-domain] Cd Length: 391 Bit Score: 55.48 E-value: 3.96e-08

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 890799132   6 MKNLKEEVTCPVCLNLMVKPVSADCGHTFCQGCITLYFesikcdKEMFSCPVCRLSYQSSNLRPNLHVANIVERLKEFKP 85
Cdd:COG5432   19 LKGLDSMLRCRICDCRISIPCETTCGHTFCSLCIRRHL------GTQPFCPVCREDPCESRLRGSSGSREINESHARNRD 92

                         90       100
                 ....*....|....*....|....*..
gi 890799132  86 SPEEEQKVFNCARHGEKLQLFCRKDMM 112
Cdd:COG5432   93 LLRKVLESLCRLPRPIKEERPCRWETV 119

RING-HC_TRIM62_C-IV

cd16608

RING finger, HC subclass, found in tripartite motif-containing protein 62 (TRIM62) and similar ...

9-62

4.22e-08

RING finger, HC subclass, found in tripartite motif-containing protein 62 (TRIM62) and similar proteins; TRIM62, also known as Ductal Epithelium Associated Ring Chromosome 1 (DEAR1), is a cytoplasmic E3 ubiquitin-protein ligase that was identified as a dominant regulator of acinar morphogenesis in the mammary gland. It is implicated in the inflammatory response of immune cells by regulating the Toll-like receptor 4 (TLR4) signaling pathway, leading to increased activity of the activator protein 1 (AP-1) transcription factor in primary macrophages. It is also involved in muscular protein homeostasis, especially during inflammation-induced atrophy, and may play a role in the pathogenesis of ICU-acquired weakness (ICUAW) by activating and maintaining inflammation in myocytes. Moreover, TRIM62 facilitates K27-linked poly-ubiquitination of CARD9 and also regulates CARD9-mediated anti-fungal immunity and intestinal inflammation. It also functions as a chromosome 1p35 tumor suppressor and negatively regulates transforming growth factor beta (TGFbeta)-driven epithelial-mesenchymal transition (EMT) by binding to and promoting the ubiquitination of SMAD3, a major effector of TGFbeta-mediated EMT. TRIM62 belongs to the C-IV subclass of the TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a C3HC4-type RING-HC finger, Bbox1 and Bbox2, and a coiled coil region, as well as a B30.2/SPRY (SplA and ryanodine receptor) domain positioned C-terminal to the RBCC domain.

Pssm-ID: 438270 [Multi-domain] Cd Length: 52 Bit Score: 49.42 E-value: 4.22e-08

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 890799132   9 LKEEVTCPVCLNLMVKPVSADCGHTFCQGCITLYFESikcdKEMFSCPVCRLSY 62
Cdd:cd16608    3 LKDELLCSICLSIYQDPVSLGCEHYFCRQCITEHWSR----SEHRDCPECRRTF 52

RING-HC_TRIM60-like_C-IV

cd16607

RING finger, HC subclass, found in tripartite motif-containing proteins TRIM60, TRIM61, TRIM75 ...

12-62

4.33e-08

RING finger, HC subclass, found in tripartite motif-containing proteins TRIM60, TRIM61, TRIM75 and similar proteins; TRIM60, also known as RING finger protein 129 (RNF129) or RING finger protein 33 (RNF33), is a cytoplasmic protein expressed in the testis. It may play an important role in the spermatogenesis process, the development of the preimplantation embryo, and in testicular functions. RNF33 interacts with the cytoplasmic kinesin motor proteins KIF3A and KIF3B suggesting possible contribution to cargo movement along the microtubule in the expressed sites. It is also involved in spermatogenesis in Sertoli cells under the regulation of nuclear factor-kappaB (NF-kappaB). TRIM75 mainly localizes within spindles, suggesting it may function in spindle organization and thereby affect meiosis. Both TRIM60 and TRIM75 belong the C-IV subclass of the TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a C3HC4-type RING-HC finger, a B2-box, and two coiled coil domains, as well as a PRY domain and a B30.2/SPRY (SplA and ryanodine receptor) domain positioned C-terminal to the RBCC domain. In contrast, TRIM61 belongs to the C-V subclass of the TRIM family that contains RBCC domains only. Its biological function remains unclear.

Pssm-ID: 438269 [Multi-domain] Cd Length: 48 Bit Score: 49.34 E-value: 4.33e-08

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 890799132  12 EVTCPVCLNLMVKPVSADCGHTFCQGCITLYFESIkcdKEMFSCPVCRLSY 62
Cdd:cd16607    1 EASCPICLDYLKDPVTINCGHNFCRSCISMSWKDL---QDTFPCPVCRFCC 48

Bbox2_TRIM43-like

cd19783

B-box-type 2 zinc finger found in tripartite motif-containing proteins TRIM43, TRIM48, TRIM49, ...

96-142

5.53e-08

B-box-type 2 zinc finger found in tripartite motif-containing proteins TRIM43, TRIM48, TRIM49, TRIM51, TRIM64, TRIM77 and similar proteins; The family includes a group of closely related uncharacterized tripartite motif-containing proteins, TRIM43, TRIM43B, TRIM48/RNF101, TRIM49/RNF18, TRIM49B, TRIM49C/TRIM49L2, TRIM49D/TRIM49L, TRIM51/SPRYD5, TRIM64, TRIM64B, TRIM64C, and TRIM77, whose biological functions remain unclear. TRIM49, also known as testis-specific RING-finger protein, has moderate similarity with SS-A/Ro52 antigen, suggesting it may be one of target proteins of autoantibodies in the sera of patients with these autoimmune disorders. All family members (except for TRIM51) belong to the C-IV subclass of TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a RING finger, Bbox2, and a coiled coil region, as well as a SPRY/B30.2 domain positioned C-terminal to the RBCC domain. TRIM51 belongs to unclassified TRIM (tripartite motif) family of proteins that do not have RING fingers. The type 2 B-box (Bbox2) zinc finger is characterized by a CHC3H2 zinc-binding consensus motif.

Pssm-ID: 380841 [Multi-domain] Cd Length: 53 Bit Score: 49.09 E-value: 5.53e-08

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
gi 890799132  96 CARHGEKLQLFCRKDMMAICWLCERSQEHRGHKTALIEEVAREYKEQ 142
Cdd:cd19783    7 CGTHRETKKLFCEADKSLLCLLCSSSQEHRAHRHYPIEWAAEEHREK 53

RING-HC_BAR

cd16497

RING finger, HC subclass, found in bifunctional apoptosis regulator (BAR); BAR, also known as ...

15-63

7.55e-08

RING finger, HC subclass, found in bifunctional apoptosis regulator (BAR); BAR, also known as RING finger protein 47, was originally identified as an inhibitor of Bax-induced apoptosis. It participates in the block of apoptosis induced by TNF-family death receptors (extrinsic pathway) and mitochondria-dependent apoptosis (intrinsic pathway). BAR is predominantly expressed by neurons in the central nervous system and is involved in the regulation of neuronal survival. It is an endoplasmic reticulum (ER)-associated RING-type E3 ubiquitin ligase that interacts with BI-1 protein and post-translationally regulates its stability, as well as functioning in ER stress. BAR contains an N-terminal C3HC4-type RING-HC finger, a SAM domain, a coiled-coil domain, and a C-terminal transmembrane (TM) domain. This model corresponds to the RING-HC finger responsible for the binding of ubiquitin conjugating enzymes (E2s).

Pssm-ID: 438160 [Multi-domain] Cd Length: 52 Bit Score: 48.66 E-value: 7.55e-08

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*....
gi 890799132  15 CPVCLNLMVKPVSADCGHTFCQGCITLYFESIKCDkemfSCPVCRLSYQ 63
Cdd:cd16497    4 CHCCYDLLVNPTTLNCGHSFCRHCLALWWKSSKKT----ECPECRQKWE 48

RING-HC_RING1-like

cd16531

RING finger, HC subclass, found in really interesting new gene proteins RING1, RING2 and ...

12-80

7.59e-08

RING finger, HC subclass, found in really interesting new gene proteins RING1, RING2 and similar proteins; RING1, also known as polycomb complex protein RING1, RING finger protein 1 (RNF1), or RING finger protein 1A (RING1A), is a transcriptional repressor that is associated with the Polycomb group (PcG) protein complex involved in stable repression of gene activity. RING2, also known as huntingtin-interacting protein 2-interacting protein 3, HIP2-interacting protein 3, protein DinG, RING finger protein 1B (RING1B), RING finger protein 2 (RNF2), or RING finger protein BAP-1, is an E3 ubiquitin-protein ligase that interacts with both nucleosomal DNA and an acidic patch on histone H4 to achieve the specific monoubiquitination of K119 on histone H2A (H2AK119ub), thereby playing a central role in histone code and gene regulation. Both RING1 and RING2 are core components of polycomb repressive complex 1 (PRC1) that functions as an E3-ubuiquitin ligase transferring the mono-ubuiquitin mark to the C-terminal tail of Histone H2A at K118/K119. PRC1 is also capable of chromatin compaction, a function not requiring histone tails, and this activity appears important in gene silencing. RING2 acts as the main E3 ubiquitin ligase on histone H2A of the PRC1 complex, while RING1 may rather act as a modulator of RNF2/RING2 activity. Members of this family contain a C3HC4-type RING-HC finger.

Pssm-ID: 438193 [Multi-domain] Cd Length: 66 Bit Score: 49.19 E-value: 7.59e-08

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 890799132  12 EVTCPVCLNLMVKP-VSADCGHTFCQGCITLYFESIKcdKEmfsCPVCRLSYQSS-NLRPNLHVANIVERL 80
Cdd:cd16531    1 ELMCPICLGIIKNTmTVKECLHRFCAECIEKALRLGN--KE---CPTCRKHLPSRrSLRPDPNFDALISKI 66

RING-HC_TRIM13_like_C-V

cd16581

RING finger, HC subclass, found in tripartite motif-containing proteins TRIM13, TRIM59 and ...

11-59

9.36e-08

RING finger, HC subclass, found in tripartite motif-containing proteins TRIM13, TRIM59 and similar proteins; TRIM13 and TRIM59, two closely related tripartite motif-containing proteins, belong to the C-V subclass of the TRIM (tripartite motif) family of proteins that are defined by an N-terminal RBCC (RING, Bbox, and coiled coil) domain, including three consecutive zinc-binding domains, a C3HC4-type RING-HC finger, Bbox1 and Bbox2, and a coiled coil region, followed by a C-terminal transmembrane domain. TRIM13, also known as B-cell chronic lymphocytic leukemia tumor suppressor Leu5, leukemia-associated protein 5, putative tumor suppressor RFP2, RING finger protein 77 (RNF77), or Ret finger protein 2, is an endoplasmic reticulum (ER) membrane anchored E3 ubiquitin-protein ligase that interacts with proteins localized to the ER, including valosin-containing protein (VCP), a protein indispensable for ER-associated degradation (ERAD). TRIM59, also known as RING finger protein 104 (RNF104) or tumor suppressor TSBF-1, is a putative E3 ubiquitin-protein ligase that functions as a novel multiple cancer biomarker for immunohistochemical detection of early tumorigenesis.

Pssm-ID: 438243 [Multi-domain] Cd Length: 50 Bit Score: 48.66 E-value: 9.36e-08

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|
gi 890799132  11 EEVTCPVCLNLMVKPVSADCGHTFCQGCI-TLYFESIKCDKEMFSCPVCR 59
Cdd:cd16581    1 EELTCSICYNIFDDPKILPCSHTFCKNCLeKLLAASGYYLLASLKCPTCR 50

RING-HC_CHFR

cd16503

RING finger, HC subclass, found in checkpoint with forkhead and RING finger domains protein ...

11-66

9.50e-08

RING finger, HC subclass, found in checkpoint with forkhead and RING finger domains protein (CHFR); CHFR, also known as RING finger protein 196 (RNF196), is a checkpoint protein that delays entry into mitosis in response to stress. It functions as an E3 ubiquitin ligase that ubiquitinates and degrades its target proteins, such as Aurora-A, Plk1, Kif22, and PARP-1, which are critical for proper mitotic transitions. It also plays an important role in cell cycle progression and tumor suppression, and is negatively regulated by SUMOylation-mediated proteasomal ubiquitylation. Moreover, CHFR is involved in the early stage of the DNA damage response, which mediates the crosstalk between ubiquitination and poly-ADP-ribosylation. CHFR contains a fork head associated (FHA) domain and a C3HC4-type RING-HC finger.

Pssm-ID: 438166 [Multi-domain] Cd Length: 55 Bit Score: 48.52 E-value: 9.50e-08

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 890799132  11 EEVTCPVCLNLMVKPVSAD-CGHTFCQGCITLYFEsikcdKEMFSCPVCRLSYQSSN 66
Cdd:cd16503    1 ENLTCSICQDLLHDCVSLQpCMHNFCAACYSDWME-----RSNTECPTCRATVQRVN 52

RING

smart00184

Ring finger; E3 ubiquitin-protein ligase activity is intrinsic to the RING domain of c-Cbl and ...

15-58

1.01e-07

Pssm-ID: 214546 [Multi-domain] Cd Length: 40 Bit Score: 48.27 E-value: 1.01e-07

                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*
gi 890799132    15 CPVCLNLMVK-PVSADCGHTFCQGCITLYFESikcdkEMFSCPVC 58
Cdd:smart00184   1 CPICLEEYLKdPVILPCGHTFCRSCIRKWLES-----GNNTCPIC 40

zf-RING_UBOX

pfam13445

RING-type zinc-finger; This zinc-finger is a typical RING-type of plant ubiquitin ligases.

15-56

1.04e-07

RING-type zinc-finger; This zinc-finger is a typical RING-type of plant ubiquitin ligases.

Pssm-ID: 463881 [Multi-domain] Cd Length: 38 Bit Score: 48.17 E-value: 1.04e-07

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 890799132   15 CPVCLNLMVKPVSaDCGHTFCQGCITlyfESIKCDKEMFSCP 56
Cdd:pfam13445   1 CPICLELFTDPVL-PCGHTFCRECLE---EMSQKKGGKFKCP 38

RING-HC_LONFs_rpt2

cd16514

second RING finger, HC subclass, found in the LON peptidase N-terminal domain and RING finger ...

15-61

1.27e-07

second RING finger, HC subclass, found in the LON peptidase N-terminal domain and RING finger protein family; The LON peptidase N-terminal domain and RING finger protein family includes LONRF1 (also known as RING finger protein 191 or RNF191), LONRF2 (also known as RING finger protein 192, RNF192, or neuroblastoma apoptosis-related protease), LONRF3 (also known as RING finger protein 127 or RNF127), which are characterized by containing two C3HC4-type RING-HC fingers, four tetratricopeptide (TPR) repeats, and an ATP-dependent protease La (LON) substrate-binding domain at the C-terminus. Their biological functions remain unclear. This model corresponds to the second RING-HC finger.

Pssm-ID: 438177 [Multi-domain] Cd Length: 45 Bit Score: 48.03 E-value: 1.27e-07

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
gi 890799132  15 CPVCLNLMVKPVSADCGHTFCQGCITLYFEsikcdkEMFSCPVCRLS 61
Cdd:cd16514    4 CSLCLRLLYEPVTTPCGHTFCRACLERCLD------HSPKCPLCRTS 44

SPRY_PRY_TRIM10

cd15827

PRY/SPRY domain of tripartite motif-binding protein 10 (TRIM10) also known as hematopoietic ...

305-481

1.49e-07

PRY/SPRY domain of tripartite motif-binding protein 10 (TRIM10) also known as hematopoietic RING finger 1 (HERF1); This domain, consisting of the distinct N-terminal PRY subdomain followed by the SPRY subdomain, is found at the C-terminus of TRIM10, also known as RING finger protein 9 (RNF9) or hematopoietic RING finger 1 (HERF1). TRIM10 domain is composed of RING/B-box/coiled-coil core and also known as RBCC protein. TRIM10/HERF1 is predominantly expressed during definitive erythropoiesis and in embryonic liver, and minimally expressed in adult liver, kidney, and colon. It is critical for erythroid cell differentiation and its down-regulation leads to cell death; inhibition of TRIM10 expression blocks terminal erythroid differentiation, while its over-expression in erythroid cells induces beta-major globin expression and erythroid differentiation.

Pssm-ID: 293999 [Multi-domain] Cd Length: 172 Bit Score: 51.37 E-value: 1.49e-07

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 890799132 305 QNNHPNIAITDDKRQVRYEdhqasnliHECENSHEG---------VLGHPAIQSGKHYW--EVDVSGKGAWVLGlsdgsy 373
Cdd:cd15827    9 QTSHPKLLLSEDHQRARFS--------YKWQNSPDNpqrfdratcVLAHDGFTGGRHTWvvSVDLAHGGSCTVG------ 74

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 890799132 374 lfcpIFHSNAERnrlfcrgiKNDSHYQPKYGFWVIGL-WK-KSVYNAFeecpftgkPSVLTLSLMvpPCRVGVFLDYAAG 451
Cdd:cd15827   75 ----VVSEDVRR--------KGELRLRPEEGVWAVRLaWGfVSALGSF--------PTRLALEEQ--PRQVRVSLDYEVG 132

                        170       180       190
                 ....*....|....*....|....*....|
gi 890799132 452 TLSFYNISNNgTLIYRFcTASFPDRVFPYF 481
Cdd:cd15827  133 WVTFVNAVTQ-EPIYTF-TASFTQKVFPFF 160

RING-HC_TRY3-like

cd23137

RING finger, HC subclass, found in Candida albicans transcriptional regulator of yeast form ...

11-59

1.85e-07

RING finger, HC subclass, found in Candida albicans transcriptional regulator of yeast form adherence 3 (TRY3) and similar proteins; TRY3 acts as a transcription factor required for yeast cell adherence to silicone substrate. It contains a typical C3HC4-type RING-HC finger.

Pssm-ID: 438499 [Multi-domain] Cd Length: 53 Bit Score: 47.85 E-value: 1.85e-07

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|
gi 890799132  11 EEVTCPVCLNLMVKPVSADCGHTFCQGCItlyfesIKCDKE-MFSCPVCR 59
Cdd:cd23137    1 DDYACPICMNVAWKPVRLECSHVFCLRCL------VKAQKQkKDNCPLCR 44

SPRY_PRY_TRIM25-like

cd13737

PRY/SPRY domain in tripartite motif-containing domain 25 (TRIM25)-like; This domain, ...

341-479

2.71e-07

PRY/SPRY domain in tripartite motif-containing domain 25 (TRIM25)-like; This domain, consisting of the distinct N-terminal PRY subdomain followed by the SPRY subdomain, is found at the C-terminus of proteins similar to TRIM25 (composed of RING/B-box/coiled-coil core and also known as RBCC proteins). TRIM25 (also called Efp) ubiquitinates the N terminus of the viral RNA receptor retinoic acid-inducible gene-I (RIG-I) in response to viral infection, leading to activation of the RIG-I signaling pathway, thus resulting in type I interferon production to limit viral replication. It has been shown that the influenza A virus targets TRIM25 and disables its antiviral function.

Pssm-ID: 293972 Cd Length: 172 Bit Score: 50.64 E-value: 2.71e-07

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 890799132 341 VLGHPAIQSGKHYWEVDVSGkgAWV-LGLSdGSYLfcpifHSNAERNRLFCRGIKNDShyqpkygfWVIGlW---KKSVY 416
Cdd:cd13737   44 VLCTRSLCEGCHYWEAEVSN--SWVcLGVT-YSYS-----HPTGKSCIFYLIGRNPYS--------WCLE-WdslKFSVW 106

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 890799132 417 NAFEECPFTGKPSVLtlslmvppcrVGVFLDYAAGTLSFYNISNNGTLIYRFCTaSFPDRVFP 479
Cdd:cd13737  107 HNNIQTVVHGSYYKT----------IGVLLDYAAGSLTFYGVANTMNLIYRFLT-TFTEPLYP 158

RING-HC_UHRF

cd16613

RING finger, HC subclass, found in ubiquitin-like PHD and RING finger domain-containing ...

14-59

3.27e-07

RING finger, HC subclass, found in ubiquitin-like PHD and RING finger domain-containing proteins, UHRF1 and UHRF2, and similar proteins; UHRF1 is a unique chromatin effector protein that integrates the recognition of both histone PTMs and DNA methylation. It is essential for cell proliferation and plays a critical role in the development and progression of many human carcinomas, such as laryngeal squamous cell carcinoma (LSCC), gastric cancer (GC), esophageal squamous cell carcinoma (ESCC), colorectal cancer, prostate cancer, and breast cancer. UHRF1 acts as a transcriptional repressor through its binding to histone H3 when it is unmodified at Arg2. Its overexpression in human lung fibroblasts results in downregulation of expression of the tumor suppressor pRB. It also plays a role in transcriptional repression of the cell cycle regulator p21. Moreover, UHRF1-dependent repression of transcription factors can facilitate the G1-S transition. It interacts with Tat-interacting protein of 60 kDa (TIP60) and induces degradation-independent ubiquitination of TIP60. It is also an N-methylpurine DNA glycosylase (MPG)-interacting protein that binds MPG in a p53 status-independent manner in the DNA base excision repair (BER) pathway. In addition, UHRF1 functions as an epigenetic regulator that is important for multiple aspects of epigenetic regulation, including maintenance of DNA methylation patterns and recognition of various histone modifications. UHRF2 was originally identified as a ubiquitin ligase acting as a small ubiquitin-like modifier (SUMO) E3 ligase that enhances zinc finger protein 131 (ZNF131) SUMOylation, but does not enhance ZNF131 ubiquitination. It also ubiquitinates PCNP, a PEST-containing nuclear protein. Moreover, UHRF2 functions as a nuclear protein involved in cell-cycle regulation and has been implicated in tumorigenesis. It interacts with cyclins, CDKs, p53, pRB, PCNA, HDAC1, DNMTs, G9a, methylated histone H3 lysine 9, and methylated DNA. It interacts with the cyclin E-CDK2 complex, ubiquitinates cyclins D1 and E1, induces G1 arrest, and is involved in the G1/S transition regulation. Furthermore, UHRF2 is a direct transcriptional target of the transcription factor E2F-1 in the induction of apoptosis. It recruits HDAC1 and binds to methyl-CpG. UHRF2 also participates in the maturation of Hepatitis B virus (HBV) by interacting with the HBV core protein and promoting its degradation. Both UHRF1 and UHRF2 contain an N-terminal ubiquitin-like domain (UBL), a tandem Tudor domain (TTD), a plant homeodomain (PHD) finger, a SET- and RING-associated (SRA) domain, and a C-terminal C3HC4-type RING-HC finger.

Pssm-ID: 438275 [Multi-domain] Cd Length: 46 Bit Score: 46.96 E-value: 3.27e-07

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*.
gi 890799132  14 TCPVCLNLMVKPVSADCGHTFCQGCITLYFESikcdkEMFSCPVCR 59
Cdd:cd16613    2 TCICCQELVYKPITTPCKHNICKSCLQRSFKA-----EVYTCPACR 42

Bbox2

cd19756

B-box-type 2 zinc finger (Bbox2); The B-box-type zinc finger is a short zinc binding domain of ...

96-132

4.10e-07

B-box-type 2 zinc finger (Bbox2); The B-box-type zinc finger is a short zinc binding domain of around 40 amino acid residues in length. It has been found in transcription factors, ribonucleoproteins and proto-oncoproteins, such as in TRIM (tripartite motif) proteins that consist of an N-terminal RING finger (originally called an A-box), followed by 1-2 B-box domains and a coiled-coil domain (also called RBCC for Ring, B-box, Coiled-Coil). The B-box-type zinc finger often presents in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction. Based on different consensus sequence and the spacing of the 7-8 zinc-binding residues, B-box-type zinc fingers can be divided into two groups, type 1 (Bbox1: C6H2) and type 2 (Bbox2: CHC3H2). The family corresponds to type 2 B-box (Bbox2).

Pssm-ID: 380814 [Multi-domain] Cd Length: 39 Bit Score: 46.25 E-value: 4.10e-07

                         10        20        30
                 ....*....|....*....|....*....|....*...
gi 890799132  96 CARHGEK-LQLFCRKDMMAICWLCERSQEHRGHKTALI 132
Cdd:cd19756    2 CPEHPEEpLKLFCETCQELVCVLCLLSGEHRGHKVVPL 39

SPRY_PRY_SPRYD4

cd12903

PRY/SPRY domain containing protein 4 (SPRYD4); This domain, consisting of the distinct ...

341-481

5.05e-07

PRY/SPRY domain containing protein 4 (SPRYD4); This domain, consisting of the distinct N-terminal PRY subdomain followed by the SPRY subdomain and is encoded by the SPRYD4 gene. SPRYD4 (SPRY containing domain 4) is ubiquitously expressed in many human tissues, most strongly in kidney, bladder, brain, thymus and stomach. Subcellular localization demonstrates that SPRYD4 protein is localized in the nucleus when overexpressed in COS-7 green monkey cell. It has remained uncharacterized thus far.

Pssm-ID: 293960 Cd Length: 169 Bit Score: 49.75 E-value: 5.05e-07

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 890799132 341 VLGHPAIQSGKHYWEVDVSGKGAWVLGLSDgsylfcpifhsnAERNRLFCRGIKNDShyqpkygfWVIGL----WKKSVY 416
Cdd:cd12903   46 VLGDTPVTSGRHYWEVTVKRSQEFRIGVAD------------VDMSRDECIGTNESS--------WVFAYaqrkWYAMVA 105

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 890799132 417 NAFEECPFTGKPSvltlslmvppcRVGVFLDYAAGTLSFYNISNNgTLIYRFcTASFPDRVFPYF 481
Cdd:cd12903  106 NETVPVPLVGKPD-----------RVGLLLDYEAGKLSLVDVEKN-SVVHTM-SAEFRGPVVPAF 157

vRING-HC-C4C4_RBBP6

cd16620

Variant RING finger, HC subclass (C4C4-type), found in retinoblastoma-binding protein 6 (RBBP6) ...

11-59

5.15e-07

Variant RING finger, HC subclass (C4C4-type), found in retinoblastoma-binding protein 6 (RBBP6) and similar proteins; RBBP6, also known as proliferation potential-related protein, protein P2P-R, retinoblastoma-binding Q protein 1 (RBQ-1), or p53-associated cellular protein of testis (PACT), is a nuclear E3 ubiquitin-protein ligase involved in multiple processes, such as the control of gene expression, mitosis, cell differentiation, and cell apoptosis. It plays a role in both promoting and inhibiting apoptosis in many human cancers, including esophageal, lung, hepatocellular, and colon cancers, familial myeloproliferative neoplasms, as well as in human immunodeficiency virus-associated nephropathy (HIVAN). It functions as an Rb- and p53-binding protein that plays an important role in chaperone-mediated ubiquitination and possibly in protein quality control. It acts as a scaffold protein to promote the assembly of the p53/TP53-MDM2 complex, resulting in an increase of MDM2-mediated ubiquitination and degradation of p53/TP53, and leading to both apoptosis and cell growth. It is also a double-stranded RNA-binding protein that plays a role in mRNA processing by regulating the human polyadenylation machinery and modulating expression of mRNAs with AU-rich 3' untranslated regions (UTRs). Moreover, RBBP6 ubiquitinates and destabilizes the transcriptional repressor ZBTB38 that negatively regulates transcription and levels of the MCM10 replication factor on chromatin. Furthermore, RBBP6 is involved in tunicamycin-induced apoptosis by mediating protein kinase (PKR) activation. RBBP6 contains an N-terminal ubiquitin-like domain and a C4C4-type RING finger, whose overall folding is similar to that of the typical C3HC4-type RING-HC finger. RBBP6 interacts with chaperones Hsp70 and Hsp40 through its N-terminal ubiquitin-like domain. It promotes the ubiquitination of p53 by Hdm2 in an E4-like manner through its RING finger. It also interacts directly with the pro-proliferative transcription factor Y-box-binding protein-1 (YB-1) via its RING finger.

Pssm-ID: 438282 [Multi-domain] Cd Length: 55 Bit Score: 46.63 E-value: 5.15e-07

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|
gi 890799132  11 EEVTCPVCLNLMVKPVSAD-CGHTFCQGCITLYFESIKcdkemFSCPVCR 59
Cdd:cd16620    2 DELKCPICKDLMKDAVLTPcCGNSFCDECIRTALLEED-----FTCPTCK 46

RING-HC_BAH1-like

cd23127

RING finger, HC subclass, found in Arabidopsis thaliana protein BENZOIC ACID HYPERSENSITIVE 1 ...

12-59

5.52e-07

RING finger, HC subclass, found in Arabidopsis thaliana protein BENZOIC ACID HYPERSENSITIVE 1 (BAH1) and similar proteins; This subfamily includes Arabidopsis thaliana BAH1 and BAH1-like. BAH1, also known as protein NITROGEN LIMITATION ADAPTATION (NLA), or RING-type E3 ubiquitin transferase BAH1, acts as an E3 ubiquitin-protein ligase that mediates E2-dependent protein ubiquitination. It plays a role in salicylic acid-mediated negative feedback regulation of salicylic acid (SA) accumulation. It may be involved in the overall regulation of SA, benzoic acid and phenylpropanoid biosynthesis. It controls the adaptability to nitrogen limitation by channeling the phenylpropanoid metabolic flux to the induced anthocyanin synthesis. BAH1-like, also known as RING finger protein 178, or RING-type E3 ubiquitin transferase BAH1-like, is a probable E3 ubiquitin-protein ligase. Members of this subfamily contain a typical C3HC4-type RING-HC finger.

Pssm-ID: 438489 [Multi-domain] Cd Length: 74 Bit Score: 47.01 E-value: 5.52e-07

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 890799132  12 EVTCPVCLNLMVKPVSADCGHTFCQGCI-----TLYFESIKCDKEMFSCPVCR 59
Cdd:cd23127    8 DLTCSICLDTVFDPVALGCGHLFCNSCAcsaasVLIFQGLKAAPPEAKCPLCR 60

RING-HC_PRT1-like

cd23132

RING finger, HC subclass, found in Arabidopsis thaliana proteolysis 1 protein (PRT1) and ...

11-62

5.99e-07

RING finger, HC subclass, found in Arabidopsis thaliana proteolysis 1 protein (PRT1) and similar proteins; PRT1, also called RING-type E3 ubiquitin transferase PRT1, is an E3 ubiquitin-protein ligase that mediates ubiquitination and subsequent proteasomal degradation of target proteins. It functions in the N-end rule pathway of protein degradation, where it specifically recognizes and ubiquitinates proteins with an N-terminal bulky aromatic amino acid (Phe). It does not act on aliphatic hydrophobic and basic N-terminal residues (Arg or Leu) containing proteins. PRT1 contains a typical C3HC4-type RING-HC finger.

Pssm-ID: 438494 [Multi-domain] Cd Length: 52 Bit Score: 46.26 E-value: 5.99e-07

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 890799132  11 EEVTCPVCLNLMVKPVSADCGHTFCQGCItlyFESIKCDKEMfSCPVCRLSY 62
Cdd:cd23132    1 EEFLCCICLDLLYKPVVLECGHVFCFWCV---HRCMNGYDES-HCPLCRRPY 48

RING-HC_RFPL4B

cd16623

RING finger, HC subclass, found in Ret finger protein-like 4B (RFPL4B) and similar proteins; ...

7-59

6.46e-07

RING finger, HC subclass, found in Ret finger protein-like 4B (RFPL4B) and similar proteins; RFPL4B, also called RING finger protein 211 (RNF211), is an uncharacterized RING finger protein containing a typical C3HC4-type RING-HC finger.

Pssm-ID: 438285 [Multi-domain] Cd Length: 63 Bit Score: 46.35 E-value: 6.46e-07

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 890799132   7 KNLKEEVTCPVCLNLMVKPVSADCGHTFCQGCITLYFeSIKCDKEMfSCPVCR 59
Cdd:cd16623    3 NRLEMEATCPICLDFFSHPISLSCAHIFCFDCIQKWM-TKREDSIL-TCPLCR 53

RING-HC_DTX3-like

cd16506

RING finger, HC subclass, found in E3 ubiquitin-protein ligase Deltex3 (DTX3), Deltex-3-like ...

14-62

1.34e-06

RING finger, HC subclass, found in E3 ubiquitin-protein ligase Deltex3 (DTX3), Deltex-3-like (DTX3L) and similar proteins; This subfamily contains Deltex3 (DTX3) and Deltex-3-like (DTX3L), both of which are E3 ubiquitin-protein ligases belonging to the Deltex (DTX) family. DTX3, also known as RING finger protein 154 (RNF154), has a biological function that remains unclear. DTX3L, also known as B-lymphoma- and BAL-associated protein (BBAP) or Rhysin-2 (Rhysin2), regulates endosomal sorting of the G protein-coupled receptor CXCR4 from endosomes to lysosomes. It also regulates subcellular localization of its partner protein, B aggressive lymphoma (BAL), by a dynamic nucleocytoplasmic trafficking mechanism. In contrast to other DTXs, both DTX3 and DTX3L contain a C3HC4-type RING-HC finger, and a previously unidentified C-terminal domain. DTX3L can associate with DTX1 through its unique N termini and further enhance self-ubiquitination.

Pssm-ID: 438169 [Multi-domain] Cd Length: 45 Bit Score: 45.05 E-value: 1.34e-06

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|
gi 890799132  14 TCPVCLNLMVKP-VSADCGHTFCQGCITLYFESIKcdkemfSCPVCRLSY 62
Cdd:cd16506    2 TCPICLDEIQNKkTLEKCKHSFCEDCIDRALQVKP------VCPVCGVVY 45

RING-HC_ScPSH1-like

cd16568

RING finger, HC subclass, found in Saccharomyces cerevisiae POB3/SPT16 histone-associated ...

9-59

1.41e-06

RING finger, HC subclass, found in Saccharomyces cerevisiae POB3/SPT16 histone-associated protein 1 (ScPSH1) and similar proteins; ScPSH1 is a Cse4-specific E3 ubiquitin ligase that interacts with the kinetochore protein Pat1 and targets the degradation of budding yeast centromeric histone H3 variant, CENP-ACse4, which is essential for faithful chromosome segregation. ScPSH1 contains a C3HC4-type RING-HC finger and a DNA directed RNA polymerase domain.

Pssm-ID: 438230 [Multi-domain] Cd Length: 54 Bit Score: 45.44 E-value: 1.41e-06

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 890799132   9 LKEEVTCPVCLNLMVKPVSADCGHTFCQGCITLYFESIkcdKEMfSCPVCR 59
Cdd:cd16568    1 ILETQECIICHEYLYEPMVTTCGHTYCYTCLNTWFKSN---RSL-SCPDCR 47

RING-HC_RNF125

cd16542

RING finger, HC subclass, found in RING finger protein 125 (RNF125); RNF125, also known as ...

15-59

1.48e-06

RING finger, HC subclass, found in RING finger protein 125 (RNF125); RNF125, also known as T-cell RING activation protein 1 (TRAC-1), is an E3 ubiquitin-protein ligase that is predominantly expressed in lymphoid cells, and functions as a positive regulator of T cell activation. It also down-modulates HIV replication and inhibits pathogen-induced cytokine production. It negatively regulates type I interferon signaling, which conjugates Lys(48)-linked ubiquitination to retinoic acid-inducible gene-I (RIG-I) and subsequently leads to the proteasome-dependent degradation of RIG-I. Further, RNF125 conjugates ubiquitin to melanoma differentiation-associated gene 5 (MDA5), a family protein of RIG-I. It thus acts as a negative regulator of RIG-I signaling, and is a direct target of miR-15b in the context of Japanese encephalitis virus (JEV) infection. Moreover, RNF125 binds to and ubiquitinates JAK1, prompting its degradation and inhibition of receptor tyrosine kinase (RTK) expression. It also negatively regulates p53 function through physical interaction and ubiquitin-mediated proteasome degradation. Mutations in RNF125 may lead to overgrowth syndromes (OGS). RNF125, together with three closely related proteins: RNF114, RNF138 and RNF166, forms a novel family of ubiquitin ligases with a C3HC4-type RING-HC finger, a C2HC-, and two C2H2-type zinc fingers, as well as a ubiquitin interacting motif (UIM). The UIM of RNF125 binds K48-linked poly-ubiquitin chains and is, together with the RING domain, required for auto-ubiquitination.

Pssm-ID: 438204 [Multi-domain] Cd Length: 50 Bit Score: 45.26 E-value: 1.48e-06

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*
gi 890799132  15 CPVCLNLMVKPVSADCGHTFCQGCITlyfESIKcdKEMFSCPVCR 59
Cdd:cd16542    4 CAVCLEVLHQPVRTRCGHVFCRPCIA---TSLR--NNTWTCPYCR 43

RING-HC_RNFT1-like

cd16532

RING finger, HC subclass, found in RING finger and transmembrane domain-containing protein ...

14-59

1.64e-06

RING finger, HC subclass, found in RING finger and transmembrane domain-containing protein RNFT1, RNFT2, and similar proteins; Both RNFT1 and RNFT2 are multi-pass membrane proteins containing a C3HC4-type RING-HC finger. Their biological roles remain unclear.

Pssm-ID: 438194 [Multi-domain] Cd Length: 41 Bit Score: 44.60 E-value: 1.64e-06

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*.
gi 890799132  14 TCPVCLNLMVKPVSADCGHTFCQGCITLYFESIKcdkemfSCPVCR 59
Cdd:cd16532    2 ICPICQDEFKDPVVLRCKHIFCEDCVSEWFERER------TCPLCR 41

Bbox2_TRIM10-like

cd19765

B-box-type 2 zinc finger found in tripartite motif-containing proteins, TRIM10, TRIM15, ...

96-132

1.79e-06

B-box-type 2 zinc finger found in tripartite motif-containing proteins, TRIM10, TRIM15, TRIM26, TRIM31 and similar proteins; This family includes TRIM10, TRIM15, TRIM26 and TRIM31. TRIM10, also known as B30-RING finger protein (RFB30), RING finger protein 9 (RNF9), or hematopoietic RING finger 1 (HERF1), is a novel hematopoiesis-specific RING finger protein required for terminal differentiation of erythroid cells. TRIM15, also termed RING finger protein 93 (RNF93), or zinc finger protein 178 (ZNF178), or zinc finger protein B7 (ZNFB7), is a focal adhesion protein that regulates focal adhesion disassembly. It localizes to focal contacts in a myosin-II-independent manner by an interaction between its coiled-coil domain and the LD2 motif of paxillin. TRIM15 can also associate with coronin 1B, cortactin, filamin binding LIM protein1, and vasodilator-stimulated phosphoprotein, which are involved in actin cytoskeleton dynamics. As an additional component of the integrin adhesome, it regulates focal adhesion turnover and cell migration. TRIM26, also known as acid finger protein (AFP), RING finger protein 95 (RNF95), or zinc finger protein 173 (ZNF173), is an E3 ubiquitin-protein ligase that negatively regulates interferon-beta production and antiviral response through polyubiquitination and degradation of nuclear transcription factor IRF3. It functions as an important regulator for RNA virus-triggered innate immune response by bridging TBK1 to NEMO (NF-kappaB essential modulator, also known as IKKgamma) and mediating TBK1 activation. It also acts as a novel tumor suppressor of hepatocellular carcinoma by regulating cancer cell proliferation, colony forming ability, migration, and invasion. TRIM31 is an E3 ubiquitin-protein ligase that primarily localizes to the cytoplasm, but is also associated with the mitochondria. It can negatively regulate cell proliferation and may be a potential biomarker of gastric cancer as it is overexpressed from the early stage of gastric carcinogenesis. TRIM31 is downregulated in non-small cell lung cancer and serves as a potential tumor suppressor. It interacts with p52 (Shc) and inhibits Src-induced anchorage-independent growth. TRIM10, TRIM15 and TRIM26 belong to the C-IV subclass of TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a RING finger, Bbox2, and a coiled coil region, as well as a B30.2/SPRY (SplA and ryanodine receptor) domain positioned C-terminal to the RBCC domain. TRIM31 belongs to the C-V subclass of TRIM family of proteins. The type 2 B-box (Bbox2) zinc finger is characterized by a CHC3H2 zinc-binding consensus motif.

Pssm-ID: 380823 [Multi-domain] Cd Length: 39 Bit Score: 44.38 E-value: 1.79e-06

                         10        20        30
                 ....*....|....*....|....*....|....*..
gi 890799132  96 CARHGEKLQLFCRKDMMAICWLCERSQEHRGHKTALI 132
Cdd:cd19765    3 CEEHGEKIHFFCEDDGKFLCVVCRESREHRTHTVSLL 39

SPRY_PRY_FSD1

cd12901

Fibronectin type III and SPRY containing 1 (FSD1) domain includes PRY at the N-terminus; This ...

341-481

2.29e-06

Fibronectin type III and SPRY containing 1 (FSD1) domain includes PRY at the N-terminus; This domain is part of the fibronectin type III and SPRY domain containing 1 (FSD1) and FSD1-like (FSD1L) proteins. These are centrosome-associated proteins that are characterized by an N-terminal coiled-coil region downstream of B-box (BBC) domain, a central fibronectin type III (FN3) domain, and C-terminal repeats in PRY/SPRY domain. The FSD1 protein associates with a subset of microtubules and may be involved in the stability and organization of microtubules during cytokinesis.

Pssm-ID: 293958 Cd Length: 207 Bit Score: 48.28 E-value: 2.29e-06

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 890799132 341 VLGHPAIQSGKHYWEV--DVSGKgAWVLGLSdgsylfcpiFHSNAERNRLfcrGIKNDShyqpkygfWVIGLwkksvyNA 418
Cdd:cd12901   76 VLGDTLIDGGQHYWEVraQKDSK-AFSVGVA---------YRSLGKFDQL---GKTNAS--------WCLHV------NN 128

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 890799132 419 FEECPFTGKPSVLTLSLMVP-PCRVGVFLDYAAGTLSFYNiSNNGTLIYRFcTASFPDRVFPYF 481
Cdd:cd12901  129 WLQNSFAAKHNNKAKTLDVPvPDRIGVYCDFDEGQLSFYN-ARTKQLLHTF-KMKFTQPVLPAF 190

RING-HC_MID2

cd16754

RING finger, HC subclass, found in midline-2 (MID2) and similar proteins; MID2, also known as ...

6-59

2.84e-06

RING finger, HC subclass, found in midline-2 (MID2) and similar proteins; MID2, also known as midin-2, midline defect 2, RING finger protein 60 (RNF60), or tripartite motif-containing protein 1 (TRIM1), is a probable E3 ubiquitin-protein ligase and is highly related to MID1 that associates with cytoplasmic microtubules along their length and throughout the cell cycle. Like MID1, MID2 associates with the microtubule network and may at least partially compensate for the loss of MID1. Both MID1 and MID2 interacts with Alpha 4, which is a regulatory subunit of PP2-type phosphatases, such as PP2A, and an integral component of the rapamycin-sensitive signaling pathway. MID2 can also substitute for MID1 to control exocytosis of lytic granules in cytotoxic T cells. Loss-of-function mutations in MID2 lead to the human X-linked intellectual disability (XLID). MID2 belongs to the C-I subclass of the TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a C3HC4-type RING-HC finger, Bbox1 and Bbox2, and a coiled coil region, as well as a COS (carboxy-terminal subgroup one signature) box, a fibronectin type III (FN3) domain, and a B30.2/SPRY (SplA and ryanodine receptor) domain positioned C-terminal to the RBCC domain. MID2 hetero-dimerizes in vitro with its paralog MID1.

Pssm-ID: 438412 [Multi-domain] Cd Length: 70 Bit Score: 44.98 E-value: 2.84e-06

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 890799132   6 MKNLKEEVTCPVCLNLMVKPVSADCGHTFCQGCI-------TLYFESIKcDKEMFSCPVCR 59
Cdd:cd16754    1 METLESELTCPICLELFEDPLLLPCAHSLCFSCAhriltsgCASGESIE-PPSAFQCPTCR 60

RING-HC_RNF213

cd16561

RING finger, HC subclass, found in RING finger protein 213 (RNF213) and similar proteins; ...

15-61

2.86e-06

RING finger, HC subclass, found in RING finger protein 213 (RNF213) and similar proteins; RNF213, also known as ALK lymphoma oligomerization partner on chromosome 17 or Moyamoya steno-occlusive disease-associated AAA+ and RING finger protein (mysterin), is an intracellular soluble protein that functions as an E3 ubiquitin-protein ligase and AAA+ ATPase, which possibly contributes to vascular development through mechanical processes in the cell. It plays a unique role in endothelial cells for proper gene expression in response to inflammatory signals from the environment. Mutations in RNF213 may be associated with Moyamoya disease (MMD), an idiopathic cerebrovascular occlusive disorder prevalent in East Asia. It also acts as a nuclear marker for acanthomorph phylogeny. RNF213 contains two tandem enzymatically active AAA+ ATPase modules and a C3HC4-type RING-HC finger. It can form a huge ring-shaped oligomeric complex.

Pssm-ID: 438223 [Multi-domain] Cd Length: 50 Bit Score: 44.19 E-value: 2.86e-06

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
gi 890799132  15 CPVCLNLMVKPVSADCGHTFCQGCITLYFEsikcdKEMfSCPVCRLS 61
Cdd:cd16561    5 CSICLEDLNDPVKLPCDHVFCEECIRQWLP-----GQM-SCPLCRTE 45

Bbox2_xNF7-like

cd19800

B-box-type 2 zinc finger found in Xenopus laevis nuclear factor 7 (xNF7) and similar proteins; ...

96-128

3.72e-06

B-box-type 2 zinc finger found in Xenopus laevis nuclear factor 7 (xNF7) and similar proteins; xNF7 is a maternally expressed novel zinc finger nuclear phosphoprotein. It acts as a transcription factor that determines dorsal-ventral body axis. xNF7 harbors a B-box motif that shows high sequence similarity with B-Box-type zinc finger 2 found in tripartite motif-containing proteins (TRIMs). The type 2 B-box (Bbox2) zinc finger is characterized by a CHC3H2 zinc-binding consensus motif.

Pssm-ID: 380858 [Multi-domain] Cd Length: 39 Bit Score: 43.54 E-value: 3.72e-06

                         10        20        30
                 ....*....|....*....|....*....|...
gi 890799132  96 CARHGEKLQLFCRKDMMAICWLCERSQEHRGHK 128
Cdd:cd19800    3 CSEHDEPLKLFCKDDKRLICVICRDSRKHRGHR 35

RING-HC_RNF10

cd16536

RING finger, HC subclass, found in RING finger protein 10 (RNF10) and similar proteins; RNF10 ...

13-68

3.90e-06

RING finger, HC subclass, found in RING finger protein 10 (RNF10) and similar proteins; RNF10 is an E3 ubiquitin-protein ligase that interacts with mesenchyme Homeobox 2 (MEOX2) transcription factor, a regulator of the proliferation, differentiation and migration of vascular smooth muscle cells and cardiomyocytes; it enhances Meox2 activation of the p21 promoter. It also regulates the expression of myelin-associated glycoprotein (MAG) genes and is required for myelin production in Schwann cells of the peripheral nervous system. Moreover, RNF10 regulates retinoic acid-induced neuronal differentiation and the cell cycle exit of P19 embryonic carcinoma cells. RNF10 contains a C3HC4-type RING-HC finger and three putative nuclear localization signals.

Pssm-ID: 438198 [Multi-domain] Cd Length: 54 Bit Score: 44.15 E-value: 3.90e-06

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 890799132  13 VTCPVCLNLMVKPVSADCGHTFCQGCITLYFESikCDKEMFSCPVCRLSYQSSNLR 68
Cdd:cd16536    1 PQCPICLEPPVAPRITRCGHIFCWPCILRYLSL--SEKKWRKCPICFESIHKKDLR 54

Bbox2_TRIM20

cd19771

B-box-type 2 zinc finger found in tripartite motif-containing protein TRIM20 and similar ...

96-128

4.03e-06

B-box-type 2 zinc finger found in tripartite motif-containing protein TRIM20 and similar proteins; TRIM20, also termed Pyrin, or Marenostrin (MEFV), is involved in the regulation of innate immunity and the inflammatory response in response to IFNG/IFN-gamma. TRIM20 belongs to unclassified TRIM family of proteins that do not have RING fingers and thus lack the characteristic tripartite (RING (R), B-box, and coiled coil (CC)) RBCC motif. It contains a pyrin domain, a Bbox2 zinc finger, and a C-terminal SPRY/B30.2 domain. The type 2 B-box (Bbox2) zinc finger is characterized by a CHC3H2 zinc-binding consensus motif.

Pssm-ID: 380829 [Multi-domain] Cd Length: 39 Bit Score: 43.61 E-value: 4.03e-06

                         10        20        30
                 ....*....|....*....|....*....|...
gi 890799132  96 CARHGEKLQLFCRKDMMAICWLCERSQEHRGHK 128
Cdd:cd19771    3 CKLHLEQLKLFCEDHREPICLICQLSQEHQGHR 35

RING-HC_COP1

cd16504

RING finger, HC subclass, found in constitutive photomorphogenesis protein 1 (COP1) and ...

13-58

4.33e-06

RING finger, HC subclass, found in constitutive photomorphogenesis protein 1 (COP1) and similar proteins; COP1, also known as RING finger and WD repeat domain protein 2 (RFWD2) or RING finger protein 200 (RNF200), is a central regulator of photomorphogenic development in plants, which targets key transcription factors for proteasome-dependent degradation. It is localized predominantly in the nucleus, but may also be present in the cytosol. Mammalian COP1 functions as an E3 ubiquitin-protein ligase that interacts with Jun transcription factors and modulates their transcriptional activity. It also interacts with and negatively regulates the tumor-suppressor protein p53. Moreover, COP1 associates with COP9 signalosome subunit 6 (CSN6), and is involved in 14-3-3sigma ubiquitin-mediated degradation. The CSN6-COP1 link enhances ubiquitin-mediated degradation of p27(Kip1), a critical CDK inhibitor involved in cell cycle regulation, to promote cancer cell growth. Furthermore, COP1 functions as the negative regulator of ETV1 and influences prognosis in triple-negative breast cancer. COP1 contains an N-terminal extension, a C3HC4-type RING-HC finger, a coiled coil domain, and seven WD40 repeats. In human COP1, a classic leucine-rich NES, and a novel bipartite NLS is bridged by the RING-HC finger.

Pssm-ID: 438167 [Multi-domain] Cd Length: 47 Bit Score: 43.77 E-value: 4.33e-06

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*.
gi 890799132  13 VTCPVCLNLMVKPVSADCGHTFCQGCITLYFESIKcdkemfSCPVC 58
Cdd:cd16504    3 FLCPICFDIIKEAFVTKCGHSFCYKCIVKHLEQKN------RCPKC 42

RING-HC_LONFs_rpt1

cd16513

first RING finger, HC subclass, found in the LON peptidase N-terminal domain and RING finger ...

11-62

5.03e-06

first RING finger, HC subclass, found in the LON peptidase N-terminal domain and RING finger protein family; The LON peptidase N-terminal domain and RING finger protein family includes LONRF1 (also known as RING finger protein 191 or RNF191), LONRF2 (also known as RING finger protein 192, RNF192, or neuroblastoma apoptosis-related protease), LONRF3 (also known as RING finger protein 127 or RNF127), which are characterized by containing two C3HC4-type RING-HC fingers, four tetratricopeptide (TPR) repeats, and an ATP-dependent protease La (LON) substrate-binding domain at the C-terminus. Their biological functions remain unclear. This model corresponds to the first RING-HC finger.

Pssm-ID: 438176 [Multi-domain] Cd Length: 47 Bit Score: 43.45 E-value: 5.03e-06

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 890799132  11 EEVTCPVCLNLMVKPVSADCGHTFCQGCItlyfesikcDKEMFS-CPVCRLSY 62
Cdd:cd16513    1 DLLSCPLCRGLLFEPVTLPCGHTFCKRCL---------ERDPSSrCRLCRLKL 44

RING-HC_RNF138

cd16544

RING finger, HC subclass, found in RING finger protein 138 (RNF138) and similar proteins; ...

11-65

5.27e-06

RING finger, HC subclass, found in RING finger protein 138 (RNF138) and similar proteins; RNF138, also known as Nemo-like kinase-associated RING finger protein (NARF) or NLK-associated RING finger protein, is an E3 ubiquitin-protein ligase that plays an important role in glioma cell proliferation, apoptosis, and cell cycle. It specifically cooperates with the E2 conjugating enzyme E2-25K (Hip-2/UbcH1), regulates the ubiquitylation and degradation of T cell factor/lymphoid enhancer factor (TCF/LEF), and further suppresses Wnt-beta-catenin signaling. RNF138, together with three closely related proteins: RNF114, RNF125 and RNF166, forms a novel family of ubiquitin ligases with a C3HC4-type RING-HC finger, a C2HC-, and two C2H2-type zinc fingers, as well as a ubiquitin interacting motif (UIM).

Pssm-ID: 438206 [Multi-domain] Cd Length: 53 Bit Score: 43.55 E-value: 5.27e-06

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 890799132  11 EEVTCPVCLNLMVKPVS-ADCGHTFCQGCITLYFesikcDKEMFSCPVCRLSYQSS 65
Cdd:cd16544    1 AELTCPVCQEVLKDPVElPPCRHIFCKACILLAL-----RSSGARCPLCRGPVGKT 51

RING-HC_RNF114

cd16540

RING finger, HC subclass, found in RING finger protein 114 (RNF114) and similar proteins; ...

14-59

5.96e-06

RING finger, HC subclass, found in RING finger protein 114 (RNF114) and similar proteins; RNF114, also known as zinc finger protein 228 (ZNF228) or zinc finger protein 313 (ZNF313), is a p21(WAF1)-targeting ubiquitin E3 ligase that interacts with X-linked inhibitor of apoptosis (XIAP)-associated factor 1 (XAF1) and may play a role in p53-mediated cell-fate decisions. It is involved in the immune response to double-stranded RNA in disease pathogenesis. Moreover, RNF114 interacts with A20 and modulates its ubiquitylation. It negatively regulates nuclear factor-kappaB (NF-kappaB)-dependent transcription and positively regulates T-cell activation. RNF114 may play a putative role in the regulation of immune responses, since it corresponds to a novel psoriasis susceptibility gene, ZNF313. RNF114, together with three closely related proteins: RNF125, RNF138 and RNF166, forms a novel family of ubiquitin ligases with a C3HC4-type RING-HC finger, a C2HC-, and two C2H2-type zinc fingers, as well as a ubiquitin interacting motif (UIM).

Pssm-ID: 438202 [Multi-domain] Cd Length: 46 Bit Score: 43.21 E-value: 5.96e-06

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*.
gi 890799132  14 TCPVCLNLMVKPVSADCGHTFCQGCITlyfESIKCDKEMfsCPVCR 59
Cdd:cd16540    3 TCPVCLEIFETPVRVPCGHVFCNACLQ---ECLKPKKPV--CAVCR 43

RING-HC_DTX3L

cd16712

RING finger, HC subclass, found in protein Deltex-3-like (DTX3L) and similar proteins; DTX3L, ...

10-62

6.58e-06

RING finger, HC subclass, found in protein Deltex-3-like (DTX3L) and similar proteins; DTX3L, also known as B-lymphoma- and BAL-associated protein (BBAP) or Rhysin-2 (Rhysin2), is a RING-domain E3 ubiquitin-protein ligase that regulates endosomal sorting of the G protein-coupled receptor CXCR4 from endosomes to lysosomes. It also regulates subcellular localization of its partner protein, B aggressive lymphoma (BAL), by a dynamic nucleocytoplasmic trafficking mechanism. DTX3L has a unique N-terminus, but lacks the highly basic N-terminal motif and the central proline-rich motif present in other Deltex (DTX) family members, such as DTX1, DTX2, and DTX4. Moreover, its C-terminal region is highly homologous to DTX3. It includes a C3HC4-type RING-HC finger, and a previously unidentified C-terminal domain. DTX3L can associate with DTX1 through its unique N-terminus and further enhance self-ubiquitination.

Pssm-ID: 438372 [Multi-domain] Cd Length: 56 Bit Score: 43.57 E-value: 6.58e-06

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 890799132  10 KEEVTCPVCLNLMVKP-VSADCGHTFCQGCITLYFEsikcDKEMfsCPVCRLSY 62
Cdd:cd16712    1 QEEDECPICMDRISNKkVLPKCKHVFCAACIDKAMK----YKPV--CPVCGTIY 48

Bbox2_TRIM35_C-IV

cd19777

B-box-type 2 zinc finger found in tripartite motif-containing protein 35 (TRIM35) and similar ...

96-134

6.67e-06

B-box-type 2 zinc finger found in tripartite motif-containing protein 35 (TRIM35) and similar proteins; TRIM35, also known as hemopoietic lineage switch protein 5 (HLS5), is a putative hepatocellular carcinoma (HCC) suppressor that inhibits phosphorylation of pyruvate kinase isoform M2 (PKM2), which is involved in aerobic glycolysis of cancer cells and further suppresses the Warburg effect and tumorigenicity in HCC. It also negatively regulates Toll-like receptor 7 (TLR7)- and TLR9-mediated type I interferon production by suppressing the stability of interferon regulatory factor 7 (IRF7). Moreover, TRIM35 regulates erythroid differentiation by modulating globin transcription factor 1 (GATA-1) activity. TRIM35 belongs to the C-IV subclass of TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a RING finger, Bbox2, and a coiled coil region, as well as a B30.2/SPRY (SplA and ryanodine receptor) domain positioned C-terminal to the RBCC domain. The type 2 B-box (Bbox2) zinc finger is characterized by a CHC3H2 zinc-binding consensus motif.

Pssm-ID: 380835 [Multi-domain] Cd Length: 44 Bit Score: 43.24 E-value: 6.67e-06

                         10        20        30
                 ....*....|....*....|....*....|....*....
gi 890799132  96 CARHGEKLQLFCRKDMMAICWLCERSQEHRGHKTALIEE 134
Cdd:cd19777    6 CRLHGETLKLFCLDDKELLCCACQSSKQHQGHRVYPVKE 44

RING-HC_CHR27-like

cd23142

RING finger, HC subclass, found in Arabidopsis thaliana protein CHROMATIN REMODELING 27 (CHR27) ...

15-59

7.09e-06

RING finger, HC subclass, found in Arabidopsis thaliana protein CHROMATIN REMODELING 27 (CHR27) and similar proteins; CHR27, also called protein SNF2-RING-HELICASE-LIKE 1, is a probable helicase-like transcription factor involved in transcriptional gene silencing. It associates with SUVR2 and contributes to transcriptional gene silencing at RNA-directed DNA methylation (RdDM) target loci but also at RdDM-independent target loci. It may be involved in nucleosome positioning to form ordered nucleosome arrays on chromatin. It associates with SUVR2 and functions redundantly with FRG2. It is required for the efficient methylation of a broad range of RdDM target loci. CHR27 contains a typical C3HC4-type RING-HC finger.

Pssm-ID: 438504 [Multi-domain] Cd Length: 55 Bit Score: 43.33 E-value: 7.09e-06

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*
gi 890799132  15 CPVCLNLMVKPVSADCGHTFCQGCITLYFESIKCDKEMFSCPVCR 59
Cdd:cd23142    3 CPICNDPPEDAVVTLCGHVFCCECVFQYLSSDRTCRQFNHCPLCR 47

RING-HC_PCGF

cd16525

RING finger, HC subclass, found in Polycomb Group RING finger homologs (PCGF1, 2, 3, 4, 5 and ...

14-59

8.00e-06

RING finger, HC subclass, found in Polycomb Group RING finger homologs (PCGF1, 2, 3, 4, 5 and 6), and similar proteins; This subfamily includes six Polycomb Group (PcG) RING finger homologs (PCGF1/NSPc1, PCGF2/Mel-18, PCGF3, PCGF4/BMI1, PCGF5, and PCGF6/MBLR) that use epigenetic mechanisms to maintain or repress expression of their target genes. They were first discovered in fruit flies and are well known for silencing Hox genes through modulation of chromatin structure during embryonic development. PCGF homologs play important roles in cell proliferation, differentiation, and tumorigenesis. They all have been found to associate with ring finger protein 2 (RNF2). The RNF2-PCGF heterodimer is catalytically competent as an E3 ubiquitin transferase and is the scaffold for the assembly of additional components. Moreover, PCGF homologs are critical components in the assembly of distinct Polycomb Repression Complex 1 (PRC1) related complexes which is involved in the maintenance of gene repression and which target different genes through distinct mechanisms. The Drosophila PRC1 core complex is formed by the Polycomb (Pc), Polyhomeotic (Ph), Posterior sex combs (Psc), and Sex combs extra (Sce, also known as Ring) subunits. In mammals, the composition of PRC1 is much more diverse and varies depending on the cellular context. All PRC1 complexes contain homologs of the Drosophila Ring protein. Ring1A/RNF1 and Ring1B/RNF2 are E3 ubiquitin ligases that mark lysine 119 of histone H2A with a single ubiquitin group (H2AK119ub). Mammalian homologs of the Drosophila Psc protein, such as PCGF2/Mel-18 or PCGF4/BMI1, regulate PRC1 enzymatic activity. PRC1 complexes can be divided into at least two classes according to the presence or absence of CBX proteins, which are homologs of Drosophila Pc. Canonical PRC1 complexes contain CBX proteins that recognize and bind H3K27me3, the mark deposited by PRC2. Therefore, canonical PRC1 complexes and PRC2 can act together to repress gene transcription and maintain this repression through cell division. Non-canonical PRC1 complexes, containing RYBP (together with additional proteins, such as L3mbtl2 or Kdm2b) rather than the CBX proteins have recently been described in mammals. PCGF homologs contain a C3HC4-type RING-HC finger.

Pssm-ID: 438188 [Multi-domain] Cd Length: 42 Bit Score: 42.60 E-value: 8.00e-06

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
gi 890799132  14 TCPVCLNLMVKPVS-ADCGHTFCQGCITLYFESIKCdkemfsCPVCR 59
Cdd:cd16525    2 TCSLCKGYLIDATTiTECLHSFCKSCIVRHLETSKN------CPVCD 42

RING-HC_RNF8

cd16535

RING finger, HC subclass, found in RING finger protein 8 (RNF8) and similar proteins; RNF8 is ...

12-82

8.23e-06

RING finger, HC subclass, found in RING finger protein 8 (RNF8) and similar proteins; RNF8 is a telomere-associated E3 ubiquitin-protein ligase that plays an important role in DNA double-strand break (DSB) repair via histone ubiquitination. It is localized in the nucleus and interacts with class III E2s (UBE2E2, UbcH6, and UBE2E3), but not with other E2s (UbcH5, UbcH7, UbcH10, hCdc34, and hBendless). It recruits UBC13 for lysine 63-based self polyubiquitylation. Its deficiency causes neuronal pathology and cognitive decline, and its loss results in neuron degeneration. RNF8, together with RNF168, catalyzes a series of ubiquitylation events on substrates such as H2A and H2AX, with the H2AK13/15 ubiquitylation being particularly important for recruitment of repair factors p53-binding protein 1 (53BP1) or the RAP80-BRCA1 complex to sites of DSBs. RNF8 mediates the ubiquitination of gammaH2AX, and recruits 53BP1 and BRCA1 to DNA damage sites which promotes DNA damage response (DDR) and inhibits chromosomal instability. Moreover, RNF8 interacts with retinoid X receptor alpha (RXR alpha) and enhances its transcription-stimulating activity. It also regulates the rate of exit from mitosis and cytokinesis. RNF8 contains an N-terminal forkhead-associated (FHA) domain and a C-terminal C3HC4-type RING-HC finger.

Pssm-ID: 438197 [Multi-domain] Cd Length: 64 Bit Score: 43.54 E-value: 8.23e-06

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 890799132  12 EVTCPVCLNLMVKPVSADCGHTFCQGCITlyfESIKCDKEmfsCPVCRLSYQSSNlrPNLHVANIVERLKE 82
Cdd:cd16535    1 ELQCSICSELFIEAVTLNCSHSFCSYCIT---EWMKRKKE---CPICRKPITSKT--RSLVLDNCIDKMVE 63

zf-C3HC4

pfam00097

Zinc finger, C3HC4 type (RING finger); The C3HC4 type zinc-finger (RING finger) is a ...

15-58

8.43e-06

Zinc finger, C3HC4 type (RING finger); The C3HC4 type zinc-finger (RING finger) is a cysteine-rich domain of 40 to 60 residues that coordinates two zinc ions, and has the consensus sequence: C-X2-C-X(9-39)-C-X(1-3)-H-X(2-3)-C-X2-C-X(4-48)-C-X2-C where X is any amino acid. Many proteins containing a RING finger play a key role in the ubiquitination pathway.

Pssm-ID: 395049 [Multi-domain] Cd Length: 40 Bit Score: 42.73 E-value: 8.43e-06

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 890799132   15 CPVCLNLMVKPV-SADCGHTFCQGCITLYFESIKcdkemFSCPVC 58
Cdd:pfam00097   1 CPICLEEPKDPVtLLPCGHLFCSKCIRSWLESGN-----VTCPLC 40

mRING-HC-C3HC3D_TRAF7

cd16644

Modified RING finger, HC subclass (C3HC3D-type), found in tumor necrosis factor (TNF) ...

15-40

1.26e-05

Modified RING finger, HC subclass (C3HC3D-type), found in tumor necrosis factor (TNF) receptor-associated factor 7 (TRAF7) and similar proteins; TRAF7, also known as RING finger and WD repeat-containing protein 1 or RING finger protein 119 (RNF119), is an E3 ubiquitin-protein ligase involved in signal transduction pathways that lead either to activation or repression of NF-kappaB transcription factor by promoting K29-linked ubiquitination of several cellular targets, including the NF-kappaB essential modulator (NEMO) and the p65 subunit of NF-kappaB transcription factor. It is also involved in K29-linked polyubiquitination that has been implicated in lysosomal degradation of proteins. Moreover, TRAF7 is required for K48-linked ubiquitination of p53, a key tumor suppressor and a master regulator of various signaling pathways, such as those related to apoptosis, cell cycle and DNA repair. It is also required for tumor necrosis factor alpha (TNFalpha)-induced Jun N-terminal kinase activation and promotes cell death by regulating polyubiquitination and lysosomal degradation of c-FLIP protein. Furthermore, TRAF7 functions as small ubiquitin-like modifier (SUMO) E3 ligase involved in other post-translational modification, such as sumoylation. It binds to and stimulates sumoylation of the proto-oncogene product c-Myb, a transcription factor regulating proliferation and differentiation of hematopoietic cells. It potentiates MEKK3-induced AP1 and CHOP activation and induces apoptosis. Meanwhile, TRAF7 mediates MyoD1 regulation of the pathway and cell-cycle progression in myoblasts. It also plays a role in Toll-like receptors (TLR) signaling. TRAF7 contains an N-terminal domain with a modified C3HC3D-type RING-HC finger and an adjacent zinc finger, and a unique C-terminal domain that comprises a coiled coil domain and seven WD40 repeats.

Pssm-ID: 438306 [Multi-domain] Cd Length: 47 Bit Score: 42.34 E-value: 1.26e-05

                         10        20
                 ....*....|....*....|....*.
gi 890799132  15 CPVCLNLMVKPVSADCGHTFCQGCIT 40
Cdd:cd16644    8 CPLCQRVFKDPVITSCGHTFCRRCAL 33

RING-HC_RAD16-like

cd16567

RING finger, HC subclass, found in Saccharomyces cerevisiae DNA repair protein RAD16, ...

15-58

1.47e-05

RING finger, HC subclass, found in Saccharomyces cerevisiae DNA repair protein RAD16, Schizosaccharomyces pombe rhp16, and similar proteins; Budding yeast RAD16, also known as ATP-dependent helicase RAD16, is encoded by a yeast excision repair gene homologous to the recombinational repair gene RAD54 and to the SNF2 gene involved in transcriptional activation. It is a component of the global genome repair (GGR) complex that promotes global genome nucleotide excision repair (GG-NER) by removing DNA damage from non-transcribing DNA. RAD16 is involved in differential repair of DNA after UV damage, and repairs preferentially the MAT-alpha locus compared with the HML-alpha locus. Fission yeast rhp16, also known as ATP-dependent helicase rhp16, is a RAD16 homolog. It is involved in GGR via nucleotide excision repair (NER), in conjunction with rhp7, after UV irradiation. Both RAD16 and rhp16 contain a C3HC4-type RING-HC finger, as well as a DEAD-like helicase domain and a helicase superfamily C-terminal domain.

Pssm-ID: 438229 [Multi-domain] Cd Length: 48 Bit Score: 42.33 E-value: 1.47e-05

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....
gi 890799132  15 CPVCLNLMVKPVSADCGHTFCQGCITLYFESIKCDKemFSCPVC 58
Cdd:cd16567    3 CGICHEEAEDPVVARCHHVFCRACVKEYIESAPGGK--VTCPTC 44

RING-HC_TRIM50_like_C-IV

cd16605

RING finger, HC subclass, found in tripartite motif-containing protein TRIM50, TRIM73, TRIM74 ...

13-59

1.64e-05

RING finger, HC subclass, found in tripartite motif-containing protein TRIM50, TRIM73, TRIM74 and similar proteins; TRIM50 is a stomach-specific E3 ubiquitin-protein ligase, encoded by the Williams-Beuren syndrome (WBS) TRIM50 gene, which regulates vesicular trafficking for acid secretion in gastric parietal cells. It colocalizes, interacts with, and increases the level of p62/SQSTM1, a multifunctional adaptor protein implicated in various cellular processes including the autophagy clearance of polyubiquitinated protein aggregates. It also promotes the formation and clearance of aggresome-associated polyubiquitinated proteins through the interaction with histone deacetylase 6 (HDAC6), a tubulin specific deacetylase that regulates microtubule-dependent aggresome formation. TRIM50 can be acetylated by PCAF and p300. TRIM50 belongs to the C-IV subclass of the TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a C3HC4-type RING-HC finger, Bbox1 and Bbox2, and a coiled coil region, as well as a B30.2/SPRY (SplA and ryanodine receptor) domain positioned C-terminal to the RBCC domain. This subfamily also includes two paralogs of TRIM50, tripartite motif-containing protein 73 (TRIM73), also known as tripartite motif-containing protein 50B (TRIM50B), and tripartite motif-containing protein 74 (TRIM74), also known as tripartite motif-containing protein 50C (TRIM50C), both of which are WBS-related genes encoding proteins that may also act as E3 ligases. In contrast with TRIM50, TRIM73 and TRIM74 belong to the C-V subclass of TRIM family of proteins that are defined by N-terminal RBCC domains only.

Pssm-ID: 438267 [Multi-domain] Cd Length: 45 Bit Score: 42.05 E-value: 1.64e-05

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*...
gi 890799132  13 VTCPVCLNLMVKPVSADCGHTFCQGCITlyfeSIKCD-KEMFSCPVCR 59
Cdd:cd16605    1 LLCPICLEVFKEPLMLQCGHSYCKSCLV----SLSGElDGQLLCPVCR 44

RING-HC_RNF169

cd16551

RING finger, HC subclass, found in RING finger protein 169 (RNF169) and similar proteins; ...

12-59

1.89e-05

RING finger, HC subclass, found in RING finger protein 169 (RNF169) and similar proteins; RNF169 is an uncharacterized E3 ubiquitin-protein ligase paralogous to RNF168. It functions as a negative regulator of the DNA damage signaling cascade. RNF169 recognizes polyubiquitin structures but does not itself contribute to double-strand break (DSB)-induced chromatin ubiquitylation. It contributes to regulation of the DSB repair pathway utilization via functionally competing with recruiting repair factors, 53BP1 and RAP80-BRCA1, for association with RNF168-modified chromatin independent of its catalytic activity, limiting the magnitude of the RNF8/RNF168-dependent signaling response to DSBs. RNF169 contains an N-terminal C3HC4-type RING-HC finger and a C-terminal MIU (motif interacting with ubiquitin) domain.

Pssm-ID: 438213 [Multi-domain] Cd Length: 55 Bit Score: 42.15 E-value: 1.89e-05

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*...
gi 890799132  12 EVTCPVCLNLMVKPVSADCGHTFCQGCITlyfESIKCDKEMFSCPVCR 59
Cdd:cd16551    1 ELTCAGCLEVPVEPATLPCGHTLCRGCAN---RALDAAEAGPTCPRCR 45

RING-HC_RNFT1

cd16741

RING finger, HC subclass, found in RING finger and transmembrane domain-containing protein 1 ...

15-59

1.93e-05

RING finger, HC subclass, found in RING finger and transmembrane domain-containing protein 1 (RNFT1); RNFT1, also known as protein PTD016, is a multi-pass membrane protein containing a C3HC4-type RING-HC finger. Its biological role remains unclear.

Pssm-ID: 438399 [Multi-domain] Cd Length: 58 Bit Score: 42.18 E-value: 1.93e-05

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*
gi 890799132  15 CPVCLNLMVKPVSADCGHTFCQGCITLYFESIKcdkemfSCPVCR 59
Cdd:cd16741   17 CAICQAEFRKPILLICQHVFCEECISLWFNREK------TCPLCR 55

RING-HC_PEX10

cd16527

RING finger, HC subclass, found in peroxin-10 (PEX10) and similar proteins; PEX10, also known ...

15-69

1.97e-05

RING finger, HC subclass, found in peroxin-10 (PEX10) and similar proteins; PEX10, also known as peroxisome biogenesis factor 10, peroxisomal biogenesis factor 10, peroxisome assembly protein 10, or RING finger protein 69 (RNF69), is an integral peroxisomal membrane protein with two transmembrane regions and a C3HC4-type RING-HC finger within its cytoplasmically exposed C-terminus. It plays an essential role in peroxisome assembly, import of target substrates, and recycling or degradation of protein complexes and amino acids. It is an essential component of the spinal locomotor circuit, and thus its mutations may be involved in peroxisomal biogenesis disorders (PBD). Mutations in human PEX10 also result in autosomal recessive ataxia. Moreover, PEX10 functions as an E3-ubiquitin ligase with an E2, UBCH5C. It mono- or poly-ubiquitinates PEX5, a key player in peroxisomal matrix protein import, in a UBC4-dependent manner, to control PEX5 receptor recycling or degradation. It also links the E2 ubiquitin conjugating enzyme PEX4 to the protein import machinery of the peroxisome.

Pssm-ID: 438190 [Multi-domain] Cd Length: 52 Bit Score: 41.83 E-value: 1.97e-05

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 890799132  15 CPVCLNLMVKPVSADCGHTFCQGCITLYfesikCDKEMFsCPVCRLSYQSSNLRP 69
Cdd:cd16527    3 CSLCLEERRHPTATPCGHLFCWSCITEW-----CNEKPE-CPLCREPFQPQRLVP 51

RING-HC_MID1

cd16753

RING finger, HC subclass, found in midline-1 (MID1) and similar proteins; MID1, also known as ...

9-59

2.48e-05

RING finger, HC subclass, found in midline-1 (MID1) and similar proteins; MID1, also known as midin, midline 1 RING finger protein, putative transcription factor XPRF, RING finger protein 59 (RNF59), or tripartite motif-containing protein 18 (TRIM18), is a microtubule-associated E3 ubiquitin-protein ligase implicated in epithelial-mesenchymal differentiation, cell migration and adhesion, and programmed cell death along specific regions of the ventral midline during embryogenesis. It monoubiquinates the alpha4 subunit of protein phosphatase 2A (PP2A), promoting proteosomal degradation of the catalytic subunit of PP2A (PP2Ac) and preventing the A and B subunits from forming an active complex. It promotes allergen and rhinovirus-induced asthma through the inhibition of PP2A activity. It is strongly upregulated in cytotoxic lymphocytes (CTLs) and directs lytic granule exocytosis and cytotoxicity of killer T cells. Loss-of-function mutations in MID1 lead to the human X-linked Opitz G/BBB (XLOS) syndrome characterized by defective midline development during embryogenesis. MID1 belongs to the C-I subclass of the TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a C3HC4-type RING-HC finger, Bbox1 and Bbox2, and a coiled coil region, as well as a COS (carboxyl-terminal subgroup one signature) box, a fibronectin type III (FN3) domain, and a B30.2/SPRY (SplA and ryanodine receptor) domain positioned C-terminal to the RBCC domain. MID1 hetero-dimerizes in vitro with its paralog MID2.

Pssm-ID: 438411 [Multi-domain] Cd Length: 72 Bit Score: 42.33 E-value: 2.48e-05

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 890799132   9 LKEEVTCPVCLNLMVKPVSADCGHTFCQGCITLYFESIKCDKE------MFSCPVCR 59
Cdd:cd16753    2 LESELTCPICLELFEDPLLLPCAHSLCFNCAHRILVSHCASNEsvesitAFQCPTCR 58

mRING-HC-C3HC3D_LNX1-like

cd16637

Modified RING finger, HC subclass (C3HC3D-type), found in ligand of Numb protein LNX1, LNX2, ...

14-59

2.49e-05

Modified RING finger, HC subclass (C3HC3D-type), found in ligand of Numb protein LNX1, LNX2, and similar proteins; The ligand of Numb protein X (LNX) family, also known as PDZ and RING (PDZRN) family, includes LNX1-5, which can interact with Numb, a key regulator of neurogenesis and neuronal differentiation. LNX5 (also known as PDZK4 or PDZRN4L) shows high sequence homology to LNX3 and LNX4, but it lacks the RING domain. LNX1-4 proteins function as E3 ubiquitin ligases and have a unique domain architecture consisting of an N-terminal RING-HC finger for E3 ubiquitin ligase activity and either two or four PDZ domains necessary for substrate-binding. LNX1/LNX2-like proteins contain a modified C3HC3D-type RING-HC finger and four PDZ domains. This model corresponds to the RING finger.

Pssm-ID: 438299 [Multi-domain] Cd Length: 42 Bit Score: 41.23 E-value: 2.49e-05

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*.
gi 890799132  14 TCPVCLNLMVKPVSADCGHTFCQGCITLYFESIKCdkemfsCPVCR 59
Cdd:cd16637    3 TCHICLQPLVEPLDTPCGHTFCYKCLTNYLKIQQC------CPLDR 42

SMC_prok_A

TIGR02169

chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of ...

117-239

2.84e-05

Pssm-ID: 274009 [Multi-domain] Cd Length: 1164 Bit Score: 46.98 E-value: 2.84e-05

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 890799132   117 LCERSQEHRGHKTALIEEVArEYKEQLQVVLQRLMADKKEFENWKDELQKDRTYWEnQIQKDVENVQSEFKRMRDiidse 196
Cdd:TIGR02169  341 LEREIEEERKRRDKLTEEYA-ELKEELEDLRAELEEVDKEFAETRDELKDYREKLE-KLKREINELKRELDRLQE----- 413

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|...
gi 890799132   197 eknELQKLRQEKEDILNNLAESESEHAQQSKLLEDFISDVEHQ 239
Cdd:TIGR02169  414 ---ELQRLSEELADLNAAIAGIEAKINELEEEKEDKALEIKKQ 453

RING-HC_ORTHRUS_rpt1

cd23138

first RING finger, HC subclass, found in Arabidopsis thaliana ORTHRUS and similar proteins; ...

11-59

3.00e-05

first RING finger, HC subclass, found in Arabidopsis thaliana ORTHRUS and similar proteins; This subfamily includes Arabidopsis thaliana ORTHRUS 1-5. They are E3 ubiquitin-protein ligases that may participate in CpG methylation-dependent transcriptional regulation and/or epigenetic transcriptional silencing. ORTHRUS 1 mediates ubiquitination with the E2 ubiquitin-conjugating enzymes UBC11, UBC8 and UBC8 homologs (e.g. UBC10, UBC11, UBC28 and UBC29) but not with UBC27, UBC30, UBC32, UBC34 and UBC36. ORTHRUS 2 and 5 mediate ubiquitination with the E2 ubiquitin-conjugating enzyme UBC11. ORTHRUS 1 and 2 promote methylation-mediated gene silencing leading, for example, to early flowering. They can bind to CpG, CpNpG, and CpNpN DNA motifs, with a strong preference for methylated forms, and with highest affinity for CpG substrates. Members of this subfamily contain two typical C3HC4-type RING-HC fingers. This model corresponds to the first one.

Pssm-ID: 438500 [Multi-domain] Cd Length: 48 Bit Score: 41.28 E-value: 3.00e-05

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*....
gi 890799132  11 EEVTCPVCLNLMVKPVSADCGHTFCQGCITLYfesikCDKEMFSCPVCR 59
Cdd:cd23138    1 DELNCSFCMQLPERPVTTPCGHNFCLKCFQKW-----MGQGKKTCGTCR 44

RING-HC_RNF166

cd16549

RING finger, HC subclass, found in RING finger protein 166 (RNF166) and similar proteins; ...

14-62

3.07e-05

RING finger, HC subclass, found in RING finger protein 166 (RNF166) and similar proteins; RNF166 is encoded by the gene RNF166 targeted by thyroid hormone receptor alpha1 (TRalpha1), which is important in brain development. It plays an important role in RNA virus-induced interferon-beta production by enhancing the ubiquitination of TRAF3 and TRAF6. RNF166, together with three closely related proteins: RNF114, RNF125 and RNF138, forms a novel family of ubiquitin ligases with a C3HC4-type RING-HC finger, a C2HC-, and two C2H2-type zinc fingers, as well as a ubiquitin interacting motif (UIM).

Pssm-ID: 438211 [Multi-domain] Cd Length: 47 Bit Score: 41.34 E-value: 3.07e-05

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|
gi 890799132  14 TCPVCLNLMVKPVS-ADCGHTFCQGCITLYFESIKCdkemfSCPVCRLSY 62
Cdd:cd16549    3 SCPICLEVYHKPVViTSCGHTFCGECLQPCLQVASP-----LCPLCRMPF 47

Bbox2_TRIM65-like

cd19793

B-box-type 2 zinc finger found in tripartite motif-containing protein 65 (TRIM65), B box and ...

96-136

3.50e-05

B-box-type 2 zinc finger found in tripartite motif-containing protein 65 (TRIM65), B box and SPRY domain-containing protein (BSPRY) and similar proteins; The family includes TRIM65 and BSPRY. TRIM65 is an E3 ubiquitin-protein ligase that interacts with the innate immune receptor MDA5 enhancing its ability to stimulate interferon-beta signaling. It functions as a potential oncogenic protein that negatively regulates p53 through ubiquitination, providing insight into development of novel approaches targeting TRIM65 for non-small cell lung carcinoma (NSCLC) treatment, and also overcoming chemotherapy resistance. Moreover, TRIM65 negatively regulates microRNA-driven suppression of mRNA translation by targeting TNRC6 proteins for ubiquitination and degradation. BSPRY is a regulatory protein for maintaining calcium homeostasis. It may regulate epithelial calcium transport by inhibiting TRPV5 activity. The type 2 B-box (Bbox2) zinc finger is characterized by a CHC3H2 zinc-binding consensus motif.

Pssm-ID: 380851 Cd Length: 43 Bit Score: 41.14 E-value: 3.50e-05

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|.
gi 890799132  96 CARHGEKLQLFCRKDMMAICWLCERSQEHRGHKTALIEEVA 136
Cdd:cd19793    3 CPEHGRELELYCRTEKRCVCAQCASKGECRGHRVTLLEERA 43

Bbox2_TRIM14

cd19768

B-box-type 2 zinc finger found in tripartite motif-containing protein 14 (TRIM14) and similar ...

94-136

3.99e-05

B-box-type 2 zinc finger found in tripartite motif-containing protein 14 (TRIM14) and similar proteins; TRIM14 is a mitochondrial adaptor that facilitates innate immune signaling. It also plays a critical role in tumor development. TRIM14 belongs to an unclassified TRIM (tripartite motif) family of proteins that do not have RING fingers and thus lack the characteristic tripartite (RING (R), B-box, and coiled coil (CC)) RBCC motif. It contains a Bbox2 zinc finger as well as a C-terminal SPRY/B30.2 domain. The type 2 B-box (Bbox2) zinc finger is characterized by a CHC3H2 zinc-binding consensus motif.

Pssm-ID: 380826 [Multi-domain] Cd Length: 44 Bit Score: 40.87 E-value: 3.99e-05

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....
gi 890799132  94 FNCARHGE-KLQLFCRKDMMAICWLCERSQEHRGHKTALIEEVA 136
Cdd:cd19768    1 RCCPEHKDrPLELFCKTCKRCVCALCPILGQHRGHDVRLIDEEA 44

RING-HC_PCGF5

cd16737

RING finger found in polycomb group RING finger protein 5 (PCGF5) and similar proteins; PCGF5, ...

13-101

4.06e-05

RING finger found in polycomb group RING finger protein 5 (PCGF5) and similar proteins; PCGF5, also known as RING finger protein 159 (RNF159), is one of six PcG RING finger (PCGF) homologs (PCGF1/NSPc1, PCGF2/Mel-18, PCGF3, PCGF4/BMI1, PCGF5, and PCGF6/MBLR) and serves as the core component of a Polycomb repressive complex 1 (PRC1). Like other PCGF homologs, PCGF5 associates with ring finger protein 2 (RNF2) to form a RNF2-PCGF heterodimer, which is catalytically competent as an E3 ubiquitin transferase and is the scaffold for the assembly of additional components. PCGF5 contains a C3HC4-type RING-HC finger.

Pssm-ID: 438395 [Multi-domain] Cd Length: 95 Bit Score: 42.44 E-value: 4.06e-05

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 890799132  13 VTCPVCLNLMVKP-VSADCGHTFCQGCITLYFEsikcdkEMFSCPVCRLSYQSSNLRPNLHVANIVERLKeFKPSPEEEQ 91
Cdd:cd16737   11 ITCRICKGYLIKPtTVTECLHTFCKSCIVQHFE------DSNDCPECGIQVHETNPLEMLRLDNTLEEII-FKLVPGLRE 83

                         90
                 ....*....|
gi 890799132  92 KVfnCARHGE 101
Cdd:cd16737   84 RE--LQREAE 91

RING-HC_ORTHRUS_rpt2

cd23139

second RING finger, HC subclass, found in Arabidopsis thaliana ORTHRUS and similar proteins; ...

9-58

5.04e-05

second RING finger, HC subclass, found in Arabidopsis thaliana ORTHRUS and similar proteins; This subfamily includes Arabidopsis thaliana ORTHRUS 1-5. They are E3 ubiquitin-protein ligases that may participate in CpG methylation-dependent transcriptional regulation and/or epigenetic transcriptional silencing. ORTHRUS 1 mediates ubiquitination with the E2 ubiquitin-conjugating enzymes UBC11, UBC8 and UBC8 homologs (e.g. UBC10, UBC11, UBC28 and UBC29) but not with UBC27, UBC30, UBC32, UBC34 and UBC36. ORTHRUS 2 and 5 mediate ubiquitination with the E2 ubiquitin-conjugating enzyme UBC11. ORTHRUS 1 and 2 promote methylation-mediated gene silencing leading, for example, to early flowering. They can bind to CpG, CpNpG, and CpNpN DNA motifs, with a strong preference for methylated forms, and with highest affinity for CpG substrates. Members of this subfamily contain two typical C3HC4-type RING-HC fingers. This model corresponds to the second one.

Pssm-ID: 438501 [Multi-domain] Cd Length: 72 Bit Score: 41.29 E-value: 5.04e-05

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 890799132   9 LKEEVTCPVCLNLMVKPVSADCGHTFCQGCITLYF-------------ESIKCDKEMFSCPVC 58
Cdd:cd23139    2 LLKEFGCQICKKVLSLPVSTPCGHNFCKACLEAKFagiadvrdrgnggRSLRARKNVKPCPCC 64

RING-HC_DTX3

cd16711

RING finger, HC subclass, found in E3 ubiquitin-protein ligase Deltex3 (DTX3) and similar ...

12-62

5.12e-05

RING finger, HC subclass, found in E3 ubiquitin-protein ligase Deltex3 (DTX3) and similar proteins; DTX3, also known as RING finger protein 154 (RNF154), is an E3 ubiquitin-protein ligase that belongs to the Deltex (DTX) family. In contrast to other DTXs, DTX3 does not contain two N-terminal Notch-binding WWE domains, but a short unique N-terminal domain, suggesting it does not interact with the intracellular domain of Notch. Its C-terminal region includes a C3HC4-type RING-HC finger, and a previously unidentified C-terminal domain.

Pssm-ID: 438371 [Multi-domain] Cd Length: 54 Bit Score: 40.86 E-value: 5.12e-05

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 890799132  12 EVTCPVCLNLMVKPVSAD-CGHTFCQGCITLYFESIKcdkemfSCPVCRLSY 62
Cdd:cd16711    1 EETCPICLGEIQNKKTLDkCKHSFCEDCITRALQVKK------ACPMCGEFY 46

Bbox2_TRIM60-like

cd19791

B-box-type 2 zinc finger found in tripartite motif-containing proteins, TRIM60, TRIM61, ...

96-127

5.39e-05

B-box-type 2 zinc finger found in tripartite motif-containing proteins, TRIM60, TRIM61, TRIM75 and similar proteins; This family includes a group of tripartite motif-containing proteins, including TRIM60, TRIM61 and TRIM75. TRIM60, also known as RING finger protein 129 (RNF129) or RING finger protein 33 (RNF33), is a cytoplasmic protein expressed in the testis. It may play an important role in the spermatogenesis process, the development of the preimplantation embryo, and in testicular functions. TRIM60 interacts with the cytoplasmic kinesin motor proteins KIF3A and KIF3B suggesting possible contribution to cargo movement along the microtubule in the expressed sites. It is also involved in spermatogenesis in Sertoli cells under the regulation of nuclear factor-kappaB (NF-kappaB). TRIM61 is closely related to TRIM60, but its biological function remains unclear. TRIM75 could be the product of a pseudogene. Its biological function remains unclear. TRIM60 and TRIM75 belong to the C-IV subclass of the TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a RING finger, Bbox2, and two coiled coil domains, as well as a B30.2/SPRY (SplA and ryanodine receptor) domain positioned C-terminal to the RBCC domain. In contrast, TRIM61 belongs to the C-V subclass of TRIM family that contains RBCC domains only. The type 2 B-box (Bbox2) zinc finger is characterized by a CHC3H2 zinc-binding consensus motif.

Pssm-ID: 380849 [Multi-domain] Cd Length: 39 Bit Score: 40.21 E-value: 5.39e-05

                         10        20        30
                 ....*....|....*....|....*....|..
gi 890799132  96 CARHGEKLQLFCRKDMMAICWLCERSQEHRGH 127
Cdd:cd19791    3 CEKHNQPLTKFCKKDLEPLCPQCSQSTDHQHH 34

RING-HC_TRIM56_C-V

cd16584

RING finger, HC subclass, found in tripartite motif-containing protein 56 (TRIM56) and similar ...

13-59

5.91e-05

RING finger, HC subclass, found in tripartite motif-containing protein 56 (TRIM56) and similar proteins; TRIM56, also known as RING finger protein 109 (RNF109), is a virus-inducible E3 ubiquitin ligase that restricts pestivirus infection. It positively regulates the Toll-like receptor 3 (TLR3) antiviral signaling pathway, and possesses antiviral activity against bovine viral diarrhea virus (BVDV), a ruminant pestivirus classified within the family Flaviviridae shared by tick-borne encephalitis virus (TBEV). It also possesses antiviral activity against two classical flaviviruses, yellow fever virus (YFV) and dengue virus (DENV), as well as a human coronavirus, HCoV-OC43, which is responsible for a significant share of common cold cases. It may not act on positive-strand RNA viruses indiscriminately. Moreover, TRIM56 is an interferon-inducible E3 ubiquitin ligase that modulates STING to confer double-stranded DNA-mediated innate immune responses. TRIM56 belongs to the C-V subclass of the TRIM (tripartite motif) family of proteins that are defined by an N-terminal RBCC (RING, Bbox, and coiled coil) domain, including three consecutive zinc-binding domains, a C3HC4-type RING-HC finger, Bbox1 and Bbox2, and a coiled coil region, as well as an uncharacterized region positioned C-terminal to the RBCC domain.

Pssm-ID: 438246 [Multi-domain] Cd Length: 56 Bit Score: 40.74 E-value: 5.91e-05

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
gi 890799132  13 VTCPVCLNLMVKPVSADCGHTFCQGCITLYFesikcDKEMFSCPVCR 59
Cdd:cd16584    2 LACKICLEQLRAPKTLPCLHTYCQDCLAQLA-----DGGRVRCPECR 43

SPRY_PRY_TRIM65

cd12896

PRY/SPRY domain in tripartite motif-containing domain 65 (TRIM65); This domain, consisting of ...

348-481

5.97e-05

PRY/SPRY domain in tripartite motif-containing domain 65 (TRIM65); This domain, consisting of the distinct N-terminal PRY subdomain followed by the SPRY subdomain, is found at the C-terminus of TRIM65 proteins (composed of RING/B-box/coiled-coil core and also known as RBCC proteins). The SPRY/PRY combination is a possible component of immune defense. This protein family has not been characterized.

Pssm-ID: 293953 [Multi-domain] Cd Length: 182 Bit Score: 43.98 E-value: 5.97e-05

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 890799132 348 QSGKHYWEVDVSGKGAwVLGLSdgsylfcpifHSNAERNRLfcRGIKNDSHYQPkyGFWVIGLWKKSvYNAFEEcpftGK 427
Cdd:cd12896   61 QHGHHYWEVEVSSHSV-TLGVT----------YPGLPRHKQ--GGHKDNIGRNP--CSWGLQIQEDS-LQAWHN----GR 120

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....
gi 890799132 428 PSVLTLslmVPPCRVGVFLDYAAGTLSFYNISNNGTLIYRFcTASFPDRVFPYF 481
Cdd:cd12896  121 AQKLQG---VSYRLLGVDLDLEAGTLTFYGLEPGTQRLHTF-HAIFTQPLYPVF 170

RING-HC_NHL-1-like

cd16524

RING finger, HC subclass, found in Caenorhabditis elegans RING finger protein NHL-1 and ...

9-59

6.18e-05

RING finger, HC subclass, found in Caenorhabditis elegans RING finger protein NHL-1 and similar proteins; NHL-1 functions as an E3 ubiquitin-protein ligase in the presence of both UBC-13 and UBC-1 within the ubiquitin pathway of Caenorhabditis elegans. It acts in chemosensory neurons to promote stress resistance in distal tissues by the transcription factor DAF-16 activation but is dispensable for the activation of heat shock factor 1 (HSF-1). NHL-1 belongs to the TRIM (tripartite motif)-NHL family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a C3HC4-type RING-HC finger, Bbox1 and Bbox2, and a coiled coil domain, as well as an NHL (named after proteins NCL-1, HT2A and Lin-41 that contain repeats folded into a six-bladed beta propeller) repeat domain positioned C-terminal to the RBCC domain.

Pssm-ID: 438187 [Multi-domain] Cd Length: 53 Bit Score: 40.49 E-value: 6.18e-05

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 890799132   9 LKEEVTCPVCLNLMVKPVSADCGHTFC-----QGCITLYFESIKcdkemfsCPVCR 59
Cdd:cd16524    2 IEQLLTCPICLDRYRRPKLLPCQHTFClspclEGLVDYVTRKLK-------CPECR 50

zf-RING_2

pfam13639

Ring finger domain;

14-59

6.53e-05

Ring finger domain;

Pssm-ID: 433370 [Multi-domain] Cd Length: 44 Bit Score: 40.08 E-value: 6.53e-05

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 890799132   14 TCPVCLNLMVKPVSA---DCGHTFCQGCITLYFESIKcdkemfSCPVCR 59
Cdd:pfam13639   2 ECPICLEEFEEGDKVvvlPCGHHFHRECLDKWLRSSN------TCPLCR 44

RING-HC_PCGF1

cd16733

RING finger, HC subclass, found in polycomb group RING finger protein 1 (PCGF1) and similar ...

6-70

6.77e-05

RING finger, HC subclass, found in polycomb group RING finger protein 1 (PCGF1) and similar proteins; PCGF1, also known as nervous system Polycomb-1 (NSPc1) or RING finger protein 68 (RNF68), is one of six PcG RING finger (PCGF) homologs (PCGF1/NSPc1, PCGF2/Mel-18, PCGF3, PCGF4/BMI1, PCGF5, and PCGF6/MBLR). It serves as the core component of a noncanonical Polycomb repressive complex 1 (PRC1)-like BCOR complex that also contains RING1, RNF2, RYBP, SKP1, as well as the BCL6 co-repressor BCOR and the histone demethylase KDM2B, and is required to maintain the transcriptionally repressive state of some genes, such as Hox genes, BCL6 and the cyclin-dependent kinase inhibitor, CDKN1A. PCGF1 promotes cell cycle progression and enhances cell proliferation as well. It is a cell growth regulator that acts as a transcriptional repressor of p21Waf1/Cip1 via the retinoid acid response element (RARE element). Moreover, PCGF1 functions as an epigenetic regulator involved in hematopoietic cell differentiation. It cooperates with the transcription factor runt-related transcription factor 1 (Runx1) in regulating differentiation and self-renewal of hematopoietic cells. Furthermore, PCGF1 represents a physical and functional link between Polycomb function and pluripotency. PCGF1 contains a C3HC4-type RING-HC finger.

Pssm-ID: 438391 [Multi-domain] Cd Length: 71 Bit Score: 41.10 E-value: 6.77e-05

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 890799132   6 MKNLKEEVTCPVCLNLMVKPVS-ADCGHTFCQGCITLYFESIKCdkemfsCPVCRLSYQSS----NLRPN 70
Cdd:cd16733    3 IKDLNEHIVCYLCAGYFIDATTiTECLHTFCKSCIVKYLQTSKY------CPMCNIKIHETqpllNLKLD 66

SPRY_PRY_TRIM76_like

cd12899

PRY/SPRY domain in tripartite motif-containing protein 76 (TRIM76)-like; This domain is ...

308-458

7.20e-05

PRY/SPRY domain in tripartite motif-containing protein 76 (TRIM76)-like; This domain is similar to the distinct PRY/SPRY subdomain found at the C-terminus of TRIM76, a Class I TRIM protein. TRIM76 (also known as cardiomyopathy-associated protein 5 or CMYA5 or myospryn or SPRYD2) is a muscle-specific member of the TRIM superfamily, but lacks the RING domain. It has been suggested that TRIM76 is involved in two distinct processes, protein kinase A signaling and vesicular trafficking.

Pssm-ID: 293956 [Multi-domain] Cd Length: 176 Bit Score: 43.62 E-value: 7.20e-05

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 890799132 308 HPNIAITDDKRQVRYEDHQASnlihECENSHE--------GVLGHPAIQSGKHYWEVDVSGKGAWVLGLSdgsylfcpif 379
Cdd:cd12899   10 HPLLSISEDGFTVVYGEEELP----ARDLSFSdnsftrcvAVMGSLIPVRGKHYWEVEVDEQTEYRVGVA---------- 75

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 890799132 380 HSNAERNRLFcrGIKNDShyqpkygfWVIGLWKKSVYNAFEecpFTGKPSVLTLSLMVPPCRVGVFLDYAAGTLSFYNI 458
Cdd:cd12899   76 FEDTQRNGYL--GANNTS--------WCMRHIITPSRHKYE---FLHNGWTPDIRITVPPKKIGILLDYDSGRLSFFNV 141

PEX10

COG5574

RING-finger-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, ...

15-59

7.67e-05

RING-finger-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones];

Pssm-ID: 227861 [Multi-domain] Cd Length: 271 Bit Score: 44.50 E-value: 7.67e-05

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*
gi 890799132  15 CPVCLNLMVKPVSADCGHTFCQGCItlyFESIKCDKEMFsCPVCR 59
Cdd:COG5574  218 CFLCLEEPEVPSCTPCGHLFCLSCL---LISWTKKKYEF-CPLCR 258

RING-H2_BRAP2

cd16457

RING finger, H2 subclass, found in BRCA1-associated protein (BRAP2) and similar proteins; ...

14-59

7.98e-05

RING finger, H2 subclass, found in BRCA1-associated protein (BRAP2) and similar proteins; BRAP2, also known as impedes mitogenic signal propagation (IMP), RING finger protein 52, or renal carcinoma antigen NY-REN-63, is a novel cytoplasmic protein interacting with the two functional nuclear localization signal (NLS) motifs of BRCA1, a nuclear protein linked to breast cancer. It also binds to the SV40 large T antigen NLS motif and the bipartite NLS motif found in mitosin. BRAP2 serves as a cytoplasmic retention protein and plays a role in the regulation of nuclear protein transport. It contains an N-terminal RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by a C3H2C3-type RING-H2 finger and a UBP-type zinc finger.

Pssm-ID: 438121 [Multi-domain] Cd Length: 44 Bit Score: 39.96 E-value: 7.98e-05

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|
gi 890799132  14 TCPVCLNLMVKPVSA----DCGHTFCQGCITLYFESikcdkemfSCPVCR 59
Cdd:cd16457    2 TCPVCLERMDESVSGiltiLCNHSFHCSCLSKWGDS--------SCPVCR 43

mRING-HC-C3HC3D_TRAF6

cd16643

Modified RING finger, HC subclass (C3HC3D-type), found in tumor necrosis factor (TNF) ...

15-57

8.20e-05

Modified RING finger, HC subclass (C3HC3D-type), found in tumor necrosis factor (TNF) receptor-associated factor 6 (TRAF6) and similar proteins; TRAF6, also known as interleukin-1 signal transducer or RING finger protein 85 (RNF85), is a cytoplasmic adapter protein that mediates signals induced by the tumor necrosis factor receptor (TNFR) superfamily and Toll-like receptor (TLR)/interleukin-1 receptor (IL-1R) family. It functions as a mediator involved in the activation of mitogen-activated protein kinase (MAPK), phosphoinositide 3-kinase (PI3K), and interferon regulatory factor pathways, as well as in IL-1R-mediated activation of NF-kappaB. TRAF6 is also an oncogene that plays a vital role in K-RAS-mediated oncogenesis. TRAF6 contains an N-terminal domain with a modified C3HC3D-type RING-HC finger and several zinc fingers, and a C-terminal TRAF domain that comprises a coiled coil domain and a conserved TRAF-C domain.

Pssm-ID: 438305 [Multi-domain] Cd Length: 58 Bit Score: 40.44 E-value: 8.20e-05

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|...
gi 890799132  15 CPVCLNLMVKPVSADCGHTFCQGCItlyFESIKcdKEMFSCPV 57
Cdd:cd16643    4 CPICLMALREPVQTPCGHRFCKACI---LKSIR--EAGHKCPV 41

RING-HC_TRIM13_C-V

cd16762

RING finger, HC subclass, found in tripartite motif-containing protein 13 (TRIM13) and similar ...

10-59

9.57e-05

RING finger, HC subclass, found in tripartite motif-containing protein 13 (TRIM13) and similar proteins; TRIM13, also known as B-cell chronic lymphocytic leukemia tumor suppressor Leu5, leukemia-associated protein 5, putative tumor suppressor RFP2, RING finger protein 77 (RNF77), or Ret finger protein 2, is an endoplasmic reticulum (ER) membrane anchored E3 ubiquitin-protein ligase that interacts with proteins localized to the ER, including valosin-containing protein (VCP), a protein indispensable for ER-associated degradation (ERAD). It also targets the known ER proteolytic substrate CD3-delta, but not the N-end rule substrate Ub-R-YFP (yellow fluorescent protein) for degradation. Moreover, TRIM13 regulates ubiquitination and degradation of NEMO to suppress tumor necrosis factor (TNF) induced nuclear factor-kappaB (NF- kappa B) activation. It is also involved in NF-kappaB p65 activation and nuclear factor of activated T-cells (NFAT)-dependent activation of c-Rel upon T-cell receptor engagement. Furthermore, TRIM13 negatively regulates melanoma differentiation-associated gene 5 (MDA5)-mediated type I interferon production. It also regulates caspase-8 ubiquitination, translocation to autophagosomes, and activation during ER stress induced cell death. Meanwhile, TRIM13 enhances ionizing radiation-induced apoptosis by increasing p53 stability and decreasing AKT kinase activity through MDM2 and AKT degradation. TRIM13 belongs to the C-V subclass of the TRIM (tripartite motif) family of proteins that are defined by an N-terminal RBCC (RING, Bbox, and coiled coil) domain, including three consecutive zinc-binding domains, a C3HC4-type RING-HC finger, Bbox1 and Bbox2, and a coiled coil region. In addition, TRIM13 contains a C-terminal transmembrane domain.

Pssm-ID: 438418 [Multi-domain] Cd Length: 56 Bit Score: 40.28 E-value: 9.57e-05

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 890799132  10 KEEVTCPVCLNLMVKPVSADCGHTFCQGCITLYFE---SIKCDKEMFSCPVCR 59
Cdd:cd16762    1 EEDLTCPICCCLFDDPRVLPCSHNFCKKCLEGILEgnvRTMLWRPPFKCPTCR 53

SPRY_PRY_TRIM25

cd13736

PRY/SPRY domain in tripartite motif-containing domain 25 (TRIM25); This domain, consisting of ...

341-493

9.92e-05

PRY/SPRY domain in tripartite motif-containing domain 25 (TRIM25); This domain, consisting of the distinct N-terminal PRY subdomain followed by the SPRY subdomain, is found at the C-terminus of TRIM25 proteins (composed of RING/B-box/coiled-coil core and also known as RBCC proteins). TRIM25 (also called Efp) ubiquitinates the N terminus of the viral RNA receptor retinoic acid-inducible gene-I (RIG-I) in response to viral infection, leading to activation of the RIG-I signaling pathway, thus resulting in type I interferon production to limit viral replication. It has been shown that the influenza A virus targets TRIM25 and disables its antiviral function.

Pssm-ID: 293971 [Multi-domain] Cd Length: 169 Bit Score: 42.95 E-value: 9.92e-05

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 890799132 341 VLGHPAIQSGKHYWEVDVSGKGAWVLGLSDGSylfcpifhsnAERNRLFCRGIKNDSHYQPKYGFWVIGLWkksvYNAFE 420
Cdd:cd13736   43 VLGLHCFKQGIHYWEVELQKNNFCGVGICYGS----------MDRQGPESRLGRNSESWCVEWFNVKISAW----HNNVE 108

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 890799132 421 ECPFTGKPSvltlslmvppcRVGVFLDYAAGTLSFYNISNNGTLIYRFCTaSFPDRVFPYFNPTGSSEPMTIC 493
Cdd:cd13736  109 KTLPSTKAT-----------RVGVLLNCDHGFVIFFAVQDKVHLMYKFKV-DFTEALYPAFWVFSAGTTLSLC 169

Bbox2_TRIM65_C-IV

cd19835

B-box-type 2 zinc finger found in tripartite motif-containing protein 65 (TRIM65) and similar ...

96-134

1.02e-04

B-box-type 2 zinc finger found in tripartite motif-containing protein 65 (TRIM65) and similar proteins; TRIM65 is an E3 ubiquitin-protein ligase that interacts with the innate immune receptor MDA5 enhancing its ability to stimulate interferon-beta signaling. It functions as a potential oncogenic protein that negatively regulates p53 through ubiquitination, providing insight into development of novel approaches targeting TRIM65 for non-small cell lung carcinoma (NSCLC) treatment, and also overcoming chemotherapy resistance. Moreover, TRIM65 negatively regulates microRNA-driven suppression of mRNA translation by targeting TNRC6 proteins for ubiquitination and degradation. TRIM65 belongs to the C-IV subclass of TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a RING finger, Bbox2, and a coiled coil region, as well as a B30.2/SPRY (SplA and ryanodine receptor) domain positioned C-terminal to the RBCC domain. The type 2 B-box (Bbox2) zinc finger is characterized by a CHC3H2 zinc-binding consensus motif.

Pssm-ID: 380893 [Multi-domain] Cd Length: 42 Bit Score: 39.72 E-value: 1.02e-04

                         10        20        30
                 ....*....|....*....|....*....|....*....
gi 890799132  96 CARHGEKLQLFCRKDMMAICWLCErSQEHRGHKTALIEE 134
Cdd:cd19835    3 CQRHGRPLELYCRTEKRCVCCKCT-VKECRNHNRVLLEE 40

RING-HC_RAG1

cd16530

RING finger, HC subclass, found in recombination activating gene-1 (RAG-1) and similar ...

13-59

1.02e-04

RING finger, HC subclass, found in recombination activating gene-1 (RAG-1) and similar proteins; RAG-1, also known as V(D)J recombination-activating protein 1, RING finger protein 74 (RNF74), or endonuclease RAG1, is the catalytic component of the RAG complex, a multiprotein complex that mediates the DNA cleavage phase during V(D)J recombination. RAG1 is a lymphoid-specific factor that mediates DNA-binding to conserved recombination signal sequences (RSS) and catalyzes DNA cleavage activities by introducing a double-strand break between the RSS and the adjacent coding segment. It also functions as an E3 ubiquitin-protein ligase that mediates monoubiquitination of histone H3, which is required for the joining step of V(D)J recombination. RAG-1 contains an N-terminal C3HC4-type RING-HC finger that mediates monoubiquitylation of histone H3, an adjacent C2H2-type zinc finger, and a nonamer binding (NBD) DNA-binding domain.

Pssm-ID: 319444 [Multi-domain] Cd Length: 46 Bit Score: 39.73 E-value: 1.02e-04

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*...
gi 890799132  13 VTCPVCLNLMVKPVSADCGHTFCQGCItlyfesIKCDKEMFS-CPVCR 59
Cdd:cd16530    3 VSCQVCEHILADPVQTPCKHLFCRTCI------LKCLKVMGSyCPSCR 44

RING-HC_UHRF1

cd16769

RING finger, HC subclass, found in ubiquitin-like PHD and RING finger domain-containing ...

4-59

1.05e-04

RING finger, HC subclass, found in ubiquitin-like PHD and RING finger domain-containing protein 1 (UHRF1); UHRF1, also known as inverted CCAAT box-binding protein of 90 kDa, nuclear protein 95, nuclear zinc finger protein Np95 (Np95), RING finger protein 106, transcription factor ICBP90, or E3 ubiquitin-protein ligase UHRF1, is a unique chromatin effector protein that integrates the recognition of both histone PTMs and DNA methylation. It is essential for cell proliferation and plays a critical role in the development and progression of many human carcinomas, such as laryngeal squamous cell carcinoma (LSCC), gastric cancer (GC), esophageal squamous cell carcinoma (ESCC), colorectal cancer, prostate cancer, and breast cancer. UHRF1 can acts as a transcriptional repressor through its binding to histone H3 when it is unmodified at Arg2. Its overexpression in human lung fibroblasts results in downregulation of expression of the tumor suppressor pRB. It also plays a role in transcriptional repression of the cell cycle regulator p21. Moreover, UHRF1-dependent repression of factors can facilitate the G1-S transition. It interacts with Tat-interacting protein of 60 kDa (TIP60) and induces degradation-independent ubiquitination of TIP60. It is also a N-methylpurine DNA glycosylase (MPG)-interacting protein that binds MPG in a p53 status-independent manner in the DNA base excision repair (BER) pathway. In addition, UHRF1 functions as an epigenetic regulator that is important for multiple aspects of epigenetic regulation, including maintenance of DNA methylation patterns and recognition of various histone modifications. UHRF1 contains an N-terminal ubiquitin-like domain (UBL), a tandem Tudor domain (TTD), a plant homeodomain (PHD) domain, a SET and RING finger associated (SRA) domain, and a C-terminal C3HC4-type RING-HC finger. It specifically binds to hemimethylated DNA, double-stranded CpG dinucleotides, and recruits the maintenance methyltransferase DNMT1 to its hemimethylated DNA substrate through its SRA domain. UHRF1-dependent H3K23 ubiquitylation has an essential role in maintenance DNA methylation and replication. The tandem Tudor domain directs UHRF1 binding to the heterochromatin mark histone H3K9me3 and the PHD domain targets UHRF1 to unmodified histone H3 in euchromatic regions. The RING-HC finger exhibits both autocatalytic E3 ubiquitin (Ub) ligase activity and activity against histone H3 and DNMT1.

Pssm-ID: 438425 [Multi-domain] Cd Length: 84 Bit Score: 40.80 E-value: 1.05e-04

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 890799132   4 QFMKNLKEEVTCPVCLNLMVKPVSADCGHTFCQGCITLYFESikcdkEMFSCPVCR 59
Cdd:cd16769    4 LFLSKVEETFQCICCQELVFRPITTVCQHNVCKDCLDRSFRA-----QVFSCPACR 54

SPRY

cd11709

SPRY domain; SPRY domains, first identified in the SP1A kinase of Dictyostelium and rabbit ...

350-481

1.26e-04

SPRY domain; SPRY domains, first identified in the SP1A kinase of Dictyostelium and rabbit Ryanodine receptor (hence the name), are homologous to B30.2. SPRY domains have been identified in at least 11 protein families, covering a wide range of functions, including regulation of cytokine signaling (SOCS), RNA metabolism (DDX1 and hnRNP), immunity to retroviruses (TRIM5alpha), intracellular calcium release (ryanodine receptors or RyR) and regulatory and developmental processes (HERC1 and Ash2L). B30.2 also contains residues in the N-terminus that form a distinct PRY domain structure; i.e. B30.2 domain consists of PRY and SPRY subdomains. B30.2 domains comprise the C-terminus of three protein families: BTNs (receptor glycoproteins of immunoglobulin superfamily); several TRIM proteins (composed of RING/B-box/coiled-coil or RBCC core); Stonutoxin (secreted poisonous protein of the stonefish Synanceia horrida). TRIM/RBCC proteins are involved in a variety of processes, including apoptosis, cell cycle regulation, cell growth, senescence, viral response, meiosis, cell differentiation, and vesicular transport. Genes belonging to this family are implicated in several human diseases that vary from cancer to rare genetic syndromes. The PRY-SPRY domain in these TRIM families is suggested to serve as the target binding site. While SPRY domains are evolutionarily ancient, B30.2 domains are a more recent adaptation where the SPRY/PRY combination is a possible component of immune defense. Mutations found in the SPRY-containing proteins have shown to cause Mediterranean fever and Opitz syndrome.

Pssm-ID: 293931 Cd Length: 118 Bit Score: 41.65 E-value: 1.26e-04

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 890799132 350 GKHYWEVDV--SGKGAWVLGLSDGSylfcpiFHSNAERnrlfcrGIKNDSHyqpkygFWVIGLWKKSVYNAFEECPFTGK 427
Cdd:cd11709    1 GKWYWEVRVdsGNGGLIQVGWATKS------FSLDGEG------GVGDDEE------SWGYDGSRLRKGHGGSSGPGGRP 62

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 890799132 428 PSvltlslmvPPCRVGVFLDYAAGTLSFYnisNNGTLIY-RFCTASF-PDRVFPYF 481
Cdd:cd11709   63 WK--------SGDVVGCLLDLDEGTLSFS---LNGKDLGvAFTNLFLkGGGLYPAV 107

PTZ00121

MAEBL; Provisional

79-246

1.40e-04

MAEBL; Provisional

Pssm-ID: 173412 [Multi-domain] Cd Length: 2084 Bit Score: 44.75 E-value: 1.40e-04

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 890799132   79 RLKEFKPSPEEEQKVFNCAR--HGEKlqlfcRKDMMAICWLCERSQEHRGHKTALIEEVAREYKEQLQVVLQRLMADKKE 156
Cdd:PTZ00121 1731 KAEEAKKEAEEDKKKAEEAKkdEEEK-----KKIAHLKKEEEKKAEEIRKEKEAVIEEELDEEDEKRRMEVDKKIKDIFD 1805

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 890799132  157 -FENWKDELQKDRTYwenqIQKDVENVQSEFKRMRDIIDS--EEKNELQKLRQEKEDILNNLAESESEHAQQSKLLEDFI 233
Cdd:PTZ00121 1806 nFANIIEGGKEGNLV----INDSKEMEDSAIKEVADSKNMqlEEADAFEKHKFNKNNENGEDGNKEADFNKEKDLKEDDE 1881

                         170
                  ....*....|....*...
gi 890799132  234 SDVEH-----QLQCSDIE 246
Cdd:PTZ00121 1882 EEIEEadeieKIDKDDIE 1899

RING-HC_UHRF2

cd16770

RING finger, HC subclass, found in ubiquitin-like PHD and RING finger domain-containing ...

10-59

1.85e-04

RING finger, HC subclass, found in ubiquitin-like PHD and RING finger domain-containing protein 2 (UHRF2); UHRF2, also known as Np95/ICBP90-like RING finger protein (NIRF), Np95-like RING finger protein, nuclear protein 97, nuclear zinc finger protein Np97, RING finger protein 107, or E3 ubiquitin-protein ligase UHRF2, was originally identified as a ubiquitin ligase acting as a small ubiquitin-like modifier (SUMO) E3 ligase that enhances zinc finger protein 131 (ZNF131) SUMOylation, but does not enhance ZNF131 ubiquitination. It also ubiquitinates PCNP, a PEST-containing nuclear protein. Moreover, UHRF2 functions as a nuclear protein involved in cell-cycle regulation and has been implicated in tumorigenesis. It interacts with cyclins, CDKs, p53, pRB, PCNA, HDAC1, DNMTs, G9a, methylated histone H3 lysine 9, and methylated DNA. It interacts with the cyclin E-CDK2 complex, ubiquitinates cyclins D1 and E1, induces G1 arrest, and is involved in the G1/S transition regulation. Furthermore, UHRF2 is a direct transcriptional target of the transcription factor E2F-1 in the induction of apoptosis. It recruits HDAC1 and binds to methyl-CpG. UHRF2 also participates in the maturation of Hepatitis B virus (HBV) through interacting with HBV core protein and promoting its degradation. UHRF2 contains an N-terminal ubiquitin-like domain (UBL), a tandem Tudor domain (TTD), a plant homeodomain (PHD) domain, a SET- and RING-associated (SRA) domain, and a C-terminal C3HC4-type RING-HC finger.

Pssm-ID: 438426 [Multi-domain] Cd Length: 65 Bit Score: 39.79 E-value: 1.85e-04

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|
gi 890799132  10 KEEVTCPVCLNLMVKPVSADCGHTFCQGCITLYFESikcdkEMFSCPVCR 59
Cdd:cd16770    1 EESFLCICCQELVYQPVTTECQHNVCKSCLQRSFKA-----EVYTCPACR 45

RING-HC_RNF112

cd16538

RING finger, HC subclass, found in RING finger protein 112 (RNF112) and similar proteins; ...

11-59

2.07e-04

RING finger, HC subclass, found in RING finger protein 112 (RNF112) and similar proteins; RNF112, also known as brain finger protein (BFP), zinc finger protein 179 (ZNF179), or neurolastin, is a peripheral membrane protein that is predominantly expressed in the central nervous system and localizes to endosomes. It contains functional GTPase and C3HC4-type RING-HC finger domains and has been identified as a brain-specific dynamin family GTPase that affects endosome size and spine density. Moreover, RNF112 acts as a downstream target of sigma-1 receptor (Sig-1R) regulation and may play a novel role in neuroprotection by mediating the neuroprotective effects of dehydroepiandrosterone (DHEA) and its sulfated analog (DHEAS).

Pssm-ID: 438200 [Multi-domain] Cd Length: 52 Bit Score: 39.21 E-value: 2.07e-04

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*....
gi 890799132  11 EEVTCPVCLNLMVKPVSADCGHTFCQGCITLYfESIKCdkEMFSCPVCR 59
Cdd:cd16538    1 EPPTCSICLERLREPISLDCGHDFCIRCFSTH-RIPGC--EPPCCPECR 46

RING-HC_ScRAD18-like

cd23148

RING finger, HC subclass, found in Saccharomyces cerevisiae radiation sensitivity protein 18 ...

14-67

2.09e-04

RING finger, HC subclass, found in Saccharomyces cerevisiae radiation sensitivity protein 18 (RAD18) and similar proteins; RAD18, also called RING-type E3 ubiquitin transferase RAD18, acts as a postreplication repair E3 ubiquitin-protein ligase that associates with the E2 ubiquitin conjugating enzyme UBC2/RAD6 to form the UBC2-RAD18 ubiquitin ligase complex involved in postreplicative repair (PRR) of damaged DNA. The UBC2-RAD18 complex cooperates with RAD5 and the UBC13-MMS2 dimer to attach mono-ubiquitin chains on 'Lys-164' of POL30, which is necessary for PRR. The UBC2-RAD18 complex is also involved in prevention of spontaneous mutations caused by 7,8-dihydro-8-oxoguanine. RAD18 is an E3 RING-finger protein belonging to the UBC2/RAD6 epistasis group. It contains a typical C3HC4-type RING-HC finger.

Pssm-ID: 438510 [Multi-domain] Cd Length: 52 Bit Score: 39.05 E-value: 2.09e-04

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 890799132  14 TCPVCLNLMVKPVSADCGHTFCQGCITLYFESiKCdkemfSCPVCRLSYQSSNL 67
Cdd:cd23148    5 RCHICKDLLKAPMRTPCNHTFCSFCIRTHLNN-DA-----RCPLCKAEVTESGL 52

RING-HC_TRIM59_C-V

cd16763

RING finger, HC subclass, found in tripartite motif-containing protein 59 (TRIM59) and similar ...

10-59

2.33e-04

RING finger, HC subclass, found in tripartite motif-containing protein 59 (TRIM59) and similar proteins; TRIM59, also known as RING finger protein 104 (RNF104) or tumor suppressor TSBF-1, is a putative E3 ubiquitin-protein ligase that functions as a novel multiple cancer biomarker for immunohistochemical detection of early tumorigenesis. It is upregulated in gastric cancer and promotes gastric carcinogenesis by interacting with and targeting the P53 tumor suppressor for its ubiquitination and degradation. It also acts as a novel accessory molecule involved in cytotoxicity of BCG-activated macrophages (BAM). Moreover, TRIM59 may serve as a multifunctional regulator for innate immune signaling pathways. It interacts with ECSIT and negatively regulates nuclear factor-kappaB (NF- kappa B) and interferon regulatory factor (IRF)-3/7-mediated signal pathways. TRIM59 belongs to the C-V subclass of the TRIM (tripartite motif) family of proteins that are defined by an N-terminal RBCC (RING, Bbox, and coiled coil) domain, including three consecutive zinc-binding domains, a C3HC4-type RING-HC finger, Bbox1 and Bbox2, and a coiled coil region. In addition, TRIM59 contains a C-terminal transmembrane domain.

Pssm-ID: 438419 [Multi-domain] Cd Length: 56 Bit Score: 39.12 E-value: 2.33e-04

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 890799132  10 KEEVTCPVCLNLMVKPVSADCGHTFCQGCItlyfESIKCDKEMFS----------CPVCR 59
Cdd:cd16763    1 EEDLTCSVCYSLFEDPRVLPCSHTFCRNCL----ENILQVSGNFSiwrplrpplkCPNCR 56

Bbox2_TRIM50-like

cd19787

B-box-type 2 zinc finger found in tripartite motif-containing protein TRIM50, TRIM73, TRIM74 ...

96-128

2.75e-04

B-box-type 2 zinc finger found in tripartite motif-containing protein TRIM50, TRIM73, TRIM74 and similar proteins; TRIM50 is a stomach-specific E3 ubiquitin-protein ligase, encoded by the Williams-Beuren syndrome (WBS) TRIM50 gene, which regulates vesicular trafficking for acid secretion in gastric parietal cells. It colocalizes, interacts with, and increases the level of p62/SQSTM1, a multifunctional adaptor protein implicated in various cellular processes including the autophagy clearance of polyubiquitinated protein aggregates. It also promotes the formation and clearance of aggresome-associated polyubiquitinated proteins through the interaction with the histone deacetylase 6 (HDAC6), a tubulin specific deacetylase that regulates microtubule-dependent aggresome formation. TRIM50 can be acetylated by PCAF and p300. TRIM50 belongs to the C-IV subclass of TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a RING finger, Bbox2, and a coiled coil region, as well as a B30.2/SPRY (SplA and ryanodine receptor) domain positioned C-terminal to the RBCC domain. The type 2 B-box (Bbox2) zinc finger is characterized by a CHC3H2 zinc-binding consensus motif. The family also includes two paralogs of TRIM50, tripartite motif-containing protein 73 (TRIM73), also known as tripartite motif-containing protein 50B (TRIM50B), and tripartite motif-containing protein 74 (TRIM74), also known as tripartite motif-containing protein 50C (TRIM50C), both of which are WBS-related genes encoding proteins and may also act as E3 ligases. In contrast with TRIM50, TRIM73 and TRIM74 belong to the C-V subclass of TRIM family of proteins that are defined by the N-terminal RBCC domains only.

Pssm-ID: 380845 [Multi-domain] Cd Length: 39 Bit Score: 38.24 E-value: 2.75e-04

                         10        20        30
                 ....*....|....*....|....*....|...
gi 890799132  96 CARHGEKLQLFCRKDMMAICWLCERSQEHRGHK 128
Cdd:cd19787    3 CPHHHNPLSLFCEKDQEVICGLCGLIGSHRQHK 35

RING-HC_TRIM9-like_C-I

cd16576

RING finger, HC subclass, found in tripartite motif-containing proteins TRIM9, TRIM67, and ...

11-59

3.12e-04

RING finger, HC subclass, found in tripartite motif-containing proteins TRIM9, TRIM67, and similar proteins; Tripartite motif-containing proteins TRIM9 and TRIM67 belong to the C-I subclass of the TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, consisting of three consecutive zinc-binding domains, a C3HC4-type RING-HC finger, Bbox1 and Bbox2, and a coiled coil region, as well as a COS (carboxyl-terminal subgroup one signature) box, a fibronectin type III (FN3) domain, and a B30.2/SPRY (SplA and ryanodine receptor) domain positioned C-terminal to the RBCC domain. TRIM9 (the human ortholog of rat Spring), also known as RING finger protein 91 (RNF91), is a brain-specific E3 ubiquitin-protein ligase collaborating with an E2 ubiquitin conjugating enzyme UBCH5b. TRIM9 plays an important role in the regulation of neuronal functions and participates in neurodegenerative disorders through its ligase activity. TRIM67, also known as TRIM9-like protein (TNL), is a protein selectively expressed in the cerebellum. It interacts with PRG-1, an important molecule in the control of hippocampal excitability dependent on presynaptic LPA2 receptor signaling, and 80K-H, also known as glucosidase II beta, a protein kinase C substrate.

Pssm-ID: 438238 [Multi-domain] Cd Length: 42 Bit Score: 38.16 E-value: 3.12e-04

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 890799132  11 EEVTCPVCLNLMVKPVSADCGHTFCQGC---ITLyfesikcdkemfSCPVCR 59
Cdd:cd16576    2 EELKCPVCGSLFTEPVILPCSHNLCLGCalnIQL------------TCPICH 41

zf-C3HC4_2

pfam13923

Zinc finger, C3HC4 type (RING finger);

15-58

3.27e-04

Zinc finger, C3HC4 type (RING finger);

Pssm-ID: 404756 [Multi-domain] Cd Length: 40 Bit Score: 38.19 E-value: 3.27e-04

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 890799132   15 CPVCLNLMVKP-VSADCGHTFCQGCITLYFESIKcdkemfSCPVC 58
Cdd:pfam13923   2 CPICMDMLKDPsTTTPCGHVFCQDCILRALRAGN------ECPLC 40

zf-B_box

pfam00643

B-box zinc finger;

91-132

3.40e-04

B-box zinc finger;

Pssm-ID: 459886 [Multi-domain] Cd Length: 42 Bit Score: 38.22 E-value: 3.40e-04

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 890799132   91 QKVFNCARHG-EKLQLFCRKDMMAICWLCERSqEHRGHKTALI 132
Cdd:pfam00643   1 SKERLCPEHEeEPLTLYCNDCQELLCEECSVG-EHRGHTVVPL 42

RING-HC_AtRMA-like

cd16745

RING finger, HC subclass, found in Arabidopsis thaliana RING membrane-anchor proteins (AtRMAs) ...

15-59

3.58e-04

RING finger, HC subclass, found in Arabidopsis thaliana RING membrane-anchor proteins (AtRMAs) and similar proteins; AtRMAs, including AtRma1, AtRma2, and AtRma3, are endoplasmic reticulum (ER)-localized Arabidopsis homologs of human outer membrane of the ER-anchor E3 ubiquitin-protein ligase, RING finger protein 5 (RNF5). AtRMAs possess E3 ubiquitin ligase activity, and may play a role in the growth and development of Arabidopsis. The AtRMA1 and AtRMA3 genes are predominantly expressed in major tissues, such as cotyledons, leaves, shoot-root junction, roots, and anthers, while AtRMA2 expression is restricted to the root tips and leaf hydathodes. AtRma1 probably functions with the Ubc4/5 subfamily of E2. AtRma2 is likely involved in the cellular regulation of ABP1 expression levels through interacting with auxin binding protein 1 (ABP1). AtRMA proteins contain an N-terminal C3HC4-type RING-HC finger and a trans-membrane-anchoring domain in their extreme C-terminal region.

Pssm-ID: 438403 [Multi-domain] Cd Length: 45 Bit Score: 38.23 E-value: 3.58e-04

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*
gi 890799132  15 CPVCLNLMVKPVSADCGHTFCQGCItlyFESIKCDKEMFSCPVCR 59
Cdd:cd16745    3 CNICLDLAQDPVVTLCGHLFCWPCL---HKWLRRQSSQPECPVCK 44

RING-HC_IRC20-like

cd23135

RING finger, HC subclass, found in Saccharomyces cerevisiae increased recombination centers ...

10-59

3.85e-04

RING finger, HC subclass, found in Saccharomyces cerevisiae increased recombination centers protein 20 (IRC20) and similar proteins; IRC20 is an uncharacterized ATP-dependent helicase that is probably involved in a pathway contributing to genomic integrity. IRC20 contains a typical C3HC4-type RING-HC finger.

Pssm-ID: 438497 [Multi-domain] Cd Length: 44 Bit Score: 38.27 E-value: 3.85e-04

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|
gi 890799132  10 KEEVTCPVCLNLMVKPVSADCGHTFCQGCITLYFesikcdKEMFSCPVCR 59
Cdd:cd23135    1 KQKLSCSICFSEIRSGAILKCGHFFCLSCIASWL------REKSTCPLCK 44

RING-HC_RING2

cd16740

RING finger, HC subclass, found in really interesting new gene 2 protein (RING2) and similar ...

7-80

3.87e-04

RING finger, HC subclass, found in really interesting new gene 2 protein (RING2) and similar proteins; RING2, also known as huntingtin-interacting protein 2-interacting protein 3, HIP2-interacting protein 3, protein DinG, RING finger protein 1B (RING1B), RING finger protein 2 (RNF2), or RING finger protein BAP-1, is an E3 ubiquitin-protein ligase that interacts with both nucleosomal DNA and an acidic patch on histone H4 to achieve the specific monoubiquitination of K119 on histone H2A (H2AK119ub), thereby playing a central role in histone code and gene regulation. RING2 is a core component of polycomb repressive complex 1 (PRC1) that functions as an E3-ubuiquitin ligase transferring the mono-ubuiquitin mark to the C-terminal tail of Histone H2A at K118/K119. PRC1 is also capable of chromatin compaction, a function not requiring histone tails, and this activity appears important in gene silencing. The enzymatic activity of RING2 is enhanced by the interaction with BMI1/PCGF4, and it is dispensable for early embryonic development and much of the gene repression activity of PRC1. Moreover, RING2 plays a key role in terminating neural precursor cell (NPC)-mediated production of subcerebral projection neurons (SCPNs) during neocortical development. It also plays a critical role in nonhomologous end-joining (NHEJ)-mediated end-to-end chromosome fusions. Furthermore, RING2 is essential for expansion of hepatic stem/progenitor cells. It promotes hepatic stem/progenitor cell expansion through simultaneous suppression of cyclin-dependent kinase inhibitors (CDKIs) Cdkn1a and Cdkn2a, known negative regulators of cell proliferation. RING2 also negatively regulates p53 expression through directly binding with both p53 and MDM2 and promoting MDM2-mediated p53 ubiquitination in selective cancer cell types to stimulate tumor development. RING2 contains a C3HC4-type RING-HC finger.

Pssm-ID: 438398 [Multi-domain] Cd Length: 77 Bit Score: 39.30 E-value: 3.87e-04

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 890799132   7 KNLKEEVTCPVCLNLMVKPVSA-DCGHTFCQGCITLYFESikCDKEmfsCPVCRLSYQSS-NLRPNLHVANIVERL 80
Cdd:cd16740    7 RSLHSELMCPICLDMLKNTMTTkECLHRFCADCIITALRS--GNKE---CPTCRKKLVSKrSLRPDPNFDALISKI 77

RING-HC_TRIM9

cd16755

RING finger, HC subclass, found in tripartite motif-containing protein 9 (TRIM9) and similar ...

10-61

4.13e-04

RING finger, HC subclass, found in tripartite motif-containing protein 9 (TRIM9) and similar proteins; TRIM9, human ortholog of rat Spring, also known as RING finger protein 91 (RNF91), is a brain-specific E3 ubiquitin-protein ligase collaborating with an E2 ubiquitin conjugating enzyme UBCH5b. TRIM9 plays an important role in the regulation of neuronal functions and participates in the neurodegenerative disorders through its ligase activity. It interacts with the WD repeat region of beta-transducin repeat-containing protein (beta-TrCP) through its N-terminal degron motif depending on the phosphorylation status, and thus negatively regulates nuclear factor-kappaB (NF-kappaB) activation in the NF-kappaB pro-inflammatory signaling pathway. Moreover, TRIM9 acts as a critical catalytic link between Netrin-1 and the exocytic soluble NSF attachment receptor protein (SNARE) machinery in murine cortical neurons. It promotes SNARE-mediated vesicle fusion and axon branching in a Netrin-dependent manner. TRIM9 belongs to the C-I subclass of the TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a C3HC4-type RING-HC finger, Bbox1 and Bbox2, and a coiled coil region, as well as a COS (carboxyl-terminal subgroup one signature) box, a fibronectin type III (FN3) domain, and a B30.2/SPRY (SplA and ryanodine receptor) domain positioned C-terminal to the RBCC domain.

Pssm-ID: 438413 [Multi-domain] Cd Length: 55 Bit Score: 38.47 E-value: 4.13e-04

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 890799132  10 KEEVTCPVCLNLMVKPVSADCGHTFCQGC---ITLYFESIKCDKEMFSCPVCRLS 61
Cdd:cd16755    1 EEELKCPVCGSFYREPIILPCSHNLCLACarnILVQTPEAESPQSCLTCPQCHRS 55

RING-HC_GEFO-like

cd16507

RING finger, HC subclass, found in Dictyostelium discoideum Ras guanine nucleotide exchange ...

5-66

4.41e-04

RING finger, HC subclass, found in Dictyostelium discoideum Ras guanine nucleotide exchange factor O (RasGEFO) and similar proteins; RasGEFO, also known as RasGEF domain-containing protein O, functions as a Ras guanine-nucleotide exchange factor (RasGEFs), activating Ras by catalyzing the replacement of GDP with GTP. RasGEFs are particularly important for signaling in development and chemotaxis in many organisms, including Dictyostelium. RasGEFO contains a C3HC4-type RING-HC finger that may be responsible for E3 ubiquitin ligase activity.

Pssm-ID: 438170 [Multi-domain] Cd Length: 58 Bit Score: 38.48 E-value: 4.41e-04

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 890799132   5 FMKNLKEEVTCPVCLNLMVKP-VSADCGHTFCQGCITLYFESIkcdkemfSCPVCRLSYQSSN 66
Cdd:cd16507    2 KSLNLLQSLTCGICQNLFKDPnTLIPCGHAFCLDCLTTNASIK-------NCIQCKVEYTTYI 57

RING-HC_RNF5-like

cd16534

RING finger, HC subclass, found in RING finger protein RNF5, RNF185 and similar proteins; RNF5 ...

15-59

6.24e-04

RING finger, HC subclass, found in RING finger protein RNF5, RNF185 and similar proteins; RNF5 and RNF185 are E3 ubiquitin-protein ligases that are anchored to the outer membrane of the endoplasmic reticulum (ER). RNF5 acts at early stages of cystic fibrosis (CF) transmembrane conductance regulator (CFTR) biosynthesis, and functions as a target for therapeutic modalities to antagonize mutant CFTR proteins in CF patients carrying the F508del allele. RNF185 controls the degradation of CFTR and CFTR F508del allele in a RING- and proteasome-dependent manner, but does not control that of other classical endoplasmic reticulum-associated degradation (ERAD) model substrates. Moreover, both RNF5 and RNF185 play important roles in cell adhesion and migration through the modulation of cell migration by ubiquitinating paxillin. Arabidopsis thaliana RING membrane-anchor proteins (AtRMAs) are also included in this family. They possess E3 ubiquitin-protein ligase activity and may play a role in the growth and development of Arabidopsis. All members of this family contain a C3HC4-type RING-HC finger.

Pssm-ID: 438196 [Multi-domain] Cd Length: 44 Bit Score: 37.67 E-value: 6.24e-04

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*
gi 890799132  15 CPVCLNLMVKPVSADCGHTFCQGCITLYFESIKCDKEmfsCPVCR 59
Cdd:cd16534    3 CNICLDTASDPVVTMCGHLFCWPCLYQWLETRPDRQT---CPVCK 44

Bbox2_TRIM46_C-I

cd19786

B-box-type 2 zinc finger found in tripartite motif-containing protein 46 (TRIM46) and similar ...

92-130

6.42e-04

B-box-type 2 zinc finger found in tripartite motif-containing protein 46 (TRIM46) and similar proteins; TRIM46, also known as gene Y protein (GeneY) or tripartite, fibronectin type-III and C-terminal SPRY motif protein (TRIFIC), is a microtubule-associated protein that specifically localizes to the proximal axon, partly overlaps with the axon initial segment (AIS) at later stages, and organizes uniform microtubule orientation in axons. It controls neuronal polarity and axon specification by driving the formation of parallel microtubule arrays. TRIM46 belongs to the C-I subclass of TRIM (tripartite motif) family of proteins, which are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a RING finger, Bbox1 and Bbox2, and a coiled coil region, as well as a COS (carboxyl-terminal subgroup one signature) box, a fibronectin type III (FN3) domain, and a B30.2/SPRY (SplA and ryanodine receptor) domain positioned C-terminal to the RBCC domain. The type 2 B-box (Bbox2) zinc finger is characterized by a CHC3H2 zinc-binding consensus motif.

Pssm-ID: 380844 [Multi-domain] Cd Length: 46 Bit Score: 37.59 E-value: 6.42e-04

                         10        20        30
                 ....*....|....*....|....*....|....*....
gi 890799132  92 KVFNCARHGEKLQLFCRKDMMAICWLCERSQEHRGHKTA 130
Cdd:cd19786    1 KGLMCPEHKEEVTHYCKTCQRLVCQLCRVRRTHAGHKIT 39

Bbox2_TRIM13_C-XI

cd19767

B-box-type 2 zinc finger found in tripartite motif-containing protein 13 (TRIM13) and similar ...

96-134

6.66e-04

B-box-type 2 zinc finger found in tripartite motif-containing protein 13 (TRIM13) and similar proteins; TRIM13, also known as B-cell chronic lymphocytic leukemia tumor suppressor Leu5, leukemia-associated protein 5, putative tumor suppressor RFP2, RING finger protein 77 (RNF77), or Ret finger protein 2, is an endoplasmic reticulum (ER) membrane-anchored E3 ubiquitin-protein ligase that interacts with proteins localized to the ER, including valosin-containing protein (VCP), a protein indispensable for ER-associated degradation (ERAD). It also targets the known ER proteolytic substrate CD3-delta, but not the N-end rule substrate Ub-R-YFP (yellow fluorescent protein) for its degradation. Moreover, TRIM13 regulates ubiquitination and degradation of NEMO to suppress tumor necrosis factor (TNF) induced nuclear factor-kappaB (NF- kappa B) activation. It is also involved in NF-kappaB p65 activation and nuclear factor of activated T-cells (NFAT)-dependent activation of c-Rel upon T-cell receptor engagement. Furthermore, TRIM13 negatively regulates lanoma differentiation-associated gene 5 (MDA5)-mediated type I interferon production. It also regulates caspase-8 ubiquitination, translocation to autophagosomes, and activation during ER stress induced cell death. Meanwhile, TRIM13 enhances ionizing radiation-induced apoptosis by increasing p53 stability and decreasing AKT kinase activity through MDM2 and AKT degradation. TRIM13 belongs to the C-XI subclass of TRIM (tripartite motif) family of proteins that are defined by an N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a RING finger, Bbox2, and a coiled coil region. In addition, TRIM13 contains a C-terminal transmembrane domain. The type 2 B-box (Bbox2) zinc finger is characterized by a CHC3H2 zinc-binding consensus motif.

Pssm-ID: 380825 Cd Length: 42 Bit Score: 37.50 E-value: 6.66e-04

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|
gi 890799132  96 CARH-GEKLQLFCRKDMMAICWLCERSQEHRGHKTALIEE 134
Cdd:cd19767    3 CKVHsGQPLNIFCSTDLKLICGFCATMGDHKKHVFCSIED 42

RING-HC_TRIM3

cd16768

RING finger, HC subclass, found in tripartite motif-containing protein 3 (TRIM3); TRIM3, also ...

10-59

6.68e-04

RING finger, HC subclass, found in tripartite motif-containing protein 3 (TRIM3); TRIM3, also known as brain-expressed RING finger protein (BERP), RING finger protein 97 (RNF97), or RING finger protein 22 (RNF22), is an E3 ubiquitin-protein ligase involved in the pathogenesis of various cancers. It functions as a tumor suppressor that regulates asymmetric cell division in glioblastoma. It binds to the cdk inhibitor p21(WAF1/CIP1) and regulates its availability that promotes cyclin D1-cdk4 nuclear accumulation. Moreover, TRIM3 plays an important role in the central nervous system (CNS). It is encoded by the gene BERP (brain-expressed RING finger protein), a unique p53-regulated gene that modulates seizure susceptibility and GABAAR cell surface expression. Furthermore, TRIM3 mediates activity-dependent turnover of postsynaptic density (PSD) scaffold proteins GKAP/SAPAP1 and is a negative regulator of dendritic spine morphology. In addition, TRIM3 may be involved in vesicular trafficking via its association with the cytoskeleton-associated-recycling or transport (CART) complex that is necessary for efficient transferrin receptor recycling, but not for epidermal growth factor receptor (EGFR) degradation. It also regulates the motility of the kinesin superfamily protein KIF21B. TRIM3 belongs to the C-VII subclass of the TRIM (tripartite motif)-NHL family that is defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a C3HC4-type RING-HC finger, Bbox1 and Bbox2, and a coiled coil domain, as well as a NHL (named after proteins NCL-1, HT2A and Lin-41 that contain repeats folded into a six-bladed beta propeller) repeat domain positioned C-terminal to the RBCC domain.

Pssm-ID: 438424 [Multi-domain] Cd Length: 48 Bit Score: 37.67 E-value: 6.68e-04

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|
gi 890799132  10 KEEVTCPVCLNLMVKPVSADCGHTFCQGCITLYfesIKCDKEMFSCPVCR 59
Cdd:cd16768    2 KQFLVCSICLDRYHNPKVLPCLHTFCERCLQNY---IPPQSLTLSCPVCR 48

mRING-HC-C3HC3D_Nrdp1

cd16634

Modified RING finger, HC subclass (C3HC3D-type), found in neuregulin receptor degradation ...

12-59

6.90e-04

Modified RING finger, HC subclass (C3HC3D-type), found in neuregulin receptor degradation protein-1 (Nrdp1) and similar proteins; Nrdp1 (referred to as FLRF in mice), also known as RING finger protein 41 (RNF41), is an E3 ubiquitin-protein ligase that plays a critical role in the regulation of cell growth and apoptosis, inflammation and production of reactive oxygen species (ROS), as well as in doxorubicin (DOX)-induced cardiac injury. It promotes the degradation of the epidermal growth factor receptor (EGFR/ErbB) family member, ErbB3, which is independent of growth factor stimulation. It also promotes M2 macrophage polarization by ubiquitinating and activating transcription factor CCAAT/enhancer-binding protein beta (C/EBPbeta) via Lys-63-linked ubiquitination. Moreover, Nrdp1 interacts with and modulates the activity of Parkin, a causative protein for early onset recessive juvenile parkinsonism (AR-JP). It also interacts with ubiquitin-specific protease 8 (USP8), which is involved in trafficking of various transmembrane proteins. Furthermore, Nrdp1 inhibits basal lysosomal degradation and enhances ectodomain shedding of JAK2-associated cytokine receptors. Its phosphorylation by the kinase Par-1b (also known as MARK2) is required for epithelial cell polarity. Nrdp1 contains an N-terminal modified C3HC3D-type RING-HC finger required for enhancing ErbB3 degradation, a B-box, a coiled-coil domain responsible for Nrdp1 oligomerization, and a C-terminal ErbB3-binding domain.

Pssm-ID: 438296 [Multi-domain] Cd Length: 43 Bit Score: 37.40 E-value: 6.90e-04

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*....
gi 890799132  12 EVTCPVCLNLMVKPVSA-DCGHTFCQGCITLYFesikcdKEMFSCPVCR 59
Cdd:cd16634    1 ELICPICSGVLEEPLQApHCEHAFCNACITEWL------SRQQTCPVDR 43

Bbox2_TRIM44

cd19784

B-box-type 2 zinc finger found in tripartite motif-containing protein 44 (TRIM44) and similar ...

96-128

7.03e-04

B-box-type 2 zinc finger found in tripartite motif-containing protein 44 (TRIM44) and similar proteins; TRIM44, also termed protein DIPB, functions as a critical regulator in tumor metastasis and progression. TRIM44 belongs to an unclassified TRIM (tripartite motif) family of proteins that do not have RING fingers and thus lack the characteristic tripartite (RING (R), B-box, and coiled coil (CC)) RBCC motif. It contains a Bbox2 domain. The type 2 B-box (Bbox2) zinc finger is characterized by a CHC3H2 zinc-binding consensus motif.

Pssm-ID: 380842 [Multi-domain] Cd Length: 39 Bit Score: 37.06 E-value: 7.03e-04

                         10        20        30
                 ....*....|....*....|....*....|...
gi 890799132  96 CARHGEKLQLFCRKDMMAICWLCERSQEHRGHK 128
Cdd:cd19784    3 CPEHGQELSLYCKEDEKIICVLCAVIGAHRQHQ 35

RING-HC_RNF146

cd16546

RING finger, HC subclass, found in RING finger protein 146 (RNF146) and similar proteins; ...

15-59

7.05e-04

RING finger, HC subclass, found in RING finger protein 146 (RNF146) and similar proteins; RNF146, also known as dactylidin, or iduna, is a cytoplasmic E3 ubiquitin-protein ligase that is responsible for PARylation-dependent ubiquitination (PARdU). It displays neuroprotective property due to its inhibition of Parthanatos, a PAR dependent cell death, via binding with Poly(ADP-ribose) (PAR). It also modulates PAR polymerase-1 (PARP-1)-mediated oxidative cell injury in cardiac myocytes. Moreover, RNF146 mediates tankyrase-dependent degradation of axin, thereby positively regulating Wnt signaling. It also facilitates DNA repair and protects against cell death induced by DNA damaging agents or gamma-irradiation by translocating to the nucleus after cellular injury and promoting the ubiquitination and degradation of various nuclear proteins involved in DNA damage repair. Furthermore, RNF146 is implicated in neurodegenerative disease and cancer development. It regulates the development and progression of non-small cell lung cancer (NSCLC) by enhancing cell growth, invasion, and survival. RNF146 contains an N-terminal C3HC4-type RING-HC finger followed by a WWE domain with a poly(ADP-ribose) (PAR) binding motif at the tail.

Pssm-ID: 438208 [Multi-domain] Cd Length: 50 Bit Score: 37.36 E-value: 7.05e-04

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*.
gi 890799132  15 CPVCLNLMVKPVSADCGHTFCQGCIT-LYFESIKcdkemfsCPVCR 59
Cdd:cd16546    3 CPICLQTCIHPVKLPCGHIFCYLCVKgVAWQSKR-------CALCR 41

SMC_prok_B

TIGR02168

chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of ...

119-300

8.23e-04

chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]

Pssm-ID: 274008 [Multi-domain] Cd Length: 1179 Bit Score: 42.35 E-value: 8.23e-04

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 890799132   119 ERSQEHRGHKTALIEEVAR--EYKEQLQVVLQRLMADKKEFENWKDEL----QKDRTYWEN------QIQKDVENVQSEF 186
Cdd:TIGR02168  323 AQLEELESKLDELAEELAEleEKLEELKEELESLEAELEELEAELEELesrlEELEEQLETlrskvaQLELQIASLNNEI 402

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 890799132   187 KRMRDIIDSEEKNeLQKLRQEKEDILNNLAESE-SEHAQQSKLLEDFISDVEHQLqcsdiEILQGVENIIKRSLTFSMKK 265
Cdd:TIGR02168  403 ERLEARLERLEDR-RERLQQEIEELLKKLEEAElKELQAELEELEEELEELQEEL-----ERLEEALEELREELEEAEQA 476

                          170       180       190
                   ....*....|....*....|....*....|....*..
gi 890799132   266 PKTIARE--QRKFRAPDLQGMLQVLQEVTEAQRYWVQ 300
Cdd:TIGR02168  477 LDAAERElaQLQARLDSLERLQENLEGFSEGVKALLK 513

rad50

TIGR00606

rad50; All proteins in this family for which functions are known are involvedin recombination, ...

117-324

8.61e-04

rad50; All proteins in this family for which functions are known are involvedin recombination, recombinational repair, and/or non-homologous end joining.They are components of an exonuclease complex with MRE11 homologs. This family is distantly related to the SbcC family of bacterial proteins.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).

Pssm-ID: 129694 [Multi-domain] Cd Length: 1311 Bit Score: 42.34 E-value: 8.61e-04

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 890799132   117 LCERSQEHRGHKTALIEEV--AREYKEQLQVVLQRLMADKKEFENWKDELQKDRTYWENQIQKDVENVQSEFKRMRDIId 194
Cdd:TIGR00606  886 FEEQLVELSTEVQSLIREIkdAKEQDSPLETFLEKDQQEKEELISSKETSNKKAQDKVNDIKEKVKNIHGYMKDIENKI- 964

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 890799132   195 sEEKNELQKLRQEKEdiLNNLAESESEHAQQSKLLEDFISDVEHQLQCSDIEilqgvENIIKRSLTFsMKKPKTIAREQR 274
Cdd:TIGR00606  965 -QDGKDDYLKQKETE--LNTVNAQLEECEKHQEKINEDMRLMRQDIDTQKIQ-----ERWLQDNLTL-RKRENELKEVEE 1035

                          170       180       190       200       210
                   ....*....|....*....|....*....|....*....|....*....|.
gi 890799132   275 KFRAPDLQ-GMLQVLQEVTEAQRYWVQVTLVQNNHpNIAITddkRQVRYED 324
Cdd:TIGR00606 1036 ELKQHLKEmGQMQVLQMKQEHQKLEENIDLIKRNH-VLALG---RQKGYEK 1082

RING-HC_RING1

cd16739

RING finger, HC subclass, found in really interesting new gene 1 protein (RING1) and similar ...

12-70

9.88e-04

RING finger, HC subclass, found in really interesting new gene 1 protein (RING1) and similar proteins; RING1, also known as polycomb complex protein RING1, RING finger protein 1 (RNF1), or RING finger protein 1A (RING1A), was identified as a transcriptional repressor that is associated with the Polycomb group (PcG) protein complex involved in stable repression of gene activity. It is a core component of polycomb repressive complex 1 (PRC1) that functions as an E3-ubuiquitin ligase that transferring the mono-ubuiquitin mark to the C-terminal tail of Histone H2A at K118/K119. PRC1 is also capable of chromatin compaction, a function not requiring histone tails, and this activity appears important in gene silencing. RING1 interacts with multiple PcG proteins and displays tumorigenic activity. It also shows zinc-dependent DNA binding activity. Moreover, RING1 inhibits transactivation of the DNA-binding protein recombination signal binding protein-Jkappa (RBP-J) by Notch through interaction with the LIM domains of KyoT2. RING1 contains a C3HC4-type RING-HC finger.

Pssm-ID: 438397 [Multi-domain] Cd Length: 70 Bit Score: 37.75 E-value: 9.88e-04

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 890799132  12 EVTCPVCLNLMVKPVSA-DCGHTFCQGCITLYFESikCDKEmfsCPVCRLSYQSS-NLRPN 70
Cdd:cd16739    3 ELMCPICLDMLKNTMTTkECLHRFCSDCIVTALRS--GNKE---CPTCRKKLVSKrSLRPD 58

mRING-HC-C3HC3D_LNX1

cd16779

Modified RING finger, HC subclass (C3HC3D-type), found in ligand of numb protein X 1 (LNX1); ...

12-40

1.01e-03

Modified RING finger, HC subclass (C3HC3D-type), found in ligand of numb protein X 1 (LNX1); LNX1, also known as numb-binding protein 1 or PDZ domain-containing RING finger protein 2, is a PDZ domain-containing RING-type E3 ubiquitin ligase responsible for the ubiquitination and degradation of Numb, a component of the Notch signaling pathway that functions in the specification of cell fates during development and is known to control cell numbers during neurogenesis in vertebrates. LNX1 contains an N-terminal modified C3HC3D-type RING-HC finger, a NPAY motif for Numb-LNX interaction, and four PDZ domains necessary for the binding of substrates, including CAR, ErbB2, SKIP, JAM4, CAST, c-Src, Claudins, RhoC, KCNA4, PAK6, PLEKHG5, PKC-alpha1, TYK2, PDZ-binding kinase (PBK), LNX2, and itself.

Pssm-ID: 438435 [Multi-domain] Cd Length: 42 Bit Score: 36.71 E-value: 1.01e-03

                         10        20
                 ....*....|....*....|....*....
gi 890799132  12 EVTCPVCLNLMVKPVSADCGHTFCQGCIT 40
Cdd:cd16779    1 DLICHICLQALIQPLDTPCGHTYCTLCLT 29

mRING-HC-C3HC3D_LNX2

cd16780

Modified RING finger, HC subclass (C3HC3D-type), found in ligand of numb protein X 2 (LNX2); ...

11-39

1.05e-03

Modified RING finger, HC subclass (C3HC3D-type), found in ligand of numb protein X 2 (LNX2); LNX2, also known as numb-binding protein 2, or PDZ domain-containing RING finger protein 1 (PDZRN1), is a PDZ domain-containing RING-type E3 ubiquitin ligase responsible for the ubiquitination and degradation of Numb, a component of the Notch signaling pathway that functions in the specification of cell fates during development and is known to control cell numbers during neurogenesis in vertebrates. It interacts with contactin-associated protein 4 (Caspr4, also known as CNTNAP4) in a PDZ domain-dependent manner, which modulates the proliferation and neuronal differentiation of neural progenitor cells (NPCs). LNX2 contains an N-terminal modified C3HC3D-type RING-HC finger, a NPAF motif for Numb/ Numblike-LNX interaction, and four PDZ domains necessary for the binding of substrates, including ErbB2, RhoC, the presynaptic protein CAST, the melanoma/cancer-testis antigen MAGEB18 and several proteins associated with cell junctions, such as JAM4 and the Coxsackievirus and adenovirus receptor (CAR).

Pssm-ID: 319694 [Multi-domain] Cd Length: 45 Bit Score: 36.78 E-value: 1.05e-03

                         10        20
                 ....*....|....*....|....*....
gi 890799132  11 EEVTCPVCLNLMVKPVSADCGHTFCQGCI 39
Cdd:cd16780    2 DDLVCHICLQPLLQPLDTPCGHTFCFKCL 30

RING-HC_PCGF3

cd16735

RING finger found in polycomb group RING finger protein 3 (PCGF3) and similar proteins; PCGF3, ...

6-60

1.11e-03

RING finger found in polycomb group RING finger protein 3 (PCGF3) and similar proteins; PCGF3, also known as RING finger protein 3A (RNF3A), is one of six PcG RING finger (PCGF) homologs (PCGF1, PCGF2/Mel-18, PCGF3, PCGF4/BMI1, PCGF5, and PCGF6) and serves as the core component of a Polycomb repressive complex 1 (PRC1). Like other PCGF homologs, PCGF3 associates with ring finger protein 2 (RNF2) to form a RNF2-PCGF heterodimer, which is catalytically competent as an E3 ubiquitin transferase and is the scaffold for the assembly of additional components. PCGF3 contains a C3HC4-type RING-HC finger.

Pssm-ID: 438393 [Multi-domain] Cd Length: 66 Bit Score: 37.43 E-value: 1.11e-03

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 890799132   6 MKNLKEEVTCPVCLNLMVKPVS-ADCGHTFCQGCITLYFEsikcdkEMFSCPVCRL 60
Cdd:cd16735    5 LKDLNAHITCRLCKGYLIDATTiTECLHTFCKSCLVKYLE------ENNTCPTCGI 54

SMC_prok_B

TIGR02168

chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of ...

134-336

1.12e-03

Pssm-ID: 274008 [Multi-domain] Cd Length: 1179 Bit Score: 41.58 E-value: 1.12e-03

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 890799132   134 EVAREYKEQLQVVLQRLMADKKEFENWKDELQKDRTYWENQI---QKDVENVQSEFKRMRdiidsEEKNELQKLRQEKED 210
Cdd:TIGR02168  305 QILRERLANLERQLEELEAQLEELESKLDELAEELAELEEKLeelKEELESLEAELEELE-----AELEELESRLEELEE 379

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 890799132   211 ILNNLAESESEHAQQSKLLEDFISDVEHQLQCSDIEILQGVENIIKRSLTFSMKKPKTIAR--EQRKFRAPDLQGMLQVL 288
Cdd:TIGR02168  380 QLETLRSKVAQLELQIASLNNEIERLEARLERLEDRRERLQQEIEELLKKLEEAELKELQAelEELEEELEELQEELERL 459

                          170       180       190       200
                   ....*....|....*....|....*....|....*....|....*...
gi 890799132   289 QEVTEAQRYwvQVTLVQNnhpniaitdDKRQVRYEDHQASNLIHECEN 336
Cdd:TIGR02168  460 EEALEELRE--ELEEAEQ---------ALDAAERELAQLQARLDSLER 496

RING-HC_RNF222

cd16564

RING finger, HC subclass, found in RING finger protein 222 (RNF222) and similar proteins; ...

14-59

1.21e-03

RING finger, HC subclass, found in RING finger protein 222 (RNF222) and similar proteins; RNF222 is an uncharacterized C3HC4-type RING-HC finger-containing protein. It may function as an E3 ubiquitin-protein ligase.

Pssm-ID: 438226 [Multi-domain] Cd Length: 50 Bit Score: 37.00 E-value: 1.21e-03

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*...
gi 890799132  14 TCPVCLNLM-VKPVSADCGHTFCQGCItlyfesIKC-DKEMFSCPVCR 59
Cdd:cd16564    2 ECPVCYEDFdDAPRILSCGHSFCEDCL------VKQlVSMTISCPICR 43

RING-HC_RNFT2

cd16742

RING finger, HC subclass, found in RING finger and transmembrane domain-containing protein 2 ...

15-59

1.24e-03

RING finger, HC subclass, found in RING finger and transmembrane domain-containing protein 2(RNFT2); RNFT2, also known as transmembrane protein 118 (TMEM118), is a multi-pass membrane protein containing a C3HC4-type RING-HC finger. Its biological role remains unclear.

Pssm-ID: 438400 [Multi-domain] Cd Length: 67 Bit Score: 37.55 E-value: 1.24e-03

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*
gi 890799132  15 CPVCLNLMVKPVSADCGHTFCQGCITLYFESIKcdkemfSCPVCR 59
Cdd:cd16742   16 CAICQAEFREPLILICQHVFCEECLCLWFDRER------TCPLCR 54

COG1340

Uncharacterized coiled-coil protein, contains DUF342 domain [Function unknown];

119-228

1.29e-03

Uncharacterized coiled-coil protein, contains DUF342 domain [Function unknown];

Pssm-ID: 440951 [Multi-domain] Cd Length: 297 Bit Score: 40.66 E-value: 1.29e-03

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 890799132 119 ERSQEHRGHKTALIEEVaREYKEQLQVVLQRLMADKKEFENWKDELQKDRT--YWENQIQKDVEnvQSEFKRM------- 189
Cdd:COG1340   57 EEAQELREKRDELNEKV-KELKEERDELNEKLNELREELDELRKELAELNKagGSIDKLRKEIE--RLEWRQQtevlspe 133

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*.
gi 890799132 190 --RDIID-----SEEKNELQKLRQEKEDILNNLAESESEHAQQSKL 228
Cdd:COG1340  134 eeKELVEkikelEKELEKAKKALEKNEKLKELRAELKELRKEAEEI 179

SMC_prok_B

TIGR02168

chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of ...

119-241

1.39e-03

Pssm-ID: 274008 [Multi-domain] Cd Length: 1179 Bit Score: 41.58 E-value: 1.39e-03

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 890799132   119 ERSQEHRGHKTALIEEVAREYKEQLQVVLQRLMADKKEFENWKDELQKDrtywENQIQKDVENVQSEFKRMRDIIDSEEK 198
Cdd:TIGR02168  763 IEELEERLEEAEEELAEAEAEIEELEAQIEQLKEELKALREALDELRAE----LTLLNEEAANLRERLESLERRIAATER 838

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|...
gi 890799132   199 nELQKLRQEKEDILNNLAESESEHAQQSKLLEDFISDVEHQLQ 241
Cdd:TIGR02168  839 -RLEDLEEQIEELSEDIESLAAEIEELEELIEELESELEALLN 880

RING-HC_MID_C-I

cd16575

RING finger, HC subclass, found in midline-1 (MID1), midline-2 (MID2) and similar proteins; ...

13-59

1.65e-03

RING finger, HC subclass, found in midline-1 (MID1), midline-2 (MID2) and similar proteins; MID1, also known as midin, midline 1 RING finger protein, putative transcription factor XPRF, RING finger protein 59 (RNF59), or tripartite motif-containing protein 18 (TRIM18), is a microtubule-associated E3 ubiquitin-protein ligase implicated in epithelial-mesenchymal differentiation, cell migration and adhesion, and programmed cell death along specific regions of the ventral midline during embryogenesis. MID2, also known as midin-2, midline defect 2, RING finger protein 60 (RNF60), or tripartite motif-containing protein 1 (TRIM1), associates with the microtubule network and may at least partially compensate for the loss of MID1. Both MID1 and MID2 interacts with Alpha 4, which is a regulatory subunit of PP2-type phosphatases, such as PP2A, and an integral component of the rapamycin-sensitive signaling pathway. They also play a central role in the regulation of granule exocytosis. Functional redundancy exists between MID1 and MID2 in cytotoxic lymphocytes (CTL). Both MID1 and MID2 belong to the C-I subclass of the TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a C3HC4-type RING-HC finger, Bbox1 and Bbox2, and a coiled coil region, as well as a COS (carboxyl-terminal subgroup one signature) box, a fibronectin type III (FN3) domain, and a B30.2/SPRY (SplA and ryanodine receptor) domain positioned C-terminal to the RBCC domain.

Pssm-ID: 438237 [Multi-domain] Cd Length: 54 Bit Score: 36.83 E-value: 1.65e-03

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 890799132  13 VTCPVCLNLMVKPVSADCGHTFCQGCI-------TLYFESIKcDKEMFSCPVCR 59
Cdd:cd16575    1 LTCPICLELFEDPLLLPCAHSLCFNCAhrilvshCASNESVE-SITAFQCPTCR 53

RING-HC_RAD5

cd23131

RING finger, HC subclass, found in radiation sensitivity protein 5 (RAD5) and similar proteins; ...

12-67

1.66e-03

RING finger, HC subclass, found in radiation sensitivity protein 5 (RAD5) and similar proteins; RAD5, also known as revertibility protein 2 (REV2), or DNA repair protein RAD5, is a probable helicase, and a member of the UBC2/RAD6 epistasis group. It functions with the DNA repair protein RAD18 in error-free postreplication DNA repair. It is involved in the maintenance of wild-type rates of instability of simple repetitive sequences such as poly(GT) repeats. It may also be involved in maintaining a balance which acts in favor of error-prone non-homologous joining during DNA double-strand breaks repairs. It recruits the UBC13-MMS2 dimer to chromatin for DNA repair. RAD5 contains a typical C3HC4-type RING-HC finger.

Pssm-ID: 438493 [Multi-domain] Cd Length: 65 Bit Score: 37.04 E-value: 1.66e-03

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 890799132  12 EVTCPVCLNLMVKPVSA---DCGHTFCQGCITLYFESIKCDKEMFSCPVCRLSYQSSNL 67
Cdd:cd23131    3 EVECSICTQEPIEVGEVvftECGHSFCEDCLLEYIEFQNKKKLDLKCPNCREPISKYRL 61

RING-H2

cd16448

H2 subclass of RING (RING-H2) fingers and its variants; The RING finger is a specialized type ...

15-59

1.70e-03

H2 subclass of RING (RING-H2) fingers and its variants; The RING finger is a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc. It is defined by the "cross-brace" motif that chelates zinc atoms by eight amino acid residues, typically Cys or His, arranged in a characteristic spacing. Canonical RING motifs have been categorized into two major subclasses, RING-HC (C3HC4-type) and RING-H2 (C3H2C3-type), according to their Cys/His content. There are also many variants of RING fingers: some have different Cys/His patterns while some lack a single Cys or His residue at typical Zn ligand positions (the fourth or eighth zinc ligand is prevalently exchanged for an Asp, which can indeed chelate Zn in a RING finger as well). This family corresponds to the H2 subclass of RING (RING-H2) finger proteins that are characterized by containing C3H2C3-type canonical RING-H2 fingers or noncanonical RING-H2 finger variants, including C4HC3- (RING-CH alias RINGv), C3H3C2-, C3H2C2D-, C3DHC3-, and C4HC2H-type modified RING-H2 fingers. The canonical RING-H2 finger has been defined as C-X2-C-X(9-39)-C-X(1-3)-H-X(2-3)-H-X2-C-X(4-48)-C-X2-C, X is any amino acid and the number of X residues varies in different fingers. It binds two Zn ions in a unique "cross-brace" arrangement, which distinguishes it from tandem zinc fingers and other similar motifs. RING-H2 finger can be found in a group of diverse proteins with a variety of cellular functions, including oncogenesis, development, viral replication, signal transduction, the cell cycle and apoptosis. Many of them are ubiquitin-protein ligases (E3s) that serves as a scaffold for binding to ubiquitin-conjugating enzymes (E2s, also referred to as ubiquitin carrier proteins or UBCs) in close proximity to substrate proteins, which enables efficient transfer of ubiquitin from E2 to the substrates.

Pssm-ID: 438112 [Multi-domain] Cd Length: 43 Bit Score: 36.23 E-value: 1.70e-03

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*...
gi 890799132  15 CPVCLNLMVKPVSA---DCGHTFCQGCITLYFESIKcdkemFSCPVCR 59
Cdd:cd16448    1 CVICLEEFEEGDVVrllPCGHVFHLACILRWLESGN-----NTCPLCR 43

RING-HC_RNF180

cd16554

RING finger, HC subclass, found in RING finger protein 180 (RNF180) and similar proteins; ...

11-59

1.77e-03

RING finger, HC subclass, found in RING finger protein 180 (RNF180) and similar proteins; RNF180, also known as Rines, is a membrane-bound E3 ubiquitin-protein ligase well conserved among vertebrates. It is a critical regulator of the monoaminergic system, as well as emotional and social behavior. It interacts with brain monoamine oxidase A (MAO-A) and targets it for ubiquitination and degradation. It also functions as a novel tumor suppressor in gastric carcinogenesis. The hypermethylated CpG site count of the RNF180 DNA promoter can be used to predict survival of gastric cancer. RNF180 contains a novel conserved dual specificity protein phosphatase Rines conserved (DSPRC) domain, a basic coiled-coil domain, a C3HC4-type RING-HC finger, and a C-terminal hydrophobic region that is predicted to be a transmembrane domain.

Pssm-ID: 438216 [Multi-domain] Cd Length: 59 Bit Score: 36.52 E-value: 1.77e-03

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|
gi 890799132  11 EEVTCPVCLNLMVKP-VSADCGHTFCQGCITLYFESIKCDkemFSCPVCR 59
Cdd:cd16554    1 ESLTCPVCLDLYYDPyMCYPCGHIFCEPCLRQLAKSSPKN---TPCPLCR 47

RING-HC_RNF5

cd16743

RING finger, HC subclass, found in RING finger protein 5 (RNF5) and similar proteins; RNF5, ...

15-59

1.78e-03

RING finger, HC subclass, found in RING finger protein 5 (RNF5) and similar proteins; RNF5, also known as protein G16 or Ram1, is an E3 ubiquitin-protein ligase anchored to the outer membrane of the endoplasmic reticulum (ER). It acts at early stages of cystic fibrosis (CF) transmembrane conductance regulator (CFTR) biosynthesis and functions as a target for therapeutic modalities to antagonize mutant CFTR proteins in CF patients carrying the F508del allele. It also regulates the turnover of specific G protein-coupled receptors by ubiquitinating JNK-associated membrane protein (JAMP) and preventing proteasome recruitment. RNF5 limits basal levels of autophagy and influences susceptibility to bacterial infection through the regulation of ATG4B stability. It is also involved in the degradation of Pendrin, a transmembrane chloride/anion exchanger highly expressed in thyroid, kidney, and inner ear. RNF5 plays an important role in cell adhesion and migration. It can modulate cell migration by ubiquitinating paxillin. Furthermore, RNF5 interacts with virus-induced signaling adaptor (VISA) at mitochondria in a viral infection-dependent manner, and further targets VISA at K362 and K461 for K48-linked ubiquitination and degradation after viral infection. It also negatively regulates virus-triggered signaling by targeting MITA, also known as STING, for ubiquitination and degradation at the mitochondria. In addition, RNF5 determines breast cancer response to ER stress-inducing chemotherapies through the regulation of the L-glutamine carrier proteins SLC1A5 and SLC38A2 (SLC1A5/38A2). It also has been implicated in muscle organization and in recognition and processing of misfolded proteins. RNF5 contains a C3HC4-type RING-HC finger.

Pssm-ID: 438401 [Multi-domain] Cd Length: 54 Bit Score: 36.40 E-value: 1.78e-03

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*
gi 890799132  15 CPVCLNLMVKPVSADCGHTFCQGCITLYFESIKCDKEmfsCPVCR 59
Cdd:cd16743    3 CNICLETARDAVVSLCGHLFCWPCLHQWLETRPERQE---CPVCK 44

RING-HC_MAT1

cd16517

RING finger, HC subclass, found in RING finger protein MAT1; MAT1, also known as ...

14-66

1.84e-03

RING finger, HC subclass, found in RING finger protein MAT1; MAT1, also known as CDK-activating kinase assembly factor MAT1, CDK7/cyclin-H assembly factor, cyclin-G1-interacting protein, menage a trois, RING finger protein 66 (RNF66), p35, or p36, is involved in cell cycle control and in RNA transcription by RNA polymerase II. It associates primarily with the catalytic subunit cyclin-dependent kinase 7 (CDK7) and the regulatory subunit cyclin H to form the CDK-activating kinase (CAK) complex that can further associate with the core-TFIIH to form the transcription factor IIH (TFIIH) basal transcription/DNA repair factor, which activates RNA polymerase II by serine phosphorylation of the repetitive C-terminal domain (CTD) of its large subunit (POLR2A), allowing its escape from the promoter, and elongation of the transcripts. MAT1 contains an N-terminal C3HC4-type RING-HC finger, a central coiled coil domain, and a C-terminal domain rich in hydrophobic residues.

Pssm-ID: 438180 [Multi-domain] Cd Length: 55 Bit Score: 36.66 E-value: 1.84e-03

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 890799132  14 TCPVC---------LNLMVKPvsadCGHTFCQGCITLYFEsikcdKEMFSCPVCRLSYQSSN 66
Cdd:cd16517    2 YCPRCkttkyrnpsLKLMVNV----CGHTLCESCVDLLFV-----RGSGPCPECGTPLRRSN 54

mRING-HC-C3HC3D_Roquin

cd16638

Modified RING finger, HC subclass (C3HC3D-type), found in Roquin-1, Roquin-2, and similar ...

14-40

1.92e-03

Modified RING finger, HC subclass (C3HC3D-type), found in Roquin-1, Roquin-2, and similar proteins; The ROQUIN family includes Roquin-1, Roquin-2, and similar proteins, which localize to the cytoplasm and upon stress, are concentrated in stress granules. They may play essential roles in preventing T-cell-mediated autoimmune disease and in microRNA-mediated repression of inducible costimulator (Icos) mRNA. They function as E3 ubiquitin ligases consisting of an N-terminal modified C3HC3D-type RING-HC finger with a potential E3 activity, a highly conserved ROQ domain required for RNA binding and localization to stress granules, and a CCCH-type zinc finger involved in RNA recognition.

Pssm-ID: 438300 [Multi-domain] Cd Length: 44 Bit Score: 36.17 E-value: 1.92e-03

                         10        20        30
                 ....*....|....*....|....*....|.
gi 890799132  14 TCPVCLNLM----VKPVSADCGHTFCQGCIT 40
Cdd:cd16638    3 SCPVCTNEFdgtqRKPISLGCGHTVCKTCLS 33

RING-HC_TRIM32_C-VII

cd16587

RING finger, HC subclass, found in tripartite motif-containing protein 32 (TRIM32) and similar ...

13-59

2.07e-03

RING finger, HC subclass, found in tripartite motif-containing protein 32 (TRIM32) and similar proteins; TRIM32, also known as 72 kDa Tat-interacting protein, zinc finger protein HT2A, or BBS11, is an E3 ubiquitin-protein ligase that promotes degradation of several targets, including actin, PIASgamma, Abl interactor 2, dysbindin, X-linked inhibitor of apoptosis (XIAP), p73 transcription factor, thin filaments and Z-bands during fasting. It plays important roles in neuronal differentiation of neural progenitor cells, as well as in controlling cell fate in skeletal muscle progenitor cells. It reduces PI3K-Akt-FoxO signaling in muscle atrophy by promoting plakoglobin-PI3K dissociation. It also functions as a pluripotency-reprogramming roadblock that facilitates cellular transition towards differentiation by modulating the levels of Oct4 and cMyc. Moreover, TRIM32 is an intrinsic influenza A virus (IAV) restriction factor which senses and targets the polymerase basic protein 1 (PB1) for ubiquitination and protein degradation. It also plays a significant role in mediating the biological activity of the HIV-1 Tat protein in vivo, binds specifically to the activation domain of HIV-1 Tat, and can also interact with the HIV-2 and EIAV Tat proteins in vivo. Furthermore, TRIM32 regulates myoblast proliferation by controlling turnover of NDRG2 (N-myc downstream-regulated gene). It negatively regulates tumor suppressor p53 to promote tumorigenesis. It also facilitates degradation of MYCN on spindle poles and induces asymmetric cell division in human neuroblastoma cells. In addition, TRIM32 plays important roles in regulation of hyperactivities and positively regulates the development of anxiety and depression disorders induced by chronic stress. It also plays a role in regeneration by affecting satellite cell cycle progression via modulation of the SUMO ligase PIASy (PIAS4). Defects in TRIM32 leads to limb-girdle muscular dystrophy type 2H (LGMD2H), sarcotubular myopathies (STM) and Bardet-Biedl syndrome. TRIM32 belongs to the C-VII subclass of the TRIM (tripartite motif)-NHL family that is defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a C3HC4-type RING-HC finger, Bbox1 and Bbox2, and a coiled coil domain, as well as a NHL (named after proteins NCL-1, HT2A and Lin-41 that contain repeats folded into a six-bladed beta propeller) repeat domain positioned C-terminal to the RBCC domain. The NHL domain mediates the interaction with Argonaute proteins and consequently allows TRIM32 to modulate the activity of certain miRNAs.

Pssm-ID: 438249 [Multi-domain] Cd Length: 51 Bit Score: 36.23 E-value: 2.07e-03

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 890799132  13 VTCPVCLNLM----VKPVSADCGHTFCQGCIT--LYFESIKCdkemFSCPVCR 59
Cdd:cd16587    1 LECPICLESFdegqLRPKLLHCGHTICEQCLEklLASLSING----VRCPFCR 49

OmpH

smart00935

Outer membrane protein (OmpH-like); This family includes outer membrane proteins such as OmpH ...

132-219

2.14e-03

Pssm-ID: 214922 [Multi-domain] Cd Length: 140 Bit Score: 38.33 E-value: 2.14e-03

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 890799132   132 IEEVAREYKEQLQVVLQRLMADKKEFENWKDEL-QKDRTYWENQIQKDVENVQSEFKRMRDIIDSEEKNELQKLRQEKED 210
Cdd:smart00935  23 LEKEFKKRQAELEKLEKELQKLKEKLQKDAATLsEAAREKKEKELQKKVQEFQRKQQKLQQDLQKRQQEELQKILDKINK 102


                   ....*....
gi 890799132   211 ILNNLAESE 219
Cdd:smart00935 103 AIKEVAKKK 111

EnvC

COG4942

Septal ring factor EnvC, activator of murein hydrolases AmiA and AmiB [Cell cycle control, ...

137-241

2.36e-03

Septal ring factor EnvC, activator of murein hydrolases AmiA and AmiB [Cell cycle control, cell division, chromosome partitioning];

Pssm-ID: 443969 [Multi-domain] Cd Length: 377 Bit Score: 40.13 E-value: 2.36e-03

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 890799132 137 REYKEQLQVVLQRLMADKKEFENWKDELQKDRtyweNQIQKDVENVQsefkrmrdiidsEEKNELQKLRQEKEDILNNLA 216
Cdd:COG4942  142 KYLAPARREQAEELRADLAELAALRAELEAER----AELEALLAELE------------EERAALEALKAERQKLLARLE 205

                         90       100       110
                 ....*....|....*....|....*....|..
gi 890799132 217 ESESEHAQQ-------SKLLEDFISDVEHQLQ 241
Cdd:COG4942  206 KELAELAAElaelqqeAEELEALIARLEAEAA 237

RING-HC_BARD1

cd16496

RING finger, HC subclass, found in BRCA1-associated RING domain protein 1 (BARD-1) and similar ...

9-77

2.56e-03

RING finger, HC subclass, found in BRCA1-associated RING domain protein 1 (BARD-1) and similar proteins; BARD-1 is a critical factor in BRCA1-mediated tumor suppression and may also serve as a target for tumorigenic lesions in some human cancers. It associates with BRCA1 (breast cancer-1) to form a heterodimeric BRCA1/BARD1 complex that is responsible for maintaining genomic stability through nuclear functions involving DNA damage signaling and repair, transcriptional regulation, and cell cycle control. The BRCA1/BARD1 complex catalyzes autoubiquitination of BRCA1 and trans ubiquitination of other protein substrates. Its E3 ligase activity is dramatically reduced in the presence of UBX domain protein 1 (UBXN1). BARD-1 contains an C3HC4-type RING-HC finger that binds BRCA1 at its N-terminus and three tandem ankyrin repeats and tandem BRCT repeat domains at its C-terminus. The BRCT repeats bind CstF-50 (cleavage stimulation factor) to modulate mRNA processing and RNAP II stability in response to DNA damage.

Pssm-ID: 438159 [Multi-domain] Cd Length: 86 Bit Score: 36.93 E-value: 2.56e-03

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 890799132   9 LKEEVTCPVCLNLMVKPVS-ADCGHTFCQGCITLYFESikcdkemfSCPVCRLSYQSSNLRPNLHVANIV 77
Cdd:cd16496   12 LENLLRCSRCASILKEPVTlGGCEHVFCRSCVGDRLGN--------GCPVCDTPAWARDLQINRQLDSMV 73

RING-HC_KEG-like

cd23140

RING finger, HC subclass, found in Arabidopsis thaliana protein KEEP ON GOING (KEG) and ...

24-59

2.75e-03

RING finger, HC subclass, found in Arabidopsis thaliana protein KEEP ON GOING (KEG) and similar proteins; KEG, also called RING-type E3 ubiquitin transferase KEG, is a RING E3 ubiquitin-protein ligase that mediates E2-dependent protein ubiquitination. It is essential for Arabidopsis growth and development. It acts as a negative regulator of abscisic acid signaling. It is required for ABSCISIC ACID-INSENSITIVE5 (ABI5) degradation, by mediating its ubiquitination. Together with EDR1, KEG may regulate endocytic trafficking and/or the formation of signaling complexes on trans-Golgi network (TGN)/ early endosome (EE) vesicles during stress responses. KEG is a multidomain protein that includes a C3HC4-type RING-HC finger, a kinase domain, ankyrin repeats, and 12 HERC2-like (for HECT and RCC1-like) repeats.

Pssm-ID: 438502 [Multi-domain] Cd Length: 57 Bit Score: 36.08 E-value: 2.75e-03

                         10        20        30
                 ....*....|....*....|....*....|....*.
gi 890799132  24 KPVSADCGHTFCQGCITLYFesIKCDKEMFSCPVCR 59
Cdd:cd23140   17 VPLLLQCGHTFCKDCLSQMF--IRCTDLTLKCPRCR 50

MukB

COG3096

Chromosome condensin MukBEF, ATPase and DNA-binding subunit MukB [Cell cycle control, cell ...

69-230

2.84e-03

Chromosome condensin MukBEF, ATPase and DNA-binding subunit MukB [Cell cycle control, cell division, chromosome partitioning];

Pssm-ID: 442330 [Multi-domain] Cd Length: 1470 Bit Score: 40.32 E-value: 2.84e-03

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 890799132   69 PNLHVANIVERLKEFKPSPEE--------EQK--VFNCAR--HGEKLQLFCrkdmmAICWLCERSQehrGHKTAliEEVA 136
Cdd:COG3096   432 PDLTPENAEDYLAAFRAKEQQateevlelEQKlsVADAARrqFEKAYELVC-----KIAGEVERSQ---AWQTA--RELL 501

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 890799132  137 REYKEQlQVVLQRLMADKKEFenwkDELQKDrtywENQiQKDVENVQSEF-KRMRDIIDSEE-----KNELQKLRQEKED 210
Cdd:COG3096   502 RRYRSQ-QALAQRLQQLRAQL----AELEQR----LRQ-QQNAERLLEEFcQRIGQQLDAAEeleelLAELEAQLEELEE 571

                         170       180
                  ....*....|....*....|
gi 890799132  211 ILNNLAESESEHAQQSKLLE 230
Cdd:COG3096   572 QAAEAVEQRSELRQQLEQLR 591

mRING-HC-C3HC3D_SCAF11

cd16636

Modified RING finger, HC subclass (C3HC3D-type), found in SR-related and CTD-associated factor ...

14-64

2.97e-03

Modified RING finger, HC subclass (C3HC3D-type), found in SR-related and CTD-associated factor 11 (SCAF11) and similar proteins; SCAF11, also known as CTD-associated SR protein 11 (CASP11), renal carcinoma antigen NY-REN-40, SC35-interacting protein 1 (Sip1), Serine/arginine-rich splicing factor 2 (SRSF2)-interacting protein, or splicing regulatory protein 129 (SRrp129), is a novel arginine-serine-rich (RS) domain-containing protein essential for pre-mRNA splicing. It functions as an auxiliary splice factor interacting with the spliceosomal component SC35, promoting RNAPII elongation. In addition to SR proteins, such as SC35, ASF/SF2, SRp75, and SRp20, SCAF11 also associates with U1-70K and U2AF65, proteins associated with 5' and 3' splice sites, respectively. SCAF11 contains an N-terminal modified C3HC3D-type RING-HC finger, an internal serine-arginine rich domain (SR domain), and a C-terminal SRI domain.

Pssm-ID: 438298 [Multi-domain] Cd Length: 52 Bit Score: 35.90 E-value: 2.97e-03

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 890799132  14 TCPVCLNLMVK---PVSADCGHTFCQGCITLYFESIKcdkemfSCPVCRLSYQS 64
Cdd:cd16636    2 RCPICLNCLLEqevAFPENCSHVFCLTCILKWAETVT------SCPIDRKPFQA 49

RING-HC_LNX4

cd16719

RING finger, HC subclass, found in ligand of numb protein X 4 (LNX4); LNX4, also known as PDZ ...

12-39

3.06e-03

RING finger, HC subclass, found in ligand of numb protein X 4 (LNX4); LNX4, also known as PDZ domain-containing RING finger protein 4 (PDZRN4), or SEMACAP3-like protein (SEMCAP3L), is an E3 ubiquitin-protein ligase responsible for the ubiquitination and degradation of Numb, a component of the Notch signaling pathway that functions in the specification of cell fates during development and is known to control cell numbers during neurogenesis in vertebrates. LNX4 contains an N-terminal C3HC4-type RING-HC finger, two PDZ domains, and a C-terminal LNX3 homology (LNX3H) domain.

Pssm-ID: 438379 [Multi-domain] Cd Length: 53 Bit Score: 35.67 E-value: 3.06e-03

                         10        20
                 ....*....|....*....|....*...
gi 890799132  12 EVTCPVCLNLMVKPVSADCGHTFCQGCI 39
Cdd:cd16719    4 DLKCKLCGKVLEEPLSTPCGHVFCAGCL 31

RING-HC_MuRF2

cd16760

RING finger, HC subclass, found in muscle-specific RING finger protein 2 (MuRF-2) and similar ...

10-59

3.08e-03

RING finger, HC subclass, found in muscle-specific RING finger protein 2 (MuRF-2) and similar proteins; MuRF-2, also known as tripartite motif-containing protein 55 (TRIM55) or RING finger protein 29 (RNF29), is a muscle-specific E3 ubiquitin-protein ligase in ubiquitin-mediated muscle protein turnover and is also a ligand of the transactivation domain of the serum response transcription factor (SRF). It is predominantly slow-fibre associated and highly expressed in embryonic skeletal muscle. MuRF-2 associates transiently with microtubules, myosin, and titin during sarcomere assembly. It has been implicated in microtubule, intermediate filament, and sarcomeric M-line maintenance in striated muscle development, as well as in signaling from the sarcomere to the nucleus. It plays an important role in the earliest stages of skeletal muscle differentiation and myofibrillogenesis. It is developmentally downregulated and is assembled at the M-line region of the sarcomere and with microtubules. MuRF-2 belongs to the C-II subclass of the TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a C3HC4-type RING-HC finger, Bbox2, and a coiled coil region, as well as a COS (carboxyl-terminal subgroup one signature) box, and an acidic residue-rich (AR) domain. It also harbors a MURF family-specific conserved box (MFC) between its RING-HC finger and Bbox domains.

Pssm-ID: 438417 [Multi-domain] Cd Length: 64 Bit Score: 36.12 E-value: 3.08e-03

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 890799132  10 KEEVTCPVCLNLMVKPVSA-DCGHTFCQGCITLYFE-----------SIKCDKEMFSCPVCR 59
Cdd:cd16760    1 EKQLICPICLEMFTKPVVIlPCQHNLCRKCANDIFQasnpylptrggTTVASGGRFRCPSCR 62

COG4372

Uncharacterized protein, contains DUF3084 domain [Function unknown];

126-340

3.21e-03

Uncharacterized protein, contains DUF3084 domain [Function unknown];

Pssm-ID: 443500 [Multi-domain] Cd Length: 370 Bit Score: 39.89 E-value: 3.21e-03

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 890799132 126 GHKTALIEEVAREYKEQLQVVLQRLMADKKEFENWKDELQKDRTYWE-------------NQIQKDVENVQSEFKRMRDI 192
Cdd:COG4372   23 GILIAALSEQLRKALFELDKLQEELEQLREELEQAREELEQLEEELEqarseleqleeelEELNEQLQAAQAELAQAQEE 102

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 890799132 193 IDSEEKnELQKLRQEKEDILN---NLAESESEHAQQSKLLEDFISDVEHQLQcsdiEILQGVENIIKRsltfsmkkpktI 269
Cdd:COG4372  103 LESLQE-EAEELQEELEELQKerqDLEQQRKQLEAQIAELQSEIAEREEELK----ELEEQLESLQEE-----------L 166

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 890799132 270 AREQRKFRAPDLQGMLQVLQE-VTEAQRYWVQVTLVQNNHPNIAITDDKRQVRYEDHQASNLIHECENSHEG 340
Cdd:COG4372  167 AALEQELQALSEAEAEQALDElLKEANRNAEKEEELAEAEKLIESLPRELAEELLEAKDSLEAKLGLALSAL 238

RING-HC_TRIM2

cd16767

RING finger, HC subclass, found in tripartite motif-containing protein 2 (TRIM2); TRIM2, also ...

10-59

3.30e-03

RING finger, HC subclass, found in tripartite motif-containing protein 2 (TRIM2); TRIM2, also known as RING finger protein 86 (RNF86), is an E3 ubiquitin-protein ligase that ubiquitinates the neurofilament light chain, a component of the intermediate filament in axons. Loss of function of TRIM2 results in early-onset axonal neuropathy. TRIM2 also plays a role in mediating the p42/p44 MAPK-dependent ubiquitination of the cell death-promoting protein Bcl-2-interacting mediator of cell death (Bim) in rapid ischemic tolerance. TRIM2 belongs to the C-VII subclass of the TRIM (tripartite motif)-NHL family that is defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a C3HC4-type RING-HC finger, Bbox1 and Bbox2, and a coiled coil domain, as well as a NHL (named after proteins NCL-1, HT2A and Lin-41 that contain repeats folded into a six-bladed beta propeller) repeat domain positioned C-terminal to the RBCC domain.

Pssm-ID: 438423 [Multi-domain] Cd Length: 51 Bit Score: 35.76 E-value: 3.30e-03

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|
gi 890799132  10 KEEVTCPVCLNLMVKPVSADCGHTFCQGCITLYfesIKCDKEMFSCPVCR 59
Cdd:cd16767    4 KQFLICSICLDRYKNPKVLPCLHTFCERCLQNY---IPAHSLTLSCPVCR 50

RING-HC_TRIM45_C-VII

cd16588

RING finger, HC subclass, found in tripartite motif-containing protein 45 (TRIM45) and similar ...

15-39

3.36e-03

RING finger, HC subclass, found in tripartite motif-containing protein 45 (TRIM45) and similar proteins; TRIM45, also known as RING finger protein 99 (RNF99), is a novel receptor for activated C-kinase (RACK1)-interacting protein that suppresses transcriptional activities of Elk-1 and AP-1 and downregulates mitogen-activated protein kinase (MAPK) signal transduction through inhibiting RACK1/PKC (protein kinase C) complex formation. It also negatively regulates tumor necrosis factor alpha (TNFalpha)-induced nuclear factor-kappaB (NF-kappa B)-mediated transcription and suppresses cell proliferation. TRIM45 belongs to the C-VII subclass of the TRIM (tripartite motif) family that is defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a C3HC4-type RING-HC finger, Bbox1 and Bbox2, and a coiled coil region, as well as a filamin-type immunoglobulin (IG-FLMN) domain and NHL repeats positioned C-terminal to the RBCC domain.

Pssm-ID: 438250 [Multi-domain] Cd Length: 59 Bit Score: 35.96 E-value: 3.36e-03

                         10        20
                 ....*....|....*....|....*
gi 890799132  15 CPVCLNLMVKPVSADCGHTFCQGCI 39
Cdd:cd16588    3 CPVCGKLFQEPRLLPCLHTLCSPCL 27

HlpA

COG2825

Periplasmic chaperone for outer membrane proteins, Skp family [Cell wall/membrane/envelope ...

132-237

3.57e-03

Periplasmic chaperone for outer membrane proteins, Skp family [Cell wall/membrane/envelope biogenesis, Posttranslational modification, protein turnover, chaperones];

Pssm-ID: 442073 [Multi-domain] Cd Length: 171 Bit Score: 38.28 E-value: 3.57e-03

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 890799132 132 IEEVAREYKEqLQVVLQRLmadKKEFENWKDELQKdrtywenqIQKDVENVQSEFKRMRDIIDSEEKNELQK-LRQEKED 210
Cdd:COG2825   31 VQRILQESPE-GKAAQKKL---EKEFKKRQAELQK--------LEKELQALQEKLQKEAATLSEEERQKKEReLQKKQQE 98

                         90       100
                 ....*....|....*....|....*...
gi 890799132 211 ILNNLAESESE-HAQQSKLLEDFISDVE 237
Cdd:COG2825   99 LQRKQQEAQQDlQKRQQELLQPILEKIQ 126

ClyA_Cry6Aa-like

cd22656

Bacillus thuringiensis crystal 6Aa (Cry6Aa) toxin, and similar proteins; This model includes ...

138-260

3.65e-03

Pssm-ID: 439154 [Multi-domain] Cd Length: 309 Bit Score: 39.28 E-value: 3.65e-03

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 890799132 138 EYKEQLQVVLQRLMADKKEFENWKDELQKDRTYWENQIQKDVENVQSEFKRMRDIIDSE----EKNELQKLRQEKEDILN 213
Cdd:cd22656  114 EAKKTIKALLDDLLKEAKKYQDKAAKVVDKLTDFENQTEKDQTALETLEKALKDLLTDEggaiARKEIKDLQKELEKLNE 193

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*....
gi 890799132 214 NLAEsesehAQQSKL--LEDFISDVEHQLQcsDIEILQGVENIIKRSLT 260
Cdd:cd22656  194 EYAA-----KLKAKIdeLKALIADDEAKLA--AALRLIADLTAADTDLD 235

RING-HC_TRIM2_like_C-VII

cd16586

RING finger, HC subclass, found in tripartite motif-containing protein TRIM2, TRIM3, and ...

13-59

3.82e-03

RING finger, HC subclass, found in tripartite motif-containing protein TRIM2, TRIM3, and similar proteins; TRIM2, also known as RING finger protein 86 (RNF86), is an E3 ubiquitin-protein ligase that ubiquitinates the neurofilament light chain, a component of the intermediate filament in axons. Loss of function of TRIM2 results in early-onset axonal neuropathy. TRIM3, also known as brain-expressed RING finger protein (BERP), RING finger protein 97 (RNF97), or RING finger protein 22 (RNF22), is an E3 ubiquitin-protein ligase involved in the pathogenesis of various cancers. It also plays an important role in the central nervous system (CNS). In addition, TRIM3 may be involved in vesicular trafficking via its association with the cytoskeleton-associated-recycling or transport (CART) complex that is necessary for efficient transferrin receptor recycling, but not for epidermal growth factor receptor (EGFR) degradation. Both TRIM2 and TRIM3 belong to the C-VII subclass of the TRIM (tripartite motif)-NHL family that is defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a C3HC4-type RING-HC finger, Bbox1 and Bbox2, and a coiled coil domain, as well as a NHL (named after proteins NCL-1, HT2A and Lin-41 that contain repeats folded into a six-bladed beta propeller) repeat domain positioned C-terminal to the RBCC domain.

Pssm-ID: 438248 [Multi-domain] Cd Length: 45 Bit Score: 35.50 E-value: 3.82e-03

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
gi 890799132  13 VTCPVCLNLMVKPVSADCGHTFCQGCITLYfesIKCDKEMFSCPVCR 59
Cdd:cd16586    2 LSCGICLERYKNPKVLPCLHTFCERCLQNY---IPAESLSLSCPVCR 45

COG4372

Uncharacterized protein, contains DUF3084 domain [Function unknown];

132-294

4.06e-03

Uncharacterized protein, contains DUF3084 domain [Function unknown];

Pssm-ID: 443500 [Multi-domain] Cd Length: 370 Bit Score: 39.50 E-value: 4.06e-03

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 890799132 132 IEEVAREYKeQLQVVLQRLMADKKEFENWKDELQKDRTYWENQIQKDVENVQSEFKRMRDIIDSEEKNELQKLRQEKEDI 211
Cdd:COG4372  117 LEELQKERQ-DLEQQRKQLEAQIAELQSEIAEREEELKELEEQLESLQEELAALEQELQALSEAEAEQALDELLKEANRN 195

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 890799132 212 LNNLAESESEHAQQSKLLEDFISDVEHQLQcSDIEILQGVENIIKRSLTFSMKKPKTIAREQRKFRAPDLQGMLQVLQEV 291
Cdd:COG4372  196 AEKEEELAEAEKLIESLPRELAEELLEAKD-SLEAKLGLALSALLDALELEEDKEELLEEVILKEIEELELAILVEKDTE 274


                 ...
gi 890799132 292 TEA 294
Cdd:COG4372  275 EEE 277

Bbox2_TRIM40_C-V

cd19781

B-box-type 2 zinc finger found in tripartite motif-containing protein 40 (TRIM40) and similar ...

96-134

4.17e-03

B-box-type 2 zinc finger found in tripartite motif-containing protein 40 (TRIM40) and similar proteins; TRIM40, also termed probable E3 NEDD8-protein ligase, or RING finger protein 35, may function as an E3 ubiquitin-protein ligase of the NEDD8 conjugation pathway. It promotes neddylation of IKBKG/NEMO, stabilizing NFKBIA, and inhibiting NF-kappaB nuclear translocation and activity. TRIM40 belongs to the C-V subclass of TRIM (tripartite motif) family of proteins that are defined by an N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a RING finger, Bbox2, and a coiled coil region. The type 2 B-box (Bbox2) zinc finger is characterized by a CHC3H2 zinc-binding consensus motif.

Pssm-ID: 380839 [Multi-domain] Cd Length: 44 Bit Score: 35.09 E-value: 4.17e-03

                         10        20        30
                 ....*....|....*....|....*....|....*....
gi 890799132  96 CARHGEKLQLFCRKDMMAICWLCERSQEHRGHKTALIEE 134
Cdd:cd19781    5 CQLHEKKVEWFCEEDQVLLCEECLKSPEHQSHHVLTIED 43

RING-HC_RBR_TRIAD1

cd16773

RING finger, HC subclass, found in two RING fingers and DRIL [double RING finger linked] 1 ...

13-45

4.24e-03

RING finger, HC subclass, found in two RING fingers and DRIL [double RING finger linked] 1 (TRIAD1); TRIAD1, also known as ariadne-2 (ARI-2), protein ariadne-2 homolog, Ariadne RBR E3 ubiquitin protein ligase 2 (ARIH2), or UbcM4-interacting protein 48, is an RBR-type E3 ubiquitin-protein ligase that catalyzes the formation of polyubiquitin chains linked via lysine-48, as well as lysine-63 residues. Its auto-ubiquitylation can be catalyzed by the E2 conjugating enzyme UBCH7. TRIAD1 has been implicated in hematopoiesis, specifically in myelopoiesis, as well as in embryogenesis. It functions as a regulator of endosomal transport and is required for the proper function of multivesicular bodies. It also acts as a novel ubiquitination target for proteasome-dependent degradation by murine double minute 2 (MDM2). As a proapoptotic protein, TRIAD1 promotes p53 activation, and inhibits MDM2-mediated p53 ubiquitination and degradation. Furthermore, TRIAD1 can inhibit the ubiquitination and proteasomal degradation of growth factor independence 1 (Gfi1), a transcriptional repressor essential for the function and development of many different hematopoietic lineages. TRIAD1 contains an RBR domain that was previously known as RING-BetweenRING-RING domain or TRIAD [two RING fingers and a DRIL (double RING finger linked)] domain. Based on current understanding of the structural biology of RBR ligases, the nomenclature of RBR has been corrected as RING-BRcat (benign-catalytic)-Rcat (required-for-catalysis) recently. The RBR (RING1-BRcat-Rcat) domain uses an auto-inhibitory mechanism to modulate ubiquitination activity, as well as a hybrid mechanism that combines aspects from both RING and HECT E3 ligase function to facilitate the ubiquitination reaction. This model corresponds to the RING domain, a C3HC4-type RING-HC finger required for RBR-mediated ubiquitination.

Pssm-ID: 438429 [Multi-domain] Cd Length: 54 Bit Score: 35.41 E-value: 4.24e-03

                         10        20        30
                 ....*....|....*....|....*....|....*
gi 890799132  13 VTCPVCLNLMVKPV--SADCGHTFCQGCITLYFES 45
Cdd:cd16773    1 VTCGVCCEDVPKDElfSLACGHYFCNDCWKQYLTV 35

RING-HC_RNF151

cd16547

RING finger, HC subclass, found in RING finger protein 151 (RNF151) and similar proteins; ...

15-59

4.42e-03

RING finger, HC subclass, found in RING finger protein 151 (RNF151) and similar proteins; RNF151 is a testis-specific RING finger protein that interacts with dysbindin, a synaptic and microtubular protein that binds brain snapin, a SNARE-binding protein that mediates intracellular membrane fusion in both neuronal and non-neuronal cells. Thus, it may be involved in acrosome formation of spermatids by interacting with multiple proteins participating in membrane biogenesis and microtubule organization. RNF151 contains a C3HC4-type RING finger domain, a putative nuclear localization signal (NLS), and a TNF receptor associated factor (TRAF)-type zinc finger domain.

Pssm-ID: 438209 [Multi-domain] Cd Length: 49 Bit Score: 35.13 E-value: 4.42e-03

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*
gi 890799132  15 CPVCLNLMVKPVSADCGHTFCQGCITLYFesikcdKEMFSCPVCR 59
Cdd:cd16547    6 CSICHGVLRCPVRLSCSHIFCKKCILQWL------KRQETCPCCR 44

RING-HC_RNF185

cd16744

RING finger, HC subclass, found in RING finger protein 185 (RNF185) and similar proteins; ...

15-69

4.67e-03

RING finger, HC subclass, found in RING finger protein 185 (RNF185) and similar proteins; RNF185 is an E3 ubiquitin-protein ligase of endoplasmic reticulum-associated degradation (ERAD) that targets cystic fibrosis transmembrane conductance regulator (CFTR). It controls the degradation of CFTR and CFTR F508del allele in a RING- and proteasome-dependent manner, but does not control that of other classical ERAD model substrates. It also negatively regulates osteogenic differentiation by targeting dishevelled2 (Dvl2), a key mediator of the Wnt signaling pathway, for degradation. Moreover, RNF185 regulates selective mitochondrial autophagy through interaction with the Bcl-2 family protein BNIP1. It also plays an important role in cell adhesion and migration through the modulation of cell migration by ubiquitinating paxillin. RNF185 contains a C3HC4-type RING-HC finger.

Pssm-ID: 438402 [Multi-domain] Cd Length: 57 Bit Score: 35.29 E-value: 4.67e-03

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 890799132  15 CPVCLNLMVKPVSADCGHTFCQGCITLYFESIKCDKemfSCPVCRLSYQSSNLRP 69
Cdd:cd16744    3 CNICLDTAKDAVVSLCGHLFCWPCLHQWLETRPNRQ---VCPVCKAGISRDKVIP 54

RING-HC_MuRF1

cd16759

RING finger, HC subclass, found in muscle-specific RING finger protein 1 (MuRF-1) and similar ...

10-59

4.74e-03

RING finger, HC subclass, found in muscle-specific RING finger protein 1 (MuRF-1) and similar proteins; MuRF-1, also known as tripartite motif-containing protein 63 (TRIM63), RING finger protein 28 (RNF28), iris RING finger protein, or striated muscle RING zinc finger, is an E3 ubiquitin-protein ligase in ubiquitin-mediated muscle protein turnover. It is predominantly fast (type II) fibre-associated in skeletal muscle and can bind to many myofibrillar proteins, including titin, nebulin, the nebulin-related protein NRAP, troponin-I (TnI), troponin-T (TnT), myosin light chain 2 (MLC-2), myotilin, and T-cap. The early and robust upregulation of MuRF-1 is triggered by disuse, denervation, starvation, sepsis, or steroid administration resulting in skeletal muscle atrophy. It also plays a role in maintaining titin M-line integrity. It associates with the periphery of the M-line lattice and may be involved in the regulation of the titin kinase domain. It also participates in muscle stress response pathways and gene expression. MuRF-1 belongs to the C-II subclass of the TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a C3HC4-type RING-HC finger, Bbox2, and a coiled coil region, as well as a COS (carboxyl-terminal subgroup one signature) box, and an acidic residue-rich (AR) domain. It also harbors a MURF family-specific conserved box (MFC) between its RING-HC finger and Bbox domains.

Pssm-ID: 319673 [Multi-domain] Cd Length: 63 Bit Score: 35.77 E-value: 4.74e-03

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 890799132  10 KEEVTCPVCLNLMVKPVSA-DCGHTFCQGCITLYFE-----------SIKCDKEMFSCPVCR 59
Cdd:cd16759    1 EKQLICPICLEMFTKPVVIlPCQHNLCRKCANDIFQaanpywqsrgtSMLGSGGRFRCPSCR 62

mRING-HC-C3HC3D_TRAF5

cd16642

Modified RING finger, HC subclass (C3HC3D-type), found in tumor necrosis factor (TNF) ...

9-57

5.32e-03

Modified RING finger, HC subclass (C3HC3D-type), found in tumor necrosis factor (TNF) receptor-associated factor 5 (TRAF5) and similar proteins; TRAF5, also known as RING finger protein 84 (RNF84), is an important signal transducer for a wide range of TNF receptor superfamily members, including tumor necrosis factor receptor 1 (TNFR1), TNFR2, CD40, and other lymphocyte costimulatory receptors, RANK/TRANCE-R, ectodysplasin-A Receptor (EDAR), lymphotoxin-beta receptor (LT-betaR), latent membrane protein 1 (LMP1), and IRE1. It functions as an activator of NF-kappaB, MAPK, and JNK, and is involved in both RANKL- and TNFalpha-induced osteoclastogenesis. It mediates CD40 signaling by associating with the cytoplasmic tail of CD40. It also negatively regulates Toll-like receptor (TLR) signaling and functions as a negative regulator of the interleukin 6 (IL-6) receptor signaling pathway that limits the differentiation of inflammatory CD4(+) T cells. TRAF5 contains an N-terminal domain with a modified C3HC3D-type RING-HC finger and several zinc fingers, and a C-terminal TRAF domain that comprises a coiled coil domain and a conserved TRAF-C domain.

Pssm-ID: 438304 [Multi-domain] Cd Length: 56 Bit Score: 35.11 E-value: 5.32e-03

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*....
gi 890799132   9 LKEEVTCPVCLNLMVKPVSADCGHTFCQGCITLYFEsikcDKEMFSCPV 57
Cdd:cd16642    1 LEDRYKCATCHFVLHNPHQTGCGHRFCQHCILSLLE----LNTTPICPI 45

RING-HC_MuRF_C-II

cd16577

RING finger, HC subclass, found in muscle-specific RING finger proteins TRIM63/MuRF-1, TRIM55 ...

15-59

7.55e-03

RING finger, HC subclass, found in muscle-specific RING finger proteins TRIM63/MuRF-1, TRIM55/MuRF-2 and TRIM54/MuRF-3; This subfamily corresponds to a group of striated muscle-specific tripartite motif (TRIM) proteins, including TRIM63/MuRF-1, TRIM55/MuRF-2, and TRIM54/MuRF-3, which function as E3 ubiquitin ligases in ubiquitin-mediated muscle protein turnover. They are tightly developmentally regulated in skeletal muscle and associate with different cytoskeleton components, such as microtubules, Z-disks and M-bands, as well as with metabolic enzymes and nuclear proteins. They also cooperate with diverse proteins implicated in selective protein degradation by the proteasome and autophagosome, and target proteins of metabolic regulation, sarcomere assembly and transcriptional regulation. Moreover, MURFs display variable fibre-type preferences. TRIM63/MuRF-1 is predominantly fast (type II) fibre-associated in skeletal muscle. TRIM55/MuRF-2 is predominantly slow-fibre associated. TRIM54/MuRF-3 is ubiquitously present. They play an active role in microtubule-mediated sarcomere assembly. MuRFs belong to the C-II subclass of the TRIM family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a C3HC4-type RING-HC finger, Bbox2, and a coiled coil region, as well as a COS (carboxyl-terminal subgroup one signature) box, and an acidic residue-rich (AR) domain positioned C-terminal to the RBCC domain. They also harbor a MURF family-specific conserved box (MFC) between its RING-HC finger and Bbox domains.

Pssm-ID: 438239 [Multi-domain] Cd Length: 56 Bit Score: 34.87 E-value: 7.55e-03

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 890799132  15 CPVCLNLMVKPVSA-DCGHTFCQGCITLYFES--------IKCDKEMFSCPVCR 59
Cdd:cd16577    3 CPICLEMFTKPVVIlPCQHNLCRKCANDIFQArnpywpttTMGSGGRFRCPSCR 56

PspA

COG1842

Phage shock protein A [Transcription, Signal transduction mechanisms];

130-241

7.80e-03

Phage shock protein A [Transcription, Signal transduction mechanisms];

Pssm-ID: 441447 [Multi-domain] Cd Length: 217 Bit Score: 37.88 E-value: 7.80e-03

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 890799132 130 ALIEEVAREYKEQLQVVLQ---RLMADKKEFENWKDELQKDRTYWENQ----IQKDVENVQSEFkrmrdiidSEEKNELQ 202
Cdd:COG1842   26 KMLDQAIRDMEEDLVEARQalaQVIANQKRLERQLEELEAEAEKWEEKarlaLEKGREDLAREA--------LERKAELE 97

                         90       100       110
                 ....*....|....*....|....*....|....*....
gi 890799132 203 KLRQEKEDILNNLAESESEHAQQSKLLEDFISDVEHQLQ 241
Cdd:COG1842   98 AQAEALEAQLAQLEEQVEKLKEALRQLESKLEELKAKKD 136

YhaN

COG4717

Uncharacterized conserved protein YhaN, contains AAA domain [Function unknown];

117-228

7.94e-03

Uncharacterized conserved protein YhaN, contains AAA domain [Function unknown];

Pssm-ID: 443752 [Multi-domain] Cd Length: 641 Bit Score: 38.98 E-value: 7.94e-03

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 890799132 117 LCERSQEHRGHKTALIEEV--AREYKEQLQVVLQRLMADKKEFENWKDELQKDRTYWENQIQKDVENVQSEFKRMRDIId 194
Cdd:COG4717  130 LYQELEALEAELAELPERLeeLEERLEELRELEEELEELEAELAELQEELEELLEQLSLATEEELQDLAEELEELQQRL- 208

                         90       100       110
                 ....*....|....*....|....*....|....
gi 890799132 195 SEEKNELQKLRQEKEDILNNLAESESEHAQQSKL 228
Cdd:COG4717  209 AELEEELEEAQEELEELEEELEQLENELEAAALE 242

RING-HC_RNF4

cd16533

RING finger, HC subclass, found in RING finger protein 4 (RNF4) and similar proteins; RNF4, ...

13-59

8.61e-03

RING finger, HC subclass, found in RING finger protein 4 (RNF4) and similar proteins; RNF4, also known as small nuclear ring finger protein (SNURF), is a SUMO-targeted E3 ubiquitin-protein ligase with a pivotal function in the DNA damage response (DDR) by interacting with the deubiquitinating enzyme ubiquitin-specific protease 11 (USP11), a known DDR-component, and further facilitating DNA repair. It plays a novel role in preventing the loss of intact chromosomes and ensures the maintenance of chromosome integrity. Moreover, RNF4 is responsible for the UbcH5A-catalyzed formation of K48 chains that target SUMO-modified promyelocytic leukemia (PML) protein for proteasomal degradation in response to arsenic treatment. It also interacts with telomeric repeat binding factor 2 (TRF2) in a small ubiquitin-like modifier (SUMO)-dependent manner and preferentially targets SUMO-conjugated TRF2 for ubiquitination through SUMO-interacting motifs (SIMs). Furthermore, RNF4 can form a complex with a Ubc13-ubiquitin conjugate and Ube2V2. It catalyzes K63-linked polyubiquitination by the Ube2V2-Ubc13 (ubiquitin-loaded) complex. Meanwhile, RNF4 negatively regulates nuclear factor kappa B (NF-kappaB) signaling by down-regulating transforming growth factor beta (TGF-beta)-activated kinase 1 (TAK1)-TAK1-binding protein2 (TAB2). RNF4 contains four SIMs followed by a C3HC4-type RING-HC finger at the C-terminus.

Pssm-ID: 438195 [Multi-domain] Cd Length: 57 Bit Score: 34.87 E-value: 8.61e-03

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 890799132  13 VTCPVCLNLMVK-------PVSADCGHTFCQGCITlyfESIkcdKEMFSCPVCR 59
Cdd:cd16533    4 VSCPICMDGYSEivqsgrlIVSTECGHVFCSQCLR---DSL---KNANTCPTCR 51

RING-HC_PML_C-V

cd16579

RING finger, HC subclass, found in promyelocytic leukemia protein (PML) and similar proteins; ...

14-59

9.14e-03

RING finger, HC subclass, found in promyelocytic leukemia protein (PML) and similar proteins; Protein PML, also known as RING finger protein 71 (RNF71) or tripartite motif-containing protein 19 (TRIM19), is predominantly a nuclear protein with a broad intrinsic antiviral activity. It is the eponymous component of PML nuclear bodies (PML NBs) and has been implicated in a wide variety of cell processes, including DNA damage signaling, apoptosis, and transcription. PML interferes with the replication of many unrelated viruses, including human immunodeficiency virus 1 (HIV-1), human foamy virus (HFV), poliovirus, influenza virus, rabies virus, EMCV, adeno-associated virus (AAV), and vesicular stomatitis virus (VSV). It also selectively interacts with misfolded proteins through distinct substrate recognition sites and conjugates these proteins with the small ubiquitin-like modifiers (SUMOs) through its SUMO ligase activity. PML belongs to the C-V subclass of the TRIM (tripartite motif) family of proteins that are defined by an N-terminal RBCC (RING, Bbox, and coiled coil) domain, including three consecutive zinc-binding domains, a C3HC4-type RING-HC finger, Bbox1 and Bbox2, and a coiled coil region, as well as an uncharacterized region positioned C-terminal to the RBCC domain.

Pssm-ID: 438241 [Multi-domain] Cd Length: 52 Bit Score: 34.45 E-value: 9.14e-03

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*.
gi 890799132  14 TCPVCLNLMVKPVSADCGHTFCQGCITlYFESIKCDKEMFSCPVCR 59
Cdd:cd16579    6 RCPGCKAEYKCPKLLPCLHTVCSGCLE-ALAEQASETTEFQCPICK 50

RING-HC_SpRad8-like

cd16572

RING finger, HC subclass, found in Schizosaccharomyces pombe DNA repair protein Rad8 (SpRad8) ...

15-59

9.28e-03

RING finger, HC subclass, found in Schizosaccharomyces pombe DNA repair protein Rad8 (SpRad8) and similar proteins; SpRad8 is a conserved protein homologous to Saccharomyces cerevisiae DNA repair protein Rad5 and human helicase-like transcription factor (HLTF) that is required for error-free postreplication repair by contributing to polyubiquitylation of PCNA. SpRad8 contains a C3HC4-type RING-HC finger responsible for the E3 ubiquitin ligase activity, a SNF2-family helicase domain including an ATP binding site, and a family-specific HIRAN domain (HIP116, Rad5p N-terminal domain) that contributes to nuclear localization.

Pssm-ID: 438234 [Multi-domain] Cd Length: 61 Bit Score: 34.79 E-value: 9.28e-03

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*.
gi 890799132  15 CPVCLN-LMVKPVSADCGHTFCQGCITLYFESIKCDKEMFSCPVCR 59
Cdd:cd16572    7 CPICAEePISELALTRCWHSACKDCLLDHIEFQKSKNEVPLCPTCR 52

Blast search parameters

Data Source:	Precalculated data, version = cdd.v.3.21
Preset Options:	Database: CDSEARCH/cdd Low complexity filter: no Composition Based Adjustment: yes E-value threshold: 0.01