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Conserved domains on  [gi|2125450422|gb|UDP24497|]
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integrase, partial [Human immunodeficiency virus 1]

Protein Classification

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 ...
 10-98 2.44e-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: 69.27  E-value: 2.44e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2125450422  10 SPGIWQLDCTHLEGKI------IIVAVHVASGYIEAEVIPAETGQETAYFILKLA---GRWPVKVVHTDNGSNFTSAAVK 80
Cdd:pfam00665   1 PNQLWQGDFTYIRIPGgggklyLLVIVDDFSREILAWALSSEMDAELVLDALERAiafRGGVPLIIHSDNGSEYTSKAFR 80

                          90
                  ....*....|....*...
gi 2125450422  81 AACWWANITQEFGIPYNP 98
Cdd:pfam00665  81 EFLKDLGIKPSFSRPGNP 98
IN_DBD_C pfam00552
Integrase DNA binding domain; Integrase mediates integration of a DNA copy of the viral genome ...
 178-221 5.09e-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: 64.34  E-value: 5.09e-14
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 2125450422 178 VYYRDSRDPIWKGPAKLLWKGEGAVVI-QDNSDIKVVPRRKAKII 221
Cdd:pfam00552   1 VKWKDLLNGLWKGPDPLLWWGRGAVCVpQDASDPQWVPERLLKRI 45
Tra5 super family cl34487
Transposase InsO and inactivated derivatives [Mobilome: prophages, transposons];
65-148 1.58e-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: 59.78  E-value: 1.58e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2125450422  65 VVHTDNGSNFTSAAVKAACWWANITQEFGIPYNPQSQGVVESMNKELKK--IIEQVRDQAEHLKTAVQMAVFIHNFKR-K 141
Cdd:COG2801   211 ILHSDNGSQYTSKAYQELLKKLGITQSMSRPGNPQDNAFIESFFGTLKYelLYRRRFESLEEAREAIEEYIEFYNHERpH 290


                  ....*..
gi 2125450422 142 GGIGGYS 148
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 ...
 10-98 2.44e-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: 69.27  E-value: 2.44e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2125450422  10 SPGIWQLDCTHLEGKI------IIVAVHVASGYIEAEVIPAETGQETAYFILKLA---GRWPVKVVHTDNGSNFTSAAVK 80
Cdd:pfam00665   1 PNQLWQGDFTYIRIPGgggklyLLVIVDDFSREILAWALSSEMDAELVLDALERAiafRGGVPLIIHSDNGSEYTSKAFR 80

                          90
                  ....*....|....*...
gi 2125450422  81 AACWWANITQEFGIPYNP 98
Cdd:pfam00665  81 EFLKDLGIKPSFSRPGNP 98
IN_DBD_C pfam00552
Integrase DNA binding domain; Integrase mediates integration of a DNA copy of the viral genome ...
 178-221 5.09e-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: 64.34  E-value: 5.09e-14
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 2125450422 178 VYYRDSRDPIWKGPAKLLWKGEGAVVI-QDNSDIKVVPRRKAKII 221
Cdd:pfam00552   1 VKWKDLLNGLWKGPDPLLWWGRGAVCVpQDASDPQWVPERLLKRI 45
Tra5 COG2801
Transposase InsO and inactivated derivatives [Mobilome: prophages, transposons];
65-148 1.58e-10

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


Pssm-ID: 442053 [Multi-domain]  Cd Length: 309  Bit Score: 59.78  E-value: 1.58e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2125450422  65 VVHTDNGSNFTSAAVKAACWWANITQEFGIPYNPQSQGVVESMNKELKK--IIEQVRDQAEHLKTAVQMAVFIHNFKR-K 141
Cdd:COG2801   211 ILHSDNGSQYTSKAYQELLKKLGITQSMSRPGNPQDNAFIESFFGTLKYelLYRRRFESLEEAREAIEEYIEFYNHERpH 290


                  ....*..
gi 2125450422 142 GGIGGYS 148
Cdd:COG2801   291 SSLGYLT 297
transpos_IS3 NF033516
IS3 family transposase;
65-112 1.76e-09

IS3 family transposase;


Pssm-ID: 468052 [Multi-domain]  Cd Length: 369  Bit Score: 56.80  E-value: 1.76e-09
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 2125450422  65 VVHTDNGSNFTSAAVKAACWWANITQEFGIPYNPQSQGVVESMNKELK 112
Cdd:NF033516  278 ILHSDNGSQYTSKAYREWLKEHGITQSMSRPGNCWDNAVAESFFGTLK 325
transpos_IS481 NF033577
IS481 family transposase; null
 8-153 2.93e-09

IS481 family transposase; null


Pssm-ID: 468094 [Multi-domain]  Cd Length: 283  Bit Score: 56.06  E-value: 2.93e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2125450422   8 DCSPGIWQLDCTHL-----EGKI-IIVAVHVASGYIEAEVIPAETGQETAYFILKLAGRWPVKV--VHTDNGSNFTSAA- 78
Cdd:NF033577  125 AHPGELWHIDIKKLgripdVGRLyLHTAIDDHSRFAYAELYPDETAETAADFLRRAFAEHGIPIrrVLTDNGSEFRSRAh 204

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2125450422  79 -VKAACWWANITQEFGIPYNPQSQGVVESMNKELK------KIIEQVRDQAEHLktavqmAVFIH--NFKRK-GGIGGYS 148
Cdd:NF033577  205 gFELALAELGIEHRRTRPYHPQTNGKVERFHRTLKdefayaRPYESLAELQAAL------DEWLHhyNHHRPhSALGGKT 278


                  ....*
gi 2125450422 149 AGERI 153
Cdd:NF033577  279 PAERF 283
 
Name Accession Description Interval E-value
rve pfam00665
Integrase core domain; Integrase mediates integration of a DNA copy of the viral genome into ...
 10-98 2.44e-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: 69.27  E-value: 2.44e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2125450422  10 SPGIWQLDCTHLEGKI------IIVAVHVASGYIEAEVIPAETGQETAYFILKLA---GRWPVKVVHTDNGSNFTSAAVK 80
Cdd:pfam00665   1 PNQLWQGDFTYIRIPGgggklyLLVIVDDFSREILAWALSSEMDAELVLDALERAiafRGGVPLIIHSDNGSEYTSKAFR 80

                          90
                  ....*....|....*...
gi 2125450422  81 AACWWANITQEFGIPYNP 98
Cdd:pfam00665  81 EFLKDLGIKPSFSRPGNP 98
IN_DBD_C pfam00552
Integrase DNA binding domain; Integrase mediates integration of a DNA copy of the viral genome ...
 178-221 5.09e-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: 64.34  E-value: 5.09e-14
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 2125450422 178 VYYRDSRDPIWKGPAKLLWKGEGAVVI-QDNSDIKVVPRRKAKII 221
Cdd:pfam00552   1 VKWKDLLNGLWKGPDPLLWWGRGAVCVpQDASDPQWVPERLLKRI 45
Tra5 COG2801
Transposase InsO and inactivated derivatives [Mobilome: prophages, transposons];
65-148 1.58e-10

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


Pssm-ID: 442053 [Multi-domain]  Cd Length: 309  Bit Score: 59.78  E-value: 1.58e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2125450422  65 VVHTDNGSNFTSAAVKAACWWANITQEFGIPYNPQSQGVVESMNKELKK--IIEQVRDQAEHLKTAVQMAVFIHNFKR-K 141
Cdd:COG2801   211 ILHSDNGSQYTSKAYQELLKKLGITQSMSRPGNPQDNAFIESFFGTLKYelLYRRRFESLEEAREAIEEYIEFYNHERpH 290


                  ....*..
gi 2125450422 142 GGIGGYS 148
Cdd:COG2801   291 SSLGYLT 297
transpos_IS3 NF033516
IS3 family transposase;
65-112 1.76e-09

IS3 family transposase;


Pssm-ID: 468052 [Multi-domain]  Cd Length: 369  Bit Score: 56.80  E-value: 1.76e-09
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 2125450422  65 VVHTDNGSNFTSAAVKAACWWANITQEFGIPYNPQSQGVVESMNKELK 112
Cdd:NF033516  278 ILHSDNGSQYTSKAYREWLKEHGITQSMSRPGNCWDNAVAESFFGTLK 325
transpos_IS481 NF033577
IS481 family transposase; null
 8-153 2.93e-09

IS481 family transposase; null


Pssm-ID: 468094 [Multi-domain]  Cd Length: 283  Bit Score: 56.06  E-value: 2.93e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2125450422   8 DCSPGIWQLDCTHL-----EGKI-IIVAVHVASGYIEAEVIPAETGQETAYFILKLAGRWPVKV--VHTDNGSNFTSAA- 78
Cdd:NF033577  125 AHPGELWHIDIKKLgripdVGRLyLHTAIDDHSRFAYAELYPDETAETAADFLRRAFAEHGIPIrrVLTDNGSEFRSRAh 204

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2125450422  79 -VKAACWWANITQEFGIPYNPQSQGVVESMNKELK------KIIEQVRDQAEHLktavqmAVFIH--NFKRK-GGIGGYS 148
Cdd:NF033577  205 gFELALAELGIEHRRTRPYHPQTNGKVERFHRTLKdefayaRPYESLAELQAAL------DEWLHhyNHHRPhSALGGKT 278


                  ....*
gi 2125450422 149 AGERI 153
Cdd:NF033577  279 PAERF 283
 
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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