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Conserved domains on  [gi|1860102257|gb|QKW32563|]
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site-specific integrase (plasmid) [Nocardiopsis flavescens]

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];
2-337 3.16e-39

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


:

Pssm-ID: 443999 [Multi-domain]  Cd Length: 291  Bit Score: 140.51  E-value: 3.16e-39
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1860102257   2 LEGWRNQ-QMARNLALSTIEGRHNAVKAFTHHADAF----PWQWSAQMVDEWLGDLRAiRHLKQSTLRNYAEAVRSFcaf 76
Cdd:COG4974     7 LEAFLEElKREKGLSPNTIKAYRRDLRRFLRFLEELgkipLAEITPEDIRAYLNYLRE-RGLSPSTINRYLAALRSF--- 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1860102257  77 ltdpaYDWAAEcEKRFGTHPvqvchewnTAHHLQESEADPSKRAFTRAELLAFFDYADDqvhrvrgagrkGWLPAFRDAA 156
Cdd:COG4974    83 -----FRYAVR-EGLLEDNP--------AAKVKLPKKPRKLPRVLTEEEIEALLEALDT-----------ETPEGLRDRA 137

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1860102257 157 LFKTAYAYGLRRREVRMLDLADFGPNPharefggyGVCYVRWGKamkGSppKRRSVLtvgpregIGgmDWIVDVLEQWVE 236
Cdd:COG4974   138 LLLLLYATGLRVSELLGLKWSDIDLDR--------GTIRVRRGK---GG--KERTVP-------LS--PEALEALREYLE 195

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1860102257 237 EARPAfthaGSPALWPSERGPRIGFSQMNTRFAAYRDAIGLDPGLDLHSLRRSYVTHLIEDGWDPRFVQEQVGHEHASTT 316
Cdd:COG4974   196 ERRPR----DSDYLFPTRRGRPLSRRAIRKILKRLAKRAGIPKRVTPHSLRHTFATHLLEAGVDLRTVQELLGHSSISTT 271

                         330       340
                  ....*....|....*....|.
gi 1860102257 317 SLYTCVSSDfrtrTLRKAMDA 337
Cdd:COG4974   272 QIYTHVSDE----ELREAVEK 288
 
Name Accession Description Interval E-value
XerD COG4974
Site-specific recombinase XerD [Replication, recombination and repair];
2-337 3.16e-39

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


Pssm-ID: 443999 [Multi-domain]  Cd Length: 291  Bit Score: 140.51  E-value: 3.16e-39
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1860102257   2 LEGWRNQ-QMARNLALSTIEGRHNAVKAFTHHADAF----PWQWSAQMVDEWLGDLRAiRHLKQSTLRNYAEAVRSFcaf 76
Cdd:COG4974     7 LEAFLEElKREKGLSPNTIKAYRRDLRRFLRFLEELgkipLAEITPEDIRAYLNYLRE-RGLSPSTINRYLAALRSF--- 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1860102257  77 ltdpaYDWAAEcEKRFGTHPvqvchewnTAHHLQESEADPSKRAFTRAELLAFFDYADDqvhrvrgagrkGWLPAFRDAA 156
Cdd:COG4974    83 -----FRYAVR-EGLLEDNP--------AAKVKLPKKPRKLPRVLTEEEIEALLEALDT-----------ETPEGLRDRA 137

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1860102257 157 LFKTAYAYGLRRREVRMLDLADFGPNPharefggyGVCYVRWGKamkGSppKRRSVLtvgpregIGgmDWIVDVLEQWVE 236
Cdd:COG4974   138 LLLLLYATGLRVSELLGLKWSDIDLDR--------GTIRVRRGK---GG--KERTVP-------LS--PEALEALREYLE 195

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1860102257 237 EARPAfthaGSPALWPSERGPRIGFSQMNTRFAAYRDAIGLDPGLDLHSLRRSYVTHLIEDGWDPRFVQEQVGHEHASTT 316
Cdd:COG4974   196 ERRPR----DSDYLFPTRRGRPLSRRAIRKILKRLAKRAGIPKRVTPHSLRHTFATHLLEAGVDLRTVQELLGHSSISTT 271

                         330       340
                  ....*....|....*....|.
gi 1860102257 317 SLYTCVSSDfrtrTLRKAMDA 337
Cdd:COG4974   272 QIYTHVSDE----ELREAVEK 288
DNA_BRE_C cd00397
DNA breaking-rejoining enzymes, C-terminal catalytic domain; The DNA breaking-rejoining enzyme ...
 136-320 5.36e-20

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: 85.61  E-value: 5.36e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1860102257 136 QVHRVRGAGRKGWLPAFRDAALFKTAYAYGLRRREVRMLDLADFGPNpharefggYGVCYVRWGKAMKGsppKRRSVLTV 215
Cdd:cd00397     1 ELEKLLDAIDEDKKIDLRDRAILLLLLETGLRISELLALKVKDIDLD--------NGTIRVRGKKTKGG---KERTVPLP 69

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1860102257 216 GPregigGMDWIVDVLEQWVEEARPAFTHAGSPALWPSERGPRIGFSQMNTRFAAYRDAIGLDPGLdlHSLRRSYVTHLI 295
Cdd:cd00397    70 KE-----LAEELKEYLKERRDKRGPLLKSLYLNKLFGTKLGERLSRRTLRRIFKKAGIEAGRKITP--HSLRHTFATNLL 142

                         170       180
                  ....*....|....*....|....*
gi 1860102257 296 EDGWDPRFVQEQVGHEHASTTSLYT 320
Cdd:cd00397   143 ENGVDIKVVQKLLGHSSISTTQRYL 167
Phage_integrase pfam00589
Phage integrase family; Members of this family cleave DNA substrates by a series of staggered ...
 135-320 1.52e-17

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: 78.90  E-value: 1.52e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1860102257 135 DQVHRVRGAGRKGWLPAfRDAALFKTAYAYGLRRREVRMLDLADFGPNPharefggyGVCYVRWGKAMKgsppKRRSVLT 214
Cdd:pfam00589   5 DEVERLLDAAETGPLSI-RDKALLELLYATGLRISELCSLRWSDIDFEN--------GVIRVHRGKGNK----ERTVPLS 71

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1860102257 215 vgpregiggmDWIVDVLEQWVEEArpAFTHAGSPALWPSERGPRIGFSQMNTRFAAYRDAIGLDPGLDLHSLRRSYVTHL 294
Cdd:pfam00589  72 ----------DAALELLKEWLSKR--LLEAPKSDYLFASKRGKPLSRQTVRKIFKRAGKEAGLELPLHPHMLRHSFATHL 139

                         170       180
                  ....*....|....*....|....*.
gi 1860102257 295 IEDGWDPRFVQEQVGHEHASTTSLYT 320
Cdd:pfam00589 140 LEAGVDLRVVQKLLGHSSISTTQIYT 165
xerC PRK00236
site-specific tyrosine recombinase XerC; Reviewed
 45-337 2.37e-16

site-specific tyrosine recombinase XerC; Reviewed


Pssm-ID: 234698 [Multi-domain]  Cd Length: 297  Bit Score: 78.27  E-value: 2.37e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1860102257  45 VDEWLGDLRAIRHLKQSTLRNYAEAVRSFCAFLtdpaydwaaecEKRFGTHPVQVchewnTAHHL-----QESEADPSKR 119
Cdd:PRK00236   10 LEAFLEYLRVERGLSPHTLRAYRRDLRAFLAFL-----------EEHGISSLQDL-----DAADLrsflaRRRRQGLSAR 73

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1860102257 120 afTRAELLA----FFDYAD----------------------------DQVHR-VRGAGRKGWLpAFRDAALFKTAYAYGL 166
Cdd:PRK00236   74 --SLARRLSalrsFYRWLVrrgllkanpaaglrapkipkrlpkpldvDQAKRlLDAIDEDDPL-ALRDRAILELLYGSGL 150

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1860102257 167 RRREVRMLDLADF-GPNPHAREFGgygvcyvrwgkamKGSppKRRSVlTVGPRegiggmdwIVDVLEQWVeEARPAFTHA 245
Cdd:PRK00236  151 RLSELVGLDIDDLdLASGTLRVLG-------------KGN--KERTV-PLGRA--------AREALEAYL-ALRPLFLPD 205

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1860102257 246 GsPALWPSERGPRIGFSQMNTRFAAYRDAIGLDPGLDLHSLRRSYVTHLIEDGWDPRFVQEQVGHEHASTTSLYTCVSSD 325
Cdd:PRK00236  206 D-DALFLGARGGRLSPRVVQRRVKKLGKKAGLPSHITPHKLRHSFATHLLESGGDLRAVQELLGHASLSTTQIYTHVDFQ 284

                         330
                  ....*....|..
gi 1860102257 326 frtrTLRKAMDA 337
Cdd:PRK00236  285 ----HLAEVYDA 292
 
Name Accession Description Interval E-value
XerD COG4974
Site-specific recombinase XerD [Replication, recombination and repair];
2-337 3.16e-39

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


Pssm-ID: 443999 [Multi-domain]  Cd Length: 291  Bit Score: 140.51  E-value: 3.16e-39
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1860102257   2 LEGWRNQ-QMARNLALSTIEGRHNAVKAFTHHADAF----PWQWSAQMVDEWLGDLRAiRHLKQSTLRNYAEAVRSFcaf 76
Cdd:COG4974     7 LEAFLEElKREKGLSPNTIKAYRRDLRRFLRFLEELgkipLAEITPEDIRAYLNYLRE-RGLSPSTINRYLAALRSF--- 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1860102257  77 ltdpaYDWAAEcEKRFGTHPvqvchewnTAHHLQESEADPSKRAFTRAELLAFFDYADDqvhrvrgagrkGWLPAFRDAA 156
Cdd:COG4974    83 -----FRYAVR-EGLLEDNP--------AAKVKLPKKPRKLPRVLTEEEIEALLEALDT-----------ETPEGLRDRA 137

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1860102257 157 LFKTAYAYGLRRREVRMLDLADFGPNPharefggyGVCYVRWGKamkGSppKRRSVLtvgpregIGgmDWIVDVLEQWVE 236
Cdd:COG4974   138 LLLLLYATGLRVSELLGLKWSDIDLDR--------GTIRVRRGK---GG--KERTVP-------LS--PEALEALREYLE 195

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1860102257 237 EARPAfthaGSPALWPSERGPRIGFSQMNTRFAAYRDAIGLDPGLDLHSLRRSYVTHLIEDGWDPRFVQEQVGHEHASTT 316
Cdd:COG4974   196 ERRPR----DSDYLFPTRRGRPLSRRAIRKILKRLAKRAGIPKRVTPHSLRHTFATHLLEAGVDLRTVQELLGHSSISTT 271

                         330       340
                  ....*....|....*....|.
gi 1860102257 317 SLYTCVSSDfrtrTLRKAMDA 337
Cdd:COG4974   272 QIYTHVSDE----ELREAVEK 288
XerC COG4973
Site-specific recombinase XerC [Replication, recombination and repair];
42-320 1.54e-28

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


Pssm-ID: 443998 [Multi-domain]  Cd Length: 287  Bit Score: 111.98  E-value: 1.54e-28
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1860102257  42 AQMVDEWLGDLRAiRHLKQSTLRNYAEAVRSFCAFLTDPAYDWAaecekrfgthpvQVCHEWNTAHHLQESEADPSKRaf 121
Cdd:COG4973     5 AEALEAYLEHLRE-RRLSPKTLEAYRRDLRRLIPLLGDADLPLE------------ELTPADVRRFLARLHRRGLSPR-- 69

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1860102257 122 TRAELL----AFFDYA----------------------------DDQVHRVRGAGRKGWLPAfRDAALFKTAYAYGLRRR 169
Cdd:COG4973    70 TLNRRLsalrSFFNWAvreglleanpaagvkapkaprklpraltVDELAQLLDALADDPLAV-RDRAIVELLYSTGLRLG 148

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1860102257 170 EVRMLDLADFgpNPHAREFggygvcYVRwGkamKGSppKRRSVlTVGPregiggmdWIVDVLEQWVEEaRPAFTHAGSPA 249
Cdd:COG4973   149 ELVGLDWEDV--DLDAGEV------RVR-G---KTG--KSRTV-PLGP--------KALAALREWLAV-RPELAAPDEGA 204

                         250       260       270       280       290       300       310
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1860102257 250 LWPSERGPRIGFSQMNTRFAAYRDAIGLDPGLDLHSLRRSYVTHLIEDGWDPRFVQEQVGHEHASTTSLYT 320
Cdd:COG4973   205 LFPSRRGTRLSPRNVQKRLRRLAKKAGLPKHVHPHDLRHSFATHLLESGGDLRAVQELLGHASISTTQIYT 275
DNA_BRE_C cd00397
DNA breaking-rejoining enzymes, C-terminal catalytic domain; The DNA breaking-rejoining enzyme ...
 136-320 5.36e-20

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: 85.61  E-value: 5.36e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1860102257 136 QVHRVRGAGRKGWLPAFRDAALFKTAYAYGLRRREVRMLDLADFGPNpharefggYGVCYVRWGKAMKGsppKRRSVLTV 215
Cdd:cd00397     1 ELEKLLDAIDEDKKIDLRDRAILLLLLETGLRISELLALKVKDIDLD--------NGTIRVRGKKTKGG---KERTVPLP 69

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1860102257 216 GPregigGMDWIVDVLEQWVEEARPAFTHAGSPALWPSERGPRIGFSQMNTRFAAYRDAIGLDPGLdlHSLRRSYVTHLI 295
Cdd:cd00397    70 KE-----LAEELKEYLKERRDKRGPLLKSLYLNKLFGTKLGERLSRRTLRRIFKKAGIEAGRKITP--HSLRHTFATNLL 142

                         170       180
                  ....*....|....*....|....*
gi 1860102257 296 EDGWDPRFVQEQVGHEHASTTSLYT 320
Cdd:cd00397   143 ENGVDIKVVQKLLGHSSISTTQRYL 167
Phage_integrase pfam00589
Phage integrase family; Members of this family cleave DNA substrates by a series of staggered ...
 135-320 1.52e-17

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: 78.90  E-value: 1.52e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1860102257 135 DQVHRVRGAGRKGWLPAfRDAALFKTAYAYGLRRREVRMLDLADFGPNPharefggyGVCYVRWGKAMKgsppKRRSVLT 214
Cdd:pfam00589   5 DEVERLLDAAETGPLSI-RDKALLELLYATGLRISELCSLRWSDIDFEN--------GVIRVHRGKGNK----ERTVPLS 71

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1860102257 215 vgpregiggmDWIVDVLEQWVEEArpAFTHAGSPALWPSERGPRIGFSQMNTRFAAYRDAIGLDPGLDLHSLRRSYVTHL 294
Cdd:pfam00589  72 ----------DAALELLKEWLSKR--LLEAPKSDYLFASKRGKPLSRQTVRKIFKRAGKEAGLELPLHPHMLRHSFATHL 139

                         170       180
                  ....*....|....*....|....*.
gi 1860102257 295 IEDGWDPRFVQEQVGHEHASTTSLYT 320
Cdd:pfam00589 140 LEAGVDLRVVQKLLGHSSISTTQIYT 165
INT_XerDC_C cd00798
XerD and XerC integrases, C-terminal catalytic domains; XerDC-like integrases are involved in ...
 151-323 1.93e-16

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: 76.01  E-value: 1.93e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1860102257 151 AFRDAALFKTAYAYGLRRREVRMLDLADFGPNPH-AREFGgygvcyvrwgkamKGSppKRRSVltvgPregIGGMdwIVD 229
Cdd:cd00798    18 GLRDRAILELLYASGLRVSELVGLDLSDVDLDEGlVRVTG-------------KGN--KERLV----P---FGSY--AVE 73

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1860102257 230 VLEQWVEEARPAFTHAGSP-ALWPSERGPRIGFSQMNTRFAAYRDAIGLDPGLDLHSLRRSYVTHLIEDGWDPRFVQEQV 308
Cdd:cd00798    74 ALEEYLEERRPLLLKKKPPdALFLNKRGKRLSRRGVWRILKKYAERAGLPKHVSPHTLRHSFATHLLEGGADLRVVQELL 153

                         170
                  ....*....|....*
gi 1860102257 309 GHEHASTTSLYTCVS 323
Cdd:cd00798   154 GHASLSTTQIYTHVS 168
xerC PRK00236
site-specific tyrosine recombinase XerC; Reviewed
 45-337 2.37e-16

site-specific tyrosine recombinase XerC; Reviewed


Pssm-ID: 234698 [Multi-domain]  Cd Length: 297  Bit Score: 78.27  E-value: 2.37e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1860102257  45 VDEWLGDLRAIRHLKQSTLRNYAEAVRSFCAFLtdpaydwaaecEKRFGTHPVQVchewnTAHHL-----QESEADPSKR 119
Cdd:PRK00236   10 LEAFLEYLRVERGLSPHTLRAYRRDLRAFLAFL-----------EEHGISSLQDL-----DAADLrsflaRRRRQGLSAR 73

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1860102257 120 afTRAELLA----FFDYAD----------------------------DQVHR-VRGAGRKGWLpAFRDAALFKTAYAYGL 166
Cdd:PRK00236   74 --SLARRLSalrsFYRWLVrrgllkanpaaglrapkipkrlpkpldvDQAKRlLDAIDEDDPL-ALRDRAILELLYGSGL 150

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1860102257 167 RRREVRMLDLADF-GPNPHAREFGgygvcyvrwgkamKGSppKRRSVlTVGPRegiggmdwIVDVLEQWVeEARPAFTHA 245
Cdd:PRK00236  151 RLSELVGLDIDDLdLASGTLRVLG-------------KGN--KERTV-PLGRA--------AREALEAYL-ALRPLFLPD 205

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1860102257 246 GsPALWPSERGPRIGFSQMNTRFAAYRDAIGLDPGLDLHSLRRSYVTHLIEDGWDPRFVQEQVGHEHASTTSLYTCVSSD 325
Cdd:PRK00236  206 D-DALFLGARGGRLSPRVVQRRVKKLGKKAGLPSHITPHKLRHSFATHLLESGGDLRAVQELLGHASLSTTQIYTHVDFQ 284

                         330
                  ....*....|..
gi 1860102257 326 frtrTLRKAMDA 337
Cdd:PRK00236  285 ----HLAEVYDA 292
xerD PRK00283
tyrosine recombinase;
151-325 4.14e-14

tyrosine recombinase;


Pssm-ID: 234713 [Multi-domain]  Cd Length: 299  Bit Score: 71.76  E-value: 4.14e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1860102257 151 AFRDAALFKTAYAYGLRRREVRMLDLADFGPNPharefggyGVCYVRwGKamkGSppKRRSVltvgPregIGGMdwIVDV 230
Cdd:PRK00283  133 GLRDRAMLELLYATGLRVSELVGLTLDDVSLRQ--------GVVRVT-GK---GN--KERLV----P---LGEE--AVYA 189

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1860102257 231 LEQWVEEARPAFTH-AGSPALWPSERG---PRIGFSQMNTRFAAYrdaIGLDP-GLDLHSLRRSYVTHLIEDGWDPRFVQ 305
Cdd:PRK00283  190 IERYLERGRPALLNgRSSDALFPSARGgqlTRQTFWHRIKHYAKR---AGIDPkKLSPHVLRHAFATHLLNHGADLRVVQ 266

                         170       180
                  ....*....|....*....|
gi 1860102257 306 EQVGHEHASTTSLYTCVSSD 325
Cdd:PRK00283  267 ELLGHSDISTTQIYTHVATE 286
xerC PRK01287
site-specific tyrosine recombinase XerC; Reviewed
 134-341 4.79e-13

site-specific tyrosine recombinase XerC; Reviewed


Pssm-ID: 234935 [Multi-domain]  Cd Length: 358  Bit Score: 69.39  E-value: 4.79e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1860102257 134 DDQVHRVRGAGRKGWLPAFRDAALFKTAYAYGLRRREVRMLDLADFGpnpharefGGYGVCYVRWGKAmkgsppKRRSVL 213
Cdd:PRK01287  139 EAETEQVLASPDLTTLQGLRDRALLELLWSTGIRRGELARLDLYDVD--------ASRGVVTVRQGKG------NKDRVV 204

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1860102257 214 TVGPRegigGMDWivdvLEQWVEEARPAFTHA-GSPALWPSERGPRIGFSQMNTRFAAYRDAIGLDPGLDLHSLRRSYVT 292
Cdd:PRK01287  205 PVGER----ALAW----LQRYLQDVRPQLAVRpDSGALFVAMDGDGLARNTLTNMVGRYIRAAGIEKAGACHLFRHAMAT 276

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*....
gi 1860102257 293 HLIEDGWDPRFVQEQVGHEHASTTSLYTCVSsdfrTRTLRKAMDATMKA 341
Cdd:PRK01287  277 QMLENGADTRHIQAILGHAKLETTQIYTRVS----IGHLQAVHASTHPA 321
INT_IntI_C cd01193
Integron integrase and similar protiens, C-terminal catalytic domain; Integron integrases ...
 135-322 5.56e-13

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: 66.53  E-value: 5.56e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1860102257 135 DQVHRVRGAGRKGwlpafRDAALFKTAYAYGLRRREV---RMLDLaDFgpnpharefgGYGVCYVRWGkamKGSppKRRS 211
Cdd:cd01193     9 DEVRRILGALTEL-----RHRLILSLLYGAGLRISELlrlRVKDI-DF----------ERGVIRVRQG---KGG--KDRV 67

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1860102257 212 VLTvgPREgiggmdwIVDVLEQWVEEARPAFTH--AGSPALWPSERGPRIGFSQMNTR-----FAAYRDAIGLDPGLDLH 284
Cdd:cd01193    68 VPL--PEK-------LLEPLRRYLKSARPKEELdpAEGRAGVLDPRTGVERRHHISETtvqraLKKAVEQAGITKRVTPH 138

                         170       180       190
                  ....*....|....*....|....*....|....*...
gi 1860102257 285 SLRRSYVTHLIEDGWDPRFVQEQVGHEHASTTSLYTCV 322
Cdd:cd01193   139 TLRHSFATHLLEAGTDIRTIQELLGHSDLSTTMIYTHV 176
INT_C_like_1 cd01184
Uncharacterized site-specific tyrosine recombinase, C-terminal catalytic domain; Tyrosine ...
 121-317 8.05e-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: 51.54  E-value: 8.05e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1860102257 121 FTRAELLAFFDYADDQVHRVRGAGRKgWLPAFrdaALFkTayayGLRRREVRMLDLADFgpnphaREFGGYGVCYVRWGK 200
Cdd:cd01184     1 FTPEELAKIFSSPLYTGCKKKDPALY-WLPLI---GLY-T----GARLNEICQLRVDDI------KEEDGIWCIDINDDA 65

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1860102257 201 AMKGS--PPKRRSVltvgPregiggmdwIVDVLEQ-----WVEE--ARPAFThagspaLWPSERGPRIGFSQ-MNTRFAA 270
Cdd:cd01184    66 EGRRLktKASRRLV----P---------IHPRLIElgfldYVEAlrADGKLF------LFPEKRDKDGKYSKaASKWFNR 126

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*....
gi 1860102257 271 YRDAIGL--DPGLDLHSLRRSYVTHLIEDGWDPRFVQEQVGHEHASTTS 317
Cdd:cd01184   127 LLRKLGIkdDERKSFHSFRHTFITALKRAGVPEELIAQIVGHSRGGVTH 175
INT_RitA_C_like cd01188
C-terminal catalytic domain of recombinase RitA, a component of the recombinase trio; ...
 153-319 1.71e-06

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: 47.62  E-value: 1.71e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1860102257 153 RDAALFKTAYAYGLRRREVRMLDLADFGPNPHAREFGGYGvcyvrwgkamKGSPpkRRSVLTVGPREGIggMDWIVDvle 232
Cdd:cd01188    21 RDYAILLLLARLGLRAGDVAGLRLDDIDWRSGTITVRQKK----------TGRP--VELPLTEPVGEAL--ADYLRD--- 83

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1860102257 233 qwveeARPAfthAGSPALWPSERGPRIGF---SQMNTRFAAYRDAIGLDPGL-DLHSLRRSYVTHLIEDGWDPRFVQEQV 308
Cdd:cd01188    84 -----GRPR---TDSREVFLRARAPYRPLsstSQISSIVRRYLRKAGIEPSHrGTHSLRHSLATRMLRAGTSLKVIADLL 155

                         170
                  ....*....|.
gi 1860102257 309 GHEHASTTSLY 319
Cdd:cd01188   156 GHRSIETTAIY 166
INT_C_like_4 cd01194
Uncharacterized site-specific tyrosine recombinase, C-terminal catalytic domain; Tyrosine ...
 149-319 4.99e-06

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


Pssm-ID: 271194 [Multi-domain]  Cd Length: 174  Bit Score: 46.21  E-value: 4.99e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1860102257 149 LPAFRDAALFKTAYAYGLRRREVRMLDLADFgpnphaREFGGYGVCYVRWgkamKGSPPKRRSVLTVGPregiggmdwIV 228
Cdd:cd01194    19 IIGLRDRAIISLMVTEGLRTVEIVRADVGDL------RQEGEGTILYVQG----KGKTSKDDFVYLRPD---------VL 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1860102257 229 DVLEQWVEeARPaFTHAGSPALwpSERGPRIGFSQMNTRFAAYR-----DAIGLDP-GLDLHSLRRSYVTHLIEDGWDPR 302
Cdd:cd01194    80 KALQAYLK-ARG-KLDFEEPLF--TSLSNNSKGQRLTTRSIRRIikkylRKAGLDDdRLTAHSLRHTAGTLALKAGKSLR 155

                         170
                  ....*....|....*..
gi 1860102257 303 FVQEQVGHEHASTTSLY 319
Cdd:cd01194   156 EVQQLLRHSDPNTTMIY 172
INT_RitB_C_like cd00797
C-terminal catalytic domain of recombinase RitB, a component of the recombinase trio; ...
 121-319 6.94e-06

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: 46.15  E-value: 6.94e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1860102257 121 FTRAELLAFFDYADdqvhrvrGAGRKGWLPAFRDAALFKTAYAYGLRRREVRMLDLADFGPNPharefggyGVCYVRWGK 200
Cdd:cd00797     1 YTDAEIRRLLAAAD-------QLPPESPLRPLTYATLFGLLYATGLRVGEALRLRLEDVDLDS--------GILTIRQTK 65

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1860102257 201 amkgsppKRRSVLtVGPREGIggmdwiVDVLEQWVEEARPAFTHAGSPALWPSERGPRIGFSQMNTRFAAYRDAIGLDP- 279
Cdd:cd00797    66 -------FGKSRL-VPLHPST------VGALRDYLARRDRLLPSPSSSYFFVSQQGGRLTGGGVYRVFRRLLRRIGLRGa 131

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1860102257 280 ----GLDLHSLRRSYVTHLI----EDGWDPR----FVQEQVGHEHASTTSLY 319
Cdd:cd00797   132 gdgrGPRLHDLRHTFAVNRLtrwyREGADVErklpVLSTYLGHVNVTDTYWY 183
INT_ICEBs1_C_like cd01189
C-terminal catalytic domain of integrases from bacterial phages and conjugate transposons; ...
 267-316 1.71e-05

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: 44.09  E-value: 1.71e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 1860102257 267 RFAAYRDAIGLdPGLDLHSLRRSYVTHLIEDGWDPRFVQEQVGHEHASTT 316
Cdd:cd01189    93 AFKKLLKKAGL-PRITPHDLRHTFASLLLEAGVPLKVIAERLGHSDISTT 141
INT_RitC_C_like cd01182
C-terminal catalytic domain of recombinase RitC, a component of the recombinase trio; ...
 151-338 4.39e-05

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: 43.81  E-value: 4.39e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1860102257 151 AFRDAALFKTAYAYGLRRREVRMLDLADF--GPNPHAREFGgygvcyvrwgkamKGSppKRRSVltvgPRegiggMDWIV 228
Cdd:cd01182    20 GRRDHALLLLLYDTGARVQELADLTIRDLrlDDPATVRLHG-------------KGR--KERTV----PL-----WKETV 75

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1860102257 229 DVLEQWVEEARPAFTHAGSPALWPSERGPRIGFSQMNTRFAAYRDAI-----GLDPGLDLHSLRRSYVTHLIEDGWDPRF 303
Cdd:cd01182    76 AALKAYLQEFHLTPDPKQLFPLFPNRRGQPLTRDGVAYILNKYVALAsnrcpSLPKRITPHTLRHTKAMHLLQAGVDLTV 155

                         170       180       190
                  ....*....|....*....|....*....|....*
gi 1860102257 304 VQEQVGHEHASTTSLYTCVSsdfrTRTLRKAMDAT 338
Cdd:cd01182   156 IRDWLGHESVETTQIYAEAD----LEMKREALEKA 186
INT_Cre_C cd00799
C-terminal catalytic domain of Cre recombinase (also called integrase); Cre-like recombinases ...
 145-333 4.77e-05

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


Pssm-ID: 271180  Cd Length: 188  Bit Score: 43.44  E-value: 4.77e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1860102257 145 RKGWLPAFRDAALFKTAYAYGLRRREV---RMLDLADFGPnpharefgGYGVCYVRWGKAMKGSPPKRRSVLTVGPREGi 221
Cdd:cd00799     9 DDTTLRGLRDRALLLLGFAGALRRSELvalRVEDLTRFVD--------GGLLIRLRRSKTDQDGEGEIKALPYGPETCP- 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1860102257 222 ggmdwiVDVLEQWVEEARpaftHAGSPALWPSERGPRIGFSQMNTR-----FAAYRDAIGLDPGL-DLHSLRRSYVTHLI 295
Cdd:cd00799    80 ------VRALRAWLEAAG----IPSGPLFRRIRRGGSVGTTRLSDRsvariVKRRAALAGLDPGDfSGHSLRRGFATEAA 149

                         170       180       190
                  ....*....|....*....|....*....|....*...
gi 1860102257 296 EDGWDPRFVQEQVGHEHASTTSLYTCVSSDFRTRTLRK 333
Cdd:cd00799   150 RAGASLPEIMAQGGHKSVATVMRYIREADRFKDNAAAK 187
INT_C_like_5 cd01195
Uncharacterized site-specific tyrosine recombinase, C-terminal catalytic domain; Tyrosine ...
 153-319 2.21e-04

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: 41.30  E-value: 2.21e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1860102257 153 RDAALFKTAYAYGLRRREVRMLDLADFGPnpharefgGYGVCYVrwgkamKGSPPKRRSVLTVGPRegigGMDWIVDVLE 232
Cdd:cd01195    21 RDEALVRLLLDNALRRSEAVALDVEDLEK--------EHRRLRI------LGKGKKQREVVTLPPT----TREALAAWLA 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1860102257 233 QWVEEARPAFThagspALWPSERGPRIGFSQMNTRFAAYRDAIGLDPGLDLHSLRRSYVTHLIEDGWD-PRFVQEQVGHE 311
Cdd:cd01195    83 ARGEAEGPLFV-----SLDRASRGRRLSPQAVYRIVRRLAERIGLGKRLSPHGLRHSAITLALDAGAGlIRKVQDFSRHA 157


                  ....*...
gi 1860102257 312 HASTTSLY 319
Cdd:cd01195   158 DLRTLQVY 165
INT_tnpA_C_Tn554 cd01186
Putative Transposase A from transposon Tn554, C-terminal catalytic domain; This family ...
 272-325 2.45e-04

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: 41.25  E-value: 2.45e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1860102257 272 RDAIGLDPgldlHSLRRSYVTHLIEDGWDPRFVQEQVGHEHASTT-SLYTCVSSD 325
Cdd:cd01186   129 RTGIDFTP----HMFRHTHATALIRAGWSIEVVARRLGHAHVQTTlNTYGHLSEE 179
INT_Rci_Hp1_C cd00796
Shufflon-specific DNA recombinase Rci and Bacteriophage Hp1_like integrase, C-terminal ...
 119-320 5.13e-04

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: 40.00  E-value: 5.13e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1860102257 119 RAFTRAELLAFFDYADDQVHrvrgagrkgwlPAFRDAALFktAYAYGLRRREVRMLDLADfgpnpharefggygvcyVRW 198
Cdd:cd00796     3 RFLTEDEEARLLAALEESTN-----------PHLRLIVLL--ALYTGARRGEILSLRWDD-----------------IDL 52

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1860102257 199 GKAMKGSP----PKRRSV-LTVGPREGIggmdwivdvleQWVEEARPAfthagsPALWPSERGPRIGFSQMNTRFAAYRD 273
Cdd:cd00796    53 EVGLIVLPetknGKPRTVpLSDEAIAIL-----------KELKRKRGK------DGFFVDGRFFGIPIASLRRAFKKARK 115

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*..
gi 1860102257 274 AIGLdPGLDLHSLRRSYVTHLIEDGWDPRFVQEQVGHEHASTTSLYT 320
Cdd:cd00796   116 RAGL-EDLRFHDLRHTFASRLVQAGVPIKTVAKILGHSSIKMTMRYA 161
xerS PRK05084
site-specific tyrosine recombinase XerS; Reviewed
 284-336 9.13e-04

site-specific tyrosine recombinase XerS; Reviewed


Pssm-ID: 235339 [Multi-domain]  Cd Length: 357  Bit Score: 40.67  E-value: 9.13e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1860102257 284 HSLRRSYVTHLIEDGWDPRFVQEQVGHEHASTTSLYTCVSSDfrtrTLRKAMD 336
Cdd:PRK05084  306 HKLRHTLATRLYDATKDQVLVADQLGHTSTETTDLYTHIVND----EQKEALD 354
PRK15417 PRK15417
integron integrase;
284-320 2.01e-03

integron integrase;


Pssm-ID: 185315 [Multi-domain]  Cd Length: 337  Bit Score: 39.64  E-value: 2.01e-03
                          10        20        30
                  ....*....|....*....|....*....|....*..
gi 1860102257 284 HSLRRSYVTHLIEDGWDPRFVQEQVGHEHASTTSLYT 320
Cdd:PRK15417  277 HTLRHSFATALLRSGYDIRTVQDLLGHSDVSTTMIYT 313
 
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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