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Conserved domains on  [gi|1788961612|ref|WP_158099566|]
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recombinase family protein, partial [Flavonifractor sp. An9]

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 ...
 7-91 3.07e-44

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 cd03770:

Pssm-ID: 445923 [Multi-domain]  Cd Length: 140  Bit Score: 139.43  E-value: 3.07e-44
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1788961612   7 TPLYERLSRDDELQGESNSISNQKKMLEDYARRSGLPNPTHFTDDGVSGTRFDRPGFLAMMEEVEAGRVEAIVIKDMSRL 86
Cdd:cd03770     1 TALYCRLSRDDDLDGESNSIENQKAILEEYAKENGLENIRHYIDDGFSGTTFDRPGFNRMIEDIEAGKIDIVIVKDMSRL 80


                  ....*
gi 1788961612  87 GRDYL 91
Cdd:cd03770    81 GRNYL 85
 
Name Accession Description Interval E-value
SR_TndX_transposase cd03770
Serine Recombinase (SR) family, TndX-like transposase subfamily, catalytic domain; composed of ...
 7-91 3.07e-44

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: 139.43  E-value: 3.07e-44
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1788961612   7 TPLYERLSRDDELQGESNSISNQKKMLEDYARRSGLPNPTHFTDDGVSGTRFDRPGFLAMMEEVEAGRVEAIVIKDMSRL 86
Cdd:cd03770     1 TALYCRLSRDDDLDGESNSIENQKAILEEYAKENGLENIRHYIDDGFSGTTFDRPGFNRMIEDIEAGKIDIVIVKDMSRL 80


                  ....*
gi 1788961612  87 GRDYL 91
Cdd:cd03770    81 GRNYL 85
SpoIVCA COG1961
Site-specific DNA recombinase SpoIVCA/DNA invertase PinE [Replication, recombination and ...
 9-91 8.27e-24

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


Pssm-ID: 441564 [Multi-domain]  Cd Length: 388  Bit Score: 92.40  E-value: 8.27e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1788961612   9 LYERLSRDDElqgESNSISNQKKMLEDYARRSGLPNPTHFTDDGVSGTRFDRPGFLAMMEEVEAGRVEAIVIKDMSRLGR 88
Cdd:COG1961     6 GYARVSTDDQ---EGLSLERQREALRAYAEKAGWEIVRIYVDEGVSGTSKDRPGLQRLLADLRAGKFDTLVVWKLDRLGR 82


                  ...
gi 1788961612  89 DYL 91
Cdd:COG1961    83 NLA 85
Resolvase smart00857
Resolvase, N terminal domain; The N-terminal domain of the resolvase family contains the ...
 9-90 1.05e-22

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: 84.98  E-value: 1.05e-22
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1788961612    9 LYERLSRDDELQGesnSISNQKKMLEDYARRSGLPNPTHFTDDGVSGTRFDRPGFLAMMEEVEAGRVEAIVIKDMSRLGR 88
Cdd:smart00857   3 GYARVSTDDQADG---SLERQLEALRAYAERNGWEVVRIYEDEGVSGKKADRPGLQRLLADLRAGDIDVLVVYKLDRLGR 79


                   ..
gi 1788961612   89 DY 90
Cdd:smart00857  80 SL 81
Resolvase pfam00239
Resolvase, N terminal domain; The N-terminal domain of the resolvase family (this family) ...
 9-89 4.71e-14

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: 62.67  E-value: 4.71e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1788961612   9 LYERLSRDDelQGESnsISNQKKMLEDYARRSGlpNPTHFTDDGVSGTRFDRPGFLAMMEEVEAGRVEAIVIKDMSRLGR 88
Cdd:pfam00239   3 GYARVSTED--QDDS--LERQLEALRAYAACNG--KIVEFEDKGVSGRKLDRPGLQRLLALLRAGKGDVLVVYKLDRLGR 76


                  .
gi 1788961612  89 D 89
Cdd:pfam00239  77 S 77
 
Name Accession Description Interval E-value
SR_TndX_transposase cd03770
Serine Recombinase (SR) family, TndX-like transposase subfamily, catalytic domain; composed of ...
 7-91 3.07e-44

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: 139.43  E-value: 3.07e-44
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1788961612   7 TPLYERLSRDDELQGESNSISNQKKMLEDYARRSGLPNPTHFTDDGVSGTRFDRPGFLAMMEEVEAGRVEAIVIKDMSRL 86
Cdd:cd03770     1 TALYCRLSRDDDLDGESNSIENQKAILEEYAKENGLENIRHYIDDGFSGTTFDRPGFNRMIEDIEAGKIDIVIVKDMSRL 80


                  ....*
gi 1788961612  87 GRDYL 91
Cdd:cd03770    81 GRNYL 85
SpoIVCA COG1961
Site-specific DNA recombinase SpoIVCA/DNA invertase PinE [Replication, recombination and ...
 9-91 8.27e-24

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


Pssm-ID: 441564 [Multi-domain]  Cd Length: 388  Bit Score: 92.40  E-value: 8.27e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1788961612   9 LYERLSRDDElqgESNSISNQKKMLEDYARRSGLPNPTHFTDDGVSGTRFDRPGFLAMMEEVEAGRVEAIVIKDMSRLGR 88
Cdd:COG1961     6 GYARVSTDDQ---EGLSLERQREALRAYAEKAGWEIVRIYVDEGVSGTSKDRPGLQRLLADLRAGKFDTLVVWKLDRLGR 82


                  ...
gi 1788961612  89 DYL 91
Cdd:COG1961    83 NLA 85
Resolvase smart00857
Resolvase, N terminal domain; The N-terminal domain of the resolvase family contains the ...
 9-90 1.05e-22

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: 84.98  E-value: 1.05e-22
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1788961612    9 LYERLSRDDELQGesnSISNQKKMLEDYARRSGLPNPTHFTDDGVSGTRFDRPGFLAMMEEVEAGRVEAIVIKDMSRLGR 88
Cdd:smart00857   3 GYARVSTDDQADG---SLERQLEALRAYAERNGWEVVRIYEDEGVSGKKADRPGLQRLLADLRAGDIDVLVVYKLDRLGR 79


                   ..
gi 1788961612   89 DY 90
Cdd:smart00857  80 SL 81
Ser_Recombinase cd00338
Serine Recombinase family, catalytic domain; a DNA binding domain may be present either N- or ...
 9-90 7.01e-21

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: 80.00  E-value: 7.01e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1788961612   9 LYERLSRDDelQGESNSISNQKKMLEDYARRSGLPNPTHFTDDGVSGTR-FDRPGFLAMMEEVEAGRVEAIVIKDMSRLG 87
Cdd:cd00338     1 IYARVSTDK--QEQGDSLERQREALREYAARNGLEVVGEYEDAGSSATSlVDRPGLQRLLADVKAGKIDVVLVEKLDRLS 78


                  ...
gi 1788961612  88 RDY 90
Cdd:cd00338    79 RNL 81
Resolvase pfam00239
Resolvase, N terminal domain; The N-terminal domain of the resolvase family (this family) ...
 9-89 4.71e-14

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: 62.67  E-value: 4.71e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1788961612   9 LYERLSRDDelQGESnsISNQKKMLEDYARRSGlpNPTHFTDDGVSGTRFDRPGFLAMMEEVEAGRVEAIVIKDMSRLGR 88
Cdd:pfam00239   3 GYARVSTED--QDDS--LERQLEALRAYAACNG--KIVEFEDKGVSGRKLDRPGLQRLLALLRAGKGDVLVVYKLDRLGR 76


                  .
gi 1788961612  89 D 89
Cdd:pfam00239  77 S 77
SR_ResInv cd03768
Serine Recombinase (SR) family, Resolvase and Invertase subfamily, catalytic domain; members ...
 10-91 2.00e-07

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: 45.16  E-value: 2.00e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1788961612  10 YERLSRDDElqgesnSISNQKKMLEDYArrsglpNPTHFTDDGVSGTRFDRPGFLAMMEEVEAGRVeaIVIKDMSRLGRD 89
Cdd:cd03768     4 YARVSTDDQ------SLERQLEALKAAG------ECDKIFEEKGSGGKKERPELQKLLEDLREGDT--LVVTKLDRLGRS 69


                  ..
gi 1788961612  90 YL 91
Cdd:cd03768    70 TK 71
SR_IS607_transposase_like cd03769
Serine Recombinase (SR) family, IS607-like transposase subfamily, catalytic domain; members ...
 7-91 5.46e-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: 44.17  E-value: 5.46e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1788961612   7 TPLYERLS---RDDELQgesnsisNQKKMLEDYARRSGLpNPTHFTDDGvSGTRFDRPGFLAMMEEVEAGRVEAIVI--K 81
Cdd:cd03769     1 TVLYARVSshdQKDDLE-------RQIERLEAYATAQGW-IVEVIKDIG-SGLNEKRKGLLKLLEDVLAGKVERVVItyK 71

                          90
                  ....*....|.
gi 1788961612  82 D-MSRLGRDYL 91
Cdd:cd03769    72 DrLARFGFELL 82
 
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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