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Conserved domains on  [gi|536165|emb|CAA84922.1|]
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TY2B [Saccharomyces cerevisiae]

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List of domain hits

Name Accession Description Interval E-value
RNase_HI_RT_Ty1 cd09272
Ty1/Copia family of RNase HI in long-term repeat retroelements; Ribonuclease H (RNase H) ...
1621-1757 8.46e-28

Ty1/Copia 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 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. The Ty1/Copia family is 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.


:

Pssm-ID: 260004  Cd Length: 140  Bit Score: 111.79  E-value: 8.46e-28
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 536165   1621 VAISDASYGNQPY-YKSQIGNIFLLNGKVIGGKSTKASLTCTSTTEAEIHAVSEAIPLLNNLSHLVQEL---NKKPIIkg 1696
Cdd:cd09272    1 EGYSDADWAGDPDdRRSTSGYVFFLGGGPISWKSKKQTTVALSSTEAEYIALAEAAKEALWLRRLLEELgipLDGPTT-- 78
                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 536165   1697 LLTDSRSTISIIKStneEKF--RNRFFGTKAMRLRDEVSGNNLYVYYIETKKNIADVMTKPLP 1757
Cdd:cd09272   79 IYCDNQSAIALAKN---PVFhsRTKHIDIRYHFIREKVEKGEIKVEYVPTEDQLADILTKPLP 138
TYA pfam01021
TYA transposon protein; Ty are yeast transposons. A 5.7kb transcript codes for p3 a fusion ...
17-114 5.95e-58

TYA transposon protein; Ty are yeast transposons. A 5.7kb transcript codes for p3 a fusion protein of TYA and TYB. The TYA protein is analogous to the gag protein of retroviruses. TYA a is cleaved to form 46kd protein which can form mature virion like particles.


:

Pssm-ID: 144563  Cd Length: 98  Bit Score: 197.20  E-value: 5.95e-58
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 536165       17 AYASVTSKEVSSNQDPLAVSASNLPEFDRDSTKVNSQQETTPGTSAVPENHHHVSPQPASVPPPQNGQYQQHGMMTPNKA 96
Cdd:pfam01021    1 ACASVTSKEVHTNQDPLDVSASKLPEYDKDSTKANSQQETTPGSSAVPENHHHASPQTAQVPLPQNGPYQQQCMMTPNQA 80
                           90
                   ....*....|....*...
gi 536165       97 MASNWAHYQQPSMMTCSH 114
Cdd:pfam01021   81 NPSGWSVYGHPSMMPYTP 98
RVT_2 super family cl06662
Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually ...
1296-1503 1.27e-34

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. This Pfam entry includes reverse transcriptases not recognized by the pfam00078 model.


The actual alignment was detected with superfamily member pfam07727:

Pssm-ID: 254387  Cd Length: 246  Bit Score: 135.28  E-value: 1.27e-34
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 536165     1296 KKVINSMFIFNKKR--DGT---HKARFVARGDIQHP-----DTYdsdmqSNTVHHYALMTSLSIALDNDYYITQLDISSA 1365
Cdd:pfam07727   13 KKPIGCKWVFKIKYnsDGEierYKARLVAKGFTQKEgidydETF-----SPVAKLTTIRLLLALAAQRGWELHQMDVKTA 87
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 536165     1366 YLYADIKEELYIRPPP---HLGLNDKLLRLRKSLYGLKQSGANWYETIKSYLI------NCCDmqevrgwSCVF-KNSQ- 1434
Cdd:pfam07727   88 FLNGELEEEVYMKQPPgfeDPGKPNKVCRLKKSLYGLKQAPRAWYQKLSSFLLklgfkqSEAD-------PCLFvKKSGg 160
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 536165     1435 --VTICLFVDDMILFSKDLNANEKIITTLKKQYDTKiiNLGesdnEIQYdILGLEIKYQ-------RSKY-MKL----GM 1500
Cdd:pfam07727  161 giIYLLLYVDDILIAGSNDELIDEFKEELSSEFEMK--DLG----ELKY-FLGIEIKRTsggiflsQRKYaKKLlkrfGM 233

                   ...
gi 536165     1501 EKS 1503
Cdd:pfam07727  234 LDC 236
rve pfam00665
Integrase core domain; Integrase mediates integration of a DNA copy of the viral genome into ...
659-778 1.50e-17

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 catalyses the DNA strand transfer reaction of the 3' ends of the viral DNA to the 5' ends of the integration site.


:

Pssm-ID: 250040  Cd Length: 119  Bit Score: 81.61  E-value: 1.50e-17
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 536165      659 EPFQYLHTDIFgPVHHLPKSAPSYFISFTDEKTRFQWVYPLhdRREESILNVFTSILAFIKNQFNARVlVIQMDRGSEYT 738
Cdd:pfam00665    4 RPNELWQMDIT-PIPISSKGGKKYLLVIVDDFSRFVVAYAL--KSKTDAELVFDLLEAALERRGGKPV-TIHSDNGSEFT 79
                           90       100       110       120
                   ....*....|....*....|....*....|....*....|
gi 536165      739 NKTLHKFFTNRGITACYTTTADSRAHGVAERLNRTLLNDC 778
Cdd:pfam00665   80 SKAFQELLKELGIKHSFSRPGNPQDNGVVERFNRTLKEEL 119
gag_pre-integrs pfam13976
GAG-pre-integrase domain; This domain is found associated with retroviral insertion elements ...
574-641 2.84e-06

GAG-pre-integrase domain; This domain is found associated with retroviral insertion elements and lies just upstream of the integrase region on the polyproteins.


:

Pssm-ID: 258228  Cd Length: 67  Bit Score: 46.97  E-value: 2.84e-06
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 536165      574 KLTINNVNKSKSV---NKYPYPLIHRMLGHANFRSIQKSLKKNAVTYLKESDIEwsnastyQCPDCLIGKS 641
Cdd:pfam13976    4 YLDISSVAGPVAAvssSKDESWLWHRRLGHPSFKSLKKLSKKGLVPGLPILKFK-------VCESCQLGKQ 67
 
Name Accession Description Interval E-value
RNase_HI_RT_Ty1 cd09272
Ty1/Copia family of RNase HI in long-term repeat retroelements; Ribonuclease H (RNase H) ...
1621-1757 8.46e-28

Ty1/Copia 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 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. The Ty1/Copia family is 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.


Pssm-ID: 260004  Cd Length: 140  Bit Score: 111.79  E-value: 8.46e-28
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 536165   1621 VAISDASYGNQPY-YKSQIGNIFLLNGKVIGGKSTKASLTCTSTTEAEIHAVSEAIPLLNNLSHLVQEL---NKKPIIkg 1696
Cdd:cd09272    1 EGYSDADWAGDPDdRRSTSGYVFFLGGGPISWKSKKQTTVALSSTEAEYIALAEAAKEALWLRRLLEELgipLDGPTT-- 78
                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 536165   1697 LLTDSRSTISIIKStneEKF--RNRFFGTKAMRLRDEVSGNNLYVYYIETKKNIADVMTKPLP 1757
Cdd:cd09272   79 IYCDNQSAIALAKN---PVFhsRTKHIDIRYHFIREKVEKGEIKVEYVPTEDQLADILTKPLP 138
TYA pfam01021
TYA transposon protein; Ty are yeast transposons. A 5.7kb transcript codes for p3 a fusion ...
17-114 5.95e-58

TYA transposon protein; Ty are yeast transposons. A 5.7kb transcript codes for p3 a fusion protein of TYA and TYB. The TYA protein is analogous to the gag protein of retroviruses. TYA a is cleaved to form 46kd protein which can form mature virion like particles.


Pssm-ID: 144563  Cd Length: 98  Bit Score: 197.20  E-value: 5.95e-58
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 536165       17 AYASVTSKEVSSNQDPLAVSASNLPEFDRDSTKVNSQQETTPGTSAVPENHHHVSPQPASVPPPQNGQYQQHGMMTPNKA 96
Cdd:pfam01021    1 ACASVTSKEVHTNQDPLDVSASKLPEYDKDSTKANSQQETTPGSSAVPENHHHASPQTAQVPLPQNGPYQQQCMMTPNQA 80
                           90
                   ....*....|....*...
gi 536165       97 MASNWAHYQQPSMMTCSH 114
Cdd:pfam01021   81 NPSGWSVYGHPSMMPYTP 98
RVT_2 pfam07727
Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually ...
1296-1503 1.27e-34

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. This Pfam entry includes reverse transcriptases not recognized by the pfam00078 model.


Pssm-ID: 254387  Cd Length: 246  Bit Score: 135.28  E-value: 1.27e-34
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 536165     1296 KKVINSMFIFNKKR--DGT---HKARFVARGDIQHP-----DTYdsdmqSNTVHHYALMTSLSIALDNDYYITQLDISSA 1365
Cdd:pfam07727   13 KKPIGCKWVFKIKYnsDGEierYKARLVAKGFTQKEgidydETF-----SPVAKLTTIRLLLALAAQRGWELHQMDVKTA 87
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 536165     1366 YLYADIKEELYIRPPP---HLGLNDKLLRLRKSLYGLKQSGANWYETIKSYLI------NCCDmqevrgwSCVF-KNSQ- 1434
Cdd:pfam07727   88 FLNGELEEEVYMKQPPgfeDPGKPNKVCRLKKSLYGLKQAPRAWYQKLSSFLLklgfkqSEAD-------PCLFvKKSGg 160
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 536165     1435 --VTICLFVDDMILFSKDLNANEKIITTLKKQYDTKiiNLGesdnEIQYdILGLEIKYQ-------RSKY-MKL----GM 1500
Cdd:pfam07727  161 giIYLLLYVDDILIAGSNDELIDEFKEELSSEFEMK--DLG----ELKY-FLGIEIKRTsggiflsQRKYaKKLlkrfGM 233

                   ...
gi 536165     1501 EKS 1503
Cdd:pfam07727  234 LDC 236
rve pfam00665
Integrase core domain; Integrase mediates integration of a DNA copy of the viral genome into ...
659-778 1.50e-17

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 catalyses the DNA strand transfer reaction of the 3' ends of the viral DNA to the 5' ends of the integration site.


Pssm-ID: 250040  Cd Length: 119  Bit Score: 81.61  E-value: 1.50e-17
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 536165      659 EPFQYLHTDIFgPVHHLPKSAPSYFISFTDEKTRFQWVYPLhdRREESILNVFTSILAFIKNQFNARVlVIQMDRGSEYT 738
Cdd:pfam00665    4 RPNELWQMDIT-PIPISSKGGKKYLLVIVDDFSRFVVAYAL--KSKTDAELVFDLLEAALERRGGKPV-TIHSDNGSEFT 79
                           90       100       110       120
                   ....*....|....*....|....*....|....*....|
gi 536165      739 NKTLHKFFTNRGITACYTTTADSRAHGVAERLNRTLLNDC 778
Cdd:pfam00665   80 SKAFQELLKELGIKHSFSRPGNPQDNGVVERFNRTLKEEL 119
gag_pre-integrs pfam13976
GAG-pre-integrase domain; This domain is found associated with retroviral insertion elements ...
574-641 2.84e-06

GAG-pre-integrase domain; This domain is found associated with retroviral insertion elements and lies just upstream of the integrase region on the polyproteins.


Pssm-ID: 258228  Cd Length: 67  Bit Score: 46.97  E-value: 2.84e-06
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 536165      574 KLTINNVNKSKSV---NKYPYPLIHRMLGHANFRSIQKSLKKNAVTYLKESDIEwsnastyQCPDCLIGKS 641
Cdd:pfam13976    4 YLDISSVAGPVAAvssSKDESWLWHRRLGHPSFKSLKKLSKKGLVPGLPILKFK-------VCESCQLGKQ 67
PRK10263 PRK10263
DNA translocase FtsK; Provisional
9-147 1.63e-05

DNA translocase FtsK; Provisional


Pssm-ID: 236669 [Multi-domain]  Cd Length: 1355  Bit Score: 48.54  E-value: 1.63e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 536165       9 NPHSLHGSAYASVTSKEVSSNQDPLaVSASNLPEFDRDSTKVNSQQETTPGTSAVPENHHHvSPQPASVPPPQNGQYQQH 88
Cdd:PRK10263  720 NPFSLDDFEFSPMKALLDDGPHEPL-FTPIVEPVQQPQQPVAPQQQYQQPQQPVAPQPQYQ-QPQQPVAPQPQYQQPQQP 797
                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 536165      89 GMMTPnkamasNWAHYQQPSmmtcshyQTSPAYYQP-DPHYPLPQYIPPLSTSSPDPIDS 147
Cdd:PRK10263  798 VAPQP------QYQQPQQPV-------APQPQYQQPqQPVAPQPQYQQPQQPVAPQPQDT 844
DUF1421 pfam07223
Protein of unknown function (DUF1421); This family represents a conserved region approximately ...
22-155 2.04e-04

Protein of unknown function (DUF1421); This family represents a conserved region approximately 350 residues long within a number of plant proteins of unknown function.


Pssm-ID: 254110 [Multi-domain]  Cd Length: 357  Bit Score: 44.16  E-value: 2.04e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 536165       22 TSKEVSSNQDPLAV-SASNLPEFDRDSTKVN--SQQETTPGTSAVPeNHHHVSPQPASVPPPQNGQYQQHGMMTPNKA-M 97
Cdd:pfam07223   20 TQKELSKLQLSHEEaQSSEAHSFHVDSTKQPpaPEQVAKHELADAP-LQQVNAALPPAPAPQSPQPDQQQQSQAPPSHqY 98
                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|....*...
gi 536165       98 ASNWAHYQQPSMMTCSHYQTSPAYYQPDPHYPLPQYIPPLSTSSPDPIDSQDQHSEVP 155
Cdd:pfam07223   99 PSQLPPQQVQSVPQQPTPQQEPYYPPPSQPQPPPAQQPQAQQPQPPPQVPQQQQYQSP 156
Amelogenin smart00818
Amelogenins, cell adhesion proteins, play a role in the biomineralisation of teeth; They seem ...
52-160 2.44e-04

Amelogenins, cell adhesion proteins, play a role in the biomineralisation of teeth; They seem to regulate formation of crystallites during the secretory stage of tooth enamel development and are thought to play a major role in the structural organisation and mineralisation of developing enamel. The extracellular matrix of the developing enamel comprises two major classes of protein: the hydrophobic amelogenins and the acidic enamelins. Circular dichroism studies of porcine amelogenin have shown that the protein consists of 3 discrete folding units: the N-terminal region appears to contain beta-strand structures, while the C-terminal region displays characteristics of a random coil conformation. Subsequent studies on the bovine protein have indicated the amelogenin structure to contain a repetitive beta-turn segment and a "beta-spiral" between Gln112 and Leu138, which sequester a (Pro, Leu, Gln) rich region. The beta-spiral offers a probable site for interactions with Ca2+ ions. Muatations in the human amelogenin gene (AMGX) cause X-linked hypoplastic amelogenesis imperfecta, a disease characterised by defective enamel. A 9bp deletion in exon 2 of AMGX results in the loss of codons for Ile5, Leu6, Phe7 and Ala8, and replacement by a new threonine codon, disrupting the 16-residue (Met1-Ala16) amelogenin signal peptide.


Pssm-ID: 197891 [Multi-domain]  Cd Length: 165  Bit Score: 42.08  E-value: 2.44e-04
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 536165        52 SQQetTPGTSAVPEnHHHVSPQPASVP-PPQNGQYQQ--HGMMTPNKAMASNW-AHYQQPSMMTcshYQTSPAYYQP--- 124
Cdd:smart00818   43 SQQ--HPPTHTLQP-HHHIPVLPAQQPvVPQQPLMPVpgQHSMTPTQHHQPNLpQPAQQPFQPQ---PLQPPQPQQPmqp 116
                            90       100       110       120
                    ....*....|....*....|....*....|....*....|....
gi 536165       125 ----DPHYPLPQY--IPPLSTSSPDPIDSQDQHSEVPQA--KTK 160
Cdd:smart00818  117 qppvHPIPPLPPQppLPPMFPMQPLPPLLPDLPLEAWPAtdKTK 160
PTZ00112 PTZ00112
origin recognition complex 1 protein; Provisional
1046-1262 5.87e-03

origin recognition complex 1 protein; Provisional


Pssm-ID: 240274 [Multi-domain]  Cd Length: 1164  Bit Score: 39.97  E-value: 5.87e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 536165    1046 YELENIKttrlGGTEEPYIQRN--SDTNIKYRTTNSTPSIDDR----SPDSDSTTPIISIETKAACDNTP-SIDTDPPEY 1118
Cdd:PTZ00112   78 PDYNQIQ----NNTHDFYIDLNerSKTPIKNNDNVTTPIKANKkekhNLDSSSSSSISSSLTNISFFSSPtSIYSCLSNS 153
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 536165    1119 RSSDHATPNIMPDKSSK-NVTADSILDDLPLPD-LTNKSPTDTSDVSKDIPHIHSRQTNSSLGGMDDSNVLTTTKSKKRS 1196
Cdd:PTZ00112  154 LSSKHSPKVIKENQSTHvNISSDNSPRNKEISNkQLKKQTNVTHTTCYDKMRRSPRNTSTIKNNTNDKNKEKNKEKDKNI 233
                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 536165    1197 LEDNETEIEVSRDTWNNKN---------MRSLEPPRSKKRINLIAAIKGVKSIKPVRTTLRYDEAITYNEDNKEK 1262
Cdd:PTZ00112  234 KKDRDGDKQTKRNSEKSKVqnshfdvriLRSYTKENKKDEKNVVSGIRSSVLLKRKSQCLRKDSYVYSNHQKKAK 308
 
Name Accession Description Interval E-value
RNase_HI_RT_Ty1 cd09272
Ty1/Copia family of RNase HI in long-term repeat retroelements; Ribonuclease H (RNase H) ...
1621-1757 8.46e-28

Ty1/Copia 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 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. The Ty1/Copia family is 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.


Pssm-ID: 260004  Cd Length: 140  Bit Score: 111.79  E-value: 8.46e-28
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 536165   1621 VAISDASYGNQPY-YKSQIGNIFLLNGKVIGGKSTKASLTCTSTTEAEIHAVSEAIPLLNNLSHLVQEL---NKKPIIkg 1696
Cdd:cd09272    1 EGYSDADWAGDPDdRRSTSGYVFFLGGGPISWKSKKQTTVALSSTEAEYIALAEAAKEALWLRRLLEELgipLDGPTT-- 78
                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 536165   1697 LLTDSRSTISIIKStneEKF--RNRFFGTKAMRLRDEVSGNNLYVYYIETKKNIADVMTKPLP 1757
Cdd:cd09272   79 IYCDNQSAIALAKN---PVFhsRTKHIDIRYHFIREKVEKGEIKVEYVPTEDQLADILTKPLP 138
TYA pfam01021
TYA transposon protein; Ty are yeast transposons. A 5.7kb transcript codes for p3 a fusion ...
17-114 5.95e-58

TYA transposon protein; Ty are yeast transposons. A 5.7kb transcript codes for p3 a fusion protein of TYA and TYB. The TYA protein is analogous to the gag protein of retroviruses. TYA a is cleaved to form 46kd protein which can form mature virion like particles.


Pssm-ID: 144563  Cd Length: 98  Bit Score: 197.20  E-value: 5.95e-58
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 536165       17 AYASVTSKEVSSNQDPLAVSASNLPEFDRDSTKVNSQQETTPGTSAVPENHHHVSPQPASVPPPQNGQYQQHGMMTPNKA 96
Cdd:pfam01021    1 ACASVTSKEVHTNQDPLDVSASKLPEYDKDSTKANSQQETTPGSSAVPENHHHASPQTAQVPLPQNGPYQQQCMMTPNQA 80
                           90
                   ....*....|....*...
gi 536165       97 MASNWAHYQQPSMMTCSH 114
Cdd:pfam01021   81 NPSGWSVYGHPSMMPYTP 98
RVT_2 pfam07727
Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually ...
1296-1503 1.27e-34

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. This Pfam entry includes reverse transcriptases not recognized by the pfam00078 model.


Pssm-ID: 254387  Cd Length: 246  Bit Score: 135.28  E-value: 1.27e-34
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 536165     1296 KKVINSMFIFNKKR--DGT---HKARFVARGDIQHP-----DTYdsdmqSNTVHHYALMTSLSIALDNDYYITQLDISSA 1365
Cdd:pfam07727   13 KKPIGCKWVFKIKYnsDGEierYKARLVAKGFTQKEgidydETF-----SPVAKLTTIRLLLALAAQRGWELHQMDVKTA 87
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 536165     1366 YLYADIKEELYIRPPP---HLGLNDKLLRLRKSLYGLKQSGANWYETIKSYLI------NCCDmqevrgwSCVF-KNSQ- 1434
Cdd:pfam07727   88 FLNGELEEEVYMKQPPgfeDPGKPNKVCRLKKSLYGLKQAPRAWYQKLSSFLLklgfkqSEAD-------PCLFvKKSGg 160
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 536165     1435 --VTICLFVDDMILFSKDLNANEKIITTLKKQYDTKiiNLGesdnEIQYdILGLEIKYQ-------RSKY-MKL----GM 1500
Cdd:pfam07727  161 giIYLLLYVDDILIAGSNDELIDEFKEELSSEFEMK--DLG----ELKY-FLGIEIKRTsggiflsQRKYaKKLlkrfGM 233

                   ...
gi 536165     1501 EKS 1503
Cdd:pfam07727  234 LDC 236
rve pfam00665
Integrase core domain; Integrase mediates integration of a DNA copy of the viral genome into ...
659-778 1.50e-17

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 catalyses the DNA strand transfer reaction of the 3' ends of the viral DNA to the 5' ends of the integration site.


Pssm-ID: 250040  Cd Length: 119  Bit Score: 81.61  E-value: 1.50e-17
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 536165      659 EPFQYLHTDIFgPVHHLPKSAPSYFISFTDEKTRFQWVYPLhdRREESILNVFTSILAFIKNQFNARVlVIQMDRGSEYT 738
Cdd:pfam00665    4 RPNELWQMDIT-PIPISSKGGKKYLLVIVDDFSRFVVAYAL--KSKTDAELVFDLLEAALERRGGKPV-TIHSDNGSEFT 79
                           90       100       110       120
                   ....*....|....*....|....*....|....*....|
gi 536165      739 NKTLHKFFTNRGITACYTTTADSRAHGVAERLNRTLLNDC 778
Cdd:pfam00665   80 SKAFQELLKELGIKHSFSRPGNPQDNGVVERFNRTLKEEL 119
gag_pre-integrs pfam13976
GAG-pre-integrase domain; This domain is found associated with retroviral insertion elements ...
574-641 2.84e-06

GAG-pre-integrase domain; This domain is found associated with retroviral insertion elements and lies just upstream of the integrase region on the polyproteins.


Pssm-ID: 258228  Cd Length: 67  Bit Score: 46.97  E-value: 2.84e-06
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 536165      574 KLTINNVNKSKSV---NKYPYPLIHRMLGHANFRSIQKSLKKNAVTYLKESDIEwsnastyQCPDCLIGKS 641
Cdd:pfam13976    4 YLDISSVAGPVAAvssSKDESWLWHRRLGHPSFKSLKKLSKKGLVPGLPILKFK-------VCESCQLGKQ 67
Neuro_bHLH pfam12533
Neuronal helix-loop-helix transcription factor; This domain family is found in eukaryotes, and ...
64-138 2.97e-03

Neuronal helix-loop-helix transcription factor; This domain family is found in eukaryotes, and is approximately 80 amino acids in length. The family is found C-terminal to pfam00010. There is a single completely conserved residue W that may be functionally important. Neuronal basic helix-loop-helix (bHLH) transcription factors such as neuroD and neurogenin have been shown to play important roles in neuronal development.


Pssm-ID: 257113  Cd Length: 120  Bit Score: 38.10  E-value: 2.97e-03
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 536165       64 PENHHHVSPQPASVPPPQNGQYQQHGMMTPNKAMASNWAHYQQPSMMTCSHYQtsPAYYQPDPHYPLPQYIPPLS 138
Cdd:pfam12533   38 PEQQQDYSHSGSSPFSQHPYPYQSPGLPSPPHGSMSSSHSLHLKPHGYCSAYE--PFYESHSPDCGSPPYDGPLS 110
PRK10263 PRK10263
DNA translocase FtsK; Provisional
9-147 1.63e-05

DNA translocase FtsK; Provisional


Pssm-ID: 236669 [Multi-domain]  Cd Length: 1355  Bit Score: 48.54  E-value: 1.63e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 536165       9 NPHSLHGSAYASVTSKEVSSNQDPLaVSASNLPEFDRDSTKVNSQQETTPGTSAVPENHHHvSPQPASVPPPQNGQYQQH 88
Cdd:PRK10263  720 NPFSLDDFEFSPMKALLDDGPHEPL-FTPIVEPVQQPQQPVAPQQQYQQPQQPVAPQPQYQ-QPQQPVAPQPQYQQPQQP 797
                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 536165      89 GMMTPnkamasNWAHYQQPSmmtcshyQTSPAYYQP-DPHYPLPQYIPPLSTSSPDPIDS 147
Cdd:PRK10263  798 VAPQP------QYQQPQQPV-------APQPQYQQPqQPVAPQPQYQQPQQPVAPQPQDT 844
PRK10263 PRK10263
DNA translocase FtsK; Provisional
55-158 2.22e-05

DNA translocase FtsK; Provisional


Pssm-ID: 236669 [Multi-domain]  Cd Length: 1355  Bit Score: 48.16  E-value: 2.22e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 536165      55 ETTPGTSAVPENHHHVSPQPasVPPPQngQYQQhgmmtPNKAMASNWaHYQQPSMMTCSHyqtsPAYYQPD-PHYPLPQY 133
Cdd:PRK10263  752 VQQPQQPVAPQQQYQQPQQP--VAPQP--QYQQ-----PQQPVAPQP-QYQQPQQPVAPQ----PQYQQPQqPVAPQPQY 817
                          90       100
                  ....*....|....*....|....*
gi 536165     134 IPPLSTSSPDPIDSQDQHSEVPQAK 158
Cdd:PRK10263  818 QQPQQPVAPQPQYQQPQQPVAPQPQ 842
DUF1421 pfam07223
Protein of unknown function (DUF1421); This family represents a conserved region approximately ...
22-155 2.04e-04

Protein of unknown function (DUF1421); This family represents a conserved region approximately 350 residues long within a number of plant proteins of unknown function.


Pssm-ID: 254110 [Multi-domain]  Cd Length: 357  Bit Score: 44.16  E-value: 2.04e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 536165       22 TSKEVSSNQDPLAV-SASNLPEFDRDSTKVN--SQQETTPGTSAVPeNHHHVSPQPASVPPPQNGQYQQHGMMTPNKA-M 97
Cdd:pfam07223   20 TQKELSKLQLSHEEaQSSEAHSFHVDSTKQPpaPEQVAKHELADAP-LQQVNAALPPAPAPQSPQPDQQQQSQAPPSHqY 98
                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|....*...
gi 536165       98 ASNWAHYQQPSMMTCSHYQTSPAYYQPDPHYPLPQYIPPLSTSSPDPIDSQDQHSEVP 155
Cdd:pfam07223   99 PSQLPPQQVQSVPQQPTPQQEPYYPPPSQPQPPPAQQPQAQQPQPPPQVPQQQQYQSP 156
Amelogenin smart00818
Amelogenins, cell adhesion proteins, play a role in the biomineralisation of teeth; They seem ...
52-160 2.44e-04

Amelogenins, cell adhesion proteins, play a role in the biomineralisation of teeth; They seem to regulate formation of crystallites during the secretory stage of tooth enamel development and are thought to play a major role in the structural organisation and mineralisation of developing enamel. The extracellular matrix of the developing enamel comprises two major classes of protein: the hydrophobic amelogenins and the acidic enamelins. Circular dichroism studies of porcine amelogenin have shown that the protein consists of 3 discrete folding units: the N-terminal region appears to contain beta-strand structures, while the C-terminal region displays characteristics of a random coil conformation. Subsequent studies on the bovine protein have indicated the amelogenin structure to contain a repetitive beta-turn segment and a "beta-spiral" between Gln112 and Leu138, which sequester a (Pro, Leu, Gln) rich region. The beta-spiral offers a probable site for interactions with Ca2+ ions. Muatations in the human amelogenin gene (AMGX) cause X-linked hypoplastic amelogenesis imperfecta, a disease characterised by defective enamel. A 9bp deletion in exon 2 of AMGX results in the loss of codons for Ile5, Leu6, Phe7 and Ala8, and replacement by a new threonine codon, disrupting the 16-residue (Met1-Ala16) amelogenin signal peptide.


Pssm-ID: 197891 [Multi-domain]  Cd Length: 165  Bit Score: 42.08  E-value: 2.44e-04
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 536165        52 SQQetTPGTSAVPEnHHHVSPQPASVP-PPQNGQYQQ--HGMMTPNKAMASNW-AHYQQPSMMTcshYQTSPAYYQP--- 124
Cdd:smart00818   43 SQQ--HPPTHTLQP-HHHIPVLPAQQPvVPQQPLMPVpgQHSMTPTQHHQPNLpQPAQQPFQPQ---PLQPPQPQQPmqp 116
                            90       100       110       120
                    ....*....|....*....|....*....|....*....|....
gi 536165       125 ----DPHYPLPQY--IPPLSTSSPDPIDSQDQHSEVPQA--KTK 160
Cdd:smart00818  117 qppvHPIPPLPPQppLPPMFPMQPLPPLLPDLPLEAWPAtdKTK 160
PTZ00112 PTZ00112
origin recognition complex 1 protein; Provisional
1046-1262 5.87e-03

origin recognition complex 1 protein; Provisional


Pssm-ID: 240274 [Multi-domain]  Cd Length: 1164  Bit Score: 39.97  E-value: 5.87e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 536165    1046 YELENIKttrlGGTEEPYIQRN--SDTNIKYRTTNSTPSIDDR----SPDSDSTTPIISIETKAACDNTP-SIDTDPPEY 1118
Cdd:PTZ00112   78 PDYNQIQ----NNTHDFYIDLNerSKTPIKNNDNVTTPIKANKkekhNLDSSSSSSISSSLTNISFFSSPtSIYSCLSNS 153
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 536165    1119 RSSDHATPNIMPDKSSK-NVTADSILDDLPLPD-LTNKSPTDTSDVSKDIPHIHSRQTNSSLGGMDDSNVLTTTKSKKRS 1196
Cdd:PTZ00112  154 LSSKHSPKVIKENQSTHvNISSDNSPRNKEISNkQLKKQTNVTHTTCYDKMRRSPRNTSTIKNNTNDKNKEKNKEKDKNI 233
                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 536165    1197 LEDNETEIEVSRDTWNNKN---------MRSLEPPRSKKRINLIAAIKGVKSIKPVRTTLRYDEAITYNEDNKEK 1262
Cdd:PTZ00112  234 KKDRDGDKQTKRNSEKSKVqnshfdvriLRSYTKENKKDEKNVVSGIRSSVLLKRKSQCLRKDSYVYSNHQKKAK 308
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.14
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Marchler-Bauer A et al. (2015), "CDD: NCBI's conserved domain database.", Nucleic Acids Res.43(D)222-6.
  • Marchler-Bauer A et al. (2011), "CDD: a Conserved Domain Database for the functional annotation of proteins.", Nucleic Acids Res.39(D)225-9.
  • Marchler-Bauer A et al. (2009), "CDD: specific functional annotation with the Conserved Domain Database.", Nucleic Acids Res.37(D)205-10.
  • Marchler-Bauer A, Bryant SH (2004), "CD-Search: protein domain annotations on the fly.", Nucleic Acids Res.32(W)327-331.
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