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Conserved domains on  [gi|1778994391|ref|WP_155105083|]
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DDE-type integrase/transposase/recombinase, partial [Escherichia coli]

Protein Classification

transposase( domain architecture ID 1000502)

transposase binds to the end of a transposon and catalyzes 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:0004803

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
DDE_3 super family cl46863
DDE superfamily endonuclease; This family of proteins are related to pfam00665 and are ...
 1-73 9.20e-41

DDE superfamily endonuclease; This family of proteins are related to pfam00665 and are probably endonucleases of the DDE superfamily. Transposase proteins are necessary for efficient DNA transposition. This domain is a member of the DDE superfamily, which contain three carboxylate residues that are believed to be responsible for coordinating metal ions needed for catalysis. The catalytic activity of this enzyme involves DNA cleavage at a specific site followed by a strand transfer reaction.


The actual alignment was detected with superfamily member PHA02517:

Pssm-ID: 481203 [Multi-domain]  Cd Length: 277  Bit Score: 134.22  E-value: 9.20e-41
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1778994391   1 KVRTTISRKAVAAGDRVNRQFVAERPDQLWVADFTYVSTWRGFVYVAFIIDVFAGYIVGWRVSSSMETTFVLD 73
Cdd:PHA02517   84 KVRTTISRKAVAAPDRVNRQFVATRPNQLWVADFTYVSTWQGWVYVAFIIDVFARRIVGWRVSSSMDTDFVLD 156
 
Name Accession Description Interval E-value
PHA02517 PHA02517
putative transposase OrfB; Reviewed
 1-73 9.20e-41

putative transposase OrfB; Reviewed


Pssm-ID: 222853 [Multi-domain]  Cd Length: 277  Bit Score: 134.22  E-value: 9.20e-41
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1778994391   1 KVRTTISRKAVAAGDRVNRQFVAERPDQLWVADFTYVSTWRGFVYVAFIIDVFAGYIVGWRVSSSMETTFVLD 73
Cdd:PHA02517   84 KVRTTISRKAVAAPDRVNRQFVATRPNQLWVADFTYVSTWQGWVYVAFIIDVFARRIVGWRVSSSMDTDFVLD 156
transpos_IS3 NF033516
IS3 family transposase;
1-73 3.55e-27

IS3 family transposase;


Pssm-ID: 468052 [Multi-domain]  Cd Length: 369  Bit Score: 100.33  E-value: 3.55e-27
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1778994391   1 KVRTTISRK-AVAAGDRVNRQFVAERPDQLWVADFTYVSTWRGFVYVAFIIDVFAGYIVGWRVSSSMETTFVLD 73
Cdd:NF033516  189 RPYTTDSGHvHPVAPNLLNRQFTATRPNQVWVTDITYIRTAEGWLYLAVVLDLFSREIVGWSVSTSMSAELVLD 262
Tra5 COG2801
Transposase InsO and inactivated derivatives [Mobilome: prophages, transposons];
1-73 9.03e-25

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


Pssm-ID: 442053 [Multi-domain]  Cd Length: 309  Bit Score: 93.29  E-value: 9.03e-25
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1778994391   1 KVRTTISRKAVAAGDrvNRQFVAERPDQLWVADFTYVSTWRGFVYVAFIIDVFAGYIVGWRVSSSMETTFVLD 73
Cdd:COG2801   125 KKYTTYSGHGGPIAP--NLLFTATAPNQVWVTDITYIPTAEGWLYLAAVIDLFSREIVGWSVSDSMDAELVVD 195
rve pfam00665
Integrase core domain; Integrase mediates integration of a DNA copy of the viral genome into ...
 26-73 4.96e-11

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: 53.09  E-value: 4.96e-11
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|
gi 1778994391 26 PDQLWVADFTYVS--TWRGFVYVAFIIDVFAGYIVGWRVSSSMETTFVLD 73
Cdd:pfam00665  1 PNQLWQGDFTYIRipGGGGKLYLLVIVDDFSREILAWALSSEMDAELVLD 50
 
Name Accession Description Interval E-value
PHA02517 PHA02517
putative transposase OrfB; Reviewed
 1-73 9.20e-41

putative transposase OrfB; Reviewed


Pssm-ID: 222853 [Multi-domain]  Cd Length: 277  Bit Score: 134.22  E-value: 9.20e-41
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1778994391   1 KVRTTISRKAVAAGDRVNRQFVAERPDQLWVADFTYVSTWRGFVYVAFIIDVFAGYIVGWRVSSSMETTFVLD 73
Cdd:PHA02517   84 KVRTTISRKAVAAPDRVNRQFVATRPNQLWVADFTYVSTWQGWVYVAFIIDVFARRIVGWRVSSSMDTDFVLD 156
transpos_IS3 NF033516
IS3 family transposase;
1-73 3.55e-27

IS3 family transposase;


Pssm-ID: 468052 [Multi-domain]  Cd Length: 369  Bit Score: 100.33  E-value: 3.55e-27
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1778994391   1 KVRTTISRK-AVAAGDRVNRQFVAERPDQLWVADFTYVSTWRGFVYVAFIIDVFAGYIVGWRVSSSMETTFVLD 73
Cdd:NF033516  189 RPYTTDSGHvHPVAPNLLNRQFTATRPNQVWVTDITYIRTAEGWLYLAVVLDLFSREIVGWSVSTSMSAELVLD 262
Tra5 COG2801
Transposase InsO and inactivated derivatives [Mobilome: prophages, transposons];
1-73 9.03e-25

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


Pssm-ID: 442053 [Multi-domain]  Cd Length: 309  Bit Score: 93.29  E-value: 9.03e-25
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1778994391   1 KVRTTISRKAVAAGDrvNRQFVAERPDQLWVADFTYVSTWRGFVYVAFIIDVFAGYIVGWRVSSSMETTFVLD 73
Cdd:COG2801   125 KKYTTYSGHGGPIAP--NLLFTATAPNQVWVTDITYIPTAEGWLYLAAVIDLFSREIVGWSVSDSMDAELVVD 195
rve pfam00665
Integrase core domain; Integrase mediates integration of a DNA copy of the viral genome into ...
 26-73 4.96e-11

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: 53.09  E-value: 4.96e-11
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|
gi 1778994391 26 PDQLWVADFTYVS--TWRGFVYVAFIIDVFAGYIVGWRVSSSMETTFVLD 73
Cdd:pfam00665  1 PNQLWQGDFTYIRipGGGGKLYLLVIVDDFSREILAWALSSEMDAELVLD 50
 
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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