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Conserved domains on  [gi|2727760042|ref|WP_343183782|]
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integrase core domain-containing protein, partial [Citrobacter freundii]

Protein Classification

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 ...
 1-64 5.40e-27

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: 98.40  E-value: 5.40e-27
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2727760042   1 SPMERFFRSLKNEWVPVTGYINFSDAAHAITDYiVGYYSSLRPHDYNGGLPPNESENRYWKNSK 64
Cdd:PHA02517  209 APAESINGLYKAEVIHRVSWKNREEVELATLEW-VAWYNNRRLHERLGYTPPAEAEKAYYASIG 271
 
Name Accession Description Interval E-value
PHA02517 PHA02517
putative transposase OrfB; Reviewed
 1-64 5.40e-27

putative transposase OrfB; Reviewed


Pssm-ID: 222853 [Multi-domain]  Cd Length: 277  Bit Score: 98.40  E-value: 5.40e-27
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2727760042   1 SPMERFFRSLKNEWVPVTGYINFSDAAHAITDYiVGYYSSLRPHDYNGGLPPNESENRYWKNSK 64
Cdd:PHA02517  209 APAESINGLYKAEVIHRVSWKNREEVELATLEW-VAWYNNRRLHERLGYTPPAEAEKAYYASIG 271
transpos_IS3 NF033516
IS3 family transposase;
2-56 7.33e-16

IS3 family transposase;


Pssm-ID: 468052 [Multi-domain]  Cd Length: 369  Bit Score: 69.52  E-value: 7.33e-16
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 2727760042   2 PMERFFRSLKNEWVPVTGYINFSDAAHAITDYIVgYYSSLRPHDYNGGLPPNESE 56
Cdd:NF033516  316 VAESFFGTLKRECLYRRRFRTLEEARQAIEEYIE-FYNHERPHSSLGYLTPAEFE 369
Tra5 COG2801
Transposase InsO and inactivated derivatives [Mobilome: prophages, transposons];
2-63 2.15e-14

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


Pssm-ID: 442053 [Multi-domain]  Cd Length: 309  Bit Score: 65.17  E-value: 2.15e-14
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2727760042   2 PMERFFRSLKNEWVPVTGYINFSDAAHAITDYIVgYYSSLRPHDYNGGLPPNESENRYWKNS 63
Cdd:COG2801   249 FIESFFGTLKYELLYRRRFESLEEAREAIEEYIE-FYNHERPHSSLGYLTPAEYEKQLAAAA 309
rve_3 pfam13683
Integrase core domain;
3-52 2.52e-07

Integrase core domain;


Pssm-ID: 433402 [Multi-domain]  Cd Length: 67  Bit Score: 42.97  E-value: 2.52e-07
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|
gi 2727760042  3 MERFFRSLKNEWVPVTGYINFSDAAHAITDYIVgYYSSLRPHDYNGGLPP 52
Cdd:pfam13683 19 VESFNGTLRDECLNEHLFSSLAEARALLAAWRE-DYNTERPHSSLGYRTP 67
transpos_IS481 NF033577
IS481 family transposase; null
 4-52 4.45e-06

IS481 family transposase; null


Pssm-ID: 468094 [Multi-domain]  Cd Length: 283  Bit Score: 41.81  E-value: 4.45e-06
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 2727760042   4 ERFFRSLKNEWVPVTGYINFSDAAHAITDYIVGYYSSlRPHDYNGGLPP 52
Cdd:NF033577  232 ERFHRTLKDEFAYARPYESLAELQAALDEWLHHYNHH-RPHSALGGKTP 279
 
Name Accession Description Interval E-value
PHA02517 PHA02517
putative transposase OrfB; Reviewed
 1-64 5.40e-27

putative transposase OrfB; Reviewed


Pssm-ID: 222853 [Multi-domain]  Cd Length: 277  Bit Score: 98.40  E-value: 5.40e-27
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2727760042   1 SPMERFFRSLKNEWVPVTGYINFSDAAHAITDYiVGYYSSLRPHDYNGGLPPNESENRYWKNSK 64
Cdd:PHA02517  209 APAESINGLYKAEVIHRVSWKNREEVELATLEW-VAWYNNRRLHERLGYTPPAEAEKAYYASIG 271
transpos_IS3 NF033516
IS3 family transposase;
2-56 7.33e-16

IS3 family transposase;


Pssm-ID: 468052 [Multi-domain]  Cd Length: 369  Bit Score: 69.52  E-value: 7.33e-16
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 2727760042   2 PMERFFRSLKNEWVPVTGYINFSDAAHAITDYIVgYYSSLRPHDYNGGLPPNESE 56
Cdd:NF033516  316 VAESFFGTLKRECLYRRRFRTLEEARQAIEEYIE-FYNHERPHSSLGYLTPAEFE 369
Tra5 COG2801
Transposase InsO and inactivated derivatives [Mobilome: prophages, transposons];
2-63 2.15e-14

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


Pssm-ID: 442053 [Multi-domain]  Cd Length: 309  Bit Score: 65.17  E-value: 2.15e-14
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2727760042   2 PMERFFRSLKNEWVPVTGYINFSDAAHAITDYIVgYYSSLRPHDYNGGLPPNESENRYWKNS 63
Cdd:COG2801   249 FIESFFGTLKYELLYRRRFESLEEAREAIEEYIE-FYNHERPHSSLGYLTPAEYEKQLAAAA 309
rve_3 pfam13683
Integrase core domain;
3-52 2.52e-07

Integrase core domain;


Pssm-ID: 433402 [Multi-domain]  Cd Length: 67  Bit Score: 42.97  E-value: 2.52e-07
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|
gi 2727760042  3 MERFFRSLKNEWVPVTGYINFSDAAHAITDYIVgYYSSLRPHDYNGGLPP 52
Cdd:pfam13683 19 VESFNGTLRDECLNEHLFSSLAEARALLAAWRE-DYNTERPHSSLGYRTP 67
transpos_IS481 NF033577
IS481 family transposase; null
 4-52 4.45e-06

IS481 family transposase; null


Pssm-ID: 468094 [Multi-domain]  Cd Length: 283  Bit Score: 41.81  E-value: 4.45e-06
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 2727760042   4 ERFFRSLKNEWVPVTGYINFSDAAHAITDYIVGYYSSlRPHDYNGGLPP 52
Cdd:NF033577  232 ERFHRTLKDEFAYARPYESLAELQAALDEWLHHYNHH-RPHSALGGKTP 279
 
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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