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Conserved domains on  [gi|285810239|tpg|DAA07024.1|]
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TPA: gag-pol fusion protein [Saccharomyces cerevisiae S288C]

Protein Classification

TYA and RNase_HI_RT_Ty1 domain-containing protein (domain architecture ID 10470242)

protein containing domains TYA, gag_pre-integrs, rve, and RNase_HI_RT_Ty1

Graphical summary

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List of domain hits

Name Accession Description Interval E-value
TYA pfam01021
TYA transposon protein; Ty are yeast transposons. A 5.7kb transcript codes for p3 a fusion ...
17-114 2.61e-62

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: 279373  Cd Length: 98  Bit Score: 210.71  E-value: 2.61e-62
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 285810239    17 AYASVTSKEVSSNQDPLAVSASNLPEFDRDSTKVNSQQETTPGTSAVPENHHHVSPQPASVPPPQNGQYQQHGMMTPNKA 96
Cdd:pfam01021    1 ACASVTSKEVPTNQDPLDVSASKLPEFDKDSTKANSQQETTPGSSAVPENHHHASPQPAQVPPPQNGPYQQQGMMTPNQA 80
                           90
                   ....*....|....*...
gi 285810239    97 MASNWAHYQQPSMMTCSH 114
Cdd:pfam01021   81 NASGWAHYGQPSMMPYSP 98
RVT_2 super family cl06662
Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually ...
1296-1489 4.76e-30

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: 311594  Cd Length: 246  Bit Score: 122.69  E-value: 4.76e-30
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 285810239  1296 KKVINSMFIFNKKRD-----GTHKARFVARGDIQHP-DTYDsDMQSNTVHHYALMTSLSIALDNDYYITQLDISSAYLYA 1369
Cdd:pfam07727   13 HKPIGCKWVFKVKRDsdgkvVRYKARLVAKGFTQKEgIDYD-ETFSPVARLESIRLLLALAAQRGWELHQMDVKSAFLNG 91
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 285810239  1370 DIKEELYIRPPP---HLGLNDKLLRLRKSLYGLKQSGANWYETIKSYLInCCDMQEVRGWSCVF----KNSQVTICLFVD 1442
Cdd:pfam07727   92 ELEEEVYVKQPPgfvVPGKPNKVCKLKKSLYGLKQAPRAWYSRLDSVLL-SLGFKRSKHDHGLFikgkGDGFLIVGLYVD 170
                          170       180       190       200       210
                   ....*....|....*....|....*....|....*....|....*....|.
gi 285810239  1443 DMILFSKDlnanEKIITTLKKQ----YDTKiiNLGESDNeiqydILGLEIK 1489
Cdd:pfam07727  171 DILITGSS----EKEINEFKEElskeFEMK--DLGELSY-----FLGIEIK 210
RNase_HI_RT_Ty1 cd09272
Ty1/Copia family of RNase HI in long-term repeat retroelements; Ribonuclease H (RNase H) ...
1621-1757 2.04e-27

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: 2.04e-27
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 285810239 1621 VAISDASYGNQPY-YKSQIGNIFLLNGKVIGGKSTKASLTCTSTTEAEIHAVSEAIPLLNNLSHLVQEL---NKKPIIkg 1696
Cdd:cd09272     1 EGYSDADWAGDPDdRRSTSGYVFFLGGGPISWKSKKQTTVALSSTEAEYIALAEAAKEALWLRRLLEELgipLDGPTT-- 78
                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 285810239 1697 LLTDSRSTISIIKStneEKF--RNRFFGTKAMRLRDEVSGNNLYVYYIETKKNIADVMTKPLP 1757
Cdd:cd09272    79 IYCDNQSAIALAKN---PVFhsRTKHIDIRYHFIREKVEKGEIKVEYVPTEDQLADILTKPLP 138
rve pfam00665
Integrase core domain; Integrase mediates integration of a DNA copy of the viral genome into ...
660-778 5.39e-16

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.


:

Pssm-ID: 307008  Cd Length: 114  Bit Score: 78.07  E-value: 5.39e-16
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 285810239   660 PFQYLHTDIFgPVHHLPKSAPSYFISFTDEKTRFQWVYPLhdRREESILNVFTSILAFIKNQFnaRVLVIQMDRGSEYTN 739
Cdd:pfam00665    1 PNELWQTDFT-YVRVPGGGGKLYLAVAVDDFSREIVAWAL--SSEMDAELVIDALKRAIAFRG--GPKIIHSDNGSEYTS 75
                           90       100       110
                   ....*....|....*....|....*....|....*....
gi 285810239   740 KTLHKFFTNRGITACYTTTADSRAHGVAERLNRTLLNDC 778
Cdd:pfam00665   76 KAFREFLAHYGITHSFSRPGNPQDNGKVERFNGTLKREF 114
gag_pre-integrs pfam13976
GAG-pre-integrase domain; This domain is found associated with retroviral insertion elements ...
574-641 6.87e-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: 316493  Cd Length: 67  Bit Score: 46.97  E-value: 6.87e-06
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 285810239   574 KLTINNVNKSKSV---NKYPYPLIHRMLGHANFRSIQKSLKKNAVTYLKESDIEwsnastyQCPDCLIGKS 641
Cdd:pfam13976    4 LLDLSSVANSSIAvasKDDETWLWHRRLGHPSFKGLKKLVKKGLLPGLPISKDL-------VCESCQLGKQ 67
 
Name Accession Description Interval E-value
TYA pfam01021
TYA transposon protein; Ty are yeast transposons. A 5.7kb transcript codes for p3 a fusion ...
17-114 2.61e-62

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: 279373  Cd Length: 98  Bit Score: 210.71  E-value: 2.61e-62
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 285810239    17 AYASVTSKEVSSNQDPLAVSASNLPEFDRDSTKVNSQQETTPGTSAVPENHHHVSPQPASVPPPQNGQYQQHGMMTPNKA 96
Cdd:pfam01021    1 ACASVTSKEVPTNQDPLDVSASKLPEFDKDSTKANSQQETTPGSSAVPENHHHASPQPAQVPPPQNGPYQQQGMMTPNQA 80
                           90
                   ....*....|....*...
gi 285810239    97 MASNWAHYQQPSMMTCSH 114
Cdd:pfam01021   81 NASGWAHYGQPSMMPYSP 98
RVT_2 pfam07727
Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually ...
1296-1489 4.76e-30

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: 311594  Cd Length: 246  Bit Score: 122.69  E-value: 4.76e-30
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 285810239  1296 KKVINSMFIFNKKRD-----GTHKARFVARGDIQHP-DTYDsDMQSNTVHHYALMTSLSIALDNDYYITQLDISSAYLYA 1369
Cdd:pfam07727   13 HKPIGCKWVFKVKRDsdgkvVRYKARLVAKGFTQKEgIDYD-ETFSPVARLESIRLLLALAAQRGWELHQMDVKSAFLNG 91
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 285810239  1370 DIKEELYIRPPP---HLGLNDKLLRLRKSLYGLKQSGANWYETIKSYLInCCDMQEVRGWSCVF----KNSQVTICLFVD 1442
Cdd:pfam07727   92 ELEEEVYVKQPPgfvVPGKPNKVCKLKKSLYGLKQAPRAWYSRLDSVLL-SLGFKRSKHDHGLFikgkGDGFLIVGLYVD 170
                          170       180       190       200       210
                   ....*....|....*....|....*....|....*....|....*....|.
gi 285810239  1443 DMILFSKDlnanEKIITTLKKQ----YDTKiiNLGESDNeiqydILGLEIK 1489
Cdd:pfam07727  171 DILITGSS----EKEINEFKEElskeFEMK--DLGELSY-----FLGIEIK 210
RNase_HI_RT_Ty1 cd09272
Ty1/Copia family of RNase HI in long-term repeat retroelements; Ribonuclease H (RNase H) ...
1621-1757 2.04e-27

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: 2.04e-27
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 285810239 1621 VAISDASYGNQPY-YKSQIGNIFLLNGKVIGGKSTKASLTCTSTTEAEIHAVSEAIPLLNNLSHLVQEL---NKKPIIkg 1696
Cdd:cd09272     1 EGYSDADWAGDPDdRRSTSGYVFFLGGGPISWKSKKQTTVALSSTEAEYIALAEAAKEALWLRRLLEELgipLDGPTT-- 78
                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 285810239 1697 LLTDSRSTISIIKStneEKF--RNRFFGTKAMRLRDEVSGNNLYVYYIETKKNIADVMTKPLP 1757
Cdd:cd09272    79 IYCDNQSAIALAKN---PVFhsRTKHIDIRYHFIREKVEKGEIKVEYVPTEDQLADILTKPLP 138
rve pfam00665
Integrase core domain; Integrase mediates integration of a DNA copy of the viral genome into ...
660-778 5.39e-16

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.


Pssm-ID: 307008  Cd Length: 114  Bit Score: 78.07  E-value: 5.39e-16
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 285810239   660 PFQYLHTDIFgPVHHLPKSAPSYFISFTDEKTRFQWVYPLhdRREESILNVFTSILAFIKNQFnaRVLVIQMDRGSEYTN 739
Cdd:pfam00665    1 PNELWQTDFT-YVRVPGGGGKLYLAVAVDDFSREIVAWAL--SSEMDAELVIDALKRAIAFRG--GPKIIHSDNGSEYTS 75
                           90       100       110
                   ....*....|....*....|....*....|....*....
gi 285810239   740 KTLHKFFTNRGITACYTTTADSRAHGVAERLNRTLLNDC 778
Cdd:pfam00665   76 KAFREFLAHYGITHSFSRPGNPQDNGKVERFNGTLKREF 114
gag_pre-integrs pfam13976
GAG-pre-integrase domain; This domain is found associated with retroviral insertion elements ...
574-641 6.87e-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: 316493  Cd Length: 67  Bit Score: 46.97  E-value: 6.87e-06
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 285810239   574 KLTINNVNKSKSV---NKYPYPLIHRMLGHANFRSIQKSLKKNAVTYLKESDIEwsnastyQCPDCLIGKS 641
Cdd:pfam13976    4 LLDLSSVANSSIAvasKDDETWLWHRRLGHPSFKGLKKLVKKGLLPGLPISKDL-------VCESCQLGKQ 67
PRK10263 PRK10263
DNA translocase FtsK; Provisional
9-147 3.92e-05

DNA translocase FtsK; Provisional


Pssm-ID: 236669  Cd Length: 1355  Bit Score: 48.54  E-value: 3.92e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 285810239    9 NPHSLHGSAYASVTSKEVSSNQDPLaVSASNLPEFDRDSTKVNSQQETTPGTSAVPENHHHvSPQPASVPPPQNGQYQQH 88
Cdd:PRK10263  720 NPFSLDDFEFSPMKALLDDGPHEPL-FTPIVEPVQQPQQPVAPQQQYQQPQQPVAPQPQYQ-QPQQPVAPQPQYQQPQQP 797
                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 285810239   89 GMMTPnkamasNWAHYQQPSmmtcshyQTSPAYYQP-DPHYPLPQYIPPLSTSSPDPIDS 147
Cdd:PRK10263  798 VAPQP------QYQQPQQPV-------APQPQYQQPqQPVAPQPQYQQPQQPVAPQPQDT 844
Amelogenin smart00818
Amelogenins, cell adhesion proteins, play a role in the biomineralisation of teeth; They seem ...
52-160 5.88e-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  Cd Length: 165  Bit Score: 42.08  E-value: 5.88e-04
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 285810239     52 SQQetTPGTSAVPEnHHHVSPQPASVP-PPQNGQYQQ--HGMMTPNKAMASNW-AHYQQPSMMTcshYQTSPAYYQP--- 124
Cdd:smart00818   43 SQQ--HPPTHTLQP-HHHIPVLPAQQPvVPQQPLMPVpgQHSMTPTQHHQPNLpQPAQQPFQPQ---PLQPPQPQQPmqp 116
                            90       100       110       120
                    ....*....|....*....|....*....|....*....|....
gi 285810239    125 ----DPHYPLPQY--IPPLSTSSPDPIDSQDQHSEVPQA--KTK 160
Cdd:smart00818  117 qppvHPIPPLPPQppLPPMFPMQPLPPLLPDLPLEAWPAtdKTK 160
 
Name Accession Description Interval E-value
TYA pfam01021
TYA transposon protein; Ty are yeast transposons. A 5.7kb transcript codes for p3 a fusion ...
17-114 2.61e-62

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: 279373  Cd Length: 98  Bit Score: 210.71  E-value: 2.61e-62
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 285810239    17 AYASVTSKEVSSNQDPLAVSASNLPEFDRDSTKVNSQQETTPGTSAVPENHHHVSPQPASVPPPQNGQYQQHGMMTPNKA 96
Cdd:pfam01021    1 ACASVTSKEVPTNQDPLDVSASKLPEFDKDSTKANSQQETTPGSSAVPENHHHASPQPAQVPPPQNGPYQQQGMMTPNQA 80
                           90
                   ....*....|....*...
gi 285810239    97 MASNWAHYQQPSMMTCSH 114
Cdd:pfam01021   81 NASGWAHYGQPSMMPYSP 98
RVT_2 pfam07727
Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually ...
1296-1489 4.76e-30

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: 311594  Cd Length: 246  Bit Score: 122.69  E-value: 4.76e-30
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 285810239  1296 KKVINSMFIFNKKRD-----GTHKARFVARGDIQHP-DTYDsDMQSNTVHHYALMTSLSIALDNDYYITQLDISSAYLYA 1369
Cdd:pfam07727   13 HKPIGCKWVFKVKRDsdgkvVRYKARLVAKGFTQKEgIDYD-ETFSPVARLESIRLLLALAAQRGWELHQMDVKSAFLNG 91
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 285810239  1370 DIKEELYIRPPP---HLGLNDKLLRLRKSLYGLKQSGANWYETIKSYLInCCDMQEVRGWSCVF----KNSQVTICLFVD 1442
Cdd:pfam07727   92 ELEEEVYVKQPPgfvVPGKPNKVCKLKKSLYGLKQAPRAWYSRLDSVLL-SLGFKRSKHDHGLFikgkGDGFLIVGLYVD 170
                          170       180       190       200       210
                   ....*....|....*....|....*....|....*....|....*....|.
gi 285810239  1443 DMILFSKDlnanEKIITTLKKQ----YDTKiiNLGESDNeiqydILGLEIK 1489
Cdd:pfam07727  171 DILITGSS----EKEINEFKEElskeFEMK--DLGELSY-----FLGIEIK 210
RNase_HI_RT_Ty1 cd09272
Ty1/Copia family of RNase HI in long-term repeat retroelements; Ribonuclease H (RNase H) ...
1621-1757 2.04e-27

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: 2.04e-27
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 285810239 1621 VAISDASYGNQPY-YKSQIGNIFLLNGKVIGGKSTKASLTCTSTTEAEIHAVSEAIPLLNNLSHLVQEL---NKKPIIkg 1696
Cdd:cd09272     1 EGYSDADWAGDPDdRRSTSGYVFFLGGGPISWKSKKQTTVALSSTEAEYIALAEAAKEALWLRRLLEELgipLDGPTT-- 78
                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 285810239 1697 LLTDSRSTISIIKStneEKF--RNRFFGTKAMRLRDEVSGNNLYVYYIETKKNIADVMTKPLP 1757
Cdd:cd09272    79 IYCDNQSAIALAKN---PVFhsRTKHIDIRYHFIREKVEKGEIKVEYVPTEDQLADILTKPLP 138
rve pfam00665
Integrase core domain; Integrase mediates integration of a DNA copy of the viral genome into ...
660-778 5.39e-16

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.


Pssm-ID: 307008  Cd Length: 114  Bit Score: 78.07  E-value: 5.39e-16
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 285810239   660 PFQYLHTDIFgPVHHLPKSAPSYFISFTDEKTRFQWVYPLhdRREESILNVFTSILAFIKNQFnaRVLVIQMDRGSEYTN 739
Cdd:pfam00665    1 PNELWQTDFT-YVRVPGGGGKLYLAVAVDDFSREIVAWAL--SSEMDAELVIDALKRAIAFRG--GPKIIHSDNGSEYTS 75
                           90       100       110
                   ....*....|....*....|....*....|....*....
gi 285810239   740 KTLHKFFTNRGITACYTTTADSRAHGVAERLNRTLLNDC 778
Cdd:pfam00665   76 KAFREFLAHYGITHSFSRPGNPQDNGKVERFNGTLKREF 114
gag_pre-integrs pfam13976
GAG-pre-integrase domain; This domain is found associated with retroviral insertion elements ...
574-641 6.87e-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: 316493  Cd Length: 67  Bit Score: 46.97  E-value: 6.87e-06
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 285810239   574 KLTINNVNKSKSV---NKYPYPLIHRMLGHANFRSIQKSLKKNAVTYLKESDIEwsnastyQCPDCLIGKS 641
Cdd:pfam13976    4 LLDLSSVANSSIAvasKDDETWLWHRRLGHPSFKGLKKLVKKGLLPGLPISKDL-------VCESCQLGKQ 67
DAZAP2 pfam11029
DAZ associated protein 2 (DAZAP2); DAZ associated protein 2 has a highly conserved sequence ...
78-132 9.97e-06

DAZ associated protein 2 (DAZAP2); DAZ associated protein 2 has a highly conserved sequence throughout evolution including a conserved polyproline region and several SH2/SH3 binding sites. It occurs as a single copy gene with a four-exon organisation and is located on chromosome 12. It encodes a ubiquitously expressed protein and binds to DAZ and DAZL1 through DAZ repeats.


Pssm-ID: 314071  Cd Length: 130  Bit Score: 47.05  E-value: 9.97e-06
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 285810239    78 PPPQNGQYQQHGMMTPNKAMASN--WAHYQQPSMMTCSHYQTSP----AYYQPDPHYPLPQ 132
Cdd:pfam11029    4 YPPAYSQIYQPRYAHPPYAASYApsYGSPYPAQQMYPPMPQMGPpppmAYQPPGPMQPPPQ 64
PRK10263 PRK10263
DNA translocase FtsK; Provisional
9-147 3.92e-05

DNA translocase FtsK; Provisional


Pssm-ID: 236669  Cd Length: 1355  Bit Score: 48.54  E-value: 3.92e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 285810239    9 NPHSLHGSAYASVTSKEVSSNQDPLaVSASNLPEFDRDSTKVNSQQETTPGTSAVPENHHHvSPQPASVPPPQNGQYQQH 88
Cdd:PRK10263  720 NPFSLDDFEFSPMKALLDDGPHEPL-FTPIVEPVQQPQQPVAPQQQYQQPQQPVAPQPQYQ-QPQQPVAPQPQYQQPQQP 797
                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 285810239   89 GMMTPnkamasNWAHYQQPSmmtcshyQTSPAYYQP-DPHYPLPQYIPPLSTSSPDPIDS 147
Cdd:PRK10263  798 VAPQP------QYQQPQQPV-------APQPQYQQPqQPVAPQPQYQQPQQPVAPQPQDT 844
PRK10263 PRK10263
DNA translocase FtsK; Provisional
55-158 5.35e-05

DNA translocase FtsK; Provisional


Pssm-ID: 236669  Cd Length: 1355  Bit Score: 48.16  E-value: 5.35e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 285810239   55 ETTPGTSAVPENHHHVSPQPasVPPPQngQYQQhgmmtPNKAMASNWaHYQQPSMMTCSHyqtsPAYYQPD-PHYPLPQY 133
Cdd:PRK10263  752 VQQPQQPVAPQQQYQQPQQP--VAPQP--QYQQ-----PQQPVAPQP-QYQQPQQPVAPQ----PQYQQPQqPVAPQPQY 817
                          90       100
                  ....*....|....*....|....*
gi 285810239  134 IPPLSTSSPDPIDSQDQHSEVPQAK 158
Cdd:PRK10263  818 QQPQQPVAPQPQYQQPQQPVAPQPQ 842
Amelogenin smart00818
Amelogenins, cell adhesion proteins, play a role in the biomineralisation of teeth; They seem ...
52-160 5.88e-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  Cd Length: 165  Bit Score: 42.08  E-value: 5.88e-04
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 285810239     52 SQQetTPGTSAVPEnHHHVSPQPASVP-PPQNGQYQQ--HGMMTPNKAMASNW-AHYQQPSMMTcshYQTSPAYYQP--- 124
Cdd:smart00818   43 SQQ--HPPTHTLQP-HHHIPVLPAQQPvVPQQPLMPVpgQHSMTPTQHHQPNLpQPAQQPFQPQ---PLQPPQPQQPmqp 116
                            90       100       110       120
                    ....*....|....*....|....*....|....*....|....
gi 285810239    125 ----DPHYPLPQY--IPPLSTSSPDPIDSQDQHSEVPQA--KTK 160
Cdd:smart00818  117 qppvHPIPPLPPQppLPPMFPMQPLPPLLPDLPLEAWPAtdKTK 160
DUF1421 pfam07223
Protein of unknown function (DUF1421); This family represents a conserved region approximately ...
52-169 1.62e-03

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: 311273  Cd Length: 389  Bit Score: 42.54  E-value: 1.62e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 285810239    52 SQQETTPGTSAVPENHHHVSPQPASVPPPQNGQYQQHGMMTPNKAMASN-WAHYQQPSMMTCSHY--QTSPAYYQPDPHY 128
Cdd:pfam07223  123 QHPENTHQQYQVPPAQQPQLPQYPPQAPHQYYQPPPQWQHQTGQQVQSQqFPQYSQPPQLQQQQYnqQVNPQQVQPPPSP 202
                           90       100       110       120
                   ....*....|....*....|....*....|....*....|.
gi 285810239   129 PLPQYIPPLSTSSPDPIDSQDQHsevPQAKTKVRNNVLPPH 169
Cdd:pfam07223  203 HHQEESAPYVPPVYPPYSPIRQP---PNPSPEPLPGSMPMQ 240
DUF1421 pfam07223
Protein of unknown function (DUF1421); This family represents a conserved region approximately ...
2-169 2.58e-03

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: 311273  Cd Length: 389  Bit Score: 42.16  E-value: 2.58e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 285810239     2 ESQQLHQNPHSLHGSAYASVTSKEVSSNQD----------PLAVSASNLP--EFDRDSTKVNSQQETTPGTSAVPENHH- 68
Cdd:pfam07223   33 ESQQSSNSQSGQEDSAQSVSASKPQDNSQShqqlplplalPHQVNAPNAPppQFQSPPPLILQQLVPVQLPTQLPQQQIn 112
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 285810239    69 -----------HV--SPQPASVPPPQNGQYQQHGMMTPNKamasnwaHYQQPSMMTCSHYQT-----SPAYYQPdPHYPL 130
Cdd:pfam07223  113 qqepyymppqqHPenTHQQYQVPPAQQPQLPQYPPQAPHQ-------YYQPPPQWQHQTGQQvqsqqFPQYSQP-PQLQQ 184
                          170       180       190       200
                   ....*....|....*....|....*....|....*....|
gi 285810239   131 PQYIPPLSTSSPDPIDSQDQHSEV-PQAktkvrNNVLPPH 169
Cdd:pfam07223  185 QQYNQQVNPQQVQPPPSPHHQEESaPYV-----PPVYPPY 219
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.16
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
  • 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, Bryant SH (2004), "CD-Search: protein domain annotations on the fly.", Nucleic Acids Res.32(W)327-331.
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