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Conserved domains on  [gi|297523853|emb|CBM41434|]
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polyprotein, partial [HIV-1 M:B 41601508923]

Protein Classification

rve and IN_DBD_C domain-containing protein( domain architecture ID 10461447)

rve and IN_DBD_C domain-containing protein

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 ...
 18-106 1.27e-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: 72.73  E-value: 1.27e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297523853   18 SPGIWQLDCTHLEGKV------ILVAVHVASGYIEAEVIPAETGQETAYFILKLA---GRWPVKIIHTDNGSNFISBTVK 88
Cdd:pfam00665   1 PNQLWQGDFTYIRIPGgggklyLLVIVDDFSREILAWALSSEMDAELVLDALERAiafRGGVPLIIHSDNGSEYTSKAFR 80

                          90
                  ....*....|....*...
gi 297523853   89 AACWWAGIKQEFGIPYNP 106
Cdd:pfam00665  81 EFLKDLGIKPSFSRPGNP 98
IN_DBD_C pfam00552
Integrase DNA binding domain; Integrase mediates integration of a DNA copy of the viral genome ...
 186-229 1.78e-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: 65.50  E-value: 1.78e-14
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 297523853  186 VYYRDSRDPLWKGPAKLLWKGEGAVVI-QDNSDIKVVPRRKVKII 229
Cdd:pfam00552   1 VKWKDLLNGLWKGPDPLLWWGRGAVCVpQDASDPQWVPERLLKRI 45
Tra5 super family cl34487
Transposase InsO and inactivated derivatives [Mobilome: prophages, transposons];
73-156 5.90e-11

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: 60.94  E-value: 5.90e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297523853  73 IIHTDNGSNFISBTVKAACWWAGIKQEFGIPYNPQSQGVVESMNKELKK--IIGQVRDQAEQLKTAVQMAVFIHNFKR-K 149
Cdd:COG2801  211 ILHSDNGSQYTSKAYQELLKKLGITQSMSRPGNPQDNAFIESFFGTLKYelLYRRRFESLEEAREAIEEYIEFYNHERpH 290


                 ....*..
gi 297523853 150 GGIGGYS 156
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 ...
 18-106 1.27e-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: 72.73  E-value: 1.27e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297523853   18 SPGIWQLDCTHLEGKV------ILVAVHVASGYIEAEVIPAETGQETAYFILKLA---GRWPVKIIHTDNGSNFISBTVK 88
Cdd:pfam00665   1 PNQLWQGDFTYIRIPGgggklyLLVIVDDFSREILAWALSSEMDAELVLDALERAiafRGGVPLIIHSDNGSEYTSKAFR 80

                          90
                  ....*....|....*...
gi 297523853   89 AACWWAGIKQEFGIPYNP 106
Cdd:pfam00665  81 EFLKDLGIKPSFSRPGNP 98
IN_DBD_C pfam00552
Integrase DNA binding domain; Integrase mediates integration of a DNA copy of the viral genome ...
 186-229 1.78e-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: 65.50  E-value: 1.78e-14
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 297523853  186 VYYRDSRDPLWKGPAKLLWKGEGAVVI-QDNSDIKVVPRRKVKII 229
Cdd:pfam00552   1 VKWKDLLNGLWKGPDPLLWWGRGAVCVpQDASDPQWVPERLLKRI 45
Tra5 COG2801
Transposase InsO and inactivated derivatives [Mobilome: prophages, transposons];
73-156 5.90e-11

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


Pssm-ID: 442053 [Multi-domain]  Cd Length: 309  Bit Score: 60.94  E-value: 5.90e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297523853  73 IIHTDNGSNFISBTVKAACWWAGIKQEFGIPYNPQSQGVVESMNKELKK--IIGQVRDQAEQLKTAVQMAVFIHNFKR-K 149
Cdd:COG2801  211 ILHSDNGSQYTSKAYQELLKKLGITQSMSRPGNPQDNAFIESFFGTLKYelLYRRRFESLEEAREAIEEYIEFYNHERpH 290


                 ....*..
gi 297523853 150 GGIGGYS 156
Cdd:COG2801  291 SSLGYLT 297
transpos_IS481 NF033577
IS481 family transposase; null
 16-161 2.03e-10

IS481 family transposase; null


Pssm-ID: 468094 [Multi-domain]  Cd Length: 283  Bit Score: 59.14  E-value: 2.03e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297523853  16 DCSPGIWQLDCTHL-----EGKV-ILVAVHVASGYIEAEVIPAETGQETAYFILKL-AGRW-PVKIIHTDNGSNFISBT- 86
Cdd:NF033577 125 AHPGELWHIDIKKLgripdVGRLyLHTAIDDHSRFAYAELYPDETAETAADFLRRAfAEHGiPIRRVLTDNGSEFRSRAh 204

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297523853  87 -VKAACWWAGIKQEFGIPYNPQSQGVVESMNKELKKIIGQVR--DQAEQLKTAvqMAVFIH--NFKRK-GGIGGYSAGER 160
Cdd:NF033577 205 gFELALAELGIEHRRTRPYHPQTNGKVERFHRTLKDEFAYARpyESLAELQAA--LDEWLHhyNHHRPhSALGGKTPAER 282


                 .
gi 297523853 161 I 161
Cdd:NF033577 283 F 283
transpos_IS3 NF033516
IS3 family transposase;
73-120 1.33e-09

IS3 family transposase;


Pssm-ID: 468052 [Multi-domain]  Cd Length: 369  Bit Score: 57.19  E-value: 1.33e-09
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*...
gi 297523853  73 IIHTDNGSNFISBTVKAACWWAGIKQEFGIPYNPQSQGVVESMNKELK 120
Cdd:NF033516 278 ILHSDNGSQYTSKAYREWLKEHGITQSMSRPGNCWDNAVAESFFGTLK 325
 
Name Accession Description Interval E-value
rve pfam00665
Integrase core domain; Integrase mediates integration of a DNA copy of the viral genome into ...
 18-106 1.27e-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: 72.73  E-value: 1.27e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297523853   18 SPGIWQLDCTHLEGKV------ILVAVHVASGYIEAEVIPAETGQETAYFILKLA---GRWPVKIIHTDNGSNFISBTVK 88
Cdd:pfam00665   1 PNQLWQGDFTYIRIPGgggklyLLVIVDDFSREILAWALSSEMDAELVLDALERAiafRGGVPLIIHSDNGSEYTSKAFR 80

                          90
                  ....*....|....*...
gi 297523853   89 AACWWAGIKQEFGIPYNP 106
Cdd:pfam00665  81 EFLKDLGIKPSFSRPGNP 98
IN_DBD_C pfam00552
Integrase DNA binding domain; Integrase mediates integration of a DNA copy of the viral genome ...
 186-229 1.78e-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: 65.50  E-value: 1.78e-14
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 297523853  186 VYYRDSRDPLWKGPAKLLWKGEGAVVI-QDNSDIKVVPRRKVKII 229
Cdd:pfam00552   1 VKWKDLLNGLWKGPDPLLWWGRGAVCVpQDASDPQWVPERLLKRI 45
Tra5 COG2801
Transposase InsO and inactivated derivatives [Mobilome: prophages, transposons];
73-156 5.90e-11

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


Pssm-ID: 442053 [Multi-domain]  Cd Length: 309  Bit Score: 60.94  E-value: 5.90e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297523853  73 IIHTDNGSNFISBTVKAACWWAGIKQEFGIPYNPQSQGVVESMNKELKK--IIGQVRDQAEQLKTAVQMAVFIHNFKR-K 149
Cdd:COG2801  211 ILHSDNGSQYTSKAYQELLKKLGITQSMSRPGNPQDNAFIESFFGTLKYelLYRRRFESLEEAREAIEEYIEFYNHERpH 290


                 ....*..
gi 297523853 150 GGIGGYS 156
Cdd:COG2801  291 SSLGYLT 297
transpos_IS481 NF033577
IS481 family transposase; null
 16-161 2.03e-10

IS481 family transposase; null


Pssm-ID: 468094 [Multi-domain]  Cd Length: 283  Bit Score: 59.14  E-value: 2.03e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297523853  16 DCSPGIWQLDCTHL-----EGKV-ILVAVHVASGYIEAEVIPAETGQETAYFILKL-AGRW-PVKIIHTDNGSNFISBT- 86
Cdd:NF033577 125 AHPGELWHIDIKKLgripdVGRLyLHTAIDDHSRFAYAELYPDETAETAADFLRRAfAEHGiPIRRVLTDNGSEFRSRAh 204

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297523853  87 -VKAACWWAGIKQEFGIPYNPQSQGVVESMNKELKKIIGQVR--DQAEQLKTAvqMAVFIH--NFKRK-GGIGGYSAGER 160
Cdd:NF033577 205 gFELALAELGIEHRRTRPYHPQTNGKVERFHRTLKDEFAYARpyESLAELQAA--LDEWLHhyNHHRPhSALGGKTPAER 282


                 .
gi 297523853 161 I 161
Cdd:NF033577 283 F 283
transpos_IS3 NF033516
IS3 family transposase;
73-120 1.33e-09

IS3 family transposase;


Pssm-ID: 468052 [Multi-domain]  Cd Length: 369  Bit Score: 57.19  E-value: 1.33e-09
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*...
gi 297523853  73 IIHTDNGSNFISBTVKAACWWAGIKQEFGIPYNPQSQGVVESMNKELK 120
Cdd:NF033516 278 ILHSDNGSQYTSKAYREWLKEHGITQSMSRPGNCWDNAVAESFFGTLK 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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