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Conserved domains on  [gi|147800844|emb|CAN71037|]
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hypothetical protein VITISV_011061 [Vitis vinifera]

Protein Classification

Ty1/Copia family ribonuclease HI( domain architecture ID 12162515)

Ty1/Copia family ribonuclease HI in long-term repeat (LTR) retroelements is involved in the 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

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
RVT_2 super family cl06662
Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually ...
 800-1043 1.49e-81

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: 400190  Cd Length: 243  Bit Score: 266.77  E-value: 1.49e-81
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 147800844   800 NGTWKLTELPEAKNAIGVKWVFRTKFNsDGSIFRHKARLVVKGFAQVARVDYGDTFALVAKHDTIRLLLALASQMGWKVY 879
Cdd:pfam07727    1 NETWTLVKLPKNVKPIGTTWVHTHKIN-DLKEVQYKARLVAQGFRQIAGEDYDKVFSPVIRLSSVRLLLAIAAEYEWPVH 79

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 147800844   880 HLNVKSAFLNGILLEEIYVQQPEGFEVIGHEHKVYKLHKAVYGLKQAPRAWYSRIDSHLIQLGFRRSENEATLYLKQNDD 959
Cdd:pfam07727   80 HMDVSSAFLNGDIDEEIYVKQPPGFNIDNESGKVWQLNKSLYGLKQAPYMWNTCITKVLMDLNFEPDTAESGMYCRGFGE 159

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 147800844   960 GlQLVVSLYVDDMLVTGSNVKLLADFKMEMQDVFEMSDLGIMNYFLGMEIYQCSWGIFISQRKYAMDILKKFKLESCKEV 1039
Cdd:pfam07727  160 N-KLIVGLYVDDMFITGSDITIINDFKLELAKHFKMKDLGDISEFLGIEFIQIAGGIRLSQHNYLNSVIKKFNLTNNNGK 238


                   ....
gi 147800844  1040 ATPL 1043
Cdd:pfam07727  239 YTPI 242
RNase_HI_RT_Ty1 cd09272
Ty1/Copia family of RNase HI in long-term repeat retroelements; Ribonuclease H (RNase H) ...
 1076-1199 1.42e-59

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: 200.77  E-value: 1.42e-59
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 147800844 1076 GYADSDWAGSVDDMKSTSGYVFTIGSGVICWNSRKQEVVAQSTIEAEYISLAAAANQAIWLRKLLADLGQEQSSPTELYC 1155
Cdd:cd09272     2 GYSDADWAGDPDDRRSTSGYVFFLGGGPISWKSKKQTTVALSSTEAEYIALAEAAKEALWLRRLLEELGIPLDGPTTIYC 81

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 147800844 1156 DNK--------------TKHINVKFHSIREAETNSLVKLHYCSTDEQLADIMTKGLPK 1199
Cdd:cd09272    82 DNQsaialaknpvfhsrTKHIDIRYHFIREKVEKGEIKVEYVPTEDQLADILTKPLPR 139
Retrotran_gag_2 super family cl26047
gag-polypeptide of LTR copia-type; This family is found in Plants and fungi, and contains ...
 69-177 8.45e-17

gag-polypeptide of LTR copia-type; This family is found in Plants and fungi, and contains LTR-polyproteins, or retrotransposons of the copia-type.


The actual alignment was detected with superfamily member pfam14223:

Pssm-ID: 464108  Cd Length: 130  Bit Score: 78.05  E-value: 8.45e-17
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 147800844    69 KAITCLHsgLADHIFTKIMNLETPKQ---------------------REFELMKMKDDESVKDYSGRLMDVVNQMRLLGE 127
Cdd:pfam14223    1 LALIVLS--LSDSLLRLVRNADTAKEawdklestyerkspankltlrRQLHSLKMKEGESVLEHINKFEELVNKLSALGV 78

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|
gi 147800844   128 AFTDQKVVEKIMVSVPQKFEAKISAIEESCDLQTLTivELTSKLHAQEQR 177
Cdd:pfam14223   79 EISDEDLVVKLLRSLPESYENFVTAIESSSDKITLE--ELISKLLDEEER 126
gag_pre-integrs pfam13976
GAG-pre-integrase domain; This domain is found associated with retroviral insertion elements ...
 412-478 2.06e-08

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: 372857  Cd Length: 67  Bit Score: 51.98  E-value: 2.06e-08
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 147800844   412 NIFYLKLDLVEGHV--FSAKIDESVVWHKSYGHFNLKSLRFMQEAGMVEDMLEISVnaQTCESCELGKQ 478
Cdd:pfam13976    1 GLYLLDLSSVANSSiaVASKDDETWLWHRRLGHPSFKGLKKLVKKGLLPGLPISKD--LVCESCQLGKQ 67
rve pfam00665
Integrase core domain; Integrase mediates integration of a DNA copy of the viral genome into ...
 515-574 3.54e-06

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: 459897 [Multi-domain]  Cd Length: 98  Bit Score: 46.54  E-value: 3.54e-06
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|
gi 147800844   515 VYFALFIDDLSRMTWVYFLKTKSQVLSMFKSFKKMVETQSGQnVKVLIIDNGGEYISKEF 574
Cdd:pfam00665   21 LYLLVIVDDFSREILAWALSSEMDAELVLDALERAIAFRGGV-PLIIHSDNGSEYTSKAF 79
DUF4219 pfam13961
Domain of unknown function (DUF4219); This domain is very short and is found at the N-terminal ...
 14-40 7.64e-06

Domain of unknown function (DUF4219); This domain is very short and is found at the N-terminal of many Gag-pol polyprotein and related proteins. There is a highly conserved YxxWxxxM sequence motif.


:

Pssm-ID: 433608  Cd Length: 27  Bit Score: 43.65  E-value: 7.64e-06
                           10        20
                   ....*....|....*....|....*..
gi 147800844    14 FNGEHYHIWAVKMRFYLRSQGLWNVVM 40
Cdd:pfam13961    1 LDGDNYETWKLRMKLYLQAQDLWEVVE 27
 
Name Accession Description Interval E-value
RVT_2 pfam07727
Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually ...
 800-1043 1.49e-81

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: 400190  Cd Length: 243  Bit Score: 266.77  E-value: 1.49e-81
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 147800844   800 NGTWKLTELPEAKNAIGVKWVFRTKFNsDGSIFRHKARLVVKGFAQVARVDYGDTFALVAKHDTIRLLLALASQMGWKVY 879
Cdd:pfam07727    1 NETWTLVKLPKNVKPIGTTWVHTHKIN-DLKEVQYKARLVAQGFRQIAGEDYDKVFSPVIRLSSVRLLLAIAAEYEWPVH 79

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 147800844   880 HLNVKSAFLNGILLEEIYVQQPEGFEVIGHEHKVYKLHKAVYGLKQAPRAWYSRIDSHLIQLGFRRSENEATLYLKQNDD 959
Cdd:pfam07727   80 HMDVSSAFLNGDIDEEIYVKQPPGFNIDNESGKVWQLNKSLYGLKQAPYMWNTCITKVLMDLNFEPDTAESGMYCRGFGE 159

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 147800844   960 GlQLVVSLYVDDMLVTGSNVKLLADFKMEMQDVFEMSDLGIMNYFLGMEIYQCSWGIFISQRKYAMDILKKFKLESCKEV 1039
Cdd:pfam07727  160 N-KLIVGLYVDDMFITGSDITIINDFKLELAKHFKMKDLGDISEFLGIEFIQIAGGIRLSQHNYLNSVIKKFNLTNNNGK 238


                   ....
gi 147800844  1040 ATPL 1043
Cdd:pfam07727  239 YTPI 242
RNase_HI_RT_Ty1 cd09272
Ty1/Copia family of RNase HI in long-term repeat retroelements; Ribonuclease H (RNase H) ...
 1076-1199 1.42e-59

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: 200.77  E-value: 1.42e-59
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 147800844 1076 GYADSDWAGSVDDMKSTSGYVFTIGSGVICWNSRKQEVVAQSTIEAEYISLAAAANQAIWLRKLLADLGQEQSSPTELYC 1155
Cdd:cd09272     2 GYSDADWAGDPDDRRSTSGYVFFLGGGPISWKSKKQTTVALSSTEAEYIALAEAAKEALWLRRLLEELGIPLDGPTTIYC 81

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 147800844 1156 DNK--------------TKHINVKFHSIREAETNSLVKLHYCSTDEQLADIMTKGLPK 1199
Cdd:cd09272    82 DNQsaialaknpvfhsrTKHIDIRYHFIREKVEKGEIKVEYVPTEDQLADILTKPLPR 139
Retrotran_gag_2 pfam14223
gag-polypeptide of LTR copia-type; This family is found in Plants and fungi, and contains ...
 69-177 8.45e-17

gag-polypeptide of LTR copia-type; This family is found in Plants and fungi, and contains LTR-polyproteins, or retrotransposons of the copia-type.


Pssm-ID: 464108  Cd Length: 130  Bit Score: 78.05  E-value: 8.45e-17
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 147800844    69 KAITCLHsgLADHIFTKIMNLETPKQ---------------------REFELMKMKDDESVKDYSGRLMDVVNQMRLLGE 127
Cdd:pfam14223    1 LALIVLS--LSDSLLRLVRNADTAKEawdklestyerkspankltlrRQLHSLKMKEGESVLEHINKFEELVNKLSALGV 78

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|
gi 147800844   128 AFTDQKVVEKIMVSVPQKFEAKISAIEESCDLQTLTivELTSKLHAQEQR 177
Cdd:pfam14223   79 EISDEDLVVKLLRSLPESYENFVTAIESSSDKITLE--ELISKLLDEEER 126
gag_pre-integrs pfam13976
GAG-pre-integrase domain; This domain is found associated with retroviral insertion elements ...
 412-478 2.06e-08

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: 372857  Cd Length: 67  Bit Score: 51.98  E-value: 2.06e-08
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 147800844   412 NIFYLKLDLVEGHV--FSAKIDESVVWHKSYGHFNLKSLRFMQEAGMVEDMLEISVnaQTCESCELGKQ 478
Cdd:pfam13976    1 GLYLLDLSSVANSSiaVASKDDETWLWHRRLGHPSFKGLKKLVKKGLLPGLPISKD--LVCESCQLGKQ 67
rve pfam00665
Integrase core domain; Integrase mediates integration of a DNA copy of the viral genome into ...
 515-574 3.54e-06

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: 459897 [Multi-domain]  Cd Length: 98  Bit Score: 46.54  E-value: 3.54e-06
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|
gi 147800844   515 VYFALFIDDLSRMTWVYFLKTKSQVLSMFKSFKKMVETQSGQnVKVLIIDNGGEYISKEF 574
Cdd:pfam00665   21 LYLLVIVDDFSREILAWALSSEMDAELVLDALERAIAFRGGV-PLIIHSDNGSEYTSKAF 79
DUF4219 pfam13961
Domain of unknown function (DUF4219); This domain is very short and is found at the N-terminal ...
 14-40 7.64e-06

Domain of unknown function (DUF4219); This domain is very short and is found at the N-terminal of many Gag-pol polyprotein and related proteins. There is a highly conserved YxxWxxxM sequence motif.


Pssm-ID: 433608  Cd Length: 27  Bit Score: 43.65  E-value: 7.64e-06
                           10        20
                   ....*....|....*....|....*..
gi 147800844    14 FNGEHYHIWAVKMRFYLRSQGLWNVVM 40
Cdd:pfam13961    1 LDGDNYETWKLRMKLYLQAQDLWEVVE 27
 
Name Accession Description Interval E-value
RVT_2 pfam07727
Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually ...
 800-1043 1.49e-81

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: 400190  Cd Length: 243  Bit Score: 266.77  E-value: 1.49e-81
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 147800844   800 NGTWKLTELPEAKNAIGVKWVFRTKFNsDGSIFRHKARLVVKGFAQVARVDYGDTFALVAKHDTIRLLLALASQMGWKVY 879
Cdd:pfam07727    1 NETWTLVKLPKNVKPIGTTWVHTHKIN-DLKEVQYKARLVAQGFRQIAGEDYDKVFSPVIRLSSVRLLLAIAAEYEWPVH 79

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 147800844   880 HLNVKSAFLNGILLEEIYVQQPEGFEVIGHEHKVYKLHKAVYGLKQAPRAWYSRIDSHLIQLGFRRSENEATLYLKQNDD 959
Cdd:pfam07727   80 HMDVSSAFLNGDIDEEIYVKQPPGFNIDNESGKVWQLNKSLYGLKQAPYMWNTCITKVLMDLNFEPDTAESGMYCRGFGE 159

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 147800844   960 GlQLVVSLYVDDMLVTGSNVKLLADFKMEMQDVFEMSDLGIMNYFLGMEIYQCSWGIFISQRKYAMDILKKFKLESCKEV 1039
Cdd:pfam07727  160 N-KLIVGLYVDDMFITGSDITIINDFKLELAKHFKMKDLGDISEFLGIEFIQIAGGIRLSQHNYLNSVIKKFNLTNNNGK 238


                   ....
gi 147800844  1040 ATPL 1043
Cdd:pfam07727  239 YTPI 242
RNase_HI_RT_Ty1 cd09272
Ty1/Copia family of RNase HI in long-term repeat retroelements; Ribonuclease H (RNase H) ...
 1076-1199 1.42e-59

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: 200.77  E-value: 1.42e-59
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 147800844 1076 GYADSDWAGSVDDMKSTSGYVFTIGSGVICWNSRKQEVVAQSTIEAEYISLAAAANQAIWLRKLLADLGQEQSSPTELYC 1155
Cdd:cd09272     2 GYSDADWAGDPDDRRSTSGYVFFLGGGPISWKSKKQTTVALSSTEAEYIALAEAAKEALWLRRLLEELGIPLDGPTTIYC 81

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 147800844 1156 DNK--------------TKHINVKFHSIREAETNSLVKLHYCSTDEQLADIMTKGLPK 1199
Cdd:cd09272    82 DNQsaialaknpvfhsrTKHIDIRYHFIREKVEKGEIKVEYVPTEDQLADILTKPLPR 139
Retrotran_gag_2 pfam14223
gag-polypeptide of LTR copia-type; This family is found in Plants and fungi, and contains ...
 69-177 8.45e-17

gag-polypeptide of LTR copia-type; This family is found in Plants and fungi, and contains LTR-polyproteins, or retrotransposons of the copia-type.


Pssm-ID: 464108  Cd Length: 130  Bit Score: 78.05  E-value: 8.45e-17
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 147800844    69 KAITCLHsgLADHIFTKIMNLETPKQ---------------------REFELMKMKDDESVKDYSGRLMDVVNQMRLLGE 127
Cdd:pfam14223    1 LALIVLS--LSDSLLRLVRNADTAKEawdklestyerkspankltlrRQLHSLKMKEGESVLEHINKFEELVNKLSALGV 78

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|
gi 147800844   128 AFTDQKVVEKIMVSVPQKFEAKISAIEESCDLQTLTivELTSKLHAQEQR 177
Cdd:pfam14223   79 EISDEDLVVKLLRSLPESYENFVTAIESSSDKITLE--ELISKLLDEEER 126
gag_pre-integrs pfam13976
GAG-pre-integrase domain; This domain is found associated with retroviral insertion elements ...
 412-478 2.06e-08

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: 372857  Cd Length: 67  Bit Score: 51.98  E-value: 2.06e-08
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 147800844   412 NIFYLKLDLVEGHV--FSAKIDESVVWHKSYGHFNLKSLRFMQEAGMVEDMLEISVnaQTCESCELGKQ 478
Cdd:pfam13976    1 GLYLLDLSSVANSSiaVASKDDETWLWHRRLGHPSFKGLKKLVKKGLLPGLPISKD--LVCESCQLGKQ 67
rve pfam00665
Integrase core domain; Integrase mediates integration of a DNA copy of the viral genome into ...
 515-574 3.54e-06

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: 459897 [Multi-domain]  Cd Length: 98  Bit Score: 46.54  E-value: 3.54e-06
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|
gi 147800844   515 VYFALFIDDLSRMTWVYFLKTKSQVLSMFKSFKKMVETQSGQnVKVLIIDNGGEYISKEF 574
Cdd:pfam00665   21 LYLLVIVDDFSREILAWALSSEMDAELVLDALERAIAFRGGV-PLIIHSDNGSEYTSKAF 79
DUF4219 pfam13961
Domain of unknown function (DUF4219); This domain is very short and is found at the N-terminal ...
 14-40 7.64e-06

Domain of unknown function (DUF4219); This domain is very short and is found at the N-terminal of many Gag-pol polyprotein and related proteins. There is a highly conserved YxxWxxxM sequence motif.


Pssm-ID: 433608  Cd Length: 27  Bit Score: 43.65  E-value: 7.64e-06
                           10        20
                   ....*....|....*....|....*..
gi 147800844    14 FNGEHYHIWAVKMRFYLRSQGLWNVVM 40
Cdd:pfam13961    1 LDGDNYETWKLRMKLYLQAQDLWEVVE 27
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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