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Conserved domains on  [gi|488378016|ref|WP_002447401|]
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MULTISPECIES: recombinase family protein [Bacillota]

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 ...
 3-135 1.02e-15

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 pfam00239:

Pssm-ID: 445923 [Multi-domain]  Cd Length: 144  Bit Score: 69.99  E-value: 1.02e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488378016    3 YGYIRPVTI--NDDLNEQKKKIETYTKK-----IVEESHANNKKRNELDLLLKKKLVS---GDAVYITDLCILADSTKQL 72
Cdd:pfam00239   2 IGYARVSTEdqDDSLERQLEALRAYAACngkivEFEDKGVSGRKLDRPGLQRLLALLRagkGDVLVVYKLDRLGRSLRDL 81

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 488378016   73 VDILDYLSQKDISLYVINLNRYIYKNIQGEFLEILHDITDFQSDVVKFRTRVGLENYTKEGKK 135
Cdd:pfam00239  82 LTLVEELREKGVDLVSLDEGIDTSTPMGRLLLTILAALAEFERALIRERTRAGLAAAAARGKL 144
 
Name Accession Description Interval E-value
Resolvase pfam00239
Resolvase, N terminal domain; The N-terminal domain of the resolvase family (this family) ...
 3-135 1.02e-15

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: 69.99  E-value: 1.02e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488378016    3 YGYIRPVTI--NDDLNEQKKKIETYTKK-----IVEESHANNKKRNELDLLLKKKLVS---GDAVYITDLCILADSTKQL 72
Cdd:pfam00239   2 IGYARVSTEdqDDSLERQLEALRAYAACngkivEFEDKGVSGRKLDRPGLQRLLALLRagkGDVLVVYKLDRLGRSLRDL 81

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 488378016   73 VDILDYLSQKDISLYVINLNRYIYKNIQGEFLEILHDITDFQSDVVKFRTRVGLENYTKEGKK 135
Cdd:pfam00239  82 LTLVEELREKGVDLVSLDEGIDTSTPMGRLLLTILAALAEFERALIRERTRAGLAAAAARGKL 144
SR_ResInv cd03768
Serine Recombinase (SR) family, Resolvase and Invertase subfamily, catalytic domain; members ...
 2-125 3.01e-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: 65.58  E-value: 3.01e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488378016   2 KYGYIRPVTINDDLNEQKKKIETY--TKKIVEESH-ANNKKRNELDLLLKKKLvSGDAVYITDLCILADSTKQLVDILDY 78
Cdd:cd03768    1 VIGYARVSTDDQSLERQLEALKAAgeCDKIFEEKGsGGKKERPELQKLLEDLR-EGDTLVVTKLDRLGRSTKDLLEIVEE 79

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*..
gi 488378016  79 LSQKDISLYVINLNRYIYKNIQGEFLEILHDITDFQSDVVKFRTRVG 125
Cdd:cd03768   80 LREKGVSLRSLTEGIDTSTPSGKLMLTILGAFAEFERELIRERTKEG 126
SpoIVCA COG1961
Site-specific DNA recombinase SpoIVCA/DNA invertase PinE [Replication, recombination and ...
 55-180 1.18e-09

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


Pssm-ID: 441564 [Multi-domain]  Cd Length: 388  Bit Score: 56.19  E-value: 1.18e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488378016  55 DAVYITDLCILADSTKQLVDILDYLSQKDISLYVINLNrYIYKNIQGEF-LEILHDITDFQSDVVKFRTRVGLENYTKEG 133
Cdd:COG1961   70 DTLVVWKLDRLGRNLADLLELVEELKERGVRLISLTEG-IDTSTPMGRLlLTILAAFAEFERELISERTRAGLAAAKARG 148

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 488378016 134 KKLGRPK---RDDKNL----------RDAIEMYMsKNYTLDEIKEKTN------ISRATLYRHLDK 180
Cdd:COG1961  149 KYLGRPPygyRDPKKLvideeeaevvRRIFELYL-EGKSLREIARELNergiptWSRSTVYRILKN 213
mpi PRK13413
master DNA invertase Mpi family serine-type recombinase;
1-178 2.83e-07

master DNA invertase Mpi family serine-type recombinase;


Pssm-ID: 184041 [Multi-domain]  Cd Length: 200  Bit Score: 48.56  E-value: 2.83e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488378016   1 MKYGYIRPVTINDDLNEQKKKIETYTKK-------IVEESHANNKKRNELDLLLKKKLV-SGDAVYITDLCILADSTKQL 72
Cdd:PRK13413   1 MIYAYIRVSTDKQTVENQRFEITNFAEKnnltidkWIEETISGTKSYKDRKLGKLLKKMrKGDILIVSELSRLGRNLMEI 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488378016  73 VDILDYLSQKDISLYVINLNRYIYKNIQGEFLEILHDIT-DFQSDVVKFRTRVGLENYTKEGKKLGRPKRDD------KN 145
Cdd:PRK13413  81 MSILNICMEKEVIVYTIKEGYELGDDINSKVLAFAFGLSaEIERNLISQRTKEALARKKAEGVTLGRPKGSTpkkyklTG 160

                        170       180       190
                 ....*....|....*....|....*....|...
gi 488378016 146 LRDAIEMYMSKNYTLDEIKEKTNISRATLYRHL 178
Cdd:PRK13413 161 KEEKIKKLLDKGTSKSEIARKLGVSRTTLARFL 193
 
Name Accession Description Interval E-value
Resolvase pfam00239
Resolvase, N terminal domain; The N-terminal domain of the resolvase family (this family) ...
 3-135 1.02e-15

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: 69.99  E-value: 1.02e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488378016    3 YGYIRPVTI--NDDLNEQKKKIETYTKK-----IVEESHANNKKRNELDLLLKKKLVS---GDAVYITDLCILADSTKQL 72
Cdd:pfam00239   2 IGYARVSTEdqDDSLERQLEALRAYAACngkivEFEDKGVSGRKLDRPGLQRLLALLRagkGDVLVVYKLDRLGRSLRDL 81

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 488378016   73 VDILDYLSQKDISLYVINLNRYIYKNIQGEFLEILHDITDFQSDVVKFRTRVGLENYTKEGKK 135
Cdd:pfam00239  82 LTLVEELREKGVDLVSLDEGIDTSTPMGRLLLTILAALAEFERALIRERTRAGLAAAAARGKL 144
SR_ResInv cd03768
Serine Recombinase (SR) family, Resolvase and Invertase subfamily, catalytic domain; members ...
 2-125 3.01e-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: 65.58  E-value: 3.01e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488378016   2 KYGYIRPVTINDDLNEQKKKIETY--TKKIVEESH-ANNKKRNELDLLLKKKLvSGDAVYITDLCILADSTKQLVDILDY 78
Cdd:cd03768    1 VIGYARVSTDDQSLERQLEALKAAgeCDKIFEEKGsGGKKERPELQKLLEDLR-EGDTLVVTKLDRLGRSTKDLLEIVEE 79

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*..
gi 488378016  79 LSQKDISLYVINLNRYIYKNIQGEFLEILHDITDFQSDVVKFRTRVG 125
Cdd:cd03768   80 LREKGVSLRSLTEGIDTSTPSGKLMLTILGAFAEFERELIRERTKEG 126
SpoIVCA COG1961
Site-specific DNA recombinase SpoIVCA/DNA invertase PinE [Replication, recombination and ...
 55-180 1.18e-09

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


Pssm-ID: 441564 [Multi-domain]  Cd Length: 388  Bit Score: 56.19  E-value: 1.18e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488378016  55 DAVYITDLCILADSTKQLVDILDYLSQKDISLYVINLNrYIYKNIQGEF-LEILHDITDFQSDVVKFRTRVGLENYTKEG 133
Cdd:COG1961   70 DTLVVWKLDRLGRNLADLLELVEELKERGVRLISLTEG-IDTSTPMGRLlLTILAAFAEFERELISERTRAGLAAAKARG 148

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 488378016 134 KKLGRPK---RDDKNL----------RDAIEMYMsKNYTLDEIKEKTN------ISRATLYRHLDK 180
Cdd:COG1961  149 KYLGRPPygyRDPKKLvideeeaevvRRIFELYL-EGKSLREIARELNergiptWSRSTVYRILKN 213
mpi PRK13413
master DNA invertase Mpi family serine-type recombinase;
1-178 2.83e-07

master DNA invertase Mpi family serine-type recombinase;


Pssm-ID: 184041 [Multi-domain]  Cd Length: 200  Bit Score: 48.56  E-value: 2.83e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488378016   1 MKYGYIRPVTINDDLNEQKKKIETYTKK-------IVEESHANNKKRNELDLLLKKKLV-SGDAVYITDLCILADSTKQL 72
Cdd:PRK13413   1 MIYAYIRVSTDKQTVENQRFEITNFAEKnnltidkWIEETISGTKSYKDRKLGKLLKKMrKGDILIVSELSRLGRNLMEI 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488378016  73 VDILDYLSQKDISLYVINLNRYIYKNIQGEFLEILHDIT-DFQSDVVKFRTRVGLENYTKEGKKLGRPKRDD------KN 145
Cdd:PRK13413  81 MSILNICMEKEVIVYTIKEGYELGDDINSKVLAFAFGLSaEIERNLISQRTKEALARKKAEGVTLGRPKGSTpkkyklTG 160

                        170       180       190
                 ....*....|....*....|....*....|...
gi 488378016 146 LRDAIEMYMSKNYTLDEIKEKTNISRATLYRHL 178
Cdd:PRK13413 161 KEEKIKKLLDKGTSKSEIARKLGVSRTTLARFL 193
 
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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