B-box-type 2 zinc finger found in tripartite motif-containing protein 19, also called promyelocytic leukemia protein (PML), and similar proteins; Protein PML, also known as RING finger protein 71 (RNF71) or tripartite motif-containing protein 19 (TRIM19), is predominantly a nuclear protein with a broad intrinsic antiviral activity. It is the eponymous component of PML nuclear bodies (PML NBs) and has been implicated in a wide variety of cell processes, including DNA damage signaling, apoptosis, and transcription. PML interferes with the replication of many unrelated viruses, including human immunodeficiency virus 1 (HIV-1), human foamy virus (HFV), poliovirus, influenza virus, rabies virus, EMCV, adeno-associated virus (AAV), and vesicular stomatitis virus (VSV). It also selectively interacts with misfolded proteins through distinct substrate recognition sites and conjugates these proteins with the small ubiquitin-like modifiers (SUMOs) through its SUMO ligase activity. PML belongs to the C-V subclass of TRIM (tripartite motif) family of proteins that are defined by an N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a RING finger, Bbox1 and Bbox2, and a coiled coil region, as well as an uncharacterized region positioned C-terminal to the RBCC domain. The type 2 B-box (Bbox2) zinc finger is characterized by a CHC3H2 zinc-binding consensus motif.

                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|.
gi 15451765 187 IFCSNPNHRTPTLtSIYCRGCSKPLCCSCALLDSSHSELKCDISAEIQQRQ 237
Cdd:cd19770   1 PFCPSPNHETQMI-SIYCRQCSKSVCCTCALLDSSHKGQHCDIKAEIQRRQ 50

B-box-type 1 zinc finger found in promyelocytic leukemia protein (PML) and similar proteins; Protein PML, also known as RING finger protein 71 (RNF71) or tripartite motif-containing protein 19 (TRIM19), is predominantly a nuclear protein with a broad intrinsic antiviral activity. It is the eponymous component of PML nuclear bodies (PML NBs) and has been implicated in a wide variety of cellular processes, including DNA damage signaling, apoptosis, and transcription. PML interferes with the replication of many unrelated viruses, including human immunodeficiency virus 1 (HIV-1), human foamy virus (HFV), poliovirus, influenza virus, rabies virus, EMCV, adeno-associated virus (AAV), and vesicular stomatitis virus (VSV). It also selectively interacts with misfolded proteins through distinct substrate recognition sites, and conjugates these proteins with the small ubiquitin-like modifiers (SUMOs) through its SUMO ligase activity. PML belongs to the C-V subclass of the TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a RING finger, Bbox1 and Bbox2, and a coiled coil region, as well as an uncharacterized region positioned C-terminal to the RBCC domain. The type 1 B-box (Bbox1) zinc finger is characterized by a C6H2 zinc-binding consensus motif.

                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*..
gi 15451765 126 QAVCTRCKES-ADFWCFECEQLLCAKCFEAHQWF---LKHEARPLAE 168
Cdd:cd19804   1 ELMCNRCSESeAEFWCSECEEFLCRKCFEAHQRFkkrKKHEALRLAE 47

B-box-type 2 zinc finger found in tripartite motif-containing protein 19, also called promyelocytic leukemia protein (PML), and similar proteins; Protein PML, also known as RING finger protein 71 (RNF71) or tripartite motif-containing protein 19 (TRIM19), is predominantly a nuclear protein with a broad intrinsic antiviral activity. It is the eponymous component of PML nuclear bodies (PML NBs) and has been implicated in a wide variety of cell processes, including DNA damage signaling, apoptosis, and transcription. PML interferes with the replication of many unrelated viruses, including human immunodeficiency virus 1 (HIV-1), human foamy virus (HFV), poliovirus, influenza virus, rabies virus, EMCV, adeno-associated virus (AAV), and vesicular stomatitis virus (VSV). It also selectively interacts with misfolded proteins through distinct substrate recognition sites and conjugates these proteins with the small ubiquitin-like modifiers (SUMOs) through its SUMO ligase activity. PML belongs to the C-V subclass of TRIM (tripartite motif) family of proteins that are defined by an N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a RING finger, Bbox1 and Bbox2, and a coiled coil region, as well as an uncharacterized region positioned C-terminal to the RBCC domain. The type 2 B-box (Bbox2) zinc finger is characterized by a CHC3H2 zinc-binding consensus motif.

                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|.
gi 15451765 187 IFCSNPNHRTPTLtSIYCRGCSKPLCCSCALLDSSHSELKCDISAEIQQRQ 237
Cdd:cd19770   1 PFCPSPNHETQMI-SIYCRQCSKSVCCTCALLDSSHKGQHCDIKAEIQRRQ 50

B-box-type 1 zinc finger found in promyelocytic leukemia protein (PML) and similar proteins; Protein PML, also known as RING finger protein 71 (RNF71) or tripartite motif-containing protein 19 (TRIM19), is predominantly a nuclear protein with a broad intrinsic antiviral activity. It is the eponymous component of PML nuclear bodies (PML NBs) and has been implicated in a wide variety of cellular processes, including DNA damage signaling, apoptosis, and transcription. PML interferes with the replication of many unrelated viruses, including human immunodeficiency virus 1 (HIV-1), human foamy virus (HFV), poliovirus, influenza virus, rabies virus, EMCV, adeno-associated virus (AAV), and vesicular stomatitis virus (VSV). It also selectively interacts with misfolded proteins through distinct substrate recognition sites, and conjugates these proteins with the small ubiquitin-like modifiers (SUMOs) through its SUMO ligase activity. PML belongs to the C-V subclass of the TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a RING finger, Bbox1 and Bbox2, and a coiled coil region, as well as an uncharacterized region positioned C-terminal to the RBCC domain. The type 1 B-box (Bbox1) zinc finger is characterized by a C6H2 zinc-binding consensus motif.

                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*..
gi 15451765 126 QAVCTRCKES-ADFWCFECEQLLCAKCFEAHQWF---LKHEARPLAE 168
Cdd:cd19804   1 ELMCNRCSESeAEFWCSECEEFLCRKCFEAHQRFkkrKKHEALRLAE 47

Exopolysaccharide export protein/domain GumC/Wzc1 [Cell wall/membrane/envelope biogenesis];

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15451765 230 SAEIQQRQEELDAMTQALQEQDSAFGAVHAQMHAAVGQLgrarAETEELIRERVRQVVAHVRAqERELLEAVDARYQRDY 309
Cdd:COG3206 262 SPVIQQLRAQLAELEAELAELSARYTPNHPDVIALRAQI----AALRAQLQQEAQRILASLEA-ELEALQAREASLQAQL 336

                        90
                ....*....|....*...
gi 15451765 310 EEMASRLGRLDAVLQRIR 327
Cdd:COG3206 337 AQLEARLAELPELEAELR 354

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)

                           10        20        30        40
                   ....*....|....*....|....*....|....*....|
gi 15451765     57 CQQC-QAEAKCPKLLPCLHTLCSGC----LEASGMQCPIC 91
Cdd:smart00184   1 CPIClEEYLKDPVILPCGHTFCRSCirkwLESGNNTCPIC 40

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]

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 15451765    53 QFLRCQQCQAEAKCPKLLPCLHTLCSGC----LEASGMqCPICQAPwplgadtpaldnvFFESLQRRLSVYRQIVDA 125
Cdd:TIGR00599  25 TSLRCHICKDFFDVPVLTSCSHTFCSLCirrcLSNQPK-CPLCRAE-------------DQESKLRSNWLVSEIVES 87

B-box-type 2 zinc finger found in tripartite motif-containing protein 19, also called promyelocytic leukemia protein (PML), and similar proteins; Protein PML, also known as RING finger protein 71 (RNF71) or tripartite motif-containing protein 19 (TRIM19), is predominantly a nuclear protein with a broad intrinsic antiviral activity. It is the eponymous component of PML nuclear bodies (PML NBs) and has been implicated in a wide variety of cell processes, including DNA damage signaling, apoptosis, and transcription. PML interferes with the replication of many unrelated viruses, including human immunodeficiency virus 1 (HIV-1), human foamy virus (HFV), poliovirus, influenza virus, rabies virus, EMCV, adeno-associated virus (AAV), and vesicular stomatitis virus (VSV). It also selectively interacts with misfolded proteins through distinct substrate recognition sites and conjugates these proteins with the small ubiquitin-like modifiers (SUMOs) through its SUMO ligase activity. PML belongs to the C-V subclass of TRIM (tripartite motif) family of proteins that are defined by an N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a RING finger, Bbox1 and Bbox2, and a coiled coil region, as well as an uncharacterized region positioned C-terminal to the RBCC domain. The type 2 B-box (Bbox2) zinc finger is characterized by a CHC3H2 zinc-binding consensus motif.

                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|.
gi 15451765 187 IFCSNPNHRTPTLtSIYCRGCSKPLCCSCALLDSSHSELKCDISAEIQQRQ 237
Cdd:cd19770   1 PFCPSPNHETQMI-SIYCRQCSKSVCCTCALLDSSHKGQHCDIKAEIQRRQ 50

B-box-type 1 zinc finger found in promyelocytic leukemia protein (PML) and similar proteins; Protein PML, also known as RING finger protein 71 (RNF71) or tripartite motif-containing protein 19 (TRIM19), is predominantly a nuclear protein with a broad intrinsic antiviral activity. It is the eponymous component of PML nuclear bodies (PML NBs) and has been implicated in a wide variety of cellular processes, including DNA damage signaling, apoptosis, and transcription. PML interferes with the replication of many unrelated viruses, including human immunodeficiency virus 1 (HIV-1), human foamy virus (HFV), poliovirus, influenza virus, rabies virus, EMCV, adeno-associated virus (AAV), and vesicular stomatitis virus (VSV). It also selectively interacts with misfolded proteins through distinct substrate recognition sites, and conjugates these proteins with the small ubiquitin-like modifiers (SUMOs) through its SUMO ligase activity. PML belongs to the C-V subclass of the TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a RING finger, Bbox1 and Bbox2, and a coiled coil region, as well as an uncharacterized region positioned C-terminal to the RBCC domain. The type 1 B-box (Bbox1) zinc finger is characterized by a C6H2 zinc-binding consensus motif.

                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*..
gi 15451765 126 QAVCTRCKES-ADFWCFECEQLLCAKCFEAHQWF---LKHEARPLAE 168
Cdd:cd19804   1 ELMCNRCSESeAEFWCSECEEFLCRKCFEAHQRFkkrKKHEALRLAE 47

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

                        10        20        30        40
                ....*....|....*....|....*....|....*....|.
gi 15451765  55 LRCQQCQAEAKCPKLLPCLHTLCSGCL----EASGMQCPIC 91
Cdd:cd16449   1 LECPICLERLKDPVLLPCGHVFCRECIrrllESGSIKCPIC 41

RING finger, HC subclass, found in tripartite motif-containing protein 3 (TRIM3); TRIM3, also known as brain-expressed RING finger protein (BERP), RING finger protein 97 (RNF97), or RING finger protein 22 (RNF22), is an E3 ubiquitin-protein ligase involved in the pathogenesis of various cancers. It functions as a tumor suppressor that regulates asymmetric cell division in glioblastoma. It binds to the cdk inhibitor p21(WAF1/CIP1) and regulates its availability that promotes cyclin D1-cdk4 nuclear accumulation. Moreover, TRIM3 plays an important role in the central nervous system (CNS). It is encoded by the gene BERP (brain-expressed RING finger protein), a unique p53-regulated gene that modulates seizure susceptibility and GABAAR cell surface expression. Furthermore, TRIM3 mediates activity-dependent turnover of postsynaptic density (PSD) scaffold proteins GKAP/SAPAP1 and is a negative regulator of dendritic spine morphology. In addition, TRIM3 may be involved in vesicular trafficking via its association with the cytoskeleton-associated-recycling or transport (CART) complex that is necessary for efficient transferrin receptor recycling, but not for epidermal growth factor receptor (EGFR) degradation. It also regulates the motility of the kinesin superfamily protein KIF21B. TRIM3 belongs to the C-VII subclass of the TRIM (tripartite motif)-NHL family that is defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a C3HC4-type RING-HC finger, Bbox1 and Bbox2, and a coiled coil domain, as well as a NHL (named after proteins NCL-1, HT2A and Lin-41 that contain repeats folded into a six-bladed beta propeller) repeat domain positioned C-terminal to the RBCC domain.

                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*.
gi 15451765  53 QFLRCQQCQAEAKCPKLLPCLHTLCSGCL------EASGMQCPICQ 92
Cdd:cd16768   3 QFLVCSICLDRYHNPKVLPCLHTFCERCLqnyippQSLTLSCPVCR 48

RING finger, HC subclass, found in tripartite motif-containing proteins TRIM9, TRIM67, and similar proteins; Tripartite motif-containing proteins TRIM9 and TRIM67 belong to the C-I subclass of the TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, consisting of three consecutive zinc-binding domains, a C3HC4-type RING-HC finger, Bbox1 and Bbox2, and a coiled coil region, as well as a COS (carboxyl-terminal subgroup one signature) box, a fibronectin type III (FN3) domain, and a B30.2/SPRY (SplA and ryanodine receptor) domain positioned C-terminal to the RBCC domain. TRIM9 (the human ortholog of rat Spring), also known as RING finger protein 91 (RNF91), is a brain-specific E3 ubiquitin-protein ligase collaborating with an E2 ubiquitin conjugating enzyme UBCH5b. TRIM9 plays an important role in the regulation of neuronal functions and participates in neurodegenerative disorders through its ligase activity. TRIM67, also known as TRIM9-like protein (TNL), is a protein selectively expressed in the cerebellum. It interacts with PRG-1, an important molecule in the control of hippocampal excitability dependent on presynaptic LPA2 receptor signaling, and 80K-H, also known as glucosidase II beta, a protein kinase C substrate.

                        10        20        30        40
                ....*....|....*....|....*....|....*....|...
gi 15451765  49 EEEfqfLRCQQCQAEAKCPKLLPCLHTLCSGCLEASGMQCPIC 91
Cdd:cd16576   1 EEE---LKCPVCGSLFTEPVILPCSHNLCLGCALNIQLTCPIC 40

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

                        10        20        30        40
                ....*....|....*....|....*....|....*....|...
gi 15451765  54 FLRCQQCQAEAKCPKLLPCLHTLCSGC----LEASGMQCPICQ 92
Cdd:cd16584   1 FLACKICLEQLRAPKTLPCLHTYCQDClaqlADGGRVRCPECR 43

Uncharacterized protein, contains DUF3084 domain [Function unknown];

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15451765 218 LDSSHSELKcDISAEIQQRQEELDAMTQALQEQDSAFGAVHAQMHAAVGQLGRARAETEELIRERVRQvvahvrAQEREL 297
Cdd:COG4372  61 LEQLEEELE-QARSELEQLEEELEELNEQLQAAQAELAQAQEELESLQEEAEELQEELEELQKERQDL------EQQRKQ 133

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15451765 298 LEAVDARYQRDYEEMASRLGRLDAVLQRIRTGSALVQRMKCYASDQEVL-DMHGFLRQALCRLRQEEPQSLQAAVRTDGF 376
Cdd:COG4372 134 LEAQIAELQSEIAEREEELKELEEQLESLQEELAALEQELQALSEAEAEqALDELLKEANRNAEKEEELAEAEKLIESLP 213

                       170
                ....*....|
gi 15451765 377 DEFKVRLQDL 386
Cdd:COG4372 214 RELAEELLEA 223

RING finger, HC subclass, found in tripartite motif-containing protein 2 (TRIM2); TRIM2, also known as RING finger protein 86 (RNF86), is an E3 ubiquitin-protein ligase that ubiquitinates the neurofilament light chain, a component of the intermediate filament in axons. Loss of function of TRIM2 results in early-onset axonal neuropathy. TRIM2 also plays a role in mediating the p42/p44 MAPK-dependent ubiquitination of the cell death-promoting protein Bcl-2-interacting mediator of cell death (Bim) in rapid ischemic tolerance. TRIM2 belongs to the C-VII subclass of the TRIM (tripartite motif)-NHL family that is defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a C3HC4-type RING-HC finger, Bbox1 and Bbox2, and a coiled coil domain, as well as a NHL (named after proteins NCL-1, HT2A and Lin-41 that contain repeats folded into a six-bladed beta propeller) repeat domain positioned C-terminal to the RBCC domain.

                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*.
gi 15451765  53 QFLRCQQCQAEAKCPKLLPCLHTLCSGCLE------ASGMQCPICQ 92
Cdd:cd16767   5 QFLICSICLDRYKNPKVLPCLHTFCERCLQnyipahSLTLSCPVCR 50

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

                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*....
gi 15451765  53 QFLRCQQCQAEAKCPKLLPCLHTLCSGCLEA----------SGMQCPIC 91
Cdd:cd16581   1 EELTCSICYNIFDDPKILPCSHTFCKNCLEKllaasgyyllASLKCPTC 49

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)

                           10        20        30        40
                   ....*....|....*....|....*....|....*....|
gi 15451765     57 CQQC-QAEAKCPKLLPCLHTLCSGC----LEASGMQCPIC 91
Cdd:smart00184   1 CPIClEEYLKDPVILPCGHTFCRSCirkwLESGNNTCPIC 40

transcriptional regulator ICP4; Provisional

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15451765   391 TQGKDAAVSKKASPEAASTPRDPIDV-DLPEEAERVKAQVQA---------LGLAEAQPMAVVQSVPGAHPVPVYAFSIK 460
Cdd:PHA03307  150 ASPPAAGASPAAVASDAASSRQAALPlSSPEETARAPSSPPAepppstppaAASPRPPRRSSPISASASSPAPAPGRSAA 229

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15451765   461 GPSYGEDVSNTTTAQKRKCS--QTQCPRKVIKMESEEGKEARLARSSPEQPRPSTSKAVSPPH-LDGPPSPRSPVIGSev 537
Cdd:PHA03307  230 DDAGASSSDSSSSESSGCGWgpENECPLPRPAPITLPTRIWEASGWNGPSSRPGPASSSSSPReRSPSPSPSSPGSGP-- 307

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15451765   538 flPNSNHVASGAGEAEERVVVISSSEDSDAENSCmepmetAEPQSSPAHSSPAHSSPAHSSPVQSLLRAQGASSLPCGTY 617
Cdd:PHA03307  308 --APSSPRASSSSSSSRESSSSSTSSSSESSRGA------AVSPGPSPSRSPSPSRPPPPADPSSPRKRPRPSRAPSSPA 379

                         250       260
                  ....*....|....*....|....*.
gi 15451765   618 HPPAWPPHQPAEQAATPDAEPHSEPP 643
Cdd:PHA03307  380 ASAGRPTRRRARAAVAGRARRRDATG 405

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]

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 15451765    53 QFLRCQQCQAEAKCPKLLPCLHTLCSGC----LEASGMqCPICQAPwplgadtpaldnvFFESLQRRLSVYRQIVDA 125
Cdd:TIGR00599  25 TSLRCHICKDFFDVPVLTSCSHTFCSLCirrcLSNQPK-CPLCRAE-------------DQESKLRSNWLVSEIVES 87

B-box-type 1 zinc finger found in transcription intermediary factor 1-alpha (TIF1-alpha); TIF1-alpha, also known as tripartite motif-containing protein 24 (TRIM24), E3 ubiquitin-protein ligase TRIM24, or RING finger protein 82, belongs to the C-VI subclass of TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a RING finger, Bbox1 and Bbox2, and a coiled coil region, as well as a plant homeodomain (PHD), and a bromodomain (Bromo) positioned C-terminal to the RBCC domain. The type 1 B-box (Bbox1) zinc finger is characterized by a C6H2 zinc-binding consensus motif. TIF1-alpha interacts specifically and in a ligand-dependent manner with the ligand binding domain (LBD) of several nuclear receptors (NRs), including retinoic X (RXR), retinoic acid (RAR), vitamin D3 (VDR), estrogen (ER), and progesterone (PR) receptors. It also associates with heterochromatin-associated factors HP1alpha, MOD1 (HP1beta), and MOD2 (HP1gamma), as well as the vertebrate Kruppel-type (C2H2) zinc finger proteins that contain the transcriptional silencing domain KRAB. TIF1-alpha is a ligand-dependent co-repressor of retinoic acid receptor (RAR) that interacts with multiple nuclear receptors in vitro via an LXXLL motif and further acts as a gatekeeper of liver carcinogenesis. It also functions as an E3-ubiquitin ligase targeting p53, and is broadly associated with chromatin silencing. Moreover, it is a chromatin regulator that recognizes specific, combinatorial histone modifications through its C-terminal PHD-Bromo region. In addition, it interacts with chromatin and estrogen receptor to activate estrogen-dependent genes associated with cellular proliferation and tumor development.

                        10        20        30
                ....*....|....*....|....*....|.
gi 15451765 128 VCTRCKESADF--WCFECEQLLCAKCFEAHQ 156
Cdd:cd19845   2 VCTSCEDNAEAngFCVECVEWLCKTCIEAHQ 32

Modified RING finger, HC subclass (C3HC5-type), found in RING finger proteins, RNF26, RNF197 (CGRRF1), RNF156 (MGRN1), RNF157 and similar proteins; This subfamily corresponds to a group of RING finger proteins containing a modified C3HC5-type RING-HC finger, which is distinguished from typical C3HC4 RING-HC finger due to the existence of the additional cysteine residue in the middle portion of the RING finger domain. Cell growth regulator with RING finger domain protein 1 (CGRRF1), also known as cell growth regulatory gene 19 protein (CGR19) or RING finger protein 197 (RNF197), functions as a novel biomarker to monitor endometrial sensitivity and response to insulin-sensitizing drugs, such as metformin, in the context of obesity. RNF26 is an E3 ubiquitin ligase that temporally regulates virus-triggered type I interferon induction by increasing the stability of Mediator of IRF3 activation, MITA, also known as STING, through K11-linked polyubiquitination after viral infection and promoting degradation of IRF3, another important component required for virus-triggered interferon induction. Mahogunin ring finger-1 (MGRN1), also known as RING finger protein 156 (RNF156), is a cytosolic E3 ubiquitin-protein ligase that inhibits signaling through the G protein-coupled melanocortin receptors-1 (MC1R), -2 (MC2R) and -4 (MC4R) via ubiquitylation-dependent and -independent processes. It suppresses chaperone-associated misfolded protein aggregation and toxicity. RNF157 is a cytoplasmic E3 ubiquitin ligase predominantly expressed in the brain. It is a homolog of the E3 ligase MGRN1. In cultured neurons, it promotes neuronal survival in an E3 ligase-dependent manner. In contrast, it supports growth and maintenance of dendrites independent of its E3 ligase activity. RNF157 interacts with and ubiquitinates the adaptor protein APBB1 (amyloid beta precursor protein-binding, family B, member 1 or Fe65), which regulates neuronal survival, but not dendritic growth downstream of RNF157. The nuclear localization of APBB1 together with its interaction partner RNA-binding protein SART3 (squamous cell carcinoma antigen recognized by T cells 3 or Tip110) is crucial to trigger apoptosis.

                        10        20        30
                ....*....|....*....|....*....|....*..
gi 15451765  57 CQQCQAEAKCPKLLPCLHT-LCSGCLEA-SGMQCPIC 91
Cdd:cd16649   3 CVVCLENPASVLLLPCRHLcLCEVCAKGlRGKTCPIC 39

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

                        10        20        30
                ....*....|....*....|....*....|....
gi 15451765  65 KCPKLLPCLHTLCSGCL----EASGMQCPICQAP 94
Cdd:cd16503  14 DCVSLQPCMHNFCAACYsdwmERSNTECPTCRAT 47

Uncharacterized protein, contains DUF3084 domain [Function unknown];

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15451765 231 AEIQQRQEELDAMTQALQEQDSAFGAVHAQMHAAVGQLGRARAETEElIRERVRQVVAHVRAQERELleavdARYQRDYE 310
Cdd:COG4372  38 FELDKLQEELEQLREELEQAREELEQLEEELEQARSELEQLEEELEE-LNEQLQAAQAELAQAQEEL-----ESLQEEAE 111

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15451765 311 EMASRLGRLDAVLQRirtgsaLVQRMKCYASDQEVLDMHGFLRQALCRLRQEEPQSLQAAVrtdgfDEFKVRLQDLSSCI 390
Cdd:COG4372 112 ELQEELEELQKERQD------LEQQRKQLEAQIAELQSEIAEREEELKELEEQLESLQEEL-----AALEQELQALSEAE 180

                       170       180       190
                ....*....|....*....|....*....|....*....
gi 15451765 391 TQGKDAAVSKKASPEAASTPRDPIDVDLPEEAERVKAQV 429
Cdd:COG4372 181 AEQALDELLKEANRNAEKEEELAEAEKLIESLPRELAEE 219

Centrosome localization domain of PPC89; The N-terminal region of the fission yeast spindle pole body protein PPC89 has low similarity to the human Cep57 protein. The CLD or centrosome localization domain of Cep57 and PPC89 is found at the N-terminus. This region localizes to the centrosome internally to gamma-tubulin, suggesting that it is either on both centrioles or on a centromatrix component. This N-terminal region can also multimerize with the N-terminus of other Cep57 molecules. The C-terminal part, Family Cep57_MT_bd, pfam06657, is the microtubule-binding region of Cep57 and PPC89.

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15451765   231 AEIQQRQEELDAMTQALQEQDSAFGAVHAQMHAAVGQLGRARAETEELIRErvrqvVAHVRAQERELLEA 300
Cdd:pfam14197   3 AENLTLQNRLDSLTRKVAVHEIELKRLRRERDSAVRQLGVAYLEIQELKAE-----NEALRKELKEQRAQ 67

B-box-type 1 zinc finger found in transcription intermediary factor 1-beta (TIF1-beta); TIF1-beta, also known as Kruppel-associated Box (KRAB)-associated protein 1 (KAP-1), KRAB-interacting protein 1 (KRIP-1), nuclear co-repressor KAP-1, RING finger protein 96, tripartite motif-containing protein 28 (TRIM28), or E3 SUMO-protein ligase TRIM28, belongs to the C-VI subclass of TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a RING finger, Bbox1 and Bbox2, and a coiled coil region, as well as a plant homeodomain (PHD), and a bromodomain (Bromo) positioned C-terminal to the RBCC domain. The type 1 B-box (Bbox1) zinc finger is characterized by a C6H2 zinc-binding consensus motif. TIF1-beta/KAP-1 acts as a nuclear co-repressor that plays a role in transcription and in the DNA damage response. Upon DNA damage, the phosphorylation of KAP-1 on serine 824 by the ataxia telangiectasia-mutated (ATM) kinase enhances cell survival and facilitates chromatin relaxation and heterochromatic DNA repair. It also regulates CHD3 nucleosome remodeling during the DNA double-strand break (DSB) response. Meanwhile, KAP-1 can be dephosphorylated by protein phosphatase PP4C in the DNA damage response. Moreover, KAP-1 is a co-activator of the orphan nuclear receptor NGFI-B (or Nur77) and is involved in NGFI-B-dependent transcription. It is also a coiled-coil binding partner, substrate and activator of the c-Fes protein tyrosine kinase. The N-terminal RBCC domains of TIF1-beta are responsible for the interaction with KRAB zinc finger proteins (KRAB-ZFPs), MDM2, MM1, C/EBPbeta, and the regulation of homo- and heterodimerization. The C-terminal PHD/Bromo domains are involved in interacting with SETDB1, Mi-2alpha and other proteins to form complexes with histone deacetylase or methyltransferase activity.

                        10        20        30
                ....*....|....*....|....*....|....*
gi 15451765 124 DAQAVCTRCKES--ADFWCFECEQLLCAKCFEAHQ 156
Cdd:cd19846   1 ETIQCCTSCEDNapATSYCVECSEPLCETCVEAHQ 35

Uncharacterized conserved protein, contains a C-terminal ATPase domain [Function unknown];

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15451765  228 DISAEIQQRQEELDAMTQALQEQDsafgavhaqmhAAVGQLGRARAETEELIRERVRQVVAHVRAQERELLEAVDARYQR 307
Cdd:COG4913  342 QLEREIERLERELEERERRRARLE-----------ALLAALGLPLPASAEEFAALRAEAAALLEALEEELEALEEALAEA 410

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|.
gi 15451765  308 DYEEMASRlGRLDAVLQRIRtgsALVQRMKCYasDQEVLDMhgflRQALCR 358
Cdd:COG4913  411 EAALRDLR-RELRELEAEIA---SLERRKSNI--PARLLAL----RDALAE 451

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

                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*
gi 15451765  55 LRCQQCQAEAKCPKLLPCLHTLCSGCLEAS---GMQCPICQAPWP 96
Cdd:cd23146   5 LKCPICLKLLNRPVLLPCDHIFCSSCITDStkvGSDCPVCKLPYH 49

B-box-type 1 zinc finger found in transcription intermediary factor 1 (TIF1) family; This family corresponds to the TIF1 family of transcriptional cofactors including TIF1-alpha (TRIM24), TIF1-beta (TRIM28), and TIF1-gamma (TRIM33), which belongs to the C-VI subclass of the TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a RING finger, Bbox1 and Bbox2, and a coiled coil region, as well as a plant homeodomain (PHD), and a bromodomain (Bromo) positioned C-terminal to the RBCC domain. The type 1 B-box (Bbox1) zinc finger is characterized by a C6H2 zinc-binding consensus motif. TIF1 proteins couple chromatin modifications to transcriptional regulation, signaling, and tumor suppression. They exert a deacetylase-dependent silencing effect when tethered to a promoter region. TIF1-alpha and TIF1-beta can homodimerize and contain a PXVXL motif necessary and sufficient for heterochromatin protein 1(HP1) binding. They bind nuclear receptors and Kruppel-associated boxes (KRAB) specifically and respectively. TIF1-gamma is structurally closely related to TIF1-alpha and TIF1-beta, but has very little functional features in common with them. It does not interact with the KRAB silencing domain of KOX1 or the heterochromatinic proteins HP1alpha, beta and gamma. It cannot bind to nuclear receptors (NRs).

                        10        20        30
                ....*....|....*....|....*....|.
gi 15451765 128 VCTRCKE--SADFWCFECEQLLCAKCFEAHQ 156
Cdd:cd19805   1 VCTSCEDnaPATSFCVECSEWLCDTCVQAHQ 31

Apolipoprotein A1/A4/E domain; These proteins contain several 22 residue repeats which form a pair of alpha helices. This family includes: Apolipoprotein A-I. Apolipoprotein A-IV. Apolipoprotein E.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15451765   224 ELKCDISAEIQQRQEELDAMTQALQEQDSAF-GAVHAQMHAAVGQL------------GRARAETEEL----------IR 280
Cdd:pfam01442  26 ELVDRLEKETEALRERLQKDLEEVRAKLEPYlEELQAKLGQNVEELrqrlepyteelrKRLNADAEELqeklapygeeLR 105

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15451765   281 ERVRQVVAHVRAQERELLEAVDARYQRDYEEMASRLG-RLDAVLQRIR-TGSALVQRMKCYASD-QEVLD 347
Cdd:pfam01442 106 ERLEQNVDALRARLAPYAEELRQKLAERLEELKESLApYAEEVQAQLSqRLQELREKLEPQAEDlREKLD 175

Modified RING finger, HC subclass (C3HC5-type), found in cell growth regulator with RING finger domain protein 1 (CGRRF1) and similar proteins; CGRRF1, also known as cell growth regulatory gene 19 protein (CGR19) or RING finger protein 197 (RNF197), functions as a novel biomarker to monitor endometrial sensitivity and response to insulin-sensitizing drugs, such as metformin, in the context of obesity. CGRRF1 contains a C-terminal modified C3HC5-type RING-HC finger, which is distinguished from typical C3HC4 RING-HC finger due to the existence of the additional cysteine residue in the middle portion of the RING finger domain.

                        10        20        30
                ....*....|....*....|....*....|....*..
gi 15451765  57 CQQCQAEAKCPKLLPCLHT-LCSGCLEASgMQCPICQ 92
Cdd:cd16787   3 CVVCQNAPVNRVLLPCRHAcVCDECFKRL-QRCPMCR 38