RNA recognition motif (RRM) found in BRCA1-associated protein (BRAP2); This subgroup corresponds to the RRM of BRAP2, also termed impedes mitogenic signal propagation (IMP), or ring finger protein 52, or renal carcinoma antigen NY-REN-63, a novel cytoplasmic protein interacting with the two functional nuclear localisation 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 may serve as a cytoplasmic retention protein and play a role in the regulation of nuclear protein transport. It contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by a C3HC4-type ring finger domain and a UBP-type zinc finger.

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 21356581 147 SNQLCLLAVPATLNCHDLLNFIAPCHAEIKHIQIVRDGSPNQFMVLLEFRSNESALEFYKSYNGSTYNSLEPDSlCHAVW 226
Cdd:cd12718   1 SEMLCMLAVPATLTCHDLLNFLAPVLPSIEHIKIIRDSTPNQYMVLIKFRSQEDADEFYKTFNGQQFNSLEEDV-CHLVY 79

                ....*
gi 21356581 227 VSEVE 231
Cdd:cd12718  80 VSRVE 84

Zn-finger in ubiquitin-hydrolases and other protein;

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 21356581   301 CMECEGTDSLWICLICGHVGCGRYQGGHAAAHFRATNHTFAMQLGTSSVWDYAGDNFVHRLFQ 363
Cdd:pfam02148   1 CSLCGNTSNLWLCLTCGHVGCGRYQNSHALEHYEETGHPLAVNLSTLTVYCYPCDDYVHDPSL 63

RNA recognition motif (RRM) found in BRCA1-associated protein (BRAP2); This subgroup corresponds to the RRM of BRAP2, also termed impedes mitogenic signal propagation (IMP), or ring finger protein 52, or renal carcinoma antigen NY-REN-63, a novel cytoplasmic protein interacting with the two functional nuclear localisation 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 may serve as a cytoplasmic retention protein and play a role in the regulation of nuclear protein transport. It contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by a C3HC4-type ring finger domain and a UBP-type zinc finger.

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 21356581 147 SNQLCLLAVPATLNCHDLLNFIAPCHAEIKHIQIVRDGSPNQFMVLLEFRSNESALEFYKSYNGSTYNSLEPDSlCHAVW 226
Cdd:cd12718   1 SEMLCMLAVPATLTCHDLLNFLAPVLPSIEHIKIIRDSTPNQYMVLIKFRSQEDADEFYKTFNGQQFNSLEEDV-CHLVY 79

                ....*
gi 21356581 227 VSEVE 231
Cdd:cd12718  80 VSRVE 84

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.

                        10        20        30        40
                ....*....|....*....|....*....|....*....|....
gi 21356581 246 PTCPVCLERMDESVDGVLTILCNHAFHASCLMKWGDSTCPVCRH 289
Cdd:cd16457   1 PTCPVCLERMDESVSGILTILCNHSFHCSCLSKWGDSSCPVCRY 44

Ubiquitin Carboxyl-terminal Hydrolase-like zinc finger;

                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*....
gi 21356581    301 CMECEGTDSLWICLICGHVGCGRYQGGHAAAHFRATNHTFAMQLGTSSV 349
Cdd:smart00290   2 CSVCGTIENLWLCLTCGQVGCGRYQNGHALEHFEETGHPLVVKLGTQRV 50

chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 21356581    364 NKSDGKLVASQTEKDEREEKIDSMQMEFTYLLTSQLDTQRKYYE--ERMERLEQEWQNHKATANDAKTEVSELQQLQQNM 441
Cdd:TIGR02168  249 KEAEEELEELTAELQELEEKLEELRLEVSELEEEIEELQKELYAlaNEISRLEQQKQILRERLANLERQLEELEAQLEEL 328

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 21356581    442 QKEKVNLERKLAQHTAKLKDVQKQLNEERELSKALQSNQSSWHGKYKLLEQQYNEFKqthdAEVTELKEQLRDIM 516
Cdd:TIGR02168  329 ESKLDELAEELAELEEKLEELKEELESLEAELEELEAELEELESRLEELEEQLETLR----SKVAQLELQIASLN 399

Predicted nucleic acid-binding protein DR0291, contains C4-type Zn-ribbon domain [General function prediction only];

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 21356581 398 QLDTQRKYYEERMERLEQEWQNHKATANDAKTEVSELQqlqqnmqKEKVNLERKLAQHTAKLKDVQKQLNE---ERELsK 474
Cdd:COG1579  21 RLEHRLKELPAELAELEDELAALEARLEAAKTELEDLE-------KEIKRLELEIEEVEARIKKYEEQLGNvrnNKEY-E 92

                        90       100       110       120
                ....*....|....*....|....*....|....*....|....
gi 21356581 475 ALQSNQSSWHGKYKLLEQQYNEF---KQTHDAEVTELKEQLRDI 515
Cdd:COG1579  93 ALQKEIESLKRRISDLEDEILELmerIEELEEELAELEAELAEL 136

Ezrin/radixin/moesin, alpha-helical domain; The ERM family consists of three closely-related proteins, ezrin, radixin and moesin. Ezrin was first identified as a constituent of microvilli, radixin as a barbed, end-capping actin-modulating protein from isolated junctional fractions, and moesin as a heparin binding protein. A tumour suppressor molecule responsible for neurofibromatosis type 2 (NF2) is highly similar to ERM proteins and has been designated merlin (moesin-ezrin-radixin-like protein). ERM molecules contain 3 domains, an N-terminal globular domain, an extended alpha-helical domain and a charged C-terminal domain (pfam00769). Ezrin, radixin and merlin also contain a polyproline linker region between the helical and C-terminal domains. The N-terminal domain is highly conserved and is also found in merlin, band 4.1 proteins and members of the band 4.1 superfamily, designated the FERM domain. ERM proteins crosslink actin filaments with plasma membranes. They co-localize with CD44 at actin filament plasma membrane interaction sites, associating with CD44 via their N-terminal domains and with actin filaments via their C-terminal domains. This is the alpha-helical domain, which is involved in intramolecular masking of protein-protein interaction sites, regulating the activity of this proteins.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 21356581   376 EKDEREEKIDSMQMEFTY----LLTSQ-----LDTQRKYYEERMERLEQEwqnhkatANDAKTEVSELQQLQQNMQKEKV 446
Cdd:pfam20492   7 EKQELEERLKQYEEETKKaqeeLEESEetaeeLEEERRQAEEEAERLEQK-------RQEAEEEKERLEESAEMEAEEKE 79

                          90       100       110
                  ....*....|....*....|....*....|.
gi 21356581   447 NLERKLAQHTAKLKDVQKQLNEERELSKALQ 477
Cdd:pfam20492  80 QLEAELAEAQEEIARLEEEVERKEEEARRLQ 110

N1R/p28-like protein; Provisional

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*...
gi 21356581  248 CPVCLERM-DESVD----GVLTiLCNHAFHASCLMKW--GDSTCPVCR 288
Cdd:PHA02929 177 CAICMEKVyDKEIKnmyfGILS-NCNHVFCIECIDIWkkEKNTCPVCR 223

RNA recognition motif (RRM) found in BRCA1-associated protein (BRAP2); This subgroup corresponds to the RRM of BRAP2, also termed impedes mitogenic signal propagation (IMP), or ring finger protein 52, or renal carcinoma antigen NY-REN-63, a novel cytoplasmic protein interacting with the two functional nuclear localisation 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 may serve as a cytoplasmic retention protein and play a role in the regulation of nuclear protein transport. It contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by a C3HC4-type ring finger domain and a UBP-type zinc finger.

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 21356581 147 SNQLCLLAVPATLNCHDLLNFIAPCHAEIKHIQIVRDGSPNQFMVLLEFRSNESALEFYKSYNGSTYNSLEPDSlCHAVW 226
Cdd:cd12718   1 SEMLCMLAVPATLTCHDLLNFLAPVLPSIEHIKIIRDSTPNQYMVLIKFRSQEDADEFYKTFNGQQFNSLEEDV-CHLVY 79

                ....*
gi 21356581 227 VSEVE 231
Cdd:cd12718  80 VSRVE 84

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.

                        10        20        30        40
                ....*....|....*....|....*....|....*....|....
gi 21356581 246 PTCPVCLERMDESVDGVLTILCNHAFHASCLMKWGDSTCPVCRH 289
Cdd:cd16457   1 PTCPVCLERMDESVSGILTILCNHSFHCSCLSKWGDSSCPVCRY 44

RNA recognition motif (RRM) found in yeast RING finger protein ETP1 and similar proteins; This subgroup corresponds to the RRM of ETP1, also termed BRAP2 homolog, or ethanol tolerance protein 1, the yeast homolog of BRCA1-associated protein (BRAP2) found in vertebrates. It may be involved in ethanol and salt-induced transcriptional activation of the NHA1 promoter and heat shock protein genes (HSP12 and HSP26), and participate in ethanol-induced turnover of the low-affinity hexose transporter Hxt3p. ETP1 contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by a C3HC4-type ring finger domain and a UBP-type zinc finger.

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 21356581 150 LCLLAVPATLNCHDLLNFIAPCHAE-IKHIQIVRDGSPNQFMVLLEFRSNESALEFYKSYNGSTYNSLEPDSlCHAVWVS 228
Cdd:cd12717   2 LAILAVPSYMTPSDLLGFVGGATLEqVSHFRLIRTSRPNRYMVLLKFRDAKSAKEFQKEFNGKKFNSIDPET-CHVVFIK 80

                ...
gi 21356581 229 EVE 231
Cdd:cd12717  81 EII 83

Ubiquitin Carboxyl-terminal Hydrolase-like zinc finger;

                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*....
gi 21356581    301 CMECEGTDSLWICLICGHVGCGRYQGGHAAAHFRATNHTFAMQLGTSSV 349
Cdd:smart00290   2 CSVCGTIENLWLCLTCGQVGCGRYQNGHALEHFEETGHPLVVKLGTQRV 50

Ring finger domain;

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 21356581   246 PTCPVCLERMDESVDgVLTILCNHAFHASCLMKW--GDSTCPVCR 288
Cdd:pfam13639   1 DECPICLEEFEEGDK-VVVLPCGHHFHRECLDKWlrSSNTCPLCR 44

chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 21356581    364 NKSDGKLVASQTEKDEREEKIDSMQMEFTYLLTSQLDTQRKYYE--ERMERLEQEWQNHKATANDAKTEVSELQQLQQNM 441
Cdd:TIGR02168  249 KEAEEELEELTAELQELEEKLEELRLEVSELEEEIEELQKELYAlaNEISRLEQQKQILRERLANLERQLEELEAQLEEL 328

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 21356581    442 QKEKVNLERKLAQHTAKLKDVQKQLNEERELSKALQSNQSSWHGKYKLLEQQYNEFKqthdAEVTELKEQLRDIM 516
Cdd:TIGR02168  329 ESKLDELAEELAELEEKLEELKEELESLEAELEELEAELEELESRLEELEEQLETLR----SKVAQLELQIASLN 399

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.

                        10        20        30        40
                ....*....|....*....|....*....|....*....|....
gi 21356581 247 TCPVCLERMdESVDGVLTILCNHAFHASCLMKW--GDSTCPVCR 288
Cdd:cd16454   1 TCAICLEEF-KEGEKVRVLPCNHLFHKDCIDPWleQHNTCPLCR 43

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

                           10        20        30        40
                   ....*....|....*....|....*....|....*....|...
gi 21356581    248 CPVCLERMDESVdgvLTILCNHAFHASCLMKW---GDSTCPVC 287
Cdd:smart00184   1 CPICLEEYLKDP---VILPCGHTFCRSCIRKWlesGNNTCPIC 40

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.

                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*..
gi 21356581 246 PTCPVCLERMDESVdGVLTIlCNHAFHASCLMKW----GDSTCPVCR 288
Cdd:cd23120   2 EECPICLEEMNSGT-GYLAD-CGHEFHLTCIREWhnksGNLDCPICR 46

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.

                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*.
gi 21356581 247 TCPVCLErmDESVDGVLTIL-CNHAFHASCLMKW---GDSTCPVCR 288
Cdd:cd16473   6 ECAICLE--NYQNGDLLRGLpCGHVFHQNCIDVWlerDNHCCPVCR 49

RING finger, H2 subclass, found in RING finger protein 126 (RNF126) and similar proteins; RNF126 is a Bag6-dependent E3 ubiquitin ligase that is involved in the mislocalized protein (MLP) pathway of quality control. It regulates the retrograde sorting of the cation-independent mannose 6-phosphate receptor (CI-MPR). Moreover, RNF126 promotes cancer cell proliferation by targeting the tumor suppressor p21 for ubiquitin-mediated degradation, and could be a novel therapeutic target in breast and prostate cancers. It is also able to ubiquitylate cytidine deaminase (AID), a poorly soluble protein that is essential for antibody diversification. In addition, RNF126 and the related protein, RNF115 associate with the epidermal growth factor receptor (EGFR) and promote ubiquitylation of EGFR, suggesting they play a role in the ubiquitin-dependent sorting and downregulation of membrane receptors. RNF126 contains an N-terminal BCA2 Zinc-finger domain (BZF), the AKT-phosphorylation sites, and the C-terminal C3H2C3-type RING-H2 finger.

                        10        20        30        40
                ....*....|....*....|....*....|....*....|....
gi 21356581 248 CPVCLErmDESV-DGVLTILCNHAFHASCLMKWGD--STCPVCR 288
Cdd:cd16801   2 CPVCKE--DYTVgENVRQLPCNHLFHNDCIVPWLEqhDTCPVCR 43

RING finger, H2 subclass, found in RING finger protein 115 (RNF115) and similar proteins; RNF115, also known as Rab7-interacting ring finger protein (Rabring 7), or zinc finger protein 364 (ZNF364), or breast cancer-associated gene 2 (BCA2), is an E3 ubiquitin-protein ligase that is an endogenous inhibitor of adenosine monophosphate-activated protein kinase (AMPK) activation and its inhibition increases the efficacy of metformin in breast cancer cells. It also functions as a co-factor in the restriction imposed by tetherin on HIV-1, and targets HIV-1 Gag for lysosomal degradation, impairing virus assembly and release, in a tetherin-independent manner. Moreover, RNF115 is a Rab7-binding protein that stimulates c-Myc degradation through mono-ubiquitination of MM-1. It also plays crucial roles as a Rab7 target protein in vesicle traffic to late endosome/lysosome and lysosome biogenesis. Furthermore, RNF115 and the related protein, RNF126 associate with the epidermal growth factor receptor (EGFR) and promote ubiquitylation of EGFR, suggesting they play a role in the ubiquitin-dependent sorting and downregulation of membrane receptors. RNF115 contains an N-terminal BCA2 Zinc-finger domain (BZF), the AKT-phosphorylation sites, and the C-terminal C3H2C3-type RING-H2 finger.

                        10        20        30        40
                ....*....|....*....|....*....|....*....|....
gi 21356581 248 CPVCLErmDESV-DGVLTILCNHAFHASCLMKWGD--STCPVCR 288
Cdd:cd16800   3 CPVCKE--DYTVgEQVRQLPCNHFFHSDCIVPWLElhDTCPVCR 44

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).

                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*....
gi 21356581 246 PTCPVCLERMDE---SVDGvltilCNHAFHASCLMKWGD--STCPVCRH 289
Cdd:cd16574   2 SSCPICLDRFENekaFLDG-----CFHAFCFTCILEWSKvkNECPLCKQ 45

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

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 21356581  241 GHTELPTCPVCLERMDESVDGVLTILCNHAFHASCLMKW----GDSTCPVCR 288
Cdd:COG5219 1468 GHEECAICYSVLDMVDRSLPSKRCATCKNKFHTRCLYKWfassARSNCPLCR 1519

RING finger, H2 subclass, found in RING finger proteins RNF38, RNF44, and similar proteins; This subfamily includes RING finger proteins RNF38, RNF44, and similar proteins. RNF38 is a nuclear E3 ubiquitin protein ligase that plays a role in regulating p53. RNF44 is an uncharacterized RING finger protein that shows high sequence similarity to RNF38. Both RNF38 and RNF44 contain a coiled-coil motif, a KIL motif (Lys-X2-Ile/Leu-X2-Ile/Leu, X can be any amino acid), and a C3H2C3-type RING-H2 finger. In addition, RNF38 harbors two potential nuclear localization signals.

                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*.
gi 21356581 246 PTCPVCLerMDESVDGVLTIL-CNHAFHASCLMKW--GDSTCPVCR 288
Cdd:cd16472   3 TQCVVCM--CDYEKRQLLRVLpCSHEFHAKCIDKWlkTNRTCPICR 46

RING finger, H2 subclass, found in RING finger protein 122 (RNF122) and similar proteins; 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. It interacts with calcium-modulating cyclophilin ligand (CAML), which is not a substrate, but a stabilizer of RNF122. RNF122 contains an N-terminal transmembrane domain and a C-terminal C3H2C3-type RING-H2 finger.

                        10        20        30        40
                ....*....|....*....|....*....|....*....|...
gi 21356581 247 TCPVCLERMdESVDGVLTILCNHAFHASCLMKWGD--STCPVC 287
Cdd:cd16676   2 TCAVCLEDF-KTKDELGVLPCQHAFHRKCLVKWLEirCVCPMC 43

RING finger, H2 subclass, found in DAZ (deleted in azoospermia)-interacting protein 3 (DZIP3) and similar proteins; DZIP3, also known as RNA-binding ubiquitin ligase of 138 kDa (RUL138) or 2A-HUB protein, is an RNA-binding E3 ubiquitin-protein ligase that interacts with coactivator-associated arginine methyltransferase 1 (CARM1) and acts as a transcriptional coactivator of estrogen receptor (ER) alpha. It is also a histone H2A ubiquitin ligase that catalyzes monoubiquitination of H2A at lysine 119, functioning as a combinatorial component of the repression machinery required for repressing a specific chemokine gene expression program, critically modulating migratory responses to Toll-like receptors (TLR) activation. DZIP3 contains a C3H2C3-type RING-H2 finger at the C-terminus.

                        10        20        30        40
                ....*....|....*....|....*....|....*....|...
gi 21356581 248 CPVCLERMdESVDGVLTILCNHAFHASCLMKW--GDSTCPVCR 288
Cdd:cd16460   3 CVICHEAF-SDGDRLLVLPCAHKFHTQCIGPWldGQQTCPTCR 44

Chromosome segregation ATPase Smc [Cell cycle control, cell division, chromosome partitioning];

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 21356581 369 KLVASQTEKDEREEKIDSMQMEFtylltSQLDTQRKYYEERMERLEQEWQNHKATANDAKTEVSELQQ-------LQQNM 441
Cdd:COG1196 240 ELEELEAELEELEAELEELEAEL-----AELEAELEELRLELEELELELEEAQAEEYELLAELARLEQdiarleeRRREL 314

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 21356581 442 QKEKVNLERKLAQHTAKLKDVQKQLNEERELSKALQSNQSSWHGKYKLLEQQYNEFKQTHDAEVTELKEQLRDIMFFLDN 521
Cdd:COG1196 315 EERLEELEEELAELEEELEELEEELEELEEELEEAEEELEEAEAELAEAEEALLEAEAELAEAEEELEELAEELLEALRA 394

                       170
                ....*....|
gi 21356581 522 QQKLANTEIA 531
Cdd:COG1196 395 AAELAAQLEE 404

RING-CH finger, H2 subclass (C4HC3-type), found in E3 ubiquitin-protein ligase listerin and similar proteins; Listerin, also known as RING finger protein 160 or zinc finger protein 294, is the mammalian homolog of yeast Ltn1. It is widely expressed in all tissues, but motor and sensory neurons and neuronal processes in the brainstem and spinal cord are primarily affected in the mutant. Listerin is required for embryonic development and plays an important role in neurodegeneration. It also functions as a critical E3 ligase involving quality control of nonstop proteins. It mediates ubiquitylation of aberrant proteins that become stalled on ribosomes during translation. Ltn1 works with several cofactors to form a large ribosomal subunit-associated quality control complex (RQC), which mediates the ubiquitylation and extraction of ribosome-stalled nascent polypeptide chains for proteasomal degradation. It appears to first associate with nascent chain-stalled 60S subunits together with two proteins of unknown function, Tae2 and Rqc1. Listerin contains a long stretch of HEAT (Huntingtin, Elongation factor 3, PR65/A subunit of protein phosphatase 2A, and TOR) or ARM (Armadillo) repeats in the N terminus and middle region, and a catalytic RING-CH finger, also known as vRING or RINGv, with an unusual arrangement of zinc-coordinating residues in the C-terminus . Its cysteines and histidines are arranged in the sequence as C4HC3-type, rather than the C3H2C3-type in canonical RING-H2 finger.

                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*...
gi 21356581 248 CPVC---LERMDESVDGVLTILCNHAFHASCLMKW----GDSTCPVCR 288
Cdd:cd16491   3 CPICysvIHGSNHSLPKLKCKTCKNKFHSACLYKWfrssNKSTCPLCR 50

chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 21356581    364 NKSDGKLVASQTEKDEREEKIDSMQMEFTylltsQLDTQRKYYEERMERLEQEWQNHKATANDAKTEVSELQQLQQNMQK 443
Cdd:TIGR02168  666 AKTNSSILERRREIEELEEKIEELEEKIA-----ELEKALAELRKELEELEEELEQLRKELEELSRQISALRKDLARLEA 740

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 21356581    444 EKVNLERKLAQHTAKLKDVQKQLNEERELSKALQSNQSSWHGKYKLLEQQYNEFK---QTHDAEVTELKEQLRDI-MFFL 519
Cdd:TIGR02168  741 EVEQLEERIAQLSKELTELEAEIEELEERLEEAEEELAEAEAEIEELEAQIEQLKeelKALREALDELRAELTLLnEEAA 820

                          170
                   ....*....|
gi 21356581    520 DNQQKLANTE 529
Cdd:TIGR02168  821 NLRERLESLE 830

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.

                        10        20        30        40
                ....*....|....*....|....*....|....*....|..
gi 21356581 248 CPVCLERMDESVdgvlTILCNHAFHASCLMKW--GDSTCPVC 287
Cdd:cd16476   3 CAICYQEMKEAR----ITPCNHFFHGLCLRKWlyVQDTCPLC 40

RING finger, H2 subclass, found in Arabidopsis thaliana protein WAV3 homolog 2 (WAVH2) and similar proteins; WAVH2, also known as RING-type E3 ubiquitin transferase WAVH2, is a probable E3 ubiquitin-protein ligase involved in the regulation of root growth. It acts as a positive regulator of root gravitropism. WAVH2 contains a C3H2C3-type RING-H2 finger.

                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*.
gi 21356581 247 TCPVCLERMDESVD-GVLTILCNHAFHASC---LMKWGDSTCPVCR 288
Cdd:cd23114   6 ECSICLETMKPGSGhAIFTAECSHSFHFECiagNVRHGNLRCPVCR 51

first RING finger, H2 subclass, found in RING finger protein 32 (RNF32) and similar proteins; RNF32 is mainly expressed in testis spermatogenesis, most likely in spermatocytes and/or in spermatids, suggesting a possible role in sperm formation. RNF32 contains two C3H2C3-type RING-H2 fingers separated by an IQ domain of unknown function. Although the biological function of RNF32 remains unclear, proteins with double RING-H2 fingers may act as scaffolds for binding several proteins that function in the same pathway. This model corresponds to the first RING-H2 finger.

                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*...
gi 21356581 248 CPVCLErmDESVDGVLTILCNHAFHASCLMKW----GDSTCPVCRHVQ 291
Cdd:cd16677   2 CPICLE--DFGLQQQVLLSCSHVFHRACLESFerfsGKKTCPMCRKEQ 47

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.

                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*...
gi 21356581 244 ELPTCPVCLERMDESVdgvltIL-CNHAFHASCLMKW--GDSTCPVCR 288
Cdd:cd16561   1 GEQECSICLEDLNDPV-----KLpCDHVFCEECIRQWlpGQMSCPLCR 43

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.

                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*..
gi 21356581 248 CPVCLERMDESVdgvlTILCNHAFHASCL-MKWGDST----CPVCRH 289
Cdd:cd16607   4 CPICLDYLKDPV----TINCGHNFCRSCIsMSWKDLQdtfpCPVCRF 46

Septal ring factor EnvC, activator of murein hydrolases AmiA and AmiB [Cell cycle control, cell division, chromosome partitioning];

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 21356581 404 KYYEERMERLEQEWQNHKATANDAKTEVSELQQLQQNMQKEKVNLERKLAQHTAKLKDVQKQLNEERELSKALQSNQSSW 483
Cdd:COG4942 146 PARREQAEELRADLAELAALRAELEAERAELEALLAELEEERAALEALKAERQKLLARLEKELAELAAELAELQQEAEEL 225

                        90
                ....*....|
gi 21356581 484 HGKYKLLEQQ 493
Cdd:COG4942 226 EALIARLEAE 235

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.

                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*
gi 21356581 248 CPVCLERMDESVDGVLTILCNHAFHASCLMKWGD---STCPVCRH 289
Cdd:cd23121   4 CAICLSDFNSDEKLRQLPKCGHIFHHHCLDRWIRynkITCPLCRA 48

RING finger, H2 subclass, found in RING finger protein 44 (RNF44) and similar proteins; RNF44 is an uncharacterized RING finger protein that shows high sequence similarity with RNF38, which is a nuclear E3 ubiquitin protein ligase that plays a role in regulating p53. RNF44 contains a coiled-coil motif, a KIL motif (Lys-X2-Ile/Leu-X2-Ile/Leu, X can be any amino acid), and a C3H2C2-type RING-H2 finger.

                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*....
gi 21356581 242 HTELPTCPVCLERMdESVDGVLTILCNHAFHASCLMKW--GDSTCPVCR 288
Cdd:cd16680   4 QSEQTLCVVCFSDF-ESRQLLRVLPCNHEFHTKCVDKWlkTNRTCPICR 51

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.

                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*..
gi 21356581 247 TCPVCLERMDESVdgvlTILCNHAFHASCLMK-WGDS----TCPVCR 288
Cdd:cd16594   7 TCPICLDYFTDPV----TLDCGHSFCRACIARcWEEPetsaSCPQCR 49

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.

                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*.
gi 21356581 247 TCPVCLERMDESvdgvLTILCNHAFHASCL--------MKWGDSTCPVCRHVQTPG 294
Cdd:cd16591   8 TCPICLELLTEP----LSLDCGHSFCQACItanhkesvNQEGESSCPVCRTSYQPE 59

RING finger, H2 subclass, found in RING finger protein 24 (RNF24) 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. RNF24 contains an N-terminal transmembrane domain and a C-terminal C3H2C3-type RING-H2 finger.