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Conserved domains on  [gi|663526247|gb|AIF16426|]
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tyrosine recombinase XerC (xerD) [uncultured marine group II/III euryarchaeote KM3_74_C08]

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];
67-363 5.12e-62

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


:

Pssm-ID: 443999 [Multi-domain]  Cd Length: 291  Bit Score: 201.38  E-value: 5.12e-62
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 663526247  67 WFECWLQRLRTEKK-SEHTIRAYTVAARTLsTTSLPGEPPLDWEQAKAISVREFHsrvdpnrgrmdAWLNGiGGLKPATV 145
Cdd:COG4974    6 LLEAFLEELKREKGlSPNTIKAYRRDLRRF-LRFLEELGKIPLAEITPEDIRAYL-----------NYLRE-RGLSPSTI 72

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 663526247 146 NARIAAASHLLQW------VGHTMPDWIQRPNRSRSLPRTLGRNELGRVRTAATQS--EDPLAQPVVTILLDTGLRVSEL 217
Cdd:COG4974   73 NRYLAALRSFFRYavreglLEDNPAAKVKLPKKPRKLPRVLTEEEIEALLEALDTEtpEGLRDRALLLLLYATGLRVSEL 152

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 663526247 218 CGLDIDDVDVEDMSALVIGGKGEKDRTVLFTQATVDAIEAWtpIRNARvqmsegEDRERSLLLSSRGRRMNPRSVQKLID 297
Cdd:COG4974  153 LGLKWSDIDLDRGTIRVRRGKGGKERTVPLSPEALEALREY--LEERR------PRDSDYLFPTRRGRPLSRRAIRKILK 224

                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 663526247 298 RLADAAEIPRsRLSPHTLRHTFATGLLERGADLVTIQRLLGHASIATTRVYLEIGDQTLREIYHRA 363
Cdd:COG4974  225 RLAKRAGIPK-RVTPHSLRHTFATHLLEAGVDLRTVQELLGHSSISTTQIYTHVSDEELREAVEKL 289
 
Name Accession Description Interval E-value
XerD COG4974
Site-specific recombinase XerD [Replication, recombination and repair];
67-363 5.12e-62

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


Pssm-ID: 443999 [Multi-domain]  Cd Length: 291  Bit Score: 201.38  E-value: 5.12e-62
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 663526247  67 WFECWLQRLRTEKK-SEHTIRAYTVAARTLsTTSLPGEPPLDWEQAKAISVREFHsrvdpnrgrmdAWLNGiGGLKPATV 145
Cdd:COG4974    6 LLEAFLEELKREKGlSPNTIKAYRRDLRRF-LRFLEELGKIPLAEITPEDIRAYL-----------NYLRE-RGLSPSTI 72

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 663526247 146 NARIAAASHLLQW------VGHTMPDWIQRPNRSRSLPRTLGRNELGRVRTAATQS--EDPLAQPVVTILLDTGLRVSEL 217
Cdd:COG4974   73 NRYLAALRSFFRYavreglLEDNPAAKVKLPKKPRKLPRVLTEEEIEALLEALDTEtpEGLRDRALLLLLYATGLRVSEL 152

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 663526247 218 CGLDIDDVDVEDMSALVIGGKGEKDRTVLFTQATVDAIEAWtpIRNARvqmsegEDRERSLLLSSRGRRMNPRSVQKLID 297
Cdd:COG4974  153 LGLKWSDIDLDRGTIRVRRGKGGKERTVPLSPEALEALREY--LEERR------PRDSDYLFPTRRGRPLSRRAIRKILK 224

                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 663526247 298 RLADAAEIPRsRLSPHTLRHTFATGLLERGADLVTIQRLLGHASIATTRVYLEIGDQTLREIYHRA 363
Cdd:COG4974  225 RLAKRAGIPK-RVTPHSLRHTFATHLLEAGVDLRTVQELLGHSSISTTQIYTHVSDEELREAVEKL 289
xerC PRK00236
site-specific tyrosine recombinase XerC; Reviewed
 71-363 1.78e-58

site-specific tyrosine recombinase XerC; Reviewed


Pssm-ID: 234698 [Multi-domain]  Cd Length: 297  Bit Score: 192.29  E-value: 1.78e-58
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 663526247  71 WLQRLRTEK-KSEHTIRAYTVAARTLSTTsLPGEPPLDWEQAKAISVREFHSRvdpnrgRMDAwlngigGLKPATVNARI 149
Cdd:PRK00236  13 FLEYLRVERgLSPHTLRAYRRDLRAFLAF-LEEHGISSLQDLDAADLRSFLAR------RRRQ------GLSARSLARRL 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 663526247 150 AAASHLLQW------VGHTMPDWIQRPNRSRSLPRTLGRNELGRVRTAATQsEDPLA---QPVVTILLDTGLRVSELCGL 220
Cdd:PRK00236  80 SALRSFYRWlvrrglLKANPAAGLRAPKIPKRLPKPLDVDQAKRLLDAIDE-DDPLAlrdRAILELLYGSGLRLSELVGL 158

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 663526247 221 DIDDVDVEDMSALVIGgKGEKDRTVLFTQATVDAIEAWTPIRNarvqmsEGEDRERSLLLSSRGRRMNPRSVQKLIDRLA 300
Cdd:PRK00236 159 DIDDLDLASGTLRVLG-KGNKERTVPLGRAAREALEAYLALRP------LFLPDDDALFLGARGGRLSPRVVQRRVKKLG 231

                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 663526247 301 DAAEIPrSRLSPHTLRHTFATGLLERGADLVTIQRLLGHASIATTRVYLEIGDQTLREIYHRA 363
Cdd:PRK00236 232 KKAGLP-SHITPHKLRHSFATHLLESGGDLRAVQELLGHASLSTTQIYTHVDFQHLAEVYDAA 293
recomb_XerC TIGR02224
tyrosine recombinase XerC; The phage integrase family describes a number of recombinases with ...
 71-364 6.32e-57

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: 188.20  E-value: 6.32e-57
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 663526247   71 WLQRLRTEKK-SEHTIRAYT----VAARTLSTTSLPgeppLDWEQAKAISVREFHSRvdpnrgRMDAwlngigGLKPATV 145
Cdd:TIGR02224   3 FLEYLRLERNySPHTVRAYRrdleAFLEFLEEEGGL----ASLAEVTAADLRSFLAE------LHAR------GLSRRSL 66

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 663526247  146 NARIAA----ASHLLQ--WVGHTMPDWIQRPNRSRSLPRTLGRNELGRV-RTAATQSEDPLA---QPVVTILLDTGLRVS 215
Cdd:TIGR02224  67 ARKLSAlrsfYRFLLRrgLIDANPAAGVRAPKQPKKLPKFLSEDEMEALlDAPEEDDEDWLAlrdRAILELLYSSGLRVS 146

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 663526247  216 ELCGLDIDDVDVEDMSALVIGgKGEKDRTVLFTQATVDAIEAWTPIRNARVQMSEGEDrerSLLLSSRGRRMNPRSVQKL 295
Cdd:TIGR02224 147 ELVGLDLSDLDLDFGEVRVRG-KGNKERIVPFGPYARDALQAYLEARRSPLLASEGQD---ALFLNRRGGRLTPRGVQYR 222

                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 663526247  296 IDRLADAAEIPRsRLSPHTLRHTFATGLLERGADLVTIQRLLGHASIATTRVYLEIGDQTLREIYHRAQ 364
Cdd:TIGR02224 223 LQQLRAKAGLPK-HVHPHALRHSFATHLLNNGADLRAVQELLGHASLSTTQIYTHVDFQHLAKVYDQAH 290
INT_XerDC_C cd00798
XerD and XerC integrases, C-terminal catalytic domains; XerDC-like integrases are involved in ...
 210-348 7.71e-47

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: 158.06  E-value: 7.71e-47
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 663526247 210 TGLRVSELCGLDIDDVDVEDMSALVIGgKGEKDRTVLFTQATVDAIEAWtpIRNARVQMSEGEDRErSLLLSSRGRRMNP 289
Cdd:cd00798   31 SGLRVSELVGLDLSDVDLDEGLVRVTG-KGNKERLVPFGSYAVEALEEY--LEERRPLLLKKKPPD-ALFLNKRGKRLSR 106

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 663526247 290 RSVQKLIDRLADAAEIPRsRLSPHTLRHTFATGLLERGADLVTIQRLLGHASIATTRVY 348
Cdd:cd00798  107 RGVWRILKKYAERAGLPK-HVSPHTLRHSFATHLLEGGADLRVVQELLGHASLSTTQIY 164
Phage_integrase pfam00589
Phage integrase family; Members of this family cleave DNA substrates by a series of staggered ...
 206-348 2.66e-35

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: 127.44  E-value: 2.66e-35
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 663526247  206 ILLDTGLRVSELCGLDIDDVDVEDMSALVIGGKGEKDRTVLFTQATVDAIEAWTPIRnarvqMSEGEDRErSLLLSSRGR 285
Cdd:pfam00589  29 LLYATGLRISELCSLRWSDIDFENGVIRVHRGKGNKERTVPLSDAALELLKEWLSKR-----LLEAPKSD-YLFASKRGK 102

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 663526247  286 RMNPRSVQKLIDRLADAAEIpRSRLSPHTLRHTFATGLLERGADLVTIQRLLGHASIATTRVY 348
Cdd:pfam00589 103 PLSRQTVRKIFKRAGKEAGL-ELPLHPHMLRHSFATHLLEAGVDLRVVQKLLGHSSISTTQIY 164
 
Name Accession Description Interval E-value
XerD COG4974
Site-specific recombinase XerD [Replication, recombination and repair];
67-363 5.12e-62

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


Pssm-ID: 443999 [Multi-domain]  Cd Length: 291  Bit Score: 201.38  E-value: 5.12e-62
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 663526247  67 WFECWLQRLRTEKK-SEHTIRAYTVAARTLsTTSLPGEPPLDWEQAKAISVREFHsrvdpnrgrmdAWLNGiGGLKPATV 145
Cdd:COG4974    6 LLEAFLEELKREKGlSPNTIKAYRRDLRRF-LRFLEELGKIPLAEITPEDIRAYL-----------NYLRE-RGLSPSTI 72

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 663526247 146 NARIAAASHLLQW------VGHTMPDWIQRPNRSRSLPRTLGRNELGRVRTAATQS--EDPLAQPVVTILLDTGLRVSEL 217
Cdd:COG4974   73 NRYLAALRSFFRYavreglLEDNPAAKVKLPKKPRKLPRVLTEEEIEALLEALDTEtpEGLRDRALLLLLYATGLRVSEL 152

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 663526247 218 CGLDIDDVDVEDMSALVIGGKGEKDRTVLFTQATVDAIEAWtpIRNARvqmsegEDRERSLLLSSRGRRMNPRSVQKLID 297
Cdd:COG4974  153 LGLKWSDIDLDRGTIRVRRGKGGKERTVPLSPEALEALREY--LEERR------PRDSDYLFPTRRGRPLSRRAIRKILK 224

                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 663526247 298 RLADAAEIPRsRLSPHTLRHTFATGLLERGADLVTIQRLLGHASIATTRVYLEIGDQTLREIYHRA 363
Cdd:COG4974  225 RLAKRAGIPK-RVTPHSLRHTFATHLLEAGVDLRTVQELLGHSSISTTQIYTHVSDEELREAVEKL 289
xerC PRK00236
site-specific tyrosine recombinase XerC; Reviewed
 71-363 1.78e-58

site-specific tyrosine recombinase XerC; Reviewed


Pssm-ID: 234698 [Multi-domain]  Cd Length: 297  Bit Score: 192.29  E-value: 1.78e-58
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 663526247  71 WLQRLRTEK-KSEHTIRAYTVAARTLSTTsLPGEPPLDWEQAKAISVREFHSRvdpnrgRMDAwlngigGLKPATVNARI 149
Cdd:PRK00236  13 FLEYLRVERgLSPHTLRAYRRDLRAFLAF-LEEHGISSLQDLDAADLRSFLAR------RRRQ------GLSARSLARRL 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 663526247 150 AAASHLLQW------VGHTMPDWIQRPNRSRSLPRTLGRNELGRVRTAATQsEDPLA---QPVVTILLDTGLRVSELCGL 220
Cdd:PRK00236  80 SALRSFYRWlvrrglLKANPAAGLRAPKIPKRLPKPLDVDQAKRLLDAIDE-DDPLAlrdRAILELLYGSGLRLSELVGL 158

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 663526247 221 DIDDVDVEDMSALVIGgKGEKDRTVLFTQATVDAIEAWTPIRNarvqmsEGEDRERSLLLSSRGRRMNPRSVQKLIDRLA 300
Cdd:PRK00236 159 DIDDLDLASGTLRVLG-KGNKERTVPLGRAAREALEAYLALRP------LFLPDDDALFLGARGGRLSPRVVQRRVKKLG 231

                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 663526247 301 DAAEIPrSRLSPHTLRHTFATGLLERGADLVTIQRLLGHASIATTRVYLEIGDQTLREIYHRA 363
Cdd:PRK00236 232 KKAGLP-SHITPHKLRHSFATHLLESGGDLRAVQELLGHASLSTTQIYTHVDFQHLAEVYDAA 293
recomb_XerC TIGR02224
tyrosine recombinase XerC; The phage integrase family describes a number of recombinases with ...
 71-364 6.32e-57

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: 188.20  E-value: 6.32e-57
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 663526247   71 WLQRLRTEKK-SEHTIRAYT----VAARTLSTTSLPgeppLDWEQAKAISVREFHSRvdpnrgRMDAwlngigGLKPATV 145
Cdd:TIGR02224   3 FLEYLRLERNySPHTVRAYRrdleAFLEFLEEEGGL----ASLAEVTAADLRSFLAE------LHAR------GLSRRSL 66

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 663526247  146 NARIAA----ASHLLQ--WVGHTMPDWIQRPNRSRSLPRTLGRNELGRV-RTAATQSEDPLA---QPVVTILLDTGLRVS 215
Cdd:TIGR02224  67 ARKLSAlrsfYRFLLRrgLIDANPAAGVRAPKQPKKLPKFLSEDEMEALlDAPEEDDEDWLAlrdRAILELLYSSGLRVS 146

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 663526247  216 ELCGLDIDDVDVEDMSALVIGgKGEKDRTVLFTQATVDAIEAWTPIRNARVQMSEGEDrerSLLLSSRGRRMNPRSVQKL 295
Cdd:TIGR02224 147 ELVGLDLSDLDLDFGEVRVRG-KGNKERIVPFGPYARDALQAYLEARRSPLLASEGQD---ALFLNRRGGRLTPRGVQYR 222

                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 663526247  296 IDRLADAAEIPRsRLSPHTLRHTFATGLLERGADLVTIQRLLGHASIATTRVYLEIGDQTLREIYHRAQ 364
Cdd:TIGR02224 223 LQQLRAKAGLPK-HVHPHALRHSFATHLLNNGADLRAVQELLGHASLSTTQIYTHVDFQHLAKVYDQAH 290
XerC COG4973
Site-specific recombinase XerC [Replication, recombination and repair];
66-360 7.74e-56

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


Pssm-ID: 443998 [Multi-domain]  Cd Length: 287  Bit Score: 185.17  E-value: 7.74e-56
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 663526247  66 PWFECWLQRLRTEKKSEHTIRAYTVAARTLstTSLPGEPPLDWEQAKAISVREFHSRVdpnRGRmdawlngigGLKPATV 145
Cdd:COG4973    6 EALEAYLEHLRERRLSPKTLEAYRRDLRRL--IPLLGDADLPLEELTPADVRRFLARL---HRR---------GLSPRTL 71

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 663526247 146 NARIAAASHLLQW------VGHTMPDWIQRPNRSRSLPRTLGRNELGRVRTAAtqSEDPLA---QPVVTILLDTGLRVSE 216
Cdd:COG4973   72 NRRLSALRSFFNWavreglLEANPAAGVKAPKAPRKLPRALTVDELAQLLDAL--ADDPLAvrdRAIVELLYSTGLRLGE 149

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 663526247 217 LCGLDIDDVDVEDmSALVIGGKGEKDRTVLFTQATVDAIEAWTPIRNARVQmsegeDRERSLLLSSRGRRMNPRSVQKLI 296
Cdd:COG4973  150 LVGLDWEDVDLDA-GEVRVRGKTGKSRTVPLGPKALAALREWLAVRPELAA-----PDEGALFPSRRGTRLSPRNVQKRL 223

                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 663526247 297 DRLADAAEIPRsRLSPHTLRHTFATGLLERGADLVTIQRLLGHASIATTRVYLEIGDQTLREIY 360
Cdd:COG4973  224 RRLAKKAGLPK-HVHPHDLRHSFATHLLESGGDLRAVQELLGHASISTTQIYTHLDFQHLAEVY 286
INT_XerDC_C cd00798
XerD and XerC integrases, C-terminal catalytic domains; XerDC-like integrases are involved in ...
 210-348 7.71e-47

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: 158.06  E-value: 7.71e-47
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 663526247 210 TGLRVSELCGLDIDDVDVEDMSALVIGgKGEKDRTVLFTQATVDAIEAWtpIRNARVQMSEGEDRErSLLLSSRGRRMNP 289
Cdd:cd00798   31 SGLRVSELVGLDLSDVDLDEGLVRVTG-KGNKERLVPFGSYAVEALEEY--LEERRPLLLKKKPPD-ALFLNKRGKRLSR 106

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 663526247 290 RSVQKLIDRLADAAEIPRsRLSPHTLRHTFATGLLERGADLVTIQRLLGHASIATTRVY 348
Cdd:cd00798  107 RGVWRILKKYAERAGLPK-HVSPHTLRHSFATHLLEGGADLRVVQELLGHASLSTTQIY 164
recomb_XerD TIGR02225
tyrosine recombinase XerD; The phage integrase family describes a number of recombinases with ...
 71-360 8.91e-44

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: 153.89  E-value: 8.91e-44
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 663526247   71 WLQRLRTEK-KSEHTIRAYtvaARTLST-TSLPGEPPLDWEQAKAISVREFHsrvdpnrgrmdAWLNGIGgLKPATVNAR 148
Cdd:TIGR02225   3 FLDYLWVERgLSQNTLEAY---RRDLEKfLEFLEERGIDLEEVDRGDIVDFL-----------AELKEAG-LSARSIARA 67

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 663526247  149 IAAASHLLQWV---GHTMPD---WIQRPNRSRSLPRTLGRNELGRVrTAATQSEDPLA---QPVVTILLDTGLRVSELCG 219
Cdd:TIGR02225  68 LSALRSFYRFLlreGIREDDpsaLIEPPKVARKLPKVLTVEEVEAL-LAAPDVDTPLGlrdRAMLELLYATGLRVSELVG 146

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 663526247  220 LDIDDVDVEDMSALVIGgKGEKDRTVLFTQATVDAIEAWtpIRNARVQMSEG-EDRERSLLLSSRGRRMNPRSVQKLIDR 298
Cdd:TIGR02225 147 LRLEDVNLDEGFVRVRG-KGNKERLVPLGEEAIEALERY--LKEARPLLLKKkVKESDALFLNRRGGPLSRQGVWKILKE 223

                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 663526247  299 LADAAEIpRSRLSPHTLRHTFATGLLERGADLVTIQRLLGHASIATTRVYLEIGDQTLREIY 360
Cdd:TIGR02225 224 YAKRAGI-EKPISPHTLRHSFATHLLENGADLRVVQELLGHADISTTQIYTHVARERLKEVH 284
xerD PRK00283
tyrosine recombinase;
138-363 8.47e-42

tyrosine recombinase;


Pssm-ID: 234713 [Multi-domain]  Cd Length: 299  Bit Score: 148.80  E-value: 8.47e-42
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 663526247 138 GGLKPATVNARIAAASHLLQWV---GHTMPD---WIQRPNRSRSLPRTLGRNELGRVrTAATQSEDPLAQ---PVVTILL 208
Cdd:PRK00283  66 GGYKATSSARRLSALRRFFQFLlreGLREDDpsaLLDSPKLPRRLPKTLSEAQVEAL-LDAPDIDTPLGLrdrAMLELLY 144

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 663526247 209 DTGLRVSELCGLDIDDVDVEDMSALVIGgKGEKDRTVLFTQATVDAIEAWtpIRNARVQMSEGEDRErSLLLSSRGRRMN 288
Cdd:PRK00283 145 ATGLRVSELVGLTLDDVSLRQGVVRVTG-KGNKERLVPLGEEAVYAIERY--LERGRPALLNGRSSD-ALFPSARGGQLT 220

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 663526247 289 PRSVQKLIDRLADAAEIPRSRLSPHTLRHTFATGLLERGADLVTIQRLLGHASIATTRVYLEIGDQTLREIYHRA 363
Cdd:PRK00283 221 RQTFWHRIKHYAKRAGIDPKKLSPHVLRHAFATHLLNHGADLRVVQELLGHSDISTTQIYTHVATERLKELHAQH 295
DNA_BRE_C cd00397
DNA breaking-rejoining enzymes, C-terminal catalytic domain; The DNA breaking-rejoining enzyme ...
 203-349 1.96e-35

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: 127.98  E-value: 1.96e-35
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 663526247 203 VVTILLDTGLRVSELCGLDIDDVDVEDMSALVIGGK--GEKDRTVLFTQATVDAIEAWTPIRNARVQMSEGEDRERSLLL 280
Cdd:cd00397   22 ILLLLLETGLRISELLALKVKDIDLDNGTIRVRGKKtkGGKERTVPLPKELAEELKEYLKERRDKRGPLLKSLYLNKLFG 101

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 663526247 281 SSRGRRMNPRSVQKLIDRLADAAEIprsRLSPHTLRHTFATGLLERGADLVTIQRLLGHASIATTRVYL 349
Cdd:cd00397  102 TKLGERLSRRTLRRIFKKAGIEAGR---KITPHSLRHTFATNLLENGVDIKVVQKLLGHSSISTTQRYL 167
Phage_integrase pfam00589
Phage integrase family; Members of this family cleave DNA substrates by a series of staggered ...
 206-348 2.66e-35

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: 127.44  E-value: 2.66e-35
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 663526247  206 ILLDTGLRVSELCGLDIDDVDVEDMSALVIGGKGEKDRTVLFTQATVDAIEAWTPIRnarvqMSEGEDRErSLLLSSRGR 285
Cdd:pfam00589  29 LLYATGLRISELCSLRWSDIDFENGVIRVHRGKGNKERTVPLSDAALELLKEWLSKR-----LLEAPKSD-YLFASKRGK 102

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 663526247  286 RMNPRSVQKLIDRLADAAEIpRSRLSPHTLRHTFATGLLERGADLVTIQRLLGHASIATTRVY 348
Cdd:pfam00589 103 PLSRQTVRKIFKRAGKEAGL-ELPLHPHMLRHSFATHLLEAGVDLRVVQKLLGHSSISTTQIY 164
INT_IntI_C cd01193
Integron integrase and similar protiens, C-terminal catalytic domain; Integron integrases ...
 176-351 8.31e-34

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: 123.92  E-value: 8.31e-34
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 663526247 176 LPRTLGRNELGRVRTAATQSEDPLAqpvVTILLDTGLRVSELCGLDIDDVDVEDMSALVIGGKGEKDRTVLFTQATVDAI 255
Cdd:cd01193    2 LPVVLSPDEVRRILGALTELRHRLI---LSLLYGAGLRISELLRLRVKDIDFERGVIRVRQGKGGKDRVVPLPEKLLEPL 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 663526247 256 EAWTPIRNARVQMSEGEDRERSLLLSSRGRR---MNPRSVQKLIDRLADAAEIpRSRLSPHTLRHTFATGLLERGADLVT 332
Cdd:cd01193   79 RRYLKSARPKEELDPAEGRAGVLDPRTGVERrhhISETTVQRALKKAVEQAGI-TKRVTPHTLRHSFATHLLEAGTDIRT 157

                        170
                 ....*....|....*....
gi 663526247 333 IQRLLGHASIATTRVYLEI 351
Cdd:cd01193  158 IQELLGHSDLSTTMIYTHV 176
INT_RitC_C_like cd01182
C-terminal catalytic domain of recombinase RitC, a component of the recombinase trio; ...
 206-358 6.79e-32

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: 118.92  E-value: 6.79e-32
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 663526247 206 ILLDTGLRVSELCGLDIDDVDVEDMSALVIGGKGEKDRTVLFTQATVDAIEAWTPIRNARvqmsEGEDRERSLLLSSRGR 285
Cdd:cd01182   29 LLYDTGARVQELADLTIRDLRLDDPATVRLHGKGRKERTVPLWKETVAALKAYLQEFHLT----PDPKQLFPLFPNRRGQ 104

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 663526247 286 RMNPRSVQKLIDRLADAA--EIP--RSRLSPHTLRHTFATGLLERGADLVTIQRLLGHASIATTRVYLEIGDQTLRE 358
Cdd:cd01182  105 PLTRDGVAYILNKYVALAsnRCPslPKRITPHTLRHTKAMHLLQAGVDLTVIRDWLGHESVETTQIYAEADLEMKRE 181
xerS PRK05084
site-specific tyrosine recombinase XerS; Reviewed
 207-358 1.25e-29

site-specific tyrosine recombinase XerS; Reviewed


Pssm-ID: 235339 [Multi-domain]  Cd Length: 357  Bit Score: 117.33  E-value: 1.25e-29
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 663526247 207 LLDTGLRVSELCGLDIDDVDVEDMSALVIGgKGEKDRTVLFTQATVDAIEAWTPIRNARVQMsegEDRERSLLLSSR--- 283
Cdd:PRK05084 204 ILGSGLRVSELVNLDLSDLNLKQMTIDVTR-KGGKRDSVNIAPFALPYLEEYLKIRASRYKA---EKQEKALFLTKYrgk 279

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 663526247 284 GRRMNPRSVQKLIDRLADAAEIPrsrLSPHTLRHTFATGLLERGADLVTIQRLLGHASIATTRVYLEIGDQTLRE 358
Cdd:PRK05084 280 PNRISARAIEKMVAKYSEAFGVR---LTPHKLRHTLATRLYDATKDQVLVADQLGHTSTETTDLYTHIVNDEQKE 351
INT_RitA_C_like cd01188
C-terminal catalytic domain of recombinase RitA, a component of the recombinase trio; ...
 203-359 2.88e-29

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: 111.95  E-value: 2.88e-29
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 663526247 203 VVTILLDTGLRVSELCGLDIDDVDVEDMSALVIGGKGEKDRTVLFTQATVDAIEAWtpIRNARvqmseGEDRERSLLLSS 282
Cdd:cd01188   25 ILLLLARLGLRAGDVAGLRLDDIDWRSGTITVRQKKTGRPVELPLTEPVGEALADY--LRDGR-----PRTDSREVFLRA 97

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 663526247 283 R---GRRMNPRSVQKLIDRLADAAEIPRSRLSPHTLRHTFATGLLERGADLVTIQRLLGHASIATTRVYLEIGDQTLREI 359
Cdd:cd01188   98 RapyRPLSSTSQISSIVRRYLRKAGIEPSHRGTHSLRHSLATRMLRAGTSLKVIADLLGHRSIETTAIYAKIDVDDLREV 177
INT_C_like_4 cd01194
Uncharacterized site-specific tyrosine recombinase, C-terminal catalytic domain; Tyrosine ...
 203-349 1.44e-21

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: 90.90  E-value: 1.44e-21
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 663526247 203 VVTILLDTGLRVSELCGLDIDDVD-VEDMSALVIGGKG--EKDRTVLFTQATVDAIEAWTpirNARVQMSEGEDRERSLL 279
Cdd:cd01194   27 IISLMVTEGLRTVEIVRADVGDLRqEGEGTILYVQGKGktSKDDFVYLRPDVLKALQAYL---KARGKLDFEEPLFTSLS 103

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 663526247 280 LSSRGRRMNPRSVQKLIDRLADAAEIPRSRLSPHTLRHTFATGLLERGADLVTIQRLLGHASIATTRVYL 349
Cdd:cd01194  104 NNSKGQRLTTRSIRRIIKKYLRKAGLDDDRLTAHSLRHTAGTLALKAGKSLREVQQLLRHSDPNTTMIYA 173
integrase_gron TIGR02249
integron integrase; Members of this family are integrases associated with integrons (and ...
 164-348 1.92e-21

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: 93.61  E-value: 1.92e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 663526247  164 PDWIQRPNRSRSLPRTLGRNELGRVRTAAtqseDPLAQPVVTILLDTGLRVSELCGLDIDDVDVEDMSALVIGGKGEKDR 243
Cdd:TIGR02249  86 MERFVRAKRPRKLPVVLTREEVRRLLEHL----EGKYRLIAKLLYGSGMRLMECLRLRIQDIDFDYGEIRIRQGKGGKDR 161

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 663526247  244 TV---------LFTQ-ATVDAIEAWTPIRN-ARVQMSEGEDR-----ERSL----LLSSRGRRMNPRS------------ 291
Cdd:TIGR02249 162 TVtlpkelippLREQiELARAYHEADLAEGyGGVYLPHALARkypnaPKEWgwqyLFPSHRLSRDPESgvirrhhinett 241

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 663526247  292 VQKLIDRLADAAEIPRSrLSPHTLRHTFATGLLERGADLVTIQRLLGHASIATTRVY 348
Cdd:TIGR02249 242 IQRAVRRAVERAGIEKP-VTCHTLRHSFATHLLESGADIRTVQELLGHSDVKTTQIY 297
INT_ICEBs1_C_like cd01189
C-terminal catalytic domain of integrases from bacterial phages and conjugate transposons; ...
 182-348 3.13e-21

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: 89.16  E-value: 3.13e-21
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 663526247 182 RNELGRVRTAATQSEDPLAqPVVTILLDTGLRVSELCGLDIDDVDvedmsalviggkgekdrtvlFTQATVDaieawtpI 261
Cdd:cd01189    1 PEELKKLLEALKKRGDRYY-LLFLLALLTGLRRGELLALTWSDID--------------------FENGTIR-------I 52

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 663526247 262 RNARVQMSEGEDRERSLLlSSRGRR---MNPRSVQKL-----IDRLADAAEIPRsrLSPHTLRHTFATGLLERGADLVTI 333
Cdd:cd01189   53 NRTLVRKKKGGYVIKPPK-TKSSIRtipLPDELIELLkelkaFKKLLKKAGLPR--ITPHDLRHTFASLLLEAGVPLKVI 129

                        170
                 ....*....|....*.
gi 663526247 334 QRLLGHASIATT-RVY 348
Cdd:cd01189  130 AERLGHSDISTTlDVY 145
INT_Rci_Hp1_C cd00796
Shufflon-specific DNA recombinase Rci and Bacteriophage Hp1_like integrase, C-terminal ...
 178-348 3.82e-21

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: 89.31  E-value: 3.82e-21
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 663526247 178 RTLGRNELGRVRTAATQSEDPLAQPVVTILLDTGLRVSELCGLDIDDVDVEDMSALVIGGKGEKDRTVLFTQATVDAIEA 257
Cdd:cd00796    3 RFLTEDEEARLLAALEESTNPHLRLIVLLALYTGARRGEILSLRWDDIDLEVGLIVLPETKNGKPRTVPLSDEAIAILKE 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 663526247 258 WtpirnarvqmsEGEDRERSLLLSSRGRRMNPRSVQKLIDRLADAAEIPRsrLSPHTLRHTFATGLLERGADLVTIQRLL 337
Cdd:cd00796   83 L-----------KRKRGKDGFFVDGRFFGIPIASLRRAFKKARKRAGLED--LRFHDLRHTFASRLVQAGVPIKTVAKIL 149

                        170
                 ....*....|.
gi 663526247 338 GHASIATTRVY 348
Cdd:cd00796  150 GHSSIKMTMRY 160
INT_C_like_5 cd01195
Uncharacterized site-specific tyrosine recombinase, C-terminal catalytic domain; Tyrosine ...
 203-348 1.62e-19

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: 84.83  E-value: 1.62e-19
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 663526247 203 VVTILLDTGLRVSELCGLDIDDVDVEDMSaLVIGGKGEKDRT-VLFTQATVDAIEAWTPIRNarvqmSEGEDRERSLLLS 281
Cdd:cd01195   25 LVRLLLDNALRRSEAVALDVEDLEKEHRR-LRILGKGKKQREvVTLPPTTREALAAWLAARG-----EAEGPLFVSLDRA 98

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 663526247 282 SRGRRMNPRSVQKLIDRLADAAEIPRsRLSPHTLRHTFATGLLERGADLVT-IQRLLGHASIATTRVY 348
Cdd:cd01195   99 SRGRRLSPQAVYRIVRRLAERIGLGK-RLSPHGLRHSAITLALDAGAGLIRkVQDFSRHADLRTLQVY 165
xerC PRK01287
site-specific tyrosine recombinase XerC; Reviewed
 203-381 3.10e-16

site-specific tyrosine recombinase XerC; Reviewed


Pssm-ID: 234935 [Multi-domain]  Cd Length: 358  Bit Score: 79.40  E-value: 3.10e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 663526247 203 VVTILLDTGLRVSELCGLDIDDVDVEDMSALVIGGKGEKDRTVLFTQATVdaieAWTP--IRNARVQMSEGEDRErSLLL 280
Cdd:PRK01287 162 LLELLWSTGIRRGELARLDLYDVDASRGVVTVRQGKGNKDRVVPVGERAL----AWLQryLQDVRPQLAVRPDSG-ALFV 236

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 663526247 281 SSRGRRMNPRSVQKLIDRLADAAEIPRSRlSPHTLRHTFATGLLERGADLVTIQRLLGHASIATTRVYLEIGDQTLREIY 360
Cdd:PRK01287 237 AMDGDGLARNTLTNMVGRYIRAAGIEKAG-ACHLFRHAMATQMLENGADTRHIQAILGHAKLETTQIYTRVSIGHLQAVH 315

                        170       180
                 ....*....|....*....|....*.
gi 663526247 361 H-----RAQRELPSGEAEETEVVDSL 381
Cdd:PRK01287 316 AsthpaERKADEKLRDADEVGLLADL 341
INTN1_C_like cd01185
Integrase IntN1 of Bacteroides mobilizable transposon NBU1 and similar proteins, C-terminal ...
 210-356 2.12e-15

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: 73.07  E-value: 2.12e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 663526247 210 TGLRVSELCGLDIDD-VDVEDMSALVIG-GKGEKDRTVLFTQATVDAIEAWTPirnarvqmseGEDRERSLLLSSRGrrm 287
Cdd:cd01185   30 TGLRFSDLKNLTWKNiVEASGRTWIRYRrKKTGKPVTVPLLPVAREILEKYKD----------DRSEGKLFPVLSNQ--- 96

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 663526247 288 nprSVQKLIDRLADAAEIPRsRLSPHTLRHTFATGLLERGADLVTIQRLLGHASIATTRVYLEIGDQTL 356
Cdd:cd01185   97 ---KINRYLKEIAKIAGIDK-HLTFHVARHTFATLLLLKGVDIETISKLLGHSSIKTTQIYAKIVDSKK 161
PRK15417 PRK15417
integron integrase;
109-348 3.14e-14

integron integrase;


Pssm-ID: 185315 [Multi-domain]  Cd Length: 337  Bit Score: 73.16  E-value: 3.14e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 663526247 109 EQAKAISVR---EFHSRVDP---NRGRMDAWLNGIGGLKPATVNARIAAASHLLQWVGHTMPD---WIQ---RPNRSRSL 176
Cdd:PRK15417  34 EQAYVHWVRafiRFHGVRHPatlGSSEVEAFLSWLANERKVSVSTHRQALAALLFFYGKVLCTdlpWLQeigRPRPSRRL 113

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 663526247 177 PRTLGRNELGRVRTAATQSEDPLAQpvvtILLDTGLRVSELCGLDIDDVDVEDMSALVIGGKGEKDRTVLFTQATVDAIE 256
Cdd:PRK15417 114 PVVLTPDEVVRILGFLEGEHRLFAQ----LLYGTGMRISEGLQLRVKDLDFDHGTIIVREGKGSKDRALMLPESLAPSLR 189

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 663526247 257 AWTPIRNARVQMSEGEDRERSLLLSSRGRR--------------------MNPRS------------VQKLIDRLADAAE 304
Cdd:PRK15417 190 EQLSRARAWWLKDQAEGRSGVALPDALERKypraghswpwfwvfaqhthsTDPRSgvvrrhhmydqtFQRAFKRAVEQAG 269

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|....
gi 663526247 305 IPRSRlSPHTLRHTFATGLLERGADLVTIQRLLGHASIATTRVY 348
Cdd:PRK15417 270 ITKPA-TPHTLRHSFATALLRSGYDIRTVQDLLGHSDVSTTMIY 312
INT_RitB_C_like cd00797
C-terminal catalytic domain of recombinase RitB, a component of the recombinase trio; ...
 184-350 4.31e-14

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: 70.41  E-value: 4.31e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 663526247 184 ELGRVRTAATQSED-----PLAQPVVTILL-DTGLRVSELCGLDIDDVDVEDMSALVIGGKGEKDRTVLFTQATVDAIEA 257
Cdd:cd00797    5 EIRRLLAAADQLPPesplrPLTYATLFGLLyATGLRVGEALRLRLEDVDLDSGILTIRQTKFGKSRLVPLHPSTVGALRD 84

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 663526247 258 WTPIRNARVQMSEGEdrerSLLLSSRGRRMNPRSVQKLIDRLADAAEIPRSRLS----PHTLRHTFATGLLER----GAD 329
Cdd:cd00797   85 YLARRDRLLPSPSSS----YFFVSQQGGRLTGGGVYRVFRRLLRRIGLRGAGDGrgprLHDLRHTFAVNRLTRwyreGAD 160

                        170       180
                 ....*....|....*....|....*...
gi 663526247 330 lvtIQRLL-------GHASIATTRVYLE 350
Cdd:cd00797  161 ---VERKLpvlstylGHVNVTDTYWYLT 185
INT_C_like_3 cd01192
Uncharacterized site-specific tyrosine recombinase, C-terminal catalytic domain; Tyrosine ...
 208-359 1.04e-13

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: 68.86  E-value: 1.04e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 663526247 208 LDTGLRVSELCGLDIDDVDVEDmSALVIGGKGEKDRTVLFTQATVDAIEAWTPIRnarvqmseGEDRERSLLLSSRGRRM 287
Cdd:cd01192   34 INTGLRISDLLSLKVEDVTNKD-KLSIKEQKTGKQKTFPLNPTLVKALKEYIDDL--------DLKRNDYLFKSLKQGPE 104

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 663526247 288 NP---RSVQKLIDRLADAAEIPRSrLSPHTLRHTFATGLLERGADLVTIQRLLGHASIATTRVYLEIGDQTLREI 359
Cdd:cd01192  105 KPisrKQAYKILKKAADDLGLNYN-IGTHSLRKTFGYHVYKQGKDIELLMKLLNHSSPSITLRYLGIDQEDVDKA 178
INT_FimBE_like cd01197
FimB and FimE and related proteins, integrase/recombinases; This CD includes proteins similar ...
 211-348 1.65e-13

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: 68.30  E-value: 1.65e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 663526247 211 GLRVSELCGLDIDDVDVEDMSALVIGGKGEKDRTVLFTQATVDAIEAWTPIRnARVQMSEGEDrersLLLSSRGRRMNPR 290
Cdd:cd01197   39 GFRVSELCDLHLSDVDLESRRLHIRRLKNGFSTTHPLRFDEREALEAWLKER-ANWKGADTDW----IFLSRRGGPLSRQ 113

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 663526247 291 SVQKLIDRLADAAEIPRSRlSPHTLRHTFATGLLERGADLVTIQRLLGHASIATTRVY 348
Cdd:cd01197  114 QAYRIIRDLGKEAGTVTQT-HPHMLRHACGYALADRGADTRLIQDYLGHRNIRHTVIY 170
INT_C_like_2 cd01191
Uncharacterized site-specific tyrosine recombinase, C-terminal catalytic domain; Tyrosine ...
 203-349 2.39e-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: 271191  Cd Length: 176  Bit Score: 64.75  E-value: 2.39e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 663526247 203 VVTILLDTGLRVSELCGLDIDDVDVedmSALVIGGKGEKDRTVLFTQATVDAIEAWTPIRNARVQMsegedrersLLLSS 282
Cdd:cd01191   25 VVRFLAATGARVSELIKIKVEHVEL---GYFDIYSKGGKLRRLYIPKKLRNEALEWLKSTNRKSGY---------IFLNR 92

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 663526247 283 RGRRMNPRSVQKLIDRLADAAEIPRSRLSPHTLRHTFATGLLERGADLVTIQRLLGHASIATTRVYL 349
Cdd:cd01191   93 FGERITTRGIAQQLKNYARKYGLNPKVVYPHSFRHRFAKNFLEKYNDIALLADLMGHESIETTRIYL 159
INT_Cre_C cd00799
C-terminal catalytic domain of Cre recombinase (also called integrase); Cre-like recombinases ...
 209-357 6.20e-12

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: 63.86  E-value: 6.20e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 663526247 209 DTGLRVSELCGLDIDDVDVEDMSALVI---------GGKGE-KDRTVLFTQATVDAIEAWTpirnARVQMSEGE-----D 273
Cdd:cd00799   27 AGALRRSELVALRVEDLTRFVDGGLLIrlrrsktdqDGEGEiKALPYGPETCPVRALRAWL----EAAGIPSGPlfrriR 102

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 663526247 274 RERSLLlssrGRRMNPRSVQKLIDRLADAAEIPRSRLSPHTLRHTFATGLLERGADLVTIQRLLGHASIATTRVYLEIGD 353
Cdd:cd00799  103 RGGSVG----TTRLSDRSVARIVKRRAALAGLDPGDFSGHSLRRGFATEAARAGASLPEIMAQGGHKSVATVMRYIREAD 178


                 ....
gi 663526247 354 QTLR 357
Cdd:cd00799  179 RFKD 182
INT_tnpA_C_Tn554 cd01186
Putative Transposase A from transposon Tn554, C-terminal catalytic domain; This family ...
 203-358 2.06e-10

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: 59.35  E-value: 2.06e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 663526247 203 VVTILLDTGLRVSELCGLDIDDVDVEDMSALVIG---------GKGEKDRTVLFTQATVDAIEAWtpirnarVQMSEGED 273
Cdd:cd01186   22 LLALLYETGLRIGEALGLRIEDIDMADNQIELVPredntnearAKSMRERRIPVSQDLIDLYADY-------LTYIYCEE 94

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 663526247 274 RERS--LLLSSRGRR----MNPRSVQKLIDRLADAAEIprsRLSPHTLRHTFATGLLERGADLVTIQRLLGHASIATT-R 346
Cdd:cd01186   95 AEFSitVFVNVKGGNqgkaMNYSDVYDLVRRLKKRTGI---DFTPHMFRHTHATALIRAGWSIEVVARRLGHAHVQTTlN 171

                        170
                 ....*....|..
gi 663526247 347 VYLEIGDQTLRE 358
Cdd:cd01186  172 TYGHLSEEDIRR 183
PRK09870 PRK09870
tyrosine recombinase; Provisional
 211-369 3.85e-10

tyrosine recombinase; Provisional


Pssm-ID: 182125  Cd Length: 200  Bit Score: 59.18  E-value: 3.85e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 663526247 211 GLRVSELCGLDIDDVDVEDMSALVIGGKGEKDRTVLFTQATVDAIEAWTPIRNARvQMSEGEdrerSLLLSSRGRRMNPR 290
Cdd:PRK09870  45 GFRASEICRLRISDIDLKAKCIYIHRLKKGFSTTHPLLNKEIQALKNWLSIRTSY-PHAESE----WVFLSRKGNPLSRQ 119

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 663526247 291 SVQKLIDRLADAAEIPRSrLSPHTLRHTFATGLLERGADLVTIQRLLGHASIATTRVYLEIGDQTLREIYHRAQRELPS 369
Cdd:PRK09870 120 QFYHIISTSGGNAGLSLE-IHPHMLRHSCGFALANMGIDTRLIQDYLGHRNIRHTVWYTASNAGRFYGIWDRARGRQRH 197
FimB COG0582
Integrase/recombinase, includes phage integrase [Replication, recombination and repair, ...
 178-364 7.96e-10

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


Pssm-ID: 440347 [Multi-domain]  Cd Length: 391  Bit Score: 60.05  E-value: 7.96e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 663526247 178 RTLGRNELGRVRTAATQSE-DPLAQPVVTILLDTGLRVSELCGLDIDDVDVEDMSALVIGG--KGEKDRTV-LFTQAtVD 253
Cdd:COG0582  204 PALTPEELPELLRALDAYRgSPVTRLALRLLLLTGVRPGELRGARWSEIDLEAALWTIPAErmKTRRPHIVpLSRQA-LE 282

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 663526247 254 AIEAWTPIRnarvqmsegedRERSLLLSSR---GRRMNPRSVQKLIDRLAdaaeipRSRLSPHTLRHTFATGLLERGADL 330
Cdd:COG0582  283 ILKELKPLT-----------GDSEYVFPSRrgpKKPMSENTLNKALRRMG------YGRFTPHGFRHTASTLLNEAGFPP 345

                        170       180       190
                 ....*....|....*....|....*....|....
gi 663526247 331 VTIQRLLGHASIATTrvyleigdqtlREIYHRAQ 364
Cdd:COG0582  346 DVIERQLAHKDGNKV-----------RAAYNRAD 368
INT_tnpB_C_Tn554 cd01187
Putative Transposase B from transposon Tn554, C-terminal catalytic domain; This family ...
 202-348 9.23e-10

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: 56.67  E-value: 9.23e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 663526247 202 PVVTILLDTGLRVSELCGLDIDDvdvedmsalvIGGKGEKDRTVLFTQATVDAIEAWT--PIRNarvqmsegedrERSLL 279
Cdd:cd01187   17 PVVQAAVFTGARASELATLKFGC----------LHAQTSDDGTFLYWLKWENKGGKQLdiPISK-----------KVAEL 75

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 663526247 280 LSSRGRRMNPRSVQKLIDRLADAaeipRSRLSPHTLRHTFATGLLERGADLVTIQRLLGHASIATTRVY 348
Cdd:cd01187   76 IKTINWTLNELSELKNISDDHGE----RFRFHTHRFRHTVATRLANSGMGILVLQQLLGHSSPEMTLRY 140
INT_C_like_1 cd01184
Uncharacterized site-specific tyrosine recombinase, C-terminal catalytic domain; Tyrosine ...
 206-348 1.43e-08

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: 53.85  E-value: 1.43e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 663526247 206 ILLDTGLRVSELCGLDIDDVdVEDMSALVIGGKGEKDRTVLFTQATVDAIeawtPIRNARVQMS--------EGEDRERS 277
Cdd:cd01184   31 IGLYTGARLNEICQLRVDDI-KEEDGIWCIDINDDAEGRRLKTKASRRLV----PIHPRLIELGfldyvealRADGKLFL 105

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 663526247 278 LLLSSRGRRMNPRSVQKLIDRLADAAEIPR-SRLSPHTLRHTFATGLLERGADLVTIQRLLGHA-SIATTRVY 348
Cdd:cd01184  106 FPEKRDKDGKYSKAASKWFNRLLRKLGIKDdERKSFHSFRHTFITALKRAGVPEELIAQIVGHSrGGVTHDTY 178
INT_C_like_6 cd01196
Uncharacterized site-specific tyrosine recombinase, C-terminal catalytic domain; Tyrosine ...
 272-359 2.76e-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: 271196  Cd Length: 183  Bit Score: 53.25  E-value: 2.76e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 663526247 272 EDRERSLLLSSRG-------RRMNPRSVQKLIDRLADAAEIPrSRLSPHTLRHTFATGLLERGADLVTIQRLLGHASIAT 344
Cdd:cd01196   89 EDPKGPLFRTTRGgtrklthNPLTQANAYRMVRRRAIAADIP-TAIGNHSFRATGITAYLKNGGTLEDAQNMANHASTRT 167

                         90
                 ....*....|....*.
gi 663526247 345 TRVYLEIGDQ-TLREI 359
Cdd:cd01196  168 TQLYDRRSDKiTLDEV 183
int PHA02601
integrase; Provisional
 56-348 3.54e-08

integrase; Provisional


Pssm-ID: 222904 [Multi-domain]  Cd Length: 333  Bit Score: 54.73  E-value: 3.54e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 663526247  56 PSRLQSLSEL--PWFECWLQRLRTEKKsehtiraytVAARTLSTTSLPGEPPLDWEQAKAISvrEFHSRvdpnRGRMDAW 133
Cdd:PHA02601  55 KEDRRRLSELlqIWWDLHGQTLEDGKA---------RLAKLLILCKGLGDPIASEFTAKDFA--DYRAR----RLSGEFK 119

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 663526247 134 LNGIGGLKPATVNARIAAAS-------HLLQWVGHTMPDWIQRPNRSRSLPRTLGRNELGRVRTAATQSEDPLAQPVVTI 206
Cdd:PHA02601 120 VNKGRPIKPATVNRELAYLSavfneliKLGKWSGPNPLDGIRPFKEAEPELAFLTKEEIERLLDACDGSRSPDLGLIAKI 199

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 663526247 207 LLDTGLRVSElcgldiddvdVEDMSALVIG--------GKGEKDRTVlftqatvdaieawtPIRNARVQMSEgedrersl 278
Cdd:PHA02601 200 CLATGARWSE----------AETLKRSQISpykitfvkTKGKKNRTV--------------PISEELYKMLP-------- 247

                        250       260       270       280       290       300       310
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 663526247 279 llSSRGRRMNP--RSVQKLIDRLAdaAEIPRSRLSpHTLRHTFATGLLERGADLVTIQRLLGHASIATTRVY 348
Cdd:PHA02601 248 --KRRGRLFKDayESFERAVKRAG--IDLPEGQAT-HVLRHTFASHFMMNGGNILVLQRILGHATIEMTMAY 314
INT_P4_C cd00801
Bacteriophage P4 integrase, C-terminal catalytic domain; P4-like integrases are found in ...
 183-349 4.29e-08

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: 52.66  E-value: 4.29e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 663526247 183 NELGRV-RTAATQSEDPLAQPVVTILLDTGLRVSELCGLDIDDVDVEDMSALVIGG--KGEKDRTVLFTQATVDAIEawt 259
Cdd:cd00801    3 DELPELwRALDTANLSPPTKLALRLLLLTGQRIGELARARWSEIDLEEKTWTIPAErtKNKRPHRVPLSDQALEILE--- 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 663526247 260 pirNARVQMSEGEdrersLLLSSRG---RRMNPRSVQKLIDRLADAAEIprsrLSPHTLRHTFATGLLERGADLVTIQRL 336
Cdd:cd00801   80 ---ELKEFTGDSG-----YLFPSRRkkkKPISENTINKALKRLGYKGKE----FTPHDLRRTFSTLLNELGIDPEVIERL 147

                        170
                 ....*....|....
gi 663526247 337 LGHA-SIATTRVYL 349
Cdd:cd00801  148 LNHVlGGVVRAAYN 161
PRK09871 PRK09871
tyrosine recombinase; Provisional
 211-348 6.80e-07

tyrosine recombinase; Provisional


Pssm-ID: 182126  Cd Length: 198  Bit Score: 49.60  E-value: 6.80e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 663526247 211 GLRVSELCGLDIDDVDVEDMSALVIGGKGEKDRTVLFTQATVDAIEAWTPIRNARvqmsEGEDRERSLLLSSRGRRMNPR 290
Cdd:PRK09871  39 GMRISELLDLHYQDLDLNEGRINIRRLKNGFSTVHPLRFDEREAVERWTQERANW----KGADRTDAIFISRRGSRLSRQ 114

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 663526247 291 SVQKLIdRLADAAEIPRSRLSPHTLRHTFATGLLERGADLVTIQRLLGHASIATTRVY 348
Cdd:PRK09871 115 QAYRII-RDAGIEAGTVTQTHPHMLRHACGYELAERGADTRLIQDYLGHRNIRHTVRY 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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