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Conserved domains on  [gi|1948509509|gb|QQA49751|]
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recombinase family protein (plasmid) [Staphylococcus pseudintermedius]

Protein Classification

recombinase family protein( domain architecture ID 18951323)

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 ...
 4-127 2.30e-59

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: 181.14  E-value: 2.30e-59
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1948509509   4 VGYARVSTQDQKLDSQIDALKEYG-CTKIFSEKVSGKKFKRTELDKCLEYLREGDTLVIYKLDRLGRTTKQLIELSQWLE 82
Cdd:cd03768     2 IGYARVSTDDQSLERQLEALKAAGeCDKIFEEKGSGGKKERPELQKLLEDLREGDTLVVTKLDRLGRSTKDLLEIVEELR 81

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*
gi 1948509509  83 DNHIELQIINMNINTKDAMGKMFFTMMSAFAELEANLLSERTKKG 127
Cdd:cd03768    82 EKGVSLRSLTEGIDTSTPSGKLMLTILGAFAEFERELIRERTKEG 126
HTH_CRP super family cl46859
helix_turn_helix, cAMP Regulatory protein C-terminus; DNA binding domain of prokaryotic ...
 138-180 1.08e-04

helix_turn_helix, cAMP Regulatory protein C-terminus; DNA binding domain of prokaryotic regulatory proteins belonging to the catabolite activator protein family.


The actual alignment was detected with superfamily member cd00569:

Pssm-ID: 481199 [Multi-domain]  Cd Length: 42  Bit Score: 38.08  E-value: 1.08e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 1948509509 138 GGRPSLPDYKKREIKFLYDERKlTGEEIAKQTGVSRSTVYRVI 180
Cdd:cd00569     1 GRPPKLTPEQIAEARRLLAAGE-SVAEIARELGVSRSTLYRYL 42
 
Name Accession Description Interval E-value
SR_ResInv cd03768
Serine Recombinase (SR) family, Resolvase and Invertase subfamily, catalytic domain; members ...
 4-127 2.30e-59

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: 181.14  E-value: 2.30e-59
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1948509509   4 VGYARVSTQDQKLDSQIDALKEYG-CTKIFSEKVSGKKFKRTELDKCLEYLREGDTLVIYKLDRLGRTTKQLIELSQWLE 82
Cdd:cd03768     2 IGYARVSTDDQSLERQLEALKAAGeCDKIFEEKGSGGKKERPELQKLLEDLREGDTLVVTKLDRLGRSTKDLLEIVEELR 81

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*
gi 1948509509  83 DNHIELQIINMNINTKDAMGKMFFTMMSAFAELEANLLSERTKKG 127
Cdd:cd03768    82 EKGVSLRSLTEGIDTSTPSGKLMLTILGAFAEFERELIRERTKEG 126
SpoIVCA COG1961
Site-specific DNA recombinase SpoIVCA/DNA invertase PinE [Replication, recombination and ...
 1-184 6.43e-50

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


Pssm-ID: 441564 [Multi-domain]  Cd Length: 388  Bit Score: 165.58  E-value: 6.43e-50
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1948509509   1 MAMVGYARVSTQDQK---LDSQIDALKEY----GCT--KIFSEK-VSGKKFKRTELDKCLEYLREG--DTLVIYKLDRLG 68
Cdd:COG1961     2 MRAAGYARVSTDDQEglsLERQREALRAYaekaGWEivRIYVDEgVSGTSKDRPGLQRLLADLRAGkfDTLVVWKLDRLG 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1948509509  69 RTTKQLIELSQWLEDNHIELQIINMNINTKDAMGKMFFTMMSAFAELEANLLSERTKKGLAAARARGRKGGRPSL-PDYK 147
Cdd:COG1961    82 RNLADLLELVEELKERGVRLISLTEGIDTSTPMGRLLLTILAAFAEFERELISERTRAGLAAAKARGKYLGRPPYgYRDP 161

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1948509509 148 K------------REIKFLYDERKlTGEEIAKQT---GV---SRSTVYRVINERK 184
Cdd:COG1961   162 KklvideeeaevvRRIFELYLEGK-SLREIARELnerGIptwSRSTVYRILKNPV 215
Resolvase pfam00239
Resolvase, N terminal domain; The N-terminal domain of the resolvase family (this family) ...
 4-137 7.52e-49

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: 155.12  E-value: 7.52e-49
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1948509509   4 VGYARVSTQDQK--LDSQIDALKEYGCTK----IFSEK-VSGKKFKRTELDKCLEYLRE--GDTLVIYKLDRLGRTTKQL 74
Cdd:pfam00239   2 IGYARVSTEDQDdsLERQLEALRAYAACNgkivEFEDKgVSGRKLDRPGLQRLLALLRAgkGDVLVVYKLDRLGRSLRDL 81

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1948509509  75 IELSQWLEDNHIELQIINMNINTKDAMGKMFFTMMSAFAELEANLLSERTKKGLAAARARGRK 137
Cdd:pfam00239  82 LTLVEELREKGVDLVSLDEGIDTSTPMGRLLLTILAALAEFERALIRERTRAGLAAAAARGKL 144
Resolvase smart00857
Resolvase, N terminal domain; The N-terminal domain of the resolvase family contains the ...
 4-137 8.18e-43

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: 140.07  E-value: 8.18e-43
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1948509509    4 VGYARVSTQDQK---LDSQIDALKEY----GCT--KIFSEK-VSGKKFKRTELDKCLEYLREGD--TLVIYKLDRLGRTT 71
Cdd:smart00857   2 AGYARVSTDDQAdgsLERQLEALRAYaernGWEvvRIYEDEgVSGKKADRPGLQRLLADLRAGDidVLVVYKLDRLGRSL 81

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1948509509   72 KQLIELSQWLEDNHIELQIINMNI-NTKDAMGKMFFTMMSAFAELEANLLSERTKKGLAAARARGRK 137
Cdd:smart00857  82 RDLLALLELLEEKGVRLVSLKEGIlDTSTPAGRLLLDILAALAEFERELISERTKAGLARAAARGRW 148
recomb_XisF NF041201
fdxN element excision recombinase XisF;
4-183 2.63e-25

fdxN element excision recombinase XisF;


Pssm-ID: 469105 [Multi-domain]  Cd Length: 463  Bit Score: 101.19  E-value: 2.63e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1948509509   4 VGYARVSTQDQK-----LDSQIDALKEYGCTKIFSEKVSGKKFKRTELDKCLEYLREG--DTLVIYKLDRLGRTTKQLIE 76
Cdd:NF041201    2 VGYARVSTREQAddghaLEQQIARLKKAGASEIFFDIESGRSDKRKGFNQLLKLVKSGkvTEIIITRIDRLTRSVVTIYK 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1948509509  77 LSQWLEDNHIELQIINM-NINTKDAMGKMFFTMMSAFAELEANLLSERTKKGLAAARARGRKGGRPslP------DYKKR 149
Cdd:NF041201   82 AIEVLQKKGVKLVILDApLDDLSSPGGWFTINQLAALAEFESRLLSERVRHGLEYFREQKKAHPKP--PfgyvriDDKYA 159

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|.
gi 1948509509 150 EIKFLYDERKLTGEEIAK-------QTGVSRSTVyRVINER 183
Cdd:NF041201  160 PDCLLYDKSELTVWEIAReiieiflENGSLRGTC-RYLNEK 199
mpi PRK13413
master DNA invertase Mpi family serine-type recombinase;
5-184 3.83e-19

master DNA invertase Mpi family serine-type recombinase;


Pssm-ID: 184041 [Multi-domain]  Cd Length: 200  Bit Score: 80.53  E-value: 3.83e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1948509509   5 GYARVSTQDQKLDSQIDALKEYGCTKIFS------EKVSG-KKFKRTELDKCLEYLREGDTLVIYKLDRLGRTTKQLIE- 76
Cdd:PRK13413    4 AYIRVSTDKQTVENQRFEITNFAEKNNLTidkwieETISGtKSYKDRKLGKLLKKMRKGDILIVSELSRLGRNLMEIMSi 83

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1948509509  77 LSQWLEDNHIELQI-----INMNINTKdamgkmffTMMSAF---AELEANLLSERTKKGLAAARARGRKGGRP--SLPDY 146
Cdd:PRK13413   84 LNICMEKEVIVYTIkegyeLGDDINSK--------VLAFAFglsAEIERNLISQRTKEALARKKAEGVTLGRPkgSTPKK 155

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|...
gi 1948509509 147 -----KKREIKFLYDERKlTGEEIAKQTGVSRSTVYRVINERK 184
Cdd:PRK13413  156 ykltgKEEKIKKLLDKGT-SKSEIARKLGVSRTTLARFLKTRG 197
transpos_IS607 NF033518
IS607 family transposase;
4-94 5.34e-10

IS607 family transposase;


Pssm-ID: 468054 [Multi-domain]  Cd Length: 187  Bit Score: 55.72  E-value: 5.34e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1948509509   4 VGYARVSTQDQK--LDSQIDALKEYgCT-------KIFSEKVSGKKFKRTELDKCLEYLREGD--TLVIYKLDRLGRTTK 72
Cdd:NF033518   57 VIYARVSSADQKddLERQVARLTQY-ATakgwqvdEVVTDIGSGLNEKRKGLLKLLDDILNGEvsRVVVEHKDRLTRFGF 135

                          90       100
                  ....*....|....*....|..
gi 1948509509  73 QLIElsQWLEDNHIELQIINMN 94
Cdd:NF033518  136 EYLE--ALFKANGVEIVVVNED 155
HTH_Hin_like cd00569
Helix-turn-helix domain of Hin and related proteins; This domain model summarizes a family of ...
 138-180 1.08e-04

Helix-turn-helix domain of Hin and related proteins; This domain model summarizes a family of DNA-binding domains unique to bacteria and represented by the Hin protein of Salmonella. The basic HTH domain is a simple fold comprised of three core helices that form a right-handed helical bundle. The principal DNA-protein interface is formed by the third helix, the recognition helix, inserting itself into the major groove of the DNA. A diverse array of HTH domains participate in a variety of functions that depend on their DNA-binding properties. HTH_Hin represents one of the simplest versions of the HTH domains; the characterization of homologous relationships between various sequence-diverse HTH domain families remains difficult. The Hin recombinase induces the site-specific inversion of a chromosomal DNA segment containing a promoter, which controls the alternate expression of two genes by reversibly switching orientation. The Hin recombinase consists of a single polypeptide chain containing a C-terminal DNA-binding domain (HTH_Hin) and a catalytic domain.


Pssm-ID: 259851 [Multi-domain]  Cd Length: 42  Bit Score: 38.08  E-value: 1.08e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 1948509509 138 GGRPSLPDYKKREIKFLYDERKlTGEEIAKQTGVSRSTVYRVI 180
Cdd:cd00569     1 GRPPKLTPEQIAEARRLLAAGE-SVAEIARELGVSRSTLYRYL 42
HTH_11 pfam08279
HTH domain; This family includes helix-turn-helix domains in a wide variety of proteins.
 151-180 1.50e-04

HTH domain; This family includes helix-turn-helix domains in a wide variety of proteins.


Pssm-ID: 429896 [Multi-domain]  Cd Length: 52  Bit Score: 38.18  E-value: 1.50e-04
                          10        20        30
                  ....*....|....*....|....*....|.
gi 1948509509 151 IKFLYDERK-LTGEEIAKQTGVSRSTVYRVI 180
Cdd:pfam08279   4 LQLLLEARGpISGQELAEKLGVSRRTIRRDI 34
BirA COG1654
Biotin operon repressor [Transcription];
151-182 2.87e-03

Biotin operon repressor [Transcription];


Pssm-ID: 441260 [Multi-domain]  Cd Length: 324  Bit Score: 37.27  E-value: 2.87e-03
                          10        20        30
                  ....*....|....*....|....*....|..
gi 1948509509 151 IKFLYDERKLTGEEIAKQTGVSRSTVYRVINE 182
Cdd:COG1654    10 LRLLADGEFHSGEELAEELGVSRAAVWKHIKA 41
PRK09863 PRK09863
putative frv operon regulatory protein; Provisional
 149-180 7.42e-03

putative frv operon regulatory protein; Provisional


Pssm-ID: 182121 [Multi-domain]  Cd Length: 584  Bit Score: 36.37  E-value: 7.42e-03
                          10        20        30
                  ....*....|....*....|....*....|....
gi 1948509509 149 REIKF--LYDERKLTGEEIAKQTGVSRSTVYRVI 180
Cdd:PRK09863    5 RELKIvdLLEQQDRSGGELAQQLGVSRRTIVRDI 38
 
Name Accession Description Interval E-value
SR_ResInv cd03768
Serine Recombinase (SR) family, Resolvase and Invertase subfamily, catalytic domain; members ...
 4-127 2.30e-59

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: 181.14  E-value: 2.30e-59
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1948509509   4 VGYARVSTQDQKLDSQIDALKEYG-CTKIFSEKVSGKKFKRTELDKCLEYLREGDTLVIYKLDRLGRTTKQLIELSQWLE 82
Cdd:cd03768     2 IGYARVSTDDQSLERQLEALKAAGeCDKIFEEKGSGGKKERPELQKLLEDLREGDTLVVTKLDRLGRSTKDLLEIVEELR 81

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*
gi 1948509509  83 DNHIELQIINMNINTKDAMGKMFFTMMSAFAELEANLLSERTKKG 127
Cdd:cd03768    82 EKGVSLRSLTEGIDTSTPSGKLMLTILGAFAEFERELIRERTKEG 126
SpoIVCA COG1961
Site-specific DNA recombinase SpoIVCA/DNA invertase PinE [Replication, recombination and ...
 1-184 6.43e-50

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


Pssm-ID: 441564 [Multi-domain]  Cd Length: 388  Bit Score: 165.58  E-value: 6.43e-50
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1948509509   1 MAMVGYARVSTQDQK---LDSQIDALKEY----GCT--KIFSEK-VSGKKFKRTELDKCLEYLREG--DTLVIYKLDRLG 68
Cdd:COG1961     2 MRAAGYARVSTDDQEglsLERQREALRAYaekaGWEivRIYVDEgVSGTSKDRPGLQRLLADLRAGkfDTLVVWKLDRLG 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1948509509  69 RTTKQLIELSQWLEDNHIELQIINMNINTKDAMGKMFFTMMSAFAELEANLLSERTKKGLAAARARGRKGGRPSL-PDYK 147
Cdd:COG1961    82 RNLADLLELVEELKERGVRLISLTEGIDTSTPMGRLLLTILAAFAEFERELISERTRAGLAAAKARGKYLGRPPYgYRDP 161

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1948509509 148 K------------REIKFLYDERKlTGEEIAKQT---GV---SRSTVYRVINERK 184
Cdd:COG1961   162 KklvideeeaevvRRIFELYLEGK-SLREIARELnerGIptwSRSTVYRILKNPV 215
Resolvase pfam00239
Resolvase, N terminal domain; The N-terminal domain of the resolvase family (this family) ...
 4-137 7.52e-49

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: 155.12  E-value: 7.52e-49
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1948509509   4 VGYARVSTQDQK--LDSQIDALKEYGCTK----IFSEK-VSGKKFKRTELDKCLEYLRE--GDTLVIYKLDRLGRTTKQL 74
Cdd:pfam00239   2 IGYARVSTEDQDdsLERQLEALRAYAACNgkivEFEDKgVSGRKLDRPGLQRLLALLRAgkGDVLVVYKLDRLGRSLRDL 81

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1948509509  75 IELSQWLEDNHIELQIINMNINTKDAMGKMFFTMMSAFAELEANLLSERTKKGLAAARARGRK 137
Cdd:pfam00239  82 LTLVEELREKGVDLVSLDEGIDTSTPMGRLLLTILAALAEFERALIRERTRAGLAAAAARGKL 144
Resolvase smart00857
Resolvase, N terminal domain; The N-terminal domain of the resolvase family contains the ...
 4-137 8.18e-43

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: 140.07  E-value: 8.18e-43
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1948509509    4 VGYARVSTQDQK---LDSQIDALKEY----GCT--KIFSEK-VSGKKFKRTELDKCLEYLREGD--TLVIYKLDRLGRTT 71
Cdd:smart00857   2 AGYARVSTDDQAdgsLERQLEALRAYaernGWEvvRIYEDEgVSGKKADRPGLQRLLADLRAGDidVLVVYKLDRLGRSL 81

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1948509509   72 KQLIELSQWLEDNHIELQIINMNI-NTKDAMGKMFFTMMSAFAELEANLLSERTKKGLAAARARGRK 137
Cdd:smart00857  82 RDLLALLELLEEKGVRLVSLKEGIlDTSTPAGRLLLDILAALAEFERELISERTKAGLARAAARGRW 148
Ser_Recombinase cd00338
Serine Recombinase family, catalytic domain; a DNA binding domain may be present either N- or ...
 6-127 8.43e-28

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: 101.18  E-value: 8.43e-28
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1948509509   6 YARVSTQDQK----LDSQIDALKEY----GCT--KIFSEKVSG--KKFKRTELDKCLEYLREG--DTLVIYKLDRLGRTT 71
Cdd:cd00338     2 YARVSTDKQEqgdsLERQREALREYaarnGLEvvGEYEDAGSSatSLVDRPGLQRLLADVKAGkiDVVLVEKLDRLSRNL 81

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1948509509  72 KQLIELSQWLEDNHIELQIINMNINTKDAMGKMFFTMMSAFAELEANLLSERTKKG 127
Cdd:cd00338    82 VDLLELLELLEAHGVRVVTADGEIDLDSEDGRLMLGILAAMAEEESKLISERTKRG 137
recomb_XisF NF041201
fdxN element excision recombinase XisF;
4-183 2.63e-25

fdxN element excision recombinase XisF;


Pssm-ID: 469105 [Multi-domain]  Cd Length: 463  Bit Score: 101.19  E-value: 2.63e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1948509509   4 VGYARVSTQDQK-----LDSQIDALKEYGCTKIFSEKVSGKKFKRTELDKCLEYLREG--DTLVIYKLDRLGRTTKQLIE 76
Cdd:NF041201    2 VGYARVSTREQAddghaLEQQIARLKKAGASEIFFDIESGRSDKRKGFNQLLKLVKSGkvTEIIITRIDRLTRSVVTIYK 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1948509509  77 LSQWLEDNHIELQIINM-NINTKDAMGKMFFTMMSAFAELEANLLSERTKKGLAAARARGRKGGRPslP------DYKKR 149
Cdd:NF041201   82 AIEVLQKKGVKLVILDApLDDLSSPGGWFTINQLAALAEFESRLLSERVRHGLEYFREQKKAHPKP--PfgyvriDDKYA 159

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|.
gi 1948509509 150 EIKFLYDERKLTGEEIAK-------QTGVSRSTVyRVINER 183
Cdd:NF041201  160 PDCLLYDKSELTVWEIAReiieiflENGSLRGTC-RYLNEK 199
mpi PRK13413
master DNA invertase Mpi family serine-type recombinase;
5-184 3.83e-19

master DNA invertase Mpi family serine-type recombinase;


Pssm-ID: 184041 [Multi-domain]  Cd Length: 200  Bit Score: 80.53  E-value: 3.83e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1948509509   5 GYARVSTQDQKLDSQIDALKEYGCTKIFS------EKVSG-KKFKRTELDKCLEYLREGDTLVIYKLDRLGRTTKQLIE- 76
Cdd:PRK13413    4 AYIRVSTDKQTVENQRFEITNFAEKNNLTidkwieETISGtKSYKDRKLGKLLKKMRKGDILIVSELSRLGRNLMEIMSi 83

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1948509509  77 LSQWLEDNHIELQI-----INMNINTKdamgkmffTMMSAF---AELEANLLSERTKKGLAAARARGRKGGRP--SLPDY 146
Cdd:PRK13413   84 LNICMEKEVIVYTIkegyeLGDDINSK--------VLAFAFglsAEIERNLISQRTKEALARKKAEGVTLGRPkgSTPKK 155

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|...
gi 1948509509 147 -----KKREIKFLYDERKlTGEEIAKQTGVSRSTVYRVINERK 184
Cdd:PRK13413  156 ykltgKEEKIKKLLDKGT-SKSEIARKLGVSRTTLARFLKTRG 197
transpos_IS607 NF033518
IS607 family transposase;
4-94 5.34e-10

IS607 family transposase;


Pssm-ID: 468054 [Multi-domain]  Cd Length: 187  Bit Score: 55.72  E-value: 5.34e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1948509509   4 VGYARVSTQDQK--LDSQIDALKEYgCT-------KIFSEKVSGKKFKRTELDKCLEYLREGD--TLVIYKLDRLGRTTK 72
Cdd:NF033518   57 VIYARVSSADQKddLERQVARLTQY-ATakgwqvdEVVTDIGSGLNEKRKGLLKLLDDILNGEvsRVVVEHKDRLTRFGF 135

                          90       100
                  ....*....|....*....|..
gi 1948509509  73 QLIElsQWLEDNHIELQIINMN 94
Cdd:NF033518  136 EYLE--ALFKANGVEIVVVNED 155
COG2452 COG2452
Predicted site-specific integrase-resolvase [Mobilome: prophages, transposons];
4-92 7.72e-10

Predicted site-specific integrase-resolvase [Mobilome: prophages, transposons];


Pssm-ID: 441988 [Multi-domain]  Cd Length: 178  Bit Score: 55.38  E-value: 7.72e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1948509509   4 VGYARVSTQDQK--LDSQIDALKEYGCTK-----IFSEKVSGKKFKRTELDKCLEyLREGDTLVIYKLDRLGRTTKQLIE 76
Cdd:COG2452    51 VIYARVSSADQKddLERQVERLEEYATAKgyqdeVIKDVGSGLNYKRKGLLKLLE-RIEVERVVVEHKDRLARFGFELLE 129

                          90
                  ....*....|....*.
gi 1948509509  77 lsQWLEDNHIELQIIN 92
Cdd:COG2452   130 --ALCEAYGVEIVVVN 143
SR_IS607_transposase_like cd03769
Serine Recombinase (SR) family, IS607-like transposase subfamily, catalytic domain; members ...
 4-99 1.96e-09

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: 53.42  E-value: 1.96e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1948509509   4 VGYARVSTQDQK--LDSQIDALKEYgCT------KIFSEKVSGKKFKRTELDKCLEYLREG--DTLVIYKLDRLGRTTKQ 73
Cdd:cd03769     2 VLYARVSSHDQKddLERQIERLEAY-ATaqgwivEVIKDIGSGLNEKRKGLLKLLEDVLAGkvERVVITYKDRLARFGFE 80

                          90       100
                  ....*....|....*....|....*.
gi 1948509509  74 LIELsqWLEDNHIELQIINMNINTKD 99
Cdd:cd03769    81 LLEE--LFKAYGVEIVVINQEENEEL 104
SR_Res_par cd03767
Serine recombinase (SR) family, Partitioning (par)-Resolvase subfamily, catalytic domain; ...
 5-69 1.47e-07

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: 48.47  E-value: 1.47e-07
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1948509509   5 GYARVSTQDQKLDSQIDALKE------YGCTKIFSEKVSGKKFKRTELDKCLEYLREGDTLVIYKLDRLGR 69
Cdd:cd03767     3 AYLRASTDEQDATRAKESLEAfatergFYIAGFYVENASGAKLDRPELFRLLDDAQSGDVLLVEQIDRLSR 73
HTH_Hin_like cd00569
Helix-turn-helix domain of Hin and related proteins; This domain model summarizes a family of ...
 138-180 1.08e-04

Helix-turn-helix domain of Hin and related proteins; This domain model summarizes a family of DNA-binding domains unique to bacteria and represented by the Hin protein of Salmonella. The basic HTH domain is a simple fold comprised of three core helices that form a right-handed helical bundle. The principal DNA-protein interface is formed by the third helix, the recognition helix, inserting itself into the major groove of the DNA. A diverse array of HTH domains participate in a variety of functions that depend on their DNA-binding properties. HTH_Hin represents one of the simplest versions of the HTH domains; the characterization of homologous relationships between various sequence-diverse HTH domain families remains difficult. The Hin recombinase induces the site-specific inversion of a chromosomal DNA segment containing a promoter, which controls the alternate expression of two genes by reversibly switching orientation. The Hin recombinase consists of a single polypeptide chain containing a C-terminal DNA-binding domain (HTH_Hin) and a catalytic domain.


Pssm-ID: 259851 [Multi-domain]  Cd Length: 42  Bit Score: 38.08  E-value: 1.08e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 1948509509 138 GGRPSLPDYKKREIKFLYDERKlTGEEIAKQTGVSRSTVYRVI 180
Cdd:cd00569     1 GRPPKLTPEQIAEARRLLAAGE-SVAEIARELGVSRSTLYRYL 42
HTH_11 pfam08279
HTH domain; This family includes helix-turn-helix domains in a wide variety of proteins.
 151-180 1.50e-04

HTH domain; This family includes helix-turn-helix domains in a wide variety of proteins.


Pssm-ID: 429896 [Multi-domain]  Cd Length: 52  Bit Score: 38.18  E-value: 1.50e-04
                          10        20        30
                  ....*....|....*....|....*....|.
gi 1948509509 151 IKFLYDERK-LTGEEIAKQTGVSRSTVYRVI 180
Cdd:pfam08279   4 LQLLLEARGpISGQELAEKLGVSRRTIRRDI 34
HTH_7 pfam02796
Helix-turn-helix domain of resolvase;
139-183 1.54e-03

Helix-turn-helix domain of resolvase;


Pssm-ID: 397088 [Multi-domain]  Cd Length: 45  Bit Score: 35.02  E-value: 1.54e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 1948509509 139 GRPS-LPDYKKREIKFLYDErKLTGEEIAKQTGVSRSTVYRVINER 183
Cdd:pfam02796   1 GRPPkLNEEDINEVITLLEE-GISIKQIAKIFGISRSTVYRYLAAS 45
BirA COG1654
Biotin operon repressor [Transcription];
151-182 2.87e-03

Biotin operon repressor [Transcription];


Pssm-ID: 441260 [Multi-domain]  Cd Length: 324  Bit Score: 37.27  E-value: 2.87e-03
                          10        20        30
                  ....*....|....*....|....*....|..
gi 1948509509 151 IKFLYDERKLTGEEIAKQTGVSRSTVYRVINE 182
Cdd:COG1654    10 LRLLADGEFHSGEELAEELGVSRAAVWKHIKA 41
HTH_LacI cd01392
Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators; ...
 164-183 4.23e-03

Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators; HTH-DNA binding domain of the LacI (lactose operon repressor) family of bacterial transcriptional regulators and their putative homologs found in plants. The LacI family has more than 500 members distributed among almost all bacterial species. The monomeric proteins of the LacI family contain common structural features that include a small DNA-binding domain with a helix-turn-helix motif in the N-terminus, a regulatory ligand-binding domain which exhibits the type I periplasmic binding protein fold in the C-terminus for oligomerization and for effector binding, and an approximately 18-amino acid linker connecting these two functional domains. In LacI-like transcriptional regulators, the ligands are monosaccharides including lactose, ribose, fructose, xylose, arabinose, galactose/glucose, and other sugars, with a few exceptions. When the C-terminal domain of the LacI family repressor binds its ligand, it undergoes a conformational change which affects the DNA-binding affinity of the repressor. In Escherichia coli, LacI represses transcription by binding with high affinity to the lac operon at a specific operator DNA sequence until it interacts with the physiological inducer allolactose or a non-degradable analog IPTG (isopropyl-beta-D-thiogalactopyranoside). Induction of the repressor lowers its affinity for the operator sequence, thereby allowing transcription of the lac operon structural genes (lacZ, lacY, and LacA). The lac repressor occurs as a tetramer made up of two functional dimers. Thus, two DNA binding domains of a dimer are required to bind the inverted repeat sequences of the operator DNA binding sites.


Pssm-ID: 143331 [Multi-domain]  Cd Length: 52  Bit Score: 33.92  E-value: 4.23e-03
                          10        20
                  ....*....|....*....|
gi 1948509509 164 EIAKQTGVSRSTVYRVINER 183
Cdd:cd01392     2 DIARAAGVSVATVSRVLNGK 21
COG4584 COG4584
Transposase [Mobilome: prophages, transposons];
146-182 5.13e-03

Transposase [Mobilome: prophages, transposons];


Pssm-ID: 443641 [Multi-domain]  Cd Length: 484  Bit Score: 36.74  E-value: 5.13e-03
                          10        20        30
                  ....*....|....*....|....*....|....*..
gi 1948509509 146 YKKREIKFLYDErKLTGEEIAKQTGVSRSTVYRVINE 182
Cdd:COG4584     5 EQIREIRRLLRE-GLSIREIARELGISRNTVRKYLRR 40
TnsD pfam15978
Tn7-like transposition protein D; TnsD is a family of putative Tn7-like transposition proteins ...
 148-183 6.26e-03

Tn7-like transposition protein D; TnsD is a family of putative Tn7-like transposition proteins type D.


Pssm-ID: 379756  Cd Length: 360  Bit Score: 36.24  E-value: 6.26e-03
                          10        20        30
                  ....*....|....*....|....*....|....*.
gi 1948509509 148 KREIKFLYDERKLTGEEIAKQTGVSRSTVYRVINER 183
Cdd:pfam15978 188 EERLKILVEDEGLSLREIAKELGVDIKTVKRYARKL 223
HTH_XRE cd00093
Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the ...
 149-183 6.26e-03

Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators.


Pssm-ID: 238045 [Multi-domain]  Cd Length: 58  Bit Score: 33.68  E-value: 6.26e-03
                          10        20        30
                  ....*....|....*....|....*....|....*
gi 1948509509 149 REIKFLYDERKLTGEEIAKQTGVSRSTVYRVINER 183
Cdd:cd00093     2 ERLKELRKEKGLTQEELAEKLGVSRSTISRIENGK 36
PRK09863 PRK09863
putative frv operon regulatory protein; Provisional
 149-180 7.42e-03

putative frv operon regulatory protein; Provisional


Pssm-ID: 182121 [Multi-domain]  Cd Length: 584  Bit Score: 36.37  E-value: 7.42e-03
                          10        20        30
                  ....*....|....*....|....*....|....
gi 1948509509 149 REIKF--LYDERKLTGEEIAKQTGVSRSTVYRVI 180
Cdd:PRK09863    5 RELKIvdLLEQQDRSGGELAQQLGVSRRTIVRDI 38
COG3355 COG3355
Predicted transcriptional regulator [Transcription];
151-182 7.77e-03

Predicted transcriptional regulator [Transcription];


Pssm-ID: 442583 [Multi-domain]  Cd Length: 131  Bit Score: 34.94  E-value: 7.77e-03
                          10        20        30
                  ....*....|....*....|....*....|..
gi 1948509509 151 IKFLYDERKLTGEEIAKQTGVSRSTVYRVINE 182
Cdd:COG3355    34 LILLENGEPLTVEELAEALDRSRSTVYRSLQK 65
YobV COG2378
Predicted DNA-binding transcriptional regulator YobV, contains HTH and WYL domains ...
 151-182 8.01e-03

Predicted DNA-binding transcriptional regulator YobV, contains HTH and WYL domains [Transcription];


Pssm-ID: 441945 [Multi-domain]  Cd Length: 314  Bit Score: 36.21  E-value: 8.01e-03
                          10        20        30
                  ....*....|....*....|....*....|..
gi 1948509509 151 IKFLYDERKLTGEEIAKQTGVSRSTVYRVINE 182
Cdd:COG2378    11 LQLLQSRRGVTAAELAERLEVSERTIYRDIDA 42
 
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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