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Conserved domains on  [gi|2038652870|emb|CAG5416322|]
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integrase/recombinase, phage integrase family protein [Streptococcus pneumoniae]

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];
46-319 2.36e-68

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


:

Pssm-ID: 443999 [Multi-domain]  Cd Length: 291  Bit Score: 215.24  E-value: 2.36e-68
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2038652870  46 LLQLFITAKQVE-GCSSKTIRYYQRTIENLFNAIKE----SVTQLTTDDLRSYLaNYQSEKDCSKANLDNIRRILSSFFA 120
Cdd:COG4974     6 LLEAFLEELKREkGLSPNTIKAYRRDLRRFLRFLEElgkiPLAEITPEDIRAYL-NYLRERGLSPSTINRYLAALRSFFR 84

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2038652870 121 WLEQEEYIIKNPIRRIKKIKTEQNVKETYTDEHLEIMRDNC-----ENLRDLAIIDLLASTGMRVGELVQLNRSDIDFEN 195
Cdd:COG4974    85 YAVREGLLEDNPAAKVKLPKKPRKLPRVLTEEEIEALLEALdtetpEGLRDRALLLLLYATGLRVSELLGLKWSDIDLDR 164

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2038652870 196 REC-VVFGKGKKERPVYFDARTKIHLRNYLNDRKD-SHPALFVTLVGKvqRLGIAGVEIRLRKLGDKLGIQK-VHPHKFR 272
Cdd:COG4974   165 GTIrVRRGKGGKERTVPLSPEALEALREYLEERRPrDSDYLFPTRRGR--PLSRRAIRKILKRLAKRAGIPKrVTPHSLR 242

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|....*..
gi 2038652870 273 RTLATKAIDKGMPIEQVQKLLGHSKIDTTLAYAMVNQNNVKHSHQKF 319
Cdd:COG4974   243 HTFATHLLEAGVDLRTVQELLGHSSISTTQIYTHVSDEELREAVEKL 289
 
Name Accession Description Interval E-value
XerD COG4974
Site-specific recombinase XerD [Replication, recombination and repair];
46-319 2.36e-68

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


Pssm-ID: 443999 [Multi-domain]  Cd Length: 291  Bit Score: 215.24  E-value: 2.36e-68
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2038652870  46 LLQLFITAKQVE-GCSSKTIRYYQRTIENLFNAIKE----SVTQLTTDDLRSYLaNYQSEKDCSKANLDNIRRILSSFFA 120
Cdd:COG4974     6 LLEAFLEELKREkGLSPNTIKAYRRDLRRFLRFLEElgkiPLAEITPEDIRAYL-NYLRERGLSPSTINRYLAALRSFFR 84

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2038652870 121 WLEQEEYIIKNPIRRIKKIKTEQNVKETYTDEHLEIMRDNC-----ENLRDLAIIDLLASTGMRVGELVQLNRSDIDFEN 195
Cdd:COG4974    85 YAVREGLLEDNPAAKVKLPKKPRKLPRVLTEEEIEALLEALdtetpEGLRDRALLLLLYATGLRVSELLGLKWSDIDLDR 164

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2038652870 196 REC-VVFGKGKKERPVYFDARTKIHLRNYLNDRKD-SHPALFVTLVGKvqRLGIAGVEIRLRKLGDKLGIQK-VHPHKFR 272
Cdd:COG4974   165 GTIrVRRGKGGKERTVPLSPEALEALREYLEERRPrDSDYLFPTRRGR--PLSRRAIRKILKRLAKRAGIPKrVTPHSLR 242

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|....*..
gi 2038652870 273 RTLATKAIDKGMPIEQVQKLLGHSKIDTTLAYAMVNQNNVKHSHQKF 319
Cdd:COG4974   243 HTFATHLLEAGVDLRTVQELLGHSSISTTQIYTHVSDEELREAVEKL 289
recomb_XerC TIGR02224
tyrosine recombinase XerC; The phage integrase family describes a number of recombinases with ...
 60-319 5.79e-50

tyrosine recombinase XerC; 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 XerC, one of two closely related chromosomal proteins along with XerD (TIGR02225). 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 homologs of XerC on other replicons, the chomosomal copy was preferred for building this model. This model does not detect all XerC, as some apparent XerC examples score in the gray zone between trusted (450) and noise (410) cutoffs, along with some XerD examples. XerC and XerD interact with cell division protein FtsK. [DNA metabolism, DNA replication, recombination, and repair]


Pssm-ID: 274042 [Multi-domain]  Cd Length: 295  Bit Score: 167.78  E-value: 5.79e-50
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2038652870  60 SSKTIRYYQRTIENLFNAIKE-----SVTQLTTDDLRSYLAnYQSEKDCSKANldnIRRILS---SFFAWLEQEEYIIKN 131
Cdd:TIGR02224  14 SPHTVRAYRRDLEAFLEFLEEegglaSLAEVTAADLRSFLA-ELHARGLSRRS---LARKLSalrSFYRFLLRRGLIDAN 89

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2038652870 132 PIRRIKKIKTE----QNVKETYTDEHLEIMRDNCE---NLRDLAIIDLLASTGMRVGELVQLNRSDIDFENRECVVFGKG 204
Cdd:TIGR02224  90 PAAGVRAPKQPkklpKFLSEDEMEALLDAPEEDDEdwlALRDRAILELLYSSGLRVSELVGLDLSDLDLDFGEVRVRGKG 169

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2038652870 205 KKERPVYFDARTKIHLRNYLNDR------KDSHPALFVTLVGKvqRLGIAGVEIRLRKLGDKLGI-QKVHPHKFRRTLAT 277
Cdd:TIGR02224 170 NKERIVPFGPYARDALQAYLEARrspllaSEGQDALFLNRRGG--RLTPRGVQYRLQQLRAKAGLpKHVHPHALRHSFAT 247

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|..
gi 2038652870 278 KAIDKGMPIEQVQKLLGHSKIDTTLAYAMVNQNNVKHSHQKF 319
Cdd:TIGR02224 248 HLLNNGADLRAVQELLGHASLSTTQIYTHVDFQHLAKVYDQA 289
xerC PRK00236
site-specific tyrosine recombinase XerC; Reviewed
 46-304 2.01e-49

site-specific tyrosine recombinase XerC; Reviewed


Pssm-ID: 234698 [Multi-domain]  Cd Length: 297  Bit Score: 166.48  E-value: 2.01e-49
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2038652870  46 LLQLFITAKQVE-GCSSKTIRYYQRTIENLFNAIKE----SVTQLTTDDLRSYLAnYQSEKDCSKANLDniRRI--LSSF 118
Cdd:PRK00236    9 ALEAFLEYLRVErGLSPHTLRAYRRDLRAFLAFLEEhgisSLQDLDAADLRSFLA-RRRRQGLSARSLA--RRLsaLRSF 85

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2038652870 119 FAWLEQEEYIIKNPIRRIKKIKTEQNV-KETYTDEHLEIMRDNCEN----LRDLAIIDLLASTGMRVGELVQLNRSDIDF 193
Cdd:PRK00236   86 YRWLVRRGLLKANPAAGLRAPKIPKRLpKPLDVDQAKRLLDAIDEDdplaLRDRAILELLYGSGLRLSELVGLDIDDLDL 165

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2038652870 194 ENRECVVFGKGKKERPVYFDARTKIHLRNYLNDR---KDSHPALFVTLVGKvqRLGIAGVEIRLRKLGDKLGI-QKVHPH 269
Cdd:PRK00236  166 ASGTLRVLGKGNKERTVPLGRAAREALEAYLALRplfLPDDDALFLGARGG--RLSPRVVQRRVKKLGKKAGLpSHITPH 243

                         250       260       270
                  ....*....|....*....|....*....|....*
gi 2038652870 270 KFRRTLATKAIDKGMPIEQVQKLLGHSKIDTTLAY 304
Cdd:PRK00236  244 KLRHSFATHLLESGGDLRAVQELLGHASLSTTQIY 278
INT_XerDC_C cd00798
XerD and XerC integrases, C-terminal catalytic domains; XerDC-like integrases are involved in ...
 164-301 4.22e-36

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: 128.01  E-value: 4.22e-36
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2038652870 164 LRDLAIIDLLASTGMRVGELVQLNRSDIDFENRECVVFGKGKKERPVYFDARTKIHLRNYLNDR------KDSHPALFVT 237
Cdd:cd00798    19 LRDRAILELLYASGLRVSELVGLDLSDVDLDEGLVRVTGKGNKERLVPFGSYAVEALEEYLEERrplllkKKPPDALFLN 98

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2038652870 238 LVGKvqRLGIAGVEIRLRKLGDKLGIQK-VHPHKFRRTLATKAIDKGMPIEQVQKLLGHSKIDTT 301
Cdd:cd00798    99 KRGK--RLSRRGVWRILKKYAERAGLPKhVSPHTLRHSFATHLLEGGADLRVVQELLGHASLSTT 161
Phage_integrase pfam00589
Phage integrase family; Members of this family cleave DNA substrates by a series of staggered ...
 151-308 8.01e-26

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: 100.86  E-value: 8.01e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2038652870 151 DEHLEIMrDNCEN----LRDLAIIDLLASTGMRVGELVQLNRSDIDFENREC-VVFGKGKKERPVYFDARTKIHLRNYLN 225
Cdd:pfam00589   5 DEVERLL-DAAETgplsIRDKALLELLYATGLRISELCSLRWSDIDFENGVIrVHRGKGNKERTVPLSDAALELLKEWLS 83

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2038652870 226 DR---KDSHPALFVTLvgKVQRLGIAGVEIRLRKLGDKLGIQK-VHPHKFRRTLATKAIDKGMPIEQVQKLLGHSKIDTT 301
Cdd:pfam00589  84 KRlleAPKSDYLFASK--RGKPLSRQTVRKIFKRAGKEAGLELpLHPHMLRHSFATHLLEAGVDLRVVQKLLGHSSISTT 161


                  ....*..
gi 2038652870 302 LAYAMVN 308
Cdd:pfam00589 162 QIYTHVA 168
 
Name Accession Description Interval E-value
XerD COG4974
Site-specific recombinase XerD [Replication, recombination and repair];
46-319 2.36e-68

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


Pssm-ID: 443999 [Multi-domain]  Cd Length: 291  Bit Score: 215.24  E-value: 2.36e-68
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2038652870  46 LLQLFITAKQVE-GCSSKTIRYYQRTIENLFNAIKE----SVTQLTTDDLRSYLaNYQSEKDCSKANLDNIRRILSSFFA 120
Cdd:COG4974     6 LLEAFLEELKREkGLSPNTIKAYRRDLRRFLRFLEElgkiPLAEITPEDIRAYL-NYLRERGLSPSTINRYLAALRSFFR 84

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2038652870 121 WLEQEEYIIKNPIRRIKKIKTEQNVKETYTDEHLEIMRDNC-----ENLRDLAIIDLLASTGMRVGELVQLNRSDIDFEN 195
Cdd:COG4974    85 YAVREGLLEDNPAAKVKLPKKPRKLPRVLTEEEIEALLEALdtetpEGLRDRALLLLLYATGLRVSELLGLKWSDIDLDR 164

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2038652870 196 REC-VVFGKGKKERPVYFDARTKIHLRNYLNDRKD-SHPALFVTLVGKvqRLGIAGVEIRLRKLGDKLGIQK-VHPHKFR 272
Cdd:COG4974   165 GTIrVRRGKGGKERTVPLSPEALEALREYLEERRPrDSDYLFPTRRGR--PLSRRAIRKILKRLAKRAGIPKrVTPHSLR 242

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|....*..
gi 2038652870 273 RTLATKAIDKGMPIEQVQKLLGHSKIDTTLAYAMVNQNNVKHSHQKF 319
Cdd:COG4974   243 HTFATHLLEAGVDLRTVQELLGHSSISTTQIYTHVSDEELREAVEKL 289
XerC COG4973
Site-specific recombinase XerC [Replication, recombination and repair];
46-304 8.04e-61

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


Pssm-ID: 443998 [Multi-domain]  Cd Length: 287  Bit Score: 195.57  E-value: 8.04e-61
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2038652870  46 LLQLFITAKQVEGCSSKTIRYYQRTIENLFNAIKE---SVTQLTTDDLRSYLANYqSEKDCSKANLDNIRRILSSFFAWL 122
Cdd:COG4973     7 ALEAYLEHLRERRLSPKTLEAYRRDLRRLIPLLGDadlPLEELTPADVRRFLARL-HRRGLSPRTLNRRLSALRSFFNWA 85

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2038652870 123 EQEEYIIKNPIRRIKKIKTEQNVKETYTDEH----LEIMRDNCENLRDLAIIDLLASTGMRVGELVQLNRSDIDFENREC 198
Cdd:COG4973    86 VREGLLEANPAAGVKAPKAPRKLPRALTVDElaqlLDALADDPLAVRDRAIVELLYSTGLRLGELVGLDWEDVDLDAGEV 165

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2038652870 199 VVFGKGKKERPVYFDARTKIHLRNYLNDRK----DSHPALFVTLVGKvqRLGIAGVEIRLRKLGDKLGI-QKVHPHKFRR 273
Cdd:COG4973   166 RVRGKTGKSRTVPLGPKALAALREWLAVRPelaaPDEGALFPSRRGT--RLSPRNVQKRLRRLAKKAGLpKHVHPHDLRH 243

                         250       260       270
                  ....*....|....*....|....*....|.
gi 2038652870 274 TLATKAIDKGMPIEQVQKLLGHSKIDTTLAY 304
Cdd:COG4973   244 SFATHLLESGGDLRAVQELLGHASISTTQIY 274
recomb_XerC TIGR02224
tyrosine recombinase XerC; The phage integrase family describes a number of recombinases with ...
 60-319 5.79e-50

tyrosine recombinase XerC; 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 XerC, one of two closely related chromosomal proteins along with XerD (TIGR02225). 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 homologs of XerC on other replicons, the chomosomal copy was preferred for building this model. This model does not detect all XerC, as some apparent XerC examples score in the gray zone between trusted (450) and noise (410) cutoffs, along with some XerD examples. XerC and XerD interact with cell division protein FtsK. [DNA metabolism, DNA replication, recombination, and repair]


Pssm-ID: 274042 [Multi-domain]  Cd Length: 295  Bit Score: 167.78  E-value: 5.79e-50
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2038652870  60 SSKTIRYYQRTIENLFNAIKE-----SVTQLTTDDLRSYLAnYQSEKDCSKANldnIRRILS---SFFAWLEQEEYIIKN 131
Cdd:TIGR02224  14 SPHTVRAYRRDLEAFLEFLEEegglaSLAEVTAADLRSFLA-ELHARGLSRRS---LARKLSalrSFYRFLLRRGLIDAN 89

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2038652870 132 PIRRIKKIKTE----QNVKETYTDEHLEIMRDNCE---NLRDLAIIDLLASTGMRVGELVQLNRSDIDFENRECVVFGKG 204
Cdd:TIGR02224  90 PAAGVRAPKQPkklpKFLSEDEMEALLDAPEEDDEdwlALRDRAILELLYSSGLRVSELVGLDLSDLDLDFGEVRVRGKG 169

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2038652870 205 KKERPVYFDARTKIHLRNYLNDR------KDSHPALFVTLVGKvqRLGIAGVEIRLRKLGDKLGI-QKVHPHKFRRTLAT 277
Cdd:TIGR02224 170 NKERIVPFGPYARDALQAYLEARrspllaSEGQDALFLNRRGG--RLTPRGVQYRLQQLRAKAGLpKHVHPHALRHSFAT 247

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|..
gi 2038652870 278 KAIDKGMPIEQVQKLLGHSKIDTTLAYAMVNQNNVKHSHQKF 319
Cdd:TIGR02224 248 HLLNNGADLRAVQELLGHASLSTTQIYTHVDFQHLAKVYDQA 289
xerC PRK00236
site-specific tyrosine recombinase XerC; Reviewed
 46-304 2.01e-49

site-specific tyrosine recombinase XerC; Reviewed


Pssm-ID: 234698 [Multi-domain]  Cd Length: 297  Bit Score: 166.48  E-value: 2.01e-49
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2038652870  46 LLQLFITAKQVE-GCSSKTIRYYQRTIENLFNAIKE----SVTQLTTDDLRSYLAnYQSEKDCSKANLDniRRI--LSSF 118
Cdd:PRK00236    9 ALEAFLEYLRVErGLSPHTLRAYRRDLRAFLAFLEEhgisSLQDLDAADLRSFLA-RRRRQGLSARSLA--RRLsaLRSF 85

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2038652870 119 FAWLEQEEYIIKNPIRRIKKIKTEQNV-KETYTDEHLEIMRDNCEN----LRDLAIIDLLASTGMRVGELVQLNRSDIDF 193
Cdd:PRK00236   86 YRWLVRRGLLKANPAAGLRAPKIPKRLpKPLDVDQAKRLLDAIDEDdplaLRDRAILELLYGSGLRLSELVGLDIDDLDL 165

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2038652870 194 ENRECVVFGKGKKERPVYFDARTKIHLRNYLNDR---KDSHPALFVTLVGKvqRLGIAGVEIRLRKLGDKLGI-QKVHPH 269
Cdd:PRK00236  166 ASGTLRVLGKGNKERTVPLGRAAREALEAYLALRplfLPDDDALFLGARGG--RLSPRVVQRRVKKLGKKAGLpSHITPH 243

                         250       260       270
                  ....*....|....*....|....*....|....*
gi 2038652870 270 KFRRTLATKAIDKGMPIEQVQKLLGHSKIDTTLAY 304
Cdd:PRK00236  244 KLRHSFATHLLESGGDLRAVQELLGHASLSTTQIY 278
INT_XerDC_C cd00798
XerD and XerC integrases, C-terminal catalytic domains; XerDC-like integrases are involved in ...
 164-301 4.22e-36

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: 128.01  E-value: 4.22e-36
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2038652870 164 LRDLAIIDLLASTGMRVGELVQLNRSDIDFENRECVVFGKGKKERPVYFDARTKIHLRNYLNDR------KDSHPALFVT 237
Cdd:cd00798    19 LRDRAILELLYASGLRVSELVGLDLSDVDLDEGLVRVTGKGNKERLVPFGSYAVEALEEYLEERrplllkKKPPDALFLN 98

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2038652870 238 LVGKvqRLGIAGVEIRLRKLGDKLGIQK-VHPHKFRRTLATKAIDKGMPIEQVQKLLGHSKIDTT 301
Cdd:cd00798    99 KRGK--RLSRRGVWRILKKYAERAGLPKhVSPHTLRHSFATHLLEGGADLRVVQELLGHASLSTT 161
recomb_XerD TIGR02225
tyrosine recombinase XerD; The phage integrase family describes a number of recombinases with ...
 48-319 6.38e-36

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: 131.16  E-value: 6.38e-36
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2038652870  48 QLFITAKQVE-GCSSKTIRYYQRTIENL---FNAIKESVTQLTTDDLRSYLanyQSEKDCSKANLDNIRRI--LSSFFAW 121
Cdd:TIGR02225   1 EQFLDYLWVErGLSQNTLEAYRRDLEKFlefLEERGIDLEEVDRGDIVDFL---AELKEAGLSARSIARALsaLRSFYRF 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2038652870 122 LEQEEYIIKNPIRRIKKIKTEQNVKETYTDEHLEIMRDNCEN-----LRDLAIIDLLASTGMRVGELVQLNRSDIDFENR 196
Cdd:TIGR02225  78 LLREGIREDDPSALIEPPKVARKLPKVLTVEEVEALLAAPDVdtplgLRDRAMLELLYATGLRVSELVGLRLEDVNLDEG 157

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2038652870 197 ECVVFGKGKKERPVYFDARTKIHLRNYLNDRKD--------SHPALFVTLVGKvqRLGIAGVEIRLRKLGDKLGIQK-VH 267
Cdd:TIGR02225 158 FVRVRGKGNKERLVPLGEEAIEALERYLKEARPlllkkkvkESDALFLNRRGG--PLSRQGVWKILKEYAKRAGIEKpIS 235

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|..
gi 2038652870 268 PHKFRRTLATKAIDKGMPIEQVQKLLGHSKIDTTLAYAMVNQNNVKHSHQKF 319
Cdd:TIGR02225 236 PHTLRHSFATHLLENGADLRVVQELLGHADISTTQIYTHVARERLKEVHKKH 287
DNA_BRE_C cd00397
DNA breaking-rejoining enzymes, C-terminal catalytic domain; The DNA breaking-rejoining enzyme ...
 158-305 3.37e-34

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: 122.97  E-value: 3.37e-34
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2038652870 158 RDNCENLRDLAIIDLLASTGMRVGELVQLNRSDIDFENRECVVFGKG---KKERPVYFDARTKIHLRNYLNDRKDSHPAL 234
Cdd:cd00397    11 EDKKIDLRDRAILLLLLETGLRISELLALKVKDIDLDNGTIRVRGKKtkgGKERTVPLPKELAEELKEYLKERRDKRGPL 90

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2038652870 235 FV---TLVGKVQRLGIAGVEIRLRKLGDKLGIQ---KVHPHKFRRTLATKAIDKGMPIEQVQKLLGHSKIDTTLAYA 305
Cdd:cd00397    91 LKslyLNKLFGTKLGERLSRRTLRRIFKKAGIEagrKITPHSLRHTFATNLLENGVDIKVVQKLLGHSSISTTQRYL 167
xerD PRK00283
tyrosine recombinase;
46-319 3.59e-27

tyrosine recombinase;


Pssm-ID: 234713 [Multi-domain]  Cd Length: 299  Bit Score: 107.97  E-value: 3.59e-27
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2038652870  46 LLQLFITAKQVE-GCSSKTIRYYQRTIENLFN---AIKESVTQLTTDDLRSYLANY--QSEKDCSKAnldniRRI--LSS 117
Cdd:PRK00283    8 LIEQFLDALWVErGLAENTLSSYRRDLELFAEwlaARGLSLAEATRDDLQAFLAELaeGGYKATSSA-----RRLsaLRR 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2038652870 118 FFAWLEQEEYIIKNPIRRIK---------KIKTEQNVKE----TYTDEHLEimrdncenLRDLAIIDLLASTGMRVGELV 184
Cdd:PRK00283   83 FFQFLLREGLREDDPSALLDspklprrlpKTLSEAQVEAlldaPDIDTPLG--------LRDRAMLELLYATGLRVSELV 154

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2038652870 185 QLNRSDIDFENRECVVFGKGKKERPVYFDARTKIHLRNYLNDRKD------SHPALFVTLVGkvQRLGIAGVEIRLRKLG 258
Cdd:PRK00283  155 GLTLDDVSLRQGVVRVTGKGNKERLVPLGEEAVYAIERYLERGRPallngrSSDALFPSARG--GQLTRQTFWHRIKHYA 232

                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2038652870 259 DKLGIQ--KVHPHKFRRTLATKAIDKGMPIEQVQKLLGHSKIDTTLAYAMVNQNNVKHSHQKF 319
Cdd:PRK00283  233 KRAGIDpkKLSPHVLRHAFATHLLNHGADLRVVQELLGHSDISTTQIYTHVATERLKELHAQH 295
Phage_integrase pfam00589
Phage integrase family; Members of this family cleave DNA substrates by a series of staggered ...
 151-308 8.01e-26

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: 100.86  E-value: 8.01e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2038652870 151 DEHLEIMrDNCEN----LRDLAIIDLLASTGMRVGELVQLNRSDIDFENREC-VVFGKGKKERPVYFDARTKIHLRNYLN 225
Cdd:pfam00589   5 DEVERLL-DAAETgplsIRDKALLELLYATGLRISELCSLRWSDIDFENGVIrVHRGKGNKERTVPLSDAALELLKEWLS 83

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2038652870 226 DR---KDSHPALFVTLvgKVQRLGIAGVEIRLRKLGDKLGIQK-VHPHKFRRTLATKAIDKGMPIEQVQKLLGHSKIDTT 301
Cdd:pfam00589  84 KRlleAPKSDYLFASK--RGKPLSRQTVRKIFKRAGKEAGLELpLHPHMLRHSFATHLLEAGVDLRVVQKLLGHSSISTT 161


                  ....*..
gi 2038652870 302 LAYAMVN 308
Cdd:pfam00589 162 QIYTHVA 168
INT_IntI_C cd01193
Integron integrase and similar protiens, C-terminal catalytic domain; Integron integrases ...
 162-304 5.82e-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: 98.89  E-value: 5.82e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2038652870 162 ENLRDLAIIDLLASTGMRVGELVQLNRSDIDFENRECVV-FGKGKKERPVYFDARTKIHLRNYLNDRKDSHPaLFVTLVG 240
Cdd:cd01193    19 TELRHRLILSLLYGAGLRISELLRLRVKDIDFERGVIRVrQGKGGKDRVVPLPEKLLEPLRRYLKSARPKEE-LDPAEGR 97

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 2038652870 241 KVQRLGIAGVEIR-----------LRKLGDKLGIQK-VHPHKFRRTLATKAIDKGMPIEQVQKLLGHSKIDTTLAY 304
Cdd:cd01193    98 AGVLDPRTGVERRhhisettvqraLKKAVEQAGITKrVTPHTLRHSFATHLLEAGTDIRTIQELLGHSDLSTTMIY 173
INT_RitC_C_like cd01182
C-terminal catalytic domain of recombinase RitC, a component of the recombinase trio; ...
 165-308 1.44e-22

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: 92.73  E-value: 1.44e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2038652870 165 RDLAIIDLLASTGMRVGELVQLNRSDIDFEN-RECVVFGKGKKERPVYFDARTKIHLRNYL---NDRKDSHPALFVTLVG 240
Cdd:cd01182    22 RDHALLLLLYDTGARVQELADLTIRDLRLDDpATVRLHGKGRKERTVPLWKETVAALKAYLqefHLTPDPKQLFPLFPNR 101

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2038652870 241 KVQRLGIAGVEIRLRKLGDKLG------IQKVHPHKFRRTLATKAIDKGMPIEQVQKLLGHSKIDTTLAYAMVN 308
Cdd:cd01182   102 RGQPLTRDGVAYILNKYVALASnrcpslPKRITPHTLRHTKAMHLLQAGVDLTVIRDWLGHESVETTQIYAEAD 175
xerC PRK01287
site-specific tyrosine recombinase XerC; Reviewed
 115-318 1.87e-22

site-specific tyrosine recombinase XerC; Reviewed


Pssm-ID: 234935 [Multi-domain]  Cd Length: 358  Bit Score: 95.97  E-value: 1.87e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2038652870 115 LSSFFAWLEQEEYIIKNPIRRIKKIKTEQNV-KETYTDEHLEIMRDNCE-----NLRDLAIIDLLASTGMRVGELVQLNR 188
Cdd:PRK01287  102 LRVWFRWLLKRHHILYNPAEDLELPKEEKRLpRQILSEAETEQVLASPDlttlqGLRDRALLELLWSTGIRRGELARLDL 181

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2038652870 189 SDIDFENRECVVF-GKGKKERPVYFDARTKIHLRNYLND-------RKDShPALFVTLVGKvqRLGIAGVEIRLRKLGDK 260
Cdd:PRK01287  182 YDVDASRGVVTVRqGKGNKDRVVPVGERALAWLQRYLQDvrpqlavRPDS-GALFVAMDGD--GLARNTLTNMVGRYIRA 258

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 2038652870 261 LGIQKVHP-HKFRRTLATKAIDKGMPIEQVQKLLGHSKIDTTLAYAMVNQNNVKHSHQK 318
Cdd:PRK01287  259 AGIEKAGAcHLFRHAMATQMLENGADTRHIQAILGHAKLETTQIYTRVSIGHLQAVHAS 317
INT_Rci_Hp1_C cd00796
Shufflon-specific DNA recombinase Rci and Bacteriophage Hp1_like integrase, C-terminal ...
 150-306 2.35e-22

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: 91.62  E-value: 2.35e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2038652870 150 TDEHLEIMRDNCENLRD---LAIIDLLASTGMRVGELVQLNRSDIDFENREcVVFG--KGKKERPVYFDARTKIHLRNYL 224
Cdd:cd00796     6 TEDEEARLLAALEESTNphlRLIVLLALYTGARRGEILSLRWDDIDLEVGL-IVLPetKNGKPRTVPLSDEAIAILKELK 84

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2038652870 225 ndRKDSHPALFVTlvGKVQRLGIAGVEIRLRKLGDKLGIQKVHPHKFRRTLATKAIDKGMPIEQVQKLLGHSKIDTTLAY 304
Cdd:cd00796    85 --RKRGKDGFFVD--GRFFGIPIASLRRAFKKARKRAGLEDLRFHDLRHTFASRLVQAGVPIKTVAKILGHSSIKMTMRY 160


                  ..
gi 2038652870 305 AM 306
Cdd:cd00796   161 AH 162
INT_RitA_C_like cd01188
C-terminal catalytic domain of recombinase RitA, a component of the recombinase trio; ...
 164-314 1.36e-21

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: 89.99  E-value: 1.36e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2038652870 164 LRDLAIIDLLASTGMRVGELVQLNRSDIDFEN-RECVVFGKGKKERPVYFDARTKIHLRNYLNDR--KDSHPALFVTLVG 240
Cdd:cd01188    20 LRDYAILLLLARLGLRAGDVAGLRLDDIDWRSgTITVRQKKTGRPVELPLTEPVGEALADYLRDGrpRTDSREVFLRARA 99

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2038652870 241 KVQRLGI-AGVEIRLRKLGDKLGIQKVH--PHKFRRTLATKAIDKGMPIEQVQKLLGHSKIDTTLAYAMVNQNNVKH 314
Cdd:cd01188   100 PYRPLSStSQISSIVRRYLRKAGIEPSHrgTHSLRHSLATRMLRAGTSLKVIADLLGHRSIETTAIYAKIDVDDLRE 176
INT_C_like_4 cd01194
Uncharacterized site-specific tyrosine recombinase, C-terminal catalytic domain; Tyrosine ...
 159-305 1.10e-20

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: 87.43  E-value: 1.10e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2038652870 159 DNCENLRDLAIIDLLASTGMRVGELVQLNRSDIDFENRECVVF--GKGK--KERPVYFDARTKIHLRNYLNDRKDSHP-- 232
Cdd:cd01194    17 DSIIGLRDRAIISLMVTEGLRTVEIVRADVGDLRQEGEGTILYvqGKGKtsKDDFVYLRPDVLKALQAYLKARGKLDFee 96

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2038652870 233 ALFVTLVGKV--QRLGIAGVEIRLRKLGDKLGI--QKVHPHKFRRTLATKAIDKGMPIEQVQKLLGHSKIDTTLAYA 305
Cdd:cd01194    97 PLFTSLSNNSkgQRLTTRSIRRIIKKYLRKAGLddDRLTAHSLRHTAGTLALKAGKSLREVQQLLRHSDPNTTMIYA 173
xerS PRK05084
site-specific tyrosine recombinase XerS; Reviewed
 160-309 2.18e-19

site-specific tyrosine recombinase XerS; Reviewed


Pssm-ID: 235339 [Multi-domain]  Cd Length: 357  Bit Score: 87.28  E-value: 2.18e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2038652870 160 NCEnlRDLAIIDLLASTGMRVGELVQLNRSDIDFENRECVVFGKGKKERPVYFDARTKIHLRNYLNDRKD--SHP----A 233
Cdd:PRK05084  193 NKE--RDLAIIALILGSGLRVSELVNLDLSDLNLKQMTIDVTRKGGKRDSVNIAPFALPYLEEYLKIRASryKAEkqekA 270

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2038652870 234 LFVTLV-GKVQRLGIAGVEIRLRKLGDKLGIqKVHPHKFRRTLATKAIDKGMPIEQVQKLLGHSKIDTTLAYAMVNQ 309
Cdd:PRK05084  271 LFLTKYrGKPNRISARAIEKMVAKYSEAFGV-RLTPHKLRHTLATRLYDATKDQVLVADQLGHTSTETTDLYTHIVN 346
FimB COG0582
Integrase/recombinase, includes phage integrase [Replication, recombination and repair, ...
 53-303 9.96e-19

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


Pssm-ID: 440347 [Multi-domain]  Cd Length: 391  Bit Score: 85.86  E-value: 9.96e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2038652870  53 AKQVEGCSSKTIRYYQRTIEN-LFNAIKE-SVTQLTTDDLRSYLANYqsEKDCSKANLDNIRRILSSFFAWLEQEEYIIK 130
Cdd:COG0582   108 EEKKPEWKEKTAAQVRRTLEKhIFPVLGDrPIAEITPPDLLAVLRPI--EARGAPETARRVRQRLRQVFRYAVARGLIER 185

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2038652870 131 NPIRRIKKIKTEQNVKE--TYTDEHL-EIMR--DNCENLRDLAI-IDLLASTGMRVGELVQLNRSDIDFENRECVVFG-- 202
Cdd:COG0582   186 NPAADLKGALPKPKVKHhpALTPEELpELLRalDAYRGSPVTRLaLRLLLLTGVRPGELRGARWSEIDLEAALWTIPAer 265

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2038652870 203 -KGKKERPVYFDARTKIHLRNYLNDRKDShPALFVTLVGKVQRLGiagvEIRLRKLGDKLGIQKVHPHKFRRTLATKAID 281
Cdd:COG0582   266 mKTRRPHIVPLSRQALEILKELKPLTGDS-EYVFPSRRGPKKPMS----ENTLNKALRRMGYGRFTPHGFRHTASTLLNE 340

                         250       260
                  ....*....|....*....|..
gi 2038652870 282 KGMPIEQVQKLLGHSKIDTTLA 303
Cdd:COG0582   341 AGFPPDVIERQLAHKDGNKVRA 362
INT_C_like_5 cd01195
Uncharacterized site-specific tyrosine recombinase, C-terminal catalytic domain; Tyrosine ...
 156-304 1.92e-17

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: 78.28  E-value: 1.92e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2038652870 156 IMRDNCENLRDLAIIDLLASTGMRVGELVQLNRSDIDFENRECVVFGKGKKER-PVYFDARTKIHLRNYLNDRKDSHPAL 234
Cdd:cd01195    12 ADRHTAKGKRDEALVRLLLDNALRRSEAVALDVEDLEKEHRRLRILGKGKKQReVVTLPPTTREALAAWLAARGEAEGPL 91

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2038652870 235 FVTLVGKVQ--RLGIAGVEIRLRKLGDKLGIQK-VHPHKFRRTLATKAIDKGMP-IEQVQKLLGHSKIDTTLAY 304
Cdd:cd01195    92 FVSLDRASRgrRLSPQAVYRIVRRLAERIGLGKrLSPHGLRHSAITLALDAGAGlIRKVQDFSRHADLRTLQVY 165
INT_tnpA_C_Tn554 cd01186
Putative Transposase A from transposon Tn554, C-terminal catalytic domain; This family ...
 159-303 4.39e-17

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: 77.84  E-value: 4.39e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2038652870 159 DNCENLRDLAIIDLLASTGMRVGELVQLNRSDIDFENRECVVFGKGKKERPVYFDART--KIHLRNYLND---------- 226
Cdd:cd01186    12 NACNNLRDKFLLALLYETGLRIGEALGLRIEDIDMADNQIELVPREDNTNEARAKSMRerRIPVSQDLIDlyadyltyiy 91

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2038652870 227 -RKDSHP-ALFVTLVGKVQ--RLGIAGVEIRLRKLGDKLGIQkVHPHKFRRTLATKAIDKGMPIEQVQKLLGHSKIDTTL 302
Cdd:cd01186    92 cEEAEFSiTVFVNVKGGNQgkAMNYSDVYDLVRRLKKRTGID-FTPHMFRHTHATALIRAGWSIEVVARRLGHAHVQTTL 170


                  .
gi 2038652870 303 A 303
Cdd:cd01186   171 N 171
INT_ICEBs1_C_like cd01189
C-terminal catalytic domain of integrases from bacterial phages and conjugate transposons; ...
 160-304 2.28e-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: 74.90  E-value: 2.28e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2038652870 160 NCENLRDLAIIDLLASTGMRVGELVQLNRSDIDFENRECVVFG--KGKKERPVYFDA-RTKIHLRN-YLNDRkdshpalf 235
Cdd:cd01189    12 KKRGDRYYLLFLLALLTGLRRGELLALTWSDIDFENGTIRINRtlVRKKKGGYVIKPpKTKSSIRTiPLPDE-------- 83

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2038652870 236 vtLVGKVQRLgiagveIRLRKLGDKLGIQKVHPHKFRRTLATKAIDKGMPIEQVQKLLGHSKIDTTLAY 304
Cdd:cd01189    84 --LIELLKEL------KAFKKLLKKAGLPRITPHDLRHTFASLLLEAGVPLKVIAERLGHSDISTTLDV 144
INTN1_C_like cd01185
Integrase IntN1 of Bacteroides mobilizable transposon NBU1 and similar proteins, C-terminal ...
 161-305 3.14e-14

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: 69.22  E-value: 3.14e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2038652870 161 CENLRDLAIIDLLasTGMRVGELVQLNRSDI-DFENRECVVFGKGKKERPVYfdarTKIH------LRNYLNDRKDShPA 233
Cdd:cd01185    17 LELVRDMFLFSCY--TGLRFSDLKNLTWKNIvEASGRTWIRYRRKKTGKPVT----VPLLpvareiLEKYKDDRSEG-KL 89

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2038652870 234 LFVTLVGKVQRlgiagveiRLRKLGDKLGIQK-VHPHKFRRTLATKAIDKGMPIEQVQKLLGHSKIDTTLAYA 305
Cdd:cd01185    90 FPVLSNQKINR--------YLKEIAKIAGIDKhLTFHVARHTFATLLLLKGVDIETISKLLGHSSIKTTQIYA 154
Phage_int_SAM_4 pfam13495
Phage integrase, N-terminal SAM-like domain;
46-127 3.47e-14

Phage integrase, N-terminal SAM-like domain;


Pssm-ID: 463898 [Multi-domain]  Cd Length: 83  Bit Score: 66.87  E-value: 3.47e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2038652870  46 LLQLFITAKQVEGCSSKTIRYYQRTIENLFNAIKE-SVTQLTTDDLRSYLANYQSEKDCSKANLDNIRRILSSFFAWLEQ 124
Cdd:pfam13495   1 LLERFREALRLRGYAERTIKAYLRWIRRFLRFHDKkHPEELTEEDIEAYLSHLANERNVSASTQNQALNALSFFYRWVLE 80


                  ...
gi 2038652870 125 EEY 127
Cdd:pfam13495  81 REL 83
INT_RitB_C_like cd00797
C-terminal catalytic domain of recombinase RitB, a component of the recombinase trio; ...
 172-304 2.18e-13

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: 67.72  E-value: 2.18e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2038652870 172 LLASTGMRVGELVQLNRSDIDFENRECVV-FGKGKKER--PVYFDARTKihLRNYLNDRKD-----SHPALFVTLVGKvq 243
Cdd:cd00797    33 LLYATGLRVGEALRLRLEDVDLDSGILTIrQTKFGKSRlvPLHPSTVGA--LRDYLARRDRllpspSSSYFFVSQQGG-- 108

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2038652870 244 RLGIAGVEIRLRKLGDKLGIQKV------HPHKFRRTLAT----------KAIDKGMPIeqVQKLLGHSKIDTTLAY 304
Cdd:cd00797   109 RLTGGGVYRVFRRLLRRIGLRGAgdgrgpRLHDLRHTFAVnrltrwyregADVERKLPV--LSTYLGHVNVTDTYWY 183
INT_C_like_3 cd01192
Uncharacterized site-specific tyrosine recombinase, C-terminal catalytic domain; Tyrosine ...
 132-314 5.34e-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: 271192 [Multi-domain]  Cd Length: 178  Bit Score: 63.47  E-value: 5.34e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2038652870 132 PIRRIKKIKteqnvketytdEHLEIMRDncENLRDLAIIDLLASTGMRVGELVQLNRSDIDFENRECVVFGKGKKERPVY 211
Cdd:cd01192     5 PIKDKKLIK-----------EIKLYLKK--ANPRNYLLFIVGINTGLRISDLLSLKVEDVTNKDKLSIKEQKTGKQKTFP 71

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2038652870 212 FDARTKIHLRNYLNDRKDSHPA-LFVTLVGKVQR-LGIAGVEIRLRKLGDKLGIQ-KVHPHKFRRTLATKAIDKGMPIEQ 288
Cdd:cd01192    72 LNPTLVKALKEYIDDLDLKRNDyLFKSLKQGPEKpISRKQAYKILKKAADDLGLNyNIGTHSLRKTFGYHVYKQGKDIEL 151

                         170       180
                  ....*....|....*....|....*.
gi 2038652870 289 VQKLLGHSKIDTTLAYAMVNQNNVKH 314
Cdd:cd01192   152 LMKLLNHSSPSITLRYLGIDQEDVDK 177
integrase_gron TIGR02249
integron integrase; Members of this family are integrases associated with integrons (and ...
 169-307 1.41e-10

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: 61.25  E-value: 1.41e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2038652870 169 IIDLLASTGMRVGELVQLNRSDIDFENRECVVF-GKGKKERPVYFDARTKIHLRNYLNDRKDSHPALFVTLVGKV----- 242
Cdd:TIGR02249 121 IAKLLYGSGMRLMECLRLRIQDIDFDYGEIRIRqGKGGKDRTVTLPKELIPPLREQIELARAYHEADLAEGYGGVylpha 200

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2038652870 243 --QRLGIAGVEIR--------------------------------LRKLGDKLGIQK-VHPHKFRRTLATKAIDKGMPIE 287
Cdd:TIGR02249 201 laRKYPNAPKEWGwqylfpshrlsrdpesgvirrhhinettiqraVRRAVERAGIEKpVTCHTLRHSFATHLLESGADIR 280

                         170       180
                  ....*....|....*....|
gi 2038652870 288 QVQKLLGHSKIDTTLAYAMV 307
Cdd:TIGR02249 281 TVQELLGHSDVKTTQIYTHV 300
INT_C_like_6 cd01196
Uncharacterized site-specific tyrosine recombinase, C-terminal catalytic domain; Tyrosine ...
 164-304 2.54e-09

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: 55.95  E-value: 2.54e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2038652870 164 LRDLAIIDLLASTGMRVGELVQLNRSDIDFENRE-CVVFG-KGKKERPVYFDARTKIHLRNYLND---RKDSHPALFVTL 238
Cdd:cd01196    20 LRDRALIALMVYSFARIGAVLAMRVEDVYDQGRRlWVRLAeKGGKQHEMPCHHDLEEYLRAYLEAaeiEEDPKGPLFRTT 99

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2038652870 239 VGKVQRLGIAGVE-------IRLRKLGDKLgIQKVHPHKFRRTLATKAIDKGMPIEQVQKLLGHSKIDTTLAY 304
Cdd:cd01196   100 RGGTRKLTHNPLTqanayrmVRRRAIAADI-PTAIGNHSFRATGITAYLKNGGTLEDAQNMANHASTRTTQLY 171
INT_Cre_C cd00799
C-terminal catalytic domain of Cre recombinase (also called integrase); Cre-like recombinases ...
 155-304 2.99e-09

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: 55.77  E-value: 2.99e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2038652870 155 EIMRDNCENLRDLAIIdLLA-STGMRVGELVQLNRSDIDFENRECVVF--GKGK-----KERPVYFDARTKI----HLRN 222
Cdd:cd00799     7 TLDDTTLRGLRDRALL-LLGfAGALRRSELVALRVEDLTRFVDGGLLIrlRRSKtdqdgEGEIKALPYGPETcpvrALRA 85

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2038652870 223 YLNDRKDSHPALFVTlVGK-----VQRLGIAGVEIRLRKLGDKLGIQKVH--PHKFRRTLATKAIDKGMPIEQVQKLLGH 295
Cdd:cd00799    86 WLEAAGIPSGPLFRR-IRRggsvgTTRLSDRSVARIVKRRAALAGLDPGDfsGHSLRRGFATEAARAGASLPEIMAQGGH 164


                  ....*....
gi 2038652870 296 SKIDTTLAY 304
Cdd:cd00799   165 KSVATVMRY 173
INT_tnpB_C_Tn554 cd01187
Putative Transposase B from transposon Tn554, C-terminal catalytic domain; This family ...
 154-306 4.68e-09

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: 54.36  E-value: 4.68e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2038652870 154 LEIMRDNCENLRD-LAIIDLLASTGMRVGELVQLnrsdiDFENRECVVfgkGKKERPVYFdarTKIHLRNYLNDRKDSHP 232
Cdd:cd01187     2 VAPNLAALDLLPQpIPVVQAAVFTGARASELATL-----KFGCLHAQT---SDDGTFLYW---LKWENKGGKQLDIPISK 70

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2038652870 233 ALFVTlvgkvqrlgIAGVEIRLRKL-------GDKLGIQKVHPHKFRRTLATKAIDKGMPIEQVQKLLGHSKIDTTLAYA 305
Cdd:cd01187    71 KVAEL---------IKTINWTLNELselknisDDHGERFRFHTHRFRHTVATRLANSGMGILVLQQLLGHSSPEMTLRYA 141


                  .
gi 2038652870 306 M 306
Cdd:cd01187   142 L 142
INT_C_like_2 cd01191
Uncharacterized site-specific tyrosine recombinase, C-terminal catalytic domain; Tyrosine ...
 169-304 2.61e-08

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: 52.81  E-value: 2.61e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2038652870 169 IIDLLASTGMRVGELVQLNRSDIDFENREcvVFGKGKKERPVYFDARTKIHLRNYLNDRKDSHPALFVTLVGKvqRLGIA 248
Cdd:cd01191    25 VVRFLAATGARVSELIKIKVEHVELGYFD--IYSKGGKLRRLYIPKKLRNEALEWLKSTNRKSGYIFLNRFGE--RITTR 100

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 2038652870 249 GVEIRLRKLGDKLGIQK--VHPHKFRRTLATKAIDKGMPIEQVQKLLGHSKIDTTLAY 304
Cdd:cd01191   101 GIAQQLKNYARKYGLNPkvVYPHSFRHRFAKNFLEKYNDIALLADLMGHESIETTRIY 158
PRK15417 PRK15417
integron integrase;
172-307 6.44e-08

integron integrase;


Pssm-ID: 185315 [Multi-domain]  Cd Length: 337  Bit Score: 53.51  E-value: 6.44e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2038652870 172 LLASTGMRVGELVQLNRSDIDFENRECVVF-GKGKKERPVYFDARTKIHLRN--------YLNDRKD--SHPALFVTLVG 240
Cdd:PRK15417  139 LLYGTGMRISEGLQLRVKDLDFDHGTIIVReGKGSKDRALMLPESLAPSLREqlsrarawWLKDQAEgrSGVALPDALER 218

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2038652870 241 KVQRLG------------------IAGVEIR-----------LRKLGDKLGIQK-VHPHKFRRTLATKAIDKGMPIEQVQ 290
Cdd:PRK15417  219 KYPRAGhswpwfwvfaqhthstdpRSGVVRRhhmydqtfqraFKRAVEQAGITKpATPHTLRHSFATALLRSGYDIRTVQ 298

                         170
                  ....*....|....*..
gi 2038652870 291 KLLGHSKIDTTLAYAMV 307
Cdd:PRK15417  299 DLLGHSDVSTTMIYTHV 315
INT_P4_C cd00801
Bacteriophage P4 integrase, C-terminal catalytic domain; P4-like integrases are found in ...
 169-297 2.11e-07

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: 50.35  E-value: 2.11e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2038652870 169 IIDLLASTGMRVGELVQLNRSDIDFENRECVV---FGKGKKERPVYFDARTKIHLRNYLNDRKDSHPaLFVTLVGKVQRL 245
Cdd:cd00801    24 ALRLLLLTGQRIGELARARWSEIDLEEKTWTIpaeRTKNKRPHRVPLSDQALEILEELKEFTGDSGY-LFPSRRKKKKPI 102

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|..
gi 2038652870 246 GIAGVEIRLRKLGDKLGIQkvHPHKFRRTLATKAIDKGMPIEQVQKLLGHSK 297
Cdd:cd00801   103 SENTINKALKRLGYKGKEF--TPHDLRRTFSTLLNELGIDPEVIERLLNHVL 152
INT_FimBE_like cd01197
FimB and FimE and related proteins, integrase/recombinases; This CD includes proteins similar ...
 165-308 3.64e-07

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: 49.43  E-value: 3.64e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2038652870 165 RDLAIIDLLASTGMRVGELVQLNRSDIDFENReCVVFGKGKK----ERPVYFDARTKihLRNYLNDRKDSHPA----LFV 236
Cdd:cd01197    27 RDYCLLLLAFRHGFRVSELCDLHLSDVDLESR-RLHIRRLKNgfstTHPLRFDEREA--LEAWLKERANWKGAdtdwIFL 103

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2038652870 237 T-LVGKVQRLGIAGVeirLRKLGDKLGIQ-KVHPHKFRRTLATKAIDKGMPIEQVQKLLGHSKIDTTLAYAMVN 308
Cdd:cd01197   104 SrRGGPLSRQQAYRI---IRDLGKEAGTVtQTHPHMLRHACGYALADRGADTRLIQDYLGHRNIRHTVIYTASN 174
Phage_int_SAM_1 pfam02899
Phage integrase, N-terminal SAM-like domain;
57-126 3.63e-04

Phage integrase, N-terminal SAM-like domain;


Pssm-ID: 427047 [Multi-domain]  Cd Length: 83  Bit Score: 38.78  E-value: 3.63e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2038652870  57 EGCSSKTIRYYQRTIENLFNAIKE---SVTQLTTDDLRSYLANYqSEKDCSKANLDNIRRILSSFFAWLEQEE 126
Cdd:pfam02899  12 RGLSPHTLRAYRRDLLAFLKFLSEggsSLEQITTSDVRAFLAEL-RAQGLSASSLARRLSALRSFYQFLIREG 83
PRK09871 PRK09871
tyrosine recombinase; Provisional
 165-308 5.62e-04

tyrosine recombinase; Provisional


Pssm-ID: 182126  Cd Length: 198  Bit Score: 40.35  E-value: 5.62e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2038652870 165 RDLAIIDLLASTGMRVGELVQLNRSDIDF-ENRECVVFGKG--KKERPVYFDARTKIHLRNYLN------DRKDshpALF 235
Cdd:PRK09871   27 RDYCLILLAYRHGMRISELLDLHYQDLDLnEGRINIRRLKNgfSTVHPLRFDEREAVERWTQERanwkgaDRTD---AIF 103

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2038652870 236 VTLVGkvQRLGIAGVEIRLRKLGDKLG-IQKVHPHKFRRTLATKAIDKGMPIEQVQKLLGHSKIDTTLAYAMVN 308
Cdd:PRK09871  104 ISRRG--SRLSRQQAYRIIRDAGIEAGtVTQTHPHMLRHACGYELAERGADTRLIQDYLGHRNIRHTVRYTASN 175
COG4342 COG4342
Phage integrase/recombinase [Mobilome: prophages, transposons];
60-296 7.19e-03

Phage integrase/recombinase [Mobilome: prophages, transposons];


Pssm-ID: 443483 [Multi-domain]  Cd Length: 278  Bit Score: 37.38  E-value: 7.19e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2038652870  60 SSKTIRYYQRTIENLFNAIKESVTQLTTDDLRSYLANYQS---EKDCSKANL----DNIRRILSSFFAWLEQEEYI---- 128
Cdd:COG4342    12 GLRVIILTEGLLEEFLEWLVKRVSEKTAKDYISALDRYLSiltPEDLREIELakekKNLVKALRNLANFLVERGIIseev 91

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2038652870 129 ---IKNPIRRIK-----KIKTEQNVKETYtdEHLEIMRDNCENLrdlaiIDLLASTGMRVGELVQL----NRSDIDFENR 196
Cdd:COG4342    92 aekIKEVLKVKRsgvdlYVPTDEEIREAL--KYLKEKDEEVYLL-----YKLLLFSGLRLSEALRLlnnfDPEKLVCEDG 164

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2038652870 197 ECVV---FGKGKKERPVYFdartkihlrnylndrkdsHPALFVTLVGKVQRLGIAGVEIRLRKLGdklgiqKVHPHKFRR 273
Cdd:COG4342   165 IARYplgWSRGSKRAFYAY------------------FPAEFARELEKLDITSYRTVKDRLRRKG------LVSAKYIRK 220

                         250       260
                  ....*....|....*....|...
gi 2038652870 274 TLATKAIDKGMPIEQVQKLLGHS 296
Cdd:COG4342   221 WVANKMIELGIPEEVIDFIQGRA 243
 
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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