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Conserved domains on  [gi|147773401|emb|CAN73437|]
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hypothetical protein VITISV_031733 [Vitis vinifera]

Protein Classification

Graphical summary

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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) ...
 1165-1304 9.64e-77

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: 249.69  E-value: 9.64e-77
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 147773401 1165 RAFSDSDWAGCPISRRSTTGYCVFLGSSLISWRTKRQKTVSLSSAEAEYRAMTGTCCELSWLRSLLKDLRILHPKPALLY 1244
Cdd:cd09272     1 EGYSDADWAGDPDDRRSTSGYVFFLGGGPISWKSKKQTTVALSSTEAEYIALAEAAKEALWLRRLLEELGIPLDGPTTIY 80

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 147773401 1245 CDNTTALHIAANPVFHERTRHIEMDCHFIREKIQDGSFVTKHIASTNQLADVFTKPLGKE 1304
Cdd:cd09272    81 CDNQSAIALAKNPVFHSRTKHIDIRYHFIREKVEKGEIKVEYVPTEDQLADILTKPLPRP 140
RVT_2 super family cl06662
Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually ...
 861-1082 3.97e-58

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: 200.90  E-value: 3.97e-58
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 147773401   861 NHTWSLTSLPLGKKPIGCRWVYKIKRhSDGTIERFKARLVAKGYTQLEGIDYHDTFSPTAKMITVRCLLALAAAQNWSLH 940
Cdd:pfam07727    1 NETWTLVKLPKNVKPIGTTWVHTHKI-NDLKEVQYKARLVAQGFRQIAGEDYDKVFSPVIRLSSVRLLLAIAAEYEWPVH 79

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 147773401   941 QLDVNNAFLHGDLHEEIYMSPPPGLR------------------RQGENLFSTAIQAA----GFVQSKADYSLFTCRKGK 998
Cdd:pfam07727   80 HMDVSSAFLNGDIDEEIYVKQPPGFNidnesgkvwqlnkslyglKQAPYMWNTCITKVlmdlNFEPDTAESGMYCRGFGE 159

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 147773401   999 SFIALLIYVDDILITGNDANAIVALKQFLHSDFRIKDLGDLKYFLGIEVSRSKKGISISQRKYTLEILKDGGFLGAKPVN 1078
Cdd:pfam07727  160 NKLIVGLYVDDMFITGSDITIINDFKLELAKHFKMKDLGDISEFLGIEFIQIAGGIRLSQHNYLNSVIKKFNLTNNNGKY 239


                   ....
gi 147773401  1079 FPME 1082
Cdd:pfam07727  240 TPII 243
gag_pre-integrs pfam13976
GAG-pre-integrase domain; This domain is found associated with retroviral insertion elements ...
 433-509 8.36e-13

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: 64.69  E-value: 8.36e-13
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 147773401   433 GLYYLvalasekpkNQTPSAAATSCrspSSQVTSSTALWHHRLGHLSSSRLDFMAK--HLLNFPFQSNNACDVCALAKQ 509
Cdd:pfam13976    1 GLYLL---------DLSSVANSSIA---VASKDDETWLWHRRLGHPSFKGLKKLVKkgLLPGLPISKDLVCESCQLGKQ 67
Retrotran_gag_2 super family cl26047
gag-polypeptide of LTR copia-type; This family is found in Plants and fungi, and contains ...
 41-173 1.85e-06

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: 48.39  E-value: 1.85e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 147773401    41 LSWILNSLSQDLADSVIFSTTAQEVWEDLRDRF-SQSNAPRIFQIERGIACLTQDQMTVAAYYTRLKKLWDELGSYNDTV 119
Cdd:pfam14223    1 LALIVLSLSDSLLRLVRNADTAKEAWDKLESTYeRKSPANKLTLRRQLHSLKMKEGESVLEHINKFEELVNKLSALGVEI 80

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|....
gi 147773401   120 CscgadyKRRRLMQFLMGLNESYNAIRGQILLMNPLPNVAKAYSSIVQEEKQRS 173
Cdd:pfam14223   81 S------DEDLVVKLLRSLPESYENFVTAIESSSDKITLEELISKLLDEEERRK 128
transpos_IS481 super family cl41329
IS481 family transposase; null
 545-634 1.51e-04

IS481 family transposase; null


The actual alignment was detected with superfamily member NF033577:

Pssm-ID: 468094 [Multi-domain]  Cd Length: 283  Bit Score: 45.27  E-value: 1.51e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 147773401  545 IRVDNGGEFFSMREFFKQK----GTTYQHSCVYTPQQNGVVERKHRHIL-ESARAFRF------QAHLPLpfWaecvsta 613
Cdd:NF033577  191 VLTDNGSEFRSRAHGFELAlaelGIEHRRTRPYHPQTNGKVERFHRTLKdEFAYARPYeslaelQAALDE--W------- 261

                          90       100
                  ....*....|....*....|..
gi 147773401  614 VHIIN-RLPTPLLSRQTPFERL 634
Cdd:NF033577  262 LHHYNhHRPHSALGGKTPAERF 283
 
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) ...
 1165-1304 9.64e-77

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: 249.69  E-value: 9.64e-77
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 147773401 1165 RAFSDSDWAGCPISRRSTTGYCVFLGSSLISWRTKRQKTVSLSSAEAEYRAMTGTCCELSWLRSLLKDLRILHPKPALLY 1244
Cdd:cd09272     1 EGYSDADWAGDPDDRRSTSGYVFFLGGGPISWKSKKQTTVALSSTEAEYIALAEAAKEALWLRRLLEELGIPLDGPTTIY 80

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 147773401 1245 CDNTTALHIAANPVFHERTRHIEMDCHFIREKIQDGSFVTKHIASTNQLADVFTKPLGKE 1304
Cdd:cd09272    81 CDNQSAIALAKNPVFHSRTKHIDIRYHFIREKVEKGEIKVEYVPTEDQLADILTKPLPRP 140
RVT_2 pfam07727
Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually ...
 861-1082 3.97e-58

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: 200.90  E-value: 3.97e-58
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 147773401   861 NHTWSLTSLPLGKKPIGCRWVYKIKRhSDGTIERFKARLVAKGYTQLEGIDYHDTFSPTAKMITVRCLLALAAAQNWSLH 940
Cdd:pfam07727    1 NETWTLVKLPKNVKPIGTTWVHTHKI-NDLKEVQYKARLVAQGFRQIAGEDYDKVFSPVIRLSSVRLLLAIAAEYEWPVH 79

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 147773401   941 QLDVNNAFLHGDLHEEIYMSPPPGLR------------------RQGENLFSTAIQAA----GFVQSKADYSLFTCRKGK 998
Cdd:pfam07727   80 HMDVSSAFLNGDIDEEIYVKQPPGFNidnesgkvwqlnkslyglKQAPYMWNTCITKVlmdlNFEPDTAESGMYCRGFGE 159

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 147773401   999 SFIALLIYVDDILITGNDANAIVALKQFLHSDFRIKDLGDLKYFLGIEVSRSKKGISISQRKYTLEILKDGGFLGAKPVN 1078
Cdd:pfam07727  160 NKLIVGLYVDDMFITGSDITIINDFKLELAKHFKMKDLGDISEFLGIEFIQIAGGIRLSQHNYLNSVIKKFNLTNNNGKY 239


                   ....
gi 147773401  1079 FPME 1082
Cdd:pfam07727  240 TPII 243
gag_pre-integrs pfam13976
GAG-pre-integrase domain; This domain is found associated with retroviral insertion elements ...
 433-509 8.36e-13

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: 64.69  E-value: 8.36e-13
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 147773401   433 GLYYLvalasekpkNQTPSAAATSCrspSSQVTSSTALWHHRLGHLSSSRLDFMAK--HLLNFPFQSNNACDVCALAKQ 509
Cdd:pfam13976    1 GLYLL---------DLSSVANSSIA---VASKDDETWLWHRRLGHPSFKGLKKLVKkgLLPGLPISKDLVCESCQLGKQ 67
Retrotran_gag_2 pfam14223
gag-polypeptide of LTR copia-type; This family is found in Plants and fungi, and contains ...
 41-173 1.85e-06

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: 48.39  E-value: 1.85e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 147773401    41 LSWILNSLSQDLADSVIFSTTAQEVWEDLRDRF-SQSNAPRIFQIERGIACLTQDQMTVAAYYTRLKKLWDELGSYNDTV 119
Cdd:pfam14223    1 LALIVLSLSDSLLRLVRNADTAKEAWDKLESTYeRKSPANKLTLRRQLHSLKMKEGESVLEHINKFEELVNKLSALGVEI 80

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|....
gi 147773401   120 CscgadyKRRRLMQFLMGLNESYNAIRGQILLMNPLPNVAKAYSSIVQEEKQRS 173
Cdd:pfam14223   81 S------DEDLVVKLLRSLPESYENFVTAIESSSDKITLEELISKLLDEEERRK 128
transpos_IS481 NF033577
IS481 family transposase; null
 545-634 1.51e-04

IS481 family transposase; null


Pssm-ID: 468094 [Multi-domain]  Cd Length: 283  Bit Score: 45.27  E-value: 1.51e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 147773401  545 IRVDNGGEFFSMREFFKQK----GTTYQHSCVYTPQQNGVVERKHRHIL-ESARAFRF------QAHLPLpfWaecvsta 613
Cdd:NF033577  191 VLTDNGSEFRSRAHGFELAlaelGIEHRRTRPYHPQTNGKVERFHRTLKdEFAYARPYeslaelQAALDE--W------- 261

                          90       100
                  ....*....|....*....|..
gi 147773401  614 VHIIN-RLPTPLLSRQTPFERL 634
Cdd:NF033577  262 LHHYNhHRPHSALGGKTPAERF 283
 
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) ...
 1165-1304 9.64e-77

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: 249.69  E-value: 9.64e-77
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 147773401 1165 RAFSDSDWAGCPISRRSTTGYCVFLGSSLISWRTKRQKTVSLSSAEAEYRAMTGTCCELSWLRSLLKDLRILHPKPALLY 1244
Cdd:cd09272     1 EGYSDADWAGDPDDRRSTSGYVFFLGGGPISWKSKKQTTVALSSTEAEYIALAEAAKEALWLRRLLEELGIPLDGPTTIY 80

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 147773401 1245 CDNTTALHIAANPVFHERTRHIEMDCHFIREKIQDGSFVTKHIASTNQLADVFTKPLGKE 1304
Cdd:cd09272    81 CDNQSAIALAKNPVFHSRTKHIDIRYHFIREKVEKGEIKVEYVPTEDQLADILTKPLPRP 140
RVT_2 pfam07727
Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually ...
 861-1082 3.97e-58

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: 200.90  E-value: 3.97e-58
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 147773401   861 NHTWSLTSLPLGKKPIGCRWVYKIKRhSDGTIERFKARLVAKGYTQLEGIDYHDTFSPTAKMITVRCLLALAAAQNWSLH 940
Cdd:pfam07727    1 NETWTLVKLPKNVKPIGTTWVHTHKI-NDLKEVQYKARLVAQGFRQIAGEDYDKVFSPVIRLSSVRLLLAIAAEYEWPVH 79

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 147773401   941 QLDVNNAFLHGDLHEEIYMSPPPGLR------------------RQGENLFSTAIQAA----GFVQSKADYSLFTCRKGK 998
Cdd:pfam07727   80 HMDVSSAFLNGDIDEEIYVKQPPGFNidnesgkvwqlnkslyglKQAPYMWNTCITKVlmdlNFEPDTAESGMYCRGFGE 159

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 147773401   999 SFIALLIYVDDILITGNDANAIVALKQFLHSDFRIKDLGDLKYFLGIEVSRSKKGISISQRKYTLEILKDGGFLGAKPVN 1078
Cdd:pfam07727  160 NKLIVGLYVDDMFITGSDITIINDFKLELAKHFKMKDLGDISEFLGIEFIQIAGGIRLSQHNYLNSVIKKFNLTNNNGKY 239


                   ....
gi 147773401  1079 FPME 1082
Cdd:pfam07727  240 TPII 243
gag_pre-integrs pfam13976
GAG-pre-integrase domain; This domain is found associated with retroviral insertion elements ...
 433-509 8.36e-13

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: 64.69  E-value: 8.36e-13
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 147773401   433 GLYYLvalasekpkNQTPSAAATSCrspSSQVTSSTALWHHRLGHLSSSRLDFMAK--HLLNFPFQSNNACDVCALAKQ 509
Cdd:pfam13976    1 GLYLL---------DLSSVANSSIA---VASKDDETWLWHRRLGHPSFKGLKKLVKkgLLPGLPISKDLVCESCQLGKQ 67
Retrotran_gag_2 pfam14223
gag-polypeptide of LTR copia-type; This family is found in Plants and fungi, and contains ...
 41-173 1.85e-06

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: 48.39  E-value: 1.85e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 147773401    41 LSWILNSLSQDLADSVIFSTTAQEVWEDLRDRF-SQSNAPRIFQIERGIACLTQDQMTVAAYYTRLKKLWDELGSYNDTV 119
Cdd:pfam14223    1 LALIVLSLSDSLLRLVRNADTAKEAWDKLESTYeRKSPANKLTLRRQLHSLKMKEGESVLEHINKFEELVNKLSALGVEI 80

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|....
gi 147773401   120 CscgadyKRRRLMQFLMGLNESYNAIRGQILLMNPLPNVAKAYSSIVQEEKQRS 173
Cdd:pfam14223   81 S------DEDLVVKLLRSLPESYENFVTAIESSSDKITLEELISKLLDEEERRK 128
transpos_IS481 NF033577
IS481 family transposase; null
 545-634 1.51e-04

IS481 family transposase; null


Pssm-ID: 468094 [Multi-domain]  Cd Length: 283  Bit Score: 45.27  E-value: 1.51e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 147773401  545 IRVDNGGEFFSMREFFKQK----GTTYQHSCVYTPQQNGVVERKHRHIL-ESARAFRF------QAHLPLpfWaecvsta 613
Cdd:NF033577  191 VLTDNGSEFRSRAHGFELAlaelGIEHRRTRPYHPQTNGKVERFHRTLKdEFAYARPYeslaelQAALDE--W------- 261

                          90       100
                  ....*....|....*....|..
gi 147773401  614 VHIIN-RLPTPLLSRQTPFERL 634
Cdd:NF033577  262 LHHYNhHRPHSALGGKTPAERF 283
Retrotrans_gag pfam03732
Retrotransposon gag protein; Gag or Capsid-like proteins from LTR retrotransposons. There is a ...
 59-140 9.61e-04

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


Pssm-ID: 367628  Cd Length: 97  Bit Score: 39.62  E-value: 9.61e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 147773401    59 STTAQEVWEDLRDRFSQSNAP--RIFQIERGIACLTQDQMTVAAYYTRLKKLWDELGSYNDTvcscgADYKRRRlmqFLM 136
Cdd:pfam03732   22 SIDAFDSWDELKDAFLKRFFPsiRKDLLRNELRSLRQGTESVREYVERFKRLARQLPHHGRD-----EEALISA---FLR 93


                   ....
gi 147773401   137 GLNE 140
Cdd:pfam03732   94 GLRP 97
 
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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