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Conserved domains on  [gi|394986186]
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Chain A, INTEGRASE

Protein Classification

transposase family protein( domain architecture ID 10461024)

transposase family protein might bind to the end of a transposon and catalyze the movement of the transposon to another part of the genome by a cut and paste mechanism or a replicative transposition mechanism

Gene Ontology:  GO:0005524|GO:0003677|GO:0046872|GO:0015074
PubMed:  11774877

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 ...
 13-100 1.62e-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: 68.11  E-value: 1.62e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 394986186   13 PGIWQLDCTHLEGKV------ILVAVHVASGYIEAEVIPAETGQETAYFLLKLA---GRWPVKTVHTDNGSNFTSTTVKA 83
Cdd:pfam00665   2 NQLWQGDFTYIRIPGgggklyLLVIVDDFSREILAWALSSEMDAELVLDALERAiafRGGVPLIIHSDNGSEYTSKAFRE 81

                          90
                  ....*....|....*..
gi 394986186   84 ACWWAGIKQEDGIPYNP 100
Cdd:pfam00665  82 FLKDLGIKPSFSRPGNP 98
Tra5 super family cl34487
Transposase InsO and inactivated derivatives [Mobilome: prophages, transposons];
67-150 5.49e-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: 59.40  E-value: 5.49e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 394986186  67 TVHTDNGSNFTSTTVKAACWWAGIKQEDGIPYNPQSQGVIESMNKELKK--IIGQVRDQAEHLKTAVQMAVFIHNHKR-K 143
Cdd:COG2801  211 ILHSDNGSQYTSKAYQELLKKLGITQSMSRPGNPQDNAFIESFFGTLKYelLYRRRFESLEEAREAIEEYIEFYNHERpH 290


                 ....*..
gi 394986186 144 GGIGGYS 150
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 ...
 13-100 1.62e-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: 68.11  E-value: 1.62e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 394986186   13 PGIWQLDCTHLEGKV------ILVAVHVASGYIEAEVIPAETGQETAYFLLKLA---GRWPVKTVHTDNGSNFTSTTVKA 83
Cdd:pfam00665   2 NQLWQGDFTYIRIPGgggklyLLVIVDDFSREILAWALSSEMDAELVLDALERAiafRGGVPLIIHSDNGSEYTSKAFRE 81

                          90
                  ....*....|....*..
gi 394986186   84 ACWWAGIKQEDGIPYNP 100
Cdd:pfam00665  82 FLKDLGIKPSFSRPGNP 98
transpos_IS481 NF033577
IS481 family transposase; null
 16-155 1.03e-11

IS481 family transposase; null


Pssm-ID: 468094 [Multi-domain]  Cd Length: 283  Bit Score: 61.07  E-value: 1.03e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 394986186  16 WQLDCTHL-----EGKV-ILVAVHVASGYIEAEVIPAETGQETAYFLLKL-AGRW-PVKTVHTDNGSNFTSTT--VKAAC 85
Cdd:NF033577 131 WHIDIKKLgripdVGRLyLHTAIDDHSRFAYAELYPDETAETAADFLRRAfAEHGiPIRRVLTDNGSEFRSRAhgFELAL 210

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 394986186  86 WWAGIKQEDGIPYNPQSQGVIESMNKELKKIIGQVR--DQAEHLKTAvqMAVFIH--NHKRK-GGIGGYSAGERI 155
Cdd:NF033577 211 AELGIEHRRTRPYHPQTNGKVERFHRTLKDEFAYARpyESLAELQAA--LDEWLHhyNHHRPhSALGGKTPAERF 283
Tra5 COG2801
Transposase InsO and inactivated derivatives [Mobilome: prophages, transposons];
67-150 5.49e-11

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


Pssm-ID: 442053 [Multi-domain]  Cd Length: 309  Bit Score: 59.40  E-value: 5.49e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 394986186  67 TVHTDNGSNFTSTTVKAACWWAGIKQEDGIPYNPQSQGVIESMNKELKK--IIGQVRDQAEHLKTAVQMAVFIHNHKR-K 143
Cdd:COG2801  211 ILHSDNGSQYTSKAYQELLKKLGITQSMSRPGNPQDNAFIESFFGTLKYelLYRRRFESLEEAREAIEEYIEFYNHERpH 290


                 ....*..
gi 394986186 144 GGIGGYS 150
Cdd:COG2801  291 SSLGYLT 297
transpos_IS3 NF033516
IS3 family transposase;
68-148 2.05e-09

IS3 family transposase;


Pssm-ID: 468052 [Multi-domain]  Cd Length: 369  Bit Score: 54.88  E-value: 2.05e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 394986186  68 VHTDNGSNFTSTTVKAACWWAGIKQEDGIPYNPQSQGVIESMNKELKK--IIGQVRDQAEHLKTAVQMAVFIHNHKR-KG 144
Cdd:NF033516 279 LHSDNGSQYTSKAYREWLKEHGITQSMSRPGNCWDNAVAESFFGTLKRecLYRRRFRTLEEARQAIEEYIEFYNHERpHS 358


                 ....
gi 394986186 145 GIGG 148
Cdd:NF033516 359 SLGY 362
 
Name Accession Description Interval E-value
rve pfam00665
Integrase core domain; Integrase mediates integration of a DNA copy of the viral genome into ...
 13-100 1.62e-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: 68.11  E-value: 1.62e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 394986186   13 PGIWQLDCTHLEGKV------ILVAVHVASGYIEAEVIPAETGQETAYFLLKLA---GRWPVKTVHTDNGSNFTSTTVKA 83
Cdd:pfam00665   2 NQLWQGDFTYIRIPGgggklyLLVIVDDFSREILAWALSSEMDAELVLDALERAiafRGGVPLIIHSDNGSEYTSKAFRE 81

                          90
                  ....*....|....*..
gi 394986186   84 ACWWAGIKQEDGIPYNP 100
Cdd:pfam00665  82 FLKDLGIKPSFSRPGNP 98
transpos_IS481 NF033577
IS481 family transposase; null
 16-155 1.03e-11

IS481 family transposase; null


Pssm-ID: 468094 [Multi-domain]  Cd Length: 283  Bit Score: 61.07  E-value: 1.03e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 394986186  16 WQLDCTHL-----EGKV-ILVAVHVASGYIEAEVIPAETGQETAYFLLKL-AGRW-PVKTVHTDNGSNFTSTT--VKAAC 85
Cdd:NF033577 131 WHIDIKKLgripdVGRLyLHTAIDDHSRFAYAELYPDETAETAADFLRRAfAEHGiPIRRVLTDNGSEFRSRAhgFELAL 210

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 394986186  86 WWAGIKQEDGIPYNPQSQGVIESMNKELKKIIGQVR--DQAEHLKTAvqMAVFIH--NHKRK-GGIGGYSAGERI 155
Cdd:NF033577 211 AELGIEHRRTRPYHPQTNGKVERFHRTLKDEFAYARpyESLAELQAA--LDEWLHhyNHHRPhSALGGKTPAERF 283
Tra5 COG2801
Transposase InsO and inactivated derivatives [Mobilome: prophages, transposons];
67-150 5.49e-11

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


Pssm-ID: 442053 [Multi-domain]  Cd Length: 309  Bit Score: 59.40  E-value: 5.49e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 394986186  67 TVHTDNGSNFTSTTVKAACWWAGIKQEDGIPYNPQSQGVIESMNKELKK--IIGQVRDQAEHLKTAVQMAVFIHNHKR-K 143
Cdd:COG2801  211 ILHSDNGSQYTSKAYQELLKKLGITQSMSRPGNPQDNAFIESFFGTLKYelLYRRRFESLEEAREAIEEYIEFYNHERpH 290


                 ....*..
gi 394986186 144 GGIGGYS 150
Cdd:COG2801  291 SSLGYLT 297
transpos_IS3 NF033516
IS3 family transposase;
68-148 2.05e-09

IS3 family transposase;


Pssm-ID: 468052 [Multi-domain]  Cd Length: 369  Bit Score: 54.88  E-value: 2.05e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 394986186  68 VHTDNGSNFTSTTVKAACWWAGIKQEDGIPYNPQSQGVIESMNKELKK--IIGQVRDQAEHLKTAVQMAVFIHNHKR-KG 144
Cdd:NF033516 279 LHSDNGSQYTSKAYREWLKEHGITQSMSRPGNCWDNAVAESFFGTLKRecLYRRRFRTLEEARQAIEEYIEFYNHERpHS 358


                 ....
gi 394986186 145 GIGG 148
Cdd:NF033516 359 SLGY 362
 
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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