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Conserved domains on  [gi|30687607|ref|NP_194477|]
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RING membrane-anchor 3 [Arabidopsis thaliana]

Protein Classification

Graphical summary

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List of domain hits

Name Accession Description Interval E-value
PLN03208 super family cl31984
E3 ubiquitin-protein ligase RMA2; Provisional
37-228 7.82e-35

E3 ubiquitin-protein ligase RMA2; Provisional


The actual alignment was detected with superfamily member PLN03208:

Pssm-ID: 178747 [Multi-domain]  Cd Length: 193  Bit Score: 123.27  E-value: 7.82e-35
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30687607   37 NESGCFDCNICLDTAHDPVVTLCGHLFCWPCIYKWLHVQLSSVS-VDQHQN-----NCPVCKSNITITSLVPLYGRGMSS 110
Cdd:PLN03208  14 DSGGDFDCNICLDQVRDPVVTLCGHLFCWPCIHKWTYASNNSRQrVDQYDHkreppKCPVCKSDVSEATLVPIYGRGQKA 93
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30687607  111 PSStfgskkqdalSTDIPRRPApsalrNPItsasslnpslqhqtlspsfhnhqYSPRGFTTTESTDLANAVMMSFLYPVI 190
Cdd:PLN03208  94 PQS----------GSNVPSRPS-----GPV-----------------------YDLRGVGQRLGEGESQRYMYRMPDPVM 135
                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....
gi 30687607  191 GMFGDLVYTRIFGTFTNTIAqPYQS------QRMMQREKSLNRV 228
Cdd:PLN03208 136 GVVCEMVYRRLFGESSSNMA-PYRDmnvrsrRRAMQAEESLSRV 178
 
Name Accession Description Interval E-value
PLN03208 PLN03208
E3 ubiquitin-protein ligase RMA2; Provisional
37-228 7.82e-35

E3 ubiquitin-protein ligase RMA2; Provisional


Pssm-ID: 178747 [Multi-domain]  Cd Length: 193  Bit Score: 123.27  E-value: 7.82e-35
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30687607   37 NESGCFDCNICLDTAHDPVVTLCGHLFCWPCIYKWLHVQLSSVS-VDQHQN-----NCPVCKSNITITSLVPLYGRGMSS 110
Cdd:PLN03208  14 DSGGDFDCNICLDQVRDPVVTLCGHLFCWPCIHKWTYASNNSRQrVDQYDHkreppKCPVCKSDVSEATLVPIYGRGQKA 93
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30687607  111 PSStfgskkqdalSTDIPRRPApsalrNPItsasslnpslqhqtlspsfhnhqYSPRGFTTTESTDLANAVMMSFLYPVI 190
Cdd:PLN03208  94 PQS----------GSNVPSRPS-----GPV-----------------------YDLRGVGQRLGEGESQRYMYRMPDPVM 135
                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....
gi 30687607  191 GMFGDLVYTRIFGTFTNTIAqPYQS------QRMMQREKSLNRV 228
Cdd:PLN03208 136 GVVCEMVYRRLFGESSSNMA-PYRDmnvrsrRRAMQAEESLSRV 178
RING-HC_AtRMA-like cd16745
RING finger, HC subclass, found in Arabidopsis thaliana RING membrane-anchor proteins (AtRMAs) ...
42-93 8.39e-29

RING finger, HC subclass, found in Arabidopsis thaliana RING membrane-anchor proteins (AtRMAs) and similar proteins; AtRMAs, including AtRma1, AtRma2, and AtRma3, are endoplasmic reticulum (ER)-localized Arabidopsis homologs of human outer membrane of the ER-anchor E3 ubiquitin-protein ligase, RING finger protein 5 (RNF5). AtRMAs possess E3 ubiquitin ligase activity, and may play a role in the growth and development of Arabidopsis. The AtRMA1 and AtRMA3 genes are predominantly expressed in major tissues, such as cotyledons, leaves, shoot-root junction, roots, and anthers, while AtRMA2 expression is restricted to the root tips and leaf hydathodes. AtRma1 probably functions with the Ubc4/5 subfamily of E2. AtRma2 is likely involved in the cellular regulation of ABP1 expression levels through interacting with auxin binding protein 1 (ABP1). AtRMA proteins contain an N-terminal C3HC4-type RING-HC finger and a trans-membrane-anchoring domain in their extreme C-terminal region.


Pssm-ID: 438403 [Multi-domain]  Cd Length: 45  Bit Score: 102.95  E-value: 8.39e-29
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|..
gi 30687607  42 FDCNICLDTAHDPVVTLCGHLFCWPCIYKWLHVQLssvsvdqHQNNCPVCKS 93
Cdd:cd16745   1 FECNICLDLAQDPVVTLCGHLFCWPCLHKWLRRQS-------SQPECPVCKA 45
PEX10 COG5574
RING-finger-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, ...
24-93 9.17e-10

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


Pssm-ID: 227861 [Multi-domain]  Cd Length: 271  Bit Score: 57.60  E-value: 9.17e-10
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30687607  24 KPNLTtaPTAGQANesgcFDCNICLDTAHDPVVTLCGHLFCWPCIykwlhvqLSSVSVDQHQnNCPVCKS 93
Cdd:COG5574 204 KKNGL--PFIPLAD----YKCFLCLEEPEVPSCTPCGHLFCLSCL-------LISWTKKKYE-FCPLCRA 259
RING smart00184
Ring finger; E3 ubiquitin-protein ligase activity is intrinsic to the RING domain of c-Cbl and ...
44-91 1.26e-09

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: 52.51  E-value: 1.26e-09
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*....
gi 30687607     44 CNICLDT-AHDPVVTLCGHLFCWPCIYKWLhvqlssvsvDQHQNNCPVC 91
Cdd:smart00184   1 CPICLEEyLKDPVILPCGHTFCRSCIRKWL---------ESGNNTCPIC 40
zf-RING_2 pfam13639
Ring finger domain;
42-92 6.28e-08

Ring finger domain;


Pssm-ID: 433370 [Multi-domain]  Cd Length: 44  Bit Score: 47.79  E-value: 6.28e-08
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 30687607    42 FDCNICLD---TAHDPVVTLCGHLFCWPCIYKWLhvqlssvsvdQHQNNCPVCK 92
Cdd:pfam13639   1 DECPICLEefeEGDKVVVLPCGHHFHRECLDKWL----------RSSNTCPLCR 44
rad18 TIGR00599
DNA repair protein rad18; All proteins in this family for which functions are known are ...
42-93 4.27e-05

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: 43.84  E-value: 4.27e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 30687607    42 FDCNICLDTAHDPVVTLCGHLFCWPCIYKWLHVqlssvsvdqhQNNCPVCKS 93
Cdd:TIGR00599  27 LRCHICKDFFDVPVLTSCSHTFCSLCIRRCLSN----------QPKCPLCRA 68
 
Name Accession Description Interval E-value
PLN03208 PLN03208
E3 ubiquitin-protein ligase RMA2; Provisional
37-228 7.82e-35

E3 ubiquitin-protein ligase RMA2; Provisional


Pssm-ID: 178747 [Multi-domain]  Cd Length: 193  Bit Score: 123.27  E-value: 7.82e-35
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30687607   37 NESGCFDCNICLDTAHDPVVTLCGHLFCWPCIYKWLHVQLSSVS-VDQHQN-----NCPVCKSNITITSLVPLYGRGMSS 110
Cdd:PLN03208  14 DSGGDFDCNICLDQVRDPVVTLCGHLFCWPCIHKWTYASNNSRQrVDQYDHkreppKCPVCKSDVSEATLVPIYGRGQKA 93
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30687607  111 PSStfgskkqdalSTDIPRRPApsalrNPItsasslnpslqhqtlspsfhnhqYSPRGFTTTESTDLANAVMMSFLYPVI 190
Cdd:PLN03208  94 PQS----------GSNVPSRPS-----GPV-----------------------YDLRGVGQRLGEGESQRYMYRMPDPVM 135
                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....
gi 30687607  191 GMFGDLVYTRIFGTFTNTIAqPYQS------QRMMQREKSLNRV 228
Cdd:PLN03208 136 GVVCEMVYRRLFGESSSNMA-PYRDmnvrsrRRAMQAEESLSRV 178
RING-HC_AtRMA-like cd16745
RING finger, HC subclass, found in Arabidopsis thaliana RING membrane-anchor proteins (AtRMAs) ...
42-93 8.39e-29

RING finger, HC subclass, found in Arabidopsis thaliana RING membrane-anchor proteins (AtRMAs) and similar proteins; AtRMAs, including AtRma1, AtRma2, and AtRma3, are endoplasmic reticulum (ER)-localized Arabidopsis homologs of human outer membrane of the ER-anchor E3 ubiquitin-protein ligase, RING finger protein 5 (RNF5). AtRMAs possess E3 ubiquitin ligase activity, and may play a role in the growth and development of Arabidopsis. The AtRMA1 and AtRMA3 genes are predominantly expressed in major tissues, such as cotyledons, leaves, shoot-root junction, roots, and anthers, while AtRMA2 expression is restricted to the root tips and leaf hydathodes. AtRma1 probably functions with the Ubc4/5 subfamily of E2. AtRma2 is likely involved in the cellular regulation of ABP1 expression levels through interacting with auxin binding protein 1 (ABP1). AtRMA proteins contain an N-terminal C3HC4-type RING-HC finger and a trans-membrane-anchoring domain in their extreme C-terminal region.


Pssm-ID: 438403 [Multi-domain]  Cd Length: 45  Bit Score: 102.95  E-value: 8.39e-29
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|..
gi 30687607  42 FDCNICLDTAHDPVVTLCGHLFCWPCIYKWLHVQLssvsvdqHQNNCPVCKS 93
Cdd:cd16745   1 FECNICLDLAQDPVVTLCGHLFCWPCLHKWLRRQS-------SQPECPVCKA 45
RING-HC_RNF5-like cd16534
RING finger, HC subclass, found in RING finger protein RNF5, RNF185 and similar proteins; RNF5 ...
42-92 4.35e-25

RING finger, HC subclass, found in RING finger protein RNF5, RNF185 and similar proteins; RNF5 and RNF185 are E3 ubiquitin-protein ligases that are anchored to the outer membrane of the endoplasmic reticulum (ER). RNF5 acts at early stages of cystic fibrosis (CF) transmembrane conductance regulator (CFTR) biosynthesis, and functions as a target for therapeutic modalities to antagonize mutant CFTR proteins in CF patients carrying the F508del allele. RNF185 controls the degradation of CFTR and CFTR F508del allele in a RING- and proteasome-dependent manner, but does not control that of other classical endoplasmic reticulum-associated degradation (ERAD) model substrates. Moreover, both RNF5 and RNF185 play important roles in cell adhesion and migration through the modulation of cell migration by ubiquitinating paxillin. Arabidopsis thaliana RING membrane-anchor proteins (AtRMAs) are also included in this family. They possess E3 ubiquitin-protein ligase activity and may play a role in the growth and development of Arabidopsis. All members of this family contain a C3HC4-type RING-HC finger.


Pssm-ID: 438196 [Multi-domain]  Cd Length: 44  Bit Score: 93.13  E-value: 4.35e-25
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|.
gi 30687607  42 FDCNICLDTAHDPVVTLCGHLFCWPCIYKWLHVQLssvsvdqHQNNCPVCK 92
Cdd:cd16534   1 FECNICLDTASDPVVTMCGHLFCWPCLYQWLETRP-------DRQTCPVCK 44
RING-HC_RNF185 cd16744
RING finger, HC subclass, found in RING finger protein 185 (RNF185) and similar proteins; ...
42-105 1.57e-22

RING finger, HC subclass, found in RING finger protein 185 (RNF185) and similar proteins; RNF185 is an E3 ubiquitin-protein ligase of endoplasmic reticulum-associated degradation (ERAD) that targets cystic fibrosis transmembrane conductance regulator (CFTR). It controls the degradation of CFTR and CFTR F508del allele in a RING- and proteasome-dependent manner, but does not control that of other classical ERAD model substrates. It also negatively regulates osteogenic differentiation by targeting dishevelled2 (Dvl2), a key mediator of the Wnt signaling pathway, for degradation. Moreover, RNF185 regulates selective mitochondrial autophagy through interaction with the Bcl-2 family protein BNIP1. It also plays an important role in cell adhesion and migration through the modulation of cell migration by ubiquitinating paxillin. RNF185 contains a C3HC4-type RING-HC finger.


Pssm-ID: 438402 [Multi-domain]  Cd Length: 57  Bit Score: 86.90  E-value: 1.57e-22
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 30687607  42 FDCNICLDTAHDPVVTLCGHLFCWPCIYKWLHVQLSsvsvdqhQNNCPVCKSNITITSLVPLYG 105
Cdd:cd16744   1 FECNICLDTAKDAVVSLCGHLFCWPCLHQWLETRPN-------RQVCPVCKAGISRDKVIPLYG 57
RING-HC_RNF5 cd16743
RING finger, HC subclass, found in RING finger protein 5 (RNF5) and similar proteins; RNF5, ...
42-102 8.23e-21

RING finger, HC subclass, found in RING finger protein 5 (RNF5) and similar proteins; RNF5, also known as protein G16 or Ram1, is an E3 ubiquitin-protein ligase anchored to the outer membrane of the endoplasmic reticulum (ER). It acts at early stages of cystic fibrosis (CF) transmembrane conductance regulator (CFTR) biosynthesis and functions as a target for therapeutic modalities to antagonize mutant CFTR proteins in CF patients carrying the F508del allele. It also regulates the turnover of specific G protein-coupled receptors by ubiquitinating JNK-associated membrane protein (JAMP) and preventing proteasome recruitment. RNF5 limits basal levels of autophagy and influences susceptibility to bacterial infection through the regulation of ATG4B stability. It is also involved in the degradation of Pendrin, a transmembrane chloride/anion exchanger highly expressed in thyroid, kidney, and inner ear. RNF5 plays an important role in cell adhesion and migration. It can modulate cell migration by ubiquitinating paxillin. Furthermore, RNF5 interacts with virus-induced signaling adaptor (VISA) at mitochondria in a viral infection-dependent manner, and further targets VISA at K362 and K461 for K48-linked ubiquitination and degradation after viral infection. It also negatively regulates virus-triggered signaling by targeting MITA, also known as STING, for ubiquitination and degradation at the mitochondria. In addition, RNF5 determines breast cancer response to ER stress-inducing chemotherapies through the regulation of the L-glutamine carrier proteins SLC1A5 and SLC38A2 (SLC1A5/38A2). It also has been implicated in muscle organization and in recognition and processing of misfolded proteins. RNF5 contains a C3HC4-type RING-HC finger.


Pssm-ID: 438401 [Multi-domain]  Cd Length: 54  Bit Score: 82.63  E-value: 8.23e-21
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 30687607  42 FDCNICLDTAHDPVVTLCGHLFCWPCIYKWLHVQlssvsvdQHQNNCPVCKSNITITSLVP 102
Cdd:cd16743   1 FECNICLETARDAVVSLCGHLFCWPCLHQWLETR-------PERQECPVCKAGISRDKVIP 54
RING-HC_HLTF cd16509
RING finger, HC subclass, found in helicase-like transcription factor (HLTF) and similar ...
42-100 9.91e-13

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


Pssm-ID: 438172 [Multi-domain]  Cd Length: 53  Bit Score: 61.17  E-value: 9.91e-13
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*....
gi 30687607  42 FDCNICLDTAHDPVVTLCGHLFCWPCIYKwlhvqlssvSVDQHQNNCPVCKSNITITSL 100
Cdd:cd16509   4 EECAICLDSLTNPVITPCAHVFCRRCICE---------VIQREKAKCPMCRAPLSASDL 53
RING-HC_BRCA1 cd16498
RING finger, HC subclass, found in breast cancer type 1 susceptibility protein (BRCA1) and ...
42-106 1.51e-11

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


Pssm-ID: 438161 [Multi-domain]  Cd Length: 94  Bit Score: 58.85  E-value: 1.51e-11
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 30687607  42 FDCNICLDTAHDPVVTLCGHLFCWPCIYKWLHVQLSSVsvdqhqnNCPVCKSNITITSLVPLYGR 106
Cdd:cd16498  17 LECPICLELLKEPVSTKCDHQFCRFCILKLLQKKKKPA-------PCPLCKKSVTKRSLQESTRF 74
RING-HC_PEX10 cd16527
RING finger, HC subclass, found in peroxin-10 (PEX10) and similar proteins; PEX10, also known ...
44-103 2.04e-11

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


Pssm-ID: 438190 [Multi-domain]  Cd Length: 52  Bit Score: 57.62  E-value: 2.04e-11
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|
gi 30687607  44 CNICLDTAHDPVVTLCGHLFCWPCIYKWLhvqlssvsvdQHQNNCPVCKSNITITSLVPL 103
Cdd:cd16527   3 CSLCLEERRHPTATPCGHLFCWSCITEWC----------NEKPECPLCREPFQPQRLVPL 52
RING-HC_RNF10 cd16536
RING finger, HC subclass, found in RING finger protein 10 (RNF10) and similar proteins; RNF10 ...
42-100 1.25e-10

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


Pssm-ID: 438198 [Multi-domain]  Cd Length: 54  Bit Score: 55.32  E-value: 1.25e-10
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*....
gi 30687607  42 FDCNICLDTAHDPVVTLCGHLFCWPCIYKWLHVQlssvsvDQHQNNCPVCKSNITITSL 100
Cdd:cd16536   1 PQCPICLEPPVAPRITRCGHIFCWPCILRYLSLS------EKKWRKCPICFESIHKKDL 53
RING-HC_RNF213 cd16561
RING finger, HC subclass, found in RING finger protein 213 (RNF213) and similar proteins; ...
43-96 1.72e-10

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


Pssm-ID: 438223 [Multi-domain]  Cd Length: 50  Bit Score: 54.98  E-value: 1.72e-10
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....
gi 30687607  43 DCNICLDTAHDPVVTLCGHLFCWPCIYKWLhvqlssvsvdQHQNNCPVCKSNIT 96
Cdd:cd16561   4 ECSICLEDLNDPVKLPCDHVFCEECIRQWL----------PGQMSCPLCRTELP 47
RING-HC_CHR27-like cd23142
RING finger, HC subclass, found in Arabidopsis thaliana protein CHROMATIN REMODELING 27 (CHR27) ...
44-100 2.82e-10

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


Pssm-ID: 438504 [Multi-domain]  Cd Length: 55  Bit Score: 54.50  E-value: 2.82e-10
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*..
gi 30687607  44 CNICLDTAHDPVVTLCGHLFCWPCIYKWlhvqLSSVSVDQHQNNCPVCKSNITITSL 100
Cdd:cd23142   3 CPICNDPPEDAVVTLCGHVFCCECVFQY----LSSDRTCRQFNHCPLCRQKLYLDDV 55
PEX10 COG5574
RING-finger-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, ...
24-93 9.17e-10

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


Pssm-ID: 227861 [Multi-domain]  Cd Length: 271  Bit Score: 57.60  E-value: 9.17e-10
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30687607  24 KPNLTtaPTAGQANesgcFDCNICLDTAHDPVVTLCGHLFCWPCIykwlhvqLSSVSVDQHQnNCPVCKS 93
Cdd:COG5574 204 KKNGL--PFIPLAD----YKCFLCLEEPEVPSCTPCGHLFCLSCL-------LISWTKKKYE-FCPLCRA 259
RING smart00184
Ring finger; E3 ubiquitin-protein ligase activity is intrinsic to the RING domain of c-Cbl and ...
44-91 1.26e-09

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: 52.51  E-value: 1.26e-09
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*....
gi 30687607     44 CNICLDT-AHDPVVTLCGHLFCWPCIYKWLhvqlssvsvDQHQNNCPVC 91
Cdd:smart00184   1 CPICLEEyLKDPVILPCGHTFCRSCIRKWL---------ESGNNTCPIC 40
RING-HC cd16449
HC subclass of RING (RING-HC) finger and its variants; The RING finger is a specialized type ...
42-91 4.49e-09

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


Pssm-ID: 438113 [Multi-domain]  Cd Length: 41  Bit Score: 50.95  E-value: 4.49e-09
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|
gi 30687607  42 FDCNICLDTAHDPVVTLCGHLFCWPCIYKWLhvqlssvsvDQHQNNCPVC 91
Cdd:cd16449   1 LECPICLERLKDPVLLPCGHVFCRECIRRLL---------ESGSIKCPIC 41
RING-HC_EHV1-like cd23130
RING finger, HC subclass, found in Equid alphaherpesvirus 1 (Equine herpesvirus 1/EHV-1) ...
42-96 6.42e-09

RING finger, HC subclass, found in Equid alphaherpesvirus 1 (Equine herpesvirus 1/EHV-1) regulatory protein and similar proteins; EHV-1 regulatory protein belongs to the Vmw110 (IPC0) protein family. It contains a typical C3HC4-type RING-HC finger and binds zinc stably.


Pssm-ID: 438492 [Multi-domain]  Cd Length: 51  Bit Score: 50.81  E-value: 6.42e-09
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*.
gi 30687607  42 FDCNICLDTAHDPVVTL-CGHLFCWPCIYKWLhvqlssvsvdQHQNNCPVCKSNIT 96
Cdd:cd23130   1 DVCPICLDDPEDEAITLpCLHQFCYTCILRWL----------QTSPTCPLCKTPVT 46
RING-HC_COP1 cd16504
RING finger, HC subclass, found in constitutive photomorphogenesis protein 1 (COP1) and ...
40-96 1.07e-08

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


Pssm-ID: 438167 [Multi-domain]  Cd Length: 47  Bit Score: 49.93  E-value: 1.07e-08
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*..
gi 30687607  40 GCFDCNICLDTAHDPVVTLCGHLFCWPCIYKWLhvqlssvsvdQHQNNCPVCKSNIT 96
Cdd:cd16504   1 NDFLCPICFDIIKEAFVTKCGHSFCYKCIVKHL----------EQKNRCPKCNFYLT 47
mRING-C3HGC3_RFWD3 cd16450
Modified RING finger, C3HGC3-type, found in RING finger and WD repeat domain-containing ...
44-104 1.60e-08

Modified RING finger, C3HGC3-type, found in RING finger and WD repeat domain-containing protein 3 (RFWD3) and similar proteins; RFWD3, also known as RING finger protein 201 (RNF201) or FLJ10520, is an E3 ubiquitin-protein ligase that forms a complex with Mdm2 and p53 to synergistically ubiquitinate p53 and acts as a positive regulator of p53 stability in response to DNA damage. It is phosphorylated by checkpoint kinase ATM/ATR and the phosphorylation mutant fails to stimulate p53 ubiquitination. RFWD3 also functions as a novel replication protein A (RPA)-associated protein involved in DNA replication checkpoint control. RFWD3 contains an N-terminal SQ-rich region followed by a RING finger domain that exhibits robust E3 ubiquitin ligase activity toward p53, a coiled-coil domain and three WD40 repeats in the C-terminus, the latter two of which may be responsible for protein-protein interaction. The RING finger in this family is a modified C3HGC3-type RING finger, but not a canonical C3H2C3-type RING-H2 finger or C3HC4-type RING-HC finger.


Pssm-ID: 438114 [Multi-domain]  Cd Length: 61  Bit Score: 49.92  E-value: 1.60e-08
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 30687607  44 CNICLD----TAHDPVVTL-CGHLFCWPCIYKWLHvqlssvsvdQHQNNCPVCKSNITITSLVPLY 104
Cdd:cd16450   5 CPICFEpwtsSGEHRLVSLkCGHLFGYSCIEKWLK---------GKGKKCPQCNKKAKRSDIRPLY 61
RING-HC_PRT1-like cd23132
RING finger, HC subclass, found in Arabidopsis thaliana proteolysis 1 protein (PRT1) and ...
42-93 1.96e-08

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


Pssm-ID: 438494 [Multi-domain]  Cd Length: 52  Bit Score: 49.34  E-value: 1.96e-08
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|..
gi 30687607  42 FDCNICLDTAHDPVVTLCGHLFCWPCIYKWLHVqlssvsvdQHQNNCPVCKS 93
Cdd:cd23132   3 FLCCICLDLLYKPVVLECGHVFCFWCVHRCMNG--------YDESHCPLCRR 46
zf-RING_2 pfam13639
Ring finger domain;
42-92 6.28e-08

Ring finger domain;


Pssm-ID: 433370 [Multi-domain]  Cd Length: 44  Bit Score: 47.79  E-value: 6.28e-08
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 30687607    42 FDCNICLD---TAHDPVVTLCGHLFCWPCIYKWLhvqlssvsvdQHQNNCPVCK 92
Cdd:pfam13639   1 DECPICLEefeEGDKVVVLPCGHHFHRECLDKWL----------RSSNTCPLCR 44
RING-HC_LONFs_rpt2 cd16514
second RING finger, HC subclass, found in the LON peptidase N-terminal domain and RING finger ...
42-93 1.22e-07

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


Pssm-ID: 438177 [Multi-domain]  Cd Length: 45  Bit Score: 46.88  E-value: 1.22e-07
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|..
gi 30687607  42 FDCNICLDTAHDPVVTLCGHLFCWPCIYKWLhvqlssvsvdQHQNNCPVCKS 93
Cdd:cd16514   2 LECSLCLRLLYEPVTTPCGHTFCRACLERCL----------DHSPKCPLCRT 43
RING-HC_RNF125 cd16542
RING finger, HC subclass, found in RING finger protein 125 (RNF125); RNF125, also known as ...
42-95 1.26e-07

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


Pssm-ID: 438204 [Multi-domain]  Cd Length: 50  Bit Score: 47.18  E-value: 1.26e-07
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....
gi 30687607  42 FDCNICLDTAHDPVVTLCGHLFCWPCIykwlhvqlsSVSVDQHQNNCPVCKSNI 95
Cdd:cd16542   2 FDCAVCLEVLHQPVRTRCGHVFCRPCI---------ATSLRNNTWTCPYCRAYL 46
RING-HC_Topors cd16574
RING finger, HC subclass, found in topoisomerase I-binding arginine/serine-rich protein ...
43-92 1.39e-07

RING finger, HC subclass, found in topoisomerase I-binding arginine/serine-rich protein (Topors) and similar proteins; Topors, also known as topoisomerase I-binding RING finger protein, tumor suppressor p53- binding protein 3, or p53-binding protein 3 (p53BP3), is a ubiquitously expressed nuclear E3 ubiquitin-protein ligase that can ligate both ubiquitin and small ubiquitin-like modifier (SUMO) to substrate proteins in the nucleus. It contains an N-terminal C3HC4-type RING-HC finger which ligates ubiquitin to its target proteins including DNA topoisomerase I, p53, NKX3.1, H2AX, and the AAV-2 Rep78/68 proteins. As a RING-dependent E3 ubiquitin ligase, Topors works with the E2 enzymes UbcH5a, UbcH5c, and UbcH6, but not with UbcH7, CDC34, or UbcH2b. Topors acts as a tumor suppressor in various malignancies. It regulates p53 modification, suggesting it may be responsible for astrocyte elevated gene-1 (AEG-1, also known as metadherin, or LYRIC) ubiquitin modification. Plk1-mediated phosphorylation of Topors inhibits Topors-mediated sumoylation of p53, whereas p53 ubiquitination is enhanced, leading to p53 degradation. It also functions as a negative regulator of the prostate tumor suppressor NKX3.1. Moreover, Topors is associated with promyelocytic leukemia nuclear bodies, and may be involved in the cellular response to camptothecin. It also plays a key role in the turnover of H2AX protein, discriminating the type of DNA damaging stress. Furthermore, Topors is a cilia-centrosomal protein associated with autosomal dominant retinal degeneration. Mutations in TOPORS cause autosomal dominant retinitis pigmentosa (adRP).


Pssm-ID: 438236 [Multi-domain]  Cd Length: 47  Bit Score: 46.89  E-value: 1.39e-07
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|..
gi 30687607  43 DCNICLDTAHDPVVTL--CGHLFCWPCIYKWlhvqlSSVSvdqhqNNCPVCK 92
Cdd:cd16574   3 SCPICLDRFENEKAFLdgCFHAFCFTCILEW-----SKVK-----NECPLCK 44
RING-HC_RNF113A_B cd16539
RING finger, HC subclass, found in RING finger proteins RNF113A, RNF113B, and similar proteins; ...
42-95 3.78e-07

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: 438201 [Multi-domain]  Cd Length: 54  Bit Score: 45.66  E-value: 3.78e-07
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....
gi 30687607  42 FDCNICLDTAHDPVVTLCGHLFCWPCIYKwlhvqlssvsVDQHQNNCPVCKSNI 95
Cdd:cd16539   6 FACFICRKPFKNPVVTKCGHYFCEKCALK----------HYRKSKKCFVCGKQT 49
RING-HC_RNFT2 cd16742
RING finger, HC subclass, found in RING finger and transmembrane domain-containing protein 2 ...
32-98 4.61e-07

RING finger, HC subclass, found in RING finger and transmembrane domain-containing protein 2(RNFT2); RNFT2, also known as transmembrane protein 118 (TMEM118), is a multi-pass membrane protein containing a C3HC4-type RING-HC finger. Its biological role remains unclear.


Pssm-ID: 438400 [Multi-domain]  Cd Length: 67  Bit Score: 46.03  E-value: 4.61e-07
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 30687607  32 TAGQANESGCFdCNICLDTAHDPVVTLCGHLFCWPCIYKWLhvqlssvsvdQHQNNCPVCKSNITIT 98
Cdd:cd16742   5 TSQQCSEAGDI-CAICQAEFREPLILICQHVFCEECLCLWF----------DRERTCPLCRSVVVET 60
zf-C3HC4_2 pfam13923
Zinc finger, C3HC4 type (RING finger);
44-91 4.85e-07

Zinc finger, C3HC4 type (RING finger);


Pssm-ID: 404756 [Multi-domain]  Cd Length: 40  Bit Score: 45.12  E-value: 4.85e-07
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 30687607    44 CNICLDTAHDP-VVTLCGHLFCWPCIYKWLhvqlssvsvdQHQNNCPVC 91
Cdd:pfam13923   2 CPICMDMLKDPsTTTPCGHVFCQDCILRAL----------EASNECPLC 40
RING-HC_TRIM62_C-IV cd16608
RING finger, HC subclass, found in tripartite motif-containing protein 62 (TRIM62) and similar ...
42-92 5.76e-07

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


Pssm-ID: 438270 [Multi-domain]  Cd Length: 52  Bit Score: 45.18  E-value: 5.76e-07
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|.
gi 30687607  42 FDCNICLDTAHDPVVTLCGHLFCWPCIYKwlHvqlssvSVDQHQNNCPVCK 92
Cdd:cd16608   7 LLCSICLSIYQDPVSLGCEHYFCRQCITE--H------WSRSEHRDCPECR 49
mRING-HC-C3HC3D_TRAF6 cd16643
Modified RING finger, HC subclass (C3HC3D-type), found in tumor necrosis factor (TNF) ...
42-83 5.83e-07

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


Pssm-ID: 438305 [Multi-domain]  Cd Length: 58  Bit Score: 45.45  E-value: 5.83e-07
                        10        20        30        40
                ....*....|....*....|....*....|....*....|..
gi 30687607  42 FDCNICLDTAHDPVVTLCGHLFCWPCIYKWLHVQLSSVSVDQ 83
Cdd:cd16643   2 YECPICLMALREPVQTPCGHRFCKACILKSIREAGHKCPVDN 43
RING-HC_ORTHRUS_rpt1 cd23138
first RING finger, HC subclass, found in Arabidopsis thaliana ORTHRUS and similar proteins; ...
42-95 6.56e-07

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


Pssm-ID: 438500 [Multi-domain]  Cd Length: 48  Bit Score: 45.13  E-value: 6.56e-07
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....
gi 30687607  42 FDCNICLDTAHDPVVTLCGHLFCWPCIYKWlhvqlssvsVDQHQNNCPVCKSNI 95
Cdd:cd23138   3 LNCSFCMQLPERPVTTPCGHNFCLKCFQKW---------MGQGKKTCGTCRSPI 47
zf-RING_UBOX pfam13445
RING-type zinc-finger; This zinc-finger is a typical RING-type of plant ubiquitin ligases.
44-89 6.86e-07

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


Pssm-ID: 463881 [Multi-domain]  Cd Length: 38  Bit Score: 44.70  E-value: 6.86e-07
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 30687607    44 CNICLDTAHDPVVTlCGHLFCWPCIYKWLhvqlssvSVDQHQNNCP 89
Cdd:pfam13445   1 CPICLELFTDPVLP-CGHTFCRECLEEMS-------QKKGGKFKCP 38
RING-HC_TRIM25_C-IV cd16597
RING finger, HC subclass, found in tripartite motif-containing protein TRIM25 and similar ...
44-92 7.57e-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: 438259 [Multi-domain]  Cd Length: 71  Bit Score: 45.38  E-value: 7.57e-07
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*....
gi 30687607  44 CNICLDTAHDPVVTLCGHLFCWPCIYKWLHVQLSSvsvdqhQNNCPVCK 92
Cdd:cd16597   8 CSICLELFKDPVTLPCGHNFCGVCIEKTWDSQHGS------EYSCPQCR 50
RING-HC_ScPSH1-like cd16568
RING finger, HC subclass, found in Saccharomyces cerevisiae POB3/SPT16 histone-associated ...
44-96 8.39e-07

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


Pssm-ID: 438230 [Multi-domain]  Cd Length: 54  Bit Score: 45.05  E-value: 8.39e-07
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|...
gi 30687607  44 CNICLDTAHDPVVTLCGHLFCWPCIYKWLHvqlssvsvDQHQNNCPVCKSNIT 96
Cdd:cd16568   7 CIICHEYLYEPMVTTCGHTYCYTCLNTWFK--------SNRSLSCPDCRTKIT 51
RING-HC_RNF170 cd16553
RING finger, HC subclass, found in RING finger protein 170 (RNF170) and similar proteins; ...
44-104 8.43e-07

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


Pssm-ID: 438215 [Multi-domain]  Cd Length: 57  Bit Score: 44.97  E-value: 8.43e-07
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 30687607  44 CNICLDTAHDPVVTLCGHLFCWPCIYK-WLH-VQLSSVSvdqhqnnCPVCKSNITItsLVPLY 104
Cdd:cd16553   4 CPICLQDARFPVETNCGHLFCGPCIITyWRHgSWLGAVS-------CPVCRQTVTL--LLPVF 57
zf-C3HC4 pfam00097
Zinc finger, C3HC4 type (RING finger); The C3HC4 type zinc-finger (RING finger) is a ...
44-91 1.65e-06

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


Pssm-ID: 395049 [Multi-domain]  Cd Length: 40  Bit Score: 43.88  E-value: 1.65e-06
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 30687607    44 CNICLDTAHDPVVTL-CGHLFCWPCIYKWLHVQlssvsvdqhQNNCPVC 91
Cdd:pfam00097   1 CPICLEEPKDPVTLLpCGHLFCSKCIRSWLESG---------NVTCPLC 40
RING-H2_PA-TM-RING cd16454
RING finger, H2 subclass, found in the PA-TM-RING ubiquitin ligase family; The PA-TM-RING ...
43-92 1.70e-06

RING finger, H2 subclass, found in the PA-TM-RING ubiquitin ligase family; The PA-TM-RING family represents a group of transmembrane-type E3 ubiquitin ligases, which has been characterized by an N-terminal transient signal peptide, a PA (protease-associated) domain, a TM (transmembrane) domain, as well as a C-terminal C3H2C3-type RING-H2 finger domain. It includes RNF13, RNF167, ZNRF4 (zinc and RING finger 4), GRAIL (gene related to anergy in lymphocytes)/RNF128, RNF130, RNF133, RNF148, RNF149 and RNF150 (which are more closely related), as well as RNF43 and ZNRF3, which have substantially longer C-terminal tail extensions compared with the others. PA-TM-RING proteins are expressed at low levels in all mammalian tissues and species, but they are not present in yeast. They play a common regulatory role in intracellular trafficking/sorting, suggesting that abrogation of their function may result in dysregulation of cellular signaling events in cancer.


Pssm-ID: 438118 [Multi-domain]  Cd Length: 43  Bit Score: 43.80  E-value: 1.70e-06
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|...
gi 30687607  43 DCNICLDT--AHDPVVTL-CGHLFCWPCIYKWLHvqlssvsvdqHQNNCPVCK 92
Cdd:cd16454   1 TCAICLEEfkEGEKVRVLpCNHLFHKDCIDPWLE----------QHNTCPLCR 43
RING-HC_ScRAD18-like cd23148
RING finger, HC subclass, found in Saccharomyces cerevisiae radiation sensitivity protein 18 ...
42-100 2.35e-06

RING finger, HC subclass, found in Saccharomyces cerevisiae radiation sensitivity protein 18 (RAD18) and similar proteins; RAD18, also called RING-type E3 ubiquitin transferase RAD18, acts as a postreplication repair E3 ubiquitin-protein ligase that associates with the E2 ubiquitin conjugating enzyme UBC2/RAD6 to form the UBC2-RAD18 ubiquitin ligase complex involved in postreplicative repair (PRR) of damaged DNA. The UBC2-RAD18 complex cooperates with RAD5 and the UBC13-MMS2 dimer to attach mono-ubiquitin chains on 'Lys-164' of POL30, which is necessary for PRR. The UBC2-RAD18 complex is also involved in prevention of spontaneous mutations caused by 7,8-dihydro-8-oxoguanine. RAD18 is an E3 RING-finger protein belonging to the UBC2/RAD6 epistasis group. It contains a typical C3HC4-type RING-HC finger.


Pssm-ID: 438510 [Multi-domain]  Cd Length: 52  Bit Score: 43.68  E-value: 2.35e-06
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*....
gi 30687607  42 FDCNICLDTAHDPVVTLCGHLFCWPCIYKWLHVqlssvsvdqhQNNCPVCKSNITITSL 100
Cdd:cd23148   4 LRCHICKDLLKAPMRTPCNHTFCSFCIRTHLNN----------DARCPLCKAEVTESGL 52
RING-HC_RAD16-like cd16567
RING finger, HC subclass, found in Saccharomyces cerevisiae DNA repair protein RAD16, ...
44-91 3.09e-06

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


Pssm-ID: 438229 [Multi-domain]  Cd Length: 48  Bit Score: 43.10  E-value: 3.09e-06
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*...
gi 30687607  44 CNICLDTAHDPVVTLCGHLFCWPCIYKWLHvqlssvSVDQHQNNCPVC 91
Cdd:cd16567   3 CGICHEEAEDPVVARCHHVFCRACVKEYIE------SAPGGKVTCPTC 44
RING-HC_IRC20-like cd23135
RING finger, HC subclass, found in Saccharomyces cerevisiae increased recombination centers ...
42-92 4.34e-06

RING finger, HC subclass, found in Saccharomyces cerevisiae increased recombination centers protein 20 (IRC20) and similar proteins; IRC20 is an uncharacterized ATP-dependent helicase that is probably involved in a pathway contributing to genomic integrity. IRC20 contains a typical C3HC4-type RING-HC finger.


Pssm-ID: 438497 [Multi-domain]  Cd Length: 44  Bit Score: 42.50  E-value: 4.34e-06
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|.
gi 30687607  42 FDCNICLDTAHDPVVTLCGHLFCWPCIYKWLhvqlssvsvdQHQNNCPVCK 92
Cdd:cd23135   4 LSCSICFSEIRSGAILKCGHFFCLSCIASWL----------REKSTCPLCK 44
mRING-HC-C3HC3D_LNX1-like cd16637
Modified RING finger, HC subclass (C3HC3D-type), found in ligand of Numb protein LNX1, LNX2, ...
42-75 4.34e-06

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


Pssm-ID: 438299 [Multi-domain]  Cd Length: 42  Bit Score: 42.77  E-value: 4.34e-06
                        10        20        30
                ....*....|....*....|....*....|....
gi 30687607  42 FDCNICLDTAHDPVVTLCGHLFCWPCIYKWLHVQ 75
Cdd:cd16637   2 LTCHICLQPLVEPLDTPCGHTFCYKCLTNYLKIQ 35
RING-HC_TRIM65_C-IV cd16609
RING finger, HC subclass, found in tripartite motif-containing protein TRIM65 and similar ...
44-94 4.91e-06

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


Pssm-ID: 438271 [Multi-domain]  Cd Length: 58  Bit Score: 42.74  E-value: 4.91e-06
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|.
gi 30687607  44 CNICLDTAHDPVVTLCGHLFCWPCIYKWLHVQlssvsvDQHQNNCPVCKSN 94
Cdd:cd16609   6 CSICLGLYQDPVTLPCQHSFCRACIEDHWRQK------DEGSFSCPECRAP 50
RING-HC_BAH1-like cd23127
RING finger, HC subclass, found in Arabidopsis thaliana protein BENZOIC ACID HYPERSENSITIVE 1 ...
44-93 4.92e-06

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


Pssm-ID: 438489 [Multi-domain]  Cd Length: 74  Bit Score: 43.16  E-value: 4.92e-06
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*...
gi 30687607  44 CNICLDTAHDPVVTLCGHLFCWPCiykwlhvQLSSVSVDQHQN--------NCPVCKS 93
Cdd:cd23127  11 CSICLDTVFDPVALGCGHLFCNSC-------ACSAASVLIFQGlkaappeaKCPLCRQ 61
RING-HC_RNF219 cd16562
RING finger, HC subclass, found in RING finger protein 219 (RNF219) and similar proteins; ...
44-95 5.07e-06

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 of 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: 438224 [Multi-domain]  Cd Length: 45  Bit Score: 42.42  E-value: 5.07e-06
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|..
gi 30687607  44 CNICLDTAHDPVVTLCGHLFCWPCIYKWLhvqlssvsvdQHQNNCPVCKSNI 95
Cdd:cd16562   4 CHICLGKVRQPVICSNNHVFCSSCMDVWL----------KNNNQCPACRVPI 45
RING-HC_TRIM40-C-V cd16583
RING finger, HC subclass, found in tripartite motif-containing protein 40 (TRIM40) and similar ...
44-92 5.53e-06

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


Pssm-ID: 438245 [Multi-domain]  Cd Length: 63  Bit Score: 42.89  E-value: 5.53e-06
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*....
gi 30687607  44 CNICLDTAHDPVVTLCGHLFCWPCIYKwlHVQLSSVSvdqHQNNCPVCK 92
Cdd:cd16583   8 CPICQEPLKEAVSTDCGHLFCRMCLTQ--HAKKASAS---GVFSCPVCR 51
RING-HC_RAD5 cd23131
RING finger, HC subclass, found in radiation sensitivity protein 5 (RAD5) and similar proteins; ...
42-103 8.01e-06

RING finger, HC subclass, found in radiation sensitivity protein 5 (RAD5) and similar proteins; RAD5, also known as revertibility protein 2 (REV2), or DNA repair protein RAD5, is a probable helicase, and a member of the UBC2/RAD6 epistasis group. It functions with the DNA repair protein RAD18 in error-free postreplication DNA repair. It is involved in the maintenance of wild-type rates of instability of simple repetitive sequences such as poly(GT) repeats. It may also be involved in maintaining a balance which acts in favor of error-prone non-homologous joining during DNA double-strand breaks repairs. It recruits the UBC13-MMS2 dimer to chromatin for DNA repair. RAD5 contains a typical C3HC4-type RING-HC finger.


Pssm-ID: 438493 [Multi-domain]  Cd Length: 65  Bit Score: 42.43  E-value: 8.01e-06
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 30687607  42 FDCNICLDTAHDP---VVTLCGHLFCWPCIYKWLHVQLSSVSvdqhQNNCPVCKSNITITSLVPL 103
Cdd:cd23131   4 VECSICTQEPIEVgevVFTECGHSFCEDCLLEYIEFQNKKKL----DLKCPNCREPISKYRLLKL 64
RING-HC_LNX3 cd16718
RING finger, HC subclass, found in ligand of numb protein X 3 (LNX3); LNX3, also known as PDZ ...
42-90 8.38e-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 C3HC4-type RING-HC finger, two PDZ domains, and a C-terminal LNX3 homology (LNX3H) domain.


Pssm-ID: 438378 [Multi-domain]  Cd Length: 47  Bit Score: 41.89  E-value: 8.38e-06
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*....
gi 30687607  42 FDCNICLDTAHDPVVTLCGHLFCWPCIYKWLhVQlssvsvdqhQNNCPV 90
Cdd:cd16718   5 FKCNLCNKVLEDPLTTPCGHVFCAGCVLPWV-VQ---------QGSCPV 43
RING-HC_TRIM7-like_C-IV cd16594
RING finger, HC subclass, found in tripartite motif-containing proteins, TRIM7, TRIM11 and ...
44-102 8.38e-06

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


Pssm-ID: 438256 [Multi-domain]  Cd Length: 61  Bit Score: 42.29  E-value: 8.38e-06
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|
gi 30687607  44 CNICLDTAHDPVVTLCGHLFCWPCIYK-WLHVQLSSvsvdqhqnNCPVCKSNITITSLVP 102
Cdd:cd16594   8 CPICLDYFTDPVTLDCGHSFCRACIARcWEEPETSA--------SCPQCRETCPQRNLRP 59
RING-HC_TRIM69_C-IV cd16611
RING finger, HC subclass, found in tripartite motif-containing protein 69 (TRIM69) and similar ...
44-92 1.01e-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 the TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a C3HC4-type RING-HC finger, Bbox1 and Bbox2, and a coiled coil region, as well as a B30.2/SPRY (SplA and ryanodine receptor) domain positioned C-terminal to the RBCC domain.


Pssm-ID: 438273 [Multi-domain]  Cd Length: 59  Bit Score: 42.05  E-value: 1.01e-05
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*....
gi 30687607  44 CNICLDTAHDPVVTLCGHLFCWPCIYKWLHVQlssvsvdQHQNNCPVCK 92
Cdd:cd16611   7 CPLCLDFFRDPVMLSCGHNFCQSCITGFWELQ-------AEDTTCPECR 48
RING-HC_RNF138 cd16544
RING finger, HC subclass, found in RING finger protein 138 (RNF138) and similar proteins; ...
42-98 1.11e-05

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


Pssm-ID: 438206 [Multi-domain]  Cd Length: 53  Bit Score: 41.62  E-value: 1.11e-05
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*...
gi 30687607  42 FDCNICLDTAHDPVVTL-CGHLFCWPCIYKwlhvqlssvSVDQHQNNCPVCKSNITIT 98
Cdd:cd16544   3 LTCPVCQEVLKDPVELPpCRHIFCKACILL---------ALRSSGARCPLCRGPVGKT 51
RING-HC_TRIM17_C-IV cd16595
RING finger, HC subclass, found in tripartite motif-containing protein TRIM17 and similar ...
44-102 1.14e-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 the TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a C3HC4-type RING-HC finger, Bbox1 and Bbox2, and a coiled coil region, as well as a B30.2/SPRY (SplA and ryanodine receptor) domain positioned C-terminal to the RBCC domain.


Pssm-ID: 438257 [Multi-domain]  Cd Length: 70  Bit Score: 42.28  E-value: 1.14e-05
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 30687607  44 CNICLDTAHDPVVTLCGHLFCWPCIYK-WLHVQLSSVSVDQHQN-NCPVCKSNITITSLVP 102
Cdd:cd16595   8 CSICLDYFTDPVMTTCGHNFCRACIQLsWEKARGKKGRRKQKGSfPCPECREMSPQRNLRP 68
RING-HC_TRIM77_C-IV cd16543
RING finger, HC subclass, found in tripartite motif-containing protein 77 (TRIM77) and similar ...
44-92 1.43e-05

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


Pssm-ID: 438205 [Multi-domain]  Cd Length: 54  Bit Score: 41.61  E-value: 1.43e-05
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|
gi 30687607  44 CNICLDTAHDPVVTLCGHLFCWPCIYK-WLHvqlssvsvDQHQNNCPVCK 92
Cdd:cd16543   6 CSICLDLLKDPVTIPCGHSFCMNCITLlWDR--------KQGVPSCPQCR 47
RING-HC_RNFT1-like cd16532
RING finger, HC subclass, found in RING finger and transmembrane domain-containing protein ...
44-92 1.47e-05

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


Pssm-ID: 438194 [Multi-domain]  Cd Length: 41  Bit Score: 41.13  E-value: 1.47e-05
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*....
gi 30687607  44 CNICLDTAHDPVVTLCGHLFCWPCIYKWLhvqlssvsvdQHQNNCPVCK 92
Cdd:cd16532   3 CPICQDEFKDPVVLRCKHIFCEDCVSEWF----------ERERTCPLCR 41
RING-HC_TRIM26_C-IV cd16598
RING finger, HC subclass, found in tripartite motif-containing protein 26 (TRIM26) and similar ...
44-102 1.49e-05

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


Pssm-ID: 438260 [Multi-domain]  Cd Length: 64  Bit Score: 41.69  E-value: 1.49e-05
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*....
gi 30687607  44 CNICLDTAHDPVVTLCGHLFCWPCIykwlhVQLSSVSVDQHQNNCPVCKSNITITSLVP 102
Cdd:cd16598   7 CSICLDYLRDPVTIDCGHNFCRSCI-----TDYCPISGGHERPVCPLCRKPFKKENIRP 60
RING-H2 cd16448
H2 subclass of RING (RING-H2) fingers and its variants; The RING finger is a specialized type ...
44-92 2.89e-05

H2 subclass of RING (RING-H2) fingers and its variants; The RING finger is a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc. It is defined by the "cross-brace" motif that chelates zinc atoms by eight amino acid residues, typically Cys or His, arranged in a characteristic spacing. Canonical RING motifs have been categorized into two major subclasses, RING-HC (C3HC4-type) and RING-H2 (C3H2C3-type), according to their Cys/His content. There are also many variants of RING fingers: some have different Cys/His patterns while some lack a single Cys or His residue at typical Zn ligand positions (the fourth or eighth zinc ligand is prevalently exchanged for an Asp, which can indeed chelate Zn in a RING finger as well). This family corresponds to the H2 subclass of RING (RING-H2) finger proteins that are characterized by containing C3H2C3-type canonical RING-H2 fingers or noncanonical RING-H2 finger variants, including C4HC3- (RING-CH alias RINGv), C3H3C2-, C3H2C2D-, C3DHC3-, and C4HC2H-type modified RING-H2 fingers. The canonical RING-H2 finger has been defined as C-X2-C-X(9-39)-C-X(1-3)-H-X(2-3)-H-X2-C-X(4-48)-C-X2-C, X is any amino acid and the number of X residues varies in different fingers. It binds two Zn ions in a unique "cross-brace" arrangement, which distinguishes it from tandem zinc fingers and other similar motifs. RING-H2 finger can be found in a group of diverse proteins with a variety of cellular functions, including oncogenesis, development, viral replication, signal transduction, the cell cycle and apoptosis. Many of them are ubiquitin-protein ligases (E3s) that serves as a scaffold for binding to ubiquitin-conjugating enzymes (E2s, also referred to as ubiquitin carrier proteins or UBCs) in close proximity to substrate proteins, which enables efficient transfer of ubiquitin from E2 to the substrates.


Pssm-ID: 438112 [Multi-domain]  Cd Length: 43  Bit Score: 40.46  E-value: 2.89e-05
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|..
gi 30687607  44 CNICLDTAHDPVV---TLCGHLFCWPCIYKWLHVQlssvsvdqhQNNCPVCK 92
Cdd:cd16448   1 CVICLEEFEEGDVvrlLPCGHVFHLACILRWLESG---------NNTCPLCR 43
RING-H2_AIRP1-like cd23116
RING finger, H2 subclass, found in Arabidopsis thaliana protein ABA INSENSITIVE RING PROTEIN 1 ...
44-91 3.36e-05

RING finger, H2 subclass, found in Arabidopsis thaliana protein ABA INSENSITIVE RING PROTEIN 1 (AIRP1) and similar proteins; This subfamily includes Arabidopsis thaliana AIRP1 and RING-H2 finger B1a (RHB1A). AIRP1, also known as RING-type E3 ubiquitin transferase AIRP1, possesses E3 ubiquitin-protein ligase activity in vitro when associated with the E2 enzyme UBC8. It plays combinatory roles with AIRP2 in the positive regulation of the abscisic acid-mediated drought stress response. RHB1A is a probable E3 ubiquitin-protein ligase. Members of this subfamily contain a C3H2C3-type RING-H2 finger.


Pssm-ID: 438478 [Multi-domain]  Cd Length: 49  Bit Score: 40.15  E-value: 3.36e-05
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|.
gi 30687607  44 CNICLD--TAHDP-VVTLCGHLFCWPCIYKWLhvqlssvsvdQHQNNCPVC 91
Cdd:cd23116   5 CPTCLEgyTEENPkLLTKCGHHFHLACIYEWM----------ERSERCPVC 45
RING-HC_RFPL4B cd16623
RING finger, HC subclass, found in Ret finger protein-like 4B (RFPL4B) and similar proteins; ...
44-92 3.44e-05

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


Pssm-ID: 438285 [Multi-domain]  Cd Length: 63  Bit Score: 40.57  E-value: 3.44e-05
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*....
gi 30687607  44 CNICLDTAHDPVVTLCGHLFCWPCIYKWLHVQLSSVSVdqhqnnCPVCK 92
Cdd:cd16623  11 CPICLDFFSHPISLSCAHIFCFDCIQKWMTKREDSILT------CPLCR 53
RING-H2_RNF139-like cd16476
RING finger, H2 subclass, found in RING finger proteins RNF139, RNF145, and similar proteins; ...
44-91 3.78e-05

RING finger, H2 subclass, found in RING finger proteins RNF139, RNF145, and similar proteins; RNF139, also known as translocation in renal carcinoma on chromosome 8 protein (TRC8), is an endoplasmic reticulum (ER)-resident multi-transmembrane protein that functions as a potent growth suppressor in mammalian cells, inducing G2/M arrest, decreased DNA synthesis and increased apoptosis. It is a tumor suppressor that has been implicated in a novel regulatory relationship linking the cholesterol/lipid biosynthetic pathway with cellular growth control. A mutation in RNF139 has been identified in families with hereditary renal (RCC) and thyroid cancers. RNF145 is an uncharacterized RING finger protein encoded by the RNF145 gene, which is expressed in T lymphocytes, and its expression is altered in acute myelomonocytic and acute promyelocytic leukemias. Although its biological function remains unclear, RNF145 shows high sequence similarity with RNF139. Both RNF139 and RNF145 contain a C3H2C3-type RING-H2 finger with possible E3-ubiquitin ligase activity.


Pssm-ID: 438139 [Multi-domain]  Cd Length: 41  Bit Score: 40.13  E-value: 3.78e-05
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*...
gi 30687607  44 CNICLDTAHDPVVTLCGHLFCWPCIYKWLHVqlssvsvdqhQNNCPVC 91
Cdd:cd16476   3 CAICYQEMKEARITPCNHFFHGLCLRKWLYV----------QDTCPLC 40
zf-C3HC4_4 pfam15227
zinc finger of C3HC4-type, RING; This is a family of primate-specific Ret finger protein-like ...
44-91 3.80e-05

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


Pssm-ID: 464570 [Multi-domain]  Cd Length: 42  Bit Score: 40.11  E-value: 3.80e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 30687607    44 CNICLDTAHDPVVTLCGHLFCWPCIYKWlhvqlsSVSVDQHQNNCPVC 91
Cdd:pfam15227   1 CPICLDYLEKPVSIECGHSFCLSCINSL------QKEPDGESLLCPQC 42
RING-H2_BRAP2 cd16457
RING finger, H2 subclass, found in BRCA1-associated protein (BRAP2) and similar proteins; ...
44-92 3.86e-05

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


Pssm-ID: 438121 [Multi-domain]  Cd Length: 44  Bit Score: 39.96  E-value: 3.86e-05
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|...
gi 30687607  44 CNICLDTAHDPV----VTLCGHLFCWPCIYKWLhvqlssvsvdqhQNNCPVCK 92
Cdd:cd16457   3 CPVCLERMDESVsgilTILCNHSFHCSCLSKWG------------DSSCPVCR 43
rad18 TIGR00599
DNA repair protein rad18; All proteins in this family for which functions are known are ...
42-93 4.27e-05

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: 43.84  E-value: 4.27e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 30687607    42 FDCNICLDTAHDPVVTLCGHLFCWPCIYKWLHVqlssvsvdqhQNNCPVCKS 93
Cdd:TIGR00599  27 LRCHICKDFFDVPVLTSCSHTFCSLCIRRCLSN----------QPKCPLCRA 68
RAD18 COG5432
RING-finger-containing E3 ubiquitin ligase [Signal transduction mechanisms];
44-92 4.34e-05

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


Pssm-ID: 227719 [Multi-domain]  Cd Length: 391  Bit Score: 43.92  E-value: 4.34e-05
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*....
gi 30687607  44 CNICLDTAHDPVVTLCGHLFCWPCIYKWLhvqlssvsvdQHQNNCPVCK 92
Cdd:COG5432  28 CRICDCRISIPCETTCGHTFCSLCIRRHL----------GTQPFCPVCR 66
RING-HC_TRIM35_C-IV cd16599
RING finger, HC subclass, found in tripartite motif-containing protein 35 (TRIM35) and similar ...
44-92 5.28e-05

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


Pssm-ID: 438261 [Multi-domain]  Cd Length: 66  Bit Score: 40.14  E-value: 5.28e-05
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|
gi 30687607  44 CNICLDTAHDPVVTLCGHLFCWPCIYK-WLHvqlssvsvdQHQNNCPVCK 92
Cdd:cd16599   7 CPICYEPFREAVTLRCGHNFCKGCVSRsWER---------QPRAPCPVCK 47
RING-HC_DTX3-like cd16506
RING finger, HC subclass, found in E3 ubiquitin-protein ligase Deltex3 (DTX3), Deltex-3-like ...
44-92 6.13e-05

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


Pssm-ID: 438169 [Multi-domain]  Cd Length: 45  Bit Score: 39.27  E-value: 6.13e-05
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|
gi 30687607  44 CNICLDTAHDP-VVTLCGHLFCWPCIYKWLhvqlssvsvdQHQNNCPVCK 92
Cdd:cd16506   3 CPICLDEIQNKkTLEKCKHSFCEDCIDRAL----------QVKPVCPVCG 42
zf-C3HC4_3 pfam13920
Zinc finger, C3HC4 type (RING finger);
44-96 6.14e-05

Zinc finger, C3HC4 type (RING finger);


Pssm-ID: 464042 [Multi-domain]  Cd Length: 50  Bit Score: 39.67  E-value: 6.14e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 30687607    44 CNICLDTAHDPVVTLCGHL-FCWPCiykwlhvqlsSVSVDQHQNNCPVCKSNIT 96
Cdd:pfam13920   5 CVICLDRPRNVVLLPCGHLcLCEEC----------AERLLRKKKKCPICRQPIE 48
mRING_PEX12 cd16451
Modified RING finger found in peroxin-12 (PEX12) and similar proteins; PEX12, also known as ...
44-104 7.23e-05

Modified RING finger found in peroxin-12 (PEX12) and similar proteins; PEX12, also known as peroxisome assembly protein 12 or peroxisome assembly factor 3 (PAF-3), is a RING finger domain-containing integral membrane peroxin required for protein import into peroxisomes. Mutations in human PEX12 result in the peroxisome deficiency Zellweger syndrome of complementation group III (CG-III), a lethal neurological disorder. PEX12 also functions as an E3-ubiquitin ligase that facilitates the PEX4-dependent monoubiquitination of PEX5, a key player in peroxisomal matrix protein import, to control PEX5 receptor recycling or degradation. PEX12 contains a modified RING finger that lacks the third, fourth, and eighth zinc-binding residues of the consensus RING finger motif, suggesting PEX12 may only bind one zinc ion.


Pssm-ID: 438115 [Multi-domain]  Cd Length: 54  Bit Score: 39.53  E-value: 7.23e-05
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 30687607  44 CNICLDT-AHDPVVTLCGHLFCWPCIYKWLhvqlssvsvdQHQNNCPVCKSNITITSLVPLY 104
Cdd:cd16451   3 CPLCRKKrTNPTALATSGYVFCYPCIYRYV----------KEHGRCPVTGYPASLDHLIKLY 54
RING-H2_RNF103 cd16473
RING finger, H2 subclass, found in RING finger protein 103 (RNF103) and similar proteins; ...
41-95 8.39e-05

RING finger, H2 subclass, found in RING finger protein 103 (RNF103) and similar proteins; RNF103, also known as KF-1 or zinc finger protein 103 homolog (Zfp-103), is an endoplasmic reticulum (ER)-resident E3 ubiquitin-protein ligase that is widely expressed in many different organs, including brain, heart, kidney, spleen, and lung. It is involved in the ER-associated degradation (ERAD) pathway by interacting with components of the ERAD pathway, including Derlin-1 and VCP. RNF103 contains several hydrophobic regions at its N-terminal and middle regions, as well as a C-terminal C3H2C3-type RING-H2 finger.


Pssm-ID: 438136 [Multi-domain]  Cd Length: 55  Bit Score: 39.18  E-value: 8.39e-05
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*...
gi 30687607  41 CFDCNICLDT--AHDPVVTL-CGHLFCWPCIYKWLHvqlssvsvdQHQNNCPVCKSNI 95
Cdd:cd16473   4 CEECAICLENyqNGDLLRGLpCGHVFHQNCIDVWLE---------RDNHCCPVCRWPV 52
RING-HC_TRIM21_C-IV cd16596
RING finger, HC subclass, found in tripartite motif-containing protein TRIM21 and similar ...
44-102 8.67e-05

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


Pssm-ID: 438258 [Multi-domain]  Cd Length: 77  Bit Score: 39.88  E-value: 8.67e-05
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*....
gi 30687607  44 CNICLDTAHDPVVTLCGHLFCWPCIYKwlhVQLSSVSVdqhqnnCPVCKSNITITSLVP 102
Cdd:cd16596  12 CPICLDPFVEPVSIECGHSFCQECISQ---VGKGGGSV------CPVCRQRFLLKNLRP 61
RING-HC_RAG1 cd16530
RING finger, HC subclass, found in recombination activating gene-1 (RAG-1) and similar ...
44-92 9.74e-05

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


Pssm-ID: 319444 [Multi-domain]  Cd Length: 46  Bit Score: 38.96  E-value: 9.74e-05
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*....
gi 30687607  44 CNICLDTAHDPVVTLCGHLFCWPCIYKWLHVQlssvsvdqhQNNCPVCK 92
Cdd:cd16530   5 CQVCEHILADPVQTPCKHLFCRTCILKCLKVM---------GSYCPSCR 44
RING-HC_TRIM5-like_C-IV cd16591
RING finger, HC subclass, found in tripartite motif-containing proteins TRIM5, TRIM6, TRIM22, ...
44-102 1.01e-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 the TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a C3HC4-type RING-HC finger, Bbox1 and Bbox2, and a coiled coil region, as well as a B30.2/SPRY (SplA and ryanodine receptor) domain positioned C-terminal to the RBCC domain. TRIM5, also known as RING finger protein 88 (RNF88), is a capsid-specific restriction factor that prevents infection from non-host-adapted retroviruses in a species-specific manner by binding to and destabilizing the retroviral capsid lattice before reverse transcription is completed. Its retroviral restriction activity correlates with the ability to activate TAK1-dependent innate immune signaling. TRIM5 also acts as a pattern recognition receptor that activates innate immune signaling in response to the retroviral capsid lattice. Moreover, TRIM5 plays a role in regulating autophagy through activation of autophagy regulator BECN1 by causing its dissociation from its inhibitors BCL2 and TAB2. It also plays a role in autophagy by acting as a selective autophagy receptor which recognizes and targets HIV-1 capsid protein p24 for autophagic destruction. TRIM6, also known as RING finger protein 89 (RNF89), is an E3-ubiquitin ligase that cooperates with the E2-ubiquitin conjugase UbE2K to catalyze the synthesis of unanchored K48-linked polyubiquitin chains, and further stimulates the interferon-I kappa B kinase epsilon (IKKepsilon) kinase-mediated antiviral response. It also regulates the transcriptional activity of Myc during the maintenance of embryonic stem (ES) cell pluripotency, and may act as a novel regulator for Myc-mediated transcription in ES cells. TRIM22, also known as 50 kDa-stimulated trans-acting factor (Staf-50) or RING finger protein 94 (RNF94), is an E3 ubiquitin-protein ligase that plays an integral role in the host innate immune response to viruses. It has been shown to inhibit the replication of a number of viruses, including HIV-1, hepatitis B, and influenza A. TRIM22 acts as a suppressor of basal HIV-1 long terminal repeat (LTR)-driven transcription by preventing the transcription factor specificity protein 1 (Sp1) binding to the HIV-1 promoter. It also controls FoxO4 activity and cell survival by directing Toll-like receptor 3 (TLR3)-stimulated cells toward type I interferon (IFN) type I gene induction or apoptosis. Moreover, TRIM22 can activate the noncanonical nuclear factor-kappaB (NF-kappaB) pathway by activating I kappa B kinase alpha (IKKalpha). It also regulates nucleotide binding oligomerization domain containing 2 (NOD2)-dependent activation of interferon-beta signaling and nuclear factor-kappaB. TRIM34, also known as interferon-responsive finger protein 1 or RING finger protein 21 (RNF21), may function as antiviral protein that contribute to the defense against retroviral infections.


Pssm-ID: 438253 [Multi-domain]  Cd Length: 72  Bit Score: 39.73  E-value: 1.01e-04
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*....
gi 30687607  44 CNICLDTAHDPVVTLCGHLFCWPCIYkwlhVQLSSVSVDQHQNNCPVCKSNITITSLVP 102
Cdd:cd16591   9 CPICLELLTEPLSLDCGHSFCQACIT----ANHKESVNQEGESSCPVCRTSYQPENLRP 63
RING-HC_RNF141 cd16545
RING finger, HC subclass, found in RING finger protein 141 (RNF141) and similar proteins; ...
43-92 1.05e-04

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/ZNF230 gene mutations may be associated with azoospermia. RNF141 contains a C3HC4-type RING finger domain that may function as an activator module in transcription.


Pssm-ID: 438207 [Multi-domain]  Cd Length: 40  Bit Score: 38.61  E-value: 1.05e-04
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|
gi 30687607  43 DCNICLDTAHDpVVTLCGHLFCWPCIYKWlhvqlssvSVDQHqnNCPVCK 92
Cdd:cd16545   2 ECCICMDRKAD-LILPCAHSYCQKCIDKW--------SDRHR--TCPICR 40
RING-HC_Bre1-like cd16499
RING finger, HC subclass, found in yeast Bre1 and its homologs from eukaryotes; Bre1 is an E3 ...
44-92 1.06e-04

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, the 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 subfamily members contain a C3HC4-type RING-HC finger at its C-terminus.


Pssm-ID: 438162 [Multi-domain]  Cd Length: 59  Bit Score: 39.08  E-value: 1.06e-04
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*....
gi 30687607  44 CNICLDTAHDPVVTLCGHLFCWPCIYKwlhvqlssvSVDQHQNNCPVCK 92
Cdd:cd16499   9 CSVCNDRFKDVIITKCGHVFCNECVQK---------RLETRQRKCPGCG 48
RING-HC_ORTHRUS_rpt2 cd23139
second RING finger, HC subclass, found in Arabidopsis thaliana ORTHRUS and similar proteins; ...
42-96 1.57e-04

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


Pssm-ID: 438501 [Multi-domain]  Cd Length: 72  Bit Score: 38.98  E-value: 1.57e-04
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 30687607  42 FDCNICLDTAHDPVVTLCGHLFCWPCI-YKWLHVQLS--------SVSVDQHQNNCPVCKSNIT 96
Cdd:cd23139   6 FGCQICKKVLSLPVSTPCGHNFCKACLeAKFAGIADVrdrgnggrSLRARKNVKPCPCCKTDIS 69
RING-HC_Cbl-like cd16502
RING finger, HC subclass, found in Casitas B-lineage lymphoma (Cbl) proteins; The Cbl adaptor ...
44-92 1.57e-04

RING finger, HC subclass, found in Casitas B-lineage lymphoma (Cbl) proteins; The Cbl adaptor protein 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 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 subfamily consist of a highly conserved N-terminal half that includes a tyrosine-kinase-binding domain (TKB, also known as the phosphotyrosine binding PTB domain, 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: 438165 [Multi-domain]  Cd Length: 43  Bit Score: 38.10  E-value: 1.57e-04
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*....
gi 30687607  44 CNICLDTAHDPVVTLCGHLFCWPCIYKWLhvqlssvsvDQHQNNCPVCK 92
Cdd:cd16502   4 CKICAENDKDVRIEPCGHLLCTPCLTSWQ---------DSDGQTCPFCR 43
RING-HC_TRY3-like cd23137
RING finger, HC subclass, found in Candida albicans transcriptional regulator of yeast form ...
42-93 1.81e-04

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


Pssm-ID: 438499 [Multi-domain]  Cd Length: 53  Bit Score: 38.22  E-value: 1.81e-04
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|..
gi 30687607  42 FDCNICLDTAHDPVVTLCGHLFCWPCIYKwlhvqlssvSVDQHQNNCPVCKS 93
Cdd:cd23137   3 YACPICMNVAWKPVRLECSHVFCLRCLVK---------AQKQKKDNCPLCRA 45
RING-H2_RNF24-like cd16469
RING finger, H2 subclass, found in RING finger proteins RNF24, RNF122, and similar proteins; ...
44-95 1.93e-04

RING finger, H2 subclass, found in RING finger proteins RNF24, RNF122, and similar proteins; This subfamily 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 undergo 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: 438132 [Multi-domain]  Cd Length: 47  Bit Score: 38.14  E-value: 1.93e-04
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*
gi 30687607  44 CNICLD--TAHDPV-VTLCGHLFCWPCIYKWLhvqlssvsvdQHQNNCPVCKSNI 95
Cdd:cd16469   3 CAVCLEefKLKEELgVCPCGHAFHTKCLKKWL----------EVRNSCPICKSPV 47
RING-HC_TRIM58_C-IV cd16606
RING finger, HC subclass, found in tripartite motif-containing protein TRIM58 and similar ...
44-93 2.00e-04

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


Pssm-ID: 438268 [Multi-domain]  Cd Length: 53  Bit Score: 38.30  E-value: 2.00e-04
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|
gi 30687607  44 CNICLDTAHDPVVTLCGHLFCWPCIYKWLHvqlSSVSVDQHQNNCPVCKS 93
Cdd:cd16606   5 CPVCLDFLQEPVSVDCGHSFCLRCISEFCE---KSDSAQGGVYACPQCRG 51
RING-HC_RNF151 cd16547
RING finger, HC subclass, found in RING finger protein 151 (RNF151) and similar proteins; ...
42-95 2.01e-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 mediates intracellular membrane fusion in both neuronal and non-neuronal cells. Thus, it may be involved in acrosome formation of spermatids by interacting with multiple proteins participating in membrane biogenesis and microtubule organization. RNF151 contains a C3HC4-type RING finger domain, a putative nuclear localization signal (NLS), and a TNF receptor associated factor (TRAF)-type zinc finger domain.


Pssm-ID: 438209 [Multi-domain]  Cd Length: 49  Bit Score: 38.21  E-value: 2.01e-04
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....
gi 30687607  42 FDCNICLDTAHDPVVTLCGHLFCWPCIYKWLhvqlssvsvdQHQNNCPVCKSNI 95
Cdd:cd16547   4 LICSICHGVLRCPVRLSCSHIFCKKCILQWL----------KRQETCPCCRKEV 47
RING-HC_BAR cd16497
RING finger, HC subclass, found in bifunctional apoptosis regulator (BAR); BAR, also known as ...
42-92 2.04e-04

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


Pssm-ID: 438160 [Multi-domain]  Cd Length: 52  Bit Score: 38.26  E-value: 2.04e-04
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|.
gi 30687607  42 FDCNICLDTAHDPVVTLCGHLFCWPCIYKWLHVqlssvsvdQHQNNCPVCK 92
Cdd:cd16497   2 FLCHCCYDLLVNPTTLNCGHSFCRHCLALWWKS--------SKKTECPECR 44
RING-HC_RNF146 cd16546
RING finger, HC subclass, found in RING finger protein 146 (RNF146) and similar proteins; ...
43-95 2.30e-04

RING finger, HC subclass, found in RING finger protein 146 (RNF146) and similar proteins; RNF146, also known as dactylidin, or iduna, is a cytoplasmic E3 ubiquitin-protein ligase that is responsible for PARylation-dependent ubiquitination (PARdU). It displays neuroprotective property due to its inhibition of Parthanatos, a PAR dependent cell death, via binding with Poly(ADP-ribose) (PAR). It also modulates PAR polymerase-1 (PARP-1)-mediated oxidative cell injury in cardiac myocytes. Moreover, RNF146 mediates tankyrase-dependent degradation of axin, thereby positively regulating Wnt signaling. It also facilitates DNA repair and protects against cell death induced by DNA damaging agents or gamma-irradiation by translocating to the nucleus after cellular injury and promoting the ubiquitination and degradation of various nuclear proteins involved in DNA damage repair. Furthermore, RNF146 is implicated in neurodegenerative disease and cancer development. It regulates the development and progression of non-small cell lung cancer (NSCLC) by enhancing cell growth, invasion, and survival. RNF146 contains an N-terminal C3HC4-type RING-HC finger followed by a WWE domain with a poly(ADP-ribose) (PAR) binding motif at the tail.


Pssm-ID: 438208 [Multi-domain]  Cd Length: 50  Bit Score: 38.14  E-value: 2.30e-04
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|...
gi 30687607  43 DCNICLDTAHDPVVTLCGHLFCWPCIYkwlhvqlssvSVDQHQNNCPVCKSNI 95
Cdd:cd16546   2 ECPICLQTCIHPVKLPCGHIFCYLCVK----------GVAWQSKRCALCRQEI 44
RING-HC_CHFR cd16503
RING finger, HC subclass, found in checkpoint with forkhead and RING finger domains protein ...
44-96 2.36e-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) domain and a C3HC4-type RING-HC finger.


Pssm-ID: 438166 [Multi-domain]  Cd Length: 55  Bit Score: 38.12  E-value: 2.36e-04
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....
gi 30687607  44 CNICLDTAHDPVVTL-CGHLFCWPCIYKWLhvqlssvsvDQHQNNCPVCKSNIT 96
Cdd:cd16503   5 CSICQDLLHDCVSLQpCMHNFCAACYSDWM---------ERSNTECPTCRATVQ 49
mRING-HC-C4C4_TRIM37_C-VIII cd16619
Modified RING finger, HC subclass (C4C4-type), found in tripartite motif-containing protein 37 ...
42-91 2.58e-04

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 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 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: 438281 [Multi-domain]  Cd Length: 43  Bit Score: 37.72  E-value: 2.58e-04
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|.
gi 30687607  42 FDCNICLDTAHDPVV-TLCGHLFCWPCIYKWLhvqlssvsvDQHQNNCPVC 91
Cdd:cd16619   1 FRCFICMEKLRDPRLcPHCSKLFCKGCIRRWL---------SEQRSSCPHC 42
RING-HC_BARD1 cd16496
RING finger, HC subclass, found in BRCA1-associated RING domain protein 1 (BARD-1) and similar ...
44-92 2.69e-04

RING finger, HC subclass, found in BRCA1-associated RING domain protein 1 (BARD-1) and similar proteins; BARD-1 is a critical factor in BRCA1-mediated tumor suppression and may also serve as a target for tumorigenic lesions in some human cancers. It associates with BRCA1 (breast cancer-1) to form a heterodimeric BRCA1/BARD1 complex that is responsible for maintaining genomic stability through nuclear functions involving DNA damage signaling and repair, transcriptional regulation, and cell cycle control. The BRCA1/BARD1 complex catalyzes autoubiquitination of BRCA1 and trans ubiquitination of other protein substrates. Its E3 ligase activity is dramatically reduced in the presence of UBX domain protein 1 (UBXN1). BARD-1 contains an C3HC4-type RING-HC finger that binds BRCA1 at its N-terminus and three tandem ankyrin repeats and tandem BRCT repeat domains at its C-terminus. The BRCT repeats bind CstF-50 (cleavage stimulation factor) to modulate mRNA processing and RNAP II stability in response to DNA damage.


Pssm-ID: 438159 [Multi-domain]  Cd Length: 86  Bit Score: 38.86  E-value: 2.69e-04
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|.
gi 30687607  44 CNICLDTAHDPVvTL--CGHLFCWPCIykwlhvqlssvsVDQHQNNCPVCK 92
Cdd:cd16496  18 CSRCASILKEPV-TLggCEHVFCRSCV------------GDRLGNGCPVCD 55
mRING-HC-C3HC3D_PHRF1 cd16635
Modified RING finger, HC subclass (C3HC3D-type), found in PHD and RING finger ...
44-90 3.21e-04

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: 438297 [Multi-domain]  Cd Length: 51  Bit Score: 37.79  E-value: 3.21e-04
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|
gi 30687607  44 CNICLDTAHDPVVTL---CGHLFCWPCIYKWlhvqlssvsvDQHQNNCPV 90
Cdd:cd16635   7 CPICLNTFRDQAVGTpesCDHIFCLDCILEW----------SKNANTCPV 46
RING-HC_LNX3-like cd16512
RING finger, HC subclass, found in ligand of Numb protein LNX3, LNX4, and similar proteins; ...
42-71 3.24e-04

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 C3HC4-type RING-HC finger and two PDZ domains.


Pssm-ID: 438175 [Multi-domain]  Cd Length: 43  Bit Score: 37.39  E-value: 3.24e-04
                        10        20        30
                ....*....|....*....|....*....|
gi 30687607  42 FDCNICLDTAHDPVVTLCGHLFCWPCIYKW 71
Cdd:cd16512   1 LKCKLCLGVLEEPLATPCGHVFCAGCVLPW 30
RING-H2_RNF145 cd16684
RING finger, H2 subclass, found in RING finger protein 145 (RNF145) and similar proteins; ...
44-91 3.29e-04

RING finger, H2 subclass, found in RING finger protein 145 (RNF145) and similar proteins; RNF145 is an uncharacterized RING finger protein encoded by the RNF145 gene, which is expressed in T lymphocytes, and its expression is altered in acute myelomonocytic and acute promyelocytic leukemias. Although its biological function remains unclear, RNF145 shows high sequence similarity with RNF139, an endoplasmic reticulum (ER)-resident multi-transmembrane protein that functions as a potent growth suppressor in mammalian cells, inducing G2/M arrest, decreased DNA synthesis and increased apoptosis. Like RNF139, RNF145 contains a C3H2C3-type RING-H2 finger with possible E3-ubiquitin ligase activity.


Pssm-ID: 319598 [Multi-domain]  Cd Length: 43  Bit Score: 37.34  E-value: 3.29e-04
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*...
gi 30687607  44 CNICLDTAHDPVVTLCGHLFCWPCIYKWLHVqlssvsvdqhQNNCPVC 91
Cdd:cd16684   5 CSICYQDMKSAVITPCSHFFHAGCLKKWLYV----------QETCPLC 42
RING-HC_RNF166 cd16549
RING finger, HC subclass, found in RING finger protein 166 (RNF166) and similar proteins; ...
42-92 3.88e-04

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


Pssm-ID: 438211 [Multi-domain]  Cd Length: 47  Bit Score: 37.10  E-value: 3.88e-04
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|..
gi 30687607  42 FDCNICLDTAHDPVVTL-CGHLFCWPCIYKWLhvQLSSvsvdqhqNNCPVCK 92
Cdd:cd16549   2 FSCPICLEVYHKPVVITsCGHTFCGECLQPCL--QVAS-------PLCPLCR 44
RING-HC_RNFT1 cd16741
RING finger, HC subclass, found in RING finger and transmembrane domain-containing protein 1 ...
29-95 3.91e-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: 438399 [Multi-domain]  Cd Length: 58  Bit Score: 37.56  E-value: 3.91e-04
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 30687607  29 TAPTAGQANESGCFdCNICLDTAHDPVVTLCGHLFCWPCIYKWLHvqlssvsvdqHQNNCPVCKSNI 95
Cdd:cd16741   3 IAASKRQCSEADDI-CAICQAEFRKPILLICQHVFCEECISLWFN----------REKTCPLCRTVI 58
RING-HC_TRIM13_like_C-V cd16581
RING finger, HC subclass, found in tripartite motif-containing proteins TRIM13, TRIM59 and ...
44-92 5.13e-04

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


Pssm-ID: 438243 [Multi-domain]  Cd Length: 50  Bit Score: 37.11  E-value: 5.13e-04
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*....
gi 30687607  44 CNICLDTAHDPVVTLCGHLFCWPCIYKWLHvqlSSVSVDQHQNNCPVCK 92
Cdd:cd16581   5 CSICYNIFDDPKILPCSHTFCKNCLEKLLA---ASGYYLLASLKCPTCR 50
RING-H2_ASR1 cd23120
RING finger, H2 subclass, found in Saccharomyces cerevisiae alcohol-sensitive RING finger ...
43-97 5.35e-04

RING finger, H2 subclass, found in Saccharomyces cerevisiae alcohol-sensitive RING finger protein 1 (ASR1) and similar proteins; ASR1 is required for tolerance to alcohol. It signals alcohol stress to the nucleus. ASR1 contains a C3H2C3-type RING-H2 finger.


Pssm-ID: 438482 [Multi-domain]  Cd Length: 54  Bit Score: 37.13  E-value: 5.35e-04
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*..
gi 30687607  43 DCNICLDTAHDPV--VTLCGHLFCWPCIYKWLHVQLSSvsvdqhqnNCPVCKSNITI 97
Cdd:cd23120   3 ECPICLEEMNSGTgyLADCGHEFHLTCIREWHNKSGNL--------DCPICRVESLL 51
RING-HC_TRIM60-like_C-IV cd16607
RING finger, HC subclass, found in tripartite motif-containing proteins TRIM60, TRIM61, TRIM75 ...
44-92 5.71e-04

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


Pssm-ID: 438269 [Multi-domain]  Cd Length: 48  Bit Score: 37.02  E-value: 5.71e-04
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|
gi 30687607  44 CNICLDTAHDPVVTLCGHLFCWPCI-YKWLHVQLSSvsvdqhqnNCPVCK 92
Cdd:cd16607   4 CPICLDYLKDPVTINCGHNFCRSCIsMSWKDLQDTF--------PCPVCR 45
RING-HC_TRIM47-like_C-IV cd16604
RING finger, HC subclass, found in tripartite motif-containing protein 47 (TRIM47) and similar ...
42-92 5.79e-04

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


Pssm-ID: 438266 [Multi-domain]  Cd Length: 49  Bit Score: 37.02  E-value: 5.79e-04
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|..
gi 30687607  42 FDCNICLDTAHDPVVTLCGHLFCWPCIYK-WLHVQLSSVSvdqhqnnCPVCK 92
Cdd:cd16604   1 LSCPICLDLLKDPVTLPCGHSFCMGCLGAlWGAGRGGRAS-------CPLCR 45
COG5540 COG5540
RING-finger-containing ubiquitin ligase [Posttranslational modification, protein turnover, ...
40-95 6.15e-04

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


Pssm-ID: 227827 [Multi-domain]  Cd Length: 374  Bit Score: 40.36  E-value: 6.15e-04
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*....
gi 30687607  40 GCfDCNICLD--TAHDPVVTL-CGHLFCWPCIYKWLhvqlssvsvDQHQNNCPVCKSNI 95
Cdd:COG5540 323 GV-ECAICMSnfIKNDRLRVLpCDHRFHVGCVDKWL---------LGYSNKCPVCRTAI 371
RING-HC_TRIM3 cd16768
RING finger, HC subclass, found in tripartite motif-containing protein 3 (TRIM3); TRIM3, also ...
44-92 6.82e-04

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


Pssm-ID: 438424 [Multi-domain]  Cd Length: 48  Bit Score: 36.52  E-value: 6.82e-04
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*....
gi 30687607  44 CNICLDTAHDPVVTLCGHLFCWPCIYKWLHVQLSSVSvdqhqnnCPVCK 92
Cdd:cd16768   7 CSICLDRYHNPKVLPCLHTFCERCLQNYIPPQSLTLS-------CPVCR 48
RING-HC_DTX3L cd16712
RING finger, HC subclass, found in protein Deltex-3-like (DTX3L) and similar proteins; DTX3L, ...
44-91 7.06e-04

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


Pssm-ID: 438372 [Multi-domain]  Cd Length: 56  Bit Score: 36.64  E-value: 7.06e-04
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*....
gi 30687607  44 CNICLDTAHDP-VVTLCGHLFCWPCIYKWLhvqlssvsvdQHQNNCPVC 91
Cdd:cd16712   6 CPICMDRISNKkVLPKCKHVFCAACIDKAM----------KYKPVCPVC 44
RING-HC_TRIM43-like_C-IV cd16603
RING finger, HC subclass, found in tripartite motif-containing proteins TRIM43, TRIM48, TRIM49, ...
44-92 7.51e-04

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


Pssm-ID: 438265 [Multi-domain]  Cd Length: 59  Bit Score: 36.69  E-value: 7.51e-04
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*....
gi 30687607  44 CNICLDTAHDPVVTLCGHLFCWPCIYkwLHVQLSSVSVdqhqnNCPVCK 92
Cdd:cd16603   7 CPICMNYFIDPVTIDCGHSFCRPCLY--LNWQDIPFLA-----QCPECR 48
RING-HC_Cbl-c cd16710
RING finger, HC subclass, found in E3 ubiquitin-protein ligase Cbl-c and similar proteins; ...
44-95 7.90e-04

RING finger, HC subclass, found in E3 ubiquitin-protein ligase Cbl-c and similar proteins; Cbl-c, also known as RING finger protein 57 (RNF57), SH3-binding protein Cbl-3, SH3-binding protein Cbl-c, or signal transduction protein Cbl-c, is an E3 ubiquitin-protein ligase expressed exclusively in epithelial cells. It contains a tyrosine-kinase-binding domain (TKB, also known as the phosphotyrosine binding PTB domain, composed of a four helix-bundle, a Ca2+ binding EF-hand and a highly variant SH2 domain), a C3HC4-type RING-HC finger, and a short proline-rich region, but lacks the ubiquitin-associated (UBA) leucine zipper motif that are present in Cbl and Cbl-b. Cbl-c acts as a regulator of epidermal growth factor receptor (EGFR)-mediated signal transduction. It also suppresses v-Src-induced transformation through ubiquitin-dependent protein degradation. Moreover, Cbl-c ubiquitinates and downregulates RETMEN2A and implicates Enigma (PDLIM7) as a positive regulator of RETMEN2A by blocking Cbl-mediated ubiquitination and degradation. The ubiquitin ligase activity of Cbl-c is increased via the interaction of its RING-HC finger domain with a LIM domain of the paxillin homolog, hydrogen peroxide induced construct 5 (Hic-5).


Pssm-ID: 438370 [Multi-domain]  Cd Length: 65  Bit Score: 36.99  E-value: 7.90e-04
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|..
gi 30687607  44 CNICLDTAHDPVVTLCGHLFCWPCIYKWLHvqlssvsvdQHQNNCPVCKSNI 95
Cdd:cd16710  16 CKICAERDKDVRIEPCGHLLCSCCLAAWQH---------SDSQTCPFCRCEI 58
RING-HC_RNF222 cd16564
RING finger, HC subclass, found in RING finger protein 222 (RNF222) and similar proteins; ...
43-97 8.07e-04

RING finger, HC subclass, found in RING finger protein 222 (RNF222) and similar proteins; RNF222 is an uncharacterized C3HC4-type RING-HC finger-containing protein. It may function as an E3 ubiquitin-protein ligase.


Pssm-ID: 438226 [Multi-domain]  Cd Length: 50  Bit Score: 36.61  E-value: 8.07e-04
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*.
gi 30687607  43 DCNICLDTAHDPVVTL-CGHLFCWPCIYKWLhvqlssvsvDQHQNNCPVCKSNITI 97
Cdd:cd16564   2 ECPVCYEDFDDAPRILsCGHSFCEDCLVKQL---------VSMTISCPICRRVTFI 48
RING-HC_TRIM72_C-IV cd16612
RING finger, HC subclass, found in tripartite motif-containing protein 72 (TRIM72) and similar ...
44-93 8.64e-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 the peroxisome proliferation-activated receptor alpha (PPAR-alpha) signaling pathway. Compensation for the absence of AKT signaling by ERK signaling during TRIM72 overexpression leads to pathological hypertrophy. Moreover, TRIM72 functions as a novel negative feedback regulator of myogenesis by targeting insulin receptor substrate-1 (IRS-1). It is transcriptionally activated by the synergism of myogenin (MyoD) and myocyte enhancer factor 2 (MEF2). TRIM72 belongs to the C-IV subclass of the TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a C3HC4-type RING-HC finger, Bbox1 and Bbox2, and a coiled coil region, as well as a B30.2/SPRY (SplA and ryanodine receptor) domain positioned C-terminal to the RBCC domain.


Pssm-ID: 438274 [Multi-domain]  Cd Length: 60  Bit Score: 36.64  E-value: 8.64e-04
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|..
gi 30687607  44 CNICLDTAHDPVVTLCGHLFCWPCiykwlhvqLSSVSVDQHQNN--CPVCKS 93
Cdd:cd16612   7 CPLCLKLFQSPVTTECGHTFCQDC--------LSRVPKEEDGGStsCPTCQA 50
RING-HC_TRIM39_C-IV cd16601
RING finger, HC subclass, found in tripartite motif-containing protein 39 (TRIM39) and similar ...
42-91 8.99e-04

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


Pssm-ID: 438263 [Multi-domain]  Cd Length: 44  Bit Score: 36.31  E-value: 8.99e-04
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|.
gi 30687607  42 FDCNICLDTAHDPVVTLCGHLFCWPCIYK-WLHVQLSSVsvdqhqnnCPVC 91
Cdd:cd16601   2 ASCSLCKEYLKDPVIIECGHNFCRACITRfWEELDGDFP--------CPQC 44
RING-HC_MID1 cd16753
RING finger, HC subclass, found in midline-1 (MID1) and similar proteins; MID1, also known as ...
44-98 1.05e-03

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


Pssm-ID: 438411 [Multi-domain]  Cd Length: 72  Bit Score: 36.94  E-value: 1.05e-03
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*....
gi 30687607  44 CNICLDTAHDPVVTLCGHLFCWPCIYKWLHVQLSSV----SVDQHQnnCPVCKSNITIT 98
Cdd:cd16753   8 CPICLELFEDPLLLPCAHSLCFNCAHRILVSHCASNesveSITAFQ--CPTCRYVITLN 64
RING-HC_TRIM38_C-IV cd16600
RING finger, HC subclass, found in tripartite motif-containing protein 38 (TRIM38) and similar ...
44-93 1.08e-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 the TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a C3HC4-type RING-HC finger, a B-box, and two coiled coil domains, as well as a B30.2/SPRY (SplA and ryanodine receptor) domain positioned C-terminal to the RBCC domain.


Pssm-ID: 438262 [Multi-domain]  Cd Length: 58  Bit Score: 36.29  E-value: 1.08e-03
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|
gi 30687607  44 CNICLDTAHDPVVTLCGHLFCWPCIYKWLHvQLSSVSVDQHQNNCPVCKS 93
Cdd:cd16600   8 CSICLQLMTEPVSINCGHSYCKRCIVSFLE-NQSQLEPGLETFSCPQCRA 56
RING-HC_MmTRIM43-like cd23133
RING finger, HC subclass, found in Mus musculus tripartite motif-containing protein 43 (TRIM43) ...
44-96 1.11e-03

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


Pssm-ID: 438495 [Multi-domain]  Cd Length: 57  Bit Score: 36.43  E-value: 1.11e-03
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|...
gi 30687607  44 CNICLDTAHDPVVTLCGHLFCWPCIykwlhvqLSSVSVDQHQNNCPVCKSNIT 96
Cdd:cd23133   6 CSICQGIFMNPVYLRCGHKFCEACL-------LLFQEDIKFPAYCPMCRQPFN 51
COG5152 COG5152
Uncharacterized conserved protein, contains RING and CCCH-type Zn-fingers [General function ...
30-67 1.18e-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: 39.29  E-value: 1.18e-03
                        10        20        30
                ....*....|....*....|....*....|....*...
gi 30687607  30 APTAGQANESGCFDCNICLDTAHDPVVTLCGHLFCWPC 67
Cdd:COG5152 185 APVISGPGEKIPFLCGICKKDYESPVVTECGHSFCSLC 222
RING-HC_TRIM41-like_C-IV cd16602
RING finger, HC subclass, found in tripartite motif-containing proteins TRIM41, TRIM52 and ...
44-102 1.24e-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 the TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a C3HC4-type RING-HC finger, Bbox1 and Bbox2, and a coiled coil region, as well as a B30.2/SPRY (SplA and ryanodine receptor) domain positioned C-terminal to the RBCC domain. In contrast, TRIM52 lacks the putative viral recognition SPRY/B30.2 domain, and thus has been classified to the C-V subclass of the TRIM family that contains only RBCC domains. TRIM41, also known as RING finger-interacting protein with C kinase (RINCK), is an E3 ubiquitin-protein ligase that promotes the ubiquitination of protein kinase C (PKC) isozymes in cells. It specifically recognizes the C1 domain of PKC isozymes. It controls the amplitude of PKC signaling by controlling the amount of PKC in the cell. TRIM52, also known as RING finger protein 102 (RNF102), is encoded by a novel, noncanonical antiviral TRIM52 gene in primate genomes with unique specificity determined by the rapidly evolving RING domain.


Pssm-ID: 438264 [Multi-domain]  Cd Length: 53  Bit Score: 36.06  E-value: 1.24e-03
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*....
gi 30687607  44 CNICLDTAHDPVVTLCGHLFCWPCIykwlhVQLSSVSvdqhqnnCPVCKSNITITSLVP 102
Cdd:cd16602   6 CAICLDYFKDPVSIGCGHNFCRVCV-----TQLWGFT-------CPQCRKSFPRRSFRP 52
RING-HC_TRIM2_like_C-VII cd16586
RING finger, HC subclass, found in tripartite motif-containing protein TRIM2, TRIM3, and ...
44-92 1.25e-03

RING finger, HC subclass, found in tripartite motif-containing protein TRIM2, TRIM3, and similar proteins; TRIM2, also known as RING finger protein 86 (RNF86), is an E3 ubiquitin-protein ligase that ubiquitinates the neurofilament light chain, a component of the intermediate filament in axons. Loss of function of TRIM2 results in early-onset axonal neuropathy. TRIM3, also known as brain-expressed RING finger protein (BERP), RING finger protein 97 (RNF97), or RING finger protein 22 (RNF22), is an E3 ubiquitin-protein ligase involved in the pathogenesis of various cancers. It also plays an important role in the central nervous system (CNS). In addition, TRIM3 may be involved in vesicular trafficking via its association with the cytoskeleton-associated-recycling or transport (CART) complex that is necessary for efficient transferrin receptor recycling, but not for epidermal growth factor receptor (EGFR) degradation. Both TRIM2 and TRIM3 belong to the C-VII subclass of the TRIM (tripartite motif)-NHL family that is defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a C3HC4-type RING-HC finger, Bbox1 and Bbox2, and a coiled coil domain, as well as a NHL (named after proteins NCL-1, HT2A and Lin-41 that contain repeats folded into a six-bladed beta propeller) repeat domain positioned C-terminal to the RBCC domain.


Pssm-ID: 438248 [Multi-domain]  Cd Length: 45  Bit Score: 35.89  E-value: 1.25e-03
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*....
gi 30687607  44 CNICLDTAHDPVVTLCGHLFCWPCIYKWLHVQLSSVSvdqhqnnCPVCK 92
Cdd:cd16586   4 CGICLERYKNPKVLPCLHTFCERCLQNYIPAESLSLS-------CPVCR 45
RING-HC_TRIM31_C-V cd16582
RING finger, HC subclass, found in tripartite motif-containing protein 31 (TRIM31) and similar ...
44-68 1.28e-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 the TRIM (tripartite motif) family of proteins that are defined by an N-terminal RBCC (RING, Bbox, and coiled coil) domain, including three consecutive zinc-binding domains, a C3HC4-type RING-HC finger, Bbox1 and Bbox2, and a coiled coil region, as well as an uncharacterized region positioned C-terminal to the RBCC domain.


Pssm-ID: 438244 [Multi-domain]  Cd Length: 44  Bit Score: 35.57  E-value: 1.28e-03
                        10        20
                ....*....|....*....|....*
gi 30687607  44 CNICLDTAHDPVVTLCGHLFCWPCI 68
Cdd:cd16582   4 CPICLDILQKPVTIDCGHNFCLQCI 28
zf-RING_5 pfam14634
zinc-RING finger domain;
44-93 1.32e-03

zinc-RING finger domain;


Pssm-ID: 434085 [Multi-domain]  Cd Length: 43  Bit Score: 35.87  E-value: 1.32e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 30687607    44 CNIC---LDTAHDPVVTLCGHLFCWPCiykwlhvqlssVSVDQHQNNCPVCKS 93
Cdd:pfam14634   2 CNKCfkeLSKTRPFYLTSCGHIFCEEC-----------LTRLLQERQCPICKK 43
RING-HC_LNX4 cd16719
RING finger, HC subclass, found in ligand of numb protein X 4 (LNX4); LNX4, also known as PDZ ...
42-71 1.33e-03

RING finger, HC subclass, found in ligand of numb protein X 4 (LNX4); LNX4, also known as PDZ domain-containing RING finger protein 4 (PDZRN4), or SEMACAP3-like protein (SEMCAP3L), is an E3 ubiquitin-protein ligase responsible for the ubiquitination and degradation of Numb, a component of the Notch signaling pathway that functions in the specification of cell fates during development and is known to control cell numbers during neurogenesis in vertebrates. LNX4 contains an N-terminal C3HC4-type RING-HC finger, two PDZ domains, and a C-terminal LNX3 homology (LNX3H) domain.


Pssm-ID: 438379 [Multi-domain]  Cd Length: 53  Bit Score: 36.06  E-value: 1.33e-03
                        10        20        30
                ....*....|....*....|....*....|
gi 30687607  42 FDCNICLDTAHDPVVTLCGHLFCWPCIYKW 71
Cdd:cd16719   5 LKCKLCGKVLEEPLSTPCGHVFCAGCLLPW 34
RING-HC_RNF114 cd16540
RING finger, HC subclass, found in RING finger protein 114 (RNF114) and similar proteins; ...
42-68 1.44e-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 the immune response to double-stranded RNA in disease pathogenesis. Moreover, RNF114 interacts with A20 and modulates its ubiquitylation. It negatively regulates nuclear factor-kappaB (NF-kappaB)-dependent transcription and positively regulates T-cell activation. RNF114 may play a putative role in the regulation of immune responses, since it corresponds to a novel psoriasis susceptibility gene, ZNF313. RNF114, together with three closely related proteins: RNF125, RNF138 and RNF166, forms a novel family of ubiquitin ligases with a C3HC4-type RING-HC finger, a C2HC-, and two C2H2-type zinc fingers, as well as a ubiquitin interacting motif (UIM).


Pssm-ID: 438202 [Multi-domain]  Cd Length: 46  Bit Score: 35.51  E-value: 1.44e-03
                        10        20
                ....*....|....*....|....*..
gi 30687607  42 FDCNICLDTAHDPVVTLCGHLFCWPCI 68
Cdd:cd16540   2 FTCPVCLEIFETPVRVPCGHVFCNACL 28
Ubox smart00504
Modified RING finger domain; Modified RING finger domain, without the full complement of Zn2 ...
42-104 1.52e-03

Modified RING finger domain; Modified RING finger domain, without the full complement of Zn2+-binding ligands. Probable involvement in E2-dependent ubiquitination.


Pssm-ID: 128780 [Multi-domain]  Cd Length: 63  Bit Score: 36.06  E-value: 1.52e-03
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 30687607     42 FDCNICLDTAHDPVVTLCGHLFCWPCIYKWLhvqlssvsvDQHqNNCPVCKSNITITSLVPLY 104
Cdd:smart00504   2 FLCPISLEVMKDPVILPSGQTYERSAIEKWL---------LSH-GTDPVTGQPLTHEDLIPNL 54
RING-HC_RNF8 cd16535
RING finger, HC subclass, found in RING finger protein 8 (RNF8) and similar proteins; RNF8 is ...
44-96 1.59e-03

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


Pssm-ID: 438197 [Multi-domain]  Cd Length: 64  Bit Score: 35.83  E-value: 1.59e-03
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|...
gi 30687607  44 CNICLDTAHDPVVTLCGHLFCWPCIYKWLHVqlssvsvdqhQNNCPVCKSNIT 96
Cdd:cd16535   4 CSICSELFIEAVTLNCSHSFCSYCITEWMKR----------KKECPICRKPIT 46
RING-HC_TRIM4_C-IV cd16590
RING finger, HC subclass, found in tripartite motif-containing protein TRIM4 and similar ...
44-70 2.18e-03

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


Pssm-ID: 438252 [Multi-domain]  Cd Length: 61  Bit Score: 35.78  E-value: 2.18e-03
                        10        20
                ....*....|....*....|....*..
gi 30687607  44 CNICLDTAHDPVVTLCGHLFCWPCIYK 70
Cdd:cd16590   9 CPICLDYFQDPVSIECGHNFCRGCLHR 35
RING-HC_LONFs_rpt1 cd16513
first RING finger, HC subclass, found in the LON peptidase N-terminal domain and RING finger ...
42-68 2.25e-03

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


Pssm-ID: 438176 [Multi-domain]  Cd Length: 47  Bit Score: 34.98  E-value: 2.25e-03
                        10        20
                ....*....|....*....|....*..
gi 30687607  42 FDCNICLDTAHDPVVTLCGHLFCWPCI 68
Cdd:cd16513   3 LSCPLCRGLLFEPVTLPCGHTFCKRCL 29
RING-HC_RNF39 cd16592
RING finger, HC subclass, found in RING finger protein 39 (RNF39) and similar proteins; RNF39, ...
44-68 2.82e-03

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


Pssm-ID: 438254 [Multi-domain]  Cd Length: 58  Bit Score: 35.12  E-value: 2.82e-03
                        10        20
                ....*....|....*....|....*
gi 30687607  44 CNICLDTAHDPVVTLCGHLFCWPCI 68
Cdd:cd16592   7 CPICLGYFKDPVILDCEHSFCRACI 31
RING-HC_AtBARD1-like cd23146
RING finger, HC subclass, found in Arabidopsis thaliana BRCA1-associated RING domain protein 1 ...
42-93 2.86e-03

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


Pssm-ID: 438508 [Multi-domain]  Cd Length: 54  Bit Score: 35.14  E-value: 2.86e-03
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|..
gi 30687607  42 FDCNICLDTAHDPVVTLCGHLFCWPCIYKWLhvqlssvsvdQHQNNCPVCKS 93
Cdd:cd23146   5 LKCPICLKLLNRPVLLPCDHIFCSSCITDST----------KVGSDCPVCKL 46
RING-HC_RING1-like cd16531
RING finger, HC subclass, found in really interesting new gene proteins RING1, RING2 and ...
44-92 3.05e-03

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


Pssm-ID: 438193 [Multi-domain]  Cd Length: 66  Bit Score: 35.32  E-value: 3.05e-03
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|
gi 30687607  44 CNICLDTAHDPVVTL-CGHLFCWPCIYKWLHVQLssvsvdqhqNNCPVCK 92
Cdd:cd16531   4 CPICLGIIKNTMTVKeCLHRFCAECIEKALRLGN---------KECPTCR 44
PHA02929 PHA02929
N1R/p28-like protein; Provisional
43-92 3.19e-03

N1R/p28-like protein; Provisional


Pssm-ID: 222944 [Multi-domain]  Cd Length: 238  Bit Score: 37.84  E-value: 3.19e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 30687607   43 DCNICLDTAHDP--------VVTLCGHLFCWPCIYKWlhvqlssvsvDQHQNNCPVCK 92
Cdd:PHA02929 176 ECAICMEKVYDKeiknmyfgILSNCNHVFCIECIDIW----------KKEKNTCPVCR 223
RING-HC_MID2 cd16754
RING finger, HC subclass, found in midline-2 (MID2) and similar proteins; MID2, also known as ...
44-97 3.55e-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 and is highly related to MID1 that associates with cytoplasmic microtubules along their length and throughout the cell cycle. Like MID1, MID2 associates with the microtubule network and may at least partially compensate for the loss of MID1. Both MID1 and MID2 interacts with Alpha 4, which is a regulatory subunit of PP2-type phosphatases, such as PP2A, and an integral component of the rapamycin-sensitive signaling pathway. MID2 can also substitute for MID1 to control exocytosis of lytic granules in cytotoxic T cells. Loss-of-function mutations in MID2 lead to the human X-linked intellectual disability (XLID). MID2 belongs to the C-I subclass of the TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a C3HC4-type RING-HC finger, Bbox1 and Bbox2, and a coiled coil region, as well as a COS (carboxy-terminal subgroup one signature) box, a fibronectin type III (FN3) domain, and a B30.2/SPRY (SplA and ryanodine receptor) domain positioned C-terminal to the RBCC domain. MID2 hetero-dimerizes in vitro with its paralog MID1.


Pssm-ID: 438412 [Multi-domain]  Cd Length: 70  Bit Score: 35.35  E-value: 3.55e-03
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*.
gi 30687607  44 CNICLDTAHDPVVTLCGHLFCWPCIYKWLHVQLSSVSVDQHQN--NCPVCKSNITI 97
Cdd:cd16754  10 CPICLELFEDPLLLPCAHSLCFSCAHRILTSGCASGESIEPPSafQCPTCRYVISL 65
RING-HC_MEX3B cd16721
RING finger, HC subclass, found in RNA-binding protein MEX3B; MEX3B, also known as RING finger ...
40-96 4.38e-03

RING finger, HC subclass, found in RNA-binding protein MEX3B; MEX3B, also known as RING finger and KH domain-containing protein 3 (RKHD3), or RING finger protein 195 (RNF195), is an RNA-binding phosphoprotein that localizes in P-bodies and stress granules, which are two structures involved in the storage and turnover of mRNAs. It regulates the spatial organization of the Rap1 pathway that orchestrates Sertoli cell functions. It has a 3' long conserved untranslated region (3'LCU)-mediated fine-tuning system for mRNA regulation in early vertebrate development such as anteroposterior (AP) patterning and signal transduction. MEX3B contains two K homology (KH) domains that provide RNA-binding capacity, and a C-terminal C3HC4-type RING-HC finger. Like other MEX-3 family proteins, MEX3B shuttles between the nucleus and the cytoplasm via the CRM1-dependent export pathway.


Pssm-ID: 438381 [Multi-domain]  Cd Length: 58  Bit Score: 34.66  E-value: 4.38e-03
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*...
gi 30687607  40 GCFDCNICLDTAHDPVVTLCGH-LFCWPCiykwlhvqlSSVSVDQHQNNCPVCKSNIT 96
Cdd:cd16721   3 GSRDCSICFESEVIAALVPCGHnLFCMEC---------ANRICEKNEPQCPVCHAAVT 51
RING-HC_RNF180 cd16554
RING finger, HC subclass, found in RING finger protein 180 (RNF180) and similar proteins; ...
44-96 4.67e-03

RING finger, HC subclass, found in RING finger protein 180 (RNF180) and similar proteins; RNF180, also known as Rines, is a membrane-bound E3 ubiquitin-protein ligase well conserved among vertebrates. It is a critical regulator of the monoaminergic system, as well as emotional and social behavior. It interacts with brain monoamine oxidase A (MAO-A) and targets it for ubiquitination and degradation. It also functions as a novel tumor suppressor in gastric carcinogenesis. The hypermethylated CpG site count of the RNF180 DNA promoter can be used to predict survival of gastric cancer. RNF180 contains a novel conserved dual specificity protein phosphatase Rines conserved (DSPRC) domain, a basic coiled-coil domain, a C3HC4-type RING-HC finger, and a C-terminal hydrophobic region that is predicted to be a transmembrane domain.


Pssm-ID: 438216 [Multi-domain]  Cd Length: 59  Bit Score: 34.60  E-value: 4.67e-03
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*
gi 30687607  44 CNICLDTAHDP-VVTLCGHLFCWPCiykwlhvqLSSVSVDQHQNN-CPVCKSNIT 96
Cdd:cd16554   5 CPVCLDLYYDPyMCYPCGHIFCEPC--------LRQLAKSSPKNTpCPLCRTTIR 51
RING-HC_RNF168 cd16550
RING finger, HC subclass, found in RING finger protein 168 (RNF168) and similar proteins; ...
44-96 5.14e-03

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


Pssm-ID: 438212 [Multi-domain]  Cd Length: 48  Bit Score: 34.27  E-value: 5.14e-03
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|...
gi 30687607  44 CNICLDTAHDPVVTLCGHLFCWPCIYKwlHVQLSSVSvdqhqnnCPVCKSNIT 96
Cdd:cd16550   3 CPICLEILVEPVTLPCNHTLCMPCFQS--TVEKASLC-------CPLCRLRIS 46
mRING-HC-C3HC3D_LNX2 cd16780
Modified RING finger, HC subclass (C3HC3D-type), found in ligand of numb protein X 2 (LNX2); ...
44-90 5.49e-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: 34.08  E-value: 5.49e-03
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*..
gi 30687607  44 CNICLDTAHDPVVTLCGHLFCWPCIYKWLhvqlssvsvdQHQNNCPV 90
Cdd:cd16780   6 CHICLQPLLQPLDTPCGHTFCFKCLRNFL----------QEKDFCPL 42
RING-H2_RHA1-like cd23121
RING finger, H2 subclass, found in Arabidopsis thaliana RING-H2 finger A1a (RHA1A), A1b (RHA1B) ...
44-92 5.77e-03

RING finger, H2 subclass, found in Arabidopsis thaliana RING-H2 finger A1a (RHA1A), A1b (RHA1B) and similar proteins; This subfamily includes Arabidopsis thaliana RHA1A, RHA1B and XERICO. RHA1A is a probable E3 ubiquitin-protein ligase that may possess E3 ubiquitin ligase activity in vitro. RHA1B possesses E3 ubiquitin-protein ligase activity when associated with the E2 enzyme UBC8 in vitro. XERICO functions on abscisic acid homeostasis at post-translational level, probably through ubiquitin/proteasome-dependent substrate-specific degradation. Members of this subfamily contain a C3H2C3-type RING-H2 finger.


Pssm-ID: 438483 [Multi-domain]  Cd Length: 50  Bit Score: 34.00  E-value: 5.77e-03
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|...
gi 30687607  44 CNICLDTAHD----PVVTLCGHLFCWPCIYKWLhvqlssvsvDQHQNNCPVCK 92
Cdd:cd23121   4 CAICLSDFNSdeklRQLPKCGHIFHHHCLDRWI---------RYNKITCPLCR 47
RING-HC_RNF169 cd16551
RING finger, HC subclass, found in RING finger protein 169 (RNF169) and similar proteins; ...
42-93 6.08e-03

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


Pssm-ID: 438213 [Multi-domain]  Cd Length: 55  Bit Score: 34.06  E-value: 6.08e-03
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|..
gi 30687607  42 FDCNICLDTAHDPVVTLCGHLFCWPCIYKWLHVQLSsvsvdqhQNNCPVCKS 93
Cdd:cd16551   2 LTCAGCLEVPVEPATLPCGHTLCRGCANRALDAAEA-------GPTCPRCRA 46
RING-Ubox_PUB cd16664
U-box domain, a modified RING finger, found in Arabidopsis plant U-box proteins (AtPUB) and ...
42-100 6.40e-03

U-box domain, a modified RING finger, found in Arabidopsis plant U-box proteins (AtPUB) and similar proteins; The plant PUB proteins, also known as U-box domain-containing proteins, are much more numerous in Arabidopsis which has 62 in comparison with the typical 6 in most animals. The majority of AtPUBs in this subfamily are known as ARM domain-containing PUB proteins, containing a C-terminally-located, tandem ARM (armadillo) repeat protein-interaction region in addition to the U-box domain. They have been implicated in the regulation of cell death and defense. They also play important roles in other plant-specific pathways, such as controlling both self-incompatibility and pseudo-self-incompatibility, as well as acting in abiotic stress. A subgroup of ARM domain-containing PUB proteins harbors a plant-specific U-box N-terminal domain.


Pssm-ID: 438326 [Multi-domain]  Cd Length: 53  Bit Score: 34.08  E-value: 6.40e-03
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*....
gi 30687607  42 FDCNICLDTAHDPVVTLCGHLFCWPCIYKWLhvqlssvsvDQHQNNCPVCKSNITITSL 100
Cdd:cd16664   4 FICPISLELMKDPVILATGQTYERAAIEKWL---------DSGNNTCPITGQPLTHTDL 53
RING-HC_RAD18 cd16529
RING finger, HC subclass, found in postreplication repair protein RAD18 and similar proteins; ...
44-100 6.43e-03

RING finger, HC subclass, found in postreplication repair protein RAD18 and similar proteins; RAD18, also known as HR18 or RING finger protein 73 (RNF73), is an E3 ubiquitin-protein ligase involved in post replication repair of UV-damaged DNA via its recruitment to stalled replication forks. It associates to the E2 ubiquitin conjugating enzyme UBE2B to form the UBE2B-RAD18 ubiquitin ligase complex involved in mono-ubiquitination of DNA-associated PCNA on K164. It also interacts with another E2 ubiquitin conjugating enzyme RAD6 to form a complex that monoubiquitinates proliferating cell nuclear antigen at stalled replication forks in DNA translesion synthesis. Moreover, Rad18 is a key factor in double-strand break DNA damage response (DDR) pathways via its association with K63-linked polyubiquitylated chromatin proteins. It can function as a mediator for DNA damage response signals to activate the G2/M checkpoint in order to maintain genome integrity and cell survival after ionizing radiation (IR) exposure. RAD18 contains a C3HC4-type RING-HC finger, a ubiquitin-binding zinc finger domain (UBZ), a SAP (SAF-A/B, Acinus and PIAS) domain, and a RAD6-binding domain (R6BD).


Pssm-ID: 438192 [Multi-domain]  Cd Length: 54  Bit Score: 34.20  E-value: 6.43e-03
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*...
gi 30687607  44 CNICLDT-AHDPVVTLCGHLFCWPCIYKWLHvqlssvsvdqHQNNCPVCKSNITITSL 100
Cdd:cd16529   7 CPICFEYfNTAMMITQCSHNYCSLCIRRFLS----------YKTQCPTCRAAVTESDL 54
RING-HC_TRAF1-like cd23125
RING finger, HC subclass, found in tumor necrosis factor (TNF) receptor-associated factor 1 ...
41-92 6.82e-03

RING finger, HC subclass, found in tumor necrosis factor (TNF) receptor-associated factor 1 (TRAF1)-like and similar proteins; TRAF1, also known as Epstein-Barr virus-induced protein 6 (EBI6), is an adapter molecule that regulates the activation of NF-kappa-B and JNK. It plays a role in the regulation of cell survival and apoptosis. The heterotrimer formed by TRAF1 and TRAF2 is part of an E3 ubiquitin-protein ligase complex that promotes ubiquitination of target proteins, such as MAP3K14. The TRAF1/TRAF2 complex recruits the antiapoptotic E3 protein-ubiquitin ligases BIRC2 and BIRC3 to TNFRSF1B/TNFR2. This subfamily corresponds a group of TRAF1-like proteins that contains an N-terminal domain with a typical C3HC4-type RING-HC finger.


Pssm-ID: 438487 [Multi-domain]  Cd Length: 51  Bit Score: 34.03  E-value: 6.82e-03
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|...
gi 30687607  41 CFDCNICLDTAHDpvvTLCGHLFCWPCIyKWLhvqlssvsVDQHQNN-CPVCK 92
Cdd:cd23125   7 CCNCKNVLKKAQQ---TLCGHRYCLACL-SWI--------VRNNKNPiCQKCK 47
COG5219 COG5219
Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only];
39-96 6.88e-03

Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only];


Pssm-ID: 227544 [Multi-domain]  Cd Length: 1525  Bit Score: 37.73  E-value: 6.88e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 30687607   39 SGCFDCNICLDTAHDPVVTL-------CGHLFCWPCIYKWLHvqlSSVSvdqhqNNCPVCKSNIT 96
Cdd:COG5219 1467 SGHEECAICYSVLDMVDRSLpskrcatCKNKFHTRCLYKWFA---SSAR-----SNCPLCRSEIT 1523
RING-HC_AtBRCA1-like cd23147
RING finger, HC subclass, found in Arabidopsis thaliana protein BREAST CANCER SUSCEPTIBILITY 1 ...
44-92 8.02e-03

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


Pssm-ID: 438509 [Multi-domain]  Cd Length: 54  Bit Score: 33.60  E-value: 8.02e-03
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*....
gi 30687607  44 CNICLDTAHDPVVTLCGHLFCWPCIYKWLHVQLSsvsvdqhqnnCPVCK 92
Cdd:cd23147   7 CPICLSLFKSAANLSCNHCFCAGCIGESLKLSAI----------CPVCK 45
RING-HC_TRIM56_C-V cd16584
RING finger, HC subclass, found in tripartite motif-containing protein 56 (TRIM56) and similar ...
42-97 8.08e-03

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


Pssm-ID: 438246 [Multi-domain]  Cd Length: 56  Bit Score: 33.81  E-value: 8.08e-03
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*.
gi 30687607  42 FDCNICLDTAHDPVVTLCGHLFCWPCIYKWlhvqlssvsVDQHQNNCPVCKSNITI 97
Cdd:cd16584   2 LACKICLEQLRAPKTLPCLHTYCQDCLAQL---------ADGGRVRCPECRETVPV 48
RING-H2_SIS3 cd23118
RING finger, H2 subclass, found in Arabidopsis thaliana protein SUGAR INSENSITIVE 3 (SIS3) and ...
44-95 8.14e-03

RING finger, H2 subclass, found in Arabidopsis thaliana protein SUGAR INSENSITIVE 3 (SIS3) and similar proteins; SIS3 is an E3 ubiquitin-protein ligase that acts as a positive regulator of sugar signaling during early seedling development. SIS3 contains a C3H2C3-type RING-H2 finger.


Pssm-ID: 438480 [Multi-domain]  Cd Length: 47  Bit Score: 33.49  E-value: 8.14e-03
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*..
gi 30687607  44 CNICLDTAHDPV---VTLCGHLFCWPCIYKWL--HVQlssvsvdqhqnnCPVCKSNI 95
Cdd:cd23118   3 CTICLEDFEDGEklrVLPCQHQFHSECVDQWLrrNPK------------CPVCRRDA 47
RING-HC_PCGF5 cd16737
RING finger found in polycomb group RING finger protein 5 (PCGF5) and similar proteins; PCGF5, ...
44-92 8.20e-03

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


Pssm-ID: 438395 [Multi-domain]  Cd Length: 95  Bit Score: 34.73  E-value: 8.20e-03
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|
gi 30687607  44 CNICLDTAHDP-VVTLCGHLFCWPCIYKwlHVQLSsvsvdqhqNNCPVCK 92
Cdd:cd16737  13 CRICKGYLIKPtTVTECLHTFCKSCIVQ--HFEDS--------NDCPECG 52
mRING-HC-C3HC3D_TRAF7 cd16644
Modified RING finger, HC subclass (C3HC3D-type), found in tumor necrosis factor (TNF) ...
44-68 8.53e-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 by promoting K29-linked ubiquitination of several cellular targets, including the NF-kappaB essential modulator (NEMO) and the p65 subunit of NF-kappaB transcription factor. It is also involved in K29-linked polyubiquitination that has been implicated in lysosomal degradation of proteins. Moreover, TRAF7 is required for K48-linked ubiquitination of p53, a key tumor suppressor and a master regulator of various signaling pathways, such as those related to apoptosis, cell cycle and DNA repair. It is also required for tumor necrosis factor alpha (TNFalpha)-induced Jun N-terminal kinase activation and promotes cell death by regulating polyubiquitination and lysosomal degradation of c-FLIP protein. Furthermore, TRAF7 functions as small ubiquitin-like modifier (SUMO) E3 ligase involved in other post-translational modification, such as sumoylation. It binds to and stimulates sumoylation of the proto-oncogene product c-Myb, a transcription factor regulating proliferation and differentiation of hematopoietic cells. It potentiates MEKK3-induced AP1 and CHOP activation and induces apoptosis. Meanwhile, TRAF7 mediates MyoD1 regulation of the pathway and cell-cycle progression in myoblasts. It also plays a role in Toll-like receptors (TLR) signaling. TRAF7 contains an N-terminal domain with a modified C3HC3D-type RING-HC finger and an adjacent zinc finger, and a unique C-terminal domain that comprises a coiled coil domain and seven WD40 repeats.


Pssm-ID: 438306 [Multi-domain]  Cd Length: 47  Bit Score: 33.48  E-value: 8.53e-03
                        10        20
                ....*....|....*....|....*
gi 30687607  44 CNICLDTAHDPVVTLCGHLFCWPCI 68
Cdd:cd16644   8 CPLCQRVFKDPVITSCGHTFCRRCA 32
RING-H2_RNF111-like cd16474
RING finger, H2 subclass, found in RING finger proteins RNF111, RNF165, and similar proteins; ...
43-92 9.40e-03

RING finger, H2 subclass, found in RING finger proteins RNF111, RNF165, and similar proteins; The family includes RING finger proteins RNF111, RNF165, and similar proteins. RNF111, also known as Arkadia, is a nuclear E3 ubiquitin-protein ligase that targets intracellular effectors and modulators of transforming growth factor beta (TGF-beta)/Nodal-related signaling for polyubiquitination and proteasome-dependent degradation. It also interacts with the clathrin-adaptor 2 (AP2) complex and regulates endocytosis of certain cell surface receptors, leading to modulation of epidermal growth factor (EGF) and possibly other signaling pathways. The N-terminal half of RNF111 harbors three SUMO-interacting motifs (SIMs). It thus functions as a SUMO-targeted ubiquitin ligase (STUbL) that directly links nonproteolytic ubiquitylation and SUMOylation in the DNA damage response, as well as triggers degradation of signal-induced polysumoylated proteins, such as the promyelocytic leukemia protein (PML). RNF165, also known as Arkadia-like 2, Arkadia2, or Ark2C, is an E3 ubiquitin ligase with homology to the C-terminal half of RNF111. It is expressed specifically in the nervous system, and can serve to amplify neuronal responses to specific signals. It acts as a positive regulator of bone morphogenetic protein (BMP)-Smad signaling that is involved in motor neuron (MN) axon elongation. Both RNF165 and RNF111 contain a C-terminal C3H2C3-type RING-H2 finger.


Pssm-ID: 438137 [Multi-domain]  Cd Length: 46  Bit Score: 33.54  E-value: 9.40e-03
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|...
gi 30687607  43 DCNICLDT--AHDPVVTL-CGHLFCWPCIYKWLhvqlssvsvdQHQNNCPVCK 92
Cdd:cd16474   2 KCTICLSDfeEGEDVRRLpCMHLFHQECVDQWL----------STNKRCPICR 44
RING-HC_UHRF cd16613
RING finger, HC subclass, found in ubiquitin-like PHD and RING finger domain-containing ...
42-92 9.68e-03

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


Pssm-ID: 438275 [Multi-domain]  Cd Length: 46  Bit Score: 33.48  E-value: 9.68e-03
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|.
gi 30687607  42 FDCNICLDTAHDPVVTLCGHLFCWPCIYKwlhvqlssvSVDQHQNNCPVCK 92
Cdd:cd16613   1 FTCICCQELVYKPITTPCKHNICKSCLQR---------SFKAEVYTCPACR 42
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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