Ty3/Gypsy family of RNase HI in long-term repeat retroelements; Ribonuclease H (RNase H) enzymes are divided into two major families, Type 1 and Type 2, based on amino acid sequence similarities and biochemical properties. RNase H is an endonuclease that cleaves the RNA strand of an RNA/DNA hybrid in a sequence non-specific manner in the presence of divalent cations. RNase H is widely present in various organisms, including bacteria, archaea and eukaryotes. RNase HI has also been observed as adjunct domains to the reverse transcriptase gene in retroviruses, in long-term repeat (LTR)-bearing retrotransposons and non-LTR retrotransposons. RNase HI in LTR retrotransposons perform degradation of the original RNA template, generation of a polypurine tract (the primer for plus-strand DNA synthesis), and final removal of RNA primers from newly synthesized minus and plus strands. The catalytic residues for RNase H enzymatic activity, three aspartatic acids and one glutamic acid residue (DEDD), are unvaried across all RNase H domains. Phylogenetic patterns of RNase HI of LTR retroelements is classified into five major families, Ty3/Gypsy, Ty1/Copia, Bel/Pao, DIRS1 and the vertebrate retroviruses. Ty3/Gypsy family widely distributed among the genomes of plants, fungi and animals. RNase H inhibitors have been explored as an anti-HIV drug target because RNase H inactivation inhibits reverse transcription.

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1937310627 1091 FLHCDASDFGIGAVLVQLDDQGQERPIAYMSKKLNSAQRNYSVTERECLAAMEAIKRFRCYLEMQEFEVITDHSSLLWLM 1170
Cdd:cd09274      1 ILETDASDYGIGAVLSQEDDDGKERPIAFFSRKLTPAERNYSTTEKELLAIVWALKKFRHYLLGRPFTVYTDHKALKYLL 80

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|.
gi 1937310627 1171 RQPDLSGRLARWVFKLQSYNFSISHRKGKDNVVPDALSRIP 1211
Cdd:cd09274     81 TQKDLNGRLARWLLLLSEFDFEIEYRPGKENVVADALSRLP 121

RING finger (Really Interesting New Gene) domain and U-box domain superfamily; 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). C4C4-, C3HC3D-, C2H2C4-, and C3HC5-type RING fingers are closely related to RING-HC fingers. In contrast, C4HC3- (RING-CH alias RINGv), C3H3C2-, C3H2C2D-, C3DHC3-, and C4HC2H-type RING fingers are more closely related to RING-H2 fingers. However, not all RING finger-containing proteins display regular RING finger features, and the RING finger family has turned out to be multifarious. The degenerate RING fingers of the Siz/PIAS RING (SP-RING) family proteins and sporulation protein RMD5, are characterized by lacking the second, fifth, and sixth Zn2+ ion-coordinating residues. They bind only one Zn2+ ion. On the other hand, the RING fingers of the human APC11 and RBX1 proteins can bind a third Zn atom since they harbor four additional Zn ligands. U-box is a modified form of the RING finger domain that lacks metal chelating Cys and His residues. It resembles the cross-brace RING structure consisting of three beta-sheets and a single alpha-helix, which would be stabilized by salt bridges instead of chelated metal ions. U-box proteins are widely distributed among eukaryotic organisms and show a higher prevalence in plants than in other organisms. RING finger/U-box-containing proteins are 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 enable efficient transfer of ubiquitin from E2 to the substrates.

                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....
gi 1937310627   27 VCHVCTETMVEGDDCLIIhECSHAFHRSCIESHLSTSSECPVCK 70
Cdd:cd16454      1 TCAICLEEFKEGEKVRVL-PCNHLFHKDCIDPWLEQHNTCPLCR 43

IS481 family transposase; null

                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1937310627 1397 QEFLQKhIFHVYGVP-EFIVSDNGSQFRAN--DFNAFLTVNGINHTYTALYSPQSNAS-ERVNRSLiagIRAFLKTDH 1470
Cdd:NF033577   174 ADFLRR-AFAEHGIPiRRVLTDNGSEFRSRahGFELALAELGIEHRRTRPYHPQTNGKvERFHRTL---KDEFAYARP 247

DNA repair protein rad18; All proteins in this family for which functions are known are involved in nucleotide excision repair.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1937310627   28 CHVCTETMvegdDCLIIHECSHAFHRSCIESHLSTSSECPVCKRACRLCDLRR-LVINANAATF---RPTIKKkgrgaMA 103
Cdd:TIGR00599   29 CHICKDFF----DVPVLTSCSHTFCSLCIRRCLSNQPKCPLCRAEDQESKLRSnWLVSEIVESFknlRPSLLE-----FL 99

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1937310627  104 RTYNTRSTSNRNLFQESDPSNTGETSMslgNEPENTQLATNDiLLDTTGNNNNRINSPIQNPEHLIRTPSNNN 176
Cdd:TIGR00599  100 RIPKTTPVENPDLAGPENSSKIELIEE---SESDGVDAEDED-LQRSATSSRALAARSTADILQLSSDPSKRN 168

Ty3/Gypsy family of RNase HI in long-term repeat retroelements; Ribonuclease H (RNase H) enzymes are divided into two major families, Type 1 and Type 2, based on amino acid sequence similarities and biochemical properties. RNase H is an endonuclease that cleaves the RNA strand of an RNA/DNA hybrid in a sequence non-specific manner in the presence of divalent cations. RNase H is widely present in various organisms, including bacteria, archaea and eukaryotes. RNase HI has also been observed as adjunct domains to the reverse transcriptase gene in retroviruses, in long-term repeat (LTR)-bearing retrotransposons and non-LTR retrotransposons. RNase HI in LTR retrotransposons perform degradation of the original RNA template, generation of a polypurine tract (the primer for plus-strand DNA synthesis), and final removal of RNA primers from newly synthesized minus and plus strands. The catalytic residues for RNase H enzymatic activity, three aspartatic acids and one glutamic acid residue (DEDD), are unvaried across all RNase H domains. Phylogenetic patterns of RNase HI of LTR retroelements is classified into five major families, Ty3/Gypsy, Ty1/Copia, Bel/Pao, DIRS1 and the vertebrate retroviruses. Ty3/Gypsy family widely distributed among the genomes of plants, fungi and animals. RNase H inhibitors have been explored as an anti-HIV drug target because RNase H inactivation inhibits reverse transcription.

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1937310627 1091 FLHCDASDFGIGAVLVQLDDQGQERPIAYMSKKLNSAQRNYSVTERECLAAMEAIKRFRCYLEMQEFEVITDHSSLLWLM 1170
Cdd:cd09274      1 ILETDASDYGIGAVLSQEDDDGKERPIAFFSRKLTPAERNYSTTEKELLAIVWALKKFRHYLLGRPFTVYTDHKALKYLL 80

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|.
gi 1937310627 1171 RQPDLSGRLARWVFKLQSYNFSISHRKGKDNVVPDALSRIP 1211
Cdd:cd09274     81 TQKDLNGRLARWLLLLSEFDFEIEYRPGKENVVADALSRLP 121

Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1937310627  837 VLKPN--KVRLC----LDARKVNAVTIK-------DAYPLPNIEGIFARLPKANLITKLDLKDAYWQIALDDKSKSLTAF 903
Cdd:pfam00078    1 IPKKGkgKYRPIsllsIDYKALNKIIVKrlkpenlDSPPQPGFRPGLAKLKKAKWFLKLDLKKAFDQVPLDELDRKLTAF 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1937310627  904 TVP----------GRPLYQFVVMPFGLCNAPQTMCRLMDEI---IPPDLRHCVFGYLDDLVIVSEDFETHLEILVRIASQ 970
Cdd:pfam00078   81 TTPpininwngelSGGRYEWKGLPQGLVLSPALFQLFMNELlrpLRKRAGLTLVRYADDILIFSKSEEEHQEALEEVLEW 160

                          170       180
                   ....*....|....*....|....*....
gi 1937310627  971 FRKANLTLNISKSKFC--VTSVNYLGFVI 997
Cdd:pfam00078  161 LKESGLKINPEKTQFFlkSKEVKYLGVTL 189

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 1937310627   27 VCHVCTETMVEGDDCLIIhECSHAFHRSCIESHLSTSSECPVCK 70
Cdd:cd16454      1 TCAICLEEFKEGEKVRVL-PCNHLFHKDCIDPWLEQHNTCPLCR 43

Retropepsins; pepsin-like aspartate proteases; The family includes pepsin-like aspartate proteases from retroviruses, retrotransposons and retroelements, as well as eukaryotic dna-damage-inducible proteins (DDIs), and bacterial aspartate peptidases. While fungal and mammalian pepsins are bilobal proteins with structurally related N and C-terminals, retropepsins are half as long as their fungal and mammalian counterparts. The monomers are structurally related to one lobe of the pepsin molecule and retropepsins function as homodimers. The active site aspartate occurs within a motif (Asp-Thr/Ser-Gly), as it does in pepsin. Retroviral aspartyl protease is synthesized as part of the POL polyprotein that contains an aspartyl protease, a reverse transcriptase, RNase H, and an integrase. The POL polyprotein undergoes specific enzymatic cleavage to yield the mature proteins. In aspartate peptidases, Asp residues are ligands of an activated water molecule in all examples where catalytic residues have been identified. This group of aspartate peptidases is classified by MEROPS as the peptidase family A2 (retropepsin family, clan AA), subfamily A2A.

                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1937310627  619 LLDTGANISCLGSDLAEiDFSKFPCYTKCKHYVKTADGHLQSVCGW-LDVEIFFKDQSKTLKLFIIPSISQRLILGIDF 696
Cdd:cd00303     13 LVDSGASVNFISESLAK-KLGLPPRLLPTPLKVKGANGSSVKTLGViLPVTIGIGGKTFTVDFYVLDLLSYDVILGRPW 90

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 1937310627    28 CHVCTETMvegDDCLIIHECSHAFHRSCIESHLSTSS-ECPVC 69
Cdd:smart00184    1 CPICLEEY---LKDPVILPCGHTFCRSCIRKWLESGNnTCPIC 40

Retrotransposon gag protein; Gag or Capsid-like proteins from LTR retrotransposons. There is a central motif QGXXEXXXXXFXXLXXH that is common to Retroviridae gag-proteins, but is poorly conserved.

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1937310627  306 HILLTGKARDWyWRYHKQ---VQSVNWDDFCDALRCQYRQYKSSFDIREEIRNRKQkPGESFDSFFDSVLVIMDRLPA-P 381
Cdd:pfam03732    4 VHSLRGAALTW-WKSLVArsiDAFDSWDELKDAFLKRFFPSIRKDLLRNELRSLRQ-GTESVREYVERFKRLARQLPHhG 81

                           90
                   ....*....|....*.
gi 1937310627  382 MSDSELIEILARNLRP 397
Cdd:pfam03732   82 RDEEALISAFLRGLRP 97

DNA repair protein rad18; All proteins in this family for which functions are known are involved in nucleotide excision repair.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1937310627   28 CHVCTETMvegdDCLIIHECSHAFHRSCIESHLSTSSECPVCKRACRLCDLRR-LVINANAATF---RPTIKKkgrgaMA 103
Cdd:TIGR00599   29 CHICKDFF----DVPVLTSCSHTFCSLCIRRCLSNQPKCPLCRAEDQESKLRSnWLVSEIVESFknlRPSLLE-----FL 99

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1937310627  104 RTYNTRSTSNRNLFQESDPSNTGETSMslgNEPENTQLATNDiLLDTTGNNNNRINSPIQNPEHLIRTPSNNN 176
Cdd:TIGR00599  100 RIPKTTPVENPDLAGPENSSKIELIEE---SESDGVDAEDED-LQRSATSSRALAARSTADILQLSSDPSKRN 168

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

                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*
gi 1937310627   28 CHVCTETMVEGDDC-LIIHECSHAFHRSCIESHLSTSSECPVCKR 71
Cdd:COG5194     34 CPECQFGMTPGDECpVVWGVCNHAFHDHCIYRWLDTKGVCPLDRQ 78

Ty3/Gypsy family of RNase HI in long-term repeat retroelements; Ribonuclease H (RNase H) enzymes are divided into two major families, Type 1 and Type 2, based on amino acid sequence similarities and biochemical properties. RNase H is an endonuclease that cleaves the RNA strand of an RNA/DNA hybrid in a sequence non-specific manner in the presence of divalent cations. RNase H is widely present in various organisms, including bacteria, archaea and eukaryotes. RNase HI has also been observed as adjunct domains to the reverse transcriptase gene in retroviruses, in long-term repeat (LTR)-bearing retrotransposons and non-LTR retrotransposons. RNase HI in LTR retrotransposons perform degradation of the original RNA template, generation of a polypurine tract (the primer for plus-strand DNA synthesis), and final removal of RNA primers from newly synthesized minus and plus strands. The catalytic residues for RNase H enzymatic activity, three aspartatic acids and one glutamic acid residue (DEDD), are unvaried across all RNase H domains. Phylogenetic patterns of RNase HI of LTR retroelements is classified into five major families, Ty3/Gypsy, Ty1/Copia, Bel/Pao, DIRS1 and the vertebrate retroviruses. Ty3/Gypsy family widely distributed among the genomes of plants, fungi and animals. RNase H inhibitors have been explored as an anti-HIV drug target because RNase H inactivation inhibits reverse transcription.

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1937310627 1091 FLHCDASDFGIGAVLVQLDDQGQERPIAYMSKKLNSAQRNYSVTERECLAAMEAIKRFRCYLEMQEFEVITDHSSLLWLM 1170
Cdd:cd09274      1 ILETDASDYGIGAVLSQEDDDGKERPIAFFSRKLTPAERNYSTTEKELLAIVWALKKFRHYLLGRPFTVYTDHKALKYLL 80

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|.
gi 1937310627 1171 RQPDLSGRLARWVFKLQSYNFSISHRKGKDNVVPDALSRIP 1211
Cdd:cd09274     81 TQKDLNGRLARWLLLLSEFDFEIEYRPGKENVVADALSRLP 121

RNase H-like domain found in reverse transcriptase;

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1937310627 1060 WTEEAQKAFENVKLLLTSAPVLTNPDFRKKFFLHCDASDFGIGAVLVQLDDQGQERPIAYMSKKLNSAQRNYSVTERECL 1139
Cdd:pfam17919    1 WTEECQKAFEKLKQALTSAPVLAHPDPDKPFILETDASDYGIGAVLSQEDDDGGERPIAYASRKLSPAERNYSTTEKELL 80

                           90       100
                   ....*....|....*....|
gi 1937310627 1140 AAMEAIKRFRCYLEMQEFEV 1159
Cdd:pfam17919   81 AIVFALKKFRHYLLGRKFTV 100

RT_ZFREV_like: A subfamily of reverse transcriptases (RTs) found in sequences similar to the intact endogenous retrovirus ZFERV from zebrafish and to Moloney murine leukemia virus RT. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs. Phylogenetic analysis suggests that ZFERV belongs to a distinct group of retroviruses.

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1937310627  794 PIKSRFYPVSPAVEKLMYGELDRMLALGVIEPSTSPWSSPMRLVLKPN--KVRLCLDARKVNAVTIKDAYPLPNIEGIFA 871
Cdd:cd03715      1 PVNQKQYPLPREAREGITPHIQELLEAGILVPCQSPWNTPILPVKKPGgnDYRMVQDLRLVNQAVLPIHPAVPNPYTLLS 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1937310627  872 RLP-KANLITKLDLKDAYWQIALDDKSKSLTAFTVPGRPlYQFVVMPFGLCNAPqTMC-----RLMDEIIPPDLRHCVFG 945
Cdd:cd03715     81 LLPpKHQWYTVLDLANAFFSLPLAPDSQPLFAFEWEGQQ-YTFTRLPQGFKNSP-TLFhealaRDLAPFPLEHEGTILLQ 158

                          170       180       190       200       210
                   ....*....|....*....|....*....|....*....|....*....|..
gi 1937310627  946 YLDDLVIVSEDFETHLEILVRIASQFRKANLTLNISKSKFCVTSVNYLGFVI 997
Cdd:cd03715    159 YVDDLLLAADSEEDCLKGTDALLTHLGELGYKVSPKKAQICRAEVKFLGVVW 210

RT_DIRS1: Reverse transcriptases (RTs) occurring in the DIRS1 group of retransposons. Members of the subfamily include the Dictyostelium DIRS-1, Volvox carteri kangaroo, and Panagrellus redivivus PAT elements. These elements differ from LTR and conventional non-LTR retrotransposons. They contain split direct repeat (SDR) termini, and have been proposed to integrate via double-stranded closed-circle DNA intermediates assisted by an encoded recombinase which is similar to gamma-site-specific integrase.

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1937310627  882 LDLKDAYWQIALDDKSKSLTAFTVPGRPlYQFVVMPFGLCNAPqtmcRLMDEIIPPDLRHC------VFGYLDDLVIVSE 955
Cdd:cd03714      1 VDLKDAYFHIPILPRSRDLLGFAWQGET-YQFKALPFGLSLAP----RVFTKVVEALLAPLrllgvrIFSYLDDLLIIAS 75

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*
gi 1937310627  956 DfETHLEILVRI--ASQFRKANLTLNISKSKFCVT-SVNYLGFVI 997
Cdd:cd03714     76 S-IKTSEAVLRHlrATLLANLGFTLNLEKSKLGPTqRITFLGLEL 119

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 1937310627   27 VCHVCTETMVEGDDCLIIhECSHAFHRSCIESHLSTSSECPVCK 70
Cdd:cd16454      1 TCAICLEEFKEGEKVRVL-PCNHLFHKDCIDPWLEQHNTCPLCR 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 1937310627   28 CHVCTETMVEGDDCLIIHECSHAFHRSCIESHLSTSSECPVC 69
Cdd:cd16461      2 CAICLSDYENGEELRRLPECKHAFHKECIDEWLKSNSTCPLC 43

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 1937310627   27 VCHVCTETMVEGDDcLIIHECSHAFHRSCIESHLS-TSSECPVCKR 71
Cdd:cd16797      2 VCAICLDEYEEGDK-LRVLPCSHAYHSKCVDPWLTqTKKTCPVCKQ 46

RING finger, H2 subclass, found in Arabidopsis thaliana MED25-binding RING-H2 protein (MBR) and similar proteins; This subfamily includes MBR1 and MBR2 (also called HAL3-interacting protein 1 or AtHIP1). They are E3 ubiquitin-protein ligases that function as regulators of MED25 stability by targeting MED25 for degradation in a RING-H2-dependent manner. Proteasome-dependent degradation of MED25 seems to activate its function as a positive regulator of FLOWERING LOCUS T (FT) and is important to induce the expression of FT, and consequently to promote flowering. MBR2 may also function downstream of HAL3 and be required for HAL3-regulated plant growth. Activation of MBR2 by HAL3 may lead to the degradation of cell cycle suppressors, resulting in enhancement of cell division and plant growth. Both MBR1 and MBR2 contain a C3H2C3-type RING-H2 finger.

                           10        20        30        40
                   ....*....|....*....|....*....|....*....|...
gi 1937310627   28 CHVCTETMVEGDDCLIIhECSHAFHRSCIESHLSTSSECPVCK 70
Cdd:cd23113      5 CCICQEEYEEGDELGTI-ECGHEYHSDCIKQWLVQKNLCPICK 46

RING finger, H2 subclass, found in RING finger protein 43 (RNF43) and similar proteins; RNF43 is a transmembrane E3 ubiquitin-protein ligase that plays an important role in frizzled (FZD)-dependent regulation of the Wnt/beta-catenin pathway. It functions as a tumor suppressor that inhibits Wnt/beta-catenin signaling by ubiquitinating FZD receptor and targeting it to the lysosomal pathway for degradation. miR-550a-5p directly targeted the 3'-UTR of gene RNF43 and regulated its expression. Moreover, RNF43 interacts with NEDD-4-like ubiquitin-protein ligase-1 (NEDL1) and regulates p53-mediated transcription. It may also be involved in cell growth control through the interaction with HAP95, a chromatin-associated protein interfacing the nuclear envelope. Mutations of RNF43 have been identified in various tumors, including colorectal cancer (CRC), endometrial cancer, mucinous ovarian tumors, gastric adenocarcinoma, pancreatic ductal adenocarcinoma, liver fluke-associated cholangiocarcinoma, hepatocellular carcinoma, and glioma. RNF43 contains an N-terminal signal peptide, a protease-associated (PA) domain, a transmembrane (TM) domain and a C3H2C3-type RING-H2 finger followed by a long C-terminal region.

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                   ....*....|....*....|....*....|....*....|...
gi 1937310627   27 VCHVCTETMVEGDDCLIIhECSHAFHRSCIESHLSTSSECPVC 69
Cdd:cd16798      5 VCAICLEEFSEGQELRII-SCSHEFHRECVDPWLHQHRTCPLC 46

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

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                   ....*....|....*....|....*....|....*....|...
gi 1937310627   28 CHVCTETMVEGDDCLIIhECSHAFHRSCIESHLSTSSECPVCK 70
Cdd:cd16474      3 CTICLSDFEEGEDVRRL-PCMHLFHQECVDQWLSTNKRCPICR 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.

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                   ....*....|....*....|....*....|....*....|...
gi 1937310627   28 CHVCTETMVegdDCLIIHECSHAFHRSCIESHL-STSSECPVC 69
Cdd:pfam00097    1 CPICLEEPK---DPVTLLPCGHLFCSKCIRSWLeSGNVTCPLC 40

Retrotransposon gag protein; Gag or Capsid-like proteins from LTR retrotransposons. There is a central motif QGXXEXXXXXFXXLXXH that is common to Retroviridae gag-proteins, but is poorly conserved.

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                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1937310627  306 HILLTGKARDWyWRYHKQ---VQSVNWDDFCDALRCQYRQYKSSFDIREEIRNRKQkPGESFDSFFDSVLVIMDRLPA-P 381
Cdd:pfam03732    4 VHSLRGAALTW-WKSLVArsiDAFDSWDELKDAFLKRFFPSIRKDLLRNELRSLRQ-GTESVREYVERFKRLARQLPHhG 81

                           90
                   ....*....|....*.
gi 1937310627  382 MSDSELIEILARNLRP 397
Cdd:pfam03732   82 RDEEALISAFLRGLRP 97

RING finger, H2 subclass, found in Tetratricopeptide repeat protein 3 (TTC3) and similar proteins; TTC3, also known as protein DCRR1, TPR repeat protein D, TPR repeat protein 3, or RING finger protein 105 (RNF105), is an E3 ubiquitin-protein ligase encoded by a gene within the Down syndrome (DS) critical region on chromosome 21. It affects differentiation and Golgi compactness in neurons through specific actin-regulating pathways. It inhibits the neuronal-like differentiation of pheocromocytoma cells by activating RhoA and by binding to Citron proteins. TTC3 is an Akt-specific E3 ligase that binds to phosphorylated Akt and facilitates its ubiquitination and degradation within the nucleus. It contains four N-terminal TPR motifs, a potential coiled-coil region and a Citron binding region in the central part, and a C-terminal C3H2C2-type RING-H2 finger.

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                   ....*....|....*....|....*....|....*....|....*
gi 1937310627   27 VCHVCTETMVEGDDCLIihECSHAFHRSCIESHLSTSSECPVCKR 71
Cdd:cd16481      1 PCIICHDDLKPDQLAKL--ECGHIFHKECIKQWLKEQSTCPTCRV 43

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

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                   ....*....|....*....|....*....|....*....|....*
gi 1937310627   28 CHVCTETMVEGDDcLIIHECSHAFHRSCIESHLSTSSECPVCKRA 72
Cdd:cd23118      3 CTICLEDFEDGEK-LRVLPCQHQFHSECVDQWLRRNPKCPVCRRD 46

IS3 family transposase;

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                   ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1937310627 1402 KHIFHVYGVPE--FIVSDNGSQFRANDFNAFLTVNGINHTYTALYSPQSNA-SERVNRSL 1458
Cdd:NF033516   265 EMAIEWRGKPEglILHSDNGSQYTSKAYREWLKEHGITQSMSRPGNCWDNAvAESFFGTL 324

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.

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                   ....*....|....*....|....*....|....*....|....
gi 1937310627   28 CHVCTETMVEGDDClIIHECSHAFHRSCIES-HLSTSSECPVCK 70
Cdd:cd16448      1 CVICLEEFEEGDVV-RLLPCGHVFHLACILRwLESGNNTCPLCR 43

RING finger, H2 subclass, found in Arabidopsis thaliana RING-type E3 ubiquitin transferase BIG BROTHER (BB) and similar proteins; BB (also known as protein ENHANCER OF DA1-1 or EOD1) is an E3 ubiquitin-protein ligase that limits organ size, and possibly seed size, in a dose-dependent manner. It negatively regulates the duration of cell proliferation in leaves and petals independently of the major phytohormones (e.g. auxin, cytokinin, gibberellin, brassinosteroids, ethylene, abscisic acid, jasmonic acid), probably by targeting growth stimulators for degradation. It limits the proliferation of root meristematic cells. BB polyubiquitinates DA1. It is involved in the promotion of leaf senescence, in addition to its function in restricting plant growth. BB-related is an E3 ubiquitin-ligase probably involved in organ size regulation. Members of this subfamily contain a C3H2C3-type RING-H2 finger.

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                   ....*....|....*....|....*....|....*....|...
gi 1937310627   28 CHVCTETMVEGDDCLIIhECSHAFHRSCIESHLSTSSECPVCK 70
Cdd:cd23115      7 CVICRLEYEEGEDLLTL-PCKHCYHSECIQQWLQINKVCPVCS 48

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.

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                   ....*....|....*....|....*....|....*....|...
gi 1937310627   28 CHVCTETMVEGDDCLIIhECSHAFHRSCIESHLSTSSECPVCK 70
Cdd:cd16669      2 CPICLLEFEEGETVKQL-PCKHSFHSDCILPWLGKTNSCPLCR 43

RING finger, H2 subclass, found in RING finger proteins RNF24, RNF122, and similar proteins; This subfamily includes RNF24, RNF122, and similar proteins. RNF24 is an intrinsic membrane protein localized in the Golgi apparatus. It specifically interacts with the ankyrin-repeats domains (ARDs) of TRPC1, -3, -4, -5, -6, and -7, and affects TRPC intracellular trafficking without affecting their activity. RNF122 is a RING finger protein associated with HEK 293T cell viability. It is localized to the endoplasmic reticulum (ER) and the Golgi apparatus, and overexpressed in anaplastic thyroid cancer cells. RNF122 functions as an E3 ubiquitin ligase that can ubiquitinate itself and undergo degradation through its RING finger in a proteasome-dependent manner. Both RNF24 and RNF122 contain an N-terminal transmembrane domain and a C-terminal C3H2C3-type RING-H2 finger.

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                   ....*....|....*....|....*....|....*....|....*.
gi 1937310627   27 VCHVCTETMVEGDDcLIIHECSHAFHRSCIESHLSTSSECPVCKRA 72
Cdd:cd16469      2 TCAVCLEEFKLKEE-LGVCPCGHAFHTKCLKKWLEVRNSCPICKSP 46

RING finger, HC subclass, found in Polycomb Group RING finger homologs (PCGF1, 2, 3, 4, 5 and 6), and similar proteins; This subfamily includes six Polycomb Group (PcG) RING finger homologs (PCGF1/NSPc1, PCGF2/Mel-18, PCGF3, PCGF4/BMI1, PCGF5, and PCGF6/MBLR) that use epigenetic mechanisms to maintain or repress expression of their target genes. They were first discovered in fruit flies and are well known for silencing Hox genes through modulation of chromatin structure during embryonic development. PCGF homologs play important roles in cell proliferation, differentiation, and tumorigenesis. They all have been found to associate with ring finger protein 2 (RNF2). The RNF2-PCGF heterodimer is catalytically competent as an E3 ubiquitin transferase and is the scaffold for the assembly of additional components. Moreover, PCGF homologs are critical components in the assembly of distinct Polycomb Repression Complex 1 (PRC1) related complexes which is involved in the maintenance of gene repression and which target different genes through distinct mechanisms. The Drosophila PRC1 core complex is formed by the Polycomb (Pc), Polyhomeotic (Ph), Posterior sex combs (Psc), and Sex combs extra (Sce, also known as Ring) subunits. In mammals, the composition of PRC1 is much more diverse and varies depending on the cellular context. All PRC1 complexes contain homologs of the Drosophila Ring protein. Ring1A/RNF1 and Ring1B/RNF2 are E3 ubiquitin ligases that mark lysine 119 of histone H2A with a single ubiquitin group (H2AK119ub). Mammalian homologs of the Drosophila Psc protein, such as PCGF2/Mel-18 or PCGF4/BMI1, regulate PRC1 enzymatic activity. PRC1 complexes can be divided into at least two classes according to the presence or absence of CBX proteins, which are homologs of Drosophila Pc. Canonical PRC1 complexes contain CBX proteins that recognize and bind H3K27me3, the mark deposited by PRC2. Therefore, canonical PRC1 complexes and PRC2 can act together to repress gene transcription and maintain this repression through cell division. Non-canonical PRC1 complexes, containing RYBP (together with additional proteins, such as L3mbtl2 or Kdm2b) rather than the CBX proteins have recently been described in mammals. PCGF homologs contain a C3HC4-type RING-HC finger.

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                   ....*....|....*....|....*....|....*....|...
gi 1937310627   27 VCHVCTETMVegdDCLIIHECSHAFHRSCIESHLSTSSECPVC 69
Cdd:cd16525      2 TCSLCKGYLI---DATTITECLHSFCKSCIVRHLETSKNCPVC 41

RING finger, H2 subclass, found in RING finger protein 11 (RNF11) and similar proteins; RNF11 is an E3 ubiquitin-protein ligase that acts both as an adaptor and a modulator of itch-mediated control of ubiquitination events underlying membrane traffic. It acts downstream of an enzymatic cascade for the ubiquitination of specific substrates. It is also a molecular adaptor of homologous to E6-associated protein C-terminus (HECT)-type ligases. RNF11 has been implicated in the regulation of several signaling pathways. It enhances transforming growth factor receptor (TGFR) signaling by both abrogating Smurf2-mediated receptor ubiquitination and by promoting the Smurf2-mediated degradation of AMSH (associated molecule with the SH3 domain of STAM), a de-ubiquitinating enzyme that enhances TGF-beta signaling and epidermal growth factor receptor (EGFR) endosomal recycling. It also acts directly on Smad4 to enhance Smad4 function, and plays a role in prolonged TGF-beta signaling. RNF11 also functions as a critical component of the A20 ubiquitin-editing protein complex that negatively regulates tumor necrosis factor (TNF)-mediated nuclear factor (NF)-kappaB activation. It interacts with Smad anchor for receptor activation (SARA) and the endosomal sorting complex required for transport (ESCRT)-0 complex, thus participating in the regulation of lysosomal degradation of EGFR. RNF11 acts as a novel GGA cargo actively participating in regulating the ubiquitination of the GGA protein family. RNF11 functions together with TAX1BP1 to target TANK-binding kinase 1 (TBK1)/IkappaB kinase IKKi, and further restricts antiviral signaling and type I interferon (IFN)-beta production. RNF11 contains an N-terminal PPPY motif that binds WW domain-containing proteins such as AIP4/itch, Nedd4 and Smurf1/2 (SMAD-specific E3 ubiquitin-protein ligase 1/2), and a C-terminal C3H2C3-type RING-H2 finger that functions as a scaffold for the coordinated transfer of ubiquitin to substrate proteins together with the E2 enzymes UbcH527 and Ubc13.

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                   ....*....|....*....|....*....|....*....|...
gi 1937310627   28 CHVCTETMVEGDdCLIIHECSHAFHRSCIESHLSTSSECPVCK 70
Cdd:cd16468      2 CVICMADFVVGD-PIRYLPCMHIYHVDCIDDWLMRSFTCPSCM 43

Integrase core domain; Integrase mediates integration of a DNA copy of the viral genome into the host chromosome. Integrase is composed of three domains. The amino-terminal domain is a zinc binding domain pfam02022. This domain is the central catalytic domain. The carboxyl terminal domain that is a non-specific DNA binding domain pfam00552. The catalytic domain acts as an endonuclease when two nucleotides are removed from the 3' ends of the blunt-ended viral DNA made by reverse transcription. This domain also catalyzes the DNA strand transfer reaction of the 3' ends of the viral DNA to the 5' ends of the integration site.

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                   ....*....|....*....|....*....|....*....|....*....|....*...
gi 1937310627 1389 RKFTSNLIQEFLQKHIFHVYGVPEFIVSDNGSQFRANDFNAFLTVNGINHTYTALYSP 1446
Cdd:pfam00665   41 SEMDAELVLDALERAIAFRGGVPLIIHSDNGSEYTSKAFREFLKDLGIKPSFSRPGNP 98