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Conserved domains on  [gi|2661943416|ref|WP_327312387|]
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MULTISPECIES: integrase core domain-containing protein [Salmonella]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
rve_3 pfam13683
Integrase core domain;
19-85 3.07e-20

Integrase core domain;


:

Pssm-ID: 433402 [Multi-domain]  Cd Length: 67  Bit Score: 76.49  E-value: 3.07e-20
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2661943416 19 HAVKLAFIQPGKPKKNVFITRFNRTYRTEILNSYLFRTLNEVREIADKGLSEYNCERPYESRNNMIP 85
Cdd:pfam13683  1 LGIEISYIAPGKPMQNGLVESFNGTLRDECLNEHLFSSLAEARALLAAWREDYNTERPHSSLGYRTP 67
rve super family cl47583
Integrase core domain; Integrase mediates integration of a DNA copy of the viral genome into ...
 1-31 8.62e-04

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.


The actual alignment was detected with superfamily member pfam00665:

Pssm-ID: 459897 [Multi-domain]  Cd Length: 98  Bit Score: 34.98  E-value: 8.62e-04
                         10        20        30
                 ....*....|....*....|....*....|.
gi 2661943416  1 MDKEPEFISLALAEWAKKHAVKLAFIQPGKP 31
Cdd:pfam00665 68 SDNGSEYTSKAFREFLKDLGIKPSFSRPGNP 98
 
Name Accession Description Interval E-value
rve_3 pfam13683
Integrase core domain;
19-85 3.07e-20

Integrase core domain;


Pssm-ID: 433402 [Multi-domain]  Cd Length: 67  Bit Score: 76.49  E-value: 3.07e-20
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2661943416 19 HAVKLAFIQPGKPKKNVFITRFNRTYRTEILNSYLFRTLNEVREIADKGLSEYNCERPYESRNNMIP 85
Cdd:pfam13683  1 LGIEISYIAPGKPMQNGLVESFNGTLRDECLNEHLFSSLAEARALLAAWREDYNTERPHSSLGYRTP 67
transpos_IS3 NF033516
IS3 family transposase;
5-89 9.77e-19

IS3 family transposase;


Pssm-ID: 468052 [Multi-domain]  Cd Length: 369  Bit Score: 78.38  E-value: 9.77e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2661943416   5 PEFISLALAEWAKKHAVKLAFIQPGKPKKNVFITRFNRTYRTEILNSYLFRTLNEVREIADKGLSEYNCERPYESRNNMI 84
Cdd:NF033516  285 SQYTSKAYREWLKEHGITQSMSRPGNCWDNAVAESFFGTLKRECLYRRRFRTLEEARQAIEEYIEFYNHERPHSSLGYLT 364


                  ....*
gi 2661943416  85 PKEYR 89
Cdd:NF033516  365 PAEFE 369
Tra5 COG2801
Transposase InsO and inactivated derivatives [Mobilome: prophages, transposons];
5-89 1.06e-17

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


Pssm-ID: 442053 [Multi-domain]  Cd Length: 309  Bit Score: 75.19  E-value: 1.06e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2661943416   5 PEFISLALAEWAKKHAVKLAFIQPGKPKKNVFITRFNRTYRTEILNSYLFRTLNEVREIADKGLSEYNCERPYESRNNMI 84
Cdd:COG2801   218 SQYTSKAYQELLKKLGITQSMSRPGNPQDNAFIESFFGTLKYELLYRRRFESLEEAREAIEEYIEFYNHERPHSSLGYLT 297


                  ....*
gi 2661943416  85 PKEYR 89
Cdd:COG2801   298 PAEYE 302
rve pfam00665
Integrase core domain; Integrase mediates integration of a DNA copy of the viral genome into ...
 1-31 8.62e-04

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: 34.98  E-value: 8.62e-04
                         10        20        30
                 ....*....|....*....|....*....|.
gi 2661943416  1 MDKEPEFISLALAEWAKKHAVKLAFIQPGKP 31
Cdd:pfam00665 68 SDNGSEYTSKAFREFLKDLGIKPSFSRPGNP 98
 
Name Accession Description Interval E-value
rve_3 pfam13683
Integrase core domain;
19-85 3.07e-20

Integrase core domain;


Pssm-ID: 433402 [Multi-domain]  Cd Length: 67  Bit Score: 76.49  E-value: 3.07e-20
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2661943416 19 HAVKLAFIQPGKPKKNVFITRFNRTYRTEILNSYLFRTLNEVREIADKGLSEYNCERPYESRNNMIP 85
Cdd:pfam13683  1 LGIEISYIAPGKPMQNGLVESFNGTLRDECLNEHLFSSLAEARALLAAWREDYNTERPHSSLGYRTP 67
transpos_IS3 NF033516
IS3 family transposase;
5-89 9.77e-19

IS3 family transposase;


Pssm-ID: 468052 [Multi-domain]  Cd Length: 369  Bit Score: 78.38  E-value: 9.77e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2661943416   5 PEFISLALAEWAKKHAVKLAFIQPGKPKKNVFITRFNRTYRTEILNSYLFRTLNEVREIADKGLSEYNCERPYESRNNMI 84
Cdd:NF033516  285 SQYTSKAYREWLKEHGITQSMSRPGNCWDNAVAESFFGTLKRECLYRRRFRTLEEARQAIEEYIEFYNHERPHSSLGYLT 364


                  ....*
gi 2661943416  85 PKEYR 89
Cdd:NF033516  365 PAEFE 369
Tra5 COG2801
Transposase InsO and inactivated derivatives [Mobilome: prophages, transposons];
5-89 1.06e-17

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


Pssm-ID: 442053 [Multi-domain]  Cd Length: 309  Bit Score: 75.19  E-value: 1.06e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2661943416   5 PEFISLALAEWAKKHAVKLAFIQPGKPKKNVFITRFNRTYRTEILNSYLFRTLNEVREIADKGLSEYNCERPYESRNNMI 84
Cdd:COG2801   218 SQYTSKAYQELLKKLGITQSMSRPGNPQDNAFIESFFGTLKYELLYRRRFESLEEAREAIEEYIEFYNHERPHSSLGYLT 297


                  ....*
gi 2661943416  85 PKEYR 89
Cdd:COG2801   298 PAEYE 302
rve pfam00665
Integrase core domain; Integrase mediates integration of a DNA copy of the viral genome into ...
 1-31 8.62e-04

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: 34.98  E-value: 8.62e-04
                         10        20        30
                 ....*....|....*....|....*....|.
gi 2661943416  1 MDKEPEFISLALAEWAKKHAVKLAFIQPGKP 31
Cdd:pfam00665 68 SDNGSEYTSKAFREFLKDLGIKPSFSRPGNP 98
 
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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