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Conserved domains on  [gi|242086515|ref|XP_002439090|]
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Protein Classification

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List of domain hits

Name Accession Description Interval E-value
SAD_SRA pfam02182
SAD/SRA domain; The domain goes by several names including SAD, SRA and YDG. It adopts a beta ...
245-407 3.01e-71

SAD/SRA domain; The domain goes by several names including SAD, SRA and YDG. It adopts a beta barrel, modified PUA-like, fold that is widely present in eukaryotic chromatin proteins and in bacteria. Versions of this domain are known to bind hemi-methylated CpG dinucleotides and also other 5mC containing dinucleotides. The domain binds DNA by flipping out the methylated cytosine base from the DNA double helix.The conserved tyrosine and aspartate residues and a glycine rich patch are critical for recognition of the flipped out base. Mammalian UHRF1 that contains this domain plays an important role in maintenance of methylation at CpG dinucleotides by recruiting DNMT1 to hemimethylated sites associated with replication forks. The SAD/SRA domain has been combined with other domains involved in the ubiquitin pathway on multiple occasions and such proteins link recognition of DNA methylation to chromatin-protein ubiquitination. The domain is also found in species that lack DNA methylation, such as certain apicomplexans, suggestive of other DNA-binding modes or functions. A highly derived and distinct version of the domain is also found in fungi where it is fused to AlkB-type 2OGFeDO domains. In bacteria, the domain is usually fused or associated with restriction endonucleases, many of which target methylated or hemi-methylated DNA.


:

Pssm-ID: 334835  Cd Length: 147  Bit Score: 229.32  E-value: 3.01e-71
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 242086515  245 HFGPIlaendPrrsiGVRVGETWEDRLECRQWGAHFPHVAGIAGQSTYGAQSVALSGGYEDDEDHGEWFLYTGSGGRDLS 324
Cdd:pfam02182   1 IFGHV-----P----GVEVGDIFPSRAELSAVGLHRPPQAGIDGMKEEGAYSIVLSGGYEDDEDNGDVLIYTGSGGRDDK 71
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 242086515  325 gnkrtnKEQSSDQKFEKLNAALRISCLKGYPVRVVRSHKEKRSSYAPESGVRYDGVYRIEKCWRKIGIQGkFKVCRYLFV 404
Cdd:pfam02182  72 ------KGQSEDQKLERGNLALANSMETGNPVRVIRGSKGKKSKYAPEKGYRYDGLYKVVKYWREKGKSG-FKVFKFKLV 144

                  ...
gi 242086515  405 RCD 407
Cdd:pfam02182 145 RLP 147
RING-HC cd16449
HC subclass of RING (RING-HC) finger and its variants; RING finger is a specialized type of ...
128-166 3.64e-09

HC subclass of RING (RING-HC) finger and its variants; 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 HC subclass of RING (RING-HC) finger proteins 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 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 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: 319363 [Multi-domain]  Cd Length: 39  Bit Score: 52.47  E-value: 3.64e-09
                         10        20        30
                 ....*....|....*....|....*....|....*....
gi 242086515 128 CVFCMKLPDRPVTTPCGHNFCLKCFQKWIQNRKRTCAKC 166
Cdd:cd16449    1 CPICLELLKDPVLLPCGHTFCRSCLRRLLKEGKKKCPIC 39
RING_Ubox super family cl17238
The superfamily of RING finger (Really Interesting New Gene) domain and U-box domain; RING ...
497-559 2.58e-08

The superfamily of RING finger (Really Interesting New Gene) domain and U-box domain; 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 as 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 pattern. Some lack a single Cys or His residues at typical Zn ligand positions. Especially, 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 finger. In contrast, C4HC3- (RING-CH alias RINGv), C3H3C2-, C3H2C2D-, C3DHC3-, and C4HC2H-type RING fingers are close to RING-H2 finger. However, not all RING finger-containing proteins display regular RING finger features, and the RING finger family has turned out to be multifarious. The degenerated RING fingers from 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. 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 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.


The actual alignment was detected with superfamily member cd16613:

Pssm-ID: 354325 [Multi-domain]  Cd Length: 46  Bit Score: 50.47  E-value: 2.58e-08
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 242086515 497 FGCSICRAVIKEPLTTPCAHNFCKTCLlgkydsqssmrersrgGRTLRAQkiVKTCPSCPTDI 559
Cdd:cd16613    1 FTCICCQEVVYQPITTPCQHNVCKGCL----------------QRSFKAE--VYSCPACRHDL 45
PHD_SF super family cl22851
PHD finger superfamily; The PHD finger superfamily includes a canonical plant homeodomain (PHD) ...
12-57 1.54e-04

PHD finger superfamily; The PHD finger superfamily includes a canonical plant homeodomain (PHD) finger typically characterized as Cys4HisCys3, and a non-canonical extended PHD finger, characterized as Cys2HisCys5HisCys2His. Variations include the RAG2 PHD finger characterized by Cys3His2Cys2His and the PHD finger 5 found in nuclear receptor-binding SET domain-containing proteins characterized by Cys4HisCys2His. The PHD finger is also termed LAP (leukemia-associated protein) motif or TTC (trithorax consensus) domain. Single or multiple copies of PHD fingers have been found in a variety of eukaryotic proteins involved in the control of gene transcription and chromatin dynamics. PHD fingers can recognize the unmodified and modified histone H3 tail, and some have been found to interact with non-histone proteins. They also function as epigenome readers controlling gene expression through molecular recruitment of multi-protein complexes of chromatin regulators and transcription factors. The PHD finger domain SF is structurally similar to the RING and FYVE_like superfamilies.


The actual alignment was detected with superfamily member cd15544:

Pssm-ID: 354958  Cd Length: 46  Bit Score: 39.70  E-value: 1.54e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*.
gi 242086515  12 CMVCRAASPPEvDLLRCSTCATPWHSPCLSKPPALADAASWSCPDC 57
Cdd:cd15544    2 CKVCRKKGDPD-NMILCDGCDKAFHLYCLRPALREVPSGDWFCPAC 46
PEX10 super family cl27118
RING-finger-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, ...
446-532 3.25e-03

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


The actual alignment was detected with superfamily member COG5574:

Pssm-ID: 227861 [Multi-domain]  Cd Length: 271  Bit Score: 39.88  E-value: 3.25e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 242086515 446 WDYDEKDGWKW---MVPPPVSKKPVLSGDPETDKQIRRSTkrahlsvaerlLKEFGCSICRAVIKEPLTTPCAHNFCKTC 522
Cdd:COG5574  173 LSLDESRLQPIlqpSNNLHTLFQVITKENLSKKNGLPFIP-----------LADYKCFLCLEEPEVPSCTPCGHLFCLSC 241
                         90
                 ....*....|
gi 242086515 523 LLGKYDSQSS 532
Cdd:COG5574  242 LLISWTKKKY 251
HRD1 super family cl34953
HRD ubiquitin ligase complex, ER membrane component [Posttranslational modification, protein ...
128-222 5.27e-03

HRD ubiquitin ligase complex, ER membrane component [Posttranslational modification, protein turnover, chaperones];


The actual alignment was detected with superfamily member COG5243:

Pssm-ID: 227568 [Multi-domain]  Cd Length: 491  Bit Score: 39.95  E-value: 5.27e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 242086515 128 CVFCMK-------------LPDRPVTTPCGHNFCLKCFQKWIQnRKRTCAKCRAQIPAKMaEQPRINSALVEVIRMAKIS 194
Cdd:COG5243  290 CTICMDemfhpdheplprgLDMTPKRLPCGHILHLHCLKNWLE-RQQTCPICRRPVIFDQ-SSPTPASPNVRNTQIATQV 367
                         90       100       110
                 ....*....|....*....|....*....|
gi 242086515 195 KNPNSAGSAVPYHYIRN--DDRPDKAFTTD 222
Cdd:COG5243  368 PNPDNTPTTTAVPGITNssNQGDPQASTFN 397
 
Name Accession Description Interval E-value
SAD_SRA pfam02182
SAD/SRA domain; The domain goes by several names including SAD, SRA and YDG. It adopts a beta ...
245-407 3.01e-71

SAD/SRA domain; The domain goes by several names including SAD, SRA and YDG. It adopts a beta barrel, modified PUA-like, fold that is widely present in eukaryotic chromatin proteins and in bacteria. Versions of this domain are known to bind hemi-methylated CpG dinucleotides and also other 5mC containing dinucleotides. The domain binds DNA by flipping out the methylated cytosine base from the DNA double helix.The conserved tyrosine and aspartate residues and a glycine rich patch are critical for recognition of the flipped out base. Mammalian UHRF1 that contains this domain plays an important role in maintenance of methylation at CpG dinucleotides by recruiting DNMT1 to hemimethylated sites associated with replication forks. The SAD/SRA domain has been combined with other domains involved in the ubiquitin pathway on multiple occasions and such proteins link recognition of DNA methylation to chromatin-protein ubiquitination. The domain is also found in species that lack DNA methylation, such as certain apicomplexans, suggestive of other DNA-binding modes or functions. A highly derived and distinct version of the domain is also found in fungi where it is fused to AlkB-type 2OGFeDO domains. In bacteria, the domain is usually fused or associated with restriction endonucleases, many of which target methylated or hemi-methylated DNA.


Pssm-ID: 334835  Cd Length: 147  Bit Score: 229.32  E-value: 3.01e-71
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 242086515  245 HFGPIlaendPrrsiGVRVGETWEDRLECRQWGAHFPHVAGIAGQSTYGAQSVALSGGYEDDEDHGEWFLYTGSGGRDLS 324
Cdd:pfam02182   1 IFGHV-----P----GVEVGDIFPSRAELSAVGLHRPPQAGIDGMKEEGAYSIVLSGGYEDDEDNGDVLIYTGSGGRDDK 71
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 242086515  325 gnkrtnKEQSSDQKFEKLNAALRISCLKGYPVRVVRSHKEKRSSYAPESGVRYDGVYRIEKCWRKIGIQGkFKVCRYLFV 404
Cdd:pfam02182  72 ------KGQSEDQKLERGNLALANSMETGNPVRVIRGSKGKKSKYAPEKGYRYDGLYKVVKYWREKGKSG-FKVFKFKLV 144

                  ...
gi 242086515  405 RCD 407
Cdd:pfam02182 145 RLP 147
SRA smart00466
SET and RING finger associated domain; Domain of unknown function in SET domain containing ...
242-409 1.64e-62

SET and RING finger associated domain; Domain of unknown function in SET domain containing proteins and in Deinococcus radiodurans DRA1533.


Pssm-ID: 197742  Cd Length: 155  Bit Score: 206.45  E-value: 1.64e-62
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 242086515   242 APDHFGPIlaendPrrsiGVRVGETWEDRLECRQWGAHFPHVAGIAGQST----YGAQSVALSGGYEDDEDHGEWFLYTG 317
Cdd:smart00466   1 MKRIFGPV-----P----GVEVGDIFFYRVELCLVGLHRPTQAGIDGLESdegePGATSVVSSGGYEDDTDDGDVLIYTG 71
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 242086515   318 SGGRDlsgnkRTNKeQSSDQKFEKLNAALRISCLKGYPVRVVRSHKeKRSSYAPESGVRYDGVYRIEKCWRKIGIQGkFK 397
Cdd:smart00466  72 QGGRD-----MTHG-QPEDQKLERGNLALEASCRKGIPVRVVRGMK-GYSKYAPGKGYIYDGLYRIVDYWREVGKSG-FL 143
                          170
                   ....*....|..
gi 242086515   398 VCRYLFVRCDNE 409
Cdd:smart00466 144 VFKFKLVRIPGQ 155
RING-HC cd16449
HC subclass of RING (RING-HC) finger and its variants; RING finger is a specialized type of ...
128-166 3.64e-09

HC subclass of RING (RING-HC) finger and its variants; 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 HC subclass of RING (RING-HC) finger proteins 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 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 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: 319363 [Multi-domain]  Cd Length: 39  Bit Score: 52.47  E-value: 3.64e-09
                         10        20        30
                 ....*....|....*....|....*....|....*....
gi 242086515 128 CVFCMKLPDRPVTTPCGHNFCLKCFQKWIQNRKRTCAKC 166
Cdd:cd16449    1 CPICLELLKDPVLLPCGHTFCRSCLRRLLKEGKKKCPIC 39
RING smart00184
Ring finger; E3 ubiquitin-protein ligase activity is intrinsic to the RING domain of c-Cbl and ...
128-166 1.68e-08

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: 50.59  E-value: 1.68e-08
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|
gi 242086515   128 CVFCM-KLPDRPVTTPCGHNFCLKCFQKWIQNRKRTCAKC 166
Cdd:smart00184   1 CPICLeEYLKDPVILPCGHTFCRSCIRKWLESGNNTCPIC 40
RING-HC_UHRF cd16613
RING finger, HC subclass, found in ubiquitin-like PHD and RING finger domain-containing ...
497-559 2.58e-08

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: 319527 [Multi-domain]  Cd Length: 46  Bit Score: 50.47  E-value: 2.58e-08
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 242086515 497 FGCSICRAVIKEPLTTPCAHNFCKTCLlgkydsqssmrersrgGRTLRAQkiVKTCPSCPTDI 559
Cdd:cd16613    1 FTCICCQEVVYQPITTPCQHNVCKGCL----------------QRSFKAE--VYSCPACRHDL 45
zf-RING_2 pfam13639
Ring finger domain;
126-167 3.45e-07

Ring finger domain;


Pssm-ID: 338865 [Multi-domain]  Cd Length: 44  Bit Score: 47.00  E-value: 3.45e-07
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 242086515  126 FSCVFC---MKLPDRPVTTPCGHNFCLKCFQKWIQnRKRTCAKCR 167
Cdd:pfam13639   1 DECPICleeFEEGDKVVILPCGHHFHRECLDKWLR-SSNTCPLCR 44
PEX10 COG5574
RING-finger-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, ...
125-168 2.38e-06

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


Pssm-ID: 227861 [Multi-domain]  Cd Length: 271  Bit Score: 49.51  E-value: 2.38e-06
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*
gi 242086515 125 NFSCVFCMKLPDRPVTTPCGHNFCLKC-FQKWIQNRKRTCAKCRA 168
Cdd:COG5574  215 DYKCFLCLEEPEVPSCTPCGHLFCLSClLISWTKKKYEFCPLCRA 259
zf-C3HC4 pfam00097
Zinc finger, C3HC4 type (RING finger); The C3HC4 type zinc-finger (RING finger) is a ...
499-555 1.46e-04

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: 333836 [Multi-domain]  Cd Length: 40  Bit Score: 39.65  E-value: 1.46e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 242086515  499 CSICRAVIKEPL-TTPCAHNFCKTCLLgkydsqSSMRERSRggrtlraqkivkTCPSC 555
Cdd:pfam00097   1 CPICLEEPKDPVtILPCGHLFCSKCIL------SWLESGNV------------TCPLC 40
PHD_BAZ1A_like cd15544
PHD finger found in bromodomain adjacent to zinc finger domain protein BAZ1A and BAZ1B; BAZ1A, ...
12-57 1.54e-04

PHD finger found in bromodomain adjacent to zinc finger domain protein BAZ1A and BAZ1B; BAZ1A, also termed ATP-dependent chromatin-remodeling protein, or ATP-utilizing chromatin assembly and remodeling factor 1 (ACF1), or CHRAC subunit ACF1, or Williams syndrome transcription factor-related chromatin-remodeling factor 180 (WCRF180), or WALp1, is a subunit of the conserved imitation switch (ISWI)-family ATP-dependent chromatin assembly and remodeling factor (ACF)/chromatin accessibility complex (CHRAC) chromatin remodeling complex, which is required for DNA replication through heterochromatin. It alters the remodeling properties of the ATPase motor protein sucrose nonfermenting-2 homolog (SNF2H). Moreover, BAZ1A and its complexes play important roles in DNA double-strand break (DSB) repair. It is essential for averting improper gene expression during spermatogenesis. It also regulates transcriptional repression of vitamin D3 receptor-regulated genes. BAZ1B, also termed Tyrosine-protein kinase BAZ1B, or Williams syndrome transcription factor (WSTF), or Williams-Beuren syndrome chromosomal region 10 protein, Williams-Beuren syndrome chromosomal region 9 protein, or WALp2, is a multifunctional protein implicated in several nuclear processes, including replication, transcription, and the DNA damage response. BAZ1B/WSTF, together with the imitation switch (ISWI) ATPase, forms a WSTF-ISWI chromatin remodeling complex (WICH), which transiently associates with the human inactive X chromosome (Xi) during late S-phase prior to BRCA1 and gamma-H2AX. Moreover, BAZ1B/WSTF, SNF2h, and nuclear myosin 1 (NM1) forms the chromatin remodeling complex B-WICH that is involved in regulating rDNA transcription. Both BAZ1A and BAZ1B contain a WAC motif, a DDT domain, BAZ 1 and BAZ 2 motifs, a WAKZ (WSTF/Acf1/KIAA0314/ZK783.4) motif, a plant homeodomain (PHD) finger, and a bromodomain.


Pssm-ID: 277019  Cd Length: 46  Bit Score: 39.70  E-value: 1.54e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*.
gi 242086515  12 CMVCRAASPPEvDLLRCSTCATPWHSPCLSKPPALADAASWSCPDC 57
Cdd:cd15544    2 CKVCRKKGDPD-NMILCDGCDKAFHLYCLRPALREVPSGDWFCPAC 46
PHD smart00249
PHD zinc finger; The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in ...
11-57 2.74e-04

PHD zinc finger; The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in epigenetics and chromatin-mediated transcriptional regulation. The PHD finger binds two zinc ions using the so-called 'cross-brace' motif and is thus structurally related to the RING finger and the FYVE finger. It is not yet known if PHD fingers have a common molecular function. Several reports suggest that it can function as a protein-protein interacton domain and it was recently demonstrated that the PHD finger of p300 can cooperate with the adjacent BROMO domain in nucleosome binding in vitro. Other reports suggesting that the PHD finger is a ubiquitin ligase have been refuted as these domains were RING fingers misidentified as PHD fingers.


Pssm-ID: 214584 [Multi-domain]  Cd Length: 47  Bit Score: 39.12  E-value: 2.74e-04
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*...
gi 242086515    11 VCMVCRAASPPEvDLLRCSTCATPWHSPCLSKPPALADAAS-WSCPDC 57
Cdd:smart00249   1 YCSVCGKPDDGG-ELLQCDGCDRWYHQTCLGPPLLEEEPDGkWYCPKC 47
RAD18 COG5432
RING-finger-containing E3 ubiquitin ligase [Signal transduction mechanisms];
499-614 4.54e-04

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


Pssm-ID: 227719 [Multi-domain]  Cd Length: 391  Bit Score: 43.15  E-value: 4.54e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 242086515 499 CSICRAVIKEPLTTPCAHNFCKTCL---LGKYDSQSSMRERSRGGRtLRAQKIVKtcpscpTDICDFLENPQINREMMEL 575
Cdd:COG5432   28 CRICDCRISIPCETTCGHTFCSLCIrrhLGTQPFCPVCREDPCESR-LRGSSGSR------EINESHARNRDLLRKVLES 100
                         90       100       110       120
                 ....*....|....*....|....*....|....*....|.
gi 242086515 576 IETLQRKAVEE--GKVASDDAEECGDGDSEENDGALVKGEE 614
Cdd:COG5432  101 LCRLPRPIKEErpCRWETVIAQDSASGDEEWEDDLASNSSP 141
PEX10 COG5574
RING-finger-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, ...
446-532 3.25e-03

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


Pssm-ID: 227861 [Multi-domain]  Cd Length: 271  Bit Score: 39.88  E-value: 3.25e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 242086515 446 WDYDEKDGWKW---MVPPPVSKKPVLSGDPETDKQIRRSTkrahlsvaerlLKEFGCSICRAVIKEPLTTPCAHNFCKTC 522
Cdd:COG5574  173 LSLDESRLQPIlqpSNNLHTLFQVITKENLSKKNGLPFIP-----------LADYKCFLCLEEPEVPSCTPCGHLFCLSC 241
                         90
                 ....*....|
gi 242086515 523 LLGKYDSQSS 532
Cdd:COG5574  242 LLISWTKKKY 251
PLN03208 PLN03208
E3 ubiquitin-protein ligase RMA2; Provisional
123-155 4.47e-03

E3 ubiquitin-protein ligase RMA2; Provisional


Pssm-ID: 178747  Cd Length: 193  Bit Score: 38.91  E-value: 4.47e-03
                         10        20        30
                 ....*....|....*....|....*....|...
gi 242086515 123 GKNFSCVFCMKLPDRPVTTPCGHNFCLKCFQKW 155
Cdd:PLN03208  16 GGDFDCNICLDQVRDPVVTLCGHLFCWPCIHKW 48
HRD1 COG5243
HRD ubiquitin ligase complex, ER membrane component [Posttranslational modification, protein ...
128-222 5.27e-03

HRD ubiquitin ligase complex, ER membrane component [Posttranslational modification, protein turnover, chaperones];


Pssm-ID: 227568 [Multi-domain]  Cd Length: 491  Bit Score: 39.95  E-value: 5.27e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 242086515 128 CVFCMK-------------LPDRPVTTPCGHNFCLKCFQKWIQnRKRTCAKCRAQIPAKMaEQPRINSALVEVIRMAKIS 194
Cdd:COG5243  290 CTICMDemfhpdheplprgLDMTPKRLPCGHILHLHCLKNWLE-RQQTCPICRRPVIFDQ-SSPTPASPNVRNTQIATQV 367
                         90       100       110
                 ....*....|....*....|....*....|
gi 242086515 195 KNPNSAGSAVPYHYIRN--DDRPDKAFTTD 222
Cdd:COG5243  368 PNPDNTPTTTAVPGITNssNQGDPQASTFN 397
rad18 TIGR00599
DNA repair protein rad18; All proteins in this family for which functions are known are ...
126-168 6.12e-03

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: 39.60  E-value: 6.12e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 242086515  126 FSCVFCMKLPDRPVTTPCGHNFCLKCFQKWIQNRKRtCAKCRA 168
Cdd:TIGR00599  27 LRCHICKDFFDVPVLTSCSHTFCSLCIRRCLSNQPK-CPLCRA 68
 
Name Accession Description Interval E-value
SAD_SRA pfam02182
SAD/SRA domain; The domain goes by several names including SAD, SRA and YDG. It adopts a beta ...
245-407 3.01e-71

SAD/SRA domain; The domain goes by several names including SAD, SRA and YDG. It adopts a beta barrel, modified PUA-like, fold that is widely present in eukaryotic chromatin proteins and in bacteria. Versions of this domain are known to bind hemi-methylated CpG dinucleotides and also other 5mC containing dinucleotides. The domain binds DNA by flipping out the methylated cytosine base from the DNA double helix.The conserved tyrosine and aspartate residues and a glycine rich patch are critical for recognition of the flipped out base. Mammalian UHRF1 that contains this domain plays an important role in maintenance of methylation at CpG dinucleotides by recruiting DNMT1 to hemimethylated sites associated with replication forks. The SAD/SRA domain has been combined with other domains involved in the ubiquitin pathway on multiple occasions and such proteins link recognition of DNA methylation to chromatin-protein ubiquitination. The domain is also found in species that lack DNA methylation, such as certain apicomplexans, suggestive of other DNA-binding modes or functions. A highly derived and distinct version of the domain is also found in fungi where it is fused to AlkB-type 2OGFeDO domains. In bacteria, the domain is usually fused or associated with restriction endonucleases, many of which target methylated or hemi-methylated DNA.


Pssm-ID: 334835  Cd Length: 147  Bit Score: 229.32  E-value: 3.01e-71
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 242086515  245 HFGPIlaendPrrsiGVRVGETWEDRLECRQWGAHFPHVAGIAGQSTYGAQSVALSGGYEDDEDHGEWFLYTGSGGRDLS 324
Cdd:pfam02182   1 IFGHV-----P----GVEVGDIFPSRAELSAVGLHRPPQAGIDGMKEEGAYSIVLSGGYEDDEDNGDVLIYTGSGGRDDK 71
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 242086515  325 gnkrtnKEQSSDQKFEKLNAALRISCLKGYPVRVVRSHKEKRSSYAPESGVRYDGVYRIEKCWRKIGIQGkFKVCRYLFV 404
Cdd:pfam02182  72 ------KGQSEDQKLERGNLALANSMETGNPVRVIRGSKGKKSKYAPEKGYRYDGLYKVVKYWREKGKSG-FKVFKFKLV 144

                  ...
gi 242086515  405 RCD 407
Cdd:pfam02182 145 RLP 147
SRA smart00466
SET and RING finger associated domain; Domain of unknown function in SET domain containing ...
242-409 1.64e-62

SET and RING finger associated domain; Domain of unknown function in SET domain containing proteins and in Deinococcus radiodurans DRA1533.


Pssm-ID: 197742  Cd Length: 155  Bit Score: 206.45  E-value: 1.64e-62
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 242086515   242 APDHFGPIlaendPrrsiGVRVGETWEDRLECRQWGAHFPHVAGIAGQST----YGAQSVALSGGYEDDEDHGEWFLYTG 317
Cdd:smart00466   1 MKRIFGPV-----P----GVEVGDIFFYRVELCLVGLHRPTQAGIDGLESdegePGATSVVSSGGYEDDTDDGDVLIYTG 71
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 242086515   318 SGGRDlsgnkRTNKeQSSDQKFEKLNAALRISCLKGYPVRVVRSHKeKRSSYAPESGVRYDGVYRIEKCWRKIGIQGkFK 397
Cdd:smart00466  72 QGGRD-----MTHG-QPEDQKLERGNLALEASCRKGIPVRVVRGMK-GYSKYAPGKGYIYDGLYRIVDYWREVGKSG-FL 143
                          170
                   ....*....|..
gi 242086515   398 VCRYLFVRCDNE 409
Cdd:smart00466 144 VFKFKLVRIPGQ 155
RING-HC cd16449
HC subclass of RING (RING-HC) finger and its variants; RING finger is a specialized type of ...
128-166 3.64e-09

HC subclass of RING (RING-HC) finger and its variants; 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 HC subclass of RING (RING-HC) finger proteins 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 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 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: 319363 [Multi-domain]  Cd Length: 39  Bit Score: 52.47  E-value: 3.64e-09
                         10        20        30
                 ....*....|....*....|....*....|....*....
gi 242086515 128 CVFCMKLPDRPVTTPCGHNFCLKCFQKWIQNRKRTCAKC 166
Cdd:cd16449    1 CPICLELLKDPVLLPCGHTFCRSCLRRLLKEGKKKCPIC 39
RING smart00184
Ring finger; E3 ubiquitin-protein ligase activity is intrinsic to the RING domain of c-Cbl and ...
128-166 1.68e-08

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: 50.59  E-value: 1.68e-08
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|
gi 242086515   128 CVFCM-KLPDRPVTTPCGHNFCLKCFQKWIQNRKRTCAKC 166
Cdd:smart00184   1 CPICLeEYLKDPVILPCGHTFCRSCIRKWLESGNNTCPIC 40
RING-HC_AtRMA_like cd16745
RING finger, HC subclass, found in Arabidopsis thaliana RING membrane-anchor proteins (AtRMAs) ...
126-168 2.10e-08

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: 319659 [Multi-domain]  Cd Length: 45  Bit Score: 50.38  E-value: 2.10e-08
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*
gi 242086515 126 FSCVFCMKLPDRPVTTPCGHNFCLKCFQKWIQ--NRKRTCAKCRA 168
Cdd:cd16745    1 FECNICLDLASDPVVTLCGHLFCWPCLYRWLQrhSENRECPVCKA 45
RING2-HC_LONFs cd16514
RING finger 2, HC subclass, found in the LON peptidase N-terminal domain and RING finger ...
126-167 2.43e-08

RING finger 2, HC subclass, found in the LON peptidase N-terminal domain and RING finger proteins family; The LON peptidase N-terminal domain and RING finger proteins family includes LONRF1 (also known as RING finger protein 191 or RNF191), LONRF2 (also known as RING finger protein 192 or 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 one N-terminal domain of the ATP-dependent protease La (LON) domain at the C-terminus. Their biological function remain unclear. This family corresponds to the second RING-HC finger.


Pssm-ID: 319428 [Multi-domain]  Cd Length: 42  Bit Score: 50.40  E-value: 2.43e-08
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|..
gi 242086515 126 FSCVFCMKLPDRPVTTPCGHNFCLKCFQKWIQNRKRtCAKCR 167
Cdd:cd16514    2 FECSLCMRLLYEPVTTPCGHTFCKKCLERCLDHSPK-CPLCK 42
RING-HC_UHRF cd16613
RING finger, HC subclass, found in ubiquitin-like PHD and RING finger domain-containing ...
497-559 2.58e-08

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: 319527 [Multi-domain]  Cd Length: 46  Bit Score: 50.47  E-value: 2.58e-08
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 242086515 497 FGCSICRAVIKEPLTTPCAHNFCKTCLlgkydsqssmrersrgGRTLRAQkiVKTCPSCPTDI 559
Cdd:cd16613    1 FTCICCQEVVYQPITTPCQHNVCKGCL----------------QRSFKAE--VYSCPACRHDL 45
RING-HC_UHRF cd16613
RING finger, HC subclass, found in ubiquitin-like PHD and RING finger domain-containing ...
126-170 2.58e-08

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: 319527 [Multi-domain]  Cd Length: 46  Bit Score: 50.47  E-value: 2.58e-08
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*
gi 242086515 126 FSCVFCMKLPDRPVTTPCGHNFCLKCFQKWIQNRKRTCAKCRAQI 170
Cdd:cd16613    1 FTCICCQEVVYQPITTPCQHNVCKGCLQRSFKAEVYSCPACRHDL 45
RING-HC_RNF168 cd16550
RING finger, HC subclass, found in RING finger protein 168 (RNF168) and similar proteins; ...
128-167 9.98e-08

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: 319464 [Multi-domain]  Cd Length: 42  Bit Score: 48.44  E-value: 9.98e-08
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|
gi 242086515 128 CVFCMKLPDRPVTTPCGHNFCLKCFQKWIQNRKRTCAKCR 167
Cdd:cd16550    1 CPICLEILVEPVTLPCKHELCLPCFQQTVEKANLCCPLCR 40
RING-HC_COP1 cd16504
RING finger, HC subclass, found in constitutive photomorphogenesis protein 1 (COP1) and ...
124-170 1.36e-07

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), was defined as 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 14-3-3 delta 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: 319418 [Multi-domain]  Cd Length: 46  Bit Score: 48.41  E-value: 1.36e-07
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
gi 242086515 124 KNFSCVFCMKLPDRPVTTPCGHNFCLKCFQKWIQNRKRtCAKCRAQI 170
Cdd:cd16504    1 NDFICPICFDIIEEAYMTKCGHSFCYKCIRTSLEQSNR-CPKCNFVL 46
RING-HC_TRIM65_C-IV cd16609
RING finger, HC subclass, found in tripartite motif-containing protein TRIM65 and similar ...
128-167 3.39e-07

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 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 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: 319523 [Multi-domain]  Cd Length: 47  Bit Score: 47.10  E-value: 3.39e-07
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*
gi 242086515 128 CVFCMKLPDRPVTTPCGHNFCLKCFQKWIQNRKR-----TCAKCR 167
Cdd:cd16609    3 CSICLELFTDPVTLPCGHNFCGECIRDHWDKCELikkgySCPQCR 47
zf-RING_2 pfam13639
Ring finger domain;
126-167 3.45e-07

Ring finger domain;


Pssm-ID: 338865 [Multi-domain]  Cd Length: 44  Bit Score: 47.00  E-value: 3.45e-07
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 242086515  126 FSCVFC---MKLPDRPVTTPCGHNFCLKCFQKWIQnRKRTCAKCR 167
Cdd:pfam13639   1 DECPICleeFEEGDKVVILPCGHHFHRECLDKWLR-SSNTCPLCR 44
RING-HC_RNF114 cd16540
RING finger, HC subclass, found in RING finger protein 114 (RNF114) and similar proteins; ...
126-167 3.99e-07

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 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: 319454 [Multi-domain]  Cd Length: 42  Bit Score: 46.75  E-value: 3.99e-07
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|..
gi 242086515 126 FSCVFCMKLPDRPVTTPCGHNFCLKCFQKWIQNRKRTCAKCR 167
Cdd:cd16540    1 FTCPVCLEVFEKPVRVPCGHVFCSACLQECLKPKKPVCGVCR 42
RING-HC_BAR cd16497
RING finger, HC subclass, found in bifunctional apoptosis regulator (BAR); BAR, also known as ...
126-167 4.14e-07

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 functions 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 family corresponds to the RING-HC finger responsible for the binding of ubiquitin conjugating enzymes (E2s).


Pssm-ID: 319411 [Multi-domain]  Cd Length: 46  Bit Score: 46.72  E-value: 4.14e-07
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|...
gi 242086515 126 FSCVFCMKLPDRPVTTPCGHNFCLKCF-QKWIQNRKRTCAKCR 167
Cdd:cd16497    1 FSCHCCYDLLVNPTTLNCGHSFCRHCLaLWWLSSKKTECPECR 43
RING-HC_TRIM25_C-IV cd16597
RING finger, HC subclass, found in tripartite motif-containing protein TRIM25 and similar ...
127-167 4.27e-07

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: 319511 [Multi-domain]  Cd Length: 44  Bit Score: 46.80  E-value: 4.27e-07
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|...
gi 242086515 127 SCVFCMKLPDRPVTTPCGHNFCLKCF-QKW-IQNRKRTCAKCR 167
Cdd:cd16597    2 TCSICLCLFDNPVTLPCGHNFCANCLeETWaDQISSLFCPQCR 44
zf-C3HC4 pfam00097
Zinc finger, C3HC4 type (RING finger); The C3HC4 type zinc-finger (RING finger) is a ...
128-166 5.22e-07

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: 333836 [Multi-domain]  Cd Length: 40  Bit Score: 46.58  E-value: 5.22e-07
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|
gi 242086515  128 CVFCMKLPDRPV-TTPCGHNFCLKCFQKWIQNRKRTCAKC 166
Cdd:pfam00097   1 CPICLEEPKDPVtILPCGHLFCSKCILSWLESGNVTCPLC 40
RING-HC_TRIM65_C-IV cd16609
RING finger, HC subclass, found in tripartite motif-containing protein TRIM65 and similar ...
499-556 6.35e-07

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 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 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: 319523 [Multi-domain]  Cd Length: 47  Bit Score: 46.33  E-value: 6.35e-07
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 242086515 499 CSICRAVIKEPLTTPCAHNFCKTCLLGKYDsqssmrersrggrtlrAQKIVKTCPSCP 556
Cdd:cd16609    3 CSICLELFTDPVTLPCGHNFCGECIRDHWD----------------KCELIKKGYSCP 44
RING-HC_RNF135_like cd16543
RING finger, HC subclass, found in RING finger protein 135 (RNF135), tripartite ...
128-167 1.09e-06

RING finger, HC subclass, found in RING finger protein 135 (RNF135), tripartite motif-containing protein 15 (TRIM15) and similar proteins; 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. TRIM15, also known as RING finger protein 93 (RNF93), 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. TRIM15 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 SPRY/B30.2 domain positioned C-terminal to the RBCC domain.


Pssm-ID: 319457 [Multi-domain]  Cd Length: 37  Bit Score: 45.52  E-value: 1.09e-06
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|
gi 242086515 128 CVFCMKLPDRPVTTPCGHNFCLKCFQKwiqNRKRTCAKCR 167
Cdd:cd16543    1 CILCQGLLFDPVTIPCGHTFCRRCLER---LPSKLCPTCR 37
mRING-HC-C3HC3D_TRAF6 cd16643
Modified RING finger, HC subclass (C3HC3D-type), found in tumor necrosis factor (TNF) ...
497-558 1.55e-06

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: 319557 [Multi-domain]  Cd Length: 58  Bit Score: 45.44  E-value: 1.55e-06
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 242086515 497 FGCSICRAVIKEPLTTPCAHNFCKTCLLgkydsqSSMRERSrggrtlraqkivktcPSCPTD 558
Cdd:cd16643    2 YECPICLMALREPVQTPCGHRFCKSCIK------KSIRDAG---------------HRCPVD 42
RING2-HC_LONFs cd16514
RING finger 2, HC subclass, found in the LON peptidase N-terminal domain and RING finger ...
496-523 1.94e-06

RING finger 2, HC subclass, found in the LON peptidase N-terminal domain and RING finger proteins family; The LON peptidase N-terminal domain and RING finger proteins family includes LONRF1 (also known as RING finger protein 191 or RNF191), LONRF2 (also known as RING finger protein 192 or 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 one N-terminal domain of the ATP-dependent protease La (LON) domain at the C-terminus. Their biological function remain unclear. This family corresponds to the second RING-HC finger.


Pssm-ID: 319428 [Multi-domain]  Cd Length: 42  Bit Score: 45.01  E-value: 1.94e-06
                         10        20
                 ....*....|....*....|....*...
gi 242086515 496 EFGCSICRAVIKEPLTTPCAHNFCKTCL 523
Cdd:cd16514    1 DFECSLCMRLLYEPVTTPCGHTFCKKCL 28
PEX10 COG5574
RING-finger-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, ...
125-168 2.38e-06

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


Pssm-ID: 227861 [Multi-domain]  Cd Length: 271  Bit Score: 49.51  E-value: 2.38e-06
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*
gi 242086515 125 NFSCVFCMKLPDRPVTTPCGHNFCLKC-FQKWIQNRKRTCAKCRA 168
Cdd:COG5574  215 DYKCFLCLEEPEVPSCTPCGHLFCLSClLISWTKKKYEFCPLCRA 259
RING-HC_LNX3_like cd16512
RING finger, HC subclass, found in ligand of Numb protein LNX3, LNX4, and similar proteins; ...
128-167 3.03e-06

RING finger, HC subclass, found in ligand of Numb protein LNX3, LNX4, 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 the substrate-binding. This family corresponds to LNX3/LNX4-like proteins, which contains a typical C3HC4-type RING-HC finger and two PDZ domains.


Pssm-ID: 319426 [Multi-domain]  Cd Length: 41  Bit Score: 44.43  E-value: 3.03e-06
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|.
gi 242086515 128 CVFCMKLPDRPVTTPCGHNFCLKCFQKWIQnRKRTC-AKCR 167
Cdd:cd16512    2 CSICLEVLEDPLTTPCGHVFCSGCILPWLV-QNGSCpVKCR 41
RING-HC_LNX3 cd16718
RING finger, HC subclass, found in ligand of numb protein X 3 (LNX3); LNX3, also known as PDZ ...
128-167 3.37e-06

RING finger, HC subclass, found in ligand of numb protein X 3 (LNX3); LNX3, also known as PDZ domain-containing RING finger protein 3 (PDZRN3), or Semaphorin cytoplasmic domain-associated protein 3 (SEMACAP3), is an E3 ubiquitin-protein ligase that was first identified as a Semaphorin-binding partner. It is also 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. LNX3 acts as a negative regulator of osteoblast differentiation by inhibiting Wnt-beta-catenin signaling. LNX3 also plays an important role in neuromuscular junction formation. It interacts with and ubiquitinates the muscle specific tyrosine kinase (MuSK), thus promoting its endocytosis and negatively regulating the cell surface expression of this key regulator of postsynaptic assembly. LNX3 contains an N-terminal typical C3HC4-type RING-HC finger, two PDZ domains, and a C-terminal LNX3 homology (LNX3H) domain.


Pssm-ID: 319632 [Multi-domain]  Cd Length: 42  Bit Score: 44.20  E-value: 3.37e-06
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|
gi 242086515 128 CVFCMKLPDRPVTTPCGHNFCLKCFQKWIQNRKRTCAKCR 167
Cdd:cd16718    2 CNLCNKVLEDPLTTPCGHVFCAGCVLPWVVQQGSCPVKCQ 41
RING-HC_TRIM25_C-IV cd16597
RING finger, HC subclass, found in tripartite motif-containing protein TRIM25 and similar ...
499-532 3.77e-06

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: 319511 [Multi-domain]  Cd Length: 44  Bit Score: 44.11  E-value: 3.77e-06
                         10        20        30
                 ....*....|....*....|....*....|....
gi 242086515 499 CSICRAVIKEPLTTPCAHNFCKTCLLGKYDSQSS 532
Cdd:cd16597    3 CSICLCLFDNPVTLPCGHNFCANCLEETWADQIS 36
RING-HC_TRIM47_C-IV cd16604
RING finger, HC subclass, found in tripartite motif-containing protein 47 (TRIM47) and similar ...
126-167 5.59e-06

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 a 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, 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.


Pssm-ID: 319518 [Multi-domain]  Cd Length: 47  Bit Score: 43.65  E-value: 5.59e-06
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
gi 242086515 126 FSCVFCMKLPDRPVTTPCGHNFCLKCFQKWIQNRKR-----TCAKCR 167
Cdd:cd16604    1 LTCPICLDALRDPVTLPCGHNYCLACLQHLWEKNGSrggayRCPECQ 47
RING-HC_LNX4 cd16719
RING finger, HC subclass, found in ligand of numb protein X 4 (LNX4); LNX4, also known as PDZ ...
128-167 8.54e-06

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 typical C3HC4-type RING-HC finger, two PDZ domains, and a C-terminal LNX3 homology (LNX3H) domain.


Pssm-ID: 319633 [Multi-domain]  Cd Length: 42  Bit Score: 43.01  E-value: 8.54e-06
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|
gi 242086515 128 CVFCMKLPDRPVTTPCGHNFCLKCFQKWIQNRKRTCAKCR 167
Cdd:cd16719    2 CKLCGKVLEEPLSTPCGHVFCAGCLLPWAVRRRRCPLQCQ 41
RING-HC_TRIM47_C-IV cd16604
RING finger, HC subclass, found in tripartite motif-containing protein 47 (TRIM47) and similar ...
497-555 8.69e-06

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 a 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, 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.


Pssm-ID: 319518 [Multi-domain]  Cd Length: 47  Bit Score: 43.27  E-value: 8.69e-06
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 242086515 497 FGCSICRAVIKEPLTTPCAHNFCKTCLlgkydsqSSMRERsRGGRTLRAqkivkTCPSC 555
Cdd:cd16604    1 LTCPICLDALRDPVTLPCGHNYCLACL-------QHLWEK-NGSRGGAY-----RCPEC 46
RING-HC_MID_C-I cd16575
RING finger, HC subclass, found in midline-1 (MID1), midline-2 (MID2) and similar proteins; ...
499-555 8.93e-06

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), is highly related to MID1. It 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 and the functional redundancy exists between MID1 and MID2 in cytotoxic lymphocytes (CTL). Both MID1 and MID2 belong to the C-I 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 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: 319489 [Multi-domain]  Cd Length: 52  Bit Score: 43.29  E-value: 8.93e-06
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 242086515 499 CSICRAVIKEPLTTPCAHNFCKTCLLGKYDSQSSMRERSRGGRTLRaqkivktCPSC 555
Cdd:cd16575    1 CPICLELFEDPILLPCSHNLCKSCAERLVVSHCGSGESGETRESFR-------CPTC 50
RING-HC_UHRF2 cd16770
RING finger, HC subclass, found in ubiquitin-like PHD and RING finger domain-containing ...
126-167 8.96e-06

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: 319684  Cd Length: 46  Bit Score: 43.09  E-value: 8.96e-06
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|..
gi 242086515 126 FSCVFCMKLPDRPVTTPCGHNFCLKCFQKWIQNRKRTCAKCR 167
Cdd:cd16770    1 FMCVCCQELVYQPVTTECLHNVCKSCLQRSFRAEVFTCPACR 42
RING-HC_UHRF1 cd16769
RING finger, HC subclass, found in ubiquitin-like PHD and RING finger domain-containing ...
126-167 1.07e-05

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: 319683  Cd Length: 47  Bit Score: 43.01  E-value: 1.07e-05
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|..
gi 242086515 126 FSCVFCMKLPDRPVTTPCGHNFCLKCFQKWIQNRKRTCAKCR 167
Cdd:cd16769    1 FQCICCQELVFRPVTTVCQHNVCKDCLDRSFRAQVYSCPACR 42
RING-HC_LNX3 cd16718
RING finger, HC subclass, found in ligand of numb protein X 3 (LNX3); LNX3, also known as PDZ ...
499-539 1.13e-05

RING finger, HC subclass, found in ligand of numb protein X 3 (LNX3); LNX3, also known as PDZ domain-containing RING finger protein 3 (PDZRN3), or Semaphorin cytoplasmic domain-associated protein 3 (SEMACAP3), is an E3 ubiquitin-protein ligase that was first identified as a Semaphorin-binding partner. It is also 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. LNX3 acts as a negative regulator of osteoblast differentiation by inhibiting Wnt-beta-catenin signaling. LNX3 also plays an important role in neuromuscular junction formation. It interacts with and ubiquitinates the muscle specific tyrosine kinase (MuSK), thus promoting its endocytosis and negatively regulating the cell surface expression of this key regulator of postsynaptic assembly. LNX3 contains an N-terminal typical C3HC4-type RING-HC finger, two PDZ domains, and a C-terminal LNX3 homology (LNX3H) domain.


Pssm-ID: 319632 [Multi-domain]  Cd Length: 42  Bit Score: 42.66  E-value: 1.13e-05
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|.
gi 242086515 499 CSICRAVIKEPLTTPCAHNFCKTCLLGKYDSQSSMRERSRG 539
Cdd:cd16718    2 CNLCNKVLEDPLTTPCGHVFCAGCVLPWVVQQGSCPVKCQR 42
RING-HC_RNF125 cd16542
RING finger, HC subclass, found in RING finger protein 125 (RNF125); RNF125, also known as ...
126-167 1.13e-05

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: 319456 [Multi-domain]  Cd Length: 42  Bit Score: 42.86  E-value: 1.13e-05
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|..
gi 242086515 126 FSCVFCMKLPDRPVTTPCGHNFCLKCFQKWIQNRKRTCAKCR 167
Cdd:cd16542    1 FDCAICLEVLHQPVRTRCGHVFCRTCIITSLKNNTWTCPYCR 42
mRING-HC-C3HC3D_TRAF6 cd16643
Modified RING finger, HC subclass (C3HC3D-type), found in tumor necrosis factor (TNF) ...
126-163 1.50e-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: 319557 [Multi-domain]  Cd Length: 58  Bit Score: 42.75  E-value: 1.50e-05
                         10        20        30
                 ....*....|....*....|....*....|....*....
gi 242086515 126 FSCVFC-MKLPDrPVTTPCGHNFCLKCFQKWIQNRKRTC 163
Cdd:cd16643    2 YECPIClMALRE-PVQTPCGHRFCKSCIKKSIRDAGHRC 39
RING-HC cd16449
HC subclass of RING (RING-HC) finger and its variants; RING finger is a specialized type of ...
499-523 1.53e-05

HC subclass of RING (RING-HC) finger and its variants; 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 HC subclass of RING (RING-HC) finger proteins 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 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 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: 319363 [Multi-domain]  Cd Length: 39  Bit Score: 42.45  E-value: 1.53e-05
                         10        20
                 ....*....|....*....|....*
gi 242086515 499 CSICRAVIKEPLTTPCAHNFCKTCL 523
Cdd:cd16449    1 CPICLELLKDPVLLPCGHTFCRSCL 25
RING-HC_TRIM10_C-IV cd16593
RING finger, HC subclass, found in tripartite motif-containing protein 10 (TRIM10) and similar ...
496-523 1.90e-05

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 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: 319507 [Multi-domain]  Cd Length: 49  Bit Score: 42.30  E-value: 1.90e-05
                         10        20
                 ....*....|....*....|....*...
gi 242086515 496 EFGCSICRAVIKEPLTTPCAHNFCKTCL 523
Cdd:cd16593    1 EVNCPICQGTLREPVTIDCGHNFCRACL 28
RING-HC_LNX4 cd16719
RING finger, HC subclass, found in ligand of numb protein X 4 (LNX4); LNX4, also known as PDZ ...
499-524 2.15e-05

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 typical C3HC4-type RING-HC finger, two PDZ domains, and a C-terminal LNX3 homology (LNX3H) domain.


Pssm-ID: 319633 [Multi-domain]  Cd Length: 42  Bit Score: 41.85  E-value: 2.15e-05
                         10        20
                 ....*....|....*....|....*.
gi 242086515 499 CSICRAVIKEPLTTPCAHNFCKTCLL 524
Cdd:cd16719    2 CKLCGKVLEEPLSTPCGHVFCAGCLL 27
RING-HC_RNF5_like cd16534
RING finger, HC subclass, found in RING finger protein RNF5, RNF185 and similar proteins; RNF5 ...
128-167 2.28e-05

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 in this family contain a C3HC4-type RING-HC finger.


Pssm-ID: 319448 [Multi-domain]  Cd Length: 43  Bit Score: 42.03  E-value: 2.28e-05
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|..
gi 242086515 128 CVFCMKLPDRPVTTPCGHNFCLKCFQKWIQNR--KRTCAKCR 167
Cdd:cd16534    2 CNICLDTAKDAVVSMCGHLFCWPCLHQWLETRpdRPTCPVCK 43
RING-HC_HLTF cd16509
RING finger, HC subclass, found in helicase-like transcription factor (HLTF) and similar ...
128-167 2.73e-05

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, or HIP116, or RING finger protein 80, or 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: 319423 [Multi-domain]  Cd Length: 43  Bit Score: 41.51  E-value: 2.73e-05
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|.
gi 242086515 128 CVFCMKLPDRPVTTPCGHNFCLKCFQKWIQNRKR-TCAKCR 167
Cdd:cd16509    3 CPICLDSLKDPVITPCAHVFCRGCIEQVIQREPNaKCPLCR 43
RING-HC_TRIM69_C-IV cd16611
RING finger, HC subclass, found in tripartite motif-containing protein 69 (TRIM69) and similar ...
127-167 2.74e-05

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 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: 319525 [Multi-domain]  Cd Length: 44  Bit Score: 41.67  E-value: 2.74e-05
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|..
gi 242086515 127 SCVFCMKLPDRPVTTPCGHNFCLKCFQK-WIQNRKRTCAKCR 167
Cdd:cd16611    3 TCPLCVEWFKDPVMLPCGHNFCRACIEDvWEGQSSFACPECR 44
RING-HC_RNF135_like cd16543
RING finger, HC subclass, found in RING finger protein 135 (RNF135), tripartite ...
499-523 2.88e-05

RING finger, HC subclass, found in RING finger protein 135 (RNF135), tripartite motif-containing protein 15 (TRIM15) and similar proteins; 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. TRIM15, also known as RING finger protein 93 (RNF93), 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. TRIM15 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 SPRY/B30.2 domain positioned C-terminal to the RBCC domain.


Pssm-ID: 319457 [Multi-domain]  Cd Length: 37  Bit Score: 41.29  E-value: 2.88e-05
                         10        20
                 ....*....|....*....|....*
gi 242086515 499 CSICRAVIKEPLTTPCAHNFCKTCL 523
Cdd:cd16543    1 CILCQGLLFDPVTIPCGHTFCRRCL 25
RING-H2 cd16448
H2 subclass of RING (RING-H2) finger and its variants; RING finger is a specialized type of ...
128-167 3.12e-05

H2 subclass of RING (RING-H2) finger and its variants; 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 as 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 pattern. Some lack a single Cys or His residues at typical Zn ligand positions. Especially, 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 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: 319362 [Multi-domain]  Cd Length: 44  Bit Score: 41.67  E-value: 3.12e-05
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....
gi 242086515 128 CVFC---MKLPDRPVT-TPCGHNFCLKCFQKWIQNRKRTCAKCR 167
Cdd:cd16448    1 CAICleeFEEGDCPVRlLPCGHVFHKSCIDKWLESGNRTCPLCR 44
RING-HC_UHRF2 cd16770
RING finger, HC subclass, found in ubiquitin-like PHD and RING finger domain-containing ...
497-559 3.15e-05

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: 319684  Cd Length: 46  Bit Score: 41.55  E-value: 3.15e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 242086515 497 FGCSICRAVIKEPLTTPCAHNFCKTCLlgkydsqssmrersrgGRTLRAQkiVKTCPSCPTDI 559
Cdd:cd16770    1 FMCVCCQELVYQPVTTECLHNVCKSCL----------------QRSFRAE--VFTCPACRYDL 45
RING-HC_LNX3_like cd16512
RING finger, HC subclass, found in ligand of Numb protein LNX3, LNX4, and similar proteins; ...
499-524 3.36e-05

RING finger, HC subclass, found in ligand of Numb protein LNX3, LNX4, 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 the substrate-binding. This family corresponds to LNX3/LNX4-like proteins, which contains a typical C3HC4-type RING-HC finger and two PDZ domains.


Pssm-ID: 319426 [Multi-domain]  Cd Length: 41  Bit Score: 41.35  E-value: 3.36e-05
                         10        20
                 ....*....|....*....|....*.
gi 242086515 499 CSICRAVIKEPLTTPCAHNFCKTCLL 524
Cdd:cd16512    2 CSICLEVLEDPLTTPCGHVFCSGCIL 27
RING-HC_TRIM17_C-IV cd16595
RING finger, HC subclass, found in tripartite motif-containing protein TRIM17 and similar ...
496-555 3.42e-05

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 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: 319509 [Multi-domain]  Cd Length: 48  Bit Score: 41.67  E-value: 3.42e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 242086515 496 EFGCSICRAVIKEPLTTPCAHNFCKTCLLGKYDSQssmrersrggrtlRAQKIVKTCPSC 555
Cdd:cd16595    1 ELCCSICLDYFKDPVILRCGHNFCRACITQFWEKQ-------------GGLQGKLTCPEC 47
RING-HC_TRIM7_C-IV cd16592
RING finger, HC subclass, found in tripartite motif-containing protein 7 (TRIM7) and similar ...
496-523 3.42e-05

RING finger, HC subclass, found in tripartite motif-containing protein 7 (TRIM7) and similar proteins; 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. TRIM7 belongs 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 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: 319506 [Multi-domain]  Cd Length: 45  Bit Score: 41.31  E-value: 3.42e-05
                         10        20
                 ....*....|....*....|....*...
gi 242086515 496 EFGCSICRAVIKEPLTTPCAHNFCKTCL 523
Cdd:cd16592    1 EASCSICLDLFRDPVSIPCGHNFCRACI 28
RING-HC_TRIM13_C-V cd16762
RING finger, HC subclass, found in tripartite motif-containing protein 13 (TRIM13) and similar ...
495-555 3.46e-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 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-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 C3HC4-type RING-HC finger, Bbox1 and Bbox2, and a coiled coil region. In addition, TRIM13 contains a C-terminal transmembrane domain.


Pssm-ID: 319676 [Multi-domain]  Cd Length: 57  Bit Score: 41.89  E-value: 3.46e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 242086515 495 KEFGCSICRAVIKEPLTTPCAHNFCKTCLLGKYDSQssmrersrgGRTLRAQKIVKTCPSC 555
Cdd:cd16762    2 EDLTCPICCSLFDDPRVLPCSHNFCKKCLEGILEGN---------VRNMLWRPAPFKCPTC 53
RING-HC_RNF166 cd16549
RING finger, HC subclass, found in RING finger protein 166 (RNF166) and similar proteins; ...
125-168 3.59e-05

RING finger, HC subclass, found in RING finger protein 166 (RNF166) and similar proteins; RNF166 is encoded by 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: 319463 [Multi-domain]  Cd Length: 47  Bit Score: 41.35  E-value: 3.59e-05
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*
gi 242086515 125 NFSCVFCMKLPDRPVT-TPCGHNFCLKCFQKWIQNRKRTCAKCRA 168
Cdd:cd16549    1 QFSCPICLEVYHKPVSiASCGHTFCGECLQPCLQVPSPLCPLCRM 45
RING-HC_TRIM59_C-V cd16763
RING finger, HC subclass, found in tripartite motif-containing protein 59 (TRIM59) and similar ...
495-555 3.62e-05

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 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 C3HC4-type RING-HC finger, Bbox1 and Bbox2, and a coiled coil region. In addition, TRIM59 contains a C-terminal transmembrane domain.


Pssm-ID: 319677 [Multi-domain]  Cd Length: 56  Bit Score: 41.76  E-value: 3.62e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 242086515 495 KEFGCSICRAVIKEPLTTPCAHNFCKTCLlgkydsqSSMRERSRGGRTLRAQKIVKTCPSC 555
Cdd:cd16763    2 EELTCSVCYSIFEDPRVLPCSHTFCRNCL-------ENVIQSSGNFSLWRPLRAPLKCPNC 55
RING-HC_TRIM13_like_C-V cd16581
RING finger, HC subclass, found in tripartite motif-containing proteins TRIM13, TRIM59 and ...
499-555 3.65e-05

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 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 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 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: 319495 [Multi-domain]  Cd Length: 45  Bit Score: 41.29  E-value: 3.65e-05
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 242086515 499 CSICRAVIKEPLTTPCAHNFCKTCLLGKYDSQSSMRersrggrtlraqkivktCPSC 555
Cdd:cd16581    5 CSICLDIFNDPRVLPCLHTFCKNCLEGRAAESGPLK-----------------CPTC 44
RING-HC_TRIM11_like_C-IV cd16594
RING finger, HC subclass, found in tripartite motif-containing proteins, TRIM11 and TRIM27, ...
127-167 3.84e-05

RING finger, HC subclass, found in tripartite motif-containing proteins, TRIM11 and TRIM27, and similar proteins; TRIM11 and TRIM27, two closely related tripartite motif-containing proteins, 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 C3HC4-type RING-HC finger, Bbox1 and Bbox2, and a coiled coil region, as well as a SPRY/B30.2 domain positioned C-terminal to the RBCC domain. 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 congenital central hypoventilation syndrome-associated polyalanine-expanded Phox2b. Trim11 modulates the function of neurogenic transcription factor Pax6 through ubiquitin-proteosome system, and thus plays an essential role for the 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, through the ubiquitin-proteasome system, 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. Furthermore, TRIM27 promote a non-canonical polyubiquitinations 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: 319508 [Multi-domain]  Cd Length: 45  Bit Score: 41.30  E-value: 3.84e-05
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|...
gi 242086515 127 SCVFCMKLPDRPVTTPCGHNFCLKCF-QKW-IQNRKRTCAKCR 167
Cdd:cd16594    3 TCPVCLEYFTDPVILDCGHNFCRACIlRCWeTRATPVSCPQCR 45
RING-HC_RNF5 cd16743
RING finger, HC subclass, found in RING finger protein 5 (RNF5) and similar proteins; RNF5, ...
126-168 4.01e-05

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: 319657 [Multi-domain]  Cd Length: 46  Bit Score: 41.47  E-value: 4.01e-05
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*
gi 242086515 126 FSCVFCMKLPDRPVTTPCGHNFCLKCFQKWIQNR--KRTCAKCRA 168
Cdd:cd16743    1 FECNICLETAREAVVSLCGHLYCWPCLHQWLETRpeRQECPVCKA 45
RING-HC_UHRF1 cd16769
RING finger, HC subclass, found in ubiquitin-like PHD and RING finger domain-containing ...
497-559 4.08e-05

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: 319683  Cd Length: 47  Bit Score: 41.47  E-value: 4.08e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 242086515 497 FGCSICRAVIKEPLTTPCAHNFCKTCLlgkydsqssmrersrgGRTLRAQkiVKTCPSCPTDI 559
Cdd:cd16769    1 FQCICCQELVFRPVTTVCQHNVCKDCL----------------DRSFRAQ--VYSCPACRYDL 45
RING-HC_TRIM7_C-IV cd16592
RING finger, HC subclass, found in tripartite motif-containing protein 7 (TRIM7) and similar ...
127-167 4.37e-05

RING finger, HC subclass, found in tripartite motif-containing protein 7 (TRIM7) and similar proteins; 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. TRIM7 belongs 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 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: 319506 [Multi-domain]  Cd Length: 45  Bit Score: 41.31  E-value: 4.37e-05
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|...
gi 242086515 127 SCVFCMKLPDRPVTTPCGHNFCLKCFQKWIQNRKRT--CAKCR 167
Cdd:cd16592    3 SCSICLDLFRDPVSIPCGHNFCRACIRRCWELQGSTfsCPQCR 45
RING-HC_BRCA1 cd16498
RING finger, HC subclass, found in breast cancer type 1 susceptibility protein (BRCA1) and ...
493-524 4.45e-05

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 tumor suppressor gene BRCA1 that regulates all DNA double-strand break (DSB) repair pathways. BRCA1 is frequently mutated in 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: 319412 [Multi-domain]  Cd Length: 48  Bit Score: 41.23  E-value: 4.45e-05
                         10        20        30
                 ....*....|....*....|....*....|..
gi 242086515 493 LLKEFGCSICRAVIKEPLTTPCAHNFCKTCLL 524
Cdd:cd16498    1 MQKNLECPICLDLMKNPVSTKCDHQFCRFCIL 32
zf-C3HC4_2 pfam13923
Zinc finger, C3HC4 type (RING finger);
128-166 5.29e-05

Zinc finger, C3HC4 type (RING finger);


Pssm-ID: 316445 [Multi-domain]  Cd Length: 40  Bit Score: 40.87  E-value: 5.29e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|
gi 242086515  128 CVFCM-KLPDRPVTTPCGHNFCLKCFQKWIQNRKRtCAKC 166
Cdd:pfam13923   2 CPICLdMLKDPSTTTPCGHVFCQKCILRALRSGNE-CPLC 40
COG5540 COG5540
RING-finger-containing ubiquitin ligase [Posttranslational modification, protein turnover, ...
123-171 5.36e-05

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


Pssm-ID: 227827 [Multi-domain]  Cd Length: 374  Bit Score: 46.14  E-value: 5.36e-05
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 242086515 123 GKNFSCVFCMK---LPDRPVTTPCGHNFCLKCFQKWIQNRKRTCAKCRAQIP 171
Cdd:COG5540  321 DKGVECAICMSnfiKNDRLRVLPCDHRFHVGCVDKWLLGYSNKCPVCRTAIP 372
RING-HC_RNF213 cd16561
RING finger, HC subclass, found in RING finger protein 213 (RNF213) and similar proteins; ...
128-167 5.61e-05

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 associate 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 forms huge ring-shaped oligomeric complex.


Pssm-ID: 319475 [Multi-domain]  Cd Length: 41  Bit Score: 40.54  E-value: 5.61e-05
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|.
gi 242086515 128 CVFCMKLPDRPVTTPCGHNFCLKCFQKWI-QNRKRTCAKCR 167
Cdd:cd16561    1 CSICLEDPKDPVSLPCDHIHCLTCLRQWFrPVGQMHCPTCR 41
RING-HC_TRIM56_C-V cd16584
RING finger, HC subclass, found in tripartite motif-containing protein 56 (TRIM56) and similar ...
126-167 7.49e-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 do 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 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 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: 319498 [Multi-domain]  Cd Length: 44  Bit Score: 40.45  E-value: 7.49e-05
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....
gi 242086515 126 FSCVFCMKLPDRPVTTPCGHNFCLKCFQKWIQNRKR--TCAKCR 167
Cdd:cd16584    1 LNCPICLEHYTKPKSLPCLHTFCEDCLEQLIDHNSRrfSCPICR 44
RING-HC_COP1 cd16504
RING finger, HC subclass, found in constitutive photomorphogenesis protein 1 (COP1) and ...
495-524 7.51e-05

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), was defined as 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 14-3-3 delta 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: 319418 [Multi-domain]  Cd Length: 46  Bit Score: 40.32  E-value: 7.51e-05
                         10        20        30
                 ....*....|....*....|....*....|
gi 242086515 495 KEFGCSICRAVIKEPLTTPCAHNFCKTCLL 524
Cdd:cd16504    1 NDFICPICFDIIEEAYMTKCGHSFCYKCIR 30
mRING-HC-C3HC3D_LNX1_like cd16637
Modified RING finger, HC subclass (C3HC3D-type), found in ligand of Numb protein LNX1, LNX2, ...
499-523 7.94e-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 the substrate-binding. This family corresponds to LNX1/LNX2-like proteins, which contains a modified C3HC3D-type RING-HC finger and four PDZ domains.


Pssm-ID: 319551 [Multi-domain]  Cd Length: 42  Bit Score: 40.40  E-value: 7.94e-05
                         10        20
                 ....*....|....*....|....*
gi 242086515 499 CSICRAVIKEPLTTPCAHNFCKTCL 523
Cdd:cd16637    4 CHICLQPLVDPLDTPCGHTFCSRCL 28
RING-HC_RNF146 cd16546
RING finger, HC subclass, found in RING finger protein 146 (RNF146) and similar proteins; ...
127-167 7.97e-05

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 regulates Wnt signaling. It also facilitates DNA repair and protects against cell death induced by DNA damaging agents or gamma-irradiation through 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: 319460 [Multi-domain]  Cd Length: 40  Bit Score: 40.45  E-value: 7.97e-05
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|.
gi 242086515 127 SCVFCMKLPDRPVTTPCGHNFCLKCFqKWIQNRKRTCAKCR 167
Cdd:cd16546    1 ECAICLQTCVHPVRLPCGHIFCYLCV-KGVAWQSKRCALCR 40
RING-HC_TRIM4_C-IV_like cd16590
RING finger, HC subclass, found in tripartite motif-containing proteins, TRIM4, TRIM75, ...
496-524 8.90e-05

RING finger, HC subclass, found in tripartite motif-containing proteins, TRIM4, TRIM75, tripartite motif family-like protein 1 (TRIML1) and similar proteins; TRIM4 and TRIM75, two closely related tripartite motif-containing proteins, 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 C3HC4-type RING-HC finger, Bbox1 and 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 it had 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. TRIM75 mainly localizes within spindles, suggesting it may function in spindle organization and thereby affect meiosis. The family also includes TRIML1 that is identical to TRIM11 and TRIM17 except for the absence of B-box domain. TRIML1, also known as RING finger protein 209 (RNF209), is a probable E3 ubiquitin-protein ligase expressed in embryo before implantation. It plays an important role in blastocyst development. By interacting with USP5 (also known as isoT), TRIML1 may exerts its influence on debranching ubiquitin from multi-chains on the stability and activity of protein substrates in the preimplantation embryo.


Pssm-ID: 319504 [Multi-domain]  Cd Length: 45  Bit Score: 40.15  E-value: 8.90e-05
                         10        20
                 ....*....|....*....|....*....
gi 242086515 496 EFGCSICRAVIKEPLTTPCAHNFCKTCLL 524
Cdd:cd16590    1 ELTCSICLDYFKDPVTIECGHNFCRGCIL 29
RING-HC_HLTF cd16509
RING finger, HC subclass, found in helicase-like transcription factor (HLTF) and similar ...
499-523 9.61e-05

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, or HIP116, or RING finger protein 80, or 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: 319423 [Multi-domain]  Cd Length: 43  Bit Score: 39.97  E-value: 9.61e-05
                         10        20
                 ....*....|....*....|....*
gi 242086515 499 CSICRAVIKEPLTTPCAHNFCKTCL 523
Cdd:cd16509    3 CPICLDSLKDPVITPCAHVFCRGCI 27
RING-HC_TRIM60_like_C-IV cd16607
RING finger, HC subclass, found in tripartite motif-containing proteins TRIM60, TRIM61 and ...
496-524 1.20e-04

RING finger, HC subclass, found in tripartite motif-containing proteins TRIM60, TRIM61 and similar proteins; TRIM60 and TRIM61 are two closely related tripartite motif-containing 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). TRIM60 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 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. In contrast to TRIM60, TRIM61 belongs to the C-V subclass of TRIM family that contains RBCC domains only. Its biological function remains unclear.


Pssm-ID: 319521 [Multi-domain]  Cd Length: 47  Bit Score: 39.96  E-value: 1.20e-04
                         10        20
                 ....*....|....*....|....*....
gi 242086515 496 EFGCSICRAVIKEPLTTPCAHNFCKTCLL 524
Cdd:cd16607    1 ESSCPICLEYLKDPVTINCGHNFCRSCLI 29
RING-HC_TRIM68_C-IV cd16610
RING finger, HC subclass, found in tripartite motif-containing protein 68 (TRIM68) and similar ...
496-525 1.38e-04

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 through 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 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: 319524 [Multi-domain]  Cd Length: 49  Bit Score: 39.91  E-value: 1.38e-04
                         10        20        30
                 ....*....|....*....|....*....|
gi 242086515 496 EFGCSICRAVIKEPLTTPCAHNFCKTCLLG 525
Cdd:cd16610    1 EVACPICMTFLREPVSIDCGHSFCHSCLSG 30
zf-C3HC4 pfam00097
Zinc finger, C3HC4 type (RING finger); The C3HC4 type zinc-finger (RING finger) is a ...
499-555 1.46e-04

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: 333836 [Multi-domain]  Cd Length: 40  Bit Score: 39.65  E-value: 1.46e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 242086515  499 CSICRAVIKEPL-TTPCAHNFCKTCLLgkydsqSSMRERSRggrtlraqkivkTCPSC 555
Cdd:pfam00097   1 CPICLEEPKDPVtILPCGHLFCSKCIL------SWLESGNV------------TCPLC 40
PHD_BAZ1A_like cd15544
PHD finger found in bromodomain adjacent to zinc finger domain protein BAZ1A and BAZ1B; BAZ1A, ...
12-57 1.54e-04

PHD finger found in bromodomain adjacent to zinc finger domain protein BAZ1A and BAZ1B; BAZ1A, also termed ATP-dependent chromatin-remodeling protein, or ATP-utilizing chromatin assembly and remodeling factor 1 (ACF1), or CHRAC subunit ACF1, or Williams syndrome transcription factor-related chromatin-remodeling factor 180 (WCRF180), or WALp1, is a subunit of the conserved imitation switch (ISWI)-family ATP-dependent chromatin assembly and remodeling factor (ACF)/chromatin accessibility complex (CHRAC) chromatin remodeling complex, which is required for DNA replication through heterochromatin. It alters the remodeling properties of the ATPase motor protein sucrose nonfermenting-2 homolog (SNF2H). Moreover, BAZ1A and its complexes play important roles in DNA double-strand break (DSB) repair. It is essential for averting improper gene expression during spermatogenesis. It also regulates transcriptional repression of vitamin D3 receptor-regulated genes. BAZ1B, also termed Tyrosine-protein kinase BAZ1B, or Williams syndrome transcription factor (WSTF), or Williams-Beuren syndrome chromosomal region 10 protein, Williams-Beuren syndrome chromosomal region 9 protein, or WALp2, is a multifunctional protein implicated in several nuclear processes, including replication, transcription, and the DNA damage response. BAZ1B/WSTF, together with the imitation switch (ISWI) ATPase, forms a WSTF-ISWI chromatin remodeling complex (WICH), which transiently associates with the human inactive X chromosome (Xi) during late S-phase prior to BRCA1 and gamma-H2AX. Moreover, BAZ1B/WSTF, SNF2h, and nuclear myosin 1 (NM1) forms the chromatin remodeling complex B-WICH that is involved in regulating rDNA transcription. Both BAZ1A and BAZ1B contain a WAC motif, a DDT domain, BAZ 1 and BAZ 2 motifs, a WAKZ (WSTF/Acf1/KIAA0314/ZK783.4) motif, a plant homeodomain (PHD) finger, and a bromodomain.


Pssm-ID: 277019  Cd Length: 46  Bit Score: 39.70  E-value: 1.54e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*.
gi 242086515  12 CMVCRAASPPEvDLLRCSTCATPWHSPCLSKPPALADAASWSCPDC 57
Cdd:cd15544    2 CKVCRKKGDPD-NMILCDGCDKAFHLYCLRPALREVPSGDWFCPAC 46
mRING-HC-C3HC3D_LNX2 cd16780
Modified RING finger, HC subclass (C3HC3D-type), found in ligand of numb protein X 2 (LNX2); ...
125-159 1.76e-04

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: 39.47  E-value: 1.76e-04
                         10        20        30
                 ....*....|....*....|....*....|....*
gi 242086515 125 NFSCVFCMKLPDRPVTTPCGHNFCLKCFQKWIQNR 159
Cdd:cd16780    3 DLVCHICLQPLLQPLDTPCGHTFCFKCLRNFLQEK 37
RING-HC_TRIM50_like_C-IV cd16605
RING finger, HC subclass, found in tripartite motif-containing protein TRIM50, TRIM73, TRIM74 ...
499-525 2.06e-04

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 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 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. 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 an N-terminal RBCC domains only.


Pssm-ID: 319519 [Multi-domain]  Cd Length: 45  Bit Score: 39.42  E-value: 2.06e-04
                         10        20
                 ....*....|....*....|....*..
gi 242086515 499 CSICRAVIKEPLTTPCAHNFCKTCLLG 525
Cdd:cd16605    3 CPICLEVFKEPLMLQCGHSYCKSCLVS 29
RING-HC_BRCA1 cd16498
RING finger, HC subclass, found in breast cancer type 1 susceptibility protein (BRCA1) and ...
124-163 2.34e-04

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 tumor suppressor gene BRCA1 that regulates all DNA double-strand break (DSB) repair pathways. BRCA1 is frequently mutated in 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: 319412 [Multi-domain]  Cd Length: 48  Bit Score: 39.31  E-value: 2.34e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|
gi 242086515 124 KNFSCVFCMKLPDRPVTTPCGHNFCLKCFQKWIQNRKRTC 163
Cdd:cd16498    3 KNLECPICLDLMKNPVSTKCDHQFCRFCILKLLSRKKGSA 42
RING-HC_TRIM40-C-V cd16583
RING finger, HC subclass, found in tripartite motif-containing protein 40 (TRIM40) and similar ...
128-168 2.35e-04

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 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 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: 319497 [Multi-domain]  Cd Length: 46  Bit Score: 39.11  E-value: 2.35e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*
gi 242086515 128 CVFCMKLPDRPVTTPCGHNFCLKCFQKWIQNRKR----TCAKCRA 168
Cdd:cd16583    2 CPICLDPLKEPVSTTCGHVFCRGCIAQHLEKASVsgvlCCPVCRK 46
RING-HC_PEX10 cd16527
RING finger, HC subclass, found in peroxin-10 (PEX10) and similar proteins; PEX10, also known ...
128-167 2.46e-04

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: 319441 [Multi-domain]  Cd Length: 40  Bit Score: 38.74  E-value: 2.46e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|
gi 242086515 128 CVFCMKLPDRPVTTPCGHNFCLKCFQKWIQNrKRTCAKCR 167
Cdd:cd16527    2 CSLCLESRRHPTATPCGHLFCWSCITEWCNE-KPECPLCR 40
PHD smart00249
PHD zinc finger; The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in ...
11-57 2.74e-04

PHD zinc finger; The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in epigenetics and chromatin-mediated transcriptional regulation. The PHD finger binds two zinc ions using the so-called 'cross-brace' motif and is thus structurally related to the RING finger and the FYVE finger. It is not yet known if PHD fingers have a common molecular function. Several reports suggest that it can function as a protein-protein interacton domain and it was recently demonstrated that the PHD finger of p300 can cooperate with the adjacent BROMO domain in nucleosome binding in vitro. Other reports suggesting that the PHD finger is a ubiquitin ligase have been refuted as these domains were RING fingers misidentified as PHD fingers.


Pssm-ID: 214584 [Multi-domain]  Cd Length: 47  Bit Score: 39.12  E-value: 2.74e-04
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*...
gi 242086515    11 VCMVCRAASPPEvDLLRCSTCATPWHSPCLSKPPALADAAS-WSCPDC 57
Cdd:smart00249   1 YCSVCGKPDDGG-ELLQCDGCDRWYHQTCLGPPLLEEEPDGkWYCPKC 47
RING-HC_TRIM4_C-IV_like cd16590
RING finger, HC subclass, found in tripartite motif-containing proteins, TRIM4, TRIM75, ...
127-167 2.90e-04

RING finger, HC subclass, found in tripartite motif-containing proteins, TRIM4, TRIM75, tripartite motif family-like protein 1 (TRIML1) and similar proteins; TRIM4 and TRIM75, two closely related tripartite motif-containing proteins, 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 C3HC4-type RING-HC finger, Bbox1 and 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 it had 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. TRIM75 mainly localizes within spindles, suggesting it may function in spindle organization and thereby affect meiosis. The family also includes TRIML1 that is identical to TRIM11 and TRIM17 except for the absence of B-box domain. TRIML1, also known as RING finger protein 209 (RNF209), is a probable E3 ubiquitin-protein ligase expressed in embryo before implantation. It plays an important role in blastocyst development. By interacting with USP5 (also known as isoT), TRIML1 may exerts its influence on debranching ubiquitin from multi-chains on the stability and activity of protein substrates in the preimplantation embryo.


Pssm-ID: 319504 [Multi-domain]  Cd Length: 45  Bit Score: 39.00  E-value: 2.90e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|...
gi 242086515 127 SCVFCMKLPDRPVTTPCGHNFCLKCFQKWIQNRKR--TCAKCR 167
Cdd:cd16590    3 TCSICLDYFKDPVTIECGHNFCRGCILQSWENLNTpfSCPECR 45
RING-HC_TRIM67 cd16758
RING finger, HC subclass, found in tripartite motif-containing protein 67 (TRIM67) and similar ...
495-522 3.07e-04

RING finger, HC subclass, found in tripartite motif-containing protein 67 (TRIM67) and similar proteins; 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. It negatively regulates Ras signaling in cell proliferation via degradation of 80K-H, leading to neural differentiation including neuritogenesis. TRIM67 belongs to the C-I 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 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: 319672 [Multi-domain]  Cd Length: 50  Bit Score: 38.90  E-value: 3.07e-04
                         10        20
                 ....*....|....*....|....*...
gi 242086515 495 KEFGCSICRAVIKEPLTTPCAHNFCKTC 522
Cdd:cd16758    2 EELKCPVCGSLFREPIILPCSHNVCLPC 29
RING-HC_TRAF2 cd16639
RING finger, HC subclass, found in tumor necrosis factor (TNF) receptor-associated factor 2 ...
128-166 3.19e-04

RING finger, HC subclass, found in tumor necrosis factor (TNF) receptor-associated factor 2 (TRAF2) and similar proteins; TRAF2, also known as tumor necrosis factor type 2 receptor-associated protein 3, is an E3 ubiquitin-protein ligase that was identified as a 75 kDa tumor necrosis factor receptor (TNF-R2)-assciated signaling protein. It interacts with members of the TNF receptor superfamily and connects the receptors to downstream signaling proteins. It also mediates K63-linked polyubiquitination of RIP1, a kinase pivotal in TNFalpha-induced NF-kappaB activation. Moreover, TRAF2 regulates peripheral CD8(+) T-cell and NKT-cell homeostasis by modulating sensitivity to IL-15. It also acts an important biological suppressor of necroptosis. It inhibits TNF-related apoptosis inducing ligand (TRAIL)- and CD95L-induced apoptosis and necroptosis. TRAF2 contains an N-terminal domain with a typical C3HC4-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: 319553  Cd Length: 42  Bit Score: 38.65  E-value: 3.19e-04
                         10        20        30
                 ....*....|....*....|....*....|....*....
gi 242086515 128 CVFCMKLPDRPVTTPCGHNFCLKCFQKWIQNRKRTCAKC 166
Cdd:cd16639    3 CSACRNVLRKPFQAQCGHRYCSSCLKWIVSSGPQKCAAC 41
RING-HC_CHFR cd16503
RING finger, HC subclass, found in checkpoint with forkhead and RING finger domains protein ...
125-167 3.27e-04

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) and a C3HC4-type RING-HC finger.


Pssm-ID: 319417 [Multi-domain]  Cd Length: 44  Bit Score: 38.55  E-value: 3.27e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....
gi 242086515 125 NFSCVFCMKLPDRPVT-TPCGHNFCLKCFQKWIQnRKRTCAKCR 167
Cdd:cd16503    2 TLLCSICQDLLHDCVSlQPCMHNFCAGCYSEWME-RSSLCPQCR 44
RING-HC_TRIM69_C-IV cd16611
RING finger, HC subclass, found in tripartite motif-containing protein 69 (TRIM69) and similar ...
496-532 3.53e-04

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 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: 319525 [Multi-domain]  Cd Length: 44  Bit Score: 38.59  E-value: 3.53e-04
                         10        20        30
                 ....*....|....*....|....*....|....*..
gi 242086515 496 EFGCSICRAVIKEPLTTPCAHNFCKTCLLGKYDSQSS 532
Cdd:cd16611    1 ELTCPLCVEWFKDPVMLPCGHNFCRACIEDVWEGQSS 37
zf-RING_UBOX pfam13445
RING-type zinc-finger; This zinc-finger is a typical RING-type of plant ubiquitin ligases.
128-166 3.65e-04

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


Pssm-ID: 338747 [Multi-domain]  Cd Length: 38  Bit Score: 38.52  E-value: 3.65e-04
                          10        20        30
                  ....*....|....*....|....*....|....*....
gi 242086515  128 CVFCMKLPDRPVTtPCGHNFCLKCFQKWIQNRKRTcAKC 166
Cdd:pfam13445   1 CPICLELFTDPVL-PCGHTFCRECLEEMSLLKGGR-FKC 37
RING-HC_RNF113A_B cd16539
RING finger, HC subclass, found in RING finger proteins RNF113A, RNF113B, and similar proteins; ...
497-527 4.04e-04

RING finger, HC subclass, found in RING finger proteins RNF113A, RNF113B, and similar proteins; RNF113A, also known as zinc finger protein 183 (ZNF183), is an E3 ubiquitin-protein ligase that physically interacts with the E2 protein, UBE2U. A nonsense mutation in RNF113A is associated with an X-linked trichothiodystrophy (TTD). Its yeast ortholog Cwc24p is predicted to have a spliceosome function and acts in a complex with Cef1p to participate in pre-U3 snoRNA splicing, indirectly affecting pre-rRNA processing. It is also important for the U2 snRNP binding to primary transcripts and co-migrates with spliceosomes. Moreover, the ortholog of RNF113A in fruit flies may also act as a spliceosome and is hypothesized to be involved in splicing, namely within the central nervous system. The ortholog in Caenorhabditis elegans is involved in DNA repair of inter-strand crosslinks. RNF113B, also known as zinc finger protein 183-like 1, shows high sequence similarity with RNF113A. Both RNF113A and RNF113B contain a CCCH-type zinc finger, which is commonly found in RNA-binding proteins involved in splicing, and a C3HC4-type RING-HC finger, which is frequently found in E3 ubiquitin ligases.


Pssm-ID: 319453 [Multi-domain]  Cd Length: 41  Bit Score: 38.37  E-value: 4.04e-04
                         10        20        30
                 ....*....|....*....|....*....|.
gi 242086515 497 FGCSICRAVIKEPLTTPCAHNFCKTCLLGKY 527
Cdd:cd16539    1 FACFICRKPFKNPVVTKCGHYFCEKCALKHY 31
zf-C3HC4_4 pfam15227
zinc finger of C3HC4-type, RING; This is a family of primate-specific Ret finger protein-like ...
128-166 4.29e-04

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: 317611 [Multi-domain]  Cd Length: 42  Bit Score: 38.15  E-value: 4.29e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 242086515  128 CVFCMKLPDRPVTTPCGHNFCLKC---FQKWIQNRKRTCAKC 166
Cdd:pfam15227   1 CPICLDYLEKPVSIECGHNFCLSCinsLQKEPDGEGFLCPLC 42
PHD_Phf1p_Phf2p_like cd15502
PHD finger found in Schizosaccharomyces pombe SWM histone demethylase complex subunits Phf1 ...
11-57 4.47e-04

PHD finger found in Schizosaccharomyces pombe SWM histone demethylase complex subunits Phf1 (Phf1p) and Phf2 (Phf2p); Phf1p and Phf2p are components of the SWM histone demethylase complex that specifically demethylates histone H3 at lysine 9 (H3K9me2), a specific tag for epigenetic transcriptional activation. They function as corepressors and play roles in regulating heterochromatin propagation and euchromatic transcription. Both Phf1p and Phf2p contain a plant homeodomain (PHD) finger.


Pssm-ID: 276977  Cd Length: 52  Bit Score: 38.57  E-value: 4.47e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 242086515  11 VCMVC-RAASPPEVDLLRCSTCATPWHSPClSKPP---ALADA--ASWSCPDC 57
Cdd:cd15502    1 VCIVCqRGHSPKSNRIVFCDGCNTPYHQLC-HDPSiddEVVEDpdAEWFCKKC 52
RAD18 COG5432
RING-finger-containing E3 ubiquitin ligase [Signal transduction mechanisms];
499-614 4.54e-04

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


Pssm-ID: 227719 [Multi-domain]  Cd Length: 391  Bit Score: 43.15  E-value: 4.54e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 242086515 499 CSICRAVIKEPLTTPCAHNFCKTCL---LGKYDSQSSMRERSRGGRtLRAQKIVKtcpscpTDICDFLENPQINREMMEL 575
Cdd:COG5432   28 CRICDCRISIPCETTCGHTFCSLCIrrhLGTQPFCPVCREDPCESR-LRGSSGSR------EINESHARNRDLLRKVLES 100
                         90       100       110       120
                 ....*....|....*....|....*....|....*....|.
gi 242086515 576 IETLQRKAVEE--GKVASDDAEECGDGDSEENDGALVKGEE 614
Cdd:COG5432  101 LCRLPRPIKEErpCRWETVIAQDSASGDEEWEDDLASNSSP 141
zf-RING_5 pfam14634
zinc-RING finger domain;
128-168 4.72e-04

zinc-RING finger domain;


Pssm-ID: 339304 [Multi-domain]  Cd Length: 43  Bit Score: 38.18  E-value: 4.72e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 242086515  128 CVFCMKLPD---RPVTTPCGHNFCLKCFQKwiQNRKRTCAKCRA 168
Cdd:pfam14634   2 CNKCFKPLSktrPFYLTSCGHIFCEECLTK--LLKERQCPICRK 43
PHD_PHF21A cd15523
PHD finger found in PHD finger protein 21A (PHF21A); PHF21A (also termed BHC80a or BRAF35-HDAC ...
11-57 5.07e-04

PHD finger found in PHD finger protein 21A (PHF21A); PHF21A (also termed BHC80a or BRAF35-HDAC complex protein BHC80) along with HDAC1/2, CtBP1, CoREST, and BRAF35, is associated with LSD1, a lysine (K)-specific histone demethylase. It inhibits LSD1-mediated histone demethylation in vitro. PHF21A is predominantly present in the central nervous system and spermatogenic cells and is one of the six components of BRAF-HDAC complex (BHC) involved in REST-dependent transcriptional repression of neuron-specific genes in non-neuronal cells. It acts as a scaffold protein in BHC in neuronal as well as non-neuronal cells and also plays a role in spermatogenesis. PHF21A contains a C-terminal plant homeodomain (PHD) finger that is responsible for the binding directly to each of five other components of BHC, and of organizing BHC mediating transcriptional repression.


Pssm-ID: 276998  Cd Length: 43  Bit Score: 38.15  E-value: 5.07e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
gi 242086515  11 VCMVCRAASppevDLLRCSTCATPWHSPCLSKPPALADAASWSCPDC 57
Cdd:cd15523    1 FCSVCRKSG----ELLMCDTCSLVYHLDCLDPPLKTIPKGMWICPKC 43
RING-HC_TRIM40-C-V cd16583
RING finger, HC subclass, found in tripartite motif-containing protein 40 (TRIM40) and similar ...
499-555 6.53e-04

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 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 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: 319497 [Multi-domain]  Cd Length: 46  Bit Score: 37.95  E-value: 6.53e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 242086515 499 CSICRAVIKEPLTTPCAHNFCKTCLLGkydsqsSMRERSRGGrtlraqkiVKTCPSC 555
Cdd:cd16583    2 CPICLDPLKEPVSTTCGHVFCRGCIAQ------HLEKASVSG--------VLCCPVC 44
RING-HC_TRIM8_C-V cd16580
RING finger, HC subclass, found in tripartite motif-containing protein 8 (TRIM8) and similar ...
499-523 6.57e-04

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 nuclear 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: 319494 [Multi-domain]  Cd Length: 44  Bit Score: 38.02  E-value: 6.57e-04
                         10        20
                 ....*....|....*....|....*
gi 242086515 499 CSICRAVIKEPLTTPCAHNFCKTCL 523
Cdd:cd16580    3 CPICLHVFVEPVQLPCKHNFCRGCI 27
RING-HC_TRIM17_C-IV cd16595
RING finger, HC subclass, found in tripartite motif-containing protein TRIM17 and similar ...
126-167 6.93e-04

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 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: 319509 [Multi-domain]  Cd Length: 48  Bit Score: 37.82  E-value: 6.93e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
gi 242086515 126 FSCVFCMKLPDRPVTTPCGHNFCLKCF-QKWIQNRKR----TCAKCR 167
Cdd:cd16595    2 LCCSICLDYFKDPVILRCGHNFCRACItQFWEKQGGLqgklTCPECR 48
RING-HC_TRIM31_C-V cd16582
RING finger, HC subclass, found in tripartite motif-containing protein 31 (TRIM31) and similar ...
126-166 7.11e-04

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 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 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: 319496 [Multi-domain]  Cd Length: 41  Bit Score: 37.44  E-value: 7.11e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|.
gi 242086515 126 FSCVFCMKLPDRPVTTPCGHNFCLKCFQKWIQNRKRtCAKC 166
Cdd:cd16582    2 VICPICLDILQKPVTIDCGHTFCLKCITQIKEGFFK-CPLC 41
RING-HC_TRIM5_like-C-IV cd16591
RING finger, HC subclass, found in tripartite motif-containing proteins TRIM5, TRIM6, TRIM22, ...
496-557 7.17e-04

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 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: 319505 [Multi-domain]  Cd Length: 49  Bit Score: 37.85  E-value: 7.17e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 242086515 496 EFGCSICRAVIKEPLTTPCAHNFCKTCLLGKYDSQSSMRERSrggrtlraqkivkTCPSCPT 557
Cdd:cd16591    1 EVTCPICLELLTEPLSLDCGHSFCRACITANHKESVLTDGES-------------SCPVCRI 49
RING-HC_RNF168 cd16550
RING finger, HC subclass, found in RING finger protein 168 (RNF168) and similar proteins; ...
499-522 7.22e-04

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: 319464 [Multi-domain]  Cd Length: 42  Bit Score: 37.66  E-value: 7.22e-04
                         10        20
                 ....*....|....*....|....
gi 242086515 499 CSICRAVIKEPLTTPCAHNFCKTC 522
Cdd:cd16550    1 CPICLEILVEPVTLPCKHELCLPC 24
RING-HC_TRIM60_like_C-IV cd16607
RING finger, HC subclass, found in tripartite motif-containing proteins TRIM60, TRIM61 and ...
127-151 7.39e-04

RING finger, HC subclass, found in tripartite motif-containing proteins TRIM60, TRIM61 and similar proteins; TRIM60 and TRIM61 are two closely related tripartite motif-containing 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). TRIM60 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 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. In contrast to TRIM60, TRIM61 belongs to the C-V subclass of TRIM family that contains RBCC domains only. Its biological function remains unclear.


Pssm-ID: 319521 [Multi-domain]  Cd Length: 47  Bit Score: 37.65  E-value: 7.39e-04
                         10        20
                 ....*....|....*....|....*
gi 242086515 127 SCVFCMKLPDRPVTTPCGHNFCLKC 151
Cdd:cd16607    3 SCPICLEYLKDPVTINCGHNFCRSC 27
RING-HC_RNF151 cd16547
RING finger, HC subclass, found in RING finger protein 151 (RNF151) and similar proteins; ...
128-167 8.52e-04

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 mediated intracellular membrane fusion in both neuronal and non-neuronal cells. Thus, it may be involved in acrosome formation of spermatids through 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: 319461 [Multi-domain]  Cd Length: 39  Bit Score: 37.49  E-value: 8.52e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|
gi 242086515 128 CVFCMKLPDRPVTTPCGHNFCLKCFQKWIQnRKRTCAKCR 167
Cdd:cd16547    1 CSICHGVLKCPYMLPCSHIFCKKCILQWLK-RQETCPCCR 39
RING-HC_TRIM72_C-IV cd16612
RING finger, HC subclass, found in tripartite motif-containing protein 72 (TRIM72) and similar ...
125-151 9.72e-04

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 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 via 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 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: 319526 [Multi-domain]  Cd Length: 47  Bit Score: 37.55  E-value: 9.72e-04
                         10        20
                 ....*....|....*....|....*..
gi 242086515 125 NFSCVFCMKLPDRPVTTPCGHNFCLKC 151
Cdd:cd16612    1 DLSCPLCLELFRAPVTPECGHTFCQAC 27
RING-HC_RNFT1 cd16741
RING finger, HC subclass, found in RING finger and transmembrane domain-containing protein 1 ...
128-167 9.79e-04

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: 319655 [Multi-domain]  Cd Length: 40  Bit Score: 37.22  E-value: 9.79e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|
gi 242086515 128 CVFCMKLPDRPVTTPCGHNFCLKCFQKWIqNRKRTCAKCR 167
Cdd:cd16741    2 CPICQAEFQKPILLICQHIFCEECISLWF-NREKTCPLCR 40
RING-HC_RNF141 cd16545
RING finger, HC subclass, found in RING finger protein 141 (RNF141) and similar proteins; ...
128-167 1.03e-03

RING finger, HC subclass, found in RING finger protein 141 (RNF141) and similar proteins; RNF141, also known as zinc finger protein 230 (ZNF230), is a RING finger protein present primarily in the nuclei of spermatogonia, the acrosome, and the tail of spermatozoa. It may have a broad function during early development of vertebrates. It plays an important role in spermatogenesis, including spermatogenic cell proliferation and sperm maturation, as well as motility and fertilization. It also exhibits DNA binding activity. RNF141 corresponding ZNF230 gene mutation may be associated with azoospermia. RNF141 contains a C3HC4-type RING finger domain that may function as an activator module in transcription.


Pssm-ID: 319459 [Multi-domain]  Cd Length: 39  Bit Score: 37.00  E-value: 1.03e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|.
gi 242086515 128 CVFCM-KLPDrpVTTPCGHNFCLKCFQKWiQNRKRTCAKCR 167
Cdd:cd16545    2 CCICMdRKPD--TILPCAHSFCQKCIDKW-SVRHRTCPICR 39
RING-HC_TRIM9 cd16755
RING finger, HC subclass, found in tripartite motif-containing protein 9 (TRIM9) and similar ...
495-522 1.22e-03

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 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 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: 319669 [Multi-domain]  Cd Length: 52  Bit Score: 37.33  E-value: 1.22e-03
                         10        20
                 ....*....|....*....|....*...
gi 242086515 495 KEFGCSICRAVIKEPLTTPCAHNFCKTC 522
Cdd:cd16755    2 EELKCPVCGSFYREPIILPCSHNLCLAC 29
mRING-HC-C3HC3D_PHRF1 cd16635
Modified RING finger, HC subclass (C3HC3D-type), found in PHD and RING finger ...
127-158 1.22e-03

Modified RING finger, HC subclass (C3HC3D-type), found in PHD and RING finger domain-containing protein 1(PHRF1) and similar proteins; PHRF1, also known as KIAA1542, or CTD-binding SR-like protein rA9, is a ubiquitin ligase which induces the ubiquitination of TGIF (TG-interacting factor) at lysine 130. It acts as a tumor suppressor that promotes the transforming growth factor (TGF)-beta cytostatic program through selective release of TGIF-driven promyelocytic leukemia protein (PML) inactivation. PHRF1 contains a plant homeodomain (PHD) finger and a modified C3HC3D-type RING-HC finger.


Pssm-ID: 319549 [Multi-domain]  Cd Length: 44  Bit Score: 37.03  E-value: 1.22e-03
                         10        20        30
                 ....*....|....*....|....*....|....*
gi 242086515 127 SCVFCM-KLPDRPVTTP--CGHNFCLKCFQKWIQN 158
Cdd:cd16635    2 SCPICLnEFTDQAVGTPesCDHYFCLDCILEWSKN 36
mRING-HC-C3HC3D_TRAF7 cd16644
Modified RING finger, HC subclass (C3HC3D-type), found in tumor necrosis factor (TNF) ...
499-526 1.42e-03

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 through 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: 319558 [Multi-domain]  Cd Length: 39  Bit Score: 36.88  E-value: 1.42e-03
                         10        20
                 ....*....|....*....|....*...
gi 242086515 499 CSICRAVIKEPLTTPCAHNFCKTCLLGK 526
Cdd:cd16644    3 CPLCQKVFKDPVITTCGHTFCRRCVLTS 30
RING-HC_MID_C-I cd16575
RING finger, HC subclass, found in midline-1 (MID1), midline-2 (MID2) and similar proteins; ...
128-156 1.47e-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), is highly related to MID1. It 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 and the functional redundancy exists between MID1 and MID2 in cytotoxic lymphocytes (CTL). Both MID1 and MID2 belong to the C-I 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 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: 319489 [Multi-domain]  Cd Length: 52  Bit Score: 37.13  E-value: 1.47e-03
                         10        20
                 ....*....|....*....|....*....
gi 242086515 128 CVFCMKLPDRPVTTPCGHNFCLKCFQKWI 156
Cdd:cd16575    1 CPICLELFEDPILLPCSHNLCKSCAERLV 29
RING-HC_TRIM46 cd16757
RING finger, HC subclass, found in tripartite motif-containing protein 46 (TRIM46) and similar ...
495-522 1.63e-03

RING finger, HC subclass, 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 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: 319671  Cd Length: 43  Bit Score: 36.73  E-value: 1.63e-03
                         10        20
                 ....*....|....*....|....*...
gi 242086515 495 KEFGCSICRAVIKEPLTTPCAHNFCKTC 522
Cdd:cd16757    3 RELLCPVCKEMYKQPLVLPCMHNVCLVC 30
RING-HC_TRIM31_C-V cd16582
RING finger, HC subclass, found in tripartite motif-containing protein 31 (TRIM31) and similar ...
496-523 1.71e-03

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 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 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: 319496 [Multi-domain]  Cd Length: 41  Bit Score: 36.67  E-value: 1.71e-03
                         10        20
                 ....*....|....*....|....*...
gi 242086515 496 EFGCSICRAVIKEPLTTPCAHNFCKTCL 523
Cdd:cd16582    1 EVICPICLDILQKPVTIDCGHTFCLKCI 28
RING-HC_ScPSH1_like cd16568
RING finger, HC subclass, found in Saccharomyces cerevisiae POB3/SPT16 histone-associated ...
138-167 1.71e-03

RING finger, HC subclass, found in Saccharomyces cerevisiae POB3/SPT16 histone-associated protein 1 (ScPSH1), Arabidopsis thaliana Protein KEEP ON GOING (AtKEG) 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. AtKEG is an E3 ubiquitin ligase essential for Arabidopsis growth and development. It maintains low levels of ABSCISIC ACID-INSENSITIVE5 (ABI5) in the absence of stress and thus functions as a negative regulator of abscisic acid (ABA) signaling. AtKEG 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: 319482 [Multi-domain]  Cd Length: 45  Bit Score: 36.71  E-value: 1.71e-03
                         10        20        30
                 ....*....|....*....|....*....|...
gi 242086515 138 PVTTPCGHNFCLKCFQKWI--QNRKR-TCAKCR 167
Cdd:cd16568   13 PMMLPCGHGFCKKCLNKMFstSSDKRlACPTCR 45
zf-C3HC4_2 pfam13923
Zinc finger, C3HC4 type (RING finger);
499-555 1.74e-03

Zinc finger, C3HC4 type (RING finger);


Pssm-ID: 316445 [Multi-domain]  Cd Length: 40  Bit Score: 36.63  E-value: 1.74e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 242086515  499 CSICRAVIKEPL-TTPCAHNFCKTCLLgkydsqssmrersrggRTLRAQKIvktCPSC 555
Cdd:pfam13923   2 CPICLDMLKDPStTTPCGHVFCQKCIL----------------RALRSGNE---CPLC 40
zf-C3HC4_3 pfam13920
Zinc finger, C3HC4 type (RING finger);
128-170 1.84e-03

Zinc finger, C3HC4 type (RING finger);


Pssm-ID: 339001 [Multi-domain]  Cd Length: 48  Bit Score: 36.59  E-value: 1.84e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 242086515  128 CVFCMKLPDRPVTTPCGHN-FCLKCFQKWIQNRKRtCAKCRAQI 170
Cdd:pfam13920   5 CVICLDRPRNVVLLPCGHLcLCEECAERLRKKKKK-CPICRQPI 47
RING-HC_AtRMA_like cd16745
RING finger, HC subclass, found in Arabidopsis thaliana RING membrane-anchor proteins (AtRMAs) ...
497-555 2.02e-03

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: 319659 [Multi-domain]  Cd Length: 45  Bit Score: 36.51  E-value: 2.02e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 242086515 497 FGCSICRAVIKEPLTTPCAHNFCKTCLLgkydsqssmrersrggRTLRAQKIVKTCPSC 555
Cdd:cd16745    1 FECNICLDLASDPVVTLCGHLFCWPCLY----------------RWLQRHSENRECPVC 43
RING-HC_TRIM26_C-IV cd16598
RING finger, HC subclass, found in tripartite motif-containing protein 26 (TRIM26) and similar ...
496-522 2.05e-03

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 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: 319512 [Multi-domain]  Cd Length: 45  Bit Score: 36.40  E-value: 2.05e-03
                         10        20
                 ....*....|....*....|....*..
gi 242086515 496 EFGCSICRAVIKEPLTTPCAHNFCKTC 522
Cdd:cd16598    1 EVTCSICLDYLRDPVTIDCGHVFCRSC 27
RING-H2_RNF24_like cd16469
RING finger, H2 subclass, found in RING finger proteins RNF24, RNF122, and similar proteins; ...
128-170 2.13e-03

RING finger, H2 subclass, found in RING finger proteins RNF24, RNF122, and similar proteins; The family includes RNF24, RNF122, and similar proteins. RNF24 is an intrinsic membrane protein localized in the Golgi apparatus. It specifically interacts with the ankyrin-repeats domains (ARDs) of TRPC1, ?3, ?4, ?5, ?6, and ?7, and affects TRPC intracellular trafficking without affecting their activity. RNF122 is a RING finger protein associated with HEK 293T cell viability. It is localized to the endoplasmic reticulum (ER) and the Golgi apparatus, and overexpressed in anaplastic thyroid cancer cells. RNF122 functions as an E3 ubiquitin ligase that can ubiquitinate itself and undergoes degradation through its RING finger in a proteasome-dependent manner. Both RNF24 and RNF122 contain an N-terminal transmembrane domain and a C-terminal C3H2C3-type RING-H2 finger.


Pssm-ID: 319383 [Multi-domain]  Cd Length: 47  Bit Score: 36.28  E-value: 2.13e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*.
gi 242086515 128 CVFCM---KLPDRPVTTPCGHNFCLKCFQKWIQNRKrTCAKCRAQI 170
Cdd:cd16469    3 CAVCLedfKKKEELGVCPCGHAFHRKCLLKWLEVRN-VCPMCNSPV 47
RING-HC_RNF151 cd16547
RING finger, HC subclass, found in RING finger protein 151 (RNF151) and similar proteins; ...
499-524 2.26e-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 mediated intracellular membrane fusion in both neuronal and non-neuronal cells. Thus, it may be involved in acrosome formation of spermatids through 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: 319461 [Multi-domain]  Cd Length: 39  Bit Score: 36.33  E-value: 2.26e-03
                         10        20
                 ....*....|....*....|....*.
gi 242086515 499 CSICRAVIKEPLTTPCAHNFCKTCLL 524
Cdd:cd16547    1 CSICHGVLKCPYMLPCSHIFCKKCIL 26
zf-RING_UBOX pfam13445
RING-type zinc-finger; This zinc-finger is a typical RING-type of plant ubiquitin ligases.
499-532 2.34e-03

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


Pssm-ID: 338747 [Multi-domain]  Cd Length: 38  Bit Score: 36.21  E-value: 2.34e-03
                          10        20        30
                  ....*....|....*....|....*....|....
gi 242086515  499 CSICRAVIKEPLTtPCAHNFCKTCLLGKYDSQSS 532
Cdd:pfam13445   1 CPICLELFTDPVL-PCGHTFCRECLEEMSLLKGG 33
RING-HC_CHFR cd16503
RING finger, HC subclass, found in checkpoint with forkhead and RING finger domains protein ...
499-555 2.48e-03

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) and a C3HC4-type RING-HC finger.


Pssm-ID: 319417 [Multi-domain]  Cd Length: 44  Bit Score: 36.23  E-value: 2.48e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 242086515 499 CSICRAVIKEPLT-TPCAHNFCKTCLlgkydsqSSMRERSrggrtlraqkivKTCPSC 555
Cdd:cd16503    5 CSICQDLLHDCVSlQPCMHNFCAGCY-------SEWMERS------------SLCPQC 43
RING-HC_TRIM42_C-III cd16578
RING finger, HC subclass, found in tripartite motif-containing protein 42 (TRIM42) and similar ...
128-154 2.55e-03

RING finger, HC subclass, found in tripartite motif-containing protein 42 (TRIM42) and similar proteins; TRIM42 belongs to the C-III 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 domain. It also has a novel cysteine-rich motif N-terminal to the RBCC domain, as well as a COS (carboxyl-terminal subgroup one signature) box and a fibronectin type-III (FN3) domain positioned C-terminal to the RBCC domain. TRIM42 can interact with TRIM27, a known cancer-associated protein. Its precise biological function remains unclear.


Pssm-ID: 319492  Cd Length: 51  Bit Score: 36.43  E-value: 2.55e-03
                         10        20
                 ....*....|....*....|....*..
gi 242086515 128 CVFCMKLPDRPVTTPCGHNFCLKCFQK 154
Cdd:cd16578    4 CPLCKGLRLHPVILPCNHSVCEKCLRR 30
RING-HC_TRIM13_C-V cd16762
RING finger, HC subclass, found in tripartite motif-containing protein 13 (TRIM13) and similar ...
124-169 2.58e-03

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 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-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 C3HC4-type RING-HC finger, Bbox1 and Bbox2, and a coiled coil region. In addition, TRIM13 contains a C-terminal transmembrane domain.


Pssm-ID: 319676 [Multi-domain]  Cd Length: 57  Bit Score: 36.50  E-value: 2.58e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 242086515 124 KNFSCVFCMKLPDRPVTTPCGHNFCLKCFQKWIQNRKRT---------CAKCRAQ 169
Cdd:cd16762    2 EDLTCPICCSLFDDPRVLPCSHNFCKKCLEGILEGNVRNmlwrpapfkCPTCRKE 56
RING-HC_GEFO_like cd16507
RING finger, HC subclass, found in Dictyostelium discoideum Ras guanine nucleotide exchange ...
127-166 2.66e-03

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, is one of the Ras guanine-nucleotide exchange factors (RasGEFs), which are the proteins that activate Ras through catalyzing the replacement of GDP with GTP. They are particularly important for signaling in development and chemotaxis in many organisms, including Dictyostelium. RasGEFO contain a C3HC4-type RING-HC finger that may be responsible for the E3 ubiquitin ligase activity.


Pssm-ID: 319421  Cd Length: 40  Bit Score: 36.03  E-value: 2.66e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|.
gi 242086515 127 SCVFCMKLPDRPVT-TPCGHNFCLKCFQKwiQNRKRTCAKC 166
Cdd:cd16507    1 TCLQCMQLFKEPMTlIPCGHTFCAACLAK--CGSSIACNMC 39
mRING-HC-C3HC3D_TRAF5 cd16642
Modified RING finger, HC subclass (C3HC3D-type), found in tumor necrosis factor (TNF) ...
499-558 2.70e-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), tumor necrosis factor receptor 2 (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 through 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: 319556 [Multi-domain]  Cd Length: 43  Bit Score: 35.89  E-value: 2.70e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 242086515 499 CSICRAVIKEPLTTPCAHNFCKTCLLGKYDSqssmrersrggrtlraqkivKTCPSCPTD 558
Cdd:cd16642    3 CATCHFVLHNPHQTGCGHRFCEHCILVLLEL--------------------NPTPACPID 42
PHD2_KDM5B cd15607
PHD finger 2 found in lysine-specific demethylase 5B (KDM5B); KDM5B (also termed Cancer/testis ...
14-57 2.71e-03

PHD finger 2 found in lysine-specific demethylase 5B (KDM5B); KDM5B (also termed Cancer/testis antigen 31 (CT31), Histone demethylase JARID1B, Jumonji/ARID domain-containing protein 1B (JARID1B), retinoblastoma-binding protein 2 homolog 1 (RBP2-H1 or RBBP2H1A), or PLU-1) is a member of the JARID subfamily within the JmjC proteins. It has a restricted expression pattern in the testis, ovary, and transiently in the mammary gland of the pregnant female and has been shown to be upregulated in breast cancer, prostate cancer, and lung cancer, suggesting a potential role in tumorigenesis. KDM5B acts as a histone demethylase that catalyzes the removal of trimethylation of lysine 4 on histone H3 (H3K4me3), induced by polychlorinated biphenyls (PCBs). It also mediates demethylation of H3K4me2 and H3K4me1. Moreover, KDM5B functions as a negative regulator of hematopoietic stem cell (HSC) self-renewal and progenitor cell activity. KDM5B has also been shown to interact with the DNA binding transcription factors BF-1 and PAX9, as well as TIEG1/KLF10 (transforming growth factor-beta inducible early gene-1/Kruppel-like transcription factor 10), and possibly function as a transcriptional corepressor. KDM5B contains the catalytic JmjC domain, JmjN, the BRIGHT domain, which is an AT-rich interacting domain (ARID), and a Cys5HisCys2 zinc finger, as well as three plant homeodomain (PHD) fingers. This model corresponds to the second PHD finger.


Pssm-ID: 277080  Cd Length: 44  Bit Score: 35.97  E-value: 2.71e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....
gi 242086515  14 VCRAASPPEVDLLRCSTCATPWHSPCLSKPPALADAASWSCPDC 57
Cdd:cd15607    1 VCVCQKAPMAPMIQCELCRDAFHSGCVTAPSDPQGPQAWLCPQC 44
RING-HC_TRIM39_C-IV cd16601
RING finger, HC subclass, found in tripartite motif-containing protein 39 (TRIM39) and similar ...
127-166 2.86e-03

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 transcriptions, which is induced by inflammatory stimulants such as tumor necrosis factor alpha (TNFalpha). 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 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: 319515 [Multi-domain]  Cd Length: 44  Bit Score: 36.19  E-value: 2.86e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|..
gi 242086515 127 SCVFCMKLPDRPVTTPCGHNFCLKCFQKWIQ--NRKRTCAKC 166
Cdd:cd16601    3 SCSVCLEYLKEPVIIECGHNFCKACITRWWEdlERDFPCPVC 44
PHD_SF cd15489
PHD finger superfamily; The PHD finger superfamily includes a canonical plant homeodomain (PHD) ...
11-57 2.92e-03

PHD finger superfamily; The PHD finger superfamily includes a canonical plant homeodomain (PHD) finger typically characterized as Cys4HisCys3, and a non-canonical extended PHD finger, characterized as Cys2HisCys5HisCys2His. Variations include the RAG2 PHD finger characterized by Cys3His2Cys2His and the PHD finger 5 found in nuclear receptor-binding SET domain-containing proteins characterized by Cys4HisCys2His. The PHD finger is also termed LAP (leukemia-associated protein) motif or TTC (trithorax consensus) domain. Single or multiple copies of PHD fingers have been found in a variety of eukaryotic proteins involved in the control of gene transcription and chromatin dynamics. PHD fingers can recognize the unmodified and modified histone H3 tail, and some have been found to interact with non-histone proteins. They also function as epigenome readers controlling gene expression through molecular recruitment of multi-protein complexes of chromatin regulators and transcription factors. The PHD finger domain SF is structurally similar to the RING and FYVE_like superfamilies.


Pssm-ID: 276966  Cd Length: 48  Bit Score: 36.14  E-value: 2.92e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*...
gi 242086515  11 VCMVCRAASPPEVDLLRCSTCATPWHSPCLSKPPALADA-ASWSCPDC 57
Cdd:cd15489    1 SCIVCGKGGDLGGELLQCDGCGKWFHADCLGPPLSSFVPnGKWICPVC 48
mRING-HC-C4C4_TRIM37_C-VIII cd16619
Modified RING finger, HC subclass (C4C4-type), found in tripartite motif-containing protein 37 ...
126-167 3.08e-03

Modified RING finger, HC subclass (C4C4-type), found in tripartite motif-containing protein 37 (TRIM37) and similar proteins; TRIM37, also known as mulibrey nanism protein, or MUL, is a peroxisomal E3 ubiquitin-protein ligase that is involved in the tumorigenesis of several cancer types, including pancreatic ductal adenocarcinoma (PDAC), hepatocellular carcinoma (HCC), breast cancer, and sporadic fibrothecoma. It mono-ubiquitinates histone H2A, a chromatin modification associated with transcriptional repression. Moreover, TRIM37 possesses anti-HIV-1 activity, and interferes with viral DNA synthesis. Mutations in the human TRIM37 gene (also known as MUL) cause Mulibrey (muscle-liver-brain-eye) nanism, a rare growth disorder of prenatal onset characterized by dysmorphic features, pericardial constriction, and hepatomegaly. TRIM37 belongs to the C-VIII 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 C4C4-type RING finger, whose overall folding is similar to that of the typical C3HC4-type RING-HC finger, Bbox1 and Bbox2, and a coiled coil region, as well as a MATH (meprin and TRAF-C homology) domain positioned C-terminal to the RBCC domain. Its MATH domain has been shown to interact with the TRAF (TNF-Receptor-Associated Factor) domain of six known TRAFs in vitro.


Pssm-ID: 319533 [Multi-domain]  Cd Length: 43  Bit Score: 35.79  E-value: 3.08e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|...
gi 242086515 126 FSCVFCMKLPDRPVTTP-CGHNFCLKCFQKWIQNRKRTCAKCR 167
Cdd:cd16619    1 FRCFICMEKLRDARLCPhCSKLCCFSCIRRWLTEQRSQCPHCR 43
RING-HC_TRIM11_like_C-IV cd16594
RING finger, HC subclass, found in tripartite motif-containing proteins, TRIM11 and TRIM27, ...
496-524 3.13e-03

RING finger, HC subclass, found in tripartite motif-containing proteins, TRIM11 and TRIM27, and similar proteins; TRIM11 and TRIM27, two closely related tripartite motif-containing proteins, 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 C3HC4-type RING-HC finger, Bbox1 and Bbox2, and a coiled coil region, as well as a SPRY/B30.2 domain positioned C-terminal to the RBCC domain. 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 congenital central hypoventilation syndrome-associated polyalanine-expanded Phox2b. Trim11 modulates the function of neurogenic transcription factor Pax6 through ubiquitin-proteosome system, and thus plays an essential role for the 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, through the ubiquitin-proteasome system, 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. Furthermore, TRIM27 promote a non-canonical polyubiquitinations 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: 319508 [Multi-domain]  Cd Length: 45  Bit Score: 35.91  E-value: 3.13e-03
                         10        20
                 ....*....|....*....|....*....
gi 242086515 496 EFGCSICRAVIKEPLTTPCAHNFCKTCLL 524
Cdd:cd16594    1 ELTCPVCLEYFTDPVILDCGHNFCRACIL 29
RING-HC_RNF113A_B cd16539
RING finger, HC subclass, found in RING finger proteins RNF113A, RNF113B, and similar proteins; ...
126-166 3.13e-03

RING finger, HC subclass, found in RING finger proteins RNF113A, RNF113B, and similar proteins; RNF113A, also known as zinc finger protein 183 (ZNF183), is an E3 ubiquitin-protein ligase that physically interacts with the E2 protein, UBE2U. A nonsense mutation in RNF113A is associated with an X-linked trichothiodystrophy (TTD). Its yeast ortholog Cwc24p is predicted to have a spliceosome function and acts in a complex with Cef1p to participate in pre-U3 snoRNA splicing, indirectly affecting pre-rRNA processing. It is also important for the U2 snRNP binding to primary transcripts and co-migrates with spliceosomes. Moreover, the ortholog of RNF113A in fruit flies may also act as a spliceosome and is hypothesized to be involved in splicing, namely within the central nervous system. The ortholog in Caenorhabditis elegans is involved in DNA repair of inter-strand crosslinks. RNF113B, also known as zinc finger protein 183-like 1, shows high sequence similarity with RNF113A. Both RNF113A and RNF113B contain a CCCH-type zinc finger, which is commonly found in RNA-binding proteins involved in splicing, and a C3HC4-type RING-HC finger, which is frequently found in E3 ubiquitin ligases.


Pssm-ID: 319453 [Multi-domain]  Cd Length: 41  Bit Score: 35.67  E-value: 3.13e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|.
gi 242086515 126 FSCVFCMKLPDRPVTTPCGHNFCLKCFQKWIQNRKRtCAKC 166
Cdd:cd16539    1 FACFICRKPFKNPVVTKCGHYFCEKCALKHYRKSKR-CFVC 40
PEX10 COG5574
RING-finger-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, ...
446-532 3.25e-03

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


Pssm-ID: 227861 [Multi-domain]  Cd Length: 271  Bit Score: 39.88  E-value: 3.25e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 242086515 446 WDYDEKDGWKW---MVPPPVSKKPVLSGDPETDKQIRRSTkrahlsvaerlLKEFGCSICRAVIKEPLTTPCAHNFCKTC 522
Cdd:COG5574  173 LSLDESRLQPIlqpSNNLHTLFQVITKENLSKKNGLPFIP-----------LADYKCFLCLEEPEVPSCTPCGHLFCLSC 241
                         90
                 ....*....|
gi 242086515 523 LLGKYDSQSS 532
Cdd:COG5574  242 LLISWTKKKY 251
PHD_UHRF1_2 cd15525
PHD finger found in ubiquitin-like PHD and RING finger domain-containing protein UHRF1 and ...
12-57 3.25e-03

PHD finger found in ubiquitin-like PHD and RING finger domain-containing protein UHRF1 and UHRF2; 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 tumour 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 RING finger.


Pssm-ID: 277000  Cd Length: 47  Bit Score: 35.81  E-value: 3.25e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
gi 242086515  12 CMVCRAASPPEVDLLrCSTCATPWHSPCLSKP-PALADAASWSCPDC 57
Cdd:cd15525    2 CHVCGGKQDPEKQLL-CDECDMAYHLYCLDPPlTSLPDDDEWYCPDC 47
RING-HC_TRIM68_C-IV cd16610
RING finger, HC subclass, found in tripartite motif-containing protein 68 (TRIM68) and similar ...
127-167 3.38e-03

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 through 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 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: 319524 [Multi-domain]  Cd Length: 49  Bit Score: 36.06  E-value: 3.38e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
gi 242086515 127 SCVFCMKLPDRPVTTPCGHNFCLKCFQK-W-----IQNRKRTCAKCR 167
Cdd:cd16610    3 ACPICMTFLREPVSIDCGHSFCHSCLSGlWevpgeSQNWGYTCPLCR 49
RING-HC_RAG1 cd16530
RING finger, HC subclass, found in recombination activating gene-1 (RAG-1) and similar ...
495-524 3.53e-03

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 the lymphoid-specific factor that mediates the DNA-binding to the conserved recombination signal sequences (RSS) and catalyzes the 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: 35.88  E-value: 3.53e-03
                         10        20        30
                 ....*....|....*....|....*....|
gi 242086515 495 KEFGCSICRAVIKEPLTTPCAHNFCKTCLL 524
Cdd:cd16530    1 KSVSCQVCEHILADPVQTPCKHLFCRTCIL 30
RING-HC_TRIM58_C-IV cd16606
RING finger, HC subclass, found in tripartite motif-containing protein TRIM58 and similar ...
128-168 3.83e-03

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: 319520 [Multi-domain]  Cd Length: 51  Bit Score: 35.77  E-value: 3.83e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
gi 242086515 128 CVFCMKLPDRPVTTPCGHNFCLKCFQKWI------QNRKRTCAKCRA 168
Cdd:cd16606    4 CPVCLDFLQEPVSVDCGHSFCLRCISEFCeksdsaQGGVYACPQCRG 50
RING-HC_TRIM41_like_C-IV cd16602
RING finger, HC subclass, found in tripartite motif-containing proteins TRIM41, TRIM52 and ...
128-167 4.04e-03

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 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 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: 319516 [Multi-domain]  Cd Length: 41  Bit Score: 35.61  E-value: 4.04e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|.
gi 242086515 128 CVFCMKLPDRPVTTPCGHNFCLKCF-QKWiqnrkRTCAKCR 167
Cdd:cd16602    5 CAICLDYFRDPVSIGCGHNFCRVCVtQLW-----FTCPQCR 40
mRING-HC-C3HC3D_LNX2 cd16780
Modified RING finger, HC subclass (C3HC3D-type), found in ligand of numb protein X 2 (LNX2); ...
496-523 4.16e-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: 35.62  E-value: 4.16e-03
                         10        20
                 ....*....|....*....|....*...
gi 242086515 496 EFGCSICRAVIKEPLTTPCAHNFCKTCL 523
Cdd:cd16780    3 DLVCHICLQPLLQPLDTPCGHTFCFKCL 30
PLN03208 PLN03208
E3 ubiquitin-protein ligase RMA2; Provisional
123-155 4.47e-03

E3 ubiquitin-protein ligase RMA2; Provisional


Pssm-ID: 178747  Cd Length: 193  Bit Score: 38.91  E-value: 4.47e-03
                         10        20        30
                 ....*....|....*....|....*....|...
gi 242086515 123 GKNFSCVFCMKLPDRPVTTPCGHNFCLKCFQKW 155
Cdd:PLN03208  16 GGDFDCNICLDQVRDPVVTLCGHLFCWPCIHKW 48
zf-C3HC4_4 pfam15227
zinc finger of C3HC4-type, RING; This is a family of primate-specific Ret finger protein-like ...
499-523 4.47e-03

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: 317611 [Multi-domain]  Cd Length: 42  Bit Score: 35.46  E-value: 4.47e-03
                          10        20
                  ....*....|....*....|....*
gi 242086515  499 CSICRAVIKEPLTTPCAHNFCKTCL 523
Cdd:pfam15227   1 CPICLDYLEKPVSIECGHNFCLSCI 25
RING-HC_TRIM9_like_C-I cd16576
RING finger, HC subclass, found in tripartite motif-containing proteins TRIM9, TRIM36, TRIM46, ...
495-555 4.53e-03

RING finger, HC subclass, found in tripartite motif-containing proteins TRIM9, TRIM36, TRIM46, TRIM67, and similar proteins; Tripartite motif-containing proteins TRIM9, TRIM36, TRIM46, and TRIM67 belong to the C-I subclass of 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 the neurodegenerative disorders through its ligase activity. TRIM36 (the human ortholog of mouse Haprin), also known as RING finger protein 98 (RNF98), or zinc-binding protein Rbcc728, is an E3 ubiquitin-protein ligase expressed in the germ plasm. It has been implicated in acrosome reaction, fertilization, and embryogenesis, as well as in the carcinogenesis. 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 forms parallel microtubule bundles in the proximal axon and plays a crucial role for the establishment and maintenance of neuronal polarity. 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: 319490 [Multi-domain]  Cd Length: 42  Bit Score: 35.44  E-value: 4.53e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 242086515 495 KEFGCSICRAVIKEPLTTPCAHNFCKTCllgkydsqssmrersrggrtlrAQKIVKTCPSC 555
Cdd:cd16576    2 EELKCPVCREFYTCPVILPCSHSICLSC----------------------ALEILLTCPQC 40
RING-HC_BRE1_like cd16499
RING finger, HC subclass, found in yeast Bre1 and its homologs from eukaryotes; Bre1 is an E3 ...
128-167 4.65e-03

RING finger, HC subclass, found in yeast Bre1 and its homologs from eukaryotes; Bre1 is an E3 ubiquitin-protein ligase that catalyzes monoubiquitination of histone H2B in concert with the E2 ubiquitin-conjugating enzyme, Rad6. The Rad6-Bre1-mediated histone H2B ubiquitylation modulates the formation of double-strand breaks (DSBs) during meiosis in yeast. it is also required, indirectly, for the methylation of histone 3 on lysine 4 (H3K4) and 79. RNF20, also known as BRE1A and RNF40, also known as BRE1B, are the mammalian homologs of Bre1. They work together to form a heterodimeric Bre1 complex that facilitate the K120 monoubiquitination of histone H2B (H2Bub1), a DNA damage-induced histone modification that is crucial for recruitment of the chromatin remodeler SNF2h to DNA double-strand break (DSB) damage sites. Moreover, Bre1 complex acts as a tumor suppressor, augmenting expression of select tumor suppressor genes and suppressing select oncogenes. Deficiency in the mammalian histone H2B ubiquitin ligase Bre1 leads to replication stress and chromosomal instability. All family members contain a C3HC4-type RING-HC finger at its C-terminus.


Pssm-ID: 319413 [Multi-domain]  Cd Length: 42  Bit Score: 35.26  E-value: 4.65e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|
gi 242086515 128 CVFCMKLPDRPVTTPCGHNFCLKCFQKWIQNRKRTCAKCR 167
Cdd:cd16499    3 CSVCNDRQKDVILTKCGHVFCKECIQERLETRQRKCPSCN 42
RING-HC_RNF219 cd16562
RING finger, HC subclass, found in RING finger protein 219 (RNF219) and similar proteins; ...
127-167 4.65e-03

RING finger, HC subclass, found in RING finger protein 219 (RNF219) and similar proteins; RNF219 may function as a modulator of late-onset Alzheimer"s disease (LOAD) associated amyloid beta A4 precursor protein (APP) endocytosis and metabolism. It genetically interacts with apolipoprotein E epsilon4 allele (APOE4). Thus a genetic variant within RNF219 was found to affect amyloid deposition in human brain and LOAD age-of-onset. Moreover, common genetic variants at the RNF219 locus had been associated with alternations in lipid metabolism, cognitive performance and central nervous system ventricle volume. RNF219 contains a C3HC4-type RING-HC finger.


Pssm-ID: 319476 [Multi-domain]  Cd Length: 42  Bit Score: 35.43  E-value: 4.65e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|.
gi 242086515 127 SCVFCMKLPDRPVTTPCGHNFCLKCFQKWIQnRKRTCAKCR 167
Cdd:cd16562    3 SCHICLGKVKQPVICPNNHVFCSSCMDLWLK-RNNQCPACR 42
RING-HC_RNF125 cd16542
RING finger, HC subclass, found in RING finger protein 125 (RNF125); RNF125, also known as ...
497-523 4.77e-03

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: 319456 [Multi-domain]  Cd Length: 42  Bit Score: 35.15  E-value: 4.77e-03
                         10        20
                 ....*....|....*....|....*..
gi 242086515 497 FGCSICRAVIKEPLTTPCAHNFCKTCL 523
Cdd:cd16542    1 FDCAICLEVLHQPVRTRCGHVFCRTCI 27
RING-HC_TRIM38_C-IV cd16600
RING finger, HC subclass, found in tripartite motif-containing protein 38 (TRIM38) and similar ...
496-555 4.80e-03

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 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: 319514 [Multi-domain]  Cd Length: 51  Bit Score: 35.63  E-value: 4.80e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 242086515 496 EFGCSICRAVIKEPLTTPCAHNFCKTCLLGKYDSQSSMRERSRggrtlraqkiVKTCPSC 555
Cdd:cd16600    1 EATCSICLHLMAEPVSISCGHSYCHACIKDFFKNLSQEEPDLE----------TFSCPQC 50
PHD_UHRF1 cd15616
PHD finger found in ubiquitin-like PHD and RING finger domain-containing protein 1 (UHRF1); ...
12-57 5.04e-03

PHD finger found in ubiquitin-like PHD and RING finger domain-containing protein 1 (UHRF1); UHRF1 (also termed 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 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 tumour 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. UHRF1 contains an N-terminal ubiquitin-like domain (UBL), a tandem Tudor domain (TTD), a plant homeodomain (PHD) finger, a SET and RING finger associated (SRA) domain, and a C-terminal RING-finger domain. 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 maintaining DNA methylation and replication. The tandem Tudor domain directs UHRF1 binding to the heterochromatin mark histone H3K9me3 and the PHD finger targets UHRF1 to unmodified histone H3 in euchromatic regions. The RING-finger domain exhibit both autocatalytic E3 ubiquitin (Ub) ligase activity and activity against histone H3 and DNMT1.


Pssm-ID: 277088  Cd Length: 47  Bit Score: 35.33  E-value: 5.04e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
gi 242086515  12 CMVCRAASPPEVDLLrCSTCATPWHSPCLSKP-PALADAASWSCPDC 57
Cdd:cd15616    2 CHVCGGKQDPDKQLM-CDECDMAFHIYCLNPPlSSIPDDEDWYCPEC 47
RING-HC_TRIM35_C-IV cd16599
RING finger, HC subclass, found in tripartite motif-containing protein 35 (TRIM35) and similar ...
128-167 5.19e-03

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 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: 319513 [Multi-domain]  Cd Length: 44  Bit Score: 35.30  E-value: 5.19e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|
gi 242086515 128 CVFCMKLPDRPVTTPCGHNFCLKCFQKWIQNRKRTCAKCR 167
Cdd:cd16599    4 CPICYDPFREAVTLRCGHNFCKGCVSRSWEVRSHTCPVCK 43
HRD1 COG5243
HRD ubiquitin ligase complex, ER membrane component [Posttranslational modification, protein ...
128-222 5.27e-03

HRD ubiquitin ligase complex, ER membrane component [Posttranslational modification, protein turnover, chaperones];


Pssm-ID: 227568 [Multi-domain]  Cd Length: 491  Bit Score: 39.95  E-value: 5.27e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 242086515 128 CVFCMK-------------LPDRPVTTPCGHNFCLKCFQKWIQnRKRTCAKCRAQIPAKMaEQPRINSALVEVIRMAKIS 194
Cdd:COG5243  290 CTICMDemfhpdheplprgLDMTPKRLPCGHILHLHCLKNWLE-RQQTCPICRRPVIFDQ-SSPTPASPNVRNTQIATQV 367
                         90       100       110
                 ....*....|....*....|....*....|
gi 242086515 195 KNPNSAGSAVPYHYIRN--DDRPDKAFTTD 222
Cdd:COG5243  368 PNPDNTPTTTAVPGITNssNQGDPQASTFN 397
mRING-HC-C3HC3D_LNX1 cd16779
Modified RING finger, HC subclass (C3HC3D-type), found in ligand of numb protein X 1 (LNX1); ...
499-523 5.41e-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: 319693 [Multi-domain]  Cd Length: 42  Bit Score: 35.17  E-value: 5.41e-03
                         10        20
                 ....*....|....*....|....*
gi 242086515 499 CSICRAVIKEPLTTPCAHNFCKTCL 523
Cdd:cd16779    4 CHICLQPLIQPLDTPCGHTYCTLCL 28
PHD_BS69 cd15537
PHD finger found in protein BS69; Protein BS69, also termed zinc finger MYND domain-containing ...
12-57 5.53e-03

PHD finger found in protein BS69; Protein BS69, also termed zinc finger MYND domain-containing protein 11 (ZMYND11 or ZMY11), is a ubiquitously expressed nuclear protein acting as a transcriptional co-repressor in association with various transcription factors. It was originally identified as an adenovirus 5 E1A-binding protein that inhibits E1A transactivation, as well as c-Myb transcription. It also mediates repression, at least in part, through interaction with the co-repressor N-CoR. Moreover, it interacts with Toll-interleukin 1 receptor domain (TIR)-containing adaptor molecule-1 (TICAM-1, also named TRIF) to facilitate NF-kappaB activation and type I IFN induction. It associates with PIAS1, a SUMO E3 enzyme, and Ubc9, a SUMO E2 enzyme, and plays an inhibitory role in muscle and neuronal differentiation. Moreover, BS69 regulates Epstein-Barr virus (EBV) latent membrane protein 1 (LMP1)/C-terminal activation region 2 (CTAR2)-mediated NF-kappaB activation by interfering with the complex formation between TNFR-associated death domain protein (TRADD) and LMP1/CTAR2. It also cooperates with tumor necrosis factor receptor (TNFR)-associated factor 3 (TRAF3) in the regulation of EBV-derived LMP1/CTAR1-induced NF-kappaB activation. Furthermore, BS69 is involved in the p53-p21Cip1-mediated senescence pathway. BS69 contains a plant homeodomain (PHD) finger, a bromodomain, a proline-tryptophan-tryptophan-proline (PWWP) domain, and a Myeloid translocation protein 8, Nervy and DEAF-1 (MYND) domain.


Pssm-ID: 277012  Cd Length: 43  Bit Score: 35.01  E-value: 5.53e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*.
gi 242086515  12 CMVCRAASppevDLLRCSTCATPWHSPCLSKPPALADAASWSCPDC 57
Cdd:cd15537    2 CFECHAPG----EVLPCSGCFRVYHSDCLSEDFRPDSTSHWTCPVC 43
RING-HC_TRIM43_like_C-IV cd16603
RING finger, HC subclass, found in tripartite motif-containing proteins TRIM43, TRIM48, TRIM49, ...
128-152 5.98e-03

RING finger, HC subclass, 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 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 target proteins of autoantibodies in the sera of patients with these autoimmune disorders. All family members 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 C3HC4-type RING-HC finger, Bbox1 and Bbox2, and a coiled coil region, as well as a SPRY/B30.2 domain positioned C-terminal to the RBCC domain.


Pssm-ID: 319517 [Multi-domain]  Cd Length: 46  Bit Score: 35.15  E-value: 5.98e-03
                         10        20
                 ....*....|....*....|....*
gi 242086515 128 CVFCMKLPDRPVTTPCGHNFCLKCF 152
Cdd:cd16603    4 CPICMNYFIDPVTIDCGHSFCRPCL 28
COG5152 COG5152
Uncharacterized conserved protein, contains RING and CCCH-type Zn-fingers [General function ...
497-527 6.00e-03

Uncharacterized conserved protein, contains RING and CCCH-type Zn-fingers [General function prediction only];


Pssm-ID: 227481 [Multi-domain]  Cd Length: 259  Bit Score: 38.90  E-value: 6.00e-03
                         10        20        30
                 ....*....|....*....|....*....|.
gi 242086515 497 FGCSICRAVIKEPLTTPCAHNFCKTCLLGKY 527
Cdd:COG5152  197 FLCGICKKDYESPVVTECGHSFCSLCAIRKY 227
rad18 TIGR00599
DNA repair protein rad18; All proteins in this family for which functions are known are ...
126-168 6.12e-03

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: 39.60  E-value: 6.12e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 242086515  126 FSCVFCMKLPDRPVTTPCGHNFCLKCFQKWIQNRKRtCAKCRA 168
Cdd:TIGR00599  27 LRCHICKDFFDVPVLTSCSHTFCSLCIRRCLSNQPK-CPLCRA 68
RING-HC_MID2 cd16754
RING finger, HC subclass, found in midline-2 (MID2) and similar proteins; MID2, also known as ...
499-522 6.21e-03

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 that is highly related to MID1 that associate 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 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: 319668 [Multi-domain]  Cd Length: 53  Bit Score: 35.40  E-value: 6.21e-03
                         10        20
                 ....*....|....*....|....
gi 242086515 499 CSICRAVIKEPLTTPCAHNFCKTC 522
Cdd:cd16754    1 CPICLELFEDPLLLPCAHSLCFSC 24
RING-HC_RNF114 cd16540
RING finger, HC subclass, found in RING finger protein 114 (RNF114) and similar proteins; ...
497-524 6.34e-03

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 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: 319454 [Multi-domain]  Cd Length: 42  Bit Score: 34.81  E-value: 6.34e-03
                         10        20
                 ....*....|....*....|....*...
gi 242086515 497 FGCSICRAVIKEPLTTPCAHNFCKTCLL 524
Cdd:cd16540    1 FTCPVCLEVFEKPVRVPCGHVFCSACLQ 28
RING-HC_TRIM21_C-IV cd16596
RING finger, HC subclass, found in tripartite motif-containing protein TRIM21 and similar ...
495-531 6.63e-03

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 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 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: 319510 [Multi-domain]  Cd Length: 44  Bit Score: 34.86  E-value: 6.63e-03
                         10        20        30
                 ....*....|....*....|....*....|....*....
gi 242086515 495 KEFGCSICRAVIKEPLTTPCAHNFCKTCL--LGKYDSQS 531
Cdd:cd16596    1 EEVTCSICLDPFVEPMSIECGHSFCQECIseVGKYGGSV 39
RING-H2_BRAP2 cd16457
RING finger, H2 subclass, found in BRCA1-associated protein (BRAP2) and similar proteins; ...
127-167 7.01e-03

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 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: 319371 [Multi-domain]  Cd Length: 44  Bit Score: 34.95  E-value: 7.01e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*
gi 242086515 127 SCVFCMKLPDRPV----TTPCGHNFCLKCFQKWIQNrkrTCAKCR 167
Cdd:cd16457    2 TCPVCLERMDESVsgilTILCNHSFHCDCLKRWGDS---TCPVCR 43
RING-HC_Cbl_like cd16502
RING finger, HC subclass, found in Casitas B-lineage lymphoma (Cbl) proteins; The Cbl adaptor ...
142-167 7.03e-03

RING finger, HC subclass, found in Casitas B-lineage lymphoma (Cbl) proteins; The Cbl adaptor proteins family contains a small class of RING-type E3 ubiquitin ligases with oncogenic activity, which is represented by three mammalian members, c-Cbl, Cbl-b and Cbl-c, as well as two invertebrate Cbl-family proteins, D-Cbl in Drosophila and Sli-1 in C. elegans. Cbl proteins function as potent negative regulators of various signaling cascades in a wide range of cell types. They play roles in ubiquitinating the activated tyrosine kinases and targeting them for degradation. D-Cbl associates with the Drosophila epidermal growth factor receptor (EGFR) and overexpression of D-Cbl in the eye of Drosophila embryos inhibits EGFR dependent photoreceptor cell development. Sli-1 is a negative regulator of the Let-23 receptor tyrosine kinase, an EGFR homolog, in vulva development. Cbl proteins in this family consist of a highly conserved N-terminal half that includes a tyrosine-kinase-binding domain (TKB, also known as the phosphotyrosine binding PTB domain, is composed of a four helix-bundle, a Ca2+ binding EF-hand and a highly variant SH2 domain) and a C3HC4-type RING-HC finger, both of which are required for Cbl-mediated downregulation of RTKs, and a divergent C-terminal region.


Pssm-ID: 319416 [Multi-domain]  Cd Length: 43  Bit Score: 35.02  E-value: 7.03e-03
                         10        20
                 ....*....|....*....|....*.
gi 242086515 142 PCGHNFCLKCFQKWIQNRKRTCAKCR 167
Cdd:cd16502   18 PCGHLLCTPCLTSWQDSDGQTCPFCR 43
RING-HC_RNF213 cd16561
RING finger, HC subclass, found in RING finger protein 213 (RNF213) and similar proteins; ...
499-523 7.33e-03

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 associate 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 forms huge ring-shaped oligomeric complex.


Pssm-ID: 319475 [Multi-domain]  Cd Length: 41  Bit Score: 34.77  E-value: 7.33e-03
                         10        20
                 ....*....|....*....|....*
gi 242086515 499 CSICRAVIKEPLTTPCAHNFCKTCL 523
Cdd:cd16561    1 CSICLEDPKDPVSLPCDHIHCLTCL 25
RING-HC_TRIM58_C-IV cd16606
RING finger, HC subclass, found in tripartite motif-containing protein TRIM58 and similar ...
499-555 7.87e-03

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: 319520 [Multi-domain]  Cd Length: 51  Bit Score: 35.00  E-value: 7.87e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 242086515 499 CSICRAVIKEPLTTPCAHNFCKTCLlgkydsqSSMRERSRGgrtlrAQKIVKTCPSC 555
Cdd:cd16606    4 CPVCLDFLQEPVSVDCGHSFCLRCI-------SEFCEKSDS-----AQGGVYACPQC 48
RING-HC_RNFT2 cd16742
RING finger, HC subclass, found in RING finger and transmembrane domain-containing protein 2 ...
499-532 8.24e-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: 319656 [Multi-domain]  Cd Length: 41  Bit Score: 34.80  E-value: 8.24e-03
                         10        20        30
                 ....*....|....*....|....*....|....
gi 242086515 499 CSICRAVIKEPLTTPCAHNFCKTCLLGKYDSQSS 532
Cdd:cd16742    3 CAICQAEFREPLILICQHVFCEECLCLWFDRERT 36
PHD1_KMT2A_like cd15506
PHD finger 1 found in histone-lysine N-methyltransferase 2A (KMT2A) and 2B (KMT2B); This ...
11-57 9.03e-03

PHD finger 1 found in histone-lysine N-methyltransferase 2A (KMT2A) and 2B (KMT2B); This family includes histone-lysine N-methyltransferase trithorax (Trx) like proteins, KMT2A (MLL1) and KMT2B (MLL2), which comprise the mammalian Trx branch of the COMPASS family, and are both essential for mammalian embryonic development. KMT2A regulates chromatin-mediated transcription through the catalysis of methylation of histone 3 lysine 4 (H3K4), and is frequently rearranged in acute leukemia. KMT2A functions as the catalytic subunit in the MLL1 complex. KMT2B is a second human homolog of Drosophila trithorax, located on chromosome 19 and functions as the catalytic subunit in the MLL2 complex. It plays a critical role in memory formation through mediating hippocampal H3K4 di- and trimethylation. It is also required for RNA polymerase II association and protection from DNA methylation at the MagohB CpG island promoter. Both KMT2A and KMT2B contain a CxxC (x for any residue) zinc finger domain, three plant homeodomain (PHD) fingers, an extended PHD (ePHD) finger, Cys2HisCys5HisCys2His, two FY (phenylalanine tyrosine)-rich domains, and a SET (Suppressor of variegation, Enhancer of zeste, Trithorax) domain. This model corresponds to the first PHD finger.


Pssm-ID: 276981  Cd Length: 47  Bit Score: 34.64  E-value: 9.03e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*....
gi 242086515  11 VCMVCraASPPEVDLLRCSTCATPWHSPCLSKPPALADAA--SWSCPDC 57
Cdd:cd15506    1 LCFLC--GSAGLNELLYCSVCCEPYHTFCLEEAERPLNINkdNWCCRRC 47
RING1-HC_LONFs cd16513
RING finger 1, HC subclass, found in the LON peptidase N-terminal domain and RING finger ...
137-167 9.08e-03

RING finger 1, HC subclass, found in the LON peptidase N-terminal domain and RING finger proteins family; The LON peptidase N-terminal domain and RING finger proteins family includes LONRF1 (also known as RING finger protein 191 or RNF191), LONRF2 (also known as RING finger protein 192 or 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 one N-terminal domain of the ATP-dependent protease La (LON) domain at the C-terminus. Their biological function remain unclear. This family corresponds to the first RING-HC finger.


Pssm-ID: 319427  Cd Length: 42  Bit Score: 34.35  E-value: 9.08e-03
                         10        20        30
                 ....*....|....*....|....*....|.
gi 242086515 137 RPVTTPCGHNFCLKCFQKWIQNRKRtCAKCR 167
Cdd:cd16513   13 LPVTSPCGHTYCKRCLEKFYASDSR-CLVCR 42
SP-RING_like cd16452
A group of variants of RING finger including SP-RING finger, SPL-RING finger, dRING finger, ...
136-167 9.13e-03

A group of variants of RING finger including SP-RING finger, SPL-RING finger, dRING finger, and RING-like Rtf2 domain; The family corresponds to a group of proteins with variants of RING fingers that are characterized by lacking the second, fifth, and sixth Zn2+ ion-coordinating residues compared with the classic C3H2C3-/C3HC4-type RING fingers. They include SP-RING finger found in the Siz/PIAS RING (SP-RING) family of SUMO E3 ligases, SPL-RING finger found in E3 SUMO-protein ligase NSE2, degenerated RING (dRING) finger found in Saccharomyces cerevisiae required for meiotic nuclear division protein 5 (Rmd5p) and homologs, and RING-like Rtf2 domain found in the replication termination factor 2 (Rtf2) protein family. The SP-RING family includes PIAS (protein inhibitor of activated STAT) proteins, Zmiz proteins, and Siz proteins from plants and fungi. The PIAS (protein inhibitor of activated STAT) protein family modulates the activity of several transcription factors and acts as an E3 ubiquitin ligase in the sumoylation pathway. NSE2, also known as MMS21 homolog (MMS21) or non-structural maintenance of chromosomes element 2 homolog (Non-SMC element 2 homolog, NSMCE2), is an autosumoylating small ubiquitin-like modifier (SUMO) ligase required for the response to DNA damage. It regulates sumoylation and nuclear-to-cytoplasmic translocation of skeletal and heart muscle-specific variant of the alpha subunit of nascent polypeptide associated complex (skNAC)-Smyd1 in myogenesis. It is also required for resisting extrinsically induced genotoxic stress. Rmd5p, also known as glucose-induced degradation protein 2 (Gid2) or sporulation protein RMD5, is an E3 ubiquitin ligase that forms the heterodimeric E3 ligase unit of the glucose induced degradation deficient (GID) complex with Gid9 (also known as Fyv10), which has a degenerated RING finger as well. The GID complex triggers polyubiquitylation and subsequent proteasomal degradation of the gluconeogenic enzymes fructose-1, 6-bisphosphate by fructose-1, 6-bisphosphatase (FBPase), phosphoenolpyruvate carboxykinase (PEPCK), and cytoplasmic malate dehydrogenase (c-MDH). The Rtf2 protein family includes a group of conserved proteins found in eukaryotes ranging from fission yeast to humans. The defining member of the family is Schizosaccharomyces pombe Rtf2 (SpRtf2), which is a proliferating cell nuclear antigen-interacting protein that functions as a key requirement for efficient replication termination at the site-specific replication barrier RTS1. It promotes termination at RTS1 by preventing replication restart. The RING-like Rtf2 domain in fission yeast is required to stabilize a paused DNA replication fork during imprinting at the mating type locus, possibly by facilitating sumoylation of PCNA. The family also includes Arabidopsis RTF2 (AtRTF2), an essential nuclear protein required for both normal embryo development and for proper expression of the GFP reporter gene. It plays a critical role in splicing the GFP pre-mRNA, and may also have a more transient regulatory role during the spliceosome cycle. The biological function of Rtf2 homologs found in eumetazoa remains unclear.


Pssm-ID: 319366 [Multi-domain]  Cd Length: 42  Bit Score: 34.63  E-value: 9.13e-03
                         10        20        30
                 ....*....|....*....|....*....|..
gi 242086515 136 DRPVTTPCGHNFCLKCFQKWIQNRKRTCAKCR 167
Cdd:cd16452   11 DPPVITPCGHTFSRAAILEWLTKKKRKCPTCR 42
RING-HC_TRIM41_like_C-IV cd16602
RING finger, HC subclass, found in tripartite motif-containing proteins TRIM41, TRIM52 and ...
495-523 9.54e-03

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 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 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: 319516 [Multi-domain]  Cd Length: 41  Bit Score: 34.46  E-value: 9.54e-03
                         10        20
                 ....*....|....*....|....*....
gi 242086515 495 KEFGCSICRAVIKEPLTTPCAHNFCKTCL 523
Cdd:cd16602    1 EEAVCAICLDYFRDPVSIGCGHNFCRVCV 29
RING-HC_RNF138 cd16544
RING finger, HC subclass, found in RING finger protein 138 (RNF138) and similar proteins; ...
125-167 9.61e-03

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: 319458 [Multi-domain]  Cd Length: 46  Bit Score: 34.78  E-value: 9.61e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....
gi 242086515 125 NFSCVFCMKLPDRPV-TTPCGHNFCLKCFQKWIQNRKRTCAKCR 167
Cdd:cd16544    2 DFSCPVCQEVLQTPIrTKKCRHVFCRKCFLLAMRRSGAHCPLCR 45
RING-H2_TTC3 cd16481
RING finger, H2 subclass, found in Tetratricopeptide repeat protein 3 (TTC3) and similar ...
127-167 9.66e-03

RING finger, H2 subclass, found in Tetratricopeptide repeat protein 3 (TTC3) and similar proteins; TTC3, also known as protein DCRR1, or TPR repeat protein D, or TPR repeat protein 3, or RING finger protein 105 (RNF105), is an E3 ubiquitin-protein ligase encoded by a gene within the Down syndrome (DS) critical region on chromosome 21. It affects differentiation and Golgi compactness in neurons through specific actin-regulating pathways. It inhibits the neuronal-like differentiation of pheocromocytoma cells by activating RhoA and by binding to Citron proteins. TTC3 is an Akt-specific E3 ligase that binds to phosphorylated Akt and facilitates its ubiquitination and degradation within the nucleus. TTC3 contains four N-terminal TPR motifs, a potential coiled-coil region and a Citron binding region in the central part, and a C-terminal C3H2C2-type RING-H2 finger.TTC3, also known as protein DCRR1, TPR repeat protein D, TPR repeat protein 3, or RING finger protein 105 (RNF105), is an E3 ubiquitin-protein ligase encoded by a gene within the Down syndrome (DS) critical region on chromosome 21. It also affects differentiation and Golgi compactness in neurons through specific actin-regulating pathways. It inhibits the neuronal-like differentiation of pheocromocytoma cells by activating RhoA and by binding to Citron proteins. TTC3 is an Akt-specific E3 ligase that binds to phosphorylated Akt and facilitates its ubiquitination and degradation within the nucleus. TTC3 contains four N-terminal TPR motifs, a potential coiled-coil region and a Citron binding region in the central part, and a C-terminal C3H2C2-type RING-H2 finger.


Pssm-ID: 319395 [Multi-domain]  Cd Length: 42  Bit Score: 34.63  E-value: 9.66e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|...
gi 242086515 127 SCVFCMKL--PDRPVTTPCGHNFCLKCFQKWIqNRKRTCAKCR 167
Cdd:cd16481    1 PCSICHEElkPGTVRKLDCGHRFHKGCIRQWL-KEQSTCPTCR 42
RING-HC_TRIM72_C-IV cd16612
RING finger, HC subclass, found in tripartite motif-containing protein 72 (TRIM72) and similar ...
496-557 9.67e-03

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 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 via 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 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: 319526 [Multi-domain]  Cd Length: 47  Bit Score: 34.47  E-value: 9.67e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 242086515 496 EFGCSICRAVIKEPLTTPCAHNFCKTCLLGKYDSQSSmrersrggrtlraqkivKTCPSCPT 557
Cdd:cd16612    1 DLSCPLCLELFRAPVTPECGHTFCQACLTRVAKEQDQ-----------------NGTTPCPT 45
RING-HC_TRIM10_C-IV cd16593
RING finger, HC subclass, found in tripartite motif-containing protein 10 (TRIM10) and similar ...
128-167 9.78e-03

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 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: 319507 [Multi-domain]  Cd Length: 49  Bit Score: 34.60  E-value: 9.78e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*.
gi 242086515 128 CVFCMKLPDRPVTTPCGHNFCLKCFQKWIQ------NRKRTCAKCR 167
Cdd:cd16593    4 CPICQGTLREPVTIDCGHNFCRACLTRYCEipgpdlEEPPTCPLCK 49
RING-HC_TRIM39_C-IV cd16601
RING finger, HC subclass, found in tripartite motif-containing protein 39 (TRIM39) and similar ...
496-523 9.92e-03

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 transcriptions, which is induced by inflammatory stimulants such as tumor necrosis factor alpha (TNFalpha). 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 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: 319515 [Multi-domain]  Cd Length: 44  Bit Score: 34.64  E-value: 9.92e-03
                         10        20
                 ....*....|....*....|....*...
gi 242086515 496 EFGCSICRAVIKEPLTTPCAHNFCKTCL 523
Cdd:cd16601    1 EASCSVCLEYLKEPVIIECGHNFCKACI 28
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.17
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
  • Marchler-Bauer A et al. (2015), "CDD: NCBI's conserved domain database.", Nucleic Acids Res.43(D)222-6.
  • Marchler-Bauer A et al. (2011), "CDD: a Conserved Domain Database for the functional annotation of proteins.", Nucleic Acids Res.39(D)225-9.
  • Marchler-Bauer A, Bryant SH (2004), "CD-Search: protein domain annotations on the fly.", Nucleic Acids Res.32(W)327-331.
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