Modified RING finger, HC subclass (C3HC3D-type), found in SR-related and CTD-associated factor 11 (SCAF11) and similar proteins; SCAF11, also known as CTD-associated SR protein 11 (CASP11), renal carcinoma antigen NY-REN-40, SC35-interacting protein 1 (Sip1), Serine/arginine-rich splicing factor 2 (SRSF2)-interacting protein, or splicing regulatory protein 129 (SRrp129), is a novel arginine-serine-rich (RS) domain-containing protein essential for pre-mRNA splicing. It functions as an auxiliary splice factor interacting with the spliceosomal component SC35, promoting RNAPII elongation. In addition to SR proteins, such as SC35, ASF/SF2, SRp75, and SRp20, SCAF11 also associates with U1-70K and U2AF65, proteins associated with 5' and 3' splice sites, respectively. SCAF11 contains an N-terminal modified C3HC3D-type RING-HC finger, an internal serine-arginine rich domain (SR domain), and a C-terminal SRI domain.

                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|..
gi 2462535617   55 DRCPICLNCLLEKEVGFPESCNHVFCMTCILKWAETLASCPIDRKPFQAVFK 106
Cdd:cd16636      1 DRCPICLNCLLEQEVAFPENCSHVFCLTCILKWAETVTSCPIDRKPFQAVYK 52

transcription termination factor Rho; Provisional

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462535617  774 PSSDLADEKVETVSQPSESPKDTIDKTKKPRTRRSRFHSPSTTWSPNKDTPQEKKRPQSPSPRRETGKESRKSQSPSPKN 853
Cdd:PRK12678    68 ATPAAPAAAARRAARAAAAARQAEQPAAEAAAAKAEAAPAARAAAAAAAEAASAPEAAQARERRERGEAARRGAARKAGE 147

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462535617  854 ESARGRKKSRSQSPKKDIARERRQSQSRSPKRDTTRESRRSEslsprRETSRENKRSQPRVKDSSPGEKSRSQSRERESD 933
Cdd:PRK12678   148 GGEQPATEARADAAERTEEEERDERRRRGDREDRQAEAERGE-----RGRREERGRDGDDRDRRDRREQGDRREERGRRD 222

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462535617  934 RDGQRRERERrtrkwsrsrshsrspsrcrtkskSSSFGRIDRDSYSPRWKGRWANDGWRCPRGNDRYRKNDPEKQNENTR 1013
Cdd:PRK12678   223 GGDRRGRRRR-----------------------RDRRDARGDDNREDRGDRDGDDGEGRGGRRGRRFRDRDRRGRRGGDG 279

                          250
                   ....*....|..
gi 2462535617 1014 KEKNDIHLDADD 1025
Cdd:PRK12678   280 GNEREPELREDD 291

Modified RING finger, HC subclass (C3HC3D-type), found in SR-related and CTD-associated factor 11 (SCAF11) and similar proteins; SCAF11, also known as CTD-associated SR protein 11 (CASP11), renal carcinoma antigen NY-REN-40, SC35-interacting protein 1 (Sip1), Serine/arginine-rich splicing factor 2 (SRSF2)-interacting protein, or splicing regulatory protein 129 (SRrp129), is a novel arginine-serine-rich (RS) domain-containing protein essential for pre-mRNA splicing. It functions as an auxiliary splice factor interacting with the spliceosomal component SC35, promoting RNAPII elongation. In addition to SR proteins, such as SC35, ASF/SF2, SRp75, and SRp20, SCAF11 also associates with U1-70K and U2AF65, proteins associated with 5' and 3' splice sites, respectively. SCAF11 contains an N-terminal modified C3HC3D-type RING-HC finger, an internal serine-arginine rich domain (SR domain), and a C-terminal SRI domain.

                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|..
gi 2462535617   55 DRCPICLNCLLEKEVGFPESCNHVFCMTCILKWAETLASCPIDRKPFQAVFK 106
Cdd:cd16636      1 DRCPICLNCLLEQEVAFPENCSHVFCLTCILKWAETVTSCPIDRKPFQAVYK 52

Ring finger domain;

                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....
gi 2462535617   55 DRCPICLNCLLEKEVGFPESCNHVFCMTCILKWAETLASCPIDR 98
Cdd:pfam13639    1 DECPICLEEFEEGDKVVVLPCGHHFHRECLDKWLRSSNTCPLCR 44

U2 snRNP auxilliary factor, large subunit, splicing factor; These splicing factors consist of an N-terminal arginine-rich low complexity domain followed by three tandem RNA recognition motifs (pfam00076). The well-characterized members of this family are auxilliary components of the U2 small nuclear ribonuclearprotein splicing factor (U2AF). These proteins are closely related to the CC1-like subfamily of splicing factors (TIGR01622). Members of this subfamily are found in plants, metazoa and fungi.

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462535617  837 RETGKESRKSQSPSPKNESARGRKKSRSQSPKKDIARERRQSQSRSPKRDTTRESRRSESLSPRRETSRENKRSQP--RV 914
Cdd:TIGR01642    3 EEPDREREKSRGRDRDRSSERPRRRSRDRSRFRDRHRRSRERSYREDSRPRDRRRYDSRSPRSLRYSSVRRSRDRPrrRS 82

                           90       100
                   ....*....|....*....|
gi 2462535617  915 KDSSPGEKSRSQSRERESDR 934
Cdd:TIGR01642   83 RSVRSIEQHRRRLRDRSPSN 102

Arginine/Serine-Rich protein 1; RSRP1 is an eukaryotic protein family. Its function is unknown.

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462535617  771 NNMPSSDLADEKVETVSQPSESPKDTIDKTKKPRTRRSRFHSPSTTWSPNKDTPQEKK-RPQSPSPRRETGKESRKSQSP 849
Cdd:pfam17069    6 NDMWPGSPQEKKSPSTSSSGSSSRLSSRSRSRSSSRSSRSHSRSSSRFSSRSRSRPRRsRSRSRSRRRHQRKYRRYSRSY 85

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462535617  850 SPKNESARGRKksrsqspkkdIARERRQSQSRSPKRDTTRESRRSESLSPRRET------SRENKRSQPRVKDSSPGEKS 923
Cdd:pfam17069   86 SRSRSRSRRRR----------YYRRSRYRYSRRYYRSPSRSRSRSRSRSRGRSYyaiwrgSRYYGFGRTVYPERSPRWRS 155

                   ....*..
gi 2462535617  924 RSQSRER 930
Cdd:pfam17069  156 RSRTRSR 162

zinc finger-like protein; Provisional

                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2462535617   52 SEADRCPICLNCLLEKEV------GFPESCNHVFCMTCILKW----AETLAS--CPIDRKPFQAV 104
Cdd:PHA02926   168 SKEKECGICYEVVYSKRLendryfGLLDSCNHIFCITCINIWhrtrRETGASdnCPICRTRFRNI 232

Modified RING finger, HC subclass (C3HC3D-type), found in SR-related and CTD-associated factor 11 (SCAF11) and similar proteins; SCAF11, also known as CTD-associated SR protein 11 (CASP11), renal carcinoma antigen NY-REN-40, SC35-interacting protein 1 (Sip1), Serine/arginine-rich splicing factor 2 (SRSF2)-interacting protein, or splicing regulatory protein 129 (SRrp129), is a novel arginine-serine-rich (RS) domain-containing protein essential for pre-mRNA splicing. It functions as an auxiliary splice factor interacting with the spliceosomal component SC35, promoting RNAPII elongation. In addition to SR proteins, such as SC35, ASF/SF2, SRp75, and SRp20, SCAF11 also associates with U1-70K and U2AF65, proteins associated with 5' and 3' splice sites, respectively. SCAF11 contains an N-terminal modified C3HC3D-type RING-HC finger, an internal serine-arginine rich domain (SR domain), and a C-terminal SRI domain.

                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|..
gi 2462535617   55 DRCPICLNCLLEKEVGFPESCNHVFCMTCILKWAETLASCPIDRKPFQAVFK 106
Cdd:cd16636      1 DRCPICLNCLLEQEVAFPENCSHVFCLTCILKWAETVTSCPIDRKPFQAVYK 52

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 2462535617   55 DRCPICLnCLLEKEVGFPESCNHVFCMTCILKWAETLASCPIDRKPF 101
Cdd:cd16574      2 SSCPICL-DRFENEKAFLDGCFHAFCFTCILEWSKVKNECPLCKQPF 47

N1R/p28-like protein; Provisional

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462535617    1 MIVSIFSNketlFQREMKKKTVCTLNMgdkKYEDMEGEENG---------------DNTISTGL-----LY--SEADRCP 58
Cdd:PHA02929   106 KVLSIINE----YNQKILKNKPSNDKI---NYIYMRKEEDMfyaiinkkgknykkfLKTIPSVLseyekLYnrSKDKECA 178

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|...
gi 2462535617   59 ICLNCLLEKEV-----GFPESCNHVFCMTCILKWAETLASCPIDRKPFQAVFK 106
Cdd:PHA02929   179 ICMEKVYDKEIknmyfGILSNCNHVFCIECIDIWKKEKNTCPVCRTPFISVIK 231

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.

                           10        20        30        40
                   ....*....|....*....|....*....|....*....|...
gi 2462535617   57 CPICLNCLLEKEVGFPESCNHVFCMTCILKWAETL-ASCPIDR 98
Cdd:cd16448      1 CVICLEEFEEGDVVRLLPCGHVFHLACILRWLESGnNTCPLCR 43

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.

                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*
gi 2462535617   57 CPICLNCLLEKevgFPESCNHVFCMTCILKW-AETLASCPIDRKP 100
Cdd:cd16643      4 CPICLMALREP---VQTPCGHRFCKACILKSiREAGHKCPVDNEP 45

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.

                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*...
gi 2462535617   56 RCPICLNcLLEKEVGFPesCNHVFCMTCILKWAETLASCPIDRKPFQA 103
Cdd:cd23147      6 KCPICLS-LFKSAANLS--CNHCFCAGCIGESLKLSAICPVCKIPATR 50

splicing factor, CC1-like family; This model represents a subfamily of RNA splicing factors including the Pad-1 protein (N. crassa), CAPER (M. musculus) and CC1.3 (H.sapiens). These proteins are characterized by an N-terminal arginine-rich, low complexity domain followed by three (or in the case of 4 H. sapiens paralogs, two) RNA recognition domains (rrm: pfam00706). These splicing factors are closely related to the U2AF splicing factor family (TIGR01642). A homologous gene from Plasmodium falciparum was identified in the course of the analysis of that genome at TIGR and was included in the seed.

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462535617  837 RETGKESRKSQSPSPKNESARGRKKSRSQSPKKDIARERRQSQSRSPKRDTTRESR--------RSESLSPRRETSRENK 908
Cdd:TIGR01622    7 RERLRDSSSAGDRDRRRDKGRERSRDRSRDRERSRSRRRDRHRDRDYYRGRERRSRsrrpnrryRPREKRRRRGDSYRRR 86

                           90       100
                   ....*....|....*....|....*..
gi 2462535617  909 RSQPRVKDSSPGEKSRSQSRERESDRD 935
Cdd:TIGR01622   87 RDDRRSRREKPRARDGTPEPLTEDERD 113

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.

                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*....
gi 2462535617   57 CPICLNcLLEKEVGFPesCNHVFCMTCILK-WAET---LASCPIDRKPF 101
Cdd:cd16604      3 CPICLD-LLKDPVTLP--CGHSFCMGCLGAlWGAGrggRASCPLCRQTF 48

RING-H2 zinc finger domain; There are 8 cysteine/ histidine residues which are proposed to be the conserved residues involved in zinc binding. The protein, of which this domain is the conserved region, participates in diverse functions relevant to chromosome metabolism and cell cycle control.

                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*
gi 2462535617   55 DRCPICLNCLLEK--EVGFPES---------CNHVFCMTCILKWAETLASCPIDR 98
Cdd:pfam12678    1 DTCAICRNPFMEPcpECQAPGDdecpvvwgeCGHAFHLHCISRWLKTNNTCPLCR 55

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

                           10        20        30        40
                   ....*....|....*....|....*....|....*....|...
gi 2462535617   56 RCPICLNcLLEKEVGFPesCNHVFCMTCILKWAETL-ASCPID 97
Cdd:cd16449      2 ECPICLE-RLKDPVLLP--CGHVFCRECIRRLLESGsIKCPIC 41

RING finger, H2 subclass, found in anaphase-promoting complex subunit 11 (APC11) and similar proteins; APC11, also known as cyclosome subunit 11, or hepatocellular carcinoma-associated RING finger protein, is a C3H2C3-type RING-H2 protein that facilitates ubiquitin chain formation by recruiting ubiquitin-charged ubiquitin conjugating enzymes (E2) through its RING-H2 domain. APC11 and its partner, the cullin-like subunit APC2, form the dynamic catalytic core of the gigantic, multisubunit 1.2-MDa anaphase-promoting complex/cyclosome (APC), also known as the cyclosome, which is a ubiquitin-protein ligase (E3) composed of at least 12 subunits and controls cell division by ubiquitinating cell cycle regulators, such as cyclin B and securin, to drive their timely degradation. APC11 can be inhibited by hydrogen peroxide, which may contribute to the delay in cell cycle progression through mitosis that is characteristic of cells subjected to oxidative stress. APC11 contains a canonical RING-H2-finger that coordinate two Zn2+ ions. In addition, it contains a third Zn2+-binding site that is not essential for its ligase activity.

                           10        20        30
                   ....*....|....*....|....*....|.
gi 2462535617   75 CNHVFCMTCILKWAETLAS---CPIDRKPFQ 102
Cdd:cd16456     32 CSHCFHMHCILKWLNSQQVqqhCPMCRQEWK 62

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 2462535617   57 CPICLNCLlEKEVGFPesCNHVFCMTCILKWAETLASCPIDR 98
Cdd:cd16561      5 CSICLEDL-NDPVKLP--CDHVFCEECIRQWLPGQMSCPLCR 43

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 2462535617   53 EADRCPICLNCLLEKEVGFPESCNHVFCMTCILKW-AETLASCPIDRKP 100
Cdd:cd16473      3 ECEECAICLENYQNGDLLRGLPCGHVFHQNCIDVWlERDNHCCPVCRWP 51

transcriptional regulator ICP4; Provisional

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462535617  773 MPSSDLADEKVETVSQPSESP---KDTIDKTKKPRTRRSRFHSPSTTWSPNKDTPqekkRPQSPSPRRETGKESRKSQSP 849
Cdd:PHA03307   223 APGRSAADDAGASSSDSSSSEssgCGWGPENECPLPRPAPITLPTRIWEASGWNG----PSSRPGPASSSSSPRERSPSP 298

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462535617  850 SPKNESARGR------KKSRSQSPKKDIARERRQSQSR-----SPKRDTTReSRRSESLSPRRETSRENKRSQPRVKDSS 918
Cdd:PHA03307   299 SPSSPGSGPApsspraSSSSSSSRESSSSSTSSSSESSrgaavSPGPSPSR-SPSPSRPPPPADPSSPRKRPRPSRAPSS 377

                          170
                   ....*....|..
gi 2462535617  919 PGEKSRSQSRER 930
Cdd:PHA03307   378 PAASAGRPTRRR 389

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.

                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*...
gi 2462535617   56 RCPICLNcLLEKEVGFPesCNHVFCMTCILKWAETLASCPIDRKPFQA 103
Cdd:cd16719      6 KCKLCGK-VLEEPLSTP--CGHVFCAGCLLPWAVQRRLCPLQCQPIAA 50

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 2462535617   57 CPICLNCLLEKEVGFPESCNHVFCMTCILKWAETLASCPIDR 98
Cdd:cd16669      2 CPICLLEFEEGETVKQLPCKHSFHSDCILPWLGKTNSCPLCR 43

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 2462535617   56 RCPICLNCLLEKE-VGFPESCNHVFCMTCILKWAETLASCPIDR 98
Cdd:cd16461      1 ECAICLSDYENGEeLRRLPECKHAFHKECIDEWLKSNSTCPLCR 44

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.

                           10        20        30        40
                   ....*....|....*....|....*....|....*....|.
gi 2462535617   57 CPICLNCLleKEVGFPESCNHVFCMTCILKWAETLA-SCPI 96
Cdd:pfam00097    1 CPICLEEP--KDPVTLLPCGHLFCSKCIRSWLESGNvTCPL 39

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.

                           10        20        30
                   ....*....|....*....|....*....|....*..
gi 2462535617   60 CLNCLLEKEVGFPESCNHVFCMTCILKWAETLASCPI 96
Cdd:cd23135      6 CSICFSEIRSGAILKCGHFFCLSCIASWLREKSTCPL 42

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).

                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|
gi 2462535617   57 CPICLNCLLEkevgfP---ESCNHVFCMTCIL-KWAETLASCPIDRKPFQ 102
Cdd:cd16544      5 CPVCQEVLKD-----PvelPPCRHIFCKACILlALRSSGARCPLCRGPVG 49

T-DNA border endonuclease VirD2;

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462535617  744 QNESEVEPSVNADLKQMNENSVTHCSENNMPSSDLADEKVETVSQPSESPKDTIDKTKKPRtRRSRFHSPSTtwSPNKDT 823
Cdd:PRK13863   254 QNESEVRLQEPAGSSIKADARIRVSLESERRAQPSASKIPVADDFGIETSYVAEGDVRKLE-GNSGTPRLAT--EVATHT 330

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462535617  824 PQEkkrpQSPSPRRETGKESRKSQSPSPKNESARGRKKSRSQSP--KKDIARERRQSQSRSPKRDTTRESRRSESLSP-- 899
Cdd:PRK13863   331 TSE----RQQRRKRPRDDEGEPSGAKRTRLNGIAVGPEANAGEQdgRDDPITSPAQPPRSNPLADPVRASIATDSLPAta 406

                          170       180       190
                   ....*....|....*....|....*....|....*..
gi 2462535617  900 RRETSRENKRSQPRVKDSSPGEKSRSQSRERESDRDG 936
Cdd:PRK13863   407 DRQQQREPSSKRPRDDDGEPSIRKRARDGRSQDGREG 443

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.

                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*
gi 2462535617   56 RCPICLNCLLEKeVGFPesCNHVFCMTCILKWAE-TLASCPIDRK 99
Cdd:cd16550      2 LCPICLEILVEP-VTLP--CNHTLCMPCFQSTVEkASLCCPLCRL 43

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

                           10        20
                   ....*....|....*....|....*...
gi 2462535617   75 CNHVFCMTCILKWAETLASCPIDRKPFQ 102
Cdd:COG5194     54 CNHAFHDHCIYRWLDTKGVCPLDRQTWV 81

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.

                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....
gi 2462535617   57 CPICLNCLLEKEVGfpeSCNHVFCMTCILKWAETLAS----CPI 96
Cdd:cd16536      3 CPICLEPPVAPRIT---RCGHIFCWPCILRYLSLSEKkwrkCPI 43

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.

                           10        20        30        40
                   ....*....|....*....|....*....|....*....|
gi 2462535617   57 CPICLNCLLEKEVGfpeSCNHVFCMTCILKWAETLASCPI 96
Cdd:cd16504      5 CPICFDIIKEAFVT---KCGHSFCYKCIVKHLEQKNRCPK 41

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.

                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|.
gi 2462535617   52 SEADRCPICLNCLlekEVGFPESCNHVFCMTCILKWAETLASCPIDRKPFQ 102
Cdd:cd23148      1 DHALRCHICKDLL---KAPMRTPCNHTFCSFCIRTHLNNDARCPLCKAEVT 48

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.

                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*...
gi 2462535617   53 EADRCPICLNCLLEkevgfPES--CNHVFCMTCILKWAE-------TLASCPIDRKPF 101
Cdd:cd16606      1 EEARCPVCLDFLQE-----PVSvdCGHSFCLRCISEFCEksdsaqgGVYACPQCRGPF 53

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.

                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*....
gi 2462535617   57 CPICLNcLLEKEVGFPesCNHVFCMTCI-LKWAETLA--SCPIDRKPFQ 102
Cdd:cd16543      6 CSICLD-LLKDPVTIP--CGHSFCMNCItLLWDRKQGvpSCPQCRESFP 51

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.

                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|...
gi 2462535617   53 EADRCPICLNCLLEkevGFPESCNHVFCMTCILKWAETLA-----SCPIDRKP 100
Cdd:cd16583      4 EEGVCPICQEPLKE---AVSTDCGHLFCRMCLTQHAKKASasgvfSCPVCRKP 53

Anaphase-promoting complex subunit 11 RING-H2 finger; Apc11 is one of the subunits of the anaphase-promoting complex or cyclosome. The APC subunits are cullin family proteins with ubiquitin ligase activity. Polyubiquitination marks proteins for degradation by the 26S proteasome and is carried out by a cascade of enzymes that includes ubiquitin-activating enzymes (E1s), ubiquitin-conjugating enzymes (E2s), and ubiquitin ligases (E3s). Apc11 acts as an E3 enzyme and is responsible for recruiting E2s to the APC and for mediating the subsequent transfer of ubiquitin to APC substrates in vivo. In Saccharomyces cerevisiae this RING-H2 finger protein defines the minimal ubiquitin ligase activity of the APC, and the integrity of the RING-H2 finger is essential for budding yeast cell viability.

                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|.
gi 2462535617   55 DRCPICLNcllekevgfpeSCNHVFCMTCILKWAETLAS---CPIDRKPFQ 102
Cdd:pfam12861   43 DDCPLVWG-----------KCSHNFHMHCILKWLHTETSkglCPMCRQTFK 82

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.

                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*...
gi 2462535617   55 DRCPICLNcllekEVGFP--ESCNHVFCMTCILK-WAETLA----SCPIDRKPFQAVF 105
Cdd:cd16553      2 MECPICLQ-----DARFPveTNCGHLFCGPCIITyWRHGSWlgavSCPVCRQTVTLLL 54

Zinc finger, C3HC4 type (RING finger);

                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....
gi 2462535617   53 EADRCPICLNclLEKEVGF-PesCNH-VFCMTCILKWAETLASCPIDRKPFQAV 104
Cdd:pfam13920    1 EDLLCVICLD--RPRNVVLlP--CGHlCLCEECAERLLRKKKKCPICRQPIESV 50

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.

                           10        20        30        40
                   ....*....|....*....|....*....|....*....|..
gi 2462535617   57 CPICLNCLLEKevgFPESCNHVFCMTCILKWAETLASCPIDR 98
Cdd:cd16637      4 CHICLQPLVEP---LDTPCGHTFCYKCLTNYLKIQQCCPLDR 42