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Conserved domains on  [gi|1894850504|gb|QNI15325|]
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recombinase family protein (plasmid) [Mycobacterium kubicae]

Protein Classification

recombinase family protein( domain architecture ID 10132968)

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|GO:0015074
PubMed:  21645851|26104451|11972771|16077726|9348666
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 ...
 2-127 4.20e-55

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: 171.12  E-value: 4.20e-55
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1894850504   2 RIGYARVSTRDQHPEAQRDALTAAG-CDQIFLDKVSGKLARRPELDKaLLSANRVGDQLVVTKLDRLGRSLEHLIELSKR 80
Cdd:cd03768     1 VIGYARVSTDDQSLERQLEALKAAGeCDKIFEEKGSGGKKERPELQK-LLEDLREGDTLVVTKLDRLGRSTKDLLEIVEE 79

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*..
gi 1894850504  81 LQGAGVDLVVLDQGIDTSTAIGRMFFQILGAVAEFEHALMSERTMDG 127
Cdd:cd03768    80 LREKGVSLRSLTEGIDTSTPSGKLMLTILGAFAEFERELIRERTKEG 126
HTH_Hin_like cd00569
Helix-turn-helix domain of Hin and related proteins; This domain model summarizes a family of ...
 139-187 2.08e-08

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: 48.48  E-value: 2.08e-08
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 1894850504 139 GQKPKLGPRQVKLAQQMYDEKDehgkrryTVEQIAAEFGVTRPTIYRHL 187
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 ...
 2-127 4.20e-55

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: 171.12  E-value: 4.20e-55
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1894850504   2 RIGYARVSTRDQHPEAQRDALTAAG-CDQIFLDKVSGKLARRPELDKaLLSANRVGDQLVVTKLDRLGRSLEHLIELSKR 80
Cdd:cd03768     1 VIGYARVSTDDQSLERQLEALKAAGeCDKIFEEKGSGGKKERPELQK-LLEDLREGDTLVVTKLDRLGRSTKDLLEIVEE 79

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*..
gi 1894850504  81 LQGAGVDLVVLDQGIDTSTAIGRMFFQILGAVAEFEHALMSERTMDG 127
Cdd:cd03768    80 LREKGVSLRSLTEGIDTSTPSGKLMLTILGAFAEFERELIRERTKEG 126
SpoIVCA COG1961
Site-specific DNA recombinase SpoIVCA/DNA invertase PinE [Replication, recombination and ...
 1-187 1.56e-48

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


Pssm-ID: 441564 [Multi-domain]  Cd Length: 388  Bit Score: 162.50  E-value: 1.56e-48
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1894850504   1 MRIGYARVSTRDQH---PEAQRDALTA----AGCD--QIFLDK-VSGKLARRPELDKAL--LSANRVgDQLVVTKLDRLG 68
Cdd:COG1961     3 RAAGYARVSTDDQEglsLERQREALRAyaekAGWEivRIYVDEgVSGTSKDRPGLQRLLadLRAGKF-DTLVVWKLDRLG 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1894850504  69 RSLEHLIELSKRLQGAGVDLVVLDQGIDTSTAIGRMFFQILGAVAEFEHALMSERTMDGLAAARARGRTGGQKPkLGPRQ 148
Cdd:COG1961    82 RNLADLLELVEELKERGVRLISLTEGIDTSTPMGRLLLTILAAFAEFERELISERTRAGLAAAKARGKYLGRPP-YGYRD 160

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1894850504 149 -------------VKLAQQMYDEkdehgkrRYTVEQIAAEF---GV---TRPTIYRHL 187
Cdd:COG1961   161 pkklvideeeaevVRRIFELYLE-------GKSLREIARELnerGIptwSRSTVYRIL 211
Resolvase pfam00239
Resolvase, N terminal domain; The N-terminal domain of the resolvase family (this family) ...
 2-136 4.41e-48

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: 153.96  E-value: 4.41e-48
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1894850504   2 RIGYARVSTRDQH--PEAQRDALTAAGCDQ----IFLDK-VSGKLARRPELDKAL-LSANRVGDQLVVTKLDRLGRSLEH 73
Cdd:pfam00239   1 AIGYARVSTEDQDdsLERQLEALRAYAACNgkivEFEDKgVSGRKLDRPGLQRLLaLLRAGKGDVLVVYKLDRLGRSLRD 80

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1894850504  74 LIELSKRLQGAGVDLVVLDQGIDTSTAIGRMFFQILGAVAEFEHALMSERTMDGLAAARARGR 136
Cdd:pfam00239  81 LLTLVEELREKGVDLVSLDEGIDTSTPMGRLLLTILAALAEFERALIRERTRAGLAAAAARGK 143
Resolvase smart00857
Resolvase, N terminal domain; The N-terminal domain of the resolvase family contains the ...
 3-136 4.82e-39

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: 130.82  E-value: 4.82e-39
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1894850504    3 IGYARVSTRDQ---HPEAQRDALTAA----GC--DQIFLDK-VSGKLARRPELdKALLSANRVGDQ--LVVTKLDRLGRS 70
Cdd:smart00857   2 AGYARVSTDDQadgSLERQLEALRAYaernGWevVRIYEDEgVSGKKADRPGL-QRLLADLRAGDIdvLVVYKLDRLGRS 80

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1894850504   71 LEHLIELSKRLQGAGVDLVVLDQGI-DTSTAIGRMFFQILGAVAEFEHALMSERTMDGLAAARARGR 136
Cdd:smart00857  81 LRDLLALLELLEEKGVRLVSLKEGIlDTSTPAGRLLLDILAALAEFERELISERTKAGLARAAARGR 147
recomb_XisF NF041201
fdxN element excision recombinase XisF;
2-175 1.99e-28

fdxN element excision recombinase XisF;


Pssm-ID: 469105 [Multi-domain]  Cd Length: 463  Bit Score: 110.05  E-value: 1.99e-28
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1894850504   2 RIGYARVSTRDQHpeAQRDALT-------AAGCDQIFLDKVSGKLARRPELDKAL-LSANRVGDQLVVTKLDRLGRS--- 70
Cdd:NF041201    1 IVGYARVSTREQA--DDGHALEqqiarlkKAGASEIFFDIESGRSDKRKGFNQLLkLVKSGKVTEIIITRIDRLTRSvvt 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1894850504  71 LEHLIELskrLQGAGVDLVVLDQG-IDTSTAIGRMFFQILGAVAEFEHALMSERTMDGLAAARARGRTGGQKPkLGprQV 149
Cdd:NF041201   79 IYKAIEV---LQKKGVKLVILDAPlDDLSSPGGWFTINQLAALAEFESRLLSERVRHGLEYFREQKKAHPKPP-FG--YV 152

                         170       180
                  ....*....|....*....|....*.
gi 1894850504 150 KLAQQMYDEKDEHGKRRYTVEQIAAE 175
Cdd:NF041201  153 RIDDKYAPDCLLYDKSELTVWEIARE 178
mpi PRK13413
master DNA invertase Mpi family serine-type recombinase;
1-187 1.05e-11

master DNA invertase Mpi family serine-type recombinase;


Pssm-ID: 184041 [Multi-domain]  Cd Length: 200  Bit Score: 60.89  E-value: 1.05e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1894850504   1 MRIGYARVSTRDQHPEAQRDALTAAgCDQ--IFLDK-----VSG-KLARRPELDKaLLSANRVGDQLVVTKLDRLGRSLE 72
Cdd:PRK13413    1 MIYAYIRVSTDKQTVENQRFEITNF-AEKnnLTIDKwieetISGtKSYKDRKLGK-LLKKMRKGDILIVSELSRLGRNLM 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1894850504  73 HLIE-----LSKRLQGAGV-DLVVLDQGIDtSTAIGRMFfqilGAVAEFEHALMSERTMDGLAAARARGRTGGQKPKLGP 146
Cdd:PRK13413   79 EIMSilnicMEKEVIVYTIkEGYELGDDIN-SKVLAFAF----GLSAEIERNLISQRTKEALARKKAEGVTLGRPKGSTP 153

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|.
gi 1894850504 147 RQVKLAQQmYDEKDEHGKRRYTVEQIAAEFGVTRPTIYRHL 187
Cdd:PRK13413  154 KKYKLTGK-EEKIKKLLDKGTSKSEIARKLGVSRTTLARFL 193
HTH_Hin_like cd00569
Helix-turn-helix domain of Hin and related proteins; This domain model summarizes a family of ...
 139-187 2.08e-08

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: 48.48  E-value: 2.08e-08
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 1894850504 139 GQKPKLGPRQVKLAQQMYDEKDehgkrryTVEQIAAEFGVTRPTIYRHL 187
Cdd:cd00569     1 GRPPKLTPEQIAEARRLLAAGE-------SVAEIARELGVSRSTLYRYL 42
HTH_7 pfam02796
Helix-turn-helix domain of resolvase;
139-189 1.50e-04

Helix-turn-helix domain of resolvase;


Pssm-ID: 397088 [Multi-domain]  Cd Length: 45  Bit Score: 38.10  E-value: 1.50e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1894850504 139 GQKPKLGPRQVKLAQQMYDEKdehgkrrYTVEQIAAEFGVTRPTIYRHLGK 189
Cdd:pfam02796   1 GRPPKLNEEDINEVITLLEEG-------ISIKQIAKIFGISRSTVYRYLAA 44
transpos_IS607 NF033518
IS607 family transposase;
3-93 2.45e-04

IS607 family transposase;


Pssm-ID: 468054 [Multi-domain]  Cd Length: 187  Bit Score: 40.32  E-value: 2.45e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1894850504   3 IGYARVSTRDQHP--EAQRDALT--AAGC----DQIFLDKVSGKLARRPELDKAL-LSANRVGDQLVVTKLDRLGR-SLE 72
Cdd:NF033518   57 VIYARVSSADQKDdlERQVARLTqyATAKgwqvDEVVTDIGSGLNEKRKGLLKLLdDILNGEVSRVVVEHKDRLTRfGFE 136

                          90       100
                  ....*....|....*....|.
gi 1894850504  73 HLIELskrLQGAGVDLVVLDQ 93
Cdd:NF033518  137 YLEAL---FKANGVEIVVVNE 154
LexA COG1974
SOS-response transcriptional repressor LexA (RecA-mediated autopeptidase) [Transcription, ...
 143-191 9.84e-03

SOS-response transcriptional repressor LexA (RecA-mediated autopeptidase) [Transcription, Signal transduction mechanisms];


Pssm-ID: 441577 [Multi-domain]  Cd Length: 199  Bit Score: 35.66  E-value: 9.84e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 1894850504 143 KLGPRQVKLAQQMYDEKDEHGkRRYTVEQIAAEFGVTRPTIYRHLgKAL 191
Cdd:COG1974     3 KLTKRQREILDFIKEYIRERG-YPPSQREIAEALGLSSSAVHRHL-KAL 49
 
Name Accession Description Interval E-value
SR_ResInv cd03768
Serine Recombinase (SR) family, Resolvase and Invertase subfamily, catalytic domain; members ...
 2-127 4.20e-55

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: 171.12  E-value: 4.20e-55
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1894850504   2 RIGYARVSTRDQHPEAQRDALTAAG-CDQIFLDKVSGKLARRPELDKaLLSANRVGDQLVVTKLDRLGRSLEHLIELSKR 80
Cdd:cd03768     1 VIGYARVSTDDQSLERQLEALKAAGeCDKIFEEKGSGGKKERPELQK-LLEDLREGDTLVVTKLDRLGRSTKDLLEIVEE 79

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*..
gi 1894850504  81 LQGAGVDLVVLDQGIDTSTAIGRMFFQILGAVAEFEHALMSERTMDG 127
Cdd:cd03768    80 LREKGVSLRSLTEGIDTSTPSGKLMLTILGAFAEFERELIRERTKEG 126
SpoIVCA COG1961
Site-specific DNA recombinase SpoIVCA/DNA invertase PinE [Replication, recombination and ...
 1-187 1.56e-48

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


Pssm-ID: 441564 [Multi-domain]  Cd Length: 388  Bit Score: 162.50  E-value: 1.56e-48
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1894850504   1 MRIGYARVSTRDQH---PEAQRDALTA----AGCD--QIFLDK-VSGKLARRPELDKAL--LSANRVgDQLVVTKLDRLG 68
Cdd:COG1961     3 RAAGYARVSTDDQEglsLERQREALRAyaekAGWEivRIYVDEgVSGTSKDRPGLQRLLadLRAGKF-DTLVVWKLDRLG 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1894850504  69 RSLEHLIELSKRLQGAGVDLVVLDQGIDTSTAIGRMFFQILGAVAEFEHALMSERTMDGLAAARARGRTGGQKPkLGPRQ 148
Cdd:COG1961    82 RNLADLLELVEELKERGVRLISLTEGIDTSTPMGRLLLTILAAFAEFERELISERTRAGLAAAKARGKYLGRPP-YGYRD 160

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1894850504 149 -------------VKLAQQMYDEkdehgkrRYTVEQIAAEF---GV---TRPTIYRHL 187
Cdd:COG1961   161 pkklvideeeaevVRRIFELYLE-------GKSLREIARELnerGIptwSRSTVYRIL 211
Resolvase pfam00239
Resolvase, N terminal domain; The N-terminal domain of the resolvase family (this family) ...
 2-136 4.41e-48

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: 153.96  E-value: 4.41e-48
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1894850504   2 RIGYARVSTRDQH--PEAQRDALTAAGCDQ----IFLDK-VSGKLARRPELDKAL-LSANRVGDQLVVTKLDRLGRSLEH 73
Cdd:pfam00239   1 AIGYARVSTEDQDdsLERQLEALRAYAACNgkivEFEDKgVSGRKLDRPGLQRLLaLLRAGKGDVLVVYKLDRLGRSLRD 80

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1894850504  74 LIELSKRLQGAGVDLVVLDQGIDTSTAIGRMFFQILGAVAEFEHALMSERTMDGLAAARARGR 136
Cdd:pfam00239  81 LLTLVEELREKGVDLVSLDEGIDTSTPMGRLLLTILAALAEFERALIRERTRAGLAAAAARGK 143
Resolvase smart00857
Resolvase, N terminal domain; The N-terminal domain of the resolvase family contains the ...
 3-136 4.82e-39

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: 130.82  E-value: 4.82e-39
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1894850504    3 IGYARVSTRDQ---HPEAQRDALTAA----GC--DQIFLDK-VSGKLARRPELdKALLSANRVGDQ--LVVTKLDRLGRS 70
Cdd:smart00857   2 AGYARVSTDDQadgSLERQLEALRAYaernGWevVRIYEDEgVSGKKADRPGL-QRLLADLRAGDIdvLVVYKLDRLGRS 80

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1894850504   71 LEHLIELSKRLQGAGVDLVVLDQGI-DTSTAIGRMFFQILGAVAEFEHALMSERTMDGLAAARARGR 136
Cdd:smart00857  81 LRDLLALLELLEEKGVRLVSLKEGIlDTSTPAGRLLLDILAALAEFERELISERTKAGLARAAARGR 147
recomb_XisF NF041201
fdxN element excision recombinase XisF;
2-175 1.99e-28

fdxN element excision recombinase XisF;


Pssm-ID: 469105 [Multi-domain]  Cd Length: 463  Bit Score: 110.05  E-value: 1.99e-28
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1894850504   2 RIGYARVSTRDQHpeAQRDALT-------AAGCDQIFLDKVSGKLARRPELDKAL-LSANRVGDQLVVTKLDRLGRS--- 70
Cdd:NF041201    1 IVGYARVSTREQA--DDGHALEqqiarlkKAGASEIFFDIESGRSDKRKGFNQLLkLVKSGKVTEIIITRIDRLTRSvvt 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1894850504  71 LEHLIELskrLQGAGVDLVVLDQG-IDTSTAIGRMFFQILGAVAEFEHALMSERTMDGLAAARARGRTGGQKPkLGprQV 149
Cdd:NF041201   79 IYKAIEV---LQKKGVKLVILDAPlDDLSSPGGWFTINQLAALAEFESRLLSERVRHGLEYFREQKKAHPKPP-FG--YV 152

                         170       180
                  ....*....|....*....|....*.
gi 1894850504 150 KLAQQMYDEKDEHGKRRYTVEQIAAE 175
Cdd:NF041201  153 RIDDKYAPDCLLYDKSELTVWEIARE 178
Ser_Recombinase cd00338
Serine Recombinase family, catalytic domain; a DNA binding domain may be present either N- or ...
 5-127 8.09e-26

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: 96.56  E-value: 8.09e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1894850504   5 YARVSTRDQH----PEAQRDALTAAgCDQ-------IFLDKVSG--KLARRPELDKAL-LSANRVGDQLVVTKLDRLGRS 70
Cdd:cd00338     2 YARVSTDKQEqgdsLERQREALREY-AARnglevvgEYEDAGSSatSLVDRPGLQRLLaDVKAGKIDVVLVEKLDRLSRN 80

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1894850504  71 LEHLIELSKRLQGAGVDLVVLDQGIDTSTAIGRMFFQILGAVAEFEHALMSERTMDG 127
Cdd:cd00338    81 LVDLLELLELLEAHGVRVVTADGEIDLDSEDGRLMLGILAAMAEEESKLISERTKRG 137
mpi PRK13413
master DNA invertase Mpi family serine-type recombinase;
1-187 1.05e-11

master DNA invertase Mpi family serine-type recombinase;


Pssm-ID: 184041 [Multi-domain]  Cd Length: 200  Bit Score: 60.89  E-value: 1.05e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1894850504   1 MRIGYARVSTRDQHPEAQRDALTAAgCDQ--IFLDK-----VSG-KLARRPELDKaLLSANRVGDQLVVTKLDRLGRSLE 72
Cdd:PRK13413    1 MIYAYIRVSTDKQTVENQRFEITNF-AEKnnLTIDKwieetISGtKSYKDRKLGK-LLKKMRKGDILIVSELSRLGRNLM 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1894850504  73 HLIE-----LSKRLQGAGV-DLVVLDQGIDtSTAIGRMFfqilGAVAEFEHALMSERTMDGLAAARARGRTGGQKPKLGP 146
Cdd:PRK13413   79 EIMSilnicMEKEVIVYTIkEGYELGDDIN-SKVLAFAF----GLSAEIERNLISQRTKEALARKKAEGVTLGRPKGSTP 153

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|.
gi 1894850504 147 RQVKLAQQmYDEKDEHGKRRYTVEQIAAEFGVTRPTIYRHL 187
Cdd:PRK13413  154 KKYKLTGK-EEKIKKLLDKGTSKSEIARKLGVSRTTLARFL 193
SR_Res_par cd03767
Serine recombinase (SR) family, Partitioning (par)-Resolvase subfamily, catalytic domain; ...
 4-113 1.07e-08

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: 51.94  E-value: 1.07e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1894850504   4 GYARVSTRDQHPEAQRDALTAAGCDQ------IFLDKVSGKLARRPELDKaLLSANRVGDQLVVTKLDRLGR-SLEHLIE 76
Cdd:cd03767     3 AYLRASTDEQDATRAKESLEAFATERgfyiagFYVENASGAKLDRPELFR-LLDDAQSGDVLLVEQIDRLSRlPLDDWET 81

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1894850504  77 LSKRLQGAGVDLVVLDQGIDTS--------------TAIGRMFFQILGAVA 113
Cdd:cd03767    82 LKASIAAKGLRVVSLDLPTSHSalaaedndftgrilSAINDMLLDLLAAMA 132
HTH_Hin_like cd00569
Helix-turn-helix domain of Hin and related proteins; This domain model summarizes a family of ...
 139-187 2.08e-08

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: 48.48  E-value: 2.08e-08
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 1894850504 139 GQKPKLGPRQVKLAQQMYDEKDehgkrryTVEQIAAEFGVTRPTIYRHL 187
Cdd:cd00569     1 GRPPKLTPEQIAEARRLLAAGE-------SVAEIARELGVSRSTLYRYL 42
SR_IS607_transposase_like cd03769
Serine Recombinase (SR) family, IS607-like transposase subfamily, catalytic domain; members ...
 3-99 1.12e-06

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: 46.10  E-value: 1.12e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1894850504   3 IGYARVSTRDQHP--EAQRDALTA-----AGCDQIFLDKVSGKLARRPELDKAL-LSANRVGDQLVVTKLDRLGR-SLEH 73
Cdd:cd03769     2 VLYARVSSHDQKDdlERQIERLEAyataqGWIVEVIKDIGSGLNEKRKGLLKLLeDVLAGKVERVVITYKDRLARfGFEL 81

                          90       100
                  ....*....|....*....|....*.
gi 1894850504  74 LIELSKRLqgaGVDLVVLDQGIDTST 99
Cdd:cd03769    82 LEELFKAY---GVEIVVINQEENEEL 104
COG2452 COG2452
Predicted site-specific integrase-resolvase [Mobilome: prophages, transposons];
3-93 3.11e-05

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


Pssm-ID: 441988 [Multi-domain]  Cd Length: 178  Bit Score: 42.67  E-value: 3.11e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1894850504   3 IGYARVSTRDQHP--EAQRDALTAAGCDQIFLDKV-----SGKLARRPELdKALLSANRVgDQLVVTKLDRLGRSLEHLI 75
Cdd:COG2452    51 VIYARVSSADQKDdlERQVERLEEYATAKGYQDEVikdvgSGLNYKRKGL-LKLLERIEV-ERVVVEHKDRLARFGFELL 128

                          90
                  ....*....|....*...
gi 1894850504  76 ElsKRLQGAGVDLVVLDQ 93
Cdd:COG2452   129 E--ALCEAYGVEIVVVNQ 144
HTH_7 pfam02796
Helix-turn-helix domain of resolvase;
139-189 1.50e-04

Helix-turn-helix domain of resolvase;


Pssm-ID: 397088 [Multi-domain]  Cd Length: 45  Bit Score: 38.10  E-value: 1.50e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1894850504 139 GQKPKLGPRQVKLAQQMYDEKdehgkrrYTVEQIAAEFGVTRPTIYRHLGK 189
Cdd:pfam02796   1 GRPPKLNEEDINEVITLLEEG-------ISIKQIAKIFGISRSTVYRYLAA 44
transpos_IS607 NF033518
IS607 family transposase;
3-93 2.45e-04

IS607 family transposase;


Pssm-ID: 468054 [Multi-domain]  Cd Length: 187  Bit Score: 40.32  E-value: 2.45e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1894850504   3 IGYARVSTRDQHP--EAQRDALT--AAGC----DQIFLDKVSGKLARRPELDKAL-LSANRVGDQLVVTKLDRLGR-SLE 72
Cdd:NF033518   57 VIYARVSSADQKDdlERQVARLTqyATAKgwqvDEVVTDIGSGLNEKRKGLLKLLdDILNGEVSRVVVEHKDRLTRfGFE 136

                          90       100
                  ....*....|....*....|.
gi 1894850504  73 HLIELskrLQGAGVDLVVLDQ 93
Cdd:NF033518  137 YLEAL---FKANGVEIVVVNE 154
HTH_22 pfam13309
HTH domain; This domain is a helix-turn-helix domain that is likely to act as a DNA-binding ...
 168-187 5.25e-03

HTH domain; This domain is a helix-turn-helix domain that is likely to act as a DNA-binding domain.


Pssm-ID: 463841 [Multi-domain]  Cd Length: 63  Bit Score: 34.36  E-value: 5.25e-03
                          10        20
                  ....*....|....*....|
gi 1894850504 168 TVEQIAAEFGVTRPTIYRHL 187
Cdd:pfam13309  43 AVEKVAKRLGVSRATVYNYL 62
LexA COG1974
SOS-response transcriptional repressor LexA (RecA-mediated autopeptidase) [Transcription, ...
 143-191 9.84e-03

SOS-response transcriptional repressor LexA (RecA-mediated autopeptidase) [Transcription, Signal transduction mechanisms];


Pssm-ID: 441577 [Multi-domain]  Cd Length: 199  Bit Score: 35.66  E-value: 9.84e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 1894850504 143 KLGPRQVKLAQQMYDEKDEHGkRRYTVEQIAAEFGVTRPTIYRHLgKAL 191
Cdd:COG1974     3 KLTKRQREILDFIKEYIRERG-YPPSQREIAEALGLSSSAVHRHL-KAL 49
 
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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