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Conserved domains on  [gi|227430781|gb|ACP28377|]
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integrase, partial [Human immunodeficiency virus 2]

Protein Classification

integrase( domain architecture ID 10488378)

integrase such as retroviral integrase that catalyzes the integration of viral DNA into host target DNA

Gene Ontology:  GO:0008907|GO:0003677|GO:0008270|GO:0006310
PubMed:  7801124
SCOP:  4000539|4000740

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 ...
 59-145 3.21e-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: 70.04  E-value: 3.21e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 227430781   59 GTWQMDCTHLEGKI------IIVAVHVASGFIEAEVIPRETGRQAALFLLKLASRW---PITHLHTDNGANFTSQDVKMV 129
Cdd:pfam00665   3 QLWQGDFTYIRIPGgggklyLLVIVDDFSREILAWALSSEMDAELVLDALERAIAFrggVPLIIHSDNGSEYTSKAFREF 82

                          90
                  ....*....|....*.
gi 227430781  130 AWWVGIEQTFGVPCNP 145
Cdd:pfam00665  83 LKDLGIKPSFSRPGNP 98
IN_DBD_C pfam00552
Integrase DNA binding domain; Integrase mediates integration of a DNA copy of the viral genome ...
 225-268 2.08e-14

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: 66.27  E-value: 2.08e-14
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 227430781  225 VYYREGRDQLWKGPGELLWKGEGAVII-KVGTEIKVVPRRKAKII 268
Cdd:pfam00552   1 VKWKDLLNGLWKGPDPLLWWGRGAVCVpQDASDPQWVPERLLKRI 45
Integrase_Zn pfam02022
Integrase Zinc binding domain; Integrase mediates integration of a DNA copy of the viral ...
 10-45 1.43e-10

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: 55.46  E-value: 1.43e-10
                          10        20        30
                  ....*....|....*....|....*....|....*.
gi 227430781   10 EEHEKYHGNVKELVHKFGIPQLVAKQIVNSCDKCQQ 45
Cdd:pfam02022   1 ELHSLHHVNAKALRKKFGITRKQARDIVQSCPTCQQ 36
transpos_IS3 super family cl41295
IS3 family transposase;
113-198 1.82e-07

IS3 family transposase;


The actual alignment was detected with superfamily member NF033516:

Pssm-ID: 468052 [Multi-domain]  Cd Length: 369  Bit Score: 51.80  E-value: 1.82e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 227430781 113 LHTDNGANFTSQDVKMVAWWVGIEQTFGVPCNPQSQGVVEAMNHHLKNQIDRLRDQAvSIETVVLMATHCMNF---KRR- 188
Cdd:NF033516 279 LHSDNGSQYTSKAYREWLKEHGITQSMSRPGNCWDNAVAESFFGTLKRECLYRRRFR-TLEEARQAIEEYIEFynhERPh 357

                         90
                 ....*....|
gi 227430781 189 GGIGDMTPAE 198
Cdd:NF033516 358 SSLGYLTPAE 367
 
Name Accession Description Interval E-value
rve pfam00665
Integrase core domain; Integrase mediates integration of a DNA copy of the viral genome into ...
 59-145 3.21e-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: 70.04  E-value: 3.21e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 227430781   59 GTWQMDCTHLEGKI------IIVAVHVASGFIEAEVIPRETGRQAALFLLKLASRW---PITHLHTDNGANFTSQDVKMV 129
Cdd:pfam00665   3 QLWQGDFTYIRIPGgggklyLLVIVDDFSREILAWALSSEMDAELVLDALERAIAFrggVPLIIHSDNGSEYTSKAFREF 82

                          90
                  ....*....|....*.
gi 227430781  130 AWWVGIEQTFGVPCNP 145
Cdd:pfam00665  83 LKDLGIKPSFSRPGNP 98
IN_DBD_C pfam00552
Integrase DNA binding domain; Integrase mediates integration of a DNA copy of the viral genome ...
 225-268 2.08e-14

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: 66.27  E-value: 2.08e-14
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 227430781  225 VYYREGRDQLWKGPGELLWKGEGAVII-KVGTEIKVVPRRKAKII 268
Cdd:pfam00552   1 VKWKDLLNGLWKGPDPLLWWGRGAVCVpQDASDPQWVPERLLKRI 45
transpos_IS481 NF033577
IS481 family transposase; null
 59-200 5.02e-12

IS481 family transposase; null


Pssm-ID: 468094 [Multi-domain]  Cd Length: 283  Bit Score: 64.92  E-value: 5.02e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 227430781  59 GTWQMDCTHL-----EGKI-IIVAVHVASGFIEAEVIPRETGRQAALFLLKL-ASRW-PITHLHTDNGANFTSqDVKMVA 130
Cdd:NF033577 129 ELWHIDIKKLgripdVGRLyLHTAIDDHSRFAYAELYPDETAETAADFLRRAfAEHGiPIRRVLTDNGSEFRS-RAHGFE 207

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 227430781 131 WWV---GIEQTFGVPCNPQSQGVVEAMNHHLKNQI------DRLRDQAVSIETVVlmatHCMNFKRR-GGIGDMTPAERL 200
Cdd:NF033577 208 LALaelGIEHRRTRPYHPQTNGKVERFHRTLKDEFayarpyESLAELQAALDEWL----HHYNHHRPhSALGGKTPAERF 283
Integrase_Zn pfam02022
Integrase Zinc binding domain; Integrase mediates integration of a DNA copy of the viral ...
 10-45 1.43e-10

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: 55.46  E-value: 1.43e-10
                          10        20        30
                  ....*....|....*....|....*....|....*.
gi 227430781   10 EEHEKYHGNVKELVHKFGIPQLVAKQIVNSCDKCQQ 45
Cdd:pfam02022   1 ELHSLHHVNAKALRKKFGITRKQARDIVQSCPTCQQ 36
Tra5 COG2801
Transposase InsO and inactivated derivatives [Mobilome: prophages, transposons];
61-199 3.16e-10

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


Pssm-ID: 442053 [Multi-domain]  Cd Length: 309  Bit Score: 59.78  E-value: 3.16e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 227430781  61 WQMDCTHL---EGK-----II------IVAVHVASgfieaevipRETGRQAALFLLKLASRWPITH---LHTDNGANFTS 123
Cdd:COG2801  152 WVTDITYIptaEGWlylaaVIdlfsreIVGWSVSD---------SMDAELVVDALEMAIERRGPPKpliLHSDNGSQYTS 222

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 227430781 124 QDVKMVAWWVGIEQTFGVPCNPQSQGVVEAMNHHLKNQIDRLRDQAvSIETVVLMATHCM---NFKRR-GGIGDMTPAER 199
Cdd:COG2801  223 KAYQELLKKLGITQSMSRPGNPQDNAFIESFFGTLKYELLYRRRFE-SLEEAREAIEEYIefyNHERPhSSLGYLTPAEY 301
transpos_IS3 NF033516
IS3 family transposase;
113-198 1.82e-07

IS3 family transposase;


Pssm-ID: 468052 [Multi-domain]  Cd Length: 369  Bit Score: 51.80  E-value: 1.82e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 227430781 113 LHTDNGANFTSQDVKMVAWWVGIEQTFGVPCNPQSQGVVEAMNHHLKNQIDRLRDQAvSIETVVLMATHCMNF---KRR- 188
Cdd:NF033516 279 LHSDNGSQYTSKAYREWLKEHGITQSMSRPGNCWDNAVAESFFGTLKRECLYRRRFR-TLEEARQAIEEYIEFynhERPh 357

                         90
                 ....*....|
gi 227430781 189 GGIGDMTPAE 198
Cdd:NF033516 358 SSLGYLTPAE 367
 
Name Accession Description Interval E-value
rve pfam00665
Integrase core domain; Integrase mediates integration of a DNA copy of the viral genome into ...
 59-145 3.21e-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: 70.04  E-value: 3.21e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 227430781   59 GTWQMDCTHLEGKI------IIVAVHVASGFIEAEVIPRETGRQAALFLLKLASRW---PITHLHTDNGANFTSQDVKMV 129
Cdd:pfam00665   3 QLWQGDFTYIRIPGgggklyLLVIVDDFSREILAWALSSEMDAELVLDALERAIAFrggVPLIIHSDNGSEYTSKAFREF 82

                          90
                  ....*....|....*.
gi 227430781  130 AWWVGIEQTFGVPCNP 145
Cdd:pfam00665  83 LKDLGIKPSFSRPGNP 98
IN_DBD_C pfam00552
Integrase DNA binding domain; Integrase mediates integration of a DNA copy of the viral genome ...
 225-268 2.08e-14

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: 66.27  E-value: 2.08e-14
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 227430781  225 VYYREGRDQLWKGPGELLWKGEGAVII-KVGTEIKVVPRRKAKII 268
Cdd:pfam00552   1 VKWKDLLNGLWKGPDPLLWWGRGAVCVpQDASDPQWVPERLLKRI 45
transpos_IS481 NF033577
IS481 family transposase; null
 59-200 5.02e-12

IS481 family transposase; null


Pssm-ID: 468094 [Multi-domain]  Cd Length: 283  Bit Score: 64.92  E-value: 5.02e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 227430781  59 GTWQMDCTHL-----EGKI-IIVAVHVASGFIEAEVIPRETGRQAALFLLKL-ASRW-PITHLHTDNGANFTSqDVKMVA 130
Cdd:NF033577 129 ELWHIDIKKLgripdVGRLyLHTAIDDHSRFAYAELYPDETAETAADFLRRAfAEHGiPIRRVLTDNGSEFRS-RAHGFE 207

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 227430781 131 WWV---GIEQTFGVPCNPQSQGVVEAMNHHLKNQI------DRLRDQAVSIETVVlmatHCMNFKRR-GGIGDMTPAERL 200
Cdd:NF033577 208 LALaelGIEHRRTRPYHPQTNGKVERFHRTLKDEFayarpyESLAELQAALDEWL----HHYNHHRPhSALGGKTPAERF 283
Integrase_Zn pfam02022
Integrase Zinc binding domain; Integrase mediates integration of a DNA copy of the viral ...
 10-45 1.43e-10

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: 55.46  E-value: 1.43e-10
                          10        20        30
                  ....*....|....*....|....*....|....*.
gi 227430781   10 EEHEKYHGNVKELVHKFGIPQLVAKQIVNSCDKCQQ 45
Cdd:pfam02022   1 ELHSLHHVNAKALRKKFGITRKQARDIVQSCPTCQQ 36
Tra5 COG2801
Transposase InsO and inactivated derivatives [Mobilome: prophages, transposons];
61-199 3.16e-10

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


Pssm-ID: 442053 [Multi-domain]  Cd Length: 309  Bit Score: 59.78  E-value: 3.16e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 227430781  61 WQMDCTHL---EGK-----II------IVAVHVASgfieaevipRETGRQAALFLLKLASRWPITH---LHTDNGANFTS 123
Cdd:COG2801  152 WVTDITYIptaEGWlylaaVIdlfsreIVGWSVSD---------SMDAELVVDALEMAIERRGPPKpliLHSDNGSQYTS 222

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 227430781 124 QDVKMVAWWVGIEQTFGVPCNPQSQGVVEAMNHHLKNQIDRLRDQAvSIETVVLMATHCM---NFKRR-GGIGDMTPAER 199
Cdd:COG2801  223 KAYQELLKKLGITQSMSRPGNPQDNAFIESFFGTLKYELLYRRRFE-SLEEAREAIEEYIefyNHERPhSSLGYLTPAEY 301
transpos_IS3 NF033516
IS3 family transposase;
113-198 1.82e-07

IS3 family transposase;


Pssm-ID: 468052 [Multi-domain]  Cd Length: 369  Bit Score: 51.80  E-value: 1.82e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 227430781 113 LHTDNGANFTSQDVKMVAWWVGIEQTFGVPCNPQSQGVVEAMNHHLKNQIDRLRDQAvSIETVVLMATHCMNF---KRR- 188
Cdd:NF033516 279 LHSDNGSQYTSKAYREWLKEHGITQSMSRPGNCWDNAVAESFFGTLKRECLYRRRFR-TLEEARQAIEEYIEFynhERPh 357

                         90
                 ....*....|
gi 227430781 189 GGIGDMTPAE 198
Cdd:NF033516 358 SSLGYLTPAE 367
 
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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