NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|2019062942|ref|WP_208497247|]
View 

recombinase family protein, partial [Klebsiella variicola]

Protein Classification

recombinase family protein( domain architecture ID 594)

recombinase family protein is a serine recombinase that catalyzes the site-specific recombination of DNA molecules by a concerted, four-strand cleavage and rejoining mechanism which involves a transient phosphoserine linkage between DNA and the enzyme

CATH:  3.40.50.1390
Gene Ontology:  GO:0000150|GO:0003677|GO:0006310
PubMed:  21645851|26104451
SCOP:  3000065

Graphical summary

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

List of domain hits

 Name Accession Description Interval E-value
Ser_Recombinase super family cl02788
Serine Recombinase family, catalytic domain; a DNA binding domain may be present either N- or ...
 2-47 1.43e-16

Serine Recombinase family, catalytic domain; a DNA binding domain may be present either N- or C-terminal to the catalytic domain. These enzymes perform site-specific recombination of DNA molecules by a concerted, four-strand cleavage and rejoining mechanism which involves a transient phosphoserine linkage between DNA and serine recombinase. Serine recombinases demonstrate functional versatility and include resolvases, invertases, integrases, and transposases. Resolvases and invertases (i.e. Tn3, gamma-delta, Tn5044 resolvases, Gin and Hin invertases) in this family contain a C-terminal DNA binding domain and comprise a major phylogenic group. Also included are phage- and bacterial-encoded recombinases such as phiC31 integrase, SpoIVCA excisionase, and Tn4451 TnpX transposase. These integrases and transposases have larger C-terminal domains compared to resolvases/invertases and are referred to as large serine recombinases. Also belonging to this family are proteins with N-terminal DNA binding domains similar to IS607- and IS1535-transposases from Helicobacter and Mycobacterium.


The actual alignment was detected with superfamily member cd03768:

Pssm-ID: 445923 [Multi-domain]  Cd Length: 126  Bit Score: 66.73  E-value: 1.43e-16
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 2019062942   2 LIGYARVSTGDQNLDLQKNALVRA-ECEQIFEDTASGKNSRRPGLRR 47
Cdd:cd03768     1 VIGYARVSTDDQSLERQLEALKAAgECDKIFEEKGSGGKKERPELQK 47
 
Name Accession Description Interval E-value
SR_ResInv cd03768
Serine Recombinase (SR) family, Resolvase and Invertase subfamily, catalytic domain; members ...
 2-47 1.43e-16

Serine Recombinase (SR) family, Resolvase and Invertase subfamily, catalytic domain; members contain a C-terminal DNA binding domain. Serine recombinases catalyze site-specific recombination of DNA molecules by a concerted, four-strand cleavage and rejoining mechanism which involves a transient phosphoserine linkage between DNA and the enzyme. They are functionally versatile and include resolvases, invertases, integrases, and transposases. Resolvases and invertases affect resolution or inversion and comprise a major phylogenic group. Resolvases (e.g. Tn3, gamma-delta, and Tn5044) normally recombine two sites in direct repeat causing deletion of the DNA between the sites. Invertases (e.g. Gin and Hin) recombine sites in inverted repeat to invert the DNA between the sites. Cointegrate resolution with gamma-delta resolvase requires the formation of a synaptosome of three resolvase dimers bound to each of two res sites on the DNA. Also included in this subfamily are some putative integrases including a sequence from bacteriophage phi-FC1.


Pssm-ID: 239737 [Multi-domain]  Cd Length: 126  Bit Score: 66.73  E-value: 1.43e-16
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 2019062942   2 LIGYARVSTGDQNLDLQKNALVRA-ECEQIFEDTASGKNSRRPGLRR 47
Cdd:cd03768     1 VIGYARVSTDDQSLERQLEALKAAgECDKIFEEKGSGGKKERPELQK 47
Resolvase pfam00239
Resolvase, N terminal domain; The N-terminal domain of the resolvase family (this family) ...
 3-47 2.77e-09

Resolvase, N terminal domain; The N-terminal domain of the resolvase family (this family) contains the active site and the dimer interface. The extended arm at the C-terminus of this domain connects to the C-terminal helix-turn-helix domain of resolvase - see pfam02796.


Pssm-ID: 425548 [Multi-domain]  Cd Length: 144  Bit Score: 48.42  E-value: 2.77e-09
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 2019062942   3 IGYARVSTGDQN--LDLQKNALVRAECEQ----IFEDT-ASGKNSRRPGLRR 47
Cdd:pfam00239   2 IGYARVSTEDQDdsLERQLEALRAYAACNgkivEFEDKgVSGRKLDRPGLQR 53
SpoIVCA COG1961
Site-specific DNA recombinase SpoIVCA/DNA invertase PinE [Replication, recombination and ...
 1-47 1.25e-08

Site-specific DNA recombinase SpoIVCA/DNA invertase PinE [Replication, recombination and repair];


Pssm-ID: 441564 [Multi-domain]  Cd Length: 388  Bit Score: 48.10  E-value: 1.25e-08
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 2019062942   1 MLIGYARVSTGDQ---NLDLQKNALVR------AECEQIFEDTA-SGKNSRRPGLRR 47
Cdd:COG1961     3 RAAGYARVSTDDQeglSLERQREALRAyaekagWEIVRIYVDEGvSGTSKDRPGLQR 59
recomb_XisF NF041201
fdxN element excision recombinase XisF;
3-45 2.33e-08

fdxN element excision recombinase XisF;


Pssm-ID: 469105 [Multi-domain]  Cd Length: 463  Bit Score: 47.26  E-value: 2.33e-08
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 2019062942   3 IGYARVSTGDQN-----LDLQKNALVRAECEQIFEDTASGKNSRRPGL 45
Cdd:NF041201    2 VGYARVSTREQAddghaLEQQIARLKKAGASEIFFDIESGRSDKRKGF 49
Resolvase smart00857
Resolvase, N terminal domain; The N-terminal domain of the resolvase family contains the ...
 3-47 9.22e-08

Resolvase, N terminal domain; The N-terminal domain of the resolvase family contains the active site and the dimer interface. The extended arm at the C-terminus of this domain connects to the C-terminal helix-turn-helix domain of resolvase.


Pssm-ID: 214861 [Multi-domain]  Cd Length: 148  Bit Score: 44.54  E-value: 9.22e-08
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*
gi 2019062942    3 IGYARVSTGDQ---NLDLQKNALVRA------ECEQIFEDTA-SGKNSRRPGLRR 47
Cdd:smart00857   2 AGYARVSTDDQadgSLERQLEALRAYaerngwEVVRIYEDEGvSGKKADRPGLQR 56
transpos_IS607 NF033518
IS607 family transposase;
3-47 6.53e-05

IS607 family transposase;


Pssm-ID: 468054 [Multi-domain]  Cd Length: 187  Bit Score: 37.23  E-value: 6.53e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 2019062942   3 IGYARVSTGDQNLDLQKN-ALVRAEC-------EQIFEDTASGKNSRRPGLRR 47
Cdd:NF033518   57 VIYARVSSADQKDDLERQvARLTQYAtakgwqvDEVVTDIGSGLNEKRKGLLK 109
 
Name Accession Description Interval E-value
SR_ResInv cd03768
Serine Recombinase (SR) family, Resolvase and Invertase subfamily, catalytic domain; members ...
 2-47 1.43e-16

Serine Recombinase (SR) family, Resolvase and Invertase subfamily, catalytic domain; members contain a C-terminal DNA binding domain. Serine recombinases catalyze site-specific recombination of DNA molecules by a concerted, four-strand cleavage and rejoining mechanism which involves a transient phosphoserine linkage between DNA and the enzyme. They are functionally versatile and include resolvases, invertases, integrases, and transposases. Resolvases and invertases affect resolution or inversion and comprise a major phylogenic group. Resolvases (e.g. Tn3, gamma-delta, and Tn5044) normally recombine two sites in direct repeat causing deletion of the DNA between the sites. Invertases (e.g. Gin and Hin) recombine sites in inverted repeat to invert the DNA between the sites. Cointegrate resolution with gamma-delta resolvase requires the formation of a synaptosome of three resolvase dimers bound to each of two res sites on the DNA. Also included in this subfamily are some putative integrases including a sequence from bacteriophage phi-FC1.


Pssm-ID: 239737 [Multi-domain]  Cd Length: 126  Bit Score: 66.73  E-value: 1.43e-16
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 2019062942   2 LIGYARVSTGDQNLDLQKNALVRA-ECEQIFEDTASGKNSRRPGLRR 47
Cdd:cd03768     1 VIGYARVSTDDQSLERQLEALKAAgECDKIFEEKGSGGKKERPELQK 47
Resolvase pfam00239
Resolvase, N terminal domain; The N-terminal domain of the resolvase family (this family) ...
 3-47 2.77e-09

Resolvase, N terminal domain; The N-terminal domain of the resolvase family (this family) contains the active site and the dimer interface. The extended arm at the C-terminus of this domain connects to the C-terminal helix-turn-helix domain of resolvase - see pfam02796.


Pssm-ID: 425548 [Multi-domain]  Cd Length: 144  Bit Score: 48.42  E-value: 2.77e-09
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 2019062942   3 IGYARVSTGDQN--LDLQKNALVRAECEQ----IFEDT-ASGKNSRRPGLRR 47
Cdd:pfam00239   2 IGYARVSTEDQDdsLERQLEALRAYAACNgkivEFEDKgVSGRKLDRPGLQR 53
SpoIVCA COG1961
Site-specific DNA recombinase SpoIVCA/DNA invertase PinE [Replication, recombination and ...
 1-47 1.25e-08

Site-specific DNA recombinase SpoIVCA/DNA invertase PinE [Replication, recombination and repair];


Pssm-ID: 441564 [Multi-domain]  Cd Length: 388  Bit Score: 48.10  E-value: 1.25e-08
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 2019062942   1 MLIGYARVSTGDQ---NLDLQKNALVR------AECEQIFEDTA-SGKNSRRPGLRR 47
Cdd:COG1961     3 RAAGYARVSTDDQeglSLERQREALRAyaekagWEIVRIYVDEGvSGTSKDRPGLQR 59
recomb_XisF NF041201
fdxN element excision recombinase XisF;
3-45 2.33e-08

fdxN element excision recombinase XisF;


Pssm-ID: 469105 [Multi-domain]  Cd Length: 463  Bit Score: 47.26  E-value: 2.33e-08
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 2019062942   3 IGYARVSTGDQN-----LDLQKNALVRAECEQIFEDTASGKNSRRPGL 45
Cdd:NF041201    2 VGYARVSTREQAddghaLEQQIARLKKAGASEIFFDIESGRSDKRKGF 49
Resolvase smart00857
Resolvase, N terminal domain; The N-terminal domain of the resolvase family contains the ...
 3-47 9.22e-08

Resolvase, N terminal domain; The N-terminal domain of the resolvase family contains the active site and the dimer interface. The extended arm at the C-terminus of this domain connects to the C-terminal helix-turn-helix domain of resolvase.


Pssm-ID: 214861 [Multi-domain]  Cd Length: 148  Bit Score: 44.54  E-value: 9.22e-08
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*
gi 2019062942    3 IGYARVSTGDQ---NLDLQKNALVRA------ECEQIFEDTA-SGKNSRRPGLRR 47
Cdd:smart00857   2 AGYARVSTDDQadgSLERQLEALRAYaerngwEVVRIYEDEGvSGKKADRPGLQR 56
SR_IS607_transposase_like cd03769
Serine Recombinase (SR) family, IS607-like transposase subfamily, catalytic domain; members ...
 3-47 6.60e-07

Serine Recombinase (SR) family, IS607-like transposase subfamily, catalytic domain; members contain a DNA binding domain with homology to MerR/SoxR located N-terminal to the catalytic domain. Serine recombinases catalyze site-specific recombination of DNA molecules by a concerted, four-strand cleavage and rejoining mechanism which involves a transient phosphoserine linkage between DNA and the enzyme. They are functionally versatile and include resolvases, invertases, integrases, and transposases. This subfamily is composed of proteins that catalyze the transposition of insertion sequence (IS) elements such as IS607 from Helicobacter and IS1535 from Mycobacterium, and similar proteins from other bacteria and several archaeal species. IS elements are DNA segments that move to new sites in prokaryotic and eukaryotic genomes causing insertion mutations and gene rearrangements.


Pssm-ID: 239738  Cd Length: 134  Bit Score: 42.25  E-value: 6.60e-07
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 2019062942   3 IGYARVSTGDQNLDL--QKNALV-----RAECEQIFEDTASGKNSRRPGLRR 47
Cdd:cd03769     2 VLYARVSSHDQKDDLerQIERLEayataQGWIVEVIKDIGSGLNEKRKGLLK 53
COG2452 COG2452
Predicted site-specific integrase-resolvase [Mobilome: prophages, transposons];
3-47 3.44e-05

Predicted site-specific integrase-resolvase [Mobilome: prophages, transposons];


Pssm-ID: 441988 [Multi-domain]  Cd Length: 178  Bit Score: 38.05  E-value: 3.44e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 2019062942   3 IGYARVSTGDQNLDL--QKNALVRAECEQ-----IFEDTASGKNSRRPGLRR 47
Cdd:COG2452    51 VIYARVSSADQKDDLerQVERLEEYATAKgyqdeVIKDVGSGLNYKRKGLLK 102
transpos_IS607 NF033518
IS607 family transposase;
3-47 6.53e-05

IS607 family transposase;


Pssm-ID: 468054 [Multi-domain]  Cd Length: 187  Bit Score: 37.23  E-value: 6.53e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 2019062942   3 IGYARVSTGDQNLDLQKN-ALVRAEC-------EQIFEDTASGKNSRRPGLRR 47
Cdd:NF033518   57 VIYARVSSADQKDDLERQvARLTQYAtakgwqvDEVVTDIGSGLNEKRKGLLK 109
 
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.
Help | Disclaimer | Write to the Help Desk
NCBI | NLM | NIH