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Conserved domains on  [gi|25121908|ref|NP_705928|]
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integrase [Human immunodeficiency virus 1]

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 ...
 57-145 3.94e-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: 459897 [Multi-domain]  Cd Length: 98  Bit Score: 72.35  E-value: 3.94e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25121908    57 SPGIWQLDCTHLEGKV------ILVAVHVASGYIEAEVIPAETGQETAYFLLKLA---GRWPVKTIHTDNGSNFTGATVR 127
Cdd:pfam00665   1 PNQLWQGDFTYIRIPGgggklyLLVIVDDFSREILAWALSSEMDAELVLDALERAiafRGGVPLIIHSDNGSEYTSKAFR 80

                          90
                  ....*....|....*...
gi 25121908   128 AACWWAGIKQEFGIPYNP 145
Cdd:pfam00665  81 EFLKDLGIKPSFSRPGNP 98
IN_DBD_C pfam00552
Integrase DNA binding domain; Integrase mediates integration of a DNA copy of the viral genome ...
 225-268 8.05e-15

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: 67.04  E-value: 8.05e-15
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 25121908   225 VYYRDSRNPLWKGPAKLLWKGEGAVVI-QDNSDIKVVPRRKAKII 268
Cdd:pfam00552   1 VKWKDLLNGLWKGPDPLLWWGRGAVCVpQDASDPQWVPERLLKRI 45
Integrase_Zn pfam02022
Integrase Zinc binding domain; Integrase mediates integration of a DNA copy of the viral ...
 10-44 9.07e-13

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: 61.23  E-value: 9.07e-13
                          10        20        30
                  ....*....|....*....|....*....|....*
gi 25121908    10 DEHEKYHSNWRAMASDFNLPPVVAKEIVASCDKCQ 44
Cdd:pfam02022   1 ELHSLHHVNAKALRKKFGITRKQARDIVQSCPTCQ 35
Tra5 super family cl34487
Transposase InsO and inactivated derivatives [Mobilome: prophages, transposons];
112-195 4.48e-10

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: 59.40  E-value: 4.48e-10
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25121908 112 TIHTDNGSNFTGATVRAACWWAGIKQEFGIPYNPQSQGVVESMNKELKK--IIGQVRDQAEHLKTAVQMAVFIHNFKR-K 188
Cdd:COG2801 211 ILHSDNGSQYTSKAYQELLKKLGITQSMSRPGNPQDNAFIESFFGTLKYelLYRRRFESLEEAREAIEEYIEFYNHERpH 290


                ....*..
gi 25121908 189 GGIGGYS 195
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 ...
 57-145 3.94e-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: 459897 [Multi-domain]  Cd Length: 98  Bit Score: 72.35  E-value: 3.94e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25121908    57 SPGIWQLDCTHLEGKV------ILVAVHVASGYIEAEVIPAETGQETAYFLLKLA---GRWPVKTIHTDNGSNFTGATVR 127
Cdd:pfam00665   1 PNQLWQGDFTYIRIPGgggklyLLVIVDDFSREILAWALSSEMDAELVLDALERAiafRGGVPLIIHSDNGSEYTSKAFR 80

                          90
                  ....*....|....*...
gi 25121908   128 AACWWAGIKQEFGIPYNP 145
Cdd:pfam00665  81 EFLKDLGIKPSFSRPGNP 98
IN_DBD_C pfam00552
Integrase DNA binding domain; Integrase mediates integration of a DNA copy of the viral genome ...
 225-268 8.05e-15

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: 67.04  E-value: 8.05e-15
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 25121908   225 VYYRDSRNPLWKGPAKLLWKGEGAVVI-QDNSDIKVVPRRKAKII 268
Cdd:pfam00552   1 VKWKDLLNGLWKGPDPLLWWGRGAVCVpQDASDPQWVPERLLKRI 45
Integrase_Zn pfam02022
Integrase Zinc binding domain; Integrase mediates integration of a DNA copy of the viral ...
 10-44 9.07e-13

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: 61.23  E-value: 9.07e-13
                          10        20        30
                  ....*....|....*....|....*....|....*
gi 25121908    10 DEHEKYHSNWRAMASDFNLPPVVAKEIVASCDKCQ 44
Cdd:pfam02022   1 ELHSLHHVNAKALRKKFGITRKQARDIVQSCPTCQ 35
transpos_IS481 NF033577
IS481 family transposase; null
 55-159 6.33e-12

IS481 family transposase; null


Pssm-ID: 468094 [Multi-domain]  Cd Length: 283  Bit Score: 64.53  E-value: 6.33e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25121908   55 DCSPGIWQLDCTHL-----EGKV-ILVAVHVASGYIEAEVIPAETGQETAYFLLKL-AGRW-PVKTIHTDNGSNFTGAT- 125
Cdd:NF033577 125 AHPGELWHIDIKKLgripdVGRLyLHTAIDDHSRFAYAELYPDETAETAADFLRRAfAEHGiPIRRVLTDNGSEFRSRAh 204

                         90       100       110
                 ....*....|....*....|....*....|....*
gi 25121908  126 -VRAACWWAGIKQEFGIPYNPQSQGVVESMNKELK 159
Cdd:NF033577 205 gFELALAELGIEHRRTRPYHPQTNGKVERFHRTLK 239
Tra5 COG2801
Transposase InsO and inactivated derivatives [Mobilome: prophages, transposons];
112-195 4.48e-10

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


Pssm-ID: 442053 [Multi-domain]  Cd Length: 309  Bit Score: 59.40  E-value: 4.48e-10
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25121908 112 TIHTDNGSNFTGATVRAACWWAGIKQEFGIPYNPQSQGVVESMNKELKK--IIGQVRDQAEHLKTAVQMAVFIHNFKR-K 188
Cdd:COG2801 211 ILHSDNGSQYTSKAYQELLKKLGITQSMSRPGNPQDNAFIESFFGTLKYelLYRRRFESLEEAREAIEEYIEFYNHERpH 290


                ....*..
gi 25121908 189 GGIGGYS 195
Cdd:COG2801 291 SSLGYLT 297
transpos_IS3 NF033516
IS3 family transposase;
113-159 5.70e-09

IS3 family transposase;


Pssm-ID: 468052 [Multi-domain]  Cd Length: 369  Bit Score: 56.42  E-value: 5.70e-09
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
gi 25121908  113 IHTDNGSNFTGATVRAACWWAGIKQEFGIPYNPQSQGVVESMNKELK 159
Cdd:NF033516 279 LHSDNGSQYTSKAYREWLKEHGITQSMSRPGNCWDNAVAESFFGTLK 325
Tra8 COG2826
Transposase and inactivated derivatives, IS30 family [Mobilome: prophages, transposons];
58-158 9.46e-06

Transposase and inactivated derivatives, IS30 family [Mobilome: prophages, transposons];


Pssm-ID: 442074 [Multi-domain]  Cd Length: 325  Bit Score: 46.41  E-value: 9.46e-06
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25121908  58 PGIWQLDCthLEGK----VILVAVHVASGYIEAEVIPAETGQETAYFLLKLAGRWP---VKTIHTDNGSNFTGatvraac 130
Cdd:COG2826 172 PGHWEGDL--IIGKrgksALLTLVERKSRFVILLKLPDKTAESVADALIRLLRKLPaflRKSITTDNGKEFAD------- 242

                        90       100       110
                ....*....|....*....|....*....|....
gi 25121908 131 wWAGIKQEFGI------PYNPQSQGVVESMNKEL 158
Cdd:COG2826 243 -HKEIEAALGIkvyfadPYSPWQRGTNENTNGLL 275
 
Name Accession Description Interval E-value
rve pfam00665
Integrase core domain; Integrase mediates integration of a DNA copy of the viral genome into ...
 57-145 3.94e-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: 459897 [Multi-domain]  Cd Length: 98  Bit Score: 72.35  E-value: 3.94e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25121908    57 SPGIWQLDCTHLEGKV------ILVAVHVASGYIEAEVIPAETGQETAYFLLKLA---GRWPVKTIHTDNGSNFTGATVR 127
Cdd:pfam00665   1 PNQLWQGDFTYIRIPGgggklyLLVIVDDFSREILAWALSSEMDAELVLDALERAiafRGGVPLIIHSDNGSEYTSKAFR 80

                          90
                  ....*....|....*...
gi 25121908   128 AACWWAGIKQEFGIPYNP 145
Cdd:pfam00665  81 EFLKDLGIKPSFSRPGNP 98
IN_DBD_C pfam00552
Integrase DNA binding domain; Integrase mediates integration of a DNA copy of the viral genome ...
 225-268 8.05e-15

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: 67.04  E-value: 8.05e-15
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 25121908   225 VYYRDSRNPLWKGPAKLLWKGEGAVVI-QDNSDIKVVPRRKAKII 268
Cdd:pfam00552   1 VKWKDLLNGLWKGPDPLLWWGRGAVCVpQDASDPQWVPERLLKRI 45
Integrase_Zn pfam02022
Integrase Zinc binding domain; Integrase mediates integration of a DNA copy of the viral ...
 10-44 9.07e-13

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: 61.23  E-value: 9.07e-13
                          10        20        30
                  ....*....|....*....|....*....|....*
gi 25121908    10 DEHEKYHSNWRAMASDFNLPPVVAKEIVASCDKCQ 44
Cdd:pfam02022   1 ELHSLHHVNAKALRKKFGITRKQARDIVQSCPTCQ 35
transpos_IS481 NF033577
IS481 family transposase; null
 55-159 6.33e-12

IS481 family transposase; null


Pssm-ID: 468094 [Multi-domain]  Cd Length: 283  Bit Score: 64.53  E-value: 6.33e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25121908   55 DCSPGIWQLDCTHL-----EGKV-ILVAVHVASGYIEAEVIPAETGQETAYFLLKL-AGRW-PVKTIHTDNGSNFTGAT- 125
Cdd:NF033577 125 AHPGELWHIDIKKLgripdVGRLyLHTAIDDHSRFAYAELYPDETAETAADFLRRAfAEHGiPIRRVLTDNGSEFRSRAh 204

                         90       100       110
                 ....*....|....*....|....*....|....*
gi 25121908  126 -VRAACWWAGIKQEFGIPYNPQSQGVVESMNKELK 159
Cdd:NF033577 205 gFELALAELGIEHRRTRPYHPQTNGKVERFHRTLK 239
Tra5 COG2801
Transposase InsO and inactivated derivatives [Mobilome: prophages, transposons];
112-195 4.48e-10

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


Pssm-ID: 442053 [Multi-domain]  Cd Length: 309  Bit Score: 59.40  E-value: 4.48e-10
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25121908 112 TIHTDNGSNFTGATVRAACWWAGIKQEFGIPYNPQSQGVVESMNKELKK--IIGQVRDQAEHLKTAVQMAVFIHNFKR-K 188
Cdd:COG2801 211 ILHSDNGSQYTSKAYQELLKKLGITQSMSRPGNPQDNAFIESFFGTLKYelLYRRRFESLEEAREAIEEYIEFYNHERpH 290


                ....*..
gi 25121908 189 GGIGGYS 195
Cdd:COG2801 291 SSLGYLT 297
transpos_IS3 NF033516
IS3 family transposase;
113-159 5.70e-09

IS3 family transposase;


Pssm-ID: 468052 [Multi-domain]  Cd Length: 369  Bit Score: 56.42  E-value: 5.70e-09
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
gi 25121908  113 IHTDNGSNFTGATVRAACWWAGIKQEFGIPYNPQSQGVVESMNKELK 159
Cdd:NF033516 279 LHSDNGSQYTSKAYREWLKEHGITQSMSRPGNCWDNAVAESFFGTLK 325
Tra8 COG2826
Transposase and inactivated derivatives, IS30 family [Mobilome: prophages, transposons];
58-158 9.46e-06

Transposase and inactivated derivatives, IS30 family [Mobilome: prophages, transposons];


Pssm-ID: 442074 [Multi-domain]  Cd Length: 325  Bit Score: 46.41  E-value: 9.46e-06
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25121908  58 PGIWQLDCthLEGK----VILVAVHVASGYIEAEVIPAETGQETAYFLLKLAGRWP---VKTIHTDNGSNFTGatvraac 130
Cdd:COG2826 172 PGHWEGDL--IIGKrgksALLTLVERKSRFVILLKLPDKTAESVADALIRLLRKLPaflRKSITTDNGKEFAD------- 242

                        90       100       110
                ....*....|....*....|....*....|....
gi 25121908 131 wWAGIKQEFGI------PYNPQSQGVVESMNKEL 158
Cdd:COG2826 243 -HKEIEAALGIkvyfadPYSPWQRGTNENTNGLL 275
 
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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