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 818942745 161 SAMLCILTVPATMTSHDLMKFVAPFYDVIEHMKIIRDSTPNQYMVLIKFRTQADADSFYMACNGRQFNSIEEDVCQLVYV 240
Cdd:cd12718    1 SEMLCMLAVPATLTCHDLLNFLAPVLPSIEHIKIIRDSTPNQYMVLIKFRSQEDADEFYKTFNGQQFNSLEEDVCHLVYV 80

                 ....
gi 818942745 241 ERAE 244
Cdd:cd12718   81 SRVE 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 818942745 263 PKCTVCLERMDESVNGILTTVCNHSFHSQCLQRWEDTTCPVCRY 306
Cdd:cd16457    1 PTCPVCLERMDESVSGILTILCNHSFHCSCLSKWGDSSCPVCRY 44

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 818942745 161 SAMLCILTVPATMTSHDLMKFVAPFYDVIEHMKIIRDSTPNQYMVLIKFRTQADADSFYMACNGRQFNSIEEDVCQLVYV 240
Cdd:cd12718    1 SEMLCMLAVPATLTCHDLLNFLAPVLPSIEHIKIIRDSTPNQYMVLIKFRSQEDADEFYKTFNGQQFNSLEEDVCHLVYV 80

                 ....
gi 818942745 241 ERAE 244
Cdd:cd12718   81 SRVE 84

Zn-finger in ubiquitin-hydrolases and other protein;

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 818942745  318 CFECGVQENLWICLICGHIGCGRYVSRHAYKHFEETQHTYAMQLTNHRVWDYAGDNYVHRLVA 380
Cdd:pfam02148   1 CSLCGNTSNLWLCLTCGHVGCGRYQNSHALEHYEETGHPLAVNLSTLTVYCYPCDDYVHDPSL 63

Ubiquitin Carboxyl-terminal Hydrolase-like zinc finger;

                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|
gi 818942745   317 KCFECGVQENLWICLICGHIGCGRYVSRHAYKHFEETQHTYAMQLTNHRV 366
Cdd:smart00290   1 RCSVCGTIENLWLCLTCGQVGCGRYQNGHALEHFEETGHPLVVKLGTQRV 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 818942745   398 QEEKIDALQLEYSYL------LTS---QLESQRIYWENKIVRIE---KDTAEEINNMKTKFKETIEKCDSLEHKLNDLLK 465
Cdd:TIGR02168  801 LREALDELRAELTLLneeaanLRErleSLERRIAATERRLEDLEeqiEELSEDIESLAAEIEELEELIEELESELEALLN 880

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818942745   466 EKQSLERKCTQLNTKLSKLTSELKEEQEMNKCLRANQLLLQNKLRDeeklLKETCEQKDLQITEIQEQLRDVmFYLEAQ- 544
Cdd:TIGR02168  881 ERASLEEALALLRSELEELSEELRELESKRSELRRELEELREKLAQ----LELRLEGLEVRIDNLQERLSEE-YSLTLEe 955

                          170
                   ....*....|....*....
gi 818942745   545 -----QKINHLPAEARQEI 558
Cdd:TIGR02168  956 aealeNKIEDDEEEARRRL 974

N1R/p28-like protein; Provisional

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818942745 193 KIIRDSTPNQYMVLIKFRTQADAdsFYMACNGRQFNSIEEDVC-QLVYVERAEVFksedgaslpvmDLTELPKCTVCLER 271
Cdd:PHA02929 117 KILKNKPSNDKINYIYMRKEEDM--FYAIINKKGKNYKKFLKTiPSVLSEYEKLY-----------NRSKDKECAICMEK 183

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|.
gi 818942745 272 -----MDESVNGILTTvCNHSFHSQCLQRW--EDTTCPVCR 305
Cdd:PHA02929 184 vydkeIKNMYFGILSN-CNHVFCIECIDIWkkEKNTCPVCR 223

Component of SCF ubiquitin ligase and anaphase-promoting complex [Posttranslational modification, protein turnover, chaperones / Cell division and chromosome partitioning];

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 818942745 255 PVMDLTelPKCTVCLERMDESVngILTTVCNHSFHSQCLQRWEDT--TCPVCR 305
Cdd:COG5194   29 HIMGTC--PECQFGMTPGDECP--VVWGVCNHAFHDHCIYRWLDTkgVCPLDR 77

phosphodiesterase; Provisional

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818942745 424 WENKIVRIEKDTAEEINNMKTKFKETIEKCDSLEHKLNDLLKEKQSLERKCTQLNTKLSKLtSELKEEQEmnkclranql 503
Cdd:PRK12704  66 IHKLRNEFEKELRERRNELQKLEKRLLQKEENLDRKLELLEKREEELEKKEKELEQKQQEL-EKKEEELE---------- 134

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 818942745 504 LLQNKLRDE-EKLLKETCEQ-KDLQITEIQEQLRdvmfyLEAQQKINHLPAEARQE 557
Cdd:PRK12704 135 ELIEEQLQElERISGLTAEEaKEILLEKVEEEAR-----HEAAVLIKEIEEEAKEE 185

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 818942745 161 SAMLCILTVPATMTSHDLMKFVAPFYDVIEHMKIIRDSTPNQYMVLIKFRTQADADSFYMACNGRQFNSIEEDVCQLVYV 240
Cdd:cd12718    1 SEMLCMLAVPATLTCHDLLNFLAPVLPSIEHIKIIRDSTPNQYMVLIKFRSQEDADEFYKTFNGQQFNSLEEDVCHLVYV 80

                 ....
gi 818942745 241 ERAE 244
Cdd:cd12718   81 SRVE 84

RNA recognition motif (RRM) found in BRCA1-associated protein (BRAP2) and similar proteins; This subfamily corresponds to the RRM domain 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. The family also includes RING finger protein ETP1 and its homologs found in fungi. ETP1, also termed BRAP2 homolog, or ethanol tolerance protein 1, is 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. Members in this family contain 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 818942745 164 LCILTVPATMTSHDLMKFVAPFYDVIEHMKIIRDSTP-NQYMVLIKFRTQADADSFYMACNGRQFNSIEEDVCQLVYVER 242
Cdd:cd12437    1 LCILAVPSYMTVADFCQFVGPFIEHISHMRILRDDGPgNRYMVLLRFDSQESADSFYQDFNGKPFSSLEPEVCHVLFVKS 80

                 ..
gi 818942745 243 AE 244
Cdd:cd12437   81 VE 82

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 818942745 263 PKCTVCLERMDESVNGILTTVCNHSFHSQCLQRWEDTTCPVCRY 306
Cdd:cd16457    1 PTCPVCLERMDESVSGILTILCNHSFHCSCLSKWGDSSCPVCRY 44

Ubiquitin Carboxyl-terminal Hydrolase-like zinc finger;

                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|
gi 818942745   317 KCFECGVQENLWICLICGHIGCGRYVSRHAYKHFEETQHTYAMQLTNHRV 366
Cdd:smart00290   1 RCSVCGTIENLWLCLTCGQVGCGRYQNGHALEHFEETGHPLVVKLGTQRV 50

RING finger, H2 subclass, found in TRAF-interacting protein (TRAIP) and similar proteins; TRAIP, also known as RING finger protein 206 (RNF206) or TRIP, is a ubiquitously expressed nucleolar E3 ubiquitin ligase important for cellular proliferation and differentiation. It is found near mitotic chromosomes and functions as a regulator of the spindle assembly checkpoint. TRAIP interacts with tumor necrosis factor (TNF)-receptor-associated factor (TRAF) proteins and inhibits TNF-alpha-mediated nuclear factor (NF)-kappaB activation. It also interacts with two tumor suppressors CYLD and spleen tyrosine kinase (Syk), and DNA polymerase eta, which facilitates translesional synthesis after DNA damage. TRAIP contains an N-terminal C3H2C2-type RING-H2 finger and an extended coiled-coil domain.

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|...
gi 818942745 265 CTVCLERMDESVNgILTTVCNHSFHSQCLQRWEDT--TCPVCR 305
Cdd:cd16480    2 CTICSDFFDNSRD-VAAIHCGHTFHYDCLLQWFDTsrTCPQCR 43

RING finger, H2 subclass, found in Saccharomyces cerevisiae transmembrane E3 ubiquitin-protein ligase 1 (TUL1) and similar proteins; This subfamily includes Saccharomyces cerevisiae TUL1, Schizosaccharomyces pombe DSC E3 ubiquitin ligase complex subunit 1 (DSC1), and Arabidopsis thaliana protein FLYING SAUCER 2 (FLY2). TUL1 is the catalytic component of DSC E3 ubiquitin ligase complexes that tag proteins present in Golgi, endosome and vacuole membranes and function in protein homeostasis under non-stress conditions, and support a role in protein quality control. It mediates ubiquitination of vacuolar proteins such as CPS1, PPN1, PEP12 and other proteins containing exposed hydrophilic residues within their transmembrane domains, leading to their sorting into internal vesicles in late endosomes. TUL1 also targets the unpalmitoylated endosomal SNARE TLG1 to the multivesicular body (MVB) pathway. DSC1, also known as defective for SREBP cleavage protein 1, is the catalytic component of the DSC E3 ubiquitin ligase complex required for the sre1 transcriptional activator proteolytic cleavage to release the soluble transcription factor from the membrane in low oxygen or sterol conditions. FLY2 acts as an E3 ubiquitin-protein ligase that may be involved in xylem development. Members of this subfamily contain a C3H2C3-type RING-H2 finger.

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|
gi 818942745 263 PKCTVCLERMDESVNGI-----LTTVCNHSFHSQCLQRWEDT--TCPVCR 305
Cdd:cd23117    5 VDCVICMSDIELPSTNSvrrdyMVTPCNHIFHTNCLERWMDIklECPTCR 54

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 818942745 265 CTVCLERM-DESVNGILTtvCNHSFHSQCLQRW--EDTTCPVCR 305
Cdd:cd16454    2 CAICLEEFkEGEKVRVLP--CNHLFHKDCIDPWleQHNTCPLCR 43

RING finger, H2 subclass, found in RING finger protein 181 (RNF181) and similar proteins; RNF181, also known as HSPC238, is a platelet E3 ubiquitin-protein ligase containing a C3H2C3-type RING-H2 finger. It interacts with the KVGFFKR motif of platelet integrin alpha(IIb)beta3, suggesting a role for RNF181-mediated ubiquitination in integrin and platelet signaling. It also suppresses the tumorigenesis of hepatocellular carcinoma (HCC) through the inhibition of extracellular signal-regulated kinase/mitogen-activated protein kinase (ERK/MAPK) signaling in the liver.

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*
gi 818942745 264 KCTVCLERMDESVNGILTTvCNHSFHSQCLQRWEDTT--CPVCRY 306
Cdd:cd16669    1 KCPICLLEFEEGETVKQLP-CKHSFHSDCILPWLGKTnsCPLCRH 44

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 818942745   265 CTVCLERMDESVngiLTTVCNHSFHSQCLQRW---EDTTCPVC 304
Cdd:smart00184   1 CPICLEEYLKDP---VILPCGHTFCRSCIRKWlesGNNTCPIC 40

RING finger, H2 subclass, found in autocrine motility factor receptor (AMFR) and similar proteins; AMFR, also known as AMF receptor, or RING finger protein 45, or ER-protein gp78, is an internalizing cell surface glycoprotein localized in both plasma membrane caveolae and the endoplasmic reticulum (ER). It is involved in the regulation of cellular adhesion, proliferation, motility and apoptosis, as well as in the process of learning and memory. AMFR also functions as a RING finger-dependent ubiquitin protein ligase (E3) implicated in the degradation from the ER. AMFR contains an N-terminal RING-H2 finger and a C-terminal ubiquitin-associated (UBA)-like CUE domain.

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....
gi 818942745 264 KCTVCLERMDESvngiLTTVCNHSFHSQCLQRW--EDTTCPVCR 305
Cdd:cd16455    2 DCAICWESMQSA----RKLPCGHLFHNSCLRSWleQDTSCPTCR 41

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

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818942745   399 EEKIDALQLEYSYL--LTSQLESQRIYWENKIVRIEKdtaeEINNMKTKFKETIEKCDSLEHKLNDLLKEKQSLERkctq 476
Cdd:TIGR02169  818 EQKLNRLTLEKEYLekEIQELQEQRIDLKEQIKSIEK----EIENLNGKKEELEEELEELEAALRDLESRLGDLKK---- 889

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|
gi 818942745   477 lntKLSKLTSELKEEQEmnkclRANQLLLQ-NKLRDEEKLLKETCEQKDLQITEIQEQLR 535
Cdd:TIGR02169  890 ---ERDELEAQLRELER-----KIEELEAQiEKKRKRLSELKAKLEALEEELSEIEDPKG 941

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 818942745 265 CTVCLERMdESVNGILTTVCNHSFHSQCLQRW--EDTTCPVCR 305
Cdd:cd16460    3 CVICHEAF-SDGDRLLVLPCAHKFHTQCIGPWldGQQTCPTCR 44

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 818942745 264 KCTVCLERMDESVNGILTTV-CNHSFHSQCLQRWEDTT---CPVCR 305
Cdd:cd23114    6 ECSICLETMKPGSGHAIFTAeCSHSFHFECIAGNVRHGnlrCPVCR 51

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.

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|...
gi 818942745 265 CTVCLERMDEsvngiLTTVCNHSFHSQCLQRWED--TTCPVCR 305
Cdd:cd16545    3 CCICMDRKAD-----LILPCAHSYCQKCIDKWSDrhRTCPICR 40

RING finger, H2 subclass, found in RING finger proteins RNF126, RNF115, and similar proteins; This subfamily includes RING finger proteins RNF126, RNF115, 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). 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. 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; this inhibition increases the efficacy of metformin in breast cancer cells. It also functions as a cofactor 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. RNF115 and 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. Both of them contain an N-terminal BCA2 Zinc-finger domain (BZF), AKT-phosphorylation sites, and a C-terminal C3H2C3-type RING-H2 finger.

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*
gi 818942745 265 CTVCLERM--DESVngiLTTVCNHSFHSQCLQRW--EDTTCPVCR 305
Cdd:cd16667    2 CAVCKEDFevGEEV---RQLPCKHLFHPDCIVPWleLHNSCPVCR 43

RING finger, H2 subclass, found in E3 ubiquitin-protein ligase RNF6 and similar proteins; RNF6 is an androgen receptor (AR)-associated protein that induces AR ubiquitination and promotes AR transcriptional activity. RNF6-induced ubiquitination may regulate AR transcriptional activity and specificity by modulating cofactor recruitment. RNF6 is overexpressed in hormone-refractory human prostate cancer tissues and required for prostate cancer cell growth under androgen-depleted conditions. Moreover, RNF6 regulates local serine/threonine kinase LIM kinase 1 (LIMK1) levels in axonal growth cones. RNF6-induced LIMK1 polyubiquitination is mediated via K48 of ubiquitin and leads to proteasomal degradation of the kinase. RNF6 also binds and upregulates the Inha promoter, and functions as a transcription regulatory protein in the mouse sertoli cell. RNF6 also acts as a potential tumor suppressor gene involved in the pathogenesis of esophageal squamous cell carcinoma (ESCC). RNF6 contains an N-terminal coiled-coil domain, a Lys-X-X-Leu/Ile-X-X-Leu/Ile (KIL) motif, and a C-terminal C3H2C3-type RING-H2 finger which is responsible for its ubiquitin ligase activity. The KIL motif is present in a subset of RING-H2 proteins from organisms as evolutionarily diverse as human, mouse, chicken, Drosophila, Caenorhabditis elegans, and Arabidopsis thaliana.

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|...
gi 818942745 265 CTVCLERMDESvNGILTTVCNHSFHSQCLQRW--EDTTCPVCR 305
Cdd:cd16673    3 CSVCINEYATG-NKLRRLPCAHEFHIHCIDRWlsENSTCPICR 44

RING finger, H2 subclass, found in RING finger protein 167 (RNF167) and similar proteins; RNF167, also known as RING105, is an endosomal/lysosomal E3 ubiquitin-protein ligase involved in alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid receptor (AMPAR) ubiquitination. It ubiquitinates AMPA-type glutamate receptor subunit GluA2 and regulates its surface expression, and thus acts as a selective regulator of AMPAR-mediated neurotransmission. It acts as an endosomal membrane protein which ubiquitylates vesicle-associated membrane protein 3 (VAMP3) and regulates endosomal trafficking. Moreover, RNF167 plays a role in the regulation of TSSC5 (tumor-suppressing subchromosomal transferable fragment cDNA, also known as ORCTL2/IMPT1/BWR1A/SLC22A1L), which can function in concert with the ubiquitin-conjugating enzyme UbcH6. RNF167 is widely conserved in metazoans and contains an N-terminal signal peptide, a protease-associated (PA) domain, two transmembrane domains (TM1 and TM2), and a C-terminal C3H2C3-type RING-H2 finger domain followed by a putative PEST sequence.

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....
gi 818942745 265 CTVCLERMDESvNGILTTVCNHSFHSQCLQRW---EDTTCPVCR 305
Cdd:cd16797    3 CAICLDEYEEG-DKLRVLPCSHAYHSKCVDPWltqTKKTCPVCK 45

RING finger, H2 subclass, found in synoviolin and similar proteins; Synoviolin, also known as synovial apoptosis inhibitor 1 (Syvn1), Hrd1, or Der3, is an endoplasmic reticulum (ER)-anchoring E3 ubiquitin ligase that functions as a suppressor of ER stress-induced apoptosis and plays a role in homeostasis maintenance. It also targets tumor suppressor gene p53 for proteasomal degradation, suggesting crosstalk between ER associated degradation (ERAD) and p53 mediated apoptotic pathway under ER stress. Moreover, synoviolin controls body weight and mitochondrial biogenesis through negative regulation of the thermogenic coactivator peroxisome proliferator-activated receptor coactivator (PGC)-1beta. It upregulates amyloid beta production by targeting a negative regulator of gamma-secretase, Retention in endoplasmic reticulum 1 (Rer1), for degradation. It is also involved in the degradation of endogenous immature nicastrin, and affects amyloid beta-protein generation. Moreover, synoviolin is highly expressed in rheumatoid synovial cells and may be involved in the pathogenesis of rheumatoid arthritis (RA). It functions as an anti-apoptotic factor that is responsible for the outgrowth of synovial cells during the development of RA. It promotes inositol-requiring enzyme 1 (IRE1) ubiquitination and degradation in synovial fibroblasts with collagen-induced arthritis. Furthermore, the upregulation of synoviolin may represent a protective response against neurodegeneration in Parkinson's disease (PD). In addition, synoviolin is involved in liver fibrogenesis. Synoviolin contains a C3H2C2-type RING-H2 finger.

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|...
gi 818942745 265 CTVCLERMDESVNGIlttVCNHSFHSQCLQRW--EDTTCPVCR 305
Cdd:cd16479    4 CIICREEMTVGAKKL---PCGHIFHLSCLRSWlqRQQTCPTCR 43

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 818942745 260 TELPKCTVCLERMdESVNGILTTVCNHSFHSQCLQRWEDT--TCPVCR 305
Cdd:cd16680    5 SEQTLCVVCFSDF-ESRQLLRVLPCNHEFHTKCVDKWLKTnrTCPICR 51

Modified RING finger, H2 subclass (C3H2C2D-type), found in zinc finger SWIM domain-containing protein 2 (ZSWIM2) and similar proteins; ZSWIM2, also known as MEKK1-related protein X (MEX) or ZZ-type zinc finger-containing protein 2, is a testis-specific E3 ubiquitin ligase that promotes death receptor-induced apoptosis through Fas, death receptor (DR) 3 and DR4 signaling. ZSWIM2 is self-ubiquitinated and targeted for degradation through the proteasome pathway. It acts as an E3 ubiquitin ligase, through the E2, Ub-conjugating enzymes UbcH5a, UbcH5c, or UbcH6. ZSWIM2 contains four putative zinc-binding domains including an N-terminal SWIM (SWI2/SNF2 and MuDR) domain critical for its ubiquitination, and two modified RING-H2 fingers separated by a ZZ zinc finger domain, which was required for interaction with UbcH5a and its self-association. This model corresponds to the second RING-H2 finger, which is not a canonical C3H2C3-type, but a modified C3H2C2D-type.

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*
gi 818942745 264 KCTVCLERMDESvNGILTTVCNHSFHSQCLQRW---EDTTCPVCR 305
Cdd:cd16486    1 QCRICLKAFQLG-QHVRTLPCRHKFHRDCIDNWllhSRNSCPIDG 44

RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs).

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 818942745 164 LCILTVPATMTSHDLMKFVAPFYDvIEHMKIIRDST-PNQYMVLIKFRTQADADSFYMACNGRQFN 228
Cdd:cd00590    1 LFVGNLPPDTTEEDLRELFSKFGE-VVSVRIVRDRDgKSKGFAFVEFESPEDAEKALEALNGTELG 65

RING finger, H2 subclass, found in RING finger protein 128 (RNF128) and similar proteins; This subfamily includes RING finger proteins RNF128, RNF133, RNF148, and similar proteins, which belong to a larger PA-TM-RING ubiquitin ligase family that has been characterized by containing an N-terminal signal peptide, a protease-associated (PA) domain, a transmembrane (TM) domain and a C-terminal C3H2C3-type RING-H2 finger followed by a putative PEST sequence. RNF128, also known as gene related to anergy in lymphocytes protein (GRAIL), is a type 1 transmembrane E3 ubiquitin-protein ligase that is a critical regulator of adaptive immunity and development. It inhibits cytokine gene transcription, is expressed in anergic CD4+ T cells, and has been implicated in primary T cell activation, survival, and differentiation, as well as in T cell anergy and oral tolerance. It induces T cell anergy through the ubiquitination activity of its cytosolic RING finger. It regulates expression of the costimulatory molecule CD40L on CD4 T cells, and ubiquitinates the costimulatory molecule CD40 ligand (CD40L) during the induction of T cell anergy. Moreover, RNF128 interacts with the luminal/extracellular portion of both CD151 and the related tetraspanin CD81 via its PA domain, which promoted ubiquitination of cytosolic lysine residues. It also down-modulates the expression of CD83 (previously described as a cell surface marker for mature dendritic cells) on CD4 T cells. Furthermore, Rho guanine dissociation inhibitor (RhoGDI) has been identified as a potential substrate of RNF128, suggesting a role for Rho effector molecules in T cell anergy. In addition, RNF128 plays a role in environmental stress responses. It promotes environmental salinity tolerance in euryhaline tilapia. RNF133 is a testis-specific endoplasmic reticulum-associated E3 ubiquitin ligase that is mainly present in the cytoplasm of elongated spermatids. It may play a role in sperm maturation through an ER-associated degradation (ERAD) pathway. RNF148 is a testis-specific E3 ubiquitin ligase that is abundantly expressed in testes and slightly expressed in pancreas. Its expression is regulated by histone deacetylases.

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*
gi 818942745 265 CTVCLERMDES-VNGILTtvCNHSFHSQCLQRW--EDTTCPVCRY 306
Cdd:cd16802    3 CAVCIEPYKPNdVVRILT--CNHLFHKNCIDPWllEHRTCPMCKC 45

Component of SCF ubiquitin ligase and anaphase-promoting complex [Posttranslational modification, protein turnover, chaperones / Cell division and chromosome partitioning];

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 818942745 255 PVMDLTelPKCTVCLERMDESVngILTTVCNHSFHSQCLQRWEDT--TCPVCR 305
Cdd:COG5194   29 HIMGTC--PECQFGMTPGDECP--VVWGVCNHAFHDHCIYRWLDTkgVCPLDR 77

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.

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*.
gi 818942745 265 CTVCLERMDESVngilTTVCNHSFHSQCLQRW-----EDTTCPVCR 305
Cdd:cd16534    3 CNICLDTASDPV----VTMCGHLFCWPCLYQWletrpDRQTCPVCK 44

helix-rich Mycoplasma protein; Members of this family occur strictly within a subset of Mycoplasma species. Members average 750 amino acids in length, including signal peptide. Sequences are predicted (Jpred 3) to be almost entirely alpha-helical. These sequences show strong periodicity (consistent with long alpha helical structures) and low complexity rich in D,E,N,Q, and K. Genes encoding these proteins are often found in tandem. The function is unknown.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818942745  425 ENKIVRIEKD--TAE-EINNMKTKFKETIEKCDSLEHKLNDLLKEKQSLERKCTQLNTKLSKLTSELKEEQEMNKCLRAN 501
Cdd:TIGR04523  39 EKKLKTIKNElkNKEkELKNLDKNLNKDEEKINNSNNKIKILEQQIKDLNDKLKKNKDKINKLNSDLSKINSEIKNDKEQ 118

                          90       100
                  ....*....|....*....|....*....
gi 818942745  502 QLLLQNKLRDEEKLLKETCEQKDLQITEI 530
Cdd:TIGR04523 119 KNKLEVELNKLEKQKKENKKNIDKFLTEI 147

RING finger, H2 subclass, found in rice E3 ubiquitin-protein ligase EL5 and similar proteins; EL5, also known as protein ELICITOR 5, is an E3 ubiquitin-protein ligase containing an N-terminal transmembrane domain and a C3H2C3-type RING-H2 finger that is a binding site for ubiquitin-conjugating enzyme (E2). It can be rapidly induced by N-acetylchitooligosaccharide elicitor. EL5 catalyzes polyubiquitination via the Lys48 residue of ubiquitin, and thus plays a crucial role as a membrane-anchored E3 in the maintenance of cell viability after the initiation of root primordial formation in rice. It also acts as an anti-cell death enzyme that might be responsible for mediating the degradation of cytotoxic proteins produced in root cells after the actions of phytohormones. Moreover, EL5 interacts with UBC5b, a rice ubiquitin carrier protein, through its RING-H2 finger. EL5 is an unstable protein, and its degradation is regulated by the C3H2C3-type RING-H2 finger in a proteasome-independent manner.

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|...
gi 818942745 265 CTVCLERMDESVNGILTTVCNHSFHSQCLQRW--EDTTCPVCR 305
Cdd:cd16461    2 CAICLSDYENGEELRRLPECKHAFHKECIDEWlkSNSTCPLCR 44

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 818942745 264 KCTVCLERMDESVngilTTVCNHSFHSQCL-QRWEDTT----CPVCRYC 307
Cdd:cd16607    3 SCPICLDYLKDPV----TINCGHNFCRSCIsMSWKDLQdtfpCPVCRFC 47

Uncharacterized protein, contains DUF3084 domain [Function unknown];

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818942745 433 KDTAEEINNMKTKFKETIEKCDSLEHKLNDLLKEKQSLERKCTQLNTKLSKLTSELKEEQEMNKCLRANQLLLQ---NKL 509
Cdd:COG4372   55 EQAREELEQLEEELEQARSELEQLEEELEELNEQLQAAQAELAQAQEELESLQEEAEELQEELEELQKERQDLEqqrKQL 134

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|..
gi 818942745 510 RDEEKLLKETCEQKDLQITEIQEQLRDVMFYLEA--QQKINHLPAEARQEIQ 559
Cdd:COG4372  135 EAQIAELQSEIAEREEELKELEEQLESLQEELAAleQELQALSEAEAEQALD 186

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 818942745 264 KCTVCLE--RMDESVNGIlttVCNHSFHSQCLQRWED--TTCPVCR 305
Cdd:cd16800    2 ECPVCKEdyTVGEQVRQL---PCNHFFHSDCIVPWLElhDTCPVCR 44