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Conserved domains on  [gi|2794006544|ref|WP_372154280|]
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recombinase family protein, partial [Vibrio sp. 10N.261.51.A1]

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

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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 ...
 8-92 1.49e-39

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 cd03767:

Pssm-ID: 445923 [Multi-domain]  Cd Length: 146  Bit Score: 127.83  E-value: 1.49e-39
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2794006544   8 YGYLRASTDEQDASRAKNDLIDFADKMGFPIACWFEENESGAQLHRPELFRLLDVAMAGDIILVEQVDRISRLNTKDWEQ 87
Cdd:cd03767     2 RAYLRASTDEQDATRAKESLEAFATERGFYIAGFYVENASGAKLDRPELFRLLDDAQSGDVLLVEQIDRLSRLPLDDWET 81


                  ....*
gi 2794006544  88 LKNII 92
Cdd:cd03767    82 LKASI 86
 
Name Accession Description Interval E-value
SR_Res_par cd03767
Serine recombinase (SR) family, Partitioning (par)-Resolvase subfamily, catalytic domain; ...
 8-92 1.49e-39

Serine recombinase (SR) family, Partitioning (par)-Resolvase subfamily, 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 subgroup is composed of proteins similar to the E. coli resolvase found in the par region of the RP4 plasmid, which encodes a highly efficient partitioning system. This protein is part of a complex stabilization system involved in the resolution of plasmid dimers during cell division. Similar to Tn3 and other resolvases, members of this family may contain a C-terminal DNA binding domain.


Pssm-ID: 239736 [Multi-domain]  Cd Length: 146  Bit Score: 127.83  E-value: 1.49e-39
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2794006544   8 YGYLRASTDEQDASRAKNDLIDFADKMGFPIACWFEENESGAQLHRPELFRLLDVAMAGDIILVEQVDRISRLNTKDWEQ 87
Cdd:cd03767     2 RAYLRASTDEQDATRAKESLEAFATERGFYIAGFYVENASGAKLDRPELFRLLDDAQSGDVLLVEQIDRLSRLPLDDWET 81


                  ....*
gi 2794006544  88 LKNII 92
Cdd:cd03767    82 LKASI 86
SpoIVCA COG1961
Site-specific DNA recombinase SpoIVCA/DNA invertase PinE [Replication, recombination and ...
 4-92 8.46e-19

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


Pssm-ID: 441564 [Multi-domain]  Cd Length: 388  Bit Score: 78.91  E-value: 8.46e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2794006544   4 NIRTYGYLRASTDEQDAS---RAKNDLIDFADKMGFPIACWFEENE-SGAQLHRPELFRLLDVAMAG--DIILVEQVDRI 77
Cdd:COG1961     1 MMRAAGYARVSTDDQEGLsleRQREALRAYAEKAGWEIVRIYVDEGvSGTSKDRPGLQRLLADLRAGkfDTLVVWKLDRL 80

                          90
                  ....*....|....*
gi 2794006544  78 SRlNTKDWEQLKNII 92
Cdd:COG1961    81 GR-NLADLLELVEEL 94
Resolvase smart00857
Resolvase, N terminal domain; The N-terminal domain of the resolvase family contains the ...
 7-92 1.10e-17

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: 72.27  E-value: 1.10e-17
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2794006544    7 TYGYLRASTDEQDAS---RAKNDLIDFADKMGFPIACWFEEN-ESGAQLHRPELFRLLDVAMAGDI--ILVEQVDRISRl 80
Cdd:smart00857   1 AAGYARVSTDDQADGsleRQLEALRAYAERNGWEVVRIYEDEgVSGKKADRPGLQRLLADLRAGDIdvLVVYKLDRLGR- 79

                           90
                   ....*....|..
gi 2794006544   81 NTKDWEQLKNII 92
Cdd:smart00857  80 SLRDLLALLELL 91
Resolvase pfam00239
Resolvase, N terminal domain; The N-terminal domain of the resolvase family (this family) ...
 8-92 9.62e-12

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: 56.89  E-value: 9.62e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2794006544   8 YGYLRASTDEQDAS--RAKNDLIDFADKMGfPIACWFEENESGAQLHRPELFRLLD--VAMAGDIILVEQVDRISRlNTK 83
Cdd:pfam00239   2 IGYARVSTEDQDDSleRQLEALRAYAACNG-KIVEFEDKGVSGRKLDRPGLQRLLAllRAGKGDVLVVYKLDRLGR-SLR 79


                  ....*....
gi 2794006544  84 DWEQLKNII 92
Cdd:pfam00239  80 DLLTLVEEL 88
mpi PRK13413
master DNA invertase Mpi family serine-type recombinase;
8-79 5.67e-10

master DNA invertase Mpi family serine-type recombinase;


Pssm-ID: 184041 [Multi-domain]  Cd Length: 200  Bit Score: 53.18  E-value: 5.67e-10
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2794006544   8 YGYLRASTDEQDASRAKNDLIDFADKMGFPIACWFEENESGAQ-LHRPELFRLLDVAMAGDIILVEQVDRISR 79
Cdd:PRK13413    3 YAYIRVSTDKQTVENQRFEITNFAEKNNLTIDKWIEETISGTKsYKDRKLGKLLKKMRKGDILIVSELSRLGR 75
 
Name Accession Description Interval E-value
SR_Res_par cd03767
Serine recombinase (SR) family, Partitioning (par)-Resolvase subfamily, catalytic domain; ...
 8-92 1.49e-39

Serine recombinase (SR) family, Partitioning (par)-Resolvase subfamily, 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 subgroup is composed of proteins similar to the E. coli resolvase found in the par region of the RP4 plasmid, which encodes a highly efficient partitioning system. This protein is part of a complex stabilization system involved in the resolution of plasmid dimers during cell division. Similar to Tn3 and other resolvases, members of this family may contain a C-terminal DNA binding domain.


Pssm-ID: 239736 [Multi-domain]  Cd Length: 146  Bit Score: 127.83  E-value: 1.49e-39
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2794006544   8 YGYLRASTDEQDASRAKNDLIDFADKMGFPIACWFEENESGAQLHRPELFRLLDVAMAGDIILVEQVDRISRLNTKDWEQ 87
Cdd:cd03767     2 RAYLRASTDEQDATRAKESLEAFATERGFYIAGFYVENASGAKLDRPELFRLLDDAQSGDVLLVEQIDRLSRLPLDDWET 81


                  ....*
gi 2794006544  88 LKNII 92
Cdd:cd03767    82 LKASI 86
SpoIVCA COG1961
Site-specific DNA recombinase SpoIVCA/DNA invertase PinE [Replication, recombination and ...
 4-92 8.46e-19

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


Pssm-ID: 441564 [Multi-domain]  Cd Length: 388  Bit Score: 78.91  E-value: 8.46e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2794006544   4 NIRTYGYLRASTDEQDAS---RAKNDLIDFADKMGFPIACWFEENE-SGAQLHRPELFRLLDVAMAG--DIILVEQVDRI 77
Cdd:COG1961     1 MMRAAGYARVSTDDQEGLsleRQREALRAYAEKAGWEIVRIYVDEGvSGTSKDRPGLQRLLADLRAGkfDTLVVWKLDRL 80

                          90
                  ....*....|....*
gi 2794006544  78 SRlNTKDWEQLKNII 92
Cdd:COG1961    81 GR-NLADLLELVEEL 94
Resolvase smart00857
Resolvase, N terminal domain; The N-terminal domain of the resolvase family contains the ...
 7-92 1.10e-17

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: 72.27  E-value: 1.10e-17
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2794006544    7 TYGYLRASTDEQDAS---RAKNDLIDFADKMGFPIACWFEEN-ESGAQLHRPELFRLLDVAMAGDI--ILVEQVDRISRl 80
Cdd:smart00857   1 AAGYARVSTDDQADGsleRQLEALRAYAERNGWEVVRIYEDEgVSGKKADRPGLQRLLADLRAGDIdvLVVYKLDRLGR- 79

                           90
                   ....*....|..
gi 2794006544   81 NTKDWEQLKNII 92
Cdd:smart00857  80 SLRDLLALLELL 91
SR_ResInv cd03768
Serine Recombinase (SR) family, Resolvase and Invertase subfamily, catalytic domain; members ...
 7-84 1.22e-14

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: 63.65  E-value: 1.22e-14
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2794006544   7 TYGYLRASTDEQDASRAKNDLIDFADkmgfpIACWFEENESGAQLHRPELFRLLDVAMAGDIILVEQVDRISRlNTKD 84
Cdd:cd03768     1 VIGYARVSTDDQSLERQLEALKAAGE-----CDKIFEEKGSGGKKERPELQKLLEDLREGDTLVVTKLDRLGR-STKD 72
Ser_Recombinase cd00338
Serine Recombinase family, catalytic domain; a DNA binding domain may be present either N- or ...
 10-92 1.89e-12

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.


Pssm-ID: 238206 [Multi-domain]  Cd Length: 137  Bit Score: 58.43  E-value: 1.89e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2794006544  10 YLRASTDEQDAS----RAKNDLIDFADKMGFPIACWFEENESGAQLH--RPELFRLLDVAMAG--DIILVEQVDRISRlN 81
Cdd:cd00338     2 YARVSTDKQEQGdsleRQREALREYAARNGLEVVGEYEDAGSSATSLvdRPGLQRLLADVKAGkiDVVLVEKLDRLSR-N 80

                          90
                  ....*....|.
gi 2794006544  82 TKDWEQLKNII 92
Cdd:cd00338    81 LVDLLELLELL 91
Resolvase pfam00239
Resolvase, N terminal domain; The N-terminal domain of the resolvase family (this family) ...
 8-92 9.62e-12

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: 56.89  E-value: 9.62e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2794006544   8 YGYLRASTDEQDAS--RAKNDLIDFADKMGfPIACWFEENESGAQLHRPELFRLLD--VAMAGDIILVEQVDRISRlNTK 83
Cdd:pfam00239   2 IGYARVSTEDQDDSleRQLEALRAYAACNG-KIVEFEDKGVSGRKLDRPGLQRLLAllRAGKGDVLVVYKLDRLGR-SLR 79


                  ....*....
gi 2794006544  84 DWEQLKNII 92
Cdd:pfam00239  80 DLLTLVEEL 88
mpi PRK13413
master DNA invertase Mpi family serine-type recombinase;
8-79 5.67e-10

master DNA invertase Mpi family serine-type recombinase;


Pssm-ID: 184041 [Multi-domain]  Cd Length: 200  Bit Score: 53.18  E-value: 5.67e-10
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2794006544   8 YGYLRASTDEQDASRAKNDLIDFADKMGFPIACWFEENESGAQ-LHRPELFRLLDVAMAGDIILVEQVDRISR 79
Cdd:PRK13413    3 YAYIRVSTDKQTVENQRFEITNFAEKNNLTIDKWIEETISGTKsYKDRKLGKLLKKMRKGDILIVSELSRLGR 75
SR_IS607_transposase_like cd03769
Serine Recombinase (SR) family, IS607-like transposase subfamily, catalytic domain; members ...
 7-83 2.19e-05

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: 39.94  E-value: 2.19e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2794006544   7 TYGYLRASTDEQ--DASRAKNDLIDFADKMGFpIACWFEENESGAQLHRPELFRLLDVAMAG--DIILVEQVDRISRLNT 82
Cdd:cd03769     1 TVLYARVSSHDQkdDLERQIERLEAYATAQGW-IVEVIKDIGSGLNEKRKGLLKLLEDVLAGkvERVVITYKDRLARFGF 79


                  .
gi 2794006544  83 K 83
Cdd:cd03769    80 E 80
SR_TndX_transposase cd03770
Serine Recombinase (SR) family, TndX-like transposase subfamily, catalytic domain; composed of ...
 7-83 8.87e-04

Serine Recombinase (SR) family, TndX-like transposase subfamily, catalytic domain; composed of large serine recombinases similar to Clostridium TndX and TnpX transposases. 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. TndX mediates the excision and circularization of the conjugative transposon Tn5397 from Clostridium difficile. TnpX is responsible for the movement of the nonconjugative chloramphenicol resistance elements of the Tn4451/3 family. Mobile genetic elements such as transposons are important vehicles for the transmission of virulence and antibiotic resistance in many microorganisms.


Pssm-ID: 239739 [Multi-domain]  Cd Length: 140  Bit Score: 35.81  E-value: 8.87e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2794006544   7 TYGYLRASTDEQDA------SRAKNDLIDFADKMGFPIACWFEE-NESGAQLHRPELFRLLDVAMAG--DIILVEQVDRI 77
Cdd:cd03770     1 TALYCRLSRDDDLDgesnsiENQKAILEEYAKENGLENIRHYIDdGFSGTTFDRPGFNRMIEDIEAGkiDIVIVKDMSRL 80


                  ....*.
gi 2794006544  78 SRLNTK 83
Cdd:cd03770    81 GRNYLK 86
 
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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