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Conserved domains on  [gi|402970321|gb|EJX86676|]
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putative DNA-invertase hin [Enterococcus faecium P1123]

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 ...
 3-128 3.71e-27

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: 99.48  E-value: 3.71e-27
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 402970321   3 IIGYARTTINDVDLTTQVDQLSDFG-CQEIFHETyeVEQNDSTAVHLESVIADMQQGDALVICQLHRLGKSTRQLTELTQ 81
Cdd:cd03768    1 VIGYARVSTDDQSLERQLEALKAAGeCDKIFEEK--GSGGKKERPELQKLLEDLREGDTLVVTKLDRLGRSTKDLLEIVE 78

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*...
gi 402970321  82 LFKDRGLHLISLDEGIDTR-EMGKIYFQLMENLANMECALIKERTLVG 128
Cdd:cd03768   79 ELREKGVSLRSLTEGIDTStPSGKLMLTILGAFAEFERELIRERTKEG 126
 
Name Accession Description Interval E-value
SR_ResInv cd03768
Serine Recombinase (SR) family, Resolvase and Invertase subfamily, catalytic domain; members ...
 3-128 3.71e-27

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: 99.48  E-value: 3.71e-27
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 402970321   3 IIGYARTTINDVDLTTQVDQLSDFG-CQEIFHETyeVEQNDSTAVHLESVIADMQQGDALVICQLHRLGKSTRQLTELTQ 81
Cdd:cd03768    1 VIGYARVSTDDQSLERQLEALKAAGeCDKIFEEK--GSGGKKERPELQKLLEDLREGDTLVVTKLDRLGRSTKDLLEIVE 78

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*...
gi 402970321  82 LFKDRGLHLISLDEGIDTR-EMGKIYFQLMENLANMECALIKERTLVG 128
Cdd:cd03768   79 ELREKGVSLRSLTEGIDTStPSGKLMLTILGAFAEFERELIRERTKEG 126
Resolvase pfam00239
Resolvase, N terminal domain; The N-terminal domain of the resolvase family (this family) ...
 3-137 4.18e-26

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: 97.34  E-value: 4.18e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 402970321    3 IIGYAR--TTINDVDLTTQVDQLSDFGCQEIFHETYEvEQNDSTAVH----LESVIADMQ--QGDALVICQLHRLGKSTR 74
Cdd:pfam00239   1 AIGYARvsTEDQDDSLERQLEALRAYAACNGKIVEFE-DKGVSGRKLdrpgLQRLLALLRagKGDVLVVYKLDRLGRSLR 79

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 402970321   75 QLTELTQLFKDRGLHLISLDEGIDTR-EMGKIYFQLMENLANMECALIKERTLVGLDEARKKGK 137
Cdd:pfam00239  80 DLLTLVEELREKGVDLVSLDEGIDTStPMGRLLLTILAALAEFERALIRERTRAGLAAAAARGK 143
SpoIVCA COG1961
Site-specific DNA recombinase SpoIVCA/DNA invertase PinE [Replication, recombination and ...
 1-156 2.01e-21

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


Pssm-ID: 441564 [Multi-domain]  Cd Length: 388  Bit Score: 90.08  E-value: 2.01e-21
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 402970321   1 MKIIGYART-TIN--DVDLTTQVDQLSDF----GCQEIfhETYeVEQNDS-TAVH---LESVIADMQQG--DALVICQLH 67
Cdd:COG1961    2 MRAAGYARVsTDDqeGLSLERQREALRAYaekaGWEIV--RIY-VDEGVSgTSKDrpgLQRLLADLRAGkfDTLVVWKLD 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 402970321  68 RLGKSTRQLTELTQLFKDRGLHLISLDEGIDTR-EMGKIYFQLMENLANMECALIKERTLVGLDEARKKGKIGGRP---- 142
Cdd:COG1961   79 RLGRNLADLLELVEELKERGVRLISLTEGIDTStPMGRLLLTILAAFAEFERELISERTRAGLAAAKARGKYLGRPpygy 158

                        170       180
                 ....*....|....*....|...
gi 402970321 143 ------KID---AKTIKKIRRLY 156
Cdd:COG1961  159 rdpkklVIDeeeAEVVRRIFELY 181
Resolvase smart00857
Resolvase, N terminal domain; The N-terminal domain of the resolvase family contains the ...
 3-137 4.04e-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: 74.20  E-value: 4.04e-17
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 402970321     3 IIGYARTTIND---VDLTTQVDQLSDF----GCQEIfhETYEVEQNDSTAVH---LESVIADMQQGD--ALVICQLHRLG 70
Cdd:smart00857   1 AAGYARVSTDDqadGSLERQLEALRAYaernGWEVV--RIYEDEGVSGKKADrpgLQRLLADLRAGDidVLVVYKLDRLG 78

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 402970321    71 KSTRQLTELTQLFKDRGLHLISLDEGI--DTREMGKIYFQLMENLANMECALIKERTLVGLDEARKKGK 137
Cdd:smart00857  79 RSLRDLLALLELLEEKGVRLVSLKEGIldTSTPAGRLLLDILAALAEFERELISERTKAGLARAAARGR 147
mpi PRK13413
master DNA invertase Mpi family serine-type recombinase;
55-182 6.50e-06

master DNA invertase Mpi family serine-type recombinase;


Pssm-ID: 184041 [Multi-domain]  Cd Length: 200  Bit Score: 44.71  E-value: 6.50e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 402970321  55 MQQGDALVICQLHRLGKSTRQLTELTQLFKDRGLHLISLDEG------IDTREMGkIYFQLMenlANMECALIKERTLVG 128
Cdd:PRK13413  59 MRKGDILIVSELSRLGRNLMEIMSILNICMEKEVIVYTIKEGyelgddINSKVLA-FAFGLS---AEIERNLISQRTKEA 134

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 402970321 129 LdeARKK--GKIGGRPKIDAKTIKKIR------RLYYEKKETIQFISSKCGVSVGTCYKYIN 182
Cdd:PRK13413 135 L--ARKKaeGVTLGRPKGSTPKKYKLTgkeekiKKLLDKGTSKSEIARKLGVSRTTLARFLK 194
 
Name Accession Description Interval E-value
SR_ResInv cd03768
Serine Recombinase (SR) family, Resolvase and Invertase subfamily, catalytic domain; members ...
 3-128 3.71e-27

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: 99.48  E-value: 3.71e-27
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 402970321   3 IIGYARTTINDVDLTTQVDQLSDFG-CQEIFHETyeVEQNDSTAVHLESVIADMQQGDALVICQLHRLGKSTRQLTELTQ 81
Cdd:cd03768    1 VIGYARVSTDDQSLERQLEALKAAGeCDKIFEEK--GSGGKKERPELQKLLEDLREGDTLVVTKLDRLGRSTKDLLEIVE 78

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*...
gi 402970321  82 LFKDRGLHLISLDEGIDTR-EMGKIYFQLMENLANMECALIKERTLVG 128
Cdd:cd03768   79 ELREKGVSLRSLTEGIDTStPSGKLMLTILGAFAEFERELIRERTKEG 126
Resolvase pfam00239
Resolvase, N terminal domain; The N-terminal domain of the resolvase family (this family) ...
 3-137 4.18e-26

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: 97.34  E-value: 4.18e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 402970321    3 IIGYAR--TTINDVDLTTQVDQLSDFGCQEIFHETYEvEQNDSTAVH----LESVIADMQ--QGDALVICQLHRLGKSTR 74
Cdd:pfam00239   1 AIGYARvsTEDQDDSLERQLEALRAYAACNGKIVEFE-DKGVSGRKLdrpgLQRLLALLRagKGDVLVVYKLDRLGRSLR 79

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 402970321   75 QLTELTQLFKDRGLHLISLDEGIDTR-EMGKIYFQLMENLANMECALIKERTLVGLDEARKKGK 137
Cdd:pfam00239  80 DLLTLVEELREKGVDLVSLDEGIDTStPMGRLLLTILAALAEFERALIRERTRAGLAAAAARGK 143
SpoIVCA COG1961
Site-specific DNA recombinase SpoIVCA/DNA invertase PinE [Replication, recombination and ...
 1-156 2.01e-21

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


Pssm-ID: 441564 [Multi-domain]  Cd Length: 388  Bit Score: 90.08  E-value: 2.01e-21
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 402970321   1 MKIIGYART-TIN--DVDLTTQVDQLSDF----GCQEIfhETYeVEQNDS-TAVH---LESVIADMQQG--DALVICQLH 67
Cdd:COG1961    2 MRAAGYARVsTDDqeGLSLERQREALRAYaekaGWEIV--RIY-VDEGVSgTSKDrpgLQRLLADLRAGkfDTLVVWKLD 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 402970321  68 RLGKSTRQLTELTQLFKDRGLHLISLDEGIDTR-EMGKIYFQLMENLANMECALIKERTLVGLDEARKKGKIGGRP---- 142
Cdd:COG1961   79 RLGRNLADLLELVEELKERGVRLISLTEGIDTStPMGRLLLTILAAFAEFERELISERTRAGLAAAKARGKYLGRPpygy 158

                        170       180
                 ....*....|....*....|...
gi 402970321 143 ------KID---AKTIKKIRRLY 156
Cdd:COG1961  159 rdpkklVIDeeeAEVVRRIFELY 181
Resolvase smart00857
Resolvase, N terminal domain; The N-terminal domain of the resolvase family contains the ...
 3-137 4.04e-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: 74.20  E-value: 4.04e-17
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 402970321     3 IIGYARTTIND---VDLTTQVDQLSDF----GCQEIfhETYEVEQNDSTAVH---LESVIADMQQGD--ALVICQLHRLG 70
Cdd:smart00857   1 AAGYARVSTDDqadGSLERQLEALRAYaernGWEVV--RIYEDEGVSGKKADrpgLQRLLADLRAGDidVLVVYKLDRLG 78

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 402970321    71 KSTRQLTELTQLFKDRGLHLISLDEGI--DTREMGKIYFQLMENLANMECALIKERTLVGLDEARKKGK 137
Cdd:smart00857  79 RSLRDLLALLELLEEKGVRLVSLKEGIldTSTPAGRLLLDILAALAEFERELISERTKAGLARAAARGR 147
Ser_Recombinase cd00338
Serine Recombinase family, catalytic domain; a DNA binding domain may be present either N- or ...
 16-125 4.32e-08

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: 49.95  E-value: 4.32e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 402970321  16 LTTQVDQLSDFGCQEIFHETYEVEQNDSTAVH------LESVIADMQQG--DALVICQLHRLGKSTRQLTELTQLFKDRG 87
Cdd:cd00338   16 LERQREALREYAARNGLEVVGEYEDAGSSATSlvdrpgLQRLLADVKAGkiDVVLVEKLDRLSRNLVDLLELLELLEAHG 95

                         90       100       110
                 ....*....|....*....|....*....|....*....
gi 402970321  88 LHLISLDEGIDT-REMGKIYFQLMENLANMECALIKERT 125
Cdd:cd00338   96 VRVVTADGEIDLdSEDGRLMLGILAAMAEEESKLISERT 134
mpi PRK13413
master DNA invertase Mpi family serine-type recombinase;
55-182 6.50e-06

master DNA invertase Mpi family serine-type recombinase;


Pssm-ID: 184041 [Multi-domain]  Cd Length: 200  Bit Score: 44.71  E-value: 6.50e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 402970321  55 MQQGDALVICQLHRLGKSTRQLTELTQLFKDRGLHLISLDEG------IDTREMGkIYFQLMenlANMECALIKERTLVG 128
Cdd:PRK13413  59 MRKGDILIVSELSRLGRNLMEIMSILNICMEKEVIVYTIKEGyelgddINSKVLA-FAFGLS---AEIERNLISQRTKEA 134

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 402970321 129 LdeARKK--GKIGGRPKIDAKTIKKIR------RLYYEKKETIQFISSKCGVSVGTCYKYIN 182
Cdd:PRK13413 135 L--ARKKaeGVTLGRPKGSTPKKYKLTgkeekiKKLLDKGTSKSEIARKLGVSRTTLARFLK 194
 
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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