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Conserved domains on  [gi|1765042309|gb|KAB5911770|]
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recombinase family protein [Bifidobacterium adolescentis]

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

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 ...
 2-126 3.33e-62

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: 188.46  E-value: 3.33e-62
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1765042309   2 TYGYARVSTGDQTTDLQRDALEKAG-CNRIFTDVASGAKAHRPELDHMLDLLREGDAVVVWKLDRLGRSLQNLVELINEF 80
Cdd:cd03768     1 VIGYARVSTDDQSLERQLEALKAAGeCDKIFEEKGSGGKKERPELQKLLEDLREGDTLVVTKLDRLGRSTKDLLEIVEEL 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*.
gi 1765042309  81 DARGVQFHSLTESIDTSTPGVTLIFNIFGSLAQFERDLIRERTRAG 126
Cdd:cd03768    81 REKGVSLRSLTEGIDTSTPSGKLMLTILGAFAEFERELIRERTKEG 126
HTH_Hin_like cd00569
Helix-turn-helix domain of Hin and related proteins; This domain model summarizes a family of ...
 138-180 1.16e-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: 48.86  E-value: 1.16e-08
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 1765042309 138 GRPVSLDRKQIKEARRLYESRsVTVDQIASMMHVSRTTIYRCL 180
Cdd:cd00569     1 GRPPKLTPEQIAEARRLLAAG-ESVAEIARELGVSRSTLYRYL 42
 
Name Accession Description Interval E-value
SR_ResInv cd03768
Serine Recombinase (SR) family, Resolvase and Invertase subfamily, catalytic domain; members ...
 2-126 3.33e-62

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: 188.46  E-value: 3.33e-62
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1765042309   2 TYGYARVSTGDQTTDLQRDALEKAG-CNRIFTDVASGAKAHRPELDHMLDLLREGDAVVVWKLDRLGRSLQNLVELINEF 80
Cdd:cd03768     1 VIGYARVSTDDQSLERQLEALKAAGeCDKIFEEKGSGGKKERPELQKLLEDLREGDTLVVTKLDRLGRSTKDLLEIVEEL 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*.
gi 1765042309  81 DARGVQFHSLTESIDTSTPGVTLIFNIFGSLAQFERDLIRERTRAG 126
Cdd:cd03768    81 REKGVSLRSLTEGIDTSTPSGKLMLTILGAFAEFERELIRERTKEG 126
SpoIVCA COG1961
Site-specific DNA recombinase SpoIVCA/DNA invertase PinE [Replication, recombination and ...
 1-182 1.40e-54

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


Pssm-ID: 441564 [Multi-domain]  Cd Length: 388  Bit Score: 177.91  E-value: 1.40e-54
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1765042309   1 MTYGYARVSTGDQ---TTDLQRDAL----EKAGCN--RIFTDVA-SGAKAHRPELDHMLDLLREG--DAVVVWKLDRLGR 68
Cdd:COG1961     3 RAAGYARVSTDDQeglSLERQREALrayaEKAGWEivRIYVDEGvSGTSKDRPGLQRLLADLRAGkfDTLVVWKLDRLGR 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1765042309  69 SLQNLVELINEFDARGVQFHSLTESIDTSTPGVTLIFNIFGSLAQFERDLIRERTRAGLEAARARGRTGGRPV------- 141
Cdd:COG1961    83 NLADLLELVEELKERGVRLISLTEGIDTSTPMGRLLLTILAAFAEFERELISERTRAGLAAAKARGKYLGRPPygyrdpk 162

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1765042309 142 --SLDRKQ---IKEARRLYESRsVTVDQIASMMH------VSRTTIYRCLQK 182
Cdd:COG1961   163 klVIDEEEaevVRRIFELYLEG-KSLREIARELNergiptWSRSTVYRILKN 213
Resolvase pfam00239
Resolvase, N terminal domain; The N-terminal domain of the resolvase family (this family) ...
 3-135 1.43e-51

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: 162.44  E-value: 1.43e-51
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1765042309   3 YGYARVSTGDQTTDL--QRDALEKAGCNR----IFTDV-ASGAKAHRPELDHMLDLLRE--GDAVVVWKLDRLGRSLQNL 73
Cdd:pfam00239   2 IGYARVSTEDQDDSLerQLEALRAYAACNgkivEFEDKgVSGRKLDRPGLQRLLALLRAgkGDVLVVYKLDRLGRSLRDL 81

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1765042309  74 VELINEFDARGVQFHSLTESIDTSTPGVTLIFNIFGSLAQFERDLIRERTRAGLEAARARGR 135
Cdd:pfam00239  82 LTLVEELREKGVDLVSLDEGIDTSTPMGRLLLTILAALAEFERALIRERTRAGLAAAAARGK 143
Resolvase smart00857
Resolvase, N terminal domain; The N-terminal domain of the resolvase family contains the ...
 2-135 2.52e-45

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: 146.61  E-value: 2.52e-45
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1765042309    2 TYGYARVSTGDQ---TTDLQRDALEKA----GCN--RIFTDVA-SGAKAHRPELDHMLDLLREGD--AVVVWKLDRLGRS 69
Cdd:smart00857   1 AAGYARVSTDDQadgSLERQLEALRAYaernGWEvvRIYEDEGvSGKKADRPGLQRLLADLRAGDidVLVVYKLDRLGRS 80

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1765042309   70 LQNLVELINEFDARGVQFHSLTESI-DTSTPGVTLIFNIFGSLAQFERDLIRERTRAGLEAARARGR 135
Cdd:smart00857  81 LRDLLALLELLEEKGVRLVSLKEGIlDTSTPAGRLLLDILAALAEFERELISERTKAGLARAAARGR 147
recomb_XisF NF041201
fdxN element excision recombinase XisF;
3-169 1.05e-31

fdxN element excision recombinase XisF;


Pssm-ID: 469105 [Multi-domain]  Cd Length: 463  Bit Score: 118.91  E-value: 1.05e-31
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1765042309   3 YGYARVSTGDQTTDlqRDALE-------KAGCNRIFTDVASGAKAHRPELDHMLDLLREG--DAVVVWKLDRLGRSLQNL 73
Cdd:NF041201    2 VGYARVSTREQADD--GHALEqqiarlkKAGASEIFFDIESGRSDKRKGFNQLLKLVKSGkvTEIIITRIDRLTRSVVTI 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1765042309  74 VELINEFDARGVQFHSLTE-SIDTSTPGVTLIFNIFGSLAQFERDLIRERTRAGLEAARARGRTGGRP----VSLDRKQI 148
Cdd:NF041201   80 YKAIEVLQKKGVKLVILDApLDDLSSPGGWFTINQLAALAEFESRLLSERVRHGLEYFREQKKAHPKPpfgyVRIDDKYA 159

                         170       180
                  ....*....|....*....|.
gi 1765042309 149 KEArRLYESRSVTVDQIASMM 169
Cdd:NF041201  160 PDC-LLYDKSELTVWEIAREI 179
mpi PRK13413
master DNA invertase Mpi family serine-type recombinase;
1-185 1.61e-20

master DNA invertase Mpi family serine-type recombinase;


Pssm-ID: 184041 [Multi-domain]  Cd Length: 200  Bit Score: 84.38  E-value: 1.61e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1765042309   1 MTYGYARVSTGDQTTDLQRDALEKAGCNRIFT------DVASGAKAHRP-ELDHMLDLLREGDAVVVWKLDRLGRSLQNL 73
Cdd:PRK13413    1 MIYAYIRVSTDKQTVENQRFEITNFAEKNNLTidkwieETISGTKSYKDrKLGKLLKKMRKGDILIVSELSRLGRNLMEI 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1765042309  74 VELINEFDARGVQFHSLTEsidtstpGVTLIFNI--------FGSLAQFERDLIRERTRAGLEAARARGRTGGRPVSLDR 145
Cdd:PRK13413   81 MSILNICMEKEVIVYTIKE-------GYELGDDInskvlafaFGLSAEIERNLISQRTKEALARKKAEGVTLGRPKGSTP 153

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*.
gi 1765042309 146 KQIK------EARRLYESRsVTVDQIASMMHVSRTTIYRCLQKNKE 185
Cdd:PRK13413  154 KKYKltgkeeKIKKLLDKG-TSKSEIARKLGVSRTTLARFLKTRGL 198
HTH_Hin_like cd00569
Helix-turn-helix domain of Hin and related proteins; This domain model summarizes a family of ...
 138-180 1.16e-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: 48.86  E-value: 1.16e-08
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 1765042309 138 GRPVSLDRKQIKEARRLYESRsVTVDQIASMMHVSRTTIYRCL 180
Cdd:cd00569     1 GRPPKLTPEQIAEARRLLAAG-ESVAEIARELGVSRSTLYRYL 42
transpos_IS607 NF033518
IS607 family transposase;
2-68 1.57e-07

IS607 family transposase;


Pssm-ID: 468054 [Multi-domain]  Cd Length: 187  Bit Score: 49.18  E-value: 1.57e-07
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1765042309   2 TYGYARVSTGDQTTDLQR--DALeKAGC-------NRIFTDVASGAKAHRPELDHMLDLLREGDA--VVVWKLDRLGR 68
Cdd:NF033518   56 TVIYARVSSADQKDDLERqvARL-TQYAtakgwqvDEVVTDIGSGLNEKRKGLLKLLDDILNGEVsrVVVEHKDRLTR 132
HTH_7 pfam02796
Helix-turn-helix domain of resolvase;
138-183 2.57e-05

Helix-turn-helix domain of resolvase;


Pssm-ID: 397088 [Multi-domain]  Cd Length: 45  Bit Score: 40.03  E-value: 2.57e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 1765042309 138 GRPVSLDRKQIKEARRLYESRSvTVDQIASMMHVSRTTIYRCLQKN 183
Cdd:pfam02796   1 GRPPKLNEEDINEVITLLEEGI-SIKQIAKIFGISRSTVYRYLAAS 45
PRK04140 PRK04140
transcriptional regulator;
129-178 1.01e-03

transcriptional regulator;


Pssm-ID: 235224 [Multi-domain]  Cd Length: 317  Bit Score: 38.68  E-value: 1.01e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 1765042309 129 AARargrtGGRPVSLDRKQIKEARrlyESRSVTVDQIASMMHVSRTTIYR 178
Cdd:PRK04140  117 AAP-----GGFYVKIDGDVLREAR---EELGLSLGELASELGVSRRTISK 158
 
Name Accession Description Interval E-value
SR_ResInv cd03768
Serine Recombinase (SR) family, Resolvase and Invertase subfamily, catalytic domain; members ...
 2-126 3.33e-62

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: 188.46  E-value: 3.33e-62
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1765042309   2 TYGYARVSTGDQTTDLQRDALEKAG-CNRIFTDVASGAKAHRPELDHMLDLLREGDAVVVWKLDRLGRSLQNLVELINEF 80
Cdd:cd03768     1 VIGYARVSTDDQSLERQLEALKAAGeCDKIFEEKGSGGKKERPELQKLLEDLREGDTLVVTKLDRLGRSTKDLLEIVEEL 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*.
gi 1765042309  81 DARGVQFHSLTESIDTSTPGVTLIFNIFGSLAQFERDLIRERTRAG 126
Cdd:cd03768    81 REKGVSLRSLTEGIDTSTPSGKLMLTILGAFAEFERELIRERTKEG 126
SpoIVCA COG1961
Site-specific DNA recombinase SpoIVCA/DNA invertase PinE [Replication, recombination and ...
 1-182 1.40e-54

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


Pssm-ID: 441564 [Multi-domain]  Cd Length: 388  Bit Score: 177.91  E-value: 1.40e-54
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1765042309   1 MTYGYARVSTGDQ---TTDLQRDAL----EKAGCN--RIFTDVA-SGAKAHRPELDHMLDLLREG--DAVVVWKLDRLGR 68
Cdd:COG1961     3 RAAGYARVSTDDQeglSLERQREALrayaEKAGWEivRIYVDEGvSGTSKDRPGLQRLLADLRAGkfDTLVVWKLDRLGR 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1765042309  69 SLQNLVELINEFDARGVQFHSLTESIDTSTPGVTLIFNIFGSLAQFERDLIRERTRAGLEAARARGRTGGRPV------- 141
Cdd:COG1961    83 NLADLLELVEELKERGVRLISLTEGIDTSTPMGRLLLTILAAFAEFERELISERTRAGLAAAKARGKYLGRPPygyrdpk 162

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1765042309 142 --SLDRKQ---IKEARRLYESRsVTVDQIASMMH------VSRTTIYRCLQK 182
Cdd:COG1961   163 klVIDEEEaevVRRIFELYLEG-KSLREIARELNergiptWSRSTVYRILKN 213
Resolvase pfam00239
Resolvase, N terminal domain; The N-terminal domain of the resolvase family (this family) ...
 3-135 1.43e-51

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: 162.44  E-value: 1.43e-51
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1765042309   3 YGYARVSTGDQTTDL--QRDALEKAGCNR----IFTDV-ASGAKAHRPELDHMLDLLRE--GDAVVVWKLDRLGRSLQNL 73
Cdd:pfam00239   2 IGYARVSTEDQDDSLerQLEALRAYAACNgkivEFEDKgVSGRKLDRPGLQRLLALLRAgkGDVLVVYKLDRLGRSLRDL 81

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1765042309  74 VELINEFDARGVQFHSLTESIDTSTPGVTLIFNIFGSLAQFERDLIRERTRAGLEAARARGR 135
Cdd:pfam00239  82 LTLVEELREKGVDLVSLDEGIDTSTPMGRLLLTILAALAEFERALIRERTRAGLAAAAARGK 143
Resolvase smart00857
Resolvase, N terminal domain; The N-terminal domain of the resolvase family contains the ...
 2-135 2.52e-45

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: 146.61  E-value: 2.52e-45
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1765042309    2 TYGYARVSTGDQ---TTDLQRDALEKA----GCN--RIFTDVA-SGAKAHRPELDHMLDLLREGD--AVVVWKLDRLGRS 69
Cdd:smart00857   1 AAGYARVSTDDQadgSLERQLEALRAYaernGWEvvRIYEDEGvSGKKADRPGLQRLLADLRAGDidVLVVYKLDRLGRS 80

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1765042309   70 LQNLVELINEFDARGVQFHSLTESI-DTSTPGVTLIFNIFGSLAQFERDLIRERTRAGLEAARARGR 135
Cdd:smart00857  81 LRDLLALLELLEEKGVRLVSLKEGIlDTSTPAGRLLLDILAALAEFERELISERTKAGLARAAARGR 147
recomb_XisF NF041201
fdxN element excision recombinase XisF;
3-169 1.05e-31

fdxN element excision recombinase XisF;


Pssm-ID: 469105 [Multi-domain]  Cd Length: 463  Bit Score: 118.91  E-value: 1.05e-31
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1765042309   3 YGYARVSTGDQTTDlqRDALE-------KAGCNRIFTDVASGAKAHRPELDHMLDLLREG--DAVVVWKLDRLGRSLQNL 73
Cdd:NF041201    2 VGYARVSTREQADD--GHALEqqiarlkKAGASEIFFDIESGRSDKRKGFNQLLKLVKSGkvTEIIITRIDRLTRSVVTI 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1765042309  74 VELINEFDARGVQFHSLTE-SIDTSTPGVTLIFNIFGSLAQFERDLIRERTRAGLEAARARGRTGGRP----VSLDRKQI 148
Cdd:NF041201   80 YKAIEVLQKKGVKLVILDApLDDLSSPGGWFTINQLAALAEFESRLLSERVRHGLEYFREQKKAHPKPpfgyVRIDDKYA 159

                         170       180
                  ....*....|....*....|.
gi 1765042309 149 KEArRLYESRSVTVDQIASMM 169
Cdd:NF041201  160 PDC-LLYDKSELTVWEIAREI 179
Ser_Recombinase cd00338
Serine Recombinase family, catalytic domain; a DNA binding domain may be present either N- or ...
 5-126 1.44e-30

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: 108.50  E-value: 1.44e-30
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1765042309   5 YARVSTGDQ----TTDLQRDALEKAgCNR-------IFTDVASGAKAH--RPELDHMLDLLREG--DAVVVWKLDRLGRS 69
Cdd:cd00338     2 YARVSTDKQeqgdSLERQREALREY-AARnglevvgEYEDAGSSATSLvdRPGLQRLLADVKAGkiDVVLVEKLDRLSRN 80

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1765042309  70 LQNLVELINEFDARGVQFHSLTESIDTSTPGVTLIFNIFGSLAQFERDLIRERTRAG 126
Cdd:cd00338    81 LVDLLELLELLEAHGVRVVTADGEIDLDSEDGRLMLGILAAMAEEESKLISERTKRG 137
mpi PRK13413
master DNA invertase Mpi family serine-type recombinase;
1-185 1.61e-20

master DNA invertase Mpi family serine-type recombinase;


Pssm-ID: 184041 [Multi-domain]  Cd Length: 200  Bit Score: 84.38  E-value: 1.61e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1765042309   1 MTYGYARVSTGDQTTDLQRDALEKAGCNRIFT------DVASGAKAHRP-ELDHMLDLLREGDAVVVWKLDRLGRSLQNL 73
Cdd:PRK13413    1 MIYAYIRVSTDKQTVENQRFEITNFAEKNNLTidkwieETISGTKSYKDrKLGKLLKKMRKGDILIVSELSRLGRNLMEI 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1765042309  74 VELINEFDARGVQFHSLTEsidtstpGVTLIFNI--------FGSLAQFERDLIRERTRAGLEAARARGRTGGRPVSLDR 145
Cdd:PRK13413   81 MSILNICMEKEVIVYTIKE-------GYELGDDInskvlafaFGLSAEIERNLISQRTKEALARKKAEGVTLGRPKGSTP 153

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*.
gi 1765042309 146 KQIK------EARRLYESRsVTVDQIASMMHVSRTTIYRCLQKNKE 185
Cdd:PRK13413  154 KKYKltgkeeKIKKLLDKG-TSKSEIARKLGVSRTTLARFLKTRGL 198
SR_IS607_transposase_like cd03769
Serine Recombinase (SR) family, IS607-like transposase subfamily, catalytic domain; members ...
 2-99 1.46e-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: 53.80  E-value: 1.46e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1765042309   2 TYGYARVSTGDQTTDLQRDA-LEKAGCNR------IFTDVASGAKAHRPELDHMLDLLREG--DAVVVWKLDRLGRSLQN 72
Cdd:cd03769     1 TVLYARVSSHDQKDDLERQIeRLEAYATAqgwiveVIKDIGSGLNEKRKGLLKLLEDVLAGkvERVVITYKDRLARFGFE 80

                          90       100
                  ....*....|....*....|....*..
gi 1765042309  73 LVELIneFDARGVQFHSLTESIDTSTP 99
Cdd:cd03769    81 LLEEL--FKAYGVEIVVINQEENEELE 105
SR_Res_par cd03767
Serine recombinase (SR) family, Partitioning (par)-Resolvase subfamily, catalytic domain; ...
 3-85 3.80e-09

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: 52.71  E-value: 3.80e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1765042309   3 YGYARVSTGDQTTDLQRDALEKAGCNR------IFTDVASGAKAHRPELDHMLDLLREGDAVVVWKLDRLGR-SLQNLVE 75
Cdd:cd03767     2 RAYLRASTDEQDATRAKESLEAFATERgfyiagFYVENASGAKLDRPELFRLLDDAQSGDVLLVEQIDRLSRlPLDDWET 81

                          90
                  ....*....|
gi 1765042309  76 LINEFDARGV 85
Cdd:cd03767    82 LKASIAAKGL 91
HTH_Hin_like cd00569
Helix-turn-helix domain of Hin and related proteins; This domain model summarizes a family of ...
 138-180 1.16e-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: 48.86  E-value: 1.16e-08
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 1765042309 138 GRPVSLDRKQIKEARRLYESRsVTVDQIASMMHVSRTTIYRCL 180
Cdd:cd00569     1 GRPPKLTPEQIAEARRLLAAG-ESVAEIARELGVSRSTLYRYL 42
COG2452 COG2452
Predicted site-specific integrase-resolvase [Mobilome: prophages, transposons];
2-75 8.40e-08

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


Pssm-ID: 441988 [Multi-domain]  Cd Length: 178  Bit Score: 49.61  E-value: 8.40e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1765042309   2 TYGYARVSTGDQTTDLQRD-------ALEKAGCNRIFTDVASGAKAHRPELDHMLDLLrEGDAVVVWKLDRLGRSLQNLV 74
Cdd:COG2452    50 TVIYARVSSADQKDDLERQverleeyATAKGYQDEVIKDVGSGLNYKRKGLLKLLERI-EVERVVVEHKDRLARFGFELL 128


                  .
gi 1765042309  75 E 75
Cdd:COG2452   129 E 129
transpos_IS607 NF033518
IS607 family transposase;
2-68 1.57e-07

IS607 family transposase;


Pssm-ID: 468054 [Multi-domain]  Cd Length: 187  Bit Score: 49.18  E-value: 1.57e-07
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1765042309   2 TYGYARVSTGDQTTDLQR--DALeKAGC-------NRIFTDVASGAKAHRPELDHMLDLLREGDA--VVVWKLDRLGR 68
Cdd:NF033518   56 TVIYARVSSADQKDDLERqvARL-TQYAtakgwqvDEVVTDIGSGLNEKRKGLLKLLDDILNGEVsrVVVEHKDRLTR 132
HTH_7 pfam02796
Helix-turn-helix domain of resolvase;
138-183 2.57e-05

Helix-turn-helix domain of resolvase;


Pssm-ID: 397088 [Multi-domain]  Cd Length: 45  Bit Score: 40.03  E-value: 2.57e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 1765042309 138 GRPVSLDRKQIKEARRLYESRSvTVDQIASMMHVSRTTIYRCLQKN 183
Cdd:pfam02796   1 GRPPKLNEEDINEVITLLEEGI-SIKQIAKIFGISRSTVYRYLAAS 45
PRK04140 PRK04140
transcriptional regulator;
129-178 1.01e-03

transcriptional regulator;


Pssm-ID: 235224 [Multi-domain]  Cd Length: 317  Bit Score: 38.68  E-value: 1.01e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 1765042309 129 AARargrtGGRPVSLDRKQIKEARrlyESRSVTVDQIASMMHVSRTTIYR 178
Cdd:PRK04140  117 AAP-----GGFYVKIDGDVLREAR---EELGLSLGELASELGVSRRTISK 158
 
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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