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Conserved domains on  [gi|1808736193|pdb|6PUW|A]
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Chain A, Chimeric Sso7d and HIV-1 integrase

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
7kD_DNA_binding pfam02294
7kD DNA-binding domain; This family contains members of the hyper-thermophilic archaebacterium ...
 23-81 1.17e-29

7kD DNA-binding domain; This family contains members of the hyper-thermophilic archaebacterium 7kD DNA-binding/endoribonuclease P2 family. There are five 7kD DNA-binding proteins, 7a-7e, found as monomers in the cell. Protein 7e shows the tightest DNA-binding ability.


:

Pssm-ID: 280458  Cd Length: 58  Bit Score: 108.94  E-value: 1.17e-29
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
6PUW_A         23 TVKFKYKGEEKEVDISKIKKVWRVGKMISFTYDEgGGKTGRGAVSEKDAPKELLQMLEK 81
Cdd:pfam02294   1 KVKFKYKGEEKEVDISKIKKVWRVGKMVSFTYDD-NGKTGRGAVSEKDAPKELLNMLGK 58
rve pfam00665
Integrase core domain; Integrase mediates integration of a DNA copy of the viral genome into ...
 152-240 7.59e-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: 7.59e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
6PUW_A        152 SPGIWQLDCTHLEGKV------ILVAVHVASGYIEAEVIPAETGQETAYFLLKLA---GRWPVKTVHTDNGSNFTSTTVK 222
Cdd:pfam00665   1 PNQLWQGDFTYIRIPGgggklyLLVIVDDFSREILAWALSSEMDAELVLDALERAiafRGGVPLIIHSDNGSEYTSKAFR 80

                          90
                  ....*....|....*...
6PUW_A        223 AACWWAGIKQEFGIPYNP 240
Cdd:pfam00665  81 EFLKDLGIKPSFSRPGNP 98
IN_DBD_C pfam00552
Integrase DNA binding domain; Integrase mediates integration of a DNA copy of the viral genome ...
 320-363 1.18e-13

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: 64.73  E-value: 1.18e-13
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
6PUW_A        320 VYYRDSRDPVWKGPAKLLWKGEGAVVI-QDNSDIKVVPRRKAKII 363
Cdd:pfam00552   1 VKWKDLLNGLWKGPDPLLWWGRGAVCVpQDASDPQWVPERLLKRI 45
Integrase_Zn pfam02022
Integrase Zinc binding domain; Integrase mediates integration of a DNA copy of the viral ...
 105-139 3.17e-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: 63.16  E-value: 3.17e-13
                          10        20        30
                  ....*....|....*....|....*....|....*
6PUW_A        105 EEHEKYHSNWRAMASDFNLPPVVAKEIVASCDKCQ 139
Cdd:pfam02022   1 ELHSLHHVNAKALRKKFGITRKQARDIVQSCPTCQ 35
Tra5 super family cl34487
Transposase InsO and inactivated derivatives [Mobilome: prophages, transposons];
207-290 3.34e-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: 60.55  E-value: 3.34e-10
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
6PUW_A      207 TVHTDNGSNFTSTTVKAACWWAGIKQEFGIPYNPQSQGVIESMNKELKK--IIGQVRDQAEHLKTAVQMAVFIHNFKR-K 283
Cdd:COG2801 211 ILHSDNGSQYTSKAYQELLKKLGITQSMSRPGNPQDNAFIESFFGTLKYelLYRRRFESLEEAREAIEEYIEFYNHERpH 290


                ....*..
6PUW_A      284 GGIGGYS 290
Cdd:COG2801 291 SSLGYLT 297
 
Name Accession Description Interval E-value
7kD_DNA_binding pfam02294
7kD DNA-binding domain; This family contains members of the hyper-thermophilic archaebacterium ...
 23-81 1.17e-29

7kD DNA-binding domain; This family contains members of the hyper-thermophilic archaebacterium 7kD DNA-binding/endoribonuclease P2 family. There are five 7kD DNA-binding proteins, 7a-7e, found as monomers in the cell. Protein 7e shows the tightest DNA-binding ability.


Pssm-ID: 280458  Cd Length: 58  Bit Score: 108.94  E-value: 1.17e-29
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
6PUW_A         23 TVKFKYKGEEKEVDISKIKKVWRVGKMISFTYDEgGGKTGRGAVSEKDAPKELLQMLEK 81
Cdd:pfam02294   1 KVKFKYKGEEKEVDISKIKKVWRVGKMVSFTYDD-NGKTGRGAVSEKDAPKELLNMLGK 58
rve pfam00665
Integrase core domain; Integrase mediates integration of a DNA copy of the viral genome into ...
 152-240 7.59e-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: 7.59e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
6PUW_A        152 SPGIWQLDCTHLEGKV------ILVAVHVASGYIEAEVIPAETGQETAYFLLKLA---GRWPVKTVHTDNGSNFTSTTVK 222
Cdd:pfam00665   1 PNQLWQGDFTYIRIPGgggklyLLVIVDDFSREILAWALSSEMDAELVLDALERAiafRGGVPLIIHSDNGSEYTSKAFR 80

                          90
                  ....*....|....*...
6PUW_A        223 AACWWAGIKQEFGIPYNP 240
Cdd:pfam00665  81 EFLKDLGIKPSFSRPGNP 98
IN_DBD_C pfam00552
Integrase DNA binding domain; Integrase mediates integration of a DNA copy of the viral genome ...
 320-363 1.18e-13

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: 64.73  E-value: 1.18e-13
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
6PUW_A        320 VYYRDSRDPVWKGPAKLLWKGEGAVVI-QDNSDIKVVPRRKAKII 363
Cdd:pfam00552   1 VKWKDLLNGLWKGPDPLLWWGRGAVCVpQDASDPQWVPERLLKRI 45
Integrase_Zn pfam02022
Integrase Zinc binding domain; Integrase mediates integration of a DNA copy of the viral ...
 105-139 3.17e-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: 63.16  E-value: 3.17e-13
                          10        20        30
                  ....*....|....*....|....*....|....*
6PUW_A        105 EEHEKYHSNWRAMASDFNLPPVVAKEIVASCDKCQ 139
Cdd:pfam02022   1 ELHSLHHVNAKALRKKFGITRKQARDIVQSCPTCQ 35
transpos_IS481 NF033577
IS481 family transposase; null
 150-254 3.21e-11

IS481 family transposase; null


Pssm-ID: 468094 [Multi-domain]  Cd Length: 283  Bit Score: 63.38  E-value: 3.21e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
6PUW_A       150 DCSPGIWQLDCTHL-----EGKV-ILVAVHVASGYIEAEVIPAETGQETAYFLLKL-AGRW-PVKTVHTDNGSNFTSTT- 220
Cdd:NF033577 125 AHPGELWHIDIKKLgripdVGRLyLHTAIDDHSRFAYAELYPDETAETAADFLRRAfAEHGiPIRRVLTDNGSEFRSRAh 204

                         90       100       110
                 ....*....|....*....|....*....|....*
6PUW_A       221 -VKAACWWAGIKQEFGIPYNPQSQGVIESMNKELK 254
Cdd:NF033577 205 gFELALAELGIEHRRTRPYHPQTNGKVERFHRTLK 239
Tra5 COG2801
Transposase InsO and inactivated derivatives [Mobilome: prophages, transposons];
207-290 3.34e-10

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


Pssm-ID: 442053 [Multi-domain]  Cd Length: 309  Bit Score: 60.55  E-value: 3.34e-10
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
6PUW_A      207 TVHTDNGSNFTSTTVKAACWWAGIKQEFGIPYNPQSQGVIESMNKELKK--IIGQVRDQAEHLKTAVQMAVFIHNFKR-K 283
Cdd:COG2801 211 ILHSDNGSQYTSKAYQELLKKLGITQSMSRPGNPQDNAFIESFFGTLKYelLYRRRFESLEEAREAIEEYIEFYNHERpH 290


                ....*..
6PUW_A      284 GGIGGYS 290
Cdd:COG2801 291 SSLGYLT 297
transpos_IS3 NF033516
IS3 family transposase;
208-254 1.92e-08

IS3 family transposase;


Pssm-ID: 468052 [Multi-domain]  Cd Length: 369  Bit Score: 55.65  E-value: 1.92e-08
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
6PUW_A       208 VHTDNGSNFTSTTVKAACWWAGIKQEFGIPYNPQSQGVIESMNKELK 254
Cdd:NF033516 279 LHSDNGSQYTSKAYREWLKEHGITQSMSRPGNCWDNAVAESFFGTLK 325
 
Name Accession Description Interval E-value
7kD_DNA_binding pfam02294
7kD DNA-binding domain; This family contains members of the hyper-thermophilic archaebacterium ...
 23-81 1.17e-29

7kD DNA-binding domain; This family contains members of the hyper-thermophilic archaebacterium 7kD DNA-binding/endoribonuclease P2 family. There are five 7kD DNA-binding proteins, 7a-7e, found as monomers in the cell. Protein 7e shows the tightest DNA-binding ability.


Pssm-ID: 280458  Cd Length: 58  Bit Score: 108.94  E-value: 1.17e-29
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
6PUW_A         23 TVKFKYKGEEKEVDISKIKKVWRVGKMISFTYDEgGGKTGRGAVSEKDAPKELLQMLEK 81
Cdd:pfam02294   1 KVKFKYKGEEKEVDISKIKKVWRVGKMVSFTYDD-NGKTGRGAVSEKDAPKELLNMLGK 58
rve pfam00665
Integrase core domain; Integrase mediates integration of a DNA copy of the viral genome into ...
 152-240 7.59e-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: 7.59e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
6PUW_A        152 SPGIWQLDCTHLEGKV------ILVAVHVASGYIEAEVIPAETGQETAYFLLKLA---GRWPVKTVHTDNGSNFTSTTVK 222
Cdd:pfam00665   1 PNQLWQGDFTYIRIPGgggklyLLVIVDDFSREILAWALSSEMDAELVLDALERAiafRGGVPLIIHSDNGSEYTSKAFR 80

                          90
                  ....*....|....*...
6PUW_A        223 AACWWAGIKQEFGIPYNP 240
Cdd:pfam00665  81 EFLKDLGIKPSFSRPGNP 98
IN_DBD_C pfam00552
Integrase DNA binding domain; Integrase mediates integration of a DNA copy of the viral genome ...
 320-363 1.18e-13

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: 64.73  E-value: 1.18e-13
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
6PUW_A        320 VYYRDSRDPVWKGPAKLLWKGEGAVVI-QDNSDIKVVPRRKAKII 363
Cdd:pfam00552   1 VKWKDLLNGLWKGPDPLLWWGRGAVCVpQDASDPQWVPERLLKRI 45
Integrase_Zn pfam02022
Integrase Zinc binding domain; Integrase mediates integration of a DNA copy of the viral ...
 105-139 3.17e-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: 63.16  E-value: 3.17e-13
                          10        20        30
                  ....*....|....*....|....*....|....*
6PUW_A        105 EEHEKYHSNWRAMASDFNLPPVVAKEIVASCDKCQ 139
Cdd:pfam02022   1 ELHSLHHVNAKALRKKFGITRKQARDIVQSCPTCQ 35
transpos_IS481 NF033577
IS481 family transposase; null
 150-254 3.21e-11

IS481 family transposase; null


Pssm-ID: 468094 [Multi-domain]  Cd Length: 283  Bit Score: 63.38  E-value: 3.21e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
6PUW_A       150 DCSPGIWQLDCTHL-----EGKV-ILVAVHVASGYIEAEVIPAETGQETAYFLLKL-AGRW-PVKTVHTDNGSNFTSTT- 220
Cdd:NF033577 125 AHPGELWHIDIKKLgripdVGRLyLHTAIDDHSRFAYAELYPDETAETAADFLRRAfAEHGiPIRRVLTDNGSEFRSRAh 204

                         90       100       110
                 ....*....|....*....|....*....|....*
6PUW_A       221 -VKAACWWAGIKQEFGIPYNPQSQGVIESMNKELK 254
Cdd:NF033577 205 gFELALAELGIEHRRTRPYHPQTNGKVERFHRTLK 239
Tra5 COG2801
Transposase InsO and inactivated derivatives [Mobilome: prophages, transposons];
207-290 3.34e-10

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


Pssm-ID: 442053 [Multi-domain]  Cd Length: 309  Bit Score: 60.55  E-value: 3.34e-10
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
6PUW_A      207 TVHTDNGSNFTSTTVKAACWWAGIKQEFGIPYNPQSQGVIESMNKELKK--IIGQVRDQAEHLKTAVQMAVFIHNFKR-K 283
Cdd:COG2801 211 ILHSDNGSQYTSKAYQELLKKLGITQSMSRPGNPQDNAFIESFFGTLKYelLYRRRFESLEEAREAIEEYIEFYNHERpH 290


                ....*..
6PUW_A      284 GGIGGYS 290
Cdd:COG2801 291 SSLGYLT 297
transpos_IS3 NF033516
IS3 family transposase;
208-254 1.92e-08

IS3 family transposase;


Pssm-ID: 468052 [Multi-domain]  Cd Length: 369  Bit Score: 55.65  E-value: 1.92e-08
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
6PUW_A       208 VHTDNGSNFTSTTVKAACWWAGIKQEFGIPYNPQSQGVIESMNKELK 254
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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