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Conserved domains on  [gi|1024883025|ref|WP_063528570|]
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MULTISPECIES: tyrosine recombinase XerC [unclassified Pseudoalteromonas]

Protein Classification

tyrosine recombinase XerC( domain architecture ID 11478354)

site-specific tyrosine recombinase XerC acts by catalyzing the cutting and rejoining of recombining DNA molecules

CATH:  1.10.443.10
Gene Ontology:  GO:0051301|GO:0009037|GO:0007059|GO:0003677|GO:0006313
PubMed:  10047575|9278480|10577069|28373867
SCOP:  4002347

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
xerC PRK00236
site-specific tyrosine recombinase XerC; Reviewed
 17-310 1.01e-139

site-specific tyrosine recombinase XerC; Reviewed


:

Pssm-ID: 234698 [Multi-domain]  Cd Length: 297  Bit Score: 396.83  E-value: 1.01e-139
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1024883025  17 RTPIQLFADYLRYEKQYSAHTVNQYTSQL----GFAALYFSKlceDWFAVQGEHIRRYSMQMRSKQLSGRTISLKLSCIR 92
Cdd:PRK00236    7 PAALEAFLEYLRVERGLSPHTLRAYRRDLraflAFLEEHGIS---SLQDLDAADLRSFLARRRRQGLSARSLARRLSALR 83

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1024883025  93 SLYKFLKAKNIASqahyHNPAEAIKGPKFSKPLPKNLDVDQMAKLLELPD-DEPLAIRDKAMMELMYSSGLRISELVGAN 171
Cdd:PRK00236   84 SFYRWLVRRGLLK----ANPAAGLRAPKIPKRLPKPLDVDQAKRLLDAIDeDDPLALRDRAILELLYGSGLRLSELVGLD 159

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1024883025 172 IQDINPTEGEILVRGKGNKERLLPVGSKALSALKAWLKIRPQFAHPDEiAVFVSSQKKRISVRQVRLRMQEWGIKQGISS 251
Cdd:PRK00236  160 IDDLDLASGTLRVLGKGNKERTVPLGRAAREALEAYLALRPLFLPDDD-ALFLGARGGRLSPRVVQRRVKKLGKKAGLPS 238

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1024883025 252 QVHPHKLRHSFASHILESSGDLRAVQELLGHSSLSATQVYTHLDFQHLAKVYDNTHPRA 310
Cdd:PRK00236  239 HITPHKLRHSFATHLLESGGDLRAVQELLGHASLSTTQIYTHVDFQHLAEVYDAAHPRA 297
 
Name Accession Description Interval E-value
xerC PRK00236
site-specific tyrosine recombinase XerC; Reviewed
 17-310 1.01e-139

site-specific tyrosine recombinase XerC; Reviewed


Pssm-ID: 234698 [Multi-domain]  Cd Length: 297  Bit Score: 396.83  E-value: 1.01e-139
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1024883025  17 RTPIQLFADYLRYEKQYSAHTVNQYTSQL----GFAALYFSKlceDWFAVQGEHIRRYSMQMRSKQLSGRTISLKLSCIR 92
Cdd:PRK00236    7 PAALEAFLEYLRVERGLSPHTLRAYRRDLraflAFLEEHGIS---SLQDLDAADLRSFLARRRRQGLSARSLARRLSALR 83

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1024883025  93 SLYKFLKAKNIASqahyHNPAEAIKGPKFSKPLPKNLDVDQMAKLLELPD-DEPLAIRDKAMMELMYSSGLRISELVGAN 171
Cdd:PRK00236   84 SFYRWLVRRGLLK----ANPAAGLRAPKIPKRLPKPLDVDQAKRLLDAIDeDDPLALRDRAILELLYGSGLRLSELVGLD 159

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1024883025 172 IQDINPTEGEILVRGKGNKERLLPVGSKALSALKAWLKIRPQFAHPDEiAVFVSSQKKRISVRQVRLRMQEWGIKQGISS 251
Cdd:PRK00236  160 IDDLDLASGTLRVLGKGNKERTVPLGRAAREALEAYLALRPLFLPDDD-ALFLGARGGRLSPRVVQRRVKKLGKKAGLPS 238

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1024883025 252 QVHPHKLRHSFASHILESSGDLRAVQELLGHSSLSATQVYTHLDFQHLAKVYDNTHPRA 310
Cdd:PRK00236  239 HITPHKLRHSFATHLLESGGDLRAVQELLGHASLSTTQIYTHVDFQHLAEVYDAAHPRA 297
recomb_XerC TIGR02224
tyrosine recombinase XerC; The phage integrase family describes a number of recombinases with ...
 21-312 1.13e-130

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: 373.87  E-value: 1.13e-130
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1024883025  21 QLFADYLRYEKQYSAHTVNQYTSQLGFAALYFSKLCE--DWFAVQGEHIRRYSMQMRSKQLSGRTISLKLSCIRSLYKFL 98
Cdd:TIGR02224   1 EAFLEYLRLERNYSPHTVRAYRRDLEAFLEFLEEEGGlaSLAEVTAADLRSFLAELHARGLSRRSLARKLSALRSFYRFL 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1024883025  99 KAKNIASQahyhNPAEAIKGPKFSKPLPKNLDVDQMAKLLELPDD---EPLAIRDKAMMELMYSSGLRISELVGANIQDI 175
Cdd:TIGR02224  81 LRRGLIDA----NPAAGVRAPKQPKKLPKFLSEDEMEALLDAPEEddeDWLALRDRAILELLYSSGLRVSELVGLDLSDL 156

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1024883025 176 NPTEGEILVRGKGNKERLLPVGSKALSALKAWLKIRPQ--FAHPDEIAVFVSSQKKRISVRQVRLRMQEWGIKQGISSQV 253
Cdd:TIGR02224 157 DLDFGEVRVRGKGNKERIVPFGPYARDALQAYLEARRSplLASEGQDALFLNRRGGRLTPRGVQYRLQQLRAKAGLPKHV 236

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1024883025 254 HPHKLRHSFASHILESSGDLRAVQELLGHSSLSATQVYTHLDFQHLAKVYDNTHPRAKK 312
Cdd:TIGR02224 237 HPHALRHSFATHLLNNGADLRAVQELLGHASLSTTQIYTHVDFQHLAKVYDQAHPRAKK 295
XerC COG4973
Site-specific recombinase XerC [Replication, recombination and repair];
15-303 1.86e-122

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


Pssm-ID: 443998 [Multi-domain]  Cd Length: 287  Bit Score: 352.73  E-value: 1.86e-122
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1024883025  15 AWRTPIQLFADYLRyEKQYSAHTVNQYTSQLGFAALYFSKLCEDWFAVQGEHIRRYSMQMRSKQLSGRTISLKLSCIRSL 94
Cdd:COG4973     3 TLAEALEAYLEHLR-ERRLSPKTLEAYRRDLRRLIPLLGDADLPLEELTPADVRRFLARLHRRGLSPRTLNRRLSALRSF 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1024883025  95 YKFLKAKNIASqahyHNPAEAIKGPKFSKPLPKNLDVDQMAKLLELPDDEPLAIRDKAMMELMYSSGLRISELVGANIQD 174
Cdd:COG4973    82 FNWAVREGLLE----ANPAAGVKAPKAPRKLPRALTVDELAQLLDALADDPLAVRDRAIVELLYSTGLRLGELVGLDWED 157

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1024883025 175 INPTEGEILVRGKGNKERLLPVGSKALSALKAWLKIRPQFAHPDEIAVFVSSQKKRISVRQVRLRMQEWGIKQGISSQVH 254
Cdd:COG4973   158 VDLDAGEVRVRGKTGKSRTVPLGPKALAALREWLAVRPELAAPDEGALFPSRRGTRLSPRNVQKRLRRLAKKAGLPKHVH 237

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|....*....
gi 1024883025 255 PHKLRHSFASHILESSGDLRAVQELLGHSSLSATQVYTHLDFQHLAKVY 303
Cdd:COG4973   238 PHDLRHSFATHLLESGGDLRAVQELLGHASISTTQIYTHLDFQHLAEVY 286
INT_XerDC_C cd00798
XerD and XerC integrases, C-terminal catalytic domains; XerDC-like integrases are involved in ...
 131-299 2.45e-90

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: 266.68  E-value: 2.45e-90
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1024883025 131 VDQMAKLLELPD-DEPLAIRDKAMMELMYSSGLRISELVGANIQDINPTEGEILVRGKGNKERLLPVGSKALSALKAWLK 209
Cdd:cd00798     1 VDEVERLLDAPDtDTPLGLRDRAILELLYASGLRVSELVGLDLSDVDLDEGLVRVTGKGNKERLVPFGSYAVEALEEYLE 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1024883025 210 IRPQFAHPDEI--AVFVSSQKKRISVRQVRLRMQEWGIKQGISSQVHPHKLRHSFASHILESSGDLRAVQELLGHSSLSA 287
Cdd:cd00798    81 ERRPLLLKKKPpdALFLNKRGKRLSRRGVWRILKKYAERAGLPKHVSPHTLRHSFATHLLEGGADLRVVQELLGHASLST 160

                         170
                  ....*....|..
gi 1024883025 288 TQVYTHLDFQHL 299
Cdd:cd00798   161 TQIYTHVSFERL 172
Phage_integrase pfam00589
Phage integrase family; Members of this family cleave DNA substrates by a series of staggered ...
 128-296 1.52e-57

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: 182.90  E-value: 1.52e-57
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1024883025 128 NLDVDQMAKLLELPDDEPLAIRDKAMMELMYSSGLRISELVGANIQDINPTEGEILV-RGKGNKERLLPVGSKALSALKA 206
Cdd:pfam00589   1 RLTEDEVERLLDAAETGPLSIRDKALLELLYATGLRISELCSLRWSDIDFENGVIRVhRGKGNKERTVPLSDAALELLKE 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1024883025 207 WLKIRPQFAHPDEiAVFVSSQKKRISVRQVRLRMQEWGIKQGISSQVHPHKLRHSFASHILESSGDLRAVQELLGHSSLS 286
Cdd:pfam00589  81 WLSKRLLEAPKSD-YLFASKRGKPLSRQTVRKIFKRAGKEAGLELPLHPHMLRHSFATHLLEAGVDLRVVQKLLGHSSIS 159

                         170
                  ....*....|
gi 1024883025 287 ATQVYTHLDF 296
Cdd:pfam00589 160 TTQIYTHVAD 169
 
Name Accession Description Interval E-value
xerC PRK00236
site-specific tyrosine recombinase XerC; Reviewed
 17-310 1.01e-139

site-specific tyrosine recombinase XerC; Reviewed


Pssm-ID: 234698 [Multi-domain]  Cd Length: 297  Bit Score: 396.83  E-value: 1.01e-139
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1024883025  17 RTPIQLFADYLRYEKQYSAHTVNQYTSQL----GFAALYFSKlceDWFAVQGEHIRRYSMQMRSKQLSGRTISLKLSCIR 92
Cdd:PRK00236    7 PAALEAFLEYLRVERGLSPHTLRAYRRDLraflAFLEEHGIS---SLQDLDAADLRSFLARRRRQGLSARSLARRLSALR 83

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1024883025  93 SLYKFLKAKNIASqahyHNPAEAIKGPKFSKPLPKNLDVDQMAKLLELPD-DEPLAIRDKAMMELMYSSGLRISELVGAN 171
Cdd:PRK00236   84 SFYRWLVRRGLLK----ANPAAGLRAPKIPKRLPKPLDVDQAKRLLDAIDeDDPLALRDRAILELLYGSGLRLSELVGLD 159

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1024883025 172 IQDINPTEGEILVRGKGNKERLLPVGSKALSALKAWLKIRPQFAHPDEiAVFVSSQKKRISVRQVRLRMQEWGIKQGISS 251
Cdd:PRK00236  160 IDDLDLASGTLRVLGKGNKERTVPLGRAAREALEAYLALRPLFLPDDD-ALFLGARGGRLSPRVVQRRVKKLGKKAGLPS 238

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1024883025 252 QVHPHKLRHSFASHILESSGDLRAVQELLGHSSLSATQVYTHLDFQHLAKVYDNTHPRA 310
Cdd:PRK00236  239 HITPHKLRHSFATHLLESGGDLRAVQELLGHASLSTTQIYTHVDFQHLAEVYDAAHPRA 297
recomb_XerC TIGR02224
tyrosine recombinase XerC; The phage integrase family describes a number of recombinases with ...
 21-312 1.13e-130

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: 373.87  E-value: 1.13e-130
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1024883025  21 QLFADYLRYEKQYSAHTVNQYTSQLGFAALYFSKLCE--DWFAVQGEHIRRYSMQMRSKQLSGRTISLKLSCIRSLYKFL 98
Cdd:TIGR02224   1 EAFLEYLRLERNYSPHTVRAYRRDLEAFLEFLEEEGGlaSLAEVTAADLRSFLAELHARGLSRRSLARKLSALRSFYRFL 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1024883025  99 KAKNIASQahyhNPAEAIKGPKFSKPLPKNLDVDQMAKLLELPDD---EPLAIRDKAMMELMYSSGLRISELVGANIQDI 175
Cdd:TIGR02224  81 LRRGLIDA----NPAAGVRAPKQPKKLPKFLSEDEMEALLDAPEEddeDWLALRDRAILELLYSSGLRVSELVGLDLSDL 156

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1024883025 176 NPTEGEILVRGKGNKERLLPVGSKALSALKAWLKIRPQ--FAHPDEIAVFVSSQKKRISVRQVRLRMQEWGIKQGISSQV 253
Cdd:TIGR02224 157 DLDFGEVRVRGKGNKERIVPFGPYARDALQAYLEARRSplLASEGQDALFLNRRGGRLTPRGVQYRLQQLRAKAGLPKHV 236

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1024883025 254 HPHKLRHSFASHILESSGDLRAVQELLGHSSLSATQVYTHLDFQHLAKVYDNTHPRAKK 312
Cdd:TIGR02224 237 HPHALRHSFATHLLNNGADLRAVQELLGHASLSTTQIYTHVDFQHLAKVYDQAHPRAKK 295
XerC COG4973
Site-specific recombinase XerC [Replication, recombination and repair];
15-303 1.86e-122

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


Pssm-ID: 443998 [Multi-domain]  Cd Length: 287  Bit Score: 352.73  E-value: 1.86e-122
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1024883025  15 AWRTPIQLFADYLRyEKQYSAHTVNQYTSQLGFAALYFSKLCEDWFAVQGEHIRRYSMQMRSKQLSGRTISLKLSCIRSL 94
Cdd:COG4973     3 TLAEALEAYLEHLR-ERRLSPKTLEAYRRDLRRLIPLLGDADLPLEELTPADVRRFLARLHRRGLSPRTLNRRLSALRSF 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1024883025  95 YKFLKAKNIASqahyHNPAEAIKGPKFSKPLPKNLDVDQMAKLLELPDDEPLAIRDKAMMELMYSSGLRISELVGANIQD 174
Cdd:COG4973    82 FNWAVREGLLE----ANPAAGVKAPKAPRKLPRALTVDELAQLLDALADDPLAVRDRAIVELLYSTGLRLGELVGLDWED 157

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1024883025 175 INPTEGEILVRGKGNKERLLPVGSKALSALKAWLKIRPQFAHPDEIAVFVSSQKKRISVRQVRLRMQEWGIKQGISSQVH 254
Cdd:COG4973   158 VDLDAGEVRVRGKTGKSRTVPLGPKALAALREWLAVRPELAAPDEGALFPSRRGTRLSPRNVQKRLRRLAKKAGLPKHVH 237

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|....*....
gi 1024883025 255 PHKLRHSFASHILESSGDLRAVQELLGHSSLSATQVYTHLDFQHLAKVY 303
Cdd:COG4973   238 PHDLRHSFATHLLESGGDLRAVQELLGHASISTTQIYTHLDFQHLAEVY 286
recomb_XerD TIGR02225
tyrosine recombinase XerD; The phage integrase family describes a number of recombinases with ...
 21-310 9.08e-97

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: 287.56  E-value: 9.08e-97
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1024883025  21 QLFADYLRYEKQYSAHTVNQYTSQLGFAALYFSKLCEDWFAVQGEHIRRYSMQMRSKQLSGRTISLKLSCIRSLYKFLKA 100
Cdd:TIGR02225   1 EQFLDYLWVERGLSQNTLEAYRRDLEKFLEFLEERGIDLEEVDRGDIVDFLAELKEAGLSARSIARALSALRSFYRFLLR 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1024883025 101 KNIASqahyHNPAEAIKGPKFSKPLPKNLDVDQMAKLLELPD-DEPLAIRDKAMMELMYSSGLRISELVGANIQDINPTE 179
Cdd:TIGR02225  81 EGIRE----DDPSALIEPPKVARKLPKVLTVEEVEALLAAPDvDTPLGLRDRAMLELLYATGLRVSELVGLRLEDVNLDE 156

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1024883025 180 GEILVRGKGNKERLLPVGSKALSALKAWLKI-RPQFA---HPDEIAVFVSSQKKRISVRQVRLRMQEWGIKQGISSQVHP 255
Cdd:TIGR02225 157 GFVRVRGKGNKERLVPLGEEAIEALERYLKEaRPLLLkkkVKESDALFLNRRGGPLSRQGVWKILKEYAKRAGIEKPISP 236

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1024883025 256 HKLRHSFASHILESSGDLRAVQELLGHSSLSATQVYTHLDFQHLAKVYDNTHPRA 310
Cdd:TIGR02225 237 HTLRHSFATHLLENGADLRVVQELLGHADISTTQIYTHVARERLKEVHKKHHPRA 291
INT_XerDC_C cd00798
XerD and XerC integrases, C-terminal catalytic domains; XerDC-like integrases are involved in ...
 131-299 2.45e-90

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: 266.68  E-value: 2.45e-90
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1024883025 131 VDQMAKLLELPD-DEPLAIRDKAMMELMYSSGLRISELVGANIQDINPTEGEILVRGKGNKERLLPVGSKALSALKAWLK 209
Cdd:cd00798     1 VDEVERLLDAPDtDTPLGLRDRAILELLYASGLRVSELVGLDLSDVDLDEGLVRVTGKGNKERLVPFGSYAVEALEEYLE 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1024883025 210 IRPQFAHPDEI--AVFVSSQKKRISVRQVRLRMQEWGIKQGISSQVHPHKLRHSFASHILESSGDLRAVQELLGHSSLSA 287
Cdd:cd00798    81 ERRPLLLKKKPpdALFLNKRGKRLSRRGVWRILKKYAERAGLPKHVSPHTLRHSFATHLLEGGADLRVVQELLGHASLST 160

                         170
                  ....*....|..
gi 1024883025 288 TQVYTHLDFQHL 299
Cdd:cd00798   161 TQIYTHVSFERL 172
XerD COG4974
Site-specific recombinase XerD [Replication, recombination and repair];
15-308 2.77e-90

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


Pssm-ID: 443999 [Multi-domain]  Cd Length: 291  Bit Score: 271.10  E-value: 2.77e-90
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1024883025  15 AWRTPIQLFADYLRYEKQYSAHTVNQYTSQLGFAALYFSKL-CEDWFAVQGEHIRRYSMQMRSKQLSGRTISLKLSCIRS 93
Cdd:COG4974     2 TLADLLEAFLEELKREKGLSPNTIKAYRRDLRRFLRFLEELgKIPLAEITPEDIRAYLNYLRERGLSPSTINRYLAALRS 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1024883025  94 LYKFLKAKNIASqahyHNPAEAIKGPKFSKPLPKNLDVDQMAKLLELPDDE-PLAIRDKAMMELMYSSGLRISELVGANI 172
Cdd:COG4974    82 FFRYAVREGLLE----DNPAAKVKLPKKPRKLPRVLTEEEIEALLEALDTEtPEGLRDRALLLLLYATGLRVSELLGLKW 157

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1024883025 173 QDINPTEGEILVR-GKGNKERLLPVGSKALSALKAWLKIRPQFAHPdeiAVFVSSQKKRISVRQVRLRMQEWGIKQGISS 251
Cdd:COG4974   158 SDIDLDRGTIRVRrGKGGKERTVPLSPEALEALREYLEERRPRDSD---YLFPTRRGRPLSRRAIRKILKRLAKRAGIPK 234

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1024883025 252 QVHPHKLRHSFASHILESSGDLRAVQELLGHSSLSATQVYTHLDFQHLAKVYDNTHP 308
Cdd:COG4974   235 RVTPHSLRHTFATHLLEAGVDLRTVQELLGHSSISTTQIYTHVSDEELREAVEKLHP 291
xerD PRK00283
tyrosine recombinase;
20-310 6.53e-89

tyrosine recombinase;


Pssm-ID: 234713 [Multi-domain]  Cd Length: 299  Bit Score: 267.83  E-value: 6.53e-89
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1024883025  20 IQLFADYLRYEKQYSAHTVNQYTSQLGFAALYFSKLCEDWFAVQGEHIRRYSMQMRSKQLSGRTISLKLSCIRSLYKFLK 99
Cdd:PRK00283    9 IEQFLDALWVERGLAENTLSSYRRDLELFAEWLAARGLSLAEATRDDLQAFLAELAEGGYKATSSARRLSALRRFFQFLL 88

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1024883025 100 AKNIASqahyHNPAEAIKGPKFSKPLPKNLDVDQMAKLLELPD-DEPLAIRDKAMMELMYSSGLRISELVGANIQDINPT 178
Cdd:PRK00283   89 REGLRE----DDPSALLDSPKLPRRLPKTLSEAQVEALLDAPDiDTPLGLRDRAMLELLYATGLRVSELVGLTLDDVSLR 164

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1024883025 179 EGEILVRGKGNKERLLPVGSKALSALKAWLKI-RPQFAH-PDEIAVFVSSQKKRISVRQVRLRMQEWGIKQGI-SSQVHP 255
Cdd:PRK00283  165 QGVVRVTGKGNKERLVPLGEEAVYAIERYLERgRPALLNgRSSDALFPSARGGQLTRQTFWHRIKHYAKRAGIdPKKLSP 244

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1024883025 256 HKLRHSFASHILESSGDLRAVQELLGHSSLSATQVYTHLDFQHLAKVYDNTHPRA 310
Cdd:PRK00283  245 HVLRHAFATHLLNHGADLRVVQELLGHSDISTTQIYTHVATERLKELHAQHHPRA 299
Phage_integrase pfam00589
Phage integrase family; Members of this family cleave DNA substrates by a series of staggered ...
 128-296 1.52e-57

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: 182.90  E-value: 1.52e-57
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1024883025 128 NLDVDQMAKLLELPDDEPLAIRDKAMMELMYSSGLRISELVGANIQDINPTEGEILV-RGKGNKERLLPVGSKALSALKA 206
Cdd:pfam00589   1 RLTEDEVERLLDAAETGPLSIRDKALLELLYATGLRISELCSLRWSDIDFENGVIRVhRGKGNKERTVPLSDAALELLKE 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1024883025 207 WLKIRPQFAHPDEiAVFVSSQKKRISVRQVRLRMQEWGIKQGISSQVHPHKLRHSFASHILESSGDLRAVQELLGHSSLS 286
Cdd:pfam00589  81 WLSKRLLEAPKSD-YLFASKRGKPLSRQTVRKIFKRAGKEAGLELPLHPHMLRHSFATHLLEAGVDLRVVQKLLGHSSIS 159

                         170
                  ....*....|
gi 1024883025 287 ATQVYTHLDF 296
Cdd:pfam00589 160 TTQIYTHVAD 169
xerC PRK01287
site-specific tyrosine recombinase XerC; Reviewed
 6-313 5.06e-51

site-specific tyrosine recombinase XerC; Reviewed


Pssm-ID: 234935 [Multi-domain]  Cd Length: 358  Bit Score: 172.24  E-value: 5.06e-51
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1024883025   6 TPDINELSDAWRTPIQLFADYLRY-----EKQYSAHTVNQYTSQLgfaaLYFSKLCEDWFAVQG--------EHIRRYSM 72
Cdd:PRK01287    5 KPRKGSLLTVAHDPKTLRQLLERFlawlqERNWSERTLKVYTEHL----YPFILWCEERGLYYAadvtlpvlERYQRYLY 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1024883025  73 QMRS---KQLSGRTISLKLSCIRSLYKFLKAKNIAsqahYHNPAEAIKGPKFSKPLPKN-LDVDQMAKLLELPD-DEPLA 147
Cdd:PRK01287   81 GYRKangEPLSTRTQRTQLSPLRVWFRWLLKRHHI----LYNPAEDLELPKEEKRLPRQiLSEAETEQVLASPDlTTLQG 156

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1024883025 148 IRDKAMMELMYSSGLRISELVGANIQDINPTEGEILVR-GKGNKERLLPVGSKALSALKAWLK-IRPQFA-HPDEIAVFV 224
Cdd:PRK01287  157 LRDRALLELLWSTGIRRGELARLDLYDVDASRGVVTVRqGKGNKDRVVPVGERALAWLQRYLQdVRPQLAvRPDSGALFV 236

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1024883025 225 SSQKKRISVRQVRLR----MQEWGIKQGISSqvhpHKLRHSFASHILESSGDLRAVQELLGHSSLSATQVYTHLDFQHLA 300
Cdd:PRK01287  237 AMDGDGLARNTLTNMvgryIRAAGIEKAGAC----HLFRHAMATQMLENGADTRHIQAILGHAKLETTQIYTRVSIGHLQ 312

                         330
                  ....*....|...
gi 1024883025 301 KVYDNTHPRAKKR 313
Cdd:PRK01287  313 AVHASTHPAERKA 325
INT_IntI_C cd01193
Integron integrase and similar protiens, C-terminal catalytic domain; Integron integrases ...
 125-294 1.24e-42

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: 145.11  E-value: 1.24e-42
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1024883025 125 LPKNLDVDQMAKLLELPDDEplaiRDKAMMELMYSSGLRISELVGANIQDINPTEGEILVR-GKGNKERLLPVGSKALSA 203
Cdd:cd01193     2 LPVVLSPDEVRRILGALTEL----RHRLILSLLYGAGLRISELLRLRVKDIDFERGVIRVRqGKGGKDRVVPLPEKLLEP 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1024883025 204 LKAWLK-IRPQFAH-------PDEIAVFVSSQKKRISVRQVRLRMQEWGIKQGISSQVHPHKLRHSFASHILESSGDLRA 275
Cdd:cd01193    78 LRRYLKsARPKEELdpaegraGVLDPRTGVERRHHISETTVQRALKKAVEQAGITKRVTPHTLRHSFATHLLEAGTDIRT 157

                         170
                  ....*....|....*....
gi 1024883025 276 VQELLGHSSLSATQVYTHL 294
Cdd:cd01193   158 IQELLGHSDLSTTMIYTHV 176
DNA_BRE_C cd00397
DNA breaking-rejoining enzymes, C-terminal catalytic domain; The DNA breaking-rejoining enzyme ...
 133-292 4.74e-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: 124.90  E-value: 4.74e-35
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1024883025 133 QMAKLLELPDDEPLA-IRDKAMMELMYSSGLRISELVGANIQDINPTEGEILVRGKG---NKERLLPVGSKALSALKAWL 208
Cdd:cd00397     1 ELEKLLDAIDEDKKIdLRDRAILLLLLETGLRISELLALKVKDIDLDNGTIRVRGKKtkgGKERTVPLPKELAEELKEYL 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1024883025 209 KIR-----PQFAHPDEIAVFVSSQKKRISVRQVRLRMQEWGIKQGIssQVHPHKLRHSFASHILESSGDLRAVQELLGHS 283
Cdd:cd00397    81 KERrdkrgPLLKSLYLNKLFGTKLGERLSRRTLRRIFKKAGIEAGR--KITPHSLRHTFATNLLENGVDIKVVQKLLGHS 158


                  ....*....
gi 1024883025 284 SLSATQVYT 292
Cdd:cd00397   159 SISTTQRYL 167
INT_RitC_C_like cd01182
C-terminal catalytic domain of recombinase RitC, a component of the recombinase trio; ...
 129-297 2.81e-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: 118.53  E-value: 2.81e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1024883025 129 LDVDQMAKLLELPDD-EPLAIRDKAMMELMYSSGLRISELVGANIQDINPTEG-EILVRGKGNKERLLPVGSKALSALKA 206
Cdd:cd01182     1 LTREEMKALLAAPDRnTSLGRRDHALLLLLYDTGARVQELADLTIRDLRLDDPaTVRLHGKGRKERTVPLWKETVAALKA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1024883025 207 WLKIRpqfaHPDEIA-----VFVSSQKKRISVRQVRLRMQEWGIK-----QGISSQVHPHKLRHSFASHILESSGDLRAV 276
Cdd:cd01182    81 YLQEF----HLTPDPkqlfpLFPNRRGQPLTRDGVAYILNKYVALasnrcPSLPKRITPHTLRHTKAMHLLQAGVDLTVI 156

                         170       180
                  ....*....|....*....|.
gi 1024883025 277 QELLGHSSLSATQVYTHLDFQ 297
Cdd:cd01182   157 RDWLGHESVETTQIYAEADLE 177
xerS PRK05084
site-specific tyrosine recombinase XerS; Reviewed
 77-295 6.54e-32

site-specific tyrosine recombinase XerS; Reviewed


Pssm-ID: 235339 [Multi-domain]  Cd Length: 357  Bit Score: 121.95  E-value: 6.54e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1024883025  77 KQLSGRTISLKLSCIRSLYKFLKakNIASQAH-----YHNPAEAIKGPKFSKPL---PKNLDvdqmAKLLElpDDEPLA- 147
Cdd:PRK05084   99 KGNSQTTINRTLSALKSLFKYLT--EEAENEDgepyfYRNVMKKIELKKKKETLaarAHNLK----QKLFL--GDEDYEf 170

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1024883025 148 ------------------------IRDKAMMELMYSSGLRISELVGANIQDINPTEGEILVRGKGNKERLLPVGSKALSA 203
Cdd:PRK05084  171 ldfidneyeqklsnralssfkknkERDLAIIALILGSGLRVSELVNLDLSDLNLKQMTIDVTRKGGKRDSVNIAPFALPY 250

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1024883025 204 LKAWLKIRPQFAHPD--EIAVFVSS---QKKRISVRQVRlRM-----QEWGIKqgissqVHPHKLRHSFASHILESSGDL 273
Cdd:PRK05084  251 LEEYLKIRASRYKAEkqEKALFLTKyrgKPNRISARAIE-KMvakysEAFGVR------LTPHKLRHTLATRLYDATKDQ 323

                         250       260
                  ....*....|....*....|..
gi 1024883025 274 RAVQELLGHSSLSATQVYTHLD 295
Cdd:PRK05084  324 VLVADQLGHTSTETTDLYTHIV 345
INT_RitA_C_like cd01188
C-terminal catalytic domain of recombinase RitA, a component of the recombinase trio; ...
 132-302 2.51e-28

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: 107.71  E-value: 2.51e-28
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1024883025 132 DQMAKLLELPD-DEPLAIRDKAMMELMYSSGLRISELVGANIQDINPTEGEILVRG-KGNKERLLPVGSKALSALKAWLK 209
Cdd:cd01188     3 DEVRRLLAAIDrLTPVGLRDYAILLLLARLGLRAGDVAGLRLDDIDWRSGTITVRQkKTGRPVELPLTEPVGEALADYLR 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1024883025 210 I-RPQFAHPDeiaVFVSSQ---KKRISVRQVRLRMQEWGIKQGISSQVH-PHKLRHSFASHILESSGDLRAVQELLGHSS 284
Cdd:cd01188    83 DgRPRTDSRE---VFLRARapyRPLSSTSQISSIVRRYLRKAGIEPSHRgTHSLRHSLATRMLRAGTSLKVIADLLGHRS 159

                         170
                  ....*....|....*...
gi 1024883025 285 LSATQVYTHLDFQHLAKV 302
Cdd:cd01188   160 IETTAIYAKIDVDDLREV 177
INT_C_like_4 cd01194
Uncharacterized site-specific tyrosine recombinase, C-terminal catalytic domain; Tyrosine ...
 129-293 1.43e-25

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: 100.14  E-value: 1.43e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1024883025 129 LDVDQMAKLLE-LPDDEPL-AIRDKAMMELMYSSGLRISELVGANIQDINPTEGE--ILVRGKG--NKERLLPVGSKALS 202
Cdd:cd01194     1 LTLEQARQLLAsLPIDDSIiGLRDRAIISLMVTEGLRTVEIVRADVGDLRQEGEGtiLYVQGKGktSKDDFVYLRPDVLK 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1024883025 203 ALKAWLKIRPqFAHPDEiAVFVS----SQKKRISVRQVRLRMQEWGIKQGI-SSQVHPHKLRHSFASHILESSGDLRAVQ 277
Cdd:cd01194    81 ALQAYLKARG-KLDFEE-PLFTSlsnnSKGQRLTTRSIRRIIKKYLRKAGLdDDRLTAHSLRHTAGTLALKAGKSLREVQ 158

                         170
                  ....*....|....*.
gi 1024883025 278 ELLGHSSLSATQVYTH 293
Cdd:cd01194   159 QLLRHSDPNTTMIYAH 174
INT_C_like_5 cd01195
Uncharacterized site-specific tyrosine recombinase, C-terminal catalytic domain; Tyrosine ...
 131-293 7.48e-25

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: 98.31  E-value: 7.48e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1024883025 131 VDQMAKLLELPDDEP-LAIRDKAMMELMYSSGLRISELVGANIQDINPTEGEILVRGKGNKER---LLPVgsKALSALKA 206
Cdd:cd01195     2 REEARQRLDAADRHTaKGKRDEALVRLLLDNALRRSEAVALDVEDLEKEHRRLRILGKGKKQRevvTLPP--TTREALAA 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1024883025 207 WLKIRPQFAHPDEIAVFVSSQKKRISVRQVRLRMQEWGIKQGISSQVHPHKLRHSFASHILESSGDL-RAVQELLGHSSL 285
Cdd:cd01195    80 WLAARGEAEGPLFVSLDRASRGRRLSPQAVYRIVRRLAERIGLGKRLSPHGLRHSAITLALDAGAGLiRKVQDFSRHADL 159


                  ....*...
gi 1024883025 286 SATQVYTH 293
Cdd:cd01195   160 RTLQVYDD 167
INT_FimBE_like cd01197
FimB and FimE and related proteins, integrase/recombinases; This CD includes proteins similar ...
 149-292 1.04e-24

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: 98.35  E-value: 1.04e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1024883025 149 RDKAMMELMYSSGLRISELVGANIQDINPTEGEILV-RGKGNKERLLPVGSKALSALKAWLKIRPQFAHPDEIAVFVSSQ 227
Cdd:cd01197    27 RDYCLLLLAFRHGFRVSELCDLHLSDVDLESRRLHIrRLKNGFSTTHPLRFDEREALEAWLKERANWKGADTDWIFLSRR 106

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1024883025 228 KKRISVRQVRLRMQEWGIKQGISSQVHPHKLRHSFASHILESSGDLRAVQELLGHSSLSATQVYT 292
Cdd:cd01197   107 GGPLSRQQAYRIIRDLGKEAGTVTQTHPHMLRHACGYALADRGADTRLIQDYLGHRNIRHTVIYT 171
integrase_gron TIGR02249
integron integrase; Members of this family are integrases associated with integrons (and ...
 114-302 1.43e-24

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: 100.93  E-value: 1.43e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1024883025 114 EAIKGPKFSKPLPKNLDVDQMAKLLE-LPDDEPLAIRdkammeLMYSSGLRISELVGANIQDINPTEGEILVR-GKGNKE 191
Cdd:TIGR02249  87 ERFVRAKRPRKLPVVLTREEVRRLLEhLEGKYRLIAK------LLYGSGMRLMECLRLRIQDIDFDYGEIRIRqGKGGKD 160

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1024883025 192 RLLPVGSKALSALKAWLKIR---------PQFAH---PDEIA--------------VFVSSQKKR--ISVRQVRLRMQEW 243
Cdd:TIGR02249 161 RTVTLPKELIPPLREQIELArayheadlaEGYGGvylPHALArkypnapkewgwqyLFPSHRLSRdpESGVIRRHHINET 240

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1024883025 244 GIKQ---------GISSQVHPHKLRHSFASHILESSGDLRAVQELLGHSSLSATQVYTHLDFQHLAKV 302
Cdd:TIGR02249 241 TIQRavrraveraGIEKPVTCHTLRHSFATHLLESGADIRTVQELLGHSDVKTTQIYTHVLNRGASGV 308
INT_Rci_Hp1_C cd00796
Shufflon-specific DNA recombinase Rci and Bacteriophage Hp1_like integrase, C-terminal ...
 132-293 2.03e-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: 2.03e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1024883025 132 DQMAKLLELPDDEPLAiRDKAMMELMYSSGLRISELVGANIQDINPTEGEI-LVRGKGNKERLLPVGSKALSALKAWLKi 210
Cdd:cd00796     8 DEEARLLAALEESTNP-HLRLIVLLALYTGARRGEILSLRWDDIDLEVGLIvLPETKNGKPRTVPLSDEAIAILKELKR- 85

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1024883025 211 rpqfaHPDEIAVFVSSQKKRISVRQVRLRMQEWGIKQGISSqVHPHKLRHSFASHILESSGDLRAVQELLGHSSLSATQV 290
Cdd:cd00796    86 -----KRGKDGFFVDGRFFGIPIASLRRAFKKARKRAGLED-LRFHDLRHTFASRLVQAGVPIKTVAKILGHSSIKMTMR 159


                  ...
gi 1024883025 291 YTH 293
Cdd:cd00796   160 YAH 162
INT_ICEBs1_C_like cd01189
C-terminal catalytic domain of integrases from bacterial phages and conjugate transposons; ...
 132-293 1.13e-18

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: 81.07  E-value: 1.13e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1024883025 132 DQMAKLLELPDDEPLaiRDKAMMELMYSSGLRISELVGANIQDINPTEGEILVRG---------------KGNK-ERLLP 195
Cdd:cd01189     2 EELKKLLEALKKRGD--RYYLLFLLALLTGLRRGELLALTWSDIDFENGTIRINRtlvrkkkggyvikppKTKSsIRTIP 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1024883025 196 VGSKALSALKAWLKIRPqfahpdeiavfvssqkkrisvrqvrlRMQEWGIKQgissqVHPHKLRHSFASHILESSGDLRA 275
Cdd:cd01189    80 LPDELIELLKELKAFKK--------------------------LLKKAGLPR-----ITPHDLRHTFASLLLEAGVPLKV 128

                         170
                  ....*....|....*....
gi 1024883025 276 VQELLGHSSLSAT-QVYTH 293
Cdd:cd01189   129 IAERLGHSDISTTlDVYAH 147
INT_RitB_C_like cd00797
C-terminal catalytic domain of recombinase RitB, a component of the recombinase trio; ...
 134-294 1.88e-18

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: 81.58  E-value: 1.88e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1024883025 134 MAKLLELPDDEPLAirdKAMME----LMYSSGLRISELVGANIQDINPTEGEILVR-GKGNKERLLPVGSKALSALKAWL 208
Cdd:cd00797    10 LAAADQLPPESPLR---PLTYAtlfgLLYATGLRVGEALRLRLEDVDLDSGILTIRqTKFGKSRLVPLHPSTVGALRDYL 86

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1024883025 209 KIRPQ-FAHPDEIAVFVSSQKKRIS---VRQVRLRM-QEWGIKqGISSQVHP--HKLRHSFASHIL----ESSGDL-RAV 276
Cdd:cd00797    87 ARRDRlLPSPSSSYFFVSQQGGRLTgggVYRVFRRLlRRIGLR-GAGDGRGPrlHDLRHTFAVNRLtrwyREGADVeRKL 165

                         170       180
                  ....*....|....*....|.
gi 1024883025 277 QEL---LGHSSLSATQVYTHL 294
Cdd:cd00797   166 PVLstyLGHVNVTDTYWYLTA 186
PRK09871 PRK09871
tyrosine recombinase; Provisional
 145-312 3.07e-18

tyrosine recombinase; Provisional


Pssm-ID: 182126  Cd Length: 198  Bit Score: 81.18  E-value: 3.07e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1024883025 145 PLAIRDKAMMELMYSSGLRISELVGANIQDINPTEGEILVRG-KGNKERLLPVGSKALSALKAWLKIRPQFAHPDEI-AV 222
Cdd:PRK09871   23 ATGARDYCLILLAYRHGMRISELLDLHYQDLDLNEGRINIRRlKNGFSTVHPLRFDEREAVERWTQERANWKGADRTdAI 102

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1024883025 223 FVSSQKKRISVRQVRLRMQEWGIKQGISSQVHPHKLRHSFASHILESSGDLRAVQELLGHSSLSATQVYTHLDFQHLAKV 302
Cdd:PRK09871  103 FISRRGSRLSRQQAYRIIRDAGIEAGTVTQTHPHMLRHACGYELAERGADTRLIQDYLGHRNIRHTVRYTASNAARFAGL 182

                         170
                  ....*....|
gi 1024883025 303 YDNTHPRAKK 312
Cdd:PRK09871  183 WERNNLINEK 192
PRK15417 PRK15417
integron integrase;
114-294 4.80e-17

integron integrase;


Pssm-ID: 185315 [Multi-domain]  Cd Length: 337  Bit Score: 80.48  E-value: 4.80e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1024883025 114 EAIKGPKFSKPLPKNLDVDQMAKLLELPDDEplairDKAMMELMYSSGLRISELVGANIQDINPTEGEILVR-GKGNKER 192
Cdd:PRK15417  102 QEIGRPRPSRRLPVVLTPDEVVRILGFLEGE-----HRLFAQLLYGTGMRISEGLQLRVKDLDFDHGTIIVReGKGSKDR 176

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1024883025 193 LL-------PVGSKALSALKAW-----LKIRPQFAHPDEIA--------------VFV----SSQKKRISVRQVRLRMQE 242
Cdd:PRK15417  177 ALmlpeslaPSLREQLSRARAWwlkdqAEGRSGVALPDALErkypraghswpwfwVFAqhthSTDPRSGVVRRHHMYDQT 256

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1024883025 243 W------GIKQ-GISSQVHPHKLRHSFASHILESSGDLRAVQELLGHSSLSATQVYTHL 294
Cdd:PRK15417  257 FqrafkrAVEQaGITKPATPHTLRHSFATALLRSGYDIRTVQDLLGHSDVSTTMIYTHV 315
PRK09870 PRK09870
tyrosine recombinase; Provisional
 132-309 2.01e-16

tyrosine recombinase; Provisional


Pssm-ID: 182125  Cd Length: 200  Bit Score: 76.13  E-value: 2.01e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1024883025 132 DQMAKLLELPDDEPLAIRDKAMMELMYSSGLRISELVGANIQDINPTEGEILV-RGKGNKERLLPVGSKALSALKAWLKI 210
Cdd:PRK09870   16 SEIESLLKAANTGPHAARNYCLTLLCFIHGFRASEICRLRISDIDLKAKCIYIhRLKKGFSTTHPLLNKEIQALKNWLSI 95

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1024883025 211 RPQFAHPDEIAVFVSSQKKRISVRQVRLRMQEWGIKQGISSQVHPHKLRHSFASHILESSGDLRAVQELLGHSSLSATQV 290
Cdd:PRK09870   96 RTSYPHAESEWVFLSRKGNPLSRQQFYHIISTSGGNAGLSLEIHPHMLRHSCGFALANMGIDTRLIQDYLGHRNIRHTVW 175

                         170
                  ....*....|....*....
gi 1024883025 291 YTHLDFQHLAKVYDNTHPR 309
Cdd:PRK09870  176 YTASNAGRFYGIWDRARGR 194
INT_Cre_C cd00799
C-terminal catalytic domain of Cre recombinase (also called integrase); Cre-like recombinases ...
 139-292 1.36e-15

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: 73.49  E-value: 1.36e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1024883025 139 ELPDDEPLAIRDKAMMELMYSSGLRISELVGANIQDINPTEGEILV----RGKGNKERL-----LPVGSK--ALSALKAW 207
Cdd:cd00799     7 TLDDTTLRGLRDRALLLLGFAGALRRSELVALRVEDLTRFVDGGLLirlrRSKTDQDGEgeikaLPYGPEtcPVRALRAW 86

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1024883025 208 LKIRPQfahpDEIAVFVSSQK------KRISVRQVRLRMQEWGIKQGI-SSQVHPHKLRHSFASHILESSGDLRAVQELL 280
Cdd:cd00799    87 LEAAGI----PSGPLFRRIRRggsvgtTRLSDRSVARIVKRRAALAGLdPGDFSGHSLRRGFATEAARAGASLPEIMAQG 162

                         170
                  ....*....|..
gi 1024883025 281 GHSSLSATQVYT 292
Cdd:cd00799   163 GHKSVATVMRYI 174
FimB COG0582
Integrase/recombinase, includes phage integrase [Replication, recombination and repair, ...
 52-296 3.25e-14

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


Pssm-ID: 440347 [Multi-domain]  Cd Length: 391  Bit Score: 72.38  E-value: 3.25e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1024883025  52 FSKLCEDWFAVQGEHIR-RYSMQMRS-------KQLSGRTIS-LKLSCIRSLYKFLKAKNIASQAHY------------- 109
Cdd:COG0582    99 FEEVAEEWLEEKKPEWKeKTAAQVRRtlekhifPVLGDRPIAeITPPDLLAVLRPIEARGAPETARRvrqrlrqvfryav 178

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1024883025 110 ------HNPAEAIKGpKFSKPLPKN---LDVDQMAKLLELPDDEPLAIRDKAMMELMYSSGLRISELVGANIQDINPTEG 180
Cdd:COG0582   179 arglieRNPAADLKG-ALPKPKVKHhpaLTPEELPELLRALDAYRGSPVTRLALRLLLLTGVRPGELRGARWSEIDLEAA 257

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1024883025 181 EILVRG---KGNKERLLPVGSKALSALKAWLKIRPQFAHpdeiaVFVS--SQKKRIS---VRQVRLRMqewGIKqgissQ 252
Cdd:COG0582   258 LWTIPAermKTRRPHIVPLSRQALEILKELKPLTGDSEY-----VFPSrrGPKKPMSentLNKALRRM---GYG-----R 324

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|....*
gi 1024883025 253 VHPHKLRHSFASHILESSGDLRAVQELLGHSSLSATQ-VYTHLDF 296
Cdd:COG0582   325 FTPHGFRHTASTLLNEAGFPPDVIERQLAHKDGNKVRaAYNRADY 369
INTN1_C_like cd01185
Integrase IntN1 of Bacteroides mobilizable transposon NBU1 and similar proteins, C-terminal ...
 132-297 1.15e-13

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: 67.67  E-value: 1.15e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1024883025 132 DQMAKL--LELPDDEPLAIRDKAMMELMYSsGLRISELVGANIQDI-NPTEGEILV--RGKGNKERLLPVgskaLSALKA 206
Cdd:cd01185     1 EELKRLmaLELSDTSRLELVRDMFLFSCYT-GLRFSDLKNLTWKNIvEASGRTWIRyrRKKTGKPVTVPL----LPVARE 75

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1024883025 207 WLKIRPQFAHPDEIavFvssqkKRISVRQVRLRMQEWGIKQGISSQVHPHKLRHSFASHILESSGDLRAVQELLGHSSLS 286
Cdd:cd01185    76 ILEKYKDDRSEGKL--F-----PVLSNQKINRYLKEIAKIAGIDKHLTFHVARHTFATLLLLKGVDIETISKLLGHSSIK 148

                         170
                  ....*....|.
gi 1024883025 287 ATQVYTHLDFQ 297
Cdd:cd01185   149 TTQIYAKIVDS 159
INT_C_like_3 cd01192
Uncharacterized site-specific tyrosine recombinase, C-terminal catalytic domain; Tyrosine ...
 160-302 6.51e-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: 65.78  E-value: 6.51e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1024883025 160 SGLRISELVGANIQDINPTEGEILVRGKGNKERLLPVGSKALSALKAWLKIRPQFAHPDEIAVFVSSQKKRISVRQVRLR 239
Cdd:cd01192    36 TGLRISDLLSLKVEDVTNKDKLSIKEQKTGKQKTFPLNPTLVKALKEYIDDLDLKRNDYLFKSLKQGPEKPISRKQAYKI 115

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1024883025 240 MQEWGIKQGISSQVHPHKLRHSFASHILESSGDLRAVQELLGHSSLSATQVYTHLDFQHLAKV 302
Cdd:cd01192   116 LKKAADDLGLNYNIGTHSLRKTFGYHVYKQGKDIELLMKLLNHSSPSITLRYLGIDQEDVDKA 178
INT_tnpA_C_Tn554 cd01186
Putative Transposase A from transposon Tn554, C-terminal catalytic domain; This family ...
 148-294 1.37e-12

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: 65.13  E-value: 1.37e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1024883025 148 IRDKAMMELMYSSGLRISELVGANIQDINPTEGEILVRGKGN----------KERLLPVGSKALSALKAWLKIRPQFAHP 217
Cdd:cd01186    17 LRDKFLLALLYETGLRIGEALGLRIEDIDMADNQIELVPREDntnearaksmRERRIPVSQDLIDLYADYLTYIYCEEAE 96

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1024883025 218 DEIAVFVSSQK-------KRISVRQ-VRLrmqewgIKQGISSQVHPHKLRHSFASHILESSGDLRAVQELLGHSSLSAT- 288
Cdd:cd01186    97 FSITVFVNVKGgnqgkamNYSDVYDlVRR------LKKRTGIDFTPHMFRHTHATALIRAGWSIEVVARRLGHAHVQTTl 170


                  ....*.
gi 1024883025 289 QVYTHL 294
Cdd:cd01186   171 NTYGHL 176
INT_C_like_2 cd01191
Uncharacterized site-specific tyrosine recombinase, C-terminal catalytic domain; Tyrosine ...
 157-291 8.93e-11

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: 59.75  E-value: 8.93e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1024883025 157 MYSSGLRISELVGANIQDINptEGEILVRGKGNKERLLPVGSKALSALKAWLKIRPQfahpDEIAVFVSSQKKRISVRQV 236
Cdd:cd01191    29 LAATGARVSELIKIKVEHVE--LGYFDIYSKGGKLRRLYIPKKLRNEALEWLKSTNR----KSGYIFLNRFGERITTRGI 102

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1024883025 237 RLRMQEWGIKQGIS-SQVHPHKLRHSFASHILESSGDLRAVQELLGHSSLSATQVY 291
Cdd:cd01191   103 AQQLKNYARKYGLNpKVVYPHSFRHRFAKNFLEKYNDIALLADLMGHESIETTRIY 158
int PHA02601
integrase; Provisional
 72-299 2.46e-10

integrase; Provisional


Pssm-ID: 222904 [Multi-domain]  Cd Length: 333  Bit Score: 60.51  E-value: 2.46e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1024883025  72 MQMRSKQLSG------------RTISLKLSCIRSLYKFLKAkniASQAHYHNPAEAIKGPKFSKPLPKNLDVDQMAKLL- 138
Cdd:PHA02601  107 ADYRARRLSGefkvnkgrpikpATVNRELAYLSAVFNELIK---LGKWSGPNPLDGIRPFKEAEPELAFLTKEEIERLLd 183

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1024883025 139 ELPDDEPLAIRDKAMMELmySSGLRISElvGANIQDINPTEGEI-LVRGKGNKERLLPVgSKALSALkawLKIRPQFAHP 217
Cdd:PHA02601  184 ACDGSRSPDLGLIAKICL--ATGARWSE--AETLKRSQISPYKItFVKTKGKKNRTVPI-SEELYKM---LPKRRGRLFK 255

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1024883025 218 DEIAVFvssqkKRIsvrqvrLRMQEWGIKQGISSqvhpHKLRHSFASHILESSGDLRAVQELLGHSSLSATQVYTHLDFQ 297
Cdd:PHA02601  256 DAYESF-----ERA------VKRAGIDLPEGQAT----HVLRHTFASHFMMNGGNILVLQRILGHATIEMTMAYAHFAPD 320


                  ..
gi 1024883025 298 HL 299
Cdd:PHA02601  321 HL 322
Phage_int_SAM_1 pfam02899
Phage integrase, N-terminal SAM-like domain;
20-102 5.63e-10

Phage integrase, N-terminal SAM-like domain;


Pssm-ID: 427047 [Multi-domain]  Cd Length: 83  Bit Score: 54.96  E-value: 5.63e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1024883025  20 IQLFADYLRYEKQYSAHTVNQYTSQLGFAALYFSKLCEDWFAVQGEHIRRYSMQMRSKQLSGRTISLKLSCIRSLYKFLK 99
Cdd:pfam02899   1 IDQFLEYLSLERGLSPHTLRAYRRDLLAFLKFLSEGGSSLEQITTSDVRAFLAELRAQGLSASSLARRLSALRSFYQFLI 80


                  ...
gi 1024883025 100 AKN 102
Cdd:pfam02899  81 REG 83
INT_C_like_6 cd01196
Uncharacterized site-specific tyrosine recombinase, C-terminal catalytic domain; Tyrosine ...
 130-291 3.84e-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: 52.48  E-value: 3.84e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1024883025 130 DVDQMAKLLELPDDE-PLAIRDKAMMELMYSSGLRISELVGANIQDINPTEGEILVR--GKGNKERLLPVGSKALSALKA 206
Cdd:cd01196     1 TAPEARRLLESIDSThPVGLRDRALIALMVYSFARIGAVLAMRVEDVYDQGRRLWVRlaEKGGKQHEMPCHHDLEEYLRA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1024883025 207 WL-KIRPQFAHPDEIAVFVSSQKKRISV---------RQVRLRMQEWGIKQGISsqvhPHKLRHSFASHILESSGDLRAV 276
Cdd:cd01196    81 YLeAAEIEEDPKGPLFRTTRGGTRKLTHnpltqanayRMVRRRAIAADIPTAIG----NHSFRATGITAYLKNGGTLEDA 156

                         170
                  ....*....|....*
gi 1024883025 277 QELLGHSSLSATQVY 291
Cdd:cd01196   157 QNMANHASTRTTQLY 171
INT_tnpB_C_Tn554 cd01187
Putative Transposase B from transposon Tn554, C-terminal catalytic domain; This family ...
 144-293 4.44e-08

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: 51.28  E-value: 4.44e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1024883025 144 EPLAIRDK-----AMMELMYSSGLRISELVGANIQDINPTEGEilvrgkgnkERLLPVGSKALSALKAWLKIrpqfAHPD 218
Cdd:cd01187     4 PNLAALDLlpqpiPVVQAAVFTGARASELATLKFGCLHAQTSD---------DGTFLYWLKWENKGGKQLDI----PISK 70

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1024883025 219 EIAVFVssqkKRISVRQVRLRMQEWGI-KQGISSQVHPHKLRHSFASHILESSGDLRAVQELLGHSSLSATQVYTH 293
Cdd:cd01187    71 KVAELI----KTINWTLNELSELKNISdDHGERFRFHTHRFRHTVATRLANSGMGILVLQQLLGHSSPEMTLRYAL 142
INT_P4_C cd00801
Bacteriophage P4 integrase, C-terminal catalytic domain; P4-like integrases are found in ...
 132-313 7.98e-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: 48.42  E-value: 7.98e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1024883025 132 DQMAKLLELPDDEPLAIRDKAMMELMYSSGLRISELVGANIQDINPTEGEILV---RGKGNKERLLPVGSKALsalkAWL 208
Cdd:cd00801     3 DELPELWRALDTANLSPPTKLALRLLLLTGQRIGELARARWSEIDLEEKTWTIpaeRTKNKRPHRVPLSDQAL----EIL 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1024883025 209 KIRPQFAHPDEIaVFVSSQKK-----RISVRQVRLRMQEWGIKQgissqvHPHKLRHSFASHILESSGDLRAVQELLGHS 283
Cdd:cd00801    79 EELKEFTGDSGY-LFPSRRKKkkpisENTINKALKRLGYKGKEF------TPHDLRRTFSTLLNELGIDPEVIERLLNHV 151

                         170       180       190
                  ....*....|....*....|....*....|
gi 1024883025 284 SLSAtqvythldfqhLAKVYDNTHPRAKKR 313
Cdd:cd00801   152 LGGV-----------VRAAYNRYDYLEERR 170
INT_Lambda_C cd00800
C-terminal catalytic domain of Lambda integrase, a tyrosine-based site-specific recombinase; ...
 147-292 1.11e-06

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


Pssm-ID: 271181 [Multi-domain]  Cd Length: 161  Bit Score: 47.72  E-value: 1.11e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1024883025 147 AIRDKA------MMELMYSSGLRISELVGANIQDInpTEGEILVR-GKGNKERLLPVGSK---ALSALKAWLKIRPQFah 216
Cdd:cd00800     5 AIYAEAppllrlAMELALLTGQRQGDLLRLKWSDI--TDGGLLVEqSKTGKKLLIPWTPSlraLVDRIRALPRKRSEY-- 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1024883025 217 pdeiaVFVSSQKKRISVRQVRLR----MQEWGIKQGISsQVHPHKLRHSFASHILESSGDLRAvQELLGHSSLSATQVYT 292
Cdd:cd00800    81 -----LINSRKGGPLSYDTLKSAwrraRKAAGLKGETE-GFTFHDLRAKAATDYAEQGGSTDA-QALLGHKSDAMTERYT 153
COG4342 COG4342
Phage integrase/recombinase [Mobilome: prophages, transposons];
90-168 4.96e-03

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


Pssm-ID: 443483 [Multi-domain]  Cd Length: 278  Bit Score: 38.15  E-value: 4.96e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1024883025  90 CIRSLYKFLKAKNIASQAHYHNPAEAIKGPKFSKPL--PKNLDVDQMAKLLELPDDEPLAIrdkamMELMYSSGLRISEL 167
Cdd:COG4342    73 ALRNLANFLVERGIISEEVAEKIKEVLKVKRSGVDLyvPTDEEIREALKYLKEKDEEVYLL-----YKLLLFSGLRLSEA 147


                  .
gi 1024883025 168 V 168
Cdd:COG4342   148 L 148
 
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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