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Conserved domains on  [gi|1752309985]
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Chain P, Integrase

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
SH3_11 pfam18103
Retroviral integrase C-terminal SH3 domain; This is the carboxy-terminal domain (CTD) found in ...
 316-378 6.95e-38

Retroviral integrase C-terminal SH3 domain; This is the carboxy-terminal domain (CTD) found in retroviral integrase, an essential retroviral enzyme that binds both termini of linear viral DNA and inserts them into a host cell chromosome. The CTD adopts an SH3-like fold. Each CTD makes contact with the phosphodiester backbone of both viral DNA molecules, essentially crosslinking the structure.


:

Pssm-ID: 375552  Cd Length: 63  Bit Score: 131.10  E-value: 6.95e-38
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1752309985 316 RSWSPVVGQLVQERVARPASLRPRWHKPSTVLKVLNPRTVVILDHLGNNRTVSIDNLKPTSHQ 378
Cdd:pfam18103   1 RSWSPVVGQLVQERVARPASLRPRWHKPSTVLEVLNPRTVVILDHLGNNRTVSIDNLKPTSHQ 63
rve pfam00665
Integrase core domain; Integrase mediates integration of a DNA copy of the viral genome into ...
 124-217 3.23e-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: 73.50  E-value: 3.23e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1752309985 124 PFDKFFIDYI-GPLPPSQGYLYVLVVVDGMTGFTWLYP-TKAPSTSATVKSLNVLTSIA--IPKVIHSDQGAAFTSSTFA 199
Cdd:pfam00665   1 PNQLWQGDFTyIRIPGGGGKLYLLVIVDDFSREILAWAlSSEMDAELVLDALERAIAFRggVPLIIHSDNGSEYTSKAFR 80

                          90
                  ....*....|....*...
gi 1752309985 200 EWAKERGIHLEFSTPYHP 217
Cdd:pfam00665  81 EFLKDLGIKPSFSRPGNP 98
Integrase_H2C2 pfam17921
Integrase zinc binding domain; This zinc binding domain is found in a wide variety of ...
 52-108 2.39e-14

Integrase zinc binding domain; This zinc binding domain is found in a wide variety of integrase proteins.


:

Pssm-ID: 465569 [Multi-domain]  Cd Length: 58  Bit Score: 66.89  E-value: 2.39e-14
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1752309985  52 PPQSDRQKIVLQAHNLA-HTGREATLLKIANLYWWPNMRKDVVKQLGRCQQCLITNAS 108
Cdd:pfam17921   1 VPKSLRKEILKEAHDSGgHLGIEKTLARLRRRYWWPGMRKDVKKYVKSCETCQRRKPS 58
 
Name Accession Description Interval E-value
SH3_11 pfam18103
Retroviral integrase C-terminal SH3 domain; This is the carboxy-terminal domain (CTD) found in ...
 316-378 6.95e-38

Retroviral integrase C-terminal SH3 domain; This is the carboxy-terminal domain (CTD) found in retroviral integrase, an essential retroviral enzyme that binds both termini of linear viral DNA and inserts them into a host cell chromosome. The CTD adopts an SH3-like fold. Each CTD makes contact with the phosphodiester backbone of both viral DNA molecules, essentially crosslinking the structure.


Pssm-ID: 375552  Cd Length: 63  Bit Score: 131.10  E-value: 6.95e-38
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1752309985 316 RSWSPVVGQLVQERVARPASLRPRWHKPSTVLKVLNPRTVVILDHLGNNRTVSIDNLKPTSHQ 378
Cdd:pfam18103   1 RSWSPVVGQLVQERVARPASLRPRWHKPSTVLEVLNPRTVVILDHLGNNRTVSIDNLKPTSHQ 63
rve pfam00665
Integrase core domain; Integrase mediates integration of a DNA copy of the viral genome into ...
 124-217 3.23e-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: 73.50  E-value: 3.23e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1752309985 124 PFDKFFIDYI-GPLPPSQGYLYVLVVVDGMTGFTWLYP-TKAPSTSATVKSLNVLTSIA--IPKVIHSDQGAAFTSSTFA 199
Cdd:pfam00665   1 PNQLWQGDFTyIRIPGGGGKLYLLVIVDDFSREILAWAlSSEMDAELVLDALERAIAFRggVPLIIHSDNGSEYTSKAFR 80

                          90
                  ....*....|....*...
gi 1752309985 200 EWAKERGIHLEFSTPYHP 217
Cdd:pfam00665  81 EFLKDLGIKPSFSRPGNP 98
Integrase_H2C2 pfam17921
Integrase zinc binding domain; This zinc binding domain is found in a wide variety of ...
 52-108 2.39e-14

Integrase zinc binding domain; This zinc binding domain is found in a wide variety of integrase proteins.


Pssm-ID: 465569 [Multi-domain]  Cd Length: 58  Bit Score: 66.89  E-value: 2.39e-14
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1752309985  52 PPQSDRQKIVLQAHNLA-HTGREATLLKIANLYWWPNMRKDVVKQLGRCQQCLITNAS 108
Cdd:pfam17921   1 VPKSLRKEILKEAHDSGgHLGIEKTLARLRRRYWWPGMRKDVKKYVKSCETCQRRKPS 58
Tra5 COG2801
Transposase InsO and inactivated derivatives [Mobilome: prophages, transposons];
121-232 2.10e-11

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


Pssm-ID: 442053 [Multi-domain]  Cd Length: 309  Bit Score: 64.40  E-value: 2.10e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1752309985 121 PQKPFDKFFID--YIgPLPpsQGYLYVLVVVDGmtgFT-----WlyptkapSTSATVKSLNVLTSI--AI-------PKV 184
Cdd:COG2801   145 ATAPNQVWVTDitYI-PTA--EGWLYLAAVIDL---FSreivgW-------SVSDSMDAELVVDALemAIerrgppkPLI 211

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*...
gi 1752309985 185 IHSDQGAAFTSSTFAEWAKERGIHLEFSTPYHPQSSGKVERKNSDIKR 232
Cdd:COG2801   212 LHSDNGSQYTSKAYQELLKKLGITQSMSRPGNPQDNAFIESFFGTLKY 259
transpos_IS481 NF033577
IS481 family transposase; null
 106-232 2.79e-09

IS481 family transposase; null


Pssm-ID: 468094 [Multi-domain]  Cd Length: 283  Bit Score: 57.60  E-value: 2.79e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1752309985 106 NASNKASGPILRPDRPQkPFDKFFID--YIGPLPpSQGYLYVLVVVDGMT--GFTWLYPTKAPSTSATVksL-NVLTSIA 180
Cdd:NF033577  110 RALDRKTGKVKRYERAH-PGELWHIDikKLGRIP-DVGRLYLHTAIDDHSrfAYAELYPDETAETAADF--LrRAFAEHG 185

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1752309985 181 IP-KVIHSDQGAAFTSST--FAEWAKERGIHLEFSTPYHPQSSGKVERKNSDIKR 232
Cdd:NF033577  186 IPiRRVLTDNGSEFRSRAhgFELALAELGIEHRRTRPYHPQTNGKVERFHRTLKD 240
transpos_IS3 NF033516
IS3 family transposase;
140-232 3.23e-09

IS3 family transposase;


Pssm-ID: 468052 [Multi-domain]  Cd Length: 369  Bit Score: 57.96  E-value: 3.23e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1752309985 140 QGYLYVLVVVDGmtgFT-----WlYPTKAPSTSATVKSLNvltsIAI-------PKVIHSDQGAAFTSSTFAEWAKERGI 207
Cdd:NF033516  230 EGWLYLAVVLDL---FSreivgW-SVSTSMSAELVLDALE----MAIewrgkpeGLILHSDNGSQYTSKAYREWLKEHGI 301

                          90       100
                  ....*....|....*....|....*
gi 1752309985 208 HLEFSTPYHPQSSGKVERKNSDIKR 232
Cdd:NF033516  302 TQSMSRPGNCWDNAVAESFFGTLKR 326
 
Name Accession Description Interval E-value
SH3_11 pfam18103
Retroviral integrase C-terminal SH3 domain; This is the carboxy-terminal domain (CTD) found in ...
 316-378 6.95e-38

Retroviral integrase C-terminal SH3 domain; This is the carboxy-terminal domain (CTD) found in retroviral integrase, an essential retroviral enzyme that binds both termini of linear viral DNA and inserts them into a host cell chromosome. The CTD adopts an SH3-like fold. Each CTD makes contact with the phosphodiester backbone of both viral DNA molecules, essentially crosslinking the structure.


Pssm-ID: 375552  Cd Length: 63  Bit Score: 131.10  E-value: 6.95e-38
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1752309985 316 RSWSPVVGQLVQERVARPASLRPRWHKPSTVLKVLNPRTVVILDHLGNNRTVSIDNLKPTSHQ 378
Cdd:pfam18103   1 RSWSPVVGQLVQERVARPASLRPRWHKPSTVLEVLNPRTVVILDHLGNNRTVSIDNLKPTSHQ 63
rve pfam00665
Integrase core domain; Integrase mediates integration of a DNA copy of the viral genome into ...
 124-217 3.23e-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: 73.50  E-value: 3.23e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1752309985 124 PFDKFFIDYI-GPLPPSQGYLYVLVVVDGMTGFTWLYP-TKAPSTSATVKSLNVLTSIA--IPKVIHSDQGAAFTSSTFA 199
Cdd:pfam00665   1 PNQLWQGDFTyIRIPGGGGKLYLLVIVDDFSREILAWAlSSEMDAELVLDALERAIAFRggVPLIIHSDNGSEYTSKAFR 80

                          90
                  ....*....|....*...
gi 1752309985 200 EWAKERGIHLEFSTPYHP 217
Cdd:pfam00665  81 EFLKDLGIKPSFSRPGNP 98
Integrase_H2C2 pfam17921
Integrase zinc binding domain; This zinc binding domain is found in a wide variety of ...
 52-108 2.39e-14

Integrase zinc binding domain; This zinc binding domain is found in a wide variety of integrase proteins.


Pssm-ID: 465569 [Multi-domain]  Cd Length: 58  Bit Score: 66.89  E-value: 2.39e-14
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1752309985  52 PPQSDRQKIVLQAHNLA-HTGREATLLKIANLYWWPNMRKDVVKQLGRCQQCLITNAS 108
Cdd:pfam17921   1 VPKSLRKEILKEAHDSGgHLGIEKTLARLRRRYWWPGMRKDVKKYVKSCETCQRRKPS 58
Tra5 COG2801
Transposase InsO and inactivated derivatives [Mobilome: prophages, transposons];
121-232 2.10e-11

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


Pssm-ID: 442053 [Multi-domain]  Cd Length: 309  Bit Score: 64.40  E-value: 2.10e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1752309985 121 PQKPFDKFFID--YIgPLPpsQGYLYVLVVVDGmtgFT-----WlyptkapSTSATVKSLNVLTSI--AI-------PKV 184
Cdd:COG2801   145 ATAPNQVWVTDitYI-PTA--EGWLYLAAVIDL---FSreivgW-------SVSDSMDAELVVDALemAIerrgppkPLI 211

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*...
gi 1752309985 185 IHSDQGAAFTSSTFAEWAKERGIHLEFSTPYHPQSSGKVERKNSDIKR 232
Cdd:COG2801   212 LHSDNGSQYTSKAYQELLKKLGITQSMSRPGNPQDNAFIESFFGTLKY 259
transpos_IS481 NF033577
IS481 family transposase; null
 106-232 2.79e-09

IS481 family transposase; null


Pssm-ID: 468094 [Multi-domain]  Cd Length: 283  Bit Score: 57.60  E-value: 2.79e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1752309985 106 NASNKASGPILRPDRPQkPFDKFFID--YIGPLPpSQGYLYVLVVVDGMT--GFTWLYPTKAPSTSATVksL-NVLTSIA 180
Cdd:NF033577  110 RALDRKTGKVKRYERAH-PGELWHIDikKLGRIP-DVGRLYLHTAIDDHSrfAYAELYPDETAETAADF--LrRAFAEHG 185

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1752309985 181 IP-KVIHSDQGAAFTSST--FAEWAKERGIHLEFSTPYHPQSSGKVERKNSDIKR 232
Cdd:NF033577  186 IPiRRVLTDNGSEFRSRAhgFELALAELGIEHRRTRPYHPQTNGKVERFHRTLKD 240
transpos_IS3 NF033516
IS3 family transposase;
140-232 3.23e-09

IS3 family transposase;


Pssm-ID: 468052 [Multi-domain]  Cd Length: 369  Bit Score: 57.96  E-value: 3.23e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1752309985 140 QGYLYVLVVVDGmtgFT-----WlYPTKAPSTSATVKSLNvltsIAI-------PKVIHSDQGAAFTSSTFAEWAKERGI 207
Cdd:NF033516  230 EGWLYLAVVLDL---FSreivgW-SVSTSMSAELVLDALE----MAIewrgkpeGLILHSDNGSQYTSKAYREWLKEHGI 301

                          90       100
                  ....*....|....*....|....*
gi 1752309985 208 HLEFSTPYHPQSSGKVERKNSDIKR 232
Cdd:NF033516  302 TQSMSRPGNCWDNAVAESFFGTLKR 326
Tra8 COG2826
Transposase and inactivated derivatives, IS30 family [Mobilome: prophages, transposons];
138-273 2.53e-03

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


Pssm-ID: 442074 [Multi-domain]  Cd Length: 325  Bit Score: 39.48  E-value: 2.53e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1752309985 138 PSQGYLYVLVVVDGMTGFTWLypTKAPS-TSATV-KSLNVLTSIAIPKVIHS---DQGAAFTSstFAEWAKERGIHLEFS 212
Cdd:COG2826   182 GKRGKSALLTLVERKSRFVIL--LKLPDkTAESVaDALIRLLRKLPAFLRKSittDNGKEFAD--HKEIEAALGIKVYFA 257

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1752309985 213 TPYHPQSSGKVER----------KNSDIKRLLTKllvgrptkwyDLLPVVQLaLNNTysP--VLKY-TPHQLLF 273
Cdd:COG2826   258 DPYSPWQRGTNENtngllrqyfpKGTDFSTVTQE----------ELDAIADR-LNNR--PrkCLGYkTPAEVFA 318
 
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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