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Conserved domains on  [gi|1493098442|ref|WP_121301315|]
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recombinase family protein [Planococcus citreus]

Protein Classification

recombinase family protein( domain architecture ID 10132964)

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:0015074|GO:0000150|GO:0003677|GO:0006310
PubMed:  11972771|16077726|9348666|21645851|26104451
SCOP:  3000065

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
SR_ResInv cd03768
Serine Recombinase (SR) family, Resolvase and Invertase subfamily, catalytic domain; members ...
 5-126 3.61e-28

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: 102.56  E-value: 3.61e-28
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1493098442   5 KFGYIRVSSKDQNEGRQLDAMKKMGINGRdIYLDKQSGKNFERANYQLLKRVIRKGDILYIHSLDRFGRNKEEILQEWND 84
Cdd:cd03768     1 VIGYARVSTDDQSLERQLEALKAAGECDK-IFEEKGSGGKKERPELQKLLEDLREGDTLVVTKLDRLGRSTKDLLEIVEE 79

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|..
gi 1493098442  85 LTKNiEADIVVLDMPLLDTTqykdSMGtfiaDLVLQILSWMA 126
Cdd:cd03768    80 LREK-GVSLRSLTEGIDTST----PSG----KLMLTILGAFA 112
 
Name Accession Description Interval E-value
SR_ResInv cd03768
Serine Recombinase (SR) family, Resolvase and Invertase subfamily, catalytic domain; members ...
 5-126 3.61e-28

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: 102.56  E-value: 3.61e-28
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1493098442   5 KFGYIRVSSKDQNEGRQLDAMKKMGINGRdIYLDKQSGKNFERANYQLLKRVIRKGDILYIHSLDRFGRNKEEILQEWND 84
Cdd:cd03768     1 VIGYARVSTDDQSLERQLEALKAAGECDK-IFEEKGSGGKKERPELQKLLEDLREGDTLVVTKLDRLGRSTKDLLEIVEE 79

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|..
gi 1493098442  85 LTKNiEADIVVLDMPLLDTTqykdSMGtfiaDLVLQILSWMA 126
Cdd:cd03768    80 LREK-GVSLRSLTEGIDTST----PSG----KLMLTILGAFA 112
SpoIVCA COG1961
Site-specific DNA recombinase SpoIVCA/DNA invertase PinE [Replication, recombination and ...
 4-154 5.40e-20

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


Pssm-ID: 441564 [Multi-domain]  Cd Length: 388  Bit Score: 86.62  E-value: 5.40e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1493098442   4 RKFGYIRVSSKDQNEG---RQLDAMK----KMGINGRDIYLDK-QSGKNFERANYQLLKRVIRKG--DILYIHSLDRFGR 73
Cdd:COG1961     3 RAAGYARVSTDDQEGLsleRQREALRayaeKAGWEIVRIYVDEgVSGTSKDRPGLQRLLADLRAGkfDTLVVWKLDRLGR 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1493098442  74 NKEEILQEWNDLTKNiEADIVVLDMPLlDTTqykDSMGtfiaDLVLQILSWMAEEERERIRKRQREGIDLALQNGIQFGR 153
Cdd:COG1961    83 NLADLLELVEELKER-GVRLISLTEGI-DTS---TPMG----RLLLTILAAFAEFERELISERTRAGLAAAKARGKYLGR 153


                  .
gi 1493098442 154 P 154
Cdd:COG1961   154 P 154
Resolvase smart00857
Resolvase, N terminal domain; The N-terminal domain of the resolvase family contains the ...
 6-148 4.33e-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: 74.58  E-value: 4.33e-17
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1493098442    6 FGYIRVSSKDQNEG---RQLDAMK----KMGINGRDIYLDK-QSGKNFERANYQLLKRVIRKGDI--LYIHSLDRFGRNK 75
Cdd:smart00857   2 AGYARVSTDDQADGsleRQLEALRayaeRNGWEVVRIYEDEgVSGKKADRPGLQRLLADLRAGDIdvLVVYKLDRLGRSL 81

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1493098442   76 EEILQEWNDLTKNiEADIVVLDMPLLDTTqykdsmgTFIADLVLQILSWMAEEERERIRKRQREGIDLALQNG 148
Cdd:smart00857  82 RDLLALLELLEEK-GVRLVSLKEGILDTS-------TPAGRLLLDILAALAEFERELISERTKAGLARAAARG 146
Resolvase pfam00239
Resolvase, N terminal domain; The N-terminal domain of the resolvase family (this family) ...
 6-148 8.43e-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: 65.75  E-value: 8.43e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1493098442   6 FGYIRVSSKDQNEG--RQLDAMKKMGINGRDI--YLDK-QSGKNFERANYQLLKRVIR--KGDILYIHSLDRFGRNKEEI 78
Cdd:pfam00239   2 IGYARVSTEDQDDSleRQLEALRAYAACNGKIveFEDKgVSGRKLDRPGLQRLLALLRagKGDVLVVYKLDRLGRSLRDL 81

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1493098442  79 LQEWNDLTKNiEADIVVLDMPLlDTTqykDSMGtfiaDLVLQILSWMAEEERERIRKRQREGIDLALQNG 148
Cdd:pfam00239  82 LTLVEELREK-GVDLVSLDEGI-DTS---TPMG----RLLLTILAALAEFERALIRERTRAGLAAAAARG 142
mpi PRK13413
master DNA invertase Mpi family serine-type recombinase;
6-89 3.36e-04

master DNA invertase Mpi family serine-type recombinase;


Pssm-ID: 184041 [Multi-domain]  Cd Length: 200  Bit Score: 40.09  E-value: 3.36e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1493098442   6 FGYIRVSSKDQ--------------NEGRQLDAMKKMGINGRDIYLDKQSGKnferanyqLLKRvIRKGDILYIHSLDRF 71
Cdd:PRK13413    3 YAYIRVSTDKQtvenqrfeitnfaeKNNLTIDKWIEETISGTKSYKDRKLGK--------LLKK-MRKGDILIVSELSRL 73

                          90
                  ....*....|....*....
gi 1493098442  72 GRNKEEILQEWND-LTKNI 89
Cdd:PRK13413   74 GRNLMEIMSILNIcMEKEV 92
 
Name Accession Description Interval E-value
SR_ResInv cd03768
Serine Recombinase (SR) family, Resolvase and Invertase subfamily, catalytic domain; members ...
 5-126 3.61e-28

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: 102.56  E-value: 3.61e-28
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1493098442   5 KFGYIRVSSKDQNEGRQLDAMKKMGINGRdIYLDKQSGKNFERANYQLLKRVIRKGDILYIHSLDRFGRNKEEILQEWND 84
Cdd:cd03768     1 VIGYARVSTDDQSLERQLEALKAAGECDK-IFEEKGSGGKKERPELQKLLEDLREGDTLVVTKLDRLGRSTKDLLEIVEE 79

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|..
gi 1493098442  85 LTKNiEADIVVLDMPLLDTTqykdSMGtfiaDLVLQILSWMA 126
Cdd:cd03768    80 LREK-GVSLRSLTEGIDTST----PSG----KLMLTILGAFA 112
SpoIVCA COG1961
Site-specific DNA recombinase SpoIVCA/DNA invertase PinE [Replication, recombination and ...
 4-154 5.40e-20

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


Pssm-ID: 441564 [Multi-domain]  Cd Length: 388  Bit Score: 86.62  E-value: 5.40e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1493098442   4 RKFGYIRVSSKDQNEG---RQLDAMK----KMGINGRDIYLDK-QSGKNFERANYQLLKRVIRKG--DILYIHSLDRFGR 73
Cdd:COG1961     3 RAAGYARVSTDDQEGLsleRQREALRayaeKAGWEIVRIYVDEgVSGTSKDRPGLQRLLADLRAGkfDTLVVWKLDRLGR 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1493098442  74 NKEEILQEWNDLTKNiEADIVVLDMPLlDTTqykDSMGtfiaDLVLQILSWMAEEERERIRKRQREGIDLALQNGIQFGR 153
Cdd:COG1961    83 NLADLLELVEELKER-GVRLISLTEGI-DTS---TPMG----RLLLTILAAFAEFERELISERTRAGLAAAKARGKYLGR 153


                  .
gi 1493098442 154 P 154
Cdd:COG1961   154 P 154
Resolvase smart00857
Resolvase, N terminal domain; The N-terminal domain of the resolvase family contains the ...
 6-148 4.33e-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: 74.58  E-value: 4.33e-17
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1493098442    6 FGYIRVSSKDQNEG---RQLDAMK----KMGINGRDIYLDK-QSGKNFERANYQLLKRVIRKGDI--LYIHSLDRFGRNK 75
Cdd:smart00857   2 AGYARVSTDDQADGsleRQLEALRayaeRNGWEVVRIYEDEgVSGKKADRPGLQRLLADLRAGDIdvLVVYKLDRLGRSL 81

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1493098442   76 EEILQEWNDLTKNiEADIVVLDMPLLDTTqykdsmgTFIADLVLQILSWMAEEERERIRKRQREGIDLALQNG 148
Cdd:smart00857  82 RDLLALLELLEEK-GVRLVSLKEGILDTS-------TPAGRLLLDILAALAEFERELISERTKAGLARAAARG 146
Resolvase pfam00239
Resolvase, N terminal domain; The N-terminal domain of the resolvase family (this family) ...
 6-148 8.43e-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: 65.75  E-value: 8.43e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1493098442   6 FGYIRVSSKDQNEG--RQLDAMKKMGINGRDI--YLDK-QSGKNFERANYQLLKRVIR--KGDILYIHSLDRFGRNKEEI 78
Cdd:pfam00239   2 IGYARVSTEDQDDSleRQLEALRAYAACNGKIveFEDKgVSGRKLDRPGLQRLLALLRagKGDVLVVYKLDRLGRSLRDL 81

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1493098442  79 LQEWNDLTKNiEADIVVLDMPLlDTTqykDSMGtfiaDLVLQILSWMAEEERERIRKRQREGIDLALQNG 148
Cdd:pfam00239  82 LTLVEELREK-GVDLVSLDEGI-DTS---TPMG----RLLLTILAALAEFERALIRERTRAGLAAAAARG 142
Ser_Recombinase cd00338
Serine Recombinase family, catalytic domain; a DNA binding domain may be present either N- or ...
 8-131 7.96e-09

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: 52.26  E-value: 7.96e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1493098442   8 YIRVSSKDQNEG----RQLDAMKK----MGINGRDIYLDKQSG--KNFERANYQ-LLKRV-IRKGDILYIHSLDRFGRNK 75
Cdd:cd00338     2 YARVSTDKQEQGdsleRQREALREyaarNGLEVVGEYEDAGSSatSLVDRPGLQrLLADVkAGKIDVVLVEKLDRLSRNL 81

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1493098442  76 EEILQeWNDLTKNIEADIVVLDMPLlDTTQYKDSMgtfiadlVLQILSWMAEEERE 131
Cdd:cd00338    82 VDLLE-LLELLEAHGVRVVTADGEI-DLDSEDGRL-------MLGILAAMAEEESK 128
SR_Res_par cd03767
Serine recombinase (SR) family, Partitioning (par)-Resolvase subfamily, catalytic domain; ...
 7-140 1.15e-04

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: 40.77  E-value: 1.15e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1493098442   7 GYIRVSSKDQNEGRQLDAMKK----MGINGRDIYLDKQSGKNFERAnyqLLKRVI---RKGDILYIHSLDRFGRNKEEil 79
Cdd:cd03767     3 AYLRASTDEQDATRAKESLEAfateRGFYIAGFYVENASGAKLDRP---ELFRLLddaQSGDVLLVEQIDRLSRLPLD-- 77

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1493098442  80 qEWNDLTKNIEAD---IVVLDMPL------LDTTQYKDSMGTFIADLVLQILSWMAEEERERIRKRQREG 140
Cdd:cd03767    78 -DWETLKASIAAKglrVVSLDLPTshsalaAEDNDFTGRILSAINDMLLDLLAAMARKDYEDRRERQKQG 146
mpi PRK13413
master DNA invertase Mpi family serine-type recombinase;
6-89 3.36e-04

master DNA invertase Mpi family serine-type recombinase;


Pssm-ID: 184041 [Multi-domain]  Cd Length: 200  Bit Score: 40.09  E-value: 3.36e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1493098442   6 FGYIRVSSKDQ--------------NEGRQLDAMKKMGINGRDIYLDKQSGKnferanyqLLKRvIRKGDILYIHSLDRF 71
Cdd:PRK13413    3 YAYIRVSTDKQtvenqrfeitnfaeKNNLTIDKWIEETISGTKSYKDRKLGK--------LLKK-MRKGDILIVSELSRL 73

                          90
                  ....*....|....*....
gi 1493098442  72 GRNKEEILQEWND-LTKNI 89
Cdd:PRK13413   74 GRNLMEIMSILNIcMEKEV 92
SR_TndX_transposase cd03770
Serine Recombinase (SR) family, TndX-like transposase subfamily, catalytic domain; composed of ...
 7-80 7.52e-03

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: 35.42  E-value: 7.52e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1493098442   7 GYIRVSSKDQNEGRQL----------DAMKKMGINGRDIYLDKQ-SGKNFERANYQLLKRVIRKG--DILYIHSLDRFGR 73
Cdd:cd03770     3 LYCRLSRDDDLDGESNsienqkaileEYAKENGLENIRHYIDDGfSGTTFDRPGFNRMIEDIEAGkiDIVIVKDMSRLGR 82


                  ....*..
gi 1493098442  74 NKEEILQ 80
Cdd:cd03770    83 NYLKVGL 89
 
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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