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Conserved domains on  [gi|297523847|emb|CBM41431|]
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polyprotein, partial [HIV-1 M:B 103108082064]

Protein Classification

Integrase_Zn and rve domain-containing protein( domain architecture ID 10488376)

protein containing domains Integrase_Zn, rve, and IN_DBD_C

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
rve pfam00665
Integrase core domain; Integrase mediates integration of a DNA copy of the viral genome into ...
 44-132 4.99e-15

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: 68.88  E-value: 4.99e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297523847   44 SPGIWQLDCTHLEGKV------ILVAVHVASGYIEAEVIPAETGQETAYFILKLA---GRWPVKTIHTDNGGNFIST*VK 114
Cdd:pfam00665   1 PNQLWQGDFTYIRIPGgggklyLLVIVDDFSREILAWALSSEMDAELVLDALERAiafRGGVPLIIHSDNGSEYTSKAFR 80

                          90
                  ....*....|....*...
gi 297523847  115 AACWWAGIKQEFGIPYNP 132
Cdd:pfam00665  81 EFLKDLGIKPSFSRPGNP 98
IN_DBD_C super family cl02895
Integrase DNA binding domain; Integrase mediates integration of a DNA copy of the viral genome ...
 212-255 7.06e-12

Integrase DNA binding 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. The central domain is the catalytic domain pfam00665. This domain is the carboxyl terminal domain that is a non-specific DNA binding domain.


The actual alignment was detected with superfamily member pfam00552:

Pssm-ID: 425747  Cd Length: 45  Bit Score: 58.95  E-value: 7.06e-12
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 297523847  212 VYYRDSRDPLW**PAKLLWKGEGAVVI-QDNSEIKVVPRRKAKII 255
Cdd:pfam00552   1 VKWKDLLNGLWKGPDPLLWWGRGAVCVpQDASDPQWVPERLLKRI 45
Integrase_Zn pfam02022
Integrase Zinc binding domain; Integrase mediates integration of a DNA copy of the viral ...
 1-31 1.19e-09

Integrase Zinc binding domain; Integrase mediates integration of a DNA copy of the viral genome into the host chromosome. Integrase is composed of three domains. This domain is the amino-terminal domain zinc binding domain. The central domain is the catalytic domain pfam00665. The carboxyl terminal domain is a DNA binding domain pfam00552.


:

Pssm-ID: 426567  Cd Length: 36  Bit Score: 52.37  E-value: 1.19e-09
                          10        20        30
                  ....*....|....*....|....*....|.
gi 297523847    1 KYHSNWRAMASDFNLPPIVAKEIVASCDKCQ 31
Cdd:pfam02022   5 LHHVNAKALRKKFGITRKQARDIVQSCPTCQ 35
Tra5 super family cl34487
Transposase InsO and inactivated derivatives [Mobilome: prophages, transposons];
99-182 1.93e-07

Transposase InsO and inactivated derivatives [Mobilome: prophages, transposons];


The actual alignment was detected with superfamily member COG2801:

Pssm-ID: 442053 [Multi-domain]  Cd Length: 309  Bit Score: 50.92  E-value: 1.93e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297523847  99 TIHTDNGGNFIST*VKAACWWAGIKQEFGIPYNPPSQGVVESMHNELKK--IIGQVRDQAEHLKTAVQMAVFIHNFKR-K 175
Cdd:COG2801  211 ILHSDNGSQYTSKAYQELLKKLGITQSMSRPGNPQDNAFIESFFGTLKYelLYRRRFESLEEAREAIEEYIEFYNHERpH 290


                 ....*..
gi 297523847 176 GGIGGYS 182
Cdd:COG2801  291 SSLGYLT 297
 
Name Accession Description Interval E-value
rve pfam00665
Integrase core domain; Integrase mediates integration of a DNA copy of the viral genome into ...
 44-132 4.99e-15

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: 68.88  E-value: 4.99e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297523847   44 SPGIWQLDCTHLEGKV------ILVAVHVASGYIEAEVIPAETGQETAYFILKLA---GRWPVKTIHTDNGGNFIST*VK 114
Cdd:pfam00665   1 PNQLWQGDFTYIRIPGgggklyLLVIVDDFSREILAWALSSEMDAELVLDALERAiafRGGVPLIIHSDNGSEYTSKAFR 80

                          90
                  ....*....|....*...
gi 297523847  115 AACWWAGIKQEFGIPYNP 132
Cdd:pfam00665  81 EFLKDLGIKPSFSRPGNP 98
IN_DBD_C pfam00552
Integrase DNA binding domain; Integrase mediates integration of a DNA copy of the viral genome ...
 212-255 7.06e-12

Integrase DNA binding 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. The central domain is the catalytic domain pfam00665. This domain is the carboxyl terminal domain that is a non-specific DNA binding domain.


Pssm-ID: 425747  Cd Length: 45  Bit Score: 58.95  E-value: 7.06e-12
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 297523847  212 VYYRDSRDPLW**PAKLLWKGEGAVVI-QDNSEIKVVPRRKAKII 255
Cdd:pfam00552   1 VKWKDLLNGLWKGPDPLLWWGRGAVCVpQDASDPQWVPERLLKRI 45
Integrase_Zn pfam02022
Integrase Zinc binding domain; Integrase mediates integration of a DNA copy of the viral ...
 1-31 1.19e-09

Integrase Zinc binding domain; Integrase mediates integration of a DNA copy of the viral genome into the host chromosome. Integrase is composed of three domains. This domain is the amino-terminal domain zinc binding domain. The central domain is the catalytic domain pfam00665. The carboxyl terminal domain is a DNA binding domain pfam00552.


Pssm-ID: 426567  Cd Length: 36  Bit Score: 52.37  E-value: 1.19e-09
                          10        20        30
                  ....*....|....*....|....*....|.
gi 297523847    1 KYHSNWRAMASDFNLPPIVAKEIVASCDKCQ 31
Cdd:pfam02022   5 LHHVNAKALRKKFGITRKQARDIVQSCPTCQ 35
Tra5 COG2801
Transposase InsO and inactivated derivatives [Mobilome: prophages, transposons];
99-182 1.93e-07

Transposase InsO and inactivated derivatives [Mobilome: prophages, transposons];


Pssm-ID: 442053 [Multi-domain]  Cd Length: 309  Bit Score: 50.92  E-value: 1.93e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297523847  99 TIHTDNGGNFIST*VKAACWWAGIKQEFGIPYNPPSQGVVESMHNELKK--IIGQVRDQAEHLKTAVQMAVFIHNFKR-K 175
Cdd:COG2801  211 ILHSDNGSQYTSKAYQELLKKLGITQSMSRPGNPQDNAFIESFFGTLKYelLYRRRFESLEEAREAIEEYIEFYNHERpH 290


                 ....*..
gi 297523847 176 GGIGGYS 182
Cdd:COG2801  291 SSLGYLT 297
transpos_IS3 NF033516
IS3 family transposase;
100-146 1.17e-05

IS3 family transposase;


Pssm-ID: 468052 [Multi-domain]  Cd Length: 369  Bit Score: 46.02  E-value: 1.17e-05
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
gi 297523847 100 IHTDNGGNFIST*VKAACWWAGIKQEFGIPYNPPSQGVVESMHNELK 146
Cdd:NF033516 279 LHSDNGSQYTSKAYREWLKEHGITQSMSRPGNCWDNAVAESFFGTLK 325
 
Name Accession Description Interval E-value
rve pfam00665
Integrase core domain; Integrase mediates integration of a DNA copy of the viral genome into ...
 44-132 4.99e-15

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: 68.88  E-value: 4.99e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297523847   44 SPGIWQLDCTHLEGKV------ILVAVHVASGYIEAEVIPAETGQETAYFILKLA---GRWPVKTIHTDNGGNFIST*VK 114
Cdd:pfam00665   1 PNQLWQGDFTYIRIPGgggklyLLVIVDDFSREILAWALSSEMDAELVLDALERAiafRGGVPLIIHSDNGSEYTSKAFR 80

                          90
                  ....*....|....*...
gi 297523847  115 AACWWAGIKQEFGIPYNP 132
Cdd:pfam00665  81 EFLKDLGIKPSFSRPGNP 98
IN_DBD_C pfam00552
Integrase DNA binding domain; Integrase mediates integration of a DNA copy of the viral genome ...
 212-255 7.06e-12

Integrase DNA binding 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. The central domain is the catalytic domain pfam00665. This domain is the carboxyl terminal domain that is a non-specific DNA binding domain.


Pssm-ID: 425747  Cd Length: 45  Bit Score: 58.95  E-value: 7.06e-12
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 297523847  212 VYYRDSRDPLW**PAKLLWKGEGAVVI-QDNSEIKVVPRRKAKII 255
Cdd:pfam00552   1 VKWKDLLNGLWKGPDPLLWWGRGAVCVpQDASDPQWVPERLLKRI 45
Integrase_Zn pfam02022
Integrase Zinc binding domain; Integrase mediates integration of a DNA copy of the viral ...
 1-31 1.19e-09

Integrase Zinc binding domain; Integrase mediates integration of a DNA copy of the viral genome into the host chromosome. Integrase is composed of three domains. This domain is the amino-terminal domain zinc binding domain. The central domain is the catalytic domain pfam00665. The carboxyl terminal domain is a DNA binding domain pfam00552.


Pssm-ID: 426567  Cd Length: 36  Bit Score: 52.37  E-value: 1.19e-09
                          10        20        30
                  ....*....|....*....|....*....|.
gi 297523847    1 KYHSNWRAMASDFNLPPIVAKEIVASCDKCQ 31
Cdd:pfam02022   5 LHHVNAKALRKKFGITRKQARDIVQSCPTCQ 35
Tra5 COG2801
Transposase InsO and inactivated derivatives [Mobilome: prophages, transposons];
99-182 1.93e-07

Transposase InsO and inactivated derivatives [Mobilome: prophages, transposons];


Pssm-ID: 442053 [Multi-domain]  Cd Length: 309  Bit Score: 50.92  E-value: 1.93e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297523847  99 TIHTDNGGNFIST*VKAACWWAGIKQEFGIPYNPPSQGVVESMHNELKK--IIGQVRDQAEHLKTAVQMAVFIHNFKR-K 175
Cdd:COG2801  211 ILHSDNGSQYTSKAYQELLKKLGITQSMSRPGNPQDNAFIESFFGTLKYelLYRRRFESLEEAREAIEEYIEFYNHERpH 290


                 ....*..
gi 297523847 176 GGIGGYS 182
Cdd:COG2801  291 SSLGYLT 297
transpos_IS3 NF033516
IS3 family transposase;
100-146 1.17e-05

IS3 family transposase;


Pssm-ID: 468052 [Multi-domain]  Cd Length: 369  Bit Score: 46.02  E-value: 1.17e-05
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
gi 297523847 100 IHTDNGGNFIST*VKAACWWAGIKQEFGIPYNPPSQGVVESMHNELK 146
Cdd:NF033516 279 LHSDNGSQYTSKAYREWLKEHGITQSMSRPGNCWDNAVAESFFGTLK 325
 
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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