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Conserved domains on  [gi|1007022593|gb|AGI12984|]
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tyrosine integrase [Mycobacterium phage Butters]

Protein Classification

tyrosine-type recombinase/integrase( domain architecture ID 11471964)

tyrosine-type recombinase/integrase cleaves DNA substrates by a series of staggered cuts, during which the protein becomes covalently linked to the DNA through a catalytic tyrosine residue at the carboxy end of the alignment.

Gene Ontology:  GO:0009009|GO:0006310
PubMed:  10047575|9278480

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
XerD COG4974
Site-specific recombinase XerD [Replication, recombination and repair];
39-304 1.85e-57

Site-specific recombinase XerD [Replication, recombination and repair];


:

Pssm-ID: 443999 [Multi-domain]  Cd Length: 291  Bit Score: 187.12  E-value: 1.85e-57
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1007022593  39 LDDW-EIWQTAQRLSRRTIDERLRVI--HLLHIET-GLQPMH-IRAAELVRWIADHEE--WSDSTACTYTSYLSAWFKWL 111
Cdd:COG4974     7 LEAFlEELKREKGLSPNTIKAYRRDLrrFLRFLEElGKIPLAeITPEDIRAYLNYLRErgLSPSTINRYLAALRSFFRYA 86

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1007022593 112 QLTDRREDNPMVKVGAPRLPDRQPRPISDADVVNLLQT---RMWASTRR--MILLALLAGLRVHEIAKIRGEDIDLSAHV 186
Cdd:COG4974    87 VREGLLEDNPAAKVKLPKKPRKLPRVLTEEEIEALLEAldtETPEGLRDraLLLLLYATGLRVSELLGLKWSDIDLDRGT 166

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1007022593 187 LWVK-GKGKRLRSVPLHPLLIEM------ASEMPAAGWWFPmrGHEGEHILSKSVSDIIGRTMKRAGVRG--TPHCLRHW 257
Cdd:COG4974   167 IRVRrGKGGKERTVPLSPEALEAlreyleERRPRDSDYLFP--TRRGRPLSRRAIRKILKRLAKRAGIPKrvTPHSLRHT 244

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|....*..
gi 1007022593 258 YATTLLDNGTDIRVVQELLRHKSIGTTQIYTKVPEGRLHDAITSLDP 304
Cdd:COG4974   245 FATHLLEAGVDLRTVQELLGHSSISTTQIYTHVSDEELREAVEKLHP 291
 
Name Accession Description Interval E-value
XerD COG4974
Site-specific recombinase XerD [Replication, recombination and repair];
39-304 1.85e-57

Site-specific recombinase XerD [Replication, recombination and repair];


Pssm-ID: 443999 [Multi-domain]  Cd Length: 291  Bit Score: 187.12  E-value: 1.85e-57
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1007022593  39 LDDW-EIWQTAQRLSRRTIDERLRVI--HLLHIET-GLQPMH-IRAAELVRWIADHEE--WSDSTACTYTSYLSAWFKWL 111
Cdd:COG4974     7 LEAFlEELKREKGLSPNTIKAYRRDLrrFLRFLEElGKIPLAeITPEDIRAYLNYLRErgLSPSTINRYLAALRSFFRYA 86

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1007022593 112 QLTDRREDNPMVKVGAPRLPDRQPRPISDADVVNLLQT---RMWASTRR--MILLALLAGLRVHEIAKIRGEDIDLSAHV 186
Cdd:COG4974    87 VREGLLEDNPAAKVKLPKKPRKLPRVLTEEEIEALLEAldtETPEGLRDraLLLLLYATGLRVSELLGLKWSDIDLDRGT 166

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1007022593 187 LWVK-GKGKRLRSVPLHPLLIEM------ASEMPAAGWWFPmrGHEGEHILSKSVSDIIGRTMKRAGVRG--TPHCLRHW 257
Cdd:COG4974   167 IRVRrGKGGKERTVPLSPEALEAlreyleERRPRDSDYLFP--TRRGRPLSRRAIRKILKRLAKRAGIPKrvTPHSLRHT 244

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|....*..
gi 1007022593 258 YATTLLDNGTDIRVVQELLRHKSIGTTQIYTKVPEGRLHDAITSLDP 304
Cdd:COG4974   245 FATHLLEAGVDLRTVQELLGHSSISTTQIYTHVSDEELREAVEKLHP 291
xerC PRK00236
site-specific tyrosine recombinase XerC; Reviewed
 39-298 7.47e-37

site-specific tyrosine recombinase XerC; Reviewed


Pssm-ID: 234698 [Multi-domain]  Cd Length: 297  Bit Score: 133.74  E-value: 7.47e-37
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1007022593  39 LDDWEIWQTAQR-LSRRTIDERLR----VIHLLHIETGLQPMHIRAAELVRWIAD--HEEWSDSTACTYTSYLSAWFKWL 111
Cdd:PRK00236   10 LEAFLEYLRVERgLSPHTLRAYRRdlraFLAFLEEHGISSLQDLDAADLRSFLARrrRQGLSARSLARRLSALRSFYRWL 89

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1007022593 112 QLTDRREDNPMVKVGAPRLPDRQPRPISDADVVNLLQTRM---WASTRRMILLALL--AGLRVHEIAKIRGEDIDLSAHV 186
Cdd:PRK00236   90 VRRGLLKANPAAGLRAPKIPKRLPKPLDVDQAKRLLDAIDeddPLALRDRAILELLygSGLRLSELVGLDIDDLDLASGT 169

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1007022593 187 LWVKGKGKRLRSVPLHPlliemasemPAAGW---WFPMRGHEGEHI----LSK--------SVSDIIGRTMKRAGVRG-- 249
Cdd:PRK00236  170 LRVLGKGNKERTVPLGR---------AAREAleaYLALRPLFLPDDdalfLGArggrlsprVVQRRVKKLGKKAGLPShi 240

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|....*....
gi 1007022593 250 TPHCLRHWYATTLLDNGTDIRVVQELLRHKSIGTTQIYTKVPEGRLHDA 298
Cdd:PRK00236  241 TPHKLRHSFATHLLESGGDLRAVQELLGHASLSTTQIYTHVDFQHLAEV 289
recomb_XerD TIGR02225
tyrosine recombinase XerD; The phage integrase family describes a number of recombinases with ...
 49-312 3.23e-34

tyrosine recombinase XerD; The phage integrase family describes a number of recombinases with tyrosine active sites that transiently bind covalently to DNA. Many are associated with mobile DNA elements, including phage, transposons, and phase variation loci. This model represents XerD, one of two closely related chromosomal proteins along with XerC (TIGR02224). XerC and XerD are site-specific recombinases which help resolve chromosome dimers to monomers for cell division after DNA replication. In species with a large chromosome and with homologs of XerD on other replicons, the chomosomal copy was preferred for building this model. This model does not detect all XerD, as some apparent XerD examples score below the trusted and noise cutoff scores. XerC and XerD interact with cell division protein FtsK. [DNA metabolism, DNA replication, recombination, and repair]


Pssm-ID: 274043 [Multi-domain]  Cd Length: 291  Bit Score: 126.54  E-value: 3.23e-34
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1007022593  49 QRLSRRTIDERLRVIHLLH---IETGLQPMHIRAAELVRWIAD-HEE-WSDSTACTYTSYLSAWFKWLQLTDRREDNPMV 123
Cdd:TIGR02225  11 RGLSQNTLEAYRRDLEKFLeflEERGIDLEEVDRGDIVDFLAElKEAgLSARSIARALSALRSFYRFLLREGIREDDPSA 90

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1007022593 124 KVGAPRLPDRQPRPISDADVVNLLQ-----TRMWASTRRMILLALLAGLRVHEIAKIRGEDIDLSAHVLWVKGKGKRLRS 198
Cdd:TIGR02225  91 LIEPPKVARKLPKVLTVEEVEALLAapdvdTPLGLRDRAMLELLYATGLRVSELVGLRLEDVNLDEGFVRVRGKGNKERL 170

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1007022593 199 VPLHPLLIE-------------MASEMPAAGWWFPMRGheGEHILSKSVSDIIGRTMKRAGVRG--TPHCLRHWYATTLL 263
Cdd:TIGR02225 171 VPLGEEAIEalerylkearpllLKKKVKESDALFLNRR--GGPLSRQGVWKILKEYAKRAGIEKpiSPHTLRHSFATHLL 248

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|....*....
gi 1007022593 264 DNGTDIRVVQELLRHKSIGTTQIYTKVPEGRLHDAitsldpWRALRPRG 312
Cdd:TIGR02225 249 ENGADLRVVQELLGHADISTTQIYTHVARERLKEV------HKKHHPRA 291
INT_XerDC_C cd00798
XerD and XerC integrases, C-terminal catalytic domains; XerDC-like integrases are involved in ...
 160-295 8.92e-30

XerD and XerC integrases, C-terminal catalytic domains; XerDC-like integrases are involved in the site-specific integration and excision of lysogenic bacteriophage genomes, transposition of conjugative transposons, termination of chromosomal replication, and stable plasmid inheritance. They share the same fold in their catalytic domain containing six conserved active site residues and the overall reaction mechanism with the DNA breaking-rejoining enzyme superfamily. In Escherichia coli, the Xer site-specific recombination system acts to convert dimeric chromosomes, which are formed by homologous recombination to monomers. Two related recombinases, XerC and XerD, bind cooperatively to a recombination site present in the E. coli chromosome. Each recombinase catalyzes the exchange of one pair of DNA strand in a reaction that proceeds through a Holliday junction intermediate. These enzymes can bridge two different and well-separated DNA sequences called arm- and core-sites. The C-terminal domain binds, cleaves, and re-ligates DNA strands at the core-sites, while the N-terminal domain is largely responsible for high-affinity binding to the arm-type sites.


Pssm-ID: 271179 [Multi-domain]  Cd Length: 172  Bit Score: 111.45  E-value: 8.92e-30
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1007022593 160 LLALL--AGLRVHEIAKIRGEDIDLSAHVLWVKGKGKRLRSVPLHPLLIE-MASEMPAAGWWFPM--------RGHEGEH 228
Cdd:cd00798    24 ILELLyaSGLRVSELVGLDLSDVDLDEGLVRVTGKGNKERLVPFGSYAVEaLEEYLEERRPLLLKkkppdalfLNKRGKR 103

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1007022593 229 ILSKSVSDIIGRTMKRAGV--RGTPHCLRHWYATTLLDNGTDIRVVQELLRHKSIGTTQIYTKVPEGRL 295
Cdd:cd00798   104 LSRRGVWRILKKYAERAGLpkHVSPHTLRHSFATHLLEGGADLRVVQELLGHASLSTTQIYTHVSFERL 172
Phage_integrase pfam00589
Phage integrase family; Members of this family cleave DNA substrates by a series of staggered ...
 153-290 1.92e-24

Phage integrase family; Members of this family cleave DNA substrates by a series of staggered cuts, during which the protein becomes covalently linked to the DNA through a catalytic tyrosine residue at the carboxy end of the alignment. The catalytic site residues in CRE recombinase are Arg-173, His-289, Arg-292 and Tyr-324.


Pssm-ID: 395471 [Multi-domain]  Cd Length: 169  Bit Score: 97.39  E-value: 1.92e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1007022593 153 ASTRRMILLALLAGLRVHEIAKIRGEDIDLSAHVLWVK-GKGKRLRSVPL--------HPLLIEMASEMPAAGWWFPmrG 223
Cdd:pfam00589  21 IRDKALLELLYATGLRISELCSLRWSDIDFENGVIRVHrGKGNKERTVPLsdaalellKEWLSKRLLEAPKSDYLFA--S 98

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1007022593 224 HEGEHILSKSVSDIIGRTMKRAGV--RGTPHCLRHWYATTLLDNGTDIRVVQELLRHKSIGTTQIYTKV 290
Cdd:pfam00589  99 KRGKPLSRQTVRKIFKRAGKEAGLelPLHPHMLRHSFATHLLEAGVDLRVVQKLLGHSSISTTQIYTHV 167
 
Name Accession Description Interval E-value
XerD COG4974
Site-specific recombinase XerD [Replication, recombination and repair];
39-304 1.85e-57

Site-specific recombinase XerD [Replication, recombination and repair];


Pssm-ID: 443999 [Multi-domain]  Cd Length: 291  Bit Score: 187.12  E-value: 1.85e-57
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1007022593  39 LDDW-EIWQTAQRLSRRTIDERLRVI--HLLHIET-GLQPMH-IRAAELVRWIADHEE--WSDSTACTYTSYLSAWFKWL 111
Cdd:COG4974     7 LEAFlEELKREKGLSPNTIKAYRRDLrrFLRFLEElGKIPLAeITPEDIRAYLNYLRErgLSPSTINRYLAALRSFFRYA 86

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1007022593 112 QLTDRREDNPMVKVGAPRLPDRQPRPISDADVVNLLQT---RMWASTRR--MILLALLAGLRVHEIAKIRGEDIDLSAHV 186
Cdd:COG4974    87 VREGLLEDNPAAKVKLPKKPRKLPRVLTEEEIEALLEAldtETPEGLRDraLLLLLYATGLRVSELLGLKWSDIDLDRGT 166

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1007022593 187 LWVK-GKGKRLRSVPLHPLLIEM------ASEMPAAGWWFPmrGHEGEHILSKSVSDIIGRTMKRAGVRG--TPHCLRHW 257
Cdd:COG4974   167 IRVRrGKGGKERTVPLSPEALEAlreyleERRPRDSDYLFP--TRRGRPLSRRAIRKILKRLAKRAGIPKrvTPHSLRHT 244

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|....*..
gi 1007022593 258 YATTLLDNGTDIRVVQELLRHKSIGTTQIYTKVPEGRLHDAITSLDP 304
Cdd:COG4974   245 FATHLLEAGVDLRTVQELLGHSSISTTQIYTHVSDEELREAVEKLHP 291
XerC COG4973
Site-specific recombinase XerC [Replication, recombination and repair];
39-299 1.24e-46

Site-specific recombinase XerC [Replication, recombination and repair];


Pssm-ID: 443998 [Multi-domain]  Cd Length: 287  Bit Score: 158.97  E-value: 1.24e-46
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1007022593  39 LDDWEIWQTAQRLSRRTIDERLRVI--HLLHIETGLQPMH-IRAAELVRWIADHEE--WSDSTACTYTSYLSAWFKWLQL 113
Cdd:COG4973     8 LEAYLEHLRERRLSPKTLEAYRRDLrrLIPLLGDADLPLEeLTPADVRRFLARLHRrgLSPRTLNRRLSALRSFFNWAVR 87

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1007022593 114 TDRREDNPMVKVGAPRLPDRQPRPISDADVVNLLQ----TRMWASTRRMILLALLAGLRVHEIAKIRGEDIDLSAHVLWV 189
Cdd:COG4973    88 EGLLEANPAAGVKAPKAPRKLPRALTVDELAQLLDaladDPLAVRDRAIVELLYSTGLRLGELVGLDWEDVDLDAGEVRV 167

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1007022593 190 KGKGKRLRSVPLHPLLIEM---------ASEMPAAGWWFPMRghEGEHILSKSVSDIIGRTMKRAGVRG--TPHCLRHWY 258
Cdd:COG4973   168 RGKTGKSRTVPLGPKALAAlrewlavrpELAAPDEGALFPSR--RGTRLSPRNVQKRLRRLAKKAGLPKhvHPHDLRHSF 245

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|.
gi 1007022593 259 ATTLLDNGTDIRVVQELLRHKSIGTTQIYTKVPEGRLHDAI 299
Cdd:COG4973   246 ATHLLESGGDLRAVQELLGHASISTTQIYTHLDFQHLAEVY 286
xerC PRK00236
site-specific tyrosine recombinase XerC; Reviewed
 39-298 7.47e-37

site-specific tyrosine recombinase XerC; Reviewed


Pssm-ID: 234698 [Multi-domain]  Cd Length: 297  Bit Score: 133.74  E-value: 7.47e-37
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1007022593  39 LDDWEIWQTAQR-LSRRTIDERLR----VIHLLHIETGLQPMHIRAAELVRWIAD--HEEWSDSTACTYTSYLSAWFKWL 111
Cdd:PRK00236   10 LEAFLEYLRVERgLSPHTLRAYRRdlraFLAFLEEHGISSLQDLDAADLRSFLARrrRQGLSARSLARRLSALRSFYRWL 89

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1007022593 112 QLTDRREDNPMVKVGAPRLPDRQPRPISDADVVNLLQTRM---WASTRRMILLALL--AGLRVHEIAKIRGEDIDLSAHV 186
Cdd:PRK00236   90 VRRGLLKANPAAGLRAPKIPKRLPKPLDVDQAKRLLDAIDeddPLALRDRAILELLygSGLRLSELVGLDIDDLDLASGT 169

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1007022593 187 LWVKGKGKRLRSVPLHPlliemasemPAAGW---WFPMRGHEGEHI----LSK--------SVSDIIGRTMKRAGVRG-- 249
Cdd:PRK00236  170 LRVLGKGNKERTVPLGR---------AAREAleaYLALRPLFLPDDdalfLGArggrlsprVVQRRVKKLGKKAGLPShi 240

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|....*....
gi 1007022593 250 TPHCLRHWYATTLLDNGTDIRVVQELLRHKSIGTTQIYTKVPEGRLHDA 298
Cdd:PRK00236  241 TPHKLRHSFATHLLESGGDLRAVQELLGHASLSTTQIYTHVDFQHLAEV 289
recomb_XerD TIGR02225
tyrosine recombinase XerD; The phage integrase family describes a number of recombinases with ...
 49-312 3.23e-34

tyrosine recombinase XerD; The phage integrase family describes a number of recombinases with tyrosine active sites that transiently bind covalently to DNA. Many are associated with mobile DNA elements, including phage, transposons, and phase variation loci. This model represents XerD, one of two closely related chromosomal proteins along with XerC (TIGR02224). XerC and XerD are site-specific recombinases which help resolve chromosome dimers to monomers for cell division after DNA replication. In species with a large chromosome and with homologs of XerD on other replicons, the chomosomal copy was preferred for building this model. This model does not detect all XerD, as some apparent XerD examples score below the trusted and noise cutoff scores. XerC and XerD interact with cell division protein FtsK. [DNA metabolism, DNA replication, recombination, and repair]


Pssm-ID: 274043 [Multi-domain]  Cd Length: 291  Bit Score: 126.54  E-value: 3.23e-34
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1007022593  49 QRLSRRTIDERLRVIHLLH---IETGLQPMHIRAAELVRWIAD-HEE-WSDSTACTYTSYLSAWFKWLQLTDRREDNPMV 123
Cdd:TIGR02225  11 RGLSQNTLEAYRRDLEKFLeflEERGIDLEEVDRGDIVDFLAElKEAgLSARSIARALSALRSFYRFLLREGIREDDPSA 90

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1007022593 124 KVGAPRLPDRQPRPISDADVVNLLQ-----TRMWASTRRMILLALLAGLRVHEIAKIRGEDIDLSAHVLWVKGKGKRLRS 198
Cdd:TIGR02225  91 LIEPPKVARKLPKVLTVEEVEALLAapdvdTPLGLRDRAMLELLYATGLRVSELVGLRLEDVNLDEGFVRVRGKGNKERL 170

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1007022593 199 VPLHPLLIE-------------MASEMPAAGWWFPMRGheGEHILSKSVSDIIGRTMKRAGVRG--TPHCLRHWYATTLL 263
Cdd:TIGR02225 171 VPLGEEAIEalerylkearpllLKKKVKESDALFLNRR--GGPLSRQGVWKILKEYAKRAGIEKpiSPHTLRHSFATHLL 248

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|....*....
gi 1007022593 264 DNGTDIRVVQELLRHKSIGTTQIYTKVPEGRLHDAitsldpWRALRPRG 312
Cdd:TIGR02225 249 ENGADLRVVQELLGHADISTTQIYTHVARERLKEV------HKKHHPRA 291
INT_XerDC_C cd00798
XerD and XerC integrases, C-terminal catalytic domains; XerDC-like integrases are involved in ...
 160-295 8.92e-30

XerD and XerC integrases, C-terminal catalytic domains; XerDC-like integrases are involved in the site-specific integration and excision of lysogenic bacteriophage genomes, transposition of conjugative transposons, termination of chromosomal replication, and stable plasmid inheritance. They share the same fold in their catalytic domain containing six conserved active site residues and the overall reaction mechanism with the DNA breaking-rejoining enzyme superfamily. In Escherichia coli, the Xer site-specific recombination system acts to convert dimeric chromosomes, which are formed by homologous recombination to monomers. Two related recombinases, XerC and XerD, bind cooperatively to a recombination site present in the E. coli chromosome. Each recombinase catalyzes the exchange of one pair of DNA strand in a reaction that proceeds through a Holliday junction intermediate. These enzymes can bridge two different and well-separated DNA sequences called arm- and core-sites. The C-terminal domain binds, cleaves, and re-ligates DNA strands at the core-sites, while the N-terminal domain is largely responsible for high-affinity binding to the arm-type sites.


Pssm-ID: 271179 [Multi-domain]  Cd Length: 172  Bit Score: 111.45  E-value: 8.92e-30
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1007022593 160 LLALL--AGLRVHEIAKIRGEDIDLSAHVLWVKGKGKRLRSVPLHPLLIE-MASEMPAAGWWFPM--------RGHEGEH 228
Cdd:cd00798    24 ILELLyaSGLRVSELVGLDLSDVDLDEGLVRVTGKGNKERLVPFGSYAVEaLEEYLEERRPLLLKkkppdalfLNKRGKR 103

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1007022593 229 ILSKSVSDIIGRTMKRAGV--RGTPHCLRHWYATTLLDNGTDIRVVQELLRHKSIGTTQIYTKVPEGRL 295
Cdd:cd00798   104 LSRRGVWRILKKYAERAGLpkHVSPHTLRHSFATHLLEGGADLRVVQELLGHASLSTTQIYTHVSFERL 172
xerD PRK00283
tyrosine recombinase;
108-312 3.21e-28

tyrosine recombinase;


Pssm-ID: 234713 [Multi-domain]  Cd Length: 299  Bit Score: 110.67  E-value: 3.21e-28
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1007022593 108 FKWLQLTDRREDNPMVKVGAPRLPDRQPRPISDADVVNLLQT---------RMWAstrrmiLLALL--AGLRVHEIAKIR 176
Cdd:PRK00283   84 FQFLLREGLREDDPSALLDSPKLPRRLPKTLSEAQVEALLDApdidtplglRDRA------MLELLyaTGLRVSELVGLT 157

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1007022593 177 GEDIDLSAHVLWVKGKGKRLRSVPLHplliEMASEM---------------PAAGWWFPmrGHEGEHILSKSVSDIIGRT 241
Cdd:PRK00283  158 LDDVSLRQGVVRVTGKGNKERLVPLG----EEAVYAierylergrpallngRSSDALFP--SARGGQLTRQTFWHRIKHY 231

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1007022593 242 MKRAGVRG---TPHCLRHWYATTLLDNGTDIRVVQELLRHKSIGTTQIYTKVPEGRLHDAitsldpWRALRPRG 312
Cdd:PRK00283  232 AKRAGIDPkklSPHVLRHAFATHLLNHGADLRVVQELLGHSDISTTQIYTHVATERLKEL------HAQHHPRA 299
DNA_BRE_C cd00397
DNA breaking-rejoining enzymes, C-terminal catalytic domain; The DNA breaking-rejoining enzyme ...
 158-288 9.22e-28

DNA breaking-rejoining enzymes, C-terminal catalytic domain; The DNA breaking-rejoining enzyme superfamily includes type IB topoisomerases and tyrosine based site-specific recombinases (integrases) that share the same fold in their catalytic domain containing conserved active site residues. The best-studied members of this diverse superfamily include Human topoisomerase I, the bacteriophage lambda integrase, the bacteriophage P1 Cre recombinase, the yeast Flp recombinase, and the bacterial XerD/C recombinases. Their overall reaction mechanism is essentially identical and involves cleavage of a single strand of a DNA duplex by nucleophilic attack of a conserved tyrosine to give a 3' phosphotyrosyl protein-DNA adduct. In the second rejoining step, a terminal 5' hydroxyl attacks the covalent adduct to release the enzyme and generate duplex DNA. The enzymes differ in that topoisomerases cleave and then rejoin the same 5' and 3' termini, whereas a site-specific recombinase transfers a 5' hydroxyl generated by recombinase cleavage to a new 3' phosphate partner located in a different duplex region. Many DNA breaking-rejoining enzymes also have N-terminal domains, which show little sequence or structure similarity.


Pssm-ID: 271175 [Multi-domain]  Cd Length: 167  Bit Score: 106.03  E-value: 9.22e-28
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1007022593 158 MILLALLAGLRVHEIAKIRGEDIDLSAHVLWVKGKG---KRLRSVPLHP--------LLIEMASEMPAAGWWFPMRG--- 223
Cdd:cd00397    22 ILLLLLETGLRISELLALKVKDIDLDNGTIRVRGKKtkgGKERTVPLPKelaeelkeYLKERRDKRGPLLKSLYLNKlfg 101

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1007022593 224 -HEGEHILSKSVSDIIGRTMKRAGVRGTPHCLRHWYATTLLDNGTDIRVVQELLRHKSIGTTQIYT 288
Cdd:cd00397   102 tKLGERLSRRTLRRIFKKAGIEAGRKITPHSLRHTFATNLLENGVDIKVVQKLLGHSSISTTQRYL 167
INT_IntI_C cd01193
Integron integrase and similar protiens, C-terminal catalytic domain; Integron integrases ...
 133-290 2.29e-25

Integron integrase and similar protiens, C-terminal catalytic domain; Integron integrases mediate site-specific DNA recombination between a proximal primary site (attI) and a secondary target site (attC) found within mobile gene cassettes encoding resistance or virulence factors. Unlike other site specific recombinases, the attC sites lack sequence conservation. Integron integrase exhibits broader DNA specificity by recognizing the non-conserved attC sites. The structure shows that DNA target site recognition are not dependent on canonical DNA but on the position of two flipped-out bases that interact in cis and in trans with the integrase. Integron-integrases are present in many natural occurring mobile elements, including transposons and conjugative plasmids. Vibrio, Shewanella, Xanthomonas, and Pseudomonas species harbor chromosomal super-integrons. All integron-integrases carry large inserts unlike the TnpF ermF-like proteins also seen in this group.


Pssm-ID: 271193 [Multi-domain]  Cd Length: 176  Bit Score: 100.04  E-value: 2.29e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1007022593 133 RQPRPISDADVVNLLQTRMWASTRRMILLALLAGLRVHEIAKIRGEDIDLSAHVLWVK-GKGKRLRSVPLHPLLIEMA-- 209
Cdd:cd01193     1 KLPVVLSPDEVRRILGALTELRHRLILSLLYGAGLRISELLRLRVKDIDFERGVIRVRqGKGGKDRVVPLPEKLLEPLrr 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1007022593 210 --SEMPAAGWWFPMRGHEGE-----------HILSKSVSDIIGRTMKRAGV--RGTPHCLRHWYATTLLDNGTDIRVVQE 274
Cdd:cd01193    81 ylKSARPKEELDPAEGRAGVldprtgverrhHISETTVQRALKKAVEQAGItkRVTPHTLRHSFATHLLEAGTDIRTIQE 160

                         170
                  ....*....|....*.
gi 1007022593 275 LLRHKSIGTTQIYTKV 290
Cdd:cd01193   161 LLGHSDLSTTMIYTHV 176
Phage_integrase pfam00589
Phage integrase family; Members of this family cleave DNA substrates by a series of staggered ...
 153-290 1.92e-24

Phage integrase family; Members of this family cleave DNA substrates by a series of staggered cuts, during which the protein becomes covalently linked to the DNA through a catalytic tyrosine residue at the carboxy end of the alignment. The catalytic site residues in CRE recombinase are Arg-173, His-289, Arg-292 and Tyr-324.


Pssm-ID: 395471 [Multi-domain]  Cd Length: 169  Bit Score: 97.39  E-value: 1.92e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1007022593 153 ASTRRMILLALLAGLRVHEIAKIRGEDIDLSAHVLWVK-GKGKRLRSVPL--------HPLLIEMASEMPAAGWWFPmrG 223
Cdd:pfam00589  21 IRDKALLELLYATGLRISELCSLRWSDIDFENGVIRVHrGKGNKERTVPLsdaalellKEWLSKRLLEAPKSDYLFA--S 98

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1007022593 224 HEGEHILSKSVSDIIGRTMKRAGV--RGTPHCLRHWYATTLLDNGTDIRVVQELLRHKSIGTTQIYTKV 290
Cdd:pfam00589  99 KRGKPLSRQTVRKIFKRAGKEAGLelPLHPHMLRHSFATHLLEAGVDLRVVQKLLGHSSISTTQIYTHV 167
INTN1_C_like cd01185
Integrase IntN1 of Bacteroides mobilizable transposon NBU1 and similar proteins, C-terminal ...
 156-292 4.50e-20

Integrase IntN1 of Bacteroides mobilizable transposon NBU1 and similar proteins, C-terminal catalytic domain; IntN1 is a tyrosine recombinase for the integration and excision of Bacteroides mobilizable transposon NBU1 from the host chromosome. IntN1 does not require strict homology between the recombining sites seen with other tyrosine recombinases. This family belongs to the superfamily of DNA breaking-rejoining enzymes, which share the same fold in their catalytic domain and the overall reaction mechanism. The catalytic domain contains six conserved active site residues. Their overall reaction mechanism involves cleavage of a single strand of a DNA duplex by nucleophilic attack of a conserved tyrosine to give a 3' phosphotyrosyl protein-DNA adduct. In the second rejoining step, a terminal 5' hydroxyl attacks the covalent adduct to release the enzyme and generate duplex DNA.


Pssm-ID: 271185 [Multi-domain]  Cd Length: 161  Bit Score: 85.39  E-value: 4.50e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1007022593 156 RRMILLALLAGLRVHEIAKIRGEDIDLSAHVLWVKG---KGKRLRSVPLHPL---LIEMASEMPAAGWWFPMrghegehI 229
Cdd:cd01185    21 RDMFLFSCYTGLRFSDLKNLTWKNIVEASGRTWIRYrrkKTGKPVTVPLLPVareILEKYKDDRSEGKLFPV-------L 93

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1007022593 230 LSKSVSDIIGRTMKRAGVR--GTPHCLRHWYATTLLDNGTDIRVVQELLRHKSIGTTQIYTKVPE 292
Cdd:cd01185    94 SNQKINRYLKEIAKIAGIDkhLTFHVARHTFATLLLLKGVDIETISKLLGHSSIKTTQIYAKIVD 158
xerC PRK01287
site-specific tyrosine recombinase XerC; Reviewed
 39-295 4.95e-20

site-specific tyrosine recombinase XerC; Reviewed


Pssm-ID: 234935 [Multi-domain]  Cd Length: 358  Bit Score: 89.42  E-value: 4.95e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1007022593  39 LDDWEIWQTAQRLSRRTID---ERLRVIHLLHIETGL-QPMHIRAAELVRW--------IADHEEWSDSTACTYTSYLSA 106
Cdd:PRK01287   25 LERFLAWLQERNWSERTLKvytEHLYPFILWCEERGLyYAADVTLPVLERYqrylygyrKANGEPLSTRTQRTQLSPLRV 104

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1007022593 107 WFKWLQLTDRREDNPMVKVGAPRLPDRQPRPI-SDAD---VVNLLQTRMWASTRRMILLALL--AGLRVHEIAKIRGEDI 180
Cdd:PRK01287  105 WFRWLLKRHHILYNPAEDLELPKEEKRLPRQIlSEAEteqVLASPDLTTLQGLRDRALLELLwsTGIRRGELARLDLYDV 184

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1007022593 181 DLSAHVLWVK-GKGKRLRSVPL---------------HPLLIEMasemPAAGWWFPmrGHEGEHILSKSVSDIIGRTMKR 244
Cdd:PRK01287  185 DASRGVVTVRqGKGNKDRVVPVgeralawlqrylqdvRPQLAVR----PDSGALFV--AMDGDGLARNTLTNMVGRYIRA 258

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1007022593 245 AGVR--GTPHCLRHWYATTLLDNGTDIRVVQELLRHKSIGTTQIYTKVPEGRL 295
Cdd:PRK01287  259 AGIEkaGACHLFRHAMATQMLENGADTRHIQAILGHAKLETTQIYTRVSIGHL 311
INT_RitA_C_like cd01188
C-terminal catalytic domain of recombinase RitA, a component of the recombinase trio; ...
 150-290 3.20e-19

C-terminal catalytic domain of recombinase RitA, a component of the recombinase trio; Recombinases RitA (also known as pAE1), RitB, and RitC are encoded by three adjacent and overlapping genes. Collectively they are known as the Recombinase in Trio (RIT). This RitA family includes various bacterial integrases and integrases from the deletion-prone region of plasmid pAE1 of Alcaligenes eutrophus H1. All three integrases contain a catalytic motif, suggesting that they are all active enzymes. However, their specific roles are not fully understood. All three families belong to the superfamily of DNA breaking-rejoining enzymes, which share the same fold in their catalytic domain and the overall reaction mechanism. The catalytic domain contains six conserved active site residues. Their overall reaction mechanism is essentially identical and involves cleavage of a single strand of a DNA duplex by nucleophilic attack of a conserved tyrosine to give a 3' phosphotyrosyl protein-DNA adduct. In the second rejoining step, a terminal 5' hydroxyl attacks the covalent adduct to release the enzyme and generate duplex DNA.


Pssm-ID: 271188 [Multi-domain]  Cd Length: 179  Bit Score: 83.45  E-value: 3.20e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1007022593 150 RMWASTRR----------MILLALLAGLRVHEIAKIRGEDIDLSAHVLWVKG-KGKRLRSVPL---------------HP 203
Cdd:cd01188     7 RLLAAIDRltpvglrdyaILLLLARLGLRAGDVAGLRLDDIDWRSGTITVRQkKTGRPVELPLtepvgealadylrdgRP 86

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1007022593 204 LLiemasempAAGWWFP--MRGHEGeHILSKSVSDIIGRTMKRAGV---RGTPHCLRHWYATTLLDNGTDIRVVQELLRH 278
Cdd:cd01188    87 RT--------DSREVFLraRAPYRP-LSSTSQISSIVRRYLRKAGIepsHRGTHSLRHSLATRMLRAGTSLKVIADLLGH 157

                         170
                  ....*....|..
gi 1007022593 279 KSIGTTQIYTKV 290
Cdd:cd01188   158 RSIETTAIYAKI 169
INT_ICEBs1_C_like cd01189
C-terminal catalytic domain of integrases from bacterial phages and conjugate transposons; ...
 158-289 3.70e-16

C-terminal catalytic domain of integrases from bacterial phages and conjugate transposons; This family of tyrosine based site-specific integrases is has origins in bacterial phages and conjugate transposons. One member is the integrase from Bacillus subtilis conjugative transposon ICEBs1. ICEBs1 can be excised and transfered to various recipients in response to DNA damage or high concentrations of potential mating partners. The family belongs to the superfamily of DNA breaking-rejoining enzymes, which share the same fold in their catalytic domain and the overall reaction mechanism. The catalytic domain contains six conserved active site residues. Their overall reaction mechanism involves cleavage of a single strand of a DNA duplex by nucleophilic attack of a conserved tyrosine to give a 3' phosphotyrosyl protein-DNA adduct. In the second rejoining step, a terminal 5' hydroxyl attacks the covalent adduct to release the enzyme and generate duplex DNA.


Pssm-ID: 271189 [Multi-domain]  Cd Length: 147  Bit Score: 74.13  E-value: 3.70e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1007022593 158 MILLALLAGLRVHEIAKIRGEDIDLSAHVL-------WVKGKGKRL---------RSVPLHPLLIEMASEMPAagwwfpm 221
Cdd:cd01189    21 LFLLALLTGLRRGELLALTWSDIDFENGTIrinrtlvRKKKGGYVIkppktkssiRTIPLPDELIELLKELKA------- 93

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1007022593 222 rghegehilsksvsdiIGRTMKRAGVRG-TPHCLRHWYATTLLDNGTDIRVVQELLRHKSIGTT-QIYTK 289
Cdd:cd01189    94 ----------------FKKLLKKAGLPRiTPHDLRHTFASLLLEAGVPLKVIAERLGHSDISTTlDVYAH 147
INT_Rci_Hp1_C cd00796
Shufflon-specific DNA recombinase Rci and Bacteriophage Hp1_like integrase, C-terminal ...
 141-288 5.69e-16

Shufflon-specific DNA recombinase Rci and Bacteriophage Hp1_like integrase, C-terminal catalytic domain; Rci protein is a tyrosine recombinase specifically involved in Shufflon type of DNA rearrangement in bacteria. The shufflon of plasmid R64 consists of four invertible DNA segments which are separated and flanked by seven 19-bp repeat sequences. RCI recombinase facilitates the site-specific recombination between any inverted repeats results in an inversion of the DNA segment(s) either independently or in groups. HP1 integrase promotes site-specific recombination of the HP1 genome into that of Haemophilus influenza. Bacteriophage Hp1_like integrases are tyrosine based site specific recombinases. They belong to the superfamily of DNA breaking-rejoining enzymes, which share the same fold in their catalytic domain and the overall reaction mechanism. The catalytic domain contains six conserved active site residues. Their overall reaction mechanism is essentially identical and involves cleavage of a single strand of a DNA duplex by nucleophilic attack of a conserved tyrosine to give a 3' phosphotyrosyl protein-DNA adduct. In the second rejoining step, a terminal 5' hydroxyl attacks the covalent adduct to release the enzyme and generate duplex DNA.


Pssm-ID: 271177 [Multi-domain]  Cd Length: 162  Bit Score: 74.29  E-value: 5.69e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1007022593 141 ADVVNLLQTRMWASTRRMILLALLAGLRVHEIAKIRGEDIDLSAHVLWVKG-KGKRLRSVPLHPLLIEMASEMPAA-GWW 218
Cdd:cd00796    11 ARLLAALEESTNPHLRLIVLLALYTGARRGEILSLRWDDIDLEVGLIVLPEtKNGKPRTVPLSDEAIAILKELKRKrGKD 90

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1007022593 219 FPMRGHEGEHILSKSVSDIIGRTMKRAGVRG-TPHCLRHWYATTLLDNGTDIRVVQELLRHKSIGTTQIYT 288
Cdd:cd00796    91 GFFVDGRFFGIPIASLRRAFKKARKRAGLEDlRFHDLRHTFASRLVQAGVPIKTVAKILGHSSIKMTMRYA 161
integrase_gron TIGR02249
integron integrase; Members of this family are integrases associated with integrons (and ...
 122-290 3.83e-15

integron integrase; Members of this family are integrases associated with integrons (and super-integrons), which are systems for incorporating and expressing cassettes of laterally transferred DNA. Incorporation occurs at an attI site. A super-integron, as in Vibrio sp., may include over 100 cassettes. This family belongs to the phage integrase family (pfam00589) that also includes recombinases XerC (TIGR02224) and XerD (TIGR02225), which are bacterial housekeeping proteins. Within this family of integron integrases, some are designated by class, e.g. IntI4, a class 4 integron integrase from Vibrio cholerae N16961. [DNA metabolism, DNA replication, recombination, and repair, Mobile and extrachromosomal element functions, Other]


Pssm-ID: 131303 [Multi-domain]  Cd Length: 315  Bit Score: 74.74  E-value: 3.83e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1007022593 122 MVKVGAPRLPDRQPRPISDADVVNLLQTrmwASTRRMILLALL--AGLRVHEIAKIRGEDIDLS--AHVLWvKGKGKRLR 197
Cdd:TIGR02249  86 MERFVRAKRPRKLPVVLTREEVRRLLEH---LEGKYRLIAKLLygSGMRLMECLRLRIQDIDFDygEIRIR-QGKGGKDR 161

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1007022593 198 SVPLHPLLIE-----------------------------MASEMPAA----GWWF----------PMRGHEGEHILSKSV 234
Cdd:TIGR02249 162 TVTLPKELIPplreqielarayheadlaegyggvylphaLARKYPNApkewGWQYlfpshrlsrdPESGVIRRHHINETT 241

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1007022593 235 sdiIGRTMKRAGVRG------TPHCLRHWYATTLLDNGTDIRVVQELLRHKSIGTTQIYTKV 290
Cdd:TIGR02249 242 ---IQRAVRRAVERAgiekpvTCHTLRHSFATHLLESGADIRTVQELLGHSDVKTTQIYTHV 300
FimB COG0582
Integrase/recombinase, includes phage integrase [Replication, recombination and repair, ...
 77-285 6.95e-15

Integrase/recombinase, includes phage integrase [Replication, recombination and repair, Mobilome: prophages, transposons];


Pssm-ID: 440347 [Multi-domain]  Cd Length: 391  Bit Score: 74.69  E-value: 6.95e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1007022593  77 IRAAELVRWIADHEE-WSDSTACTYTSYLSAWFKWLQLTDRREDNPM--VKVGAPRLPDRQPRPISDADVVNLLQT---- 149
Cdd:COG0582   142 ITPPDLLAVLRPIEArGAPETARRVRQRLRQVFRYAVARGLIERNPAadLKGALPKPKVKHHPALTPEELPELLRAlday 221

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1007022593 150 RMWASTRRMILLALLAGLRVHEIAKIRGEDIDLSAHVLWV---KGKGKRLRSVPLHPLLIEMASEMPA----AGWWFPMR 222
Cdd:COG0582   222 RGSPVTRLALRLLLLTGVRPGELRGARWSEIDLEAALWTIpaeRMKTRRPHIVPLSRQALEILKELKPltgdSEYVFPSR 301

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1007022593 223 GHEGEHILSKSVSdiigRTMKRAGVRG-TPHCLRHWYATTLLDNGTDIRVVQELLRHKSIGTTQ 285
Cdd:COG0582   302 RGPKKPMSENTLN----KALRRMGYGRfTPHGFRHTASTLLNEAGFPPDVIERQLAHKDGNKVR 361
INT_C_like_4 cd01194
Uncharacterized site-specific tyrosine recombinase, C-terminal catalytic domain; Tyrosine ...
 156-287 8.01e-15

Uncharacterized site-specific tyrosine recombinase, C-terminal catalytic domain; Tyrosine recombinase (integrase) belongs to a DNA breaking-rejoining enzyme superfamily. The catalytic domain contains six conserved active site residues. The recombination reaction involves cleavage of a single strand of a DNA duplex by nucleophilic attack of a conserved tyrosine to give a 3' phosphotyrosyl protein-DNA adduct. In the second rejoining step, a terminal 5' hydroxyl attacks the covalent adduct to release the enzyme and generate duplex DNA. Many DNA breaking-rejoining enzymes also have N-terminal domains, which show little sequence or structure similarity.


Pssm-ID: 271194 [Multi-domain]  Cd Length: 174  Bit Score: 71.25  E-value: 8.01e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1007022593 156 RRMILLALLAGLRVHEIAKIRGEDID--LSAHVLWVKGKGKRLRS--VPLHPLLIE-------MASEMPAAGWWFPMRGH 224
Cdd:cd01194    25 RAIISLMVTEGLRTVEIVRADVGDLRqeGEGTILYVQGKGKTSKDdfVYLRPDVLKalqaylkARGKLDFEEPLFTSLSN 104

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1007022593 225 --EGEHILSKSVSDIIGRTMKRAGV---RGTPHCLRHWYATTLLDNGTDIRVVQELLRHKSIGTTQIY 287
Cdd:cd01194   105 nsKGQRLTTRSIRRIIKKYLRKAGLdddRLTAHSLRHTAGTLALKAGKSLREVQQLLRHSDPNTTMIY 172
INT_C_like_1 cd01184
Uncharacterized site-specific tyrosine recombinase, C-terminal catalytic domain; Tyrosine ...
 158-289 1.57e-14

Uncharacterized site-specific tyrosine recombinase, C-terminal catalytic domain; Tyrosine recombinase (integrase) belongs to a DNA breaking-rejoining enzyme superfamily. The catalytic domain containing six conserved active site residues. The recombination reaction involves cleavage of a single strand of a DNA duplex by nucleophilic attack of a conserved tyrosine to give a 3' phosphotyrosyl protein-DNA adduct. In the second rejoining step, a terminal 5' hydroxyl attacks the covalent adduct to release the enzyme and generate duplex DNA. Many DNA breaking-rejoining enzymes also have N-terminal domains, which show little sequence or structure similarity.


Pssm-ID: 271184 [Multi-domain]  Cd Length: 180  Bit Score: 70.41  E-value: 1.57e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1007022593 158 MILLALLAGLRVHEIAKIRGEDIDLSAHVlWV-----KGKGKRL------RSVPLHPLLIEM-----ASEMPAAG--WWF 219
Cdd:cd01184    28 LPLIGLYTGARLNEICQLRVDDIKEEDGI-WCidindDAEGRRLktkasrRLVPIHPRLIELgfldyVEALRADGklFLF 106

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1007022593 220 PMRGHEGEHiLSKSVSDIIGRTMKRAGVRGTP----HCLRHWYATTLLDNGTDIRVVQELLRHK-SIGTTQIYTK 289
Cdd:cd01184   107 PEKRDKDGK-YSKAASKWFNRLLRKLGIKDDErksfHSFRHTFITALKRAGVPEELIAQIVGHSrGGVTHDTYGK 180
INT_RitC_C_like cd01182
C-terminal catalytic domain of recombinase RitC, a component of the recombinase trio; ...
 149-290 2.63e-14

C-terminal catalytic domain of recombinase RitC, a component of the recombinase trio; Recombinases belonging to the RitA (also known as pAE1 due to its presence in the deletion prone region of plasmid pAE1 of Alcaligenes eutrophus H1), RitB, and RitC families are associated in a complex referred to as a Recombinase in Trio (RIT) element. These RIT elements consist of three adjacent and unidirectional overlapping genes, one from each family (ritABC in order of transcription). All three integrases contain a catalytic motif, suggesting that they are all active enzymes. However, their specific roles are not yet fully understood. All three families belong to the superfamily of DNA breaking-rejoining enzymes, which share the same fold in their catalytic domain and the overall reaction mechanism.


Pssm-ID: 271183 [Multi-domain]  Cd Length: 186  Bit Score: 70.00  E-value: 2.63e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1007022593 149 TRMWASTRRMILLALL--AGLRVHEIAKIRGEDIDLS--AHVLwVKGKGKRLRSVPLHP--------LLIEMASEMPAAG 216
Cdd:cd01182    15 RNTSLGRRDHALLLLLydTGARVQELADLTIRDLRLDdpATVR-LHGKGRKERTVPLWKetvaalkaYLQEFHLTPDPKQ 93

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1007022593 217 WW--FPMRGHEG------EHILSKSVSDIIGR--TMKRagvRGTPHCLRHWYATTLLDNGTDIRVVQELLRHKSIGTTQI 286
Cdd:cd01182    94 LFplFPNRRGQPltrdgvAYILNKYVALASNRcpSLPK---RITPHTLRHTKAMHLLQAGVDLTVIRDWLGHESVETTQI 170


                  ....
gi 1007022593 287 YTKV 290
Cdd:cd01182   171 YAEA 174
INT_tnpA_C_Tn554 cd01186
Putative Transposase A from transposon Tn554, C-terminal catalytic domain; This family ...
 156-284 4.12e-14

Putative Transposase A from transposon Tn554, C-terminal catalytic domain; This family includes putative Transposase A from transposon Tn554. It belongs to a DNA breaking-rejoining enzyme superfamily. The catalytic domain contains six conserved active site residues. The recombination reaction involves cleavage of a single strand of a DNA duplex by nucleophilic attack of a conserved tyrosine to give a 3' phosphotyrosyl protein-DNA adduct. In the second rejoining step, a terminal 5' hydroxyl attacks the covalent adduct to release the enzyme and generate duplex DNA. Many DNA breaking-rejoining enzymes also have N-terminal domains, which show little sequence or structure similarity.


Pssm-ID: 271186 [Multi-domain]  Cd Length: 184  Bit Score: 69.37  E-value: 4.12e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1007022593 156 RRMILLALLA--GLRVHEIAKIRGEDIDLSAHVLWVKGKG----------KRLRSVPLHPLLIEMASEMPAAGWWFP--- 220
Cdd:cd01186    18 RDKFLLALLYetGLRIGEALGLRIEDIDMADNQIELVPREdntnearaksMRERRIPVSQDLIDLYADYLTYIYCEEaef 97

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1007022593 221 --------MRGHEGEHILSKSVSDIIGRTMKRAGVRGTPHCLRHWYATTLLDNGTDIRVVQELLRHKSIGTT 284
Cdd:cd01186    98 sitvfvnvKGGNQGKAMNYSDVYDLVRRLKKRTGIDFTPHMFRHTHATALIRAGWSIEVVARRLGHAHVQTT 169
xerS PRK05084
site-specific tyrosine recombinase XerS; Reviewed
 156-303 3.74e-13

site-specific tyrosine recombinase XerS; Reviewed


Pssm-ID: 235339 [Multi-domain]  Cd Length: 357  Bit Score: 69.18  E-value: 3.74e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1007022593 156 RRMILLALL--AGLRVHEIAKIRGEDIDLSAHVLWVKGKGKRLRSVPL----HPLLIE---------MASEMPAAgwWFP 220
Cdd:PRK05084  196 RDLAIIALIlgSGLRVSELVNLDLSDLNLKQMTIDVTRKGGKRDSVNIapfaLPYLEEylkirasryKAEKQEKA--LFL 273

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1007022593 221 MRGHEGEHILSK-SVSDIIGRTMKRAGVRGTPHCLRHWYATTLLDNGTDIRVVQELLRHKSIGTTQIYTKVPEGRLHDAI 299
Cdd:PRK05084  274 TKYRGKPNRISArAIEKMVAKYSEAFGVRLTPHKLRHTLATRLYDATKDQVLVADQLGHTSTETTDLYTHIVNDEQKEAL 353


                  ....
gi 1007022593 300 TSLD 303
Cdd:PRK05084  354 DRLE 357
INT_C_like_5 cd01195
Uncharacterized site-specific tyrosine recombinase, C-terminal catalytic domain; Tyrosine ...
 148-287 9.95e-12

Uncharacterized site-specific tyrosine recombinase, C-terminal catalytic domain; Tyrosine recombinase (integrase) belongs to a DNA breaking-rejoining enzyme superfamily. The catalytic domain contains six conserved active site residues. The recombination reaction involves cleavage of a single strand of a DNA duplex by nucleophilic attack of a conserved tyrosine to give a 3' phosphotyrosyl protein-DNA adduct. In the second rejoining step, a terminal 5' hydroxyl attacks the covalent adduct to release the enzyme and generate duplex DNA. Many DNA breaking-rejoining enzymes also have N-terminal domains, which show little sequence or structure similarity.


Pssm-ID: 271195 [Multi-domain]  Cd Length: 170  Bit Score: 62.49  E-value: 9.95e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1007022593 148 QTRMWASTRRMILLALLAGLRVHEIAKIRGEDIDLSAHVLWVKGKGKRLRSVPLHPlliemASEMPAAGWWFPMRGHE-- 225
Cdd:cd01195    15 HTAKGKRDEALVRLLLDNALRRSEAVALDVEDLEKEHRRLRILGKGKKQREVVTLP-----PTTREALAAWLAARGEAeg 89

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1007022593 226 ----------GEHILS-KSVSDIIGRTMKRAGV--RGTPHCLRHWYATTLLDNGTD-IRVVQELLRHKSIGTTQIY 287
Cdd:cd01195    90 plfvsldrasRGRRLSpQAVYRIVRRLAERIGLgkRLSPHGLRHSAITLALDAGAGlIRKVQDFSRHADLRTLQVY 165
INT_P4_C cd00801
Bacteriophage P4 integrase, C-terminal catalytic domain; P4-like integrases are found in ...
 146-279 2.07e-11

Bacteriophage P4 integrase, C-terminal catalytic domain; P4-like integrases are found in temperate bacteriophages, integrative plasmids, pathogenicity and symbiosis islands, and other mobile genetic elements. The P4 integrase mediates integrative and excisive site-specific recombination between two sites, called attachment sites, located on the phage genome and the bacterial chromosome. The phage attachment site is often found adjacent to the integrase gene, while the host attachment sites are typically situated near tRNA genes. This family belongs to the superfamily of DNA breaking-rejoining enzymes, which share the same fold in their catalytic domain and the overall reaction mechanism. The catalytic domain contains six conserved active site residues. Their overall reaction mechanism involves cleavage of a single strand of a DNA duplex by nucleophilic attack of a conserved tyrosine to give a 3' phosphotyrosyl protein-DNA adduct. In the second rejoining step, a terminal 5' hydroxyl attacks the covalent adduct to release the enzyme and generate duplex DNA.


Pssm-ID: 271182 [Multi-domain]  Cd Length: 180  Bit Score: 61.90  E-value: 2.07e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1007022593 146 LLQTRMWASTRRMILLALLAGLRVHEIAKIRGEDIDLSAHVlWV----KGKGKRLRSVPLHPLLIEMASEMPA----AGW 217
Cdd:cd00801    12 LDTANLSPPTKLALRLLLLTGQRIGELARARWSEIDLEEKT-WTipaeRTKNKRPHRVPLSDQALEILEELKEftgdSGY 90

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1007022593 218 WFPMRGHEGEHILSKSVSDIIGRTMKRAGVRgTPHCLRHWYATTLLDNGTDIRVVQELLRHK 279
Cdd:cd00801    91 LFPSRRKKKKPISENTINKALKRLGYKGKEF-TPHDLRRTFSTLLNELGIDPEVIERLLNHV 151
PRK09870 PRK09870
tyrosine recombinase; Provisional
 153-296 2.64e-11

tyrosine recombinase; Provisional


Pssm-ID: 182125  Cd Length: 200  Bit Score: 61.88  E-value: 2.64e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1007022593 153 ASTRRMILLALLAGLRVHEIAKIRGEDIDLSAHVLWVKGKGKRLRSVplHPLL------------IEMASEMPAAGWWFP 220
Cdd:PRK09870   32 ARNYCLTLLCFIHGFRASEICRLRISDIDLKAKCIYIHRLKKGFSTT--HPLLnkeiqalknwlsIRTSYPHAESEWVFL 109

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1007022593 221 MRghEGEHILSKSVSDIIGRTMKRAG--VRGTPHCLRHWYATTLLDNGTDIRVVQELLRHKSIGTTQIYTKVPEGRLH 296
Cdd:PRK09870  110 SR--KGNPLSRQQFYHIISTSGGNAGlsLEIHPHMLRHSCGFALANMGIDTRLIQDYLGHRNIRHTVWYTASNAGRFY 185
PRK15417 PRK15417
integron integrase;
82-290 7.06e-11

integron integrase;


Pssm-ID: 185315 [Multi-domain]  Cd Length: 337  Bit Score: 62.37  E-value: 7.06e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1007022593  82 LVRWIADHEEWSDSTACT--------YTSYLSAWFKWLQltdrrednpmvKVGAPRLPDRQPRPISDADVVNLLQTrMWA 153
Cdd:PRK15417   64 FLSWLANERKVSVSTHRQalaallffYGKVLCTDLPWLQ-----------EIGRPRPSRRLPVVLTPDEVVRILGF-LEG 131

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1007022593 154 STRRMILLALLAGLRVHEIAKIRGEDIDLSAHVLWVK-GKGKRLRSV----PLHPLLIEMASEmpAAGWW---------- 218
Cdd:PRK15417  132 EHRLFAQLLYGTGMRISEGLQLRVKDLDFDHGTIIVReGKGSKDRALmlpeSLAPSLREQLSR--ARAWWlkdqaegrsg 209

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1007022593 219 ----------FPMRGH----------------------EGEHILSKSVSDIIGRTMKRAGVR--GTPHCLRHWYATTLLD 264
Cdd:PRK15417  210 valpdalerkYPRAGHswpwfwvfaqhthstdprsgvvRRHHMYDQTFQRAFKRAVEQAGITkpATPHTLRHSFATALLR 289

                         250       260
                  ....*....|....*....|....*.
gi 1007022593 265 NGTDIRVVQELLRHKSIGTTQIYTKV 290
Cdd:PRK15417  290 SGYDIRTVQDLLGHSDVSTTMIYTHV 315
int PHA02601
integrase; Provisional
 160-307 9.22e-11

integrase; Provisional


Pssm-ID: 222904 [Multi-domain]  Cd Length: 333  Bit Score: 62.05  E-value: 9.22e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1007022593 160 LLALLAGLRVHEIAKIRGEDIdLSAHVLWVKGKGKRLRSVPLHPLLIEMASEmpAAGWWFPMRGHEGEhilsksvsdiig 239
Cdd:PHA02601  198 KICLATGARWSEAETLKRSQI-SPYKITFVKTKGKKNRTVPISEELYKMLPK--RRGRLFKDAYESFE------------ 262

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1007022593 240 RTMKRAGVRGTP----HCLRHWYATTLLDNGTDIRVVQELLRHKSIGTTQIYTKVPEGRLHDAITsLDPWRA 307
Cdd:PHA02601  263 RAVKRAGIDLPEgqatHVLRHTFASHFMMNGGNILVLQRILGHATIEMTMAYAHFAPDHLEDAVS-LNPLSN 333
INT_FimBE_like cd01197
FimB and FimE and related proteins, integrase/recombinases; This CD includes proteins similar ...
 133-288 3.17e-10

FimB and FimE and related proteins, integrase/recombinases; This CD includes proteins similar to E.coli FimE and FimB and Proteus mirabilis MrpI. FimB and FimE are the regulatory proteins during expression of type 1 fimbriae in Escherichia coli. The fimB and fimE proteins direct the phase switch into the 'on' and 'off' position. MrpI is the regulatory protein of proteus mirabilis fimbriae expression. This family belongs to the integrase/recombinase superfamily.


Pssm-ID: 271197 [Multi-domain]  Cd Length: 181  Bit Score: 58.29  E-value: 3.17e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1007022593 133 RQPRPISDADVVNLLQTRMWAST----RRMILLALLAGLRVHEIAKIRGEDIDLSAHVLWVKGKGKRLRSVplHPL---- 204
Cdd:cd01197     2 KQRKYLTGKEVQALLQAACRGRTpardYCLLLLAFRHGFRVSELCDLHLSDVDLESRRLHIRRLKNGFSTT--HPLrfde 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1007022593 205 -------LIEMASEMPAAGWWFPMrGHEGEHILSKSVSDIIGRTMKRAGV--RGTPHCLRHWYATTLLDNGTDIRVVQEL 275
Cdd:cd01197    80 realeawLKERANWKGADTDWIFL-SRRGGPLSRQQAYRIIRDLGKEAGTvtQTHPHMLRHACGYALADRGADTRLIQDY 158

                         170
                  ....*....|...
gi 1007022593 276 LRHKSIGTTQIYT 288
Cdd:cd01197   159 LGHRNIRHTVIYT 171
INT_RitB_C_like cd00797
C-terminal catalytic domain of recombinase RitB, a component of the recombinase trio; ...
 151-292 2.16e-08

C-terminal catalytic domain of recombinase RitB, a component of the recombinase trio; Recombinases belonging to the RitA (also known as pAE1 due to its presence in the deletion prone region of plasmid pAE1 of Alcaligenes eutrophus H1), RitB, and RitC families are associated in a complex referred to as a Recombinase in Trio (RIT) element. These RIT elements consist of three adjacent and unidirectional overlapping genes, one from each family (ritABC in order of transcription). All three integrases contain a catalytic motif, suggesting that they are all active enzymes. However, their specific roles are not yet fully understood. All three families belong to the superfamily of DNA breaking-rejoining enzymes, which share the same fold in their catalytic domain and the overall reaction mechanism.


Pssm-ID: 271178 [Multi-domain]  Cd Length: 198  Bit Score: 53.46  E-value: 2.16e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1007022593 151 MWAST-RRMILLALLAGLRVHEIAKIRGEDIDLSAHVLWVK-GKGKRLRSVPLHPLLIEM----------ASEMPAAGWW 218
Cdd:cd00797    22 LRPLTyATLFGLLYATGLRVGEALRLRLEDVDLDSGILTIRqTKFGKSRLVPLHPSTVGAlrdylarrdrLLPSPSSSYF 101

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1007022593 219 FPmrGHEGEHILSKSVSDIIGRTMKRAGVRGTP-------HCLRHWYATTLL----DNGTDIR----VVQELLRHKSIGT 283
Cdd:cd00797   102 FV--SQQGGRLTGGGVYRVFRRLLRRIGLRGAGdgrgprlHDLRHTFAVNRLtrwyREGADVErklpVLSTYLGHVNVTD 179

                         170
                  ....*....|
gi 1007022593 284 TQIY-TKVPE 292
Cdd:cd00797   180 TYWYlTATPE 189
INT_C_like_3 cd01192
Uncharacterized site-specific tyrosine recombinase, C-terminal catalytic domain; Tyrosine ...
 137-287 1.27e-07

Uncharacterized site-specific tyrosine recombinase, C-terminal catalytic domain; Tyrosine recombinase (integrase) belongs to a DNA breaking-rejoining enzyme superfamily. The catalytic domain contains six conserved active site residues. The recombination reaction involves cleavage of a single strand of a DNA duplex by nucleophilic attack of a conserved tyrosine to give a 3' phosphotyrosyl protein-DNA adduct. In the second rejoining step, a terminal 5' hydroxyl attacks the covalent adduct to release the enzyme and generate duplex DNA. Many DNA breaking-rejoining enzymes also have N-terminal domains, which show little sequence or structure similarity.


Pssm-ID: 271192 [Multi-domain]  Cd Length: 178  Bit Score: 50.75  E-value: 1.27e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1007022593 137 PISDADVVNLLQTRMWASTRRM---ILLALLAGLRVHEIAKIRGEDIDLSAHvLWVKGK--GKRlRSVPLHPLL------ 205
Cdd:cd01192     5 PIKDKKLIKEIKLYLKKANPRNyllFIVGINTGLRISDLLSLKVEDVTNKDK-LSIKEQktGKQ-KTFPLNPTLvkalke 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1007022593 206 -IEMASEMPAAGWWFPMRGHEGEHILSKSVSDI---IGRTMKRAGVRGTpHCLRHWYATTLLDNGTDIRVVQELLRHKSI 281
Cdd:cd01192    83 yIDDLDLKRNDYLFKSLKQGPEKPISRKQAYKIlkkAADDLGLNYNIGT-HSLRKTFGYHVYKQGKDIELLMKLLNHSSP 161


                  ....*.
gi 1007022593 282 GTTQIY 287
Cdd:cd01192   162 SITLRY 167
INT_C_like_2 cd01191
Uncharacterized site-specific tyrosine recombinase, C-terminal catalytic domain; Tyrosine ...
 166-287 3.65e-06

Uncharacterized site-specific tyrosine recombinase, C-terminal catalytic domain; Tyrosine recombinase (integrase) belongs to a DNA breaking-rejoining enzyme superfamily. The catalytic domain contains six conserved active site residues. The recombination reaction involves cleavage of a single strand of a DNA duplex by nucleophilic attack of a conserved tyrosine to give a 3' phosphotyrosyl protein-DNA adduct. In the second rejoining step, a terminal 5' hydroxyl attacks the covalent adduct to release the enzyme and generate duplex DNA. Many DNA breaking-rejoining enzymes also have N-terminal domains, which show little sequence or structure similarity.


Pssm-ID: 271191  Cd Length: 176  Bit Score: 46.65  E-value: 3.65e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1007022593 166 GLRVHEIAKIRGEDIDLSAHVLWVKGkGKrLRSVPLHPLLIEMASEmpaagwWFPMRGHE---------GEHILSKSVSD 236
Cdd:cd01191    33 GARVSELIKIKVEHVELGYFDIYSKG-GK-LRRLYIPKKLRNEALE------WLKSTNRKsgyiflnrfGERITTRGIAQ 104

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1007022593 237 IIGRTMKRAGVRGT---PHCLRHWYATTLLDNGTDIRVVQELLRHKSIGTTQIY 287
Cdd:cd01191   105 QLKNYARKYGLNPKvvyPHSFRHRFAKNFLEKYNDIALLADLMGHESIETTRIY 158
INT_Cre_C cd00799
C-terminal catalytic domain of Cre recombinase (also called integrase); Cre-like recombinases ...
 226-302 6.23e-05

C-terminal catalytic domain of Cre recombinase (also called integrase); Cre-like recombinases are tyrosine based site specific recombinases. They belong to the superfamily of DNA breaking-rejoining enzymes, which share the same fold in their catalytic domain and the overall reaction mechanism. The bacteriophage P1 Cre recombinase maintains the circular phage replicon in a monomeric state by catalyzing a site-specific recombination between two loxP sites. The catalytic core domain of Cre recombinase is linked to a more divergent helical N-terminal domain, which interacts primarily with the DNA major groove proximal to the crossover region.


Pssm-ID: 271180  Cd Length: 188  Bit Score: 43.06  E-value: 6.23e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1007022593 226 GEHILSKSVSDIIGRTMKRAGVRG---TPHCLRHWYATTLLDNGTDIRVVQELLRHKSIGTTQIYTKVPEGRLHDAITSL 302
Cdd:cd00799   109 TTRLSDRSVARIVKRRAALAGLDPgdfSGHSLRRGFATEAARAGASLPEIMAQGGHKSVATVMRYIREADRFKDNAAAKL 188
INT_StrepXerD_C_like cd01190
Putative XerD in Streptococcus pneumonia and similar proteins, C-terminal catalytic domain; ...
 141-288 7.61e-05

Putative XerD in Streptococcus pneumonia and similar proteins, C-terminal catalytic domain; This family includes a putative XerD recombinase in Streptococcus pneumonia and similar tyrosine recombinases. However, the members of this family contain unusual active site motifs from the XerD from Escherichia coli. E. coli XerD and homologous enzymes show four conserved amino acids R-H-R-H that are spaced along the C-terminal domain. The putative S. pneumoniae XerD contains three unique replacements at the conserved positions resulting in L-Q-R-L. Severe growth defects in a loss-of-function xerD mutant demonstrate an important in vivo function of the S. pneumoniae XerD protein. This family belongs to the superfamily of DNA breaking-rejoining enzymes, which share the same fold in their catalytic domain and the overall reaction mechanism. The catalytic domain contains six conserved active site residues. Their overall reaction mechanism involves cleavage of a single strand of a DNA duplex by nucleophilic attack of a conserved tyrosine to give a 3' phosphotyrosyl protein-DNA adduct. In the second rejoining step, a terminal 5' hydroxyl attacks the covalent adduct to release the enzyme and generate duplex DNA.


Pssm-ID: 271190  Cd Length: 150  Bit Score: 42.33  E-value: 7.61e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1007022593 141 ADVVNLLQT--RMWASTRRMILLALLAGLRVHEIAKIRGEDIDLSAHVLWV-KGKGKRLRSVPlHPLLIEMASEMPAAGW 217
Cdd:cd01190     3 PEILDLSSFyqGDFLKGQLIALLILELGLTPSEIANLKWADFDLDFQVLTIeKGGIKRVLPLP-KKLLPFLEQHIKADYL 81

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1007022593 218 WFPMRG-HEGEHILSKSVSDIIGRTMKrAGVrgTPHCLRHWYATTLLDNGTDIRVVQELLRHKSIGTTQIYT 288
Cdd:cd01190    82 EFDHEGkAYSRQWLFNQLKKFLNSIGL-SGL--TAQKLREQYILKQKEAGKSIYELAKLLGLKSPVTLEKYY 150
INT_Lambda_C cd00800
C-terminal catalytic domain of Lambda integrase, a tyrosine-based site-specific recombinase; ...
 156-290 7.94e-05

C-terminal catalytic domain of Lambda integrase, a tyrosine-based site-specific recombinase; Lambda-type integrases catalyze site-specific integration and excision of temperate bacteriophages and other mobile genetic elements to and from the bacterial host chromosome. They are tyrosine-based site-specific recombinase and belong to the superfamily of DNA breaking-rejoining enzymes, which share the same fold in their catalytic domain and the overall reaction mechanism. The phage lambda integrase can bridge two different and well-separated DNA sequences called arm- and core-sites. The C-terminal domain binds, cleaves and re-ligates DNA strands at the core-sites, while the N-terminal domain is largely responsible for high-affinity binding to the arm-type sites.


Pssm-ID: 271181 [Multi-domain]  Cd Length: 161  Bit Score: 42.33  E-value: 7.94e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1007022593 156 RRMILLALLAGLRVHEIAKIRGEDIDlSAHVLWVKGK-GKRLRsVPLHPLLIEMASEMPAAGWWFPM---RGHEGEHILS 231
Cdd:cd00800    15 RLAMELALLTGQRQGDLLRLKWSDIT-DGGLLVEQSKtGKKLL-IPWTPSLRALVDRIRALPRKRSEyliNSRKGGPLSY 92

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1007022593 232 KSVSDIIGRTMKRAGVRGTP-----HCLRHWYATTLLDNGTDiRVVQELLRHKSIGTTQIYTKV 290
Cdd:cd00800    93 DTLKSAWRRARKAAGLKGETegftfHDLRAKAATDYAEQGGS-TDAQALLGHKSDAMTERYTRK 155
PRK09871 PRK09871
tyrosine recombinase; Provisional
 158-288 1.09e-04

tyrosine recombinase; Provisional


Pssm-ID: 182126  Cd Length: 198  Bit Score: 42.66  E-value: 1.09e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1007022593 158 MILLALLAGLRVHEIAKIRGEDIDLSAHVLWVKgkgkRLRS--VPLHPLL------IEMASEMpAAGWWFPMR------G 223
Cdd:PRK09871   31 LILLAYRHGMRISELLDLHYQDLDLNEGRINIR----RLKNgfSTVHPLRfdereaVERWTQE-RANWKGADRtdaifiS 105

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1007022593 224 HEGEHILSKSVSDIIGRTMKRAGVRGT--PHCLRHWYATTLLDNGTDIRVVQELLRHKSIGTTQIYT 288
Cdd:PRK09871  106 RRGSRLSRQQAYRIIRDAGIEAGTVTQthPHMLRHACGYELAERGADTRLIQDYLGHRNIRHTVRYT 172
INT_tnpB_C_Tn554 cd01187
Putative Transposase B from transposon Tn554, C-terminal catalytic domain; This family ...
 157-287 1.45e-04

Putative Transposase B from transposon Tn554, C-terminal catalytic domain; This family includes putative Transposase B from transposon Tn554. It belongs to a DNA breaking-rejoining enzyme superfamily. The catalytic domain containing six conserved active site residues. The recombination reaction involves cleavage of a single strand of a DNA duplex by nucleophilic attack of a conserved tyrosine to give a 3' phosphotyrosyl protein-DNA adduct. In the second rejoining step, a terminal 5' hydroxyl attacks the covalent adduct to release the enzyme and generate duplex DNA. Many DNA breaking-rejoining enzymes also have N-terminal domains, which show little sequence or structure similarity.


Pssm-ID: 271187 [Multi-domain]  Cd Length: 142  Bit Score: 41.26  E-value: 1.45e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1007022593 157 RMILLALLAGLRVHEIAK-----IRGEDIDLSAHVLWVKG--KGKRLRSVPLHPLLIEMAsempaAGWwfpmRGHEGEHI 229
Cdd:cd01187    17 PVVQAAVFTGARASELATlkfgcLHAQTSDDGTFLYWLKWenKGGKQLDIPISKKVAELI-----KTI----NWTLNELS 87

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1007022593 230 LSKSVSDIIGRTMkragvRGTPHCLRHWYATTLLDNGTDIRVVQELLRHKSIGTTQIY 287
Cdd:cd01187    88 ELKNISDDHGERF-----RFHTHRFRHTVATRLANSGMGILVLQQLLGHSSPEMTLRY 140
INT_C_like_6 cd01196
Uncharacterized site-specific tyrosine recombinase, C-terminal catalytic domain; Tyrosine ...
 156-300 1.47e-03

Uncharacterized site-specific tyrosine recombinase, C-terminal catalytic domain; Tyrosine recombinase (integrase) belongs to a DNA breaking-rejoining enzyme superfamily. The catalytic domain contains six conserved active site residues. The recombination reaction involves cleavage of a single strand of a DNA duplex by nucleophilic attack of a conserved tyrosine to give a 3' phosphotyrosyl protein-DNA adduct. In the second rejoining step, a terminal 5' hydroxyl attacks the covalent adduct to release the enzyme and generate duplex DNA. Many DNA breaking-rejoining enzymes also have N-terminal domains, which show little sequence or structure similarity.


Pssm-ID: 271196  Cd Length: 183  Bit Score: 39.00  E-value: 1.47e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1007022593 156 RRMILLALLAGLRVHEIAKIRGEDIDLSAHVLWV--KGKGKRLRSVPLHPLLIEM------ASEM---PAAGWWFPMRGh 224
Cdd:cd01196    23 RALIALMVYSFARIGAVLAMRVEDVYDQGRRLWVrlAEKGGKQHEMPCHHDLEEYlrayleAAEIeedPKGPLFRTTRG- 101

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1007022593 225 eGEHILSKS------VSDIIGRTMKRAGV--RGTPHCLRHWYATTLLDNGTDIRVVQELLRHKSIGTTQIYTkvpegRLH 296
Cdd:cd01196   102 -GTRKLTHNpltqanAYRMVRRRAIAADIptAIGNHSFRATGITAYLKNGGTLEDAQNMANHASTRTTQLYD-----RRS 175


                  ....
gi 1007022593 297 DAIT 300
Cdd:cd01196   176 DKIT 179
xerD PRK02436
site-specific tyrosine recombinase XerD;
160-212 3.03e-03

site-specific tyrosine recombinase XerD;


Pssm-ID: 235038 [Multi-domain]  Cd Length: 245  Bit Score: 38.43  E-value: 3.03e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1007022593 160 LLALLA---GLRVHEIAKIRGEDIDLSAHVLWV-KGKGKRLRSVPlHPLLIEMASEM 212
Cdd:PRK02436  116 LIALLIlelGLTPSEIAGLKVADIDLDFQVLTIeKAGGKRVLTLP-EALLPFLEAIL 171
 
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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