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Conserved domains on  [gi|499653598|ref|WP_011334332|]
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MULTISPECIES: site-specific integrase [Pseudomonas]

Protein Classification

site-specific integrase( domain architecture ID 10092423)

tyrosine based site-specific recombinase (integrase) is involved in cleavage of a single strand of a DNA duplex by nucleophilic attack of a conserved tyrosine to give a 3' phosphotyrosyl protein-DNA adduct

CATH:  1.10.443.10
Gene Ontology:  GO:0015074|GO:0003677|GO:0006310
PubMed:  10047575|9278480|10577069
SCOP:  4002347

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
INT_Cre_C cd00799
C-terminal catalytic domain of Cre recombinase (also called integrase); Cre-like recombinases ...
 133-297 4.28e-53

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: 172.10  E-value: 4.28e-53
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499653598 133 LRACRDRALILLGFWRGFRSDELCRVQIEHVQAHAGNGITLYLPRSKGDRENLGQTYQAPALLKLCPVQAYIEWITEAAL 212
Cdd:cd00799   13 LRGLRDRALLLLGFAGALRRSELVALRVEDLTRFVDGGLLIRLRRSKTDQDGEGEIKALPYGPETCPVRALRAWLEAAGI 92

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499653598 213 VRGPVFRAVDRWGNLSEEGLHANSVIPLLRQALERAGISAERYTSHSLRRGFATWAHQSGWDLKSLMSYVGWKDMKSAMR 292
Cdd:cd00799   93 PSGPLFRRIRRGGSVGTTRLSDRSVARIVKRRAALAGLDPGDFSGHSLRRGFATEAARAGASLPEIMAQGGHKSVATVMR 172


                 ....*
gi 499653598 293 YVEAS 297
Cdd:cd00799  173 YIREA 177
 
Name Accession Description Interval E-value
INT_Cre_C cd00799
C-terminal catalytic domain of Cre recombinase (also called integrase); Cre-like recombinases ...
 133-297 4.28e-53

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: 172.10  E-value: 4.28e-53
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499653598 133 LRACRDRALILLGFWRGFRSDELCRVQIEHVQAHAGNGITLYLPRSKGDRENLGQTYQAPALLKLCPVQAYIEWITEAAL 212
Cdd:cd00799   13 LRGLRDRALLLLGFAGALRRSELVALRVEDLTRFVDGGLLIRLRRSKTDQDGEGEIKALPYGPETCPVRALRAWLEAAGI 92

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499653598 213 VRGPVFRAVDRWGNLSEEGLHANSVIPLLRQALERAGISAERYTSHSLRRGFATWAHQSGWDLKSLMSYVGWKDMKSAMR 292
Cdd:cd00799   93 PSGPLFRRIRRGGSVGTTRLSDRSVARIVKRRAALAGLDPGDFSGHSLRRGFATEAARAGASLPEIMAQGGHKSVATVMR 172


                 ....*
gi 499653598 293 YVEAS 297
Cdd:cd00799  173 YIREA 177
XerD COG4974
Site-specific recombinase XerD [Replication, recombination and repair];
4-298 7.69e-25

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


Pssm-ID: 443999 [Multi-domain]  Cd Length: 291  Bit Score: 101.22  E-value: 7.69e-25
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499653598   4 IDRYLQA-----ATRDNTRRSYRAAIEHFE---SAWGGFLPA--TADSVARYLVAHAG-VLSVNTLKLRLSALAQWHNsq 72
Cdd:COG4974    7 LEAFLEElkrekGLSPNTIKAYRRDLRRFLrflEELGKIPLAeiTPEDIRAYLNYLRErGLSPSTINRYLAALRSFFR-- 84

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499653598  73 gFAdptkspvvrkVFKGIRALHPAQEKQAEPLQLRdleQTVAWLEQEMKDAREQQDRPLLLRAcRDRALILLGFWRGFRS 152
Cdd:COG4974   85 -YA----------VREGLLEDNPAAKVKLPKKPRK---LPRVLTEEEIEALLEALDTETPEGL-RDRALLLLLYATGLRV 149

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499653598 153 DELCRVQIEHVQAHAGngiTLYLPRSKGDRENLgqTYQAPALLKLcpVQAYIEWITEAAlvRGPVFRavdrwgNLSEEGL 232
Cdd:COG4974  150 SELLGLKWSDIDLDRG---TIRVRRGKGGKERT--VPLSPEALEA--LREYLEERRPRD--SDYLFP------TRRGRPL 214

                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 499653598 233 HANSVIPLLRQALERAGISaERYTSHSLRRGFATWAHQSGWDLKSLMSYVGWKDMKSAMRYVEASP 298
Cdd:COG4974  215 SRRAIRKILKRLAKRAGIP-KRVTPHSLRHTFATHLLEAGVDLRTVQELLGHSSISTTQIYTHVSD 279
Phage_integrase pfam00589
Phage integrase family; Members of this family cleave DNA substrates by a series of staggered ...
 135-294 5.56e-13

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: 65.80  E-value: 5.56e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499653598  135 ACRDRALILLGFWRGFRSDELCRVQIEHVQAHAGngiTLYLPRSKGDRENlgqtyQAPALLKLCpvQAYIEWIT---EAA 211
Cdd:pfam00589  20 SIRDKALLELLYATGLRISELCSLRWSDIDFENG---VIRVHRGKGNKER-----TVPLSDAAL--ELLKEWLSkrlLEA 89

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499653598  212 LVRGPVFRAVDRWGnlseegLHANSVIPLLRQALERAGISaERYTSHSLRRGFATWAHQSGWDLKSLMSYVGWKDMKSAM 291
Cdd:pfam00589  90 PKSDYLFASKRGKP------LSRQTVRKIFKRAGKEAGLE-LPLHPHMLRHSFATHLLEAGVDLRVVQKLLGHSSISTTQ 162


                  ...
gi 499653598  292 RYV 294
Cdd:pfam00589 163 IYT 165
PRK09870 PRK09870
tyrosine recombinase; Provisional
 135-302 7.11e-04

tyrosine recombinase; Provisional


Pssm-ID: 182125  Cd Length: 200  Bit Score: 39.92  E-value: 7.11e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499653598 135 ACRDRALILLGFWRGFRSDELCRVQIEHVQAHAGngiTLYLPRSKGdrenlGQTYQAPALLKlcPVQAYIEWITeaalVR 214
Cdd:PRK09870  31 AARNYCLTLLCFIHGFRASEICRLRISDIDLKAK---CIYIHRLKK-----GFSTTHPLLNK--EIQALKNWLS----IR 96

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499653598 215 GPVFRAVDRWGNLSEEG--LHANSVIPLLRQALERAGISAERYtSHSLRR--GFATwaHQSGWDLKSLMSYVGWKDMKSA 290
Cdd:PRK09870  97 TSYPHAESEWVFLSRKGnpLSRQQFYHIISTSGGNAGLSLEIH-PHMLRHscGFAL--ANMGIDTRLIQDYLGHRNIRHT 173

                        170
                 ....*....|....
gi 499653598 291 MRYV--EASPFHGM 302
Cdd:PRK09870 174 VWYTasNAGRFYGI 187
 
Name Accession Description Interval E-value
INT_Cre_C cd00799
C-terminal catalytic domain of Cre recombinase (also called integrase); Cre-like recombinases ...
 133-297 4.28e-53

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: 172.10  E-value: 4.28e-53
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499653598 133 LRACRDRALILLGFWRGFRSDELCRVQIEHVQAHAGNGITLYLPRSKGDRENLGQTYQAPALLKLCPVQAYIEWITEAAL 212
Cdd:cd00799   13 LRGLRDRALLLLGFAGALRRSELVALRVEDLTRFVDGGLLIRLRRSKTDQDGEGEIKALPYGPETCPVRALRAWLEAAGI 92

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499653598 213 VRGPVFRAVDRWGNLSEEGLHANSVIPLLRQALERAGISAERYTSHSLRRGFATWAHQSGWDLKSLMSYVGWKDMKSAMR 292
Cdd:cd00799   93 PSGPLFRRIRRGGSVGTTRLSDRSVARIVKRRAALAGLDPGDFSGHSLRRGFATEAARAGASLPEIMAQGGHKSVATVMR 172


                 ....*
gi 499653598 293 YVEAS 297
Cdd:cd00799  173 YIREA 177
XerD COG4974
Site-specific recombinase XerD [Replication, recombination and repair];
4-298 7.69e-25

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


Pssm-ID: 443999 [Multi-domain]  Cd Length: 291  Bit Score: 101.22  E-value: 7.69e-25
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499653598   4 IDRYLQA-----ATRDNTRRSYRAAIEHFE---SAWGGFLPA--TADSVARYLVAHAG-VLSVNTLKLRLSALAQWHNsq 72
Cdd:COG4974    7 LEAFLEElkrekGLSPNTIKAYRRDLRRFLrflEELGKIPLAeiTPEDIRAYLNYLRErGLSPSTINRYLAALRSFFR-- 84

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499653598  73 gFAdptkspvvrkVFKGIRALHPAQEKQAEPLQLRdleQTVAWLEQEMKDAREQQDRPLLLRAcRDRALILLGFWRGFRS 152
Cdd:COG4974   85 -YA----------VREGLLEDNPAAKVKLPKKPRK---LPRVLTEEEIEALLEALDTETPEGL-RDRALLLLLYATGLRV 149

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499653598 153 DELCRVQIEHVQAHAGngiTLYLPRSKGDRENLgqTYQAPALLKLcpVQAYIEWITEAAlvRGPVFRavdrwgNLSEEGL 232
Cdd:COG4974  150 SELLGLKWSDIDLDRG---TIRVRRGKGGKERT--VPLSPEALEA--LREYLEERRPRD--SDYLFP------TRRGRPL 214

                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 499653598 233 HANSVIPLLRQALERAGISaERYTSHSLRRGFATWAHQSGWDLKSLMSYVGWKDMKSAMRYVEASP 298
Cdd:COG4974  215 SRRAIRKILKRLAKRAGIP-KRVTPHSLRHTFATHLLEAGVDLRTVQELLGHSSISTTQIYTHVSD 279
XerC COG4973
Site-specific recombinase XerC [Replication, recombination and repair];
4-300 2.65e-21

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


Pssm-ID: 443998 [Multi-domain]  Cd Length: 287  Bit Score: 91.56  E-value: 2.65e-21
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499653598   4 IDRYLQAAT----RDNTRRSYRAAIEHFESAWGGFLPA----TADSVARYLVA-HAGVLSVNTLKLRLSALA---QWHNS 71
Cdd:COG4973    8 LEAYLEHLRerrlSPKTLEAYRRDLRRLIPLLGDADLPleelTPADVRRFLARlHRRGLSPRTLNRRLSALRsffNWAVR 87

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499653598  72 QGFADPTkspvvrkVFKGIRAlhPAQEKQaEPLQLrDLEQTVAWLEQEMKDAReqqdrplllrACRDRALILLGFWRGFR 151
Cdd:COG4973   88 EGLLEAN-------PAAGVKA--PKAPRK-LPRAL-TVDELAQLLDALADDPL----------AVRDRAIVELLYSTGLR 146

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499653598 152 SDELCRVQIEHVQAHAGngiTLYLpRSKGDREN---LGQTYQApALLKLCPVQAYIEWITEAALVRGPvfravdrwgnlS 228
Cdd:COG4973  147 LGELVGLDWEDVDLDAG---EVRV-RGKTGKSRtvpLGPKALA-ALREWLAVRPELAAPDEGALFPSR-----------R 210

                        250       260       270       280       290       300       310
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 499653598 229 EEGLHANSVIPLLRQALERAGISaERYTSHSLRRGFATWAHQSGWDLKSLMSYVGWKDMKSAMRYVEASPFH 300
Cdd:COG4973  211 GTRLSPRNVQKRLRRLAKKAGLP-KHVHPHDLRHSFATHLLESGGDLRAVQELLGHASISTTQIYTHLDFQH 281
DNA_BRE_C cd00397
DNA breaking-rejoining enzymes, C-terminal catalytic domain; The DNA breaking-rejoining enzyme ...
 126-294 5.92e-15

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: 71.36  E-value: 5.92e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499653598 126 QQDRPLLLRACRDRALILLGFWRGFRSDELCRVQIEHVQAHaGNGITLylpRSKGDRENLGQTYQAPALLKlcpvQAYIE 205
Cdd:cd00397    7 DAIDEDKKIDLRDRAILLLLLETGLRISELLALKVKDIDLD-NGTIRV---RGKKTKGGKERTVPLPKELA----EELKE 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499653598 206 WITEAALVRGPVFRAVDRWgNLSEEGLHANSVIPLLRQALERAGISA-ERYTSHSLRRGFATWAHQSGWDLKSLMSYVGW 284
Cdd:cd00397   79 YLKERRDKRGPLLKSLYLN-KLFGTKLGERLSRRTLRRIFKKAGIEAgRKITPHSLRHTFATNLLENGVDIKVVQKLLGH 157

                        170
                 ....*....|
gi 499653598 285 KDMKSAMRYV 294
Cdd:cd00397  158 SSISTTQRYL 167
Phage_integrase pfam00589
Phage integrase family; Members of this family cleave DNA substrates by a series of staggered ...
 135-294 5.56e-13

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: 65.80  E-value: 5.56e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499653598  135 ACRDRALILLGFWRGFRSDELCRVQIEHVQAHAGngiTLYLPRSKGDRENlgqtyQAPALLKLCpvQAYIEWIT---EAA 211
Cdd:pfam00589  20 SIRDKALLELLYATGLRISELCSLRWSDIDFENG---VIRVHRGKGNKER-----TVPLSDAAL--ELLKEWLSkrlLEA 89

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499653598  212 LVRGPVFRAVDRWGnlseegLHANSVIPLLRQALERAGISaERYTSHSLRRGFATWAHQSGWDLKSLMSYVGWKDMKSAM 291
Cdd:pfam00589  90 PKSDYLFASKRGKP------LSRQTVRKIFKRAGKEAGLE-LPLHPHMLRHSFATHLLEAGVDLRVVQKLLGHSSISTTQ 162


                  ...
gi 499653598  292 RYV 294
Cdd:pfam00589 163 IYT 165
INT_IntI_C cd01193
Integron integrase and similar protiens, C-terminal catalytic domain; Integron integrases ...
 137-293 8.04e-08

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: 51.12  E-value: 8.04e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499653598 137 RDRALILLGFWRGFRSDELCRVQIEHVQAHAGngiTLYLPRSKG--DRenlgQTYQAPALLKlcPVQAYIEWiteaALVR 214
Cdd:cd01193   22 RHRLILSLLYGAGLRISELLRLRVKDIDFERG---VIRVRQGKGgkDR----VVPLPEKLLE--PLRRYLKS----ARPK 88

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499653598 215 GPVFRAVDRWGNLSEEG-------LHANSVIPLLRQALERAGIsAERYTSHSLRRGFATWAHQSGWDLKSLMSYVGWKDM 287
Cdd:cd01193   89 EELDPAEGRAGVLDPRTgverrhhISETTVQRALKKAVEQAGI-TKRVTPHTLRHSFATHLLEAGTDIRTIQELLGHSDL 167


                 ....*.
gi 499653598 288 KSAMRY 293
Cdd:cd01193  168 STTMIY 173
INT_C_like_4 cd01194
Uncharacterized site-specific tyrosine recombinase, C-terminal catalytic domain; Tyrosine ...
 137-293 3.84e-07

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


Pssm-ID: 271194 [Multi-domain]  Cd Length: 174  Bit Score: 49.29  E-value: 3.84e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499653598 137 RDRALILLGFWRGFRSDELCRVQIEHVQaHAGNGITLYLpRSKGDRENLGQTYQAPALLKlcPVQAYIEwiteaalVRG- 215
Cdd:cd01194   23 RDRAIISLMVTEGLRTVEIVRADVGDLR-QEGEGTILYV-QGKGKTSKDDFVYLRPDVLK--ALQAYLK-------ARGk 91

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499653598 216 -----PVFRAVDRwgNLSEEGLHANSVIPLLRQALERAGISAERYTSHSLRRGFATWAHQSGWDLKSLMSYVGWKDMKSA 290
Cdd:cd01194   92 ldfeePLFTSLSN--NSKGQRLTTRSIRRIIKKYLRKAGLDDDRLTAHSLRHTAGTLALKAGKSLREVQQLLRHSDPNTT 169


                 ...
gi 499653598 291 MRY 293
Cdd:cd01194  170 MIY 172
INT_Rci_Hp1_C cd00796
Shufflon-specific DNA recombinase Rci and Bacteriophage Hp1_like integrase, C-terminal ...
 132-294 8.48e-07

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: 48.09  E-value: 8.48e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499653598 132 LLRACRD------RALILLGFWRGFRSDELCRVQIEHVqahAGNGITLYLPRSKGDRenlgqtyqaPALLKLCP-VQAYI 204
Cdd:cd00796   13 LLAALEEstnphlRLIVLLALYTGARRGEILSLRWDDI---DLEVGLIVLPETKNGK---------PRTVPLSDeAIAIL 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499653598 205 EWITEAAlvRGPVFRAVDRWGNLSEEGLHANsviplLRQALERAGIsaERYTSHSLRRGFATWAHQSGWDLKSLMSYVGW 284
Cdd:cd00796   81 KELKRKR--GKDGFFVDGRFFGIPIASLRRA-----FKKARKRAGL--EDLRFHDLRHTFASRLVQAGVPIKTVAKILGH 151

                        170
                 ....*....|
gi 499653598 285 KDMKSAMRYV 294
Cdd:cd00796  152 SSIKMTMRYA 161
INT_C_like_5 cd01195
Uncharacterized site-specific tyrosine recombinase, C-terminal catalytic domain; Tyrosine ...
 137-296 7.00e-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: 271195 [Multi-domain]  Cd Length: 170  Bit Score: 45.54  E-value: 7.00e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499653598 137 RDRALILLGFWRGFRSDELCRVQIEHVQAHAGNgitlyLPRSKGdrenlGQTYQAPALLKLCPVQAYIEWITEAALVRGP 216
Cdd:cd01195   21 RDEALVRLLLDNALRRSEAVALDVEDLEKEHRR-----LRILGK-----GKKQREVVTLPPTTREALAAWLAARGEAEGP 90

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499653598 217 VFRAVDRwgNLSEEGLHANSVIPLLRQALERAGIsAERYTSHSLRRGFATWAHQSGWDLKSLM-SYVGWKDMKSAMRYVE 295
Cdd:cd01195   91 LFVSLDR--ASRGRRLSPQAVYRIVRRLAERIGL-GKRLSPHGLRHSAITLALDAGAGLIRKVqDFSRHADLRTLQVYDD 167


                 .
gi 499653598 296 A 296
Cdd:cd01195  168 Q 168
INT_ICEBs1_C_like cd01189
C-terminal catalytic domain of integrases from bacterial phages and conjugate transposons; ...
 241-293 1.07e-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: 44.47  E-value: 1.07e-05
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 499653598 241 LRQALERAGIsaERYTSHSLRRGFATWAHQSGWDLKSLMSYVGWKDMKSAMRY 293
Cdd:cd01189   94 FKKLLKKAGL--PRITPHDLRHTFASLLLEAGVPLKVIAERLGHSDISTTLDV 144
INT_RitA_C_like cd01188
C-terminal catalytic domain of recombinase RitA, a component of the recombinase trio; ...
 136-294 1.05e-04

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: 42.23  E-value: 1.05e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499653598 136 CRDRALILLGFWRGFRSDELCRVQIEHVQAHAGNgITLYlpRSKGdrenlgqtyQAPALLKLC-PV-QAYIEWITEAalv 213
Cdd:cd01188   20 LRDYAILLLLARLGLRAGDVAGLRLDDIDWRSGT-ITVR--QKKT---------GRPVELPLTePVgEALADYLRDG--- 84

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499653598 214 RGP-----VF-RAVDRWGNLSEEgLHANSVIpllRQALERAGISAERYTSHSLRRGFATWAHQSGWDLKSLMSYVGWKDM 287
Cdd:cd01188   85 RPRtdsreVFlRARAPYRPLSST-SQISSIV---RRYLRKAGIEPSHRGTHSLRHSLATRMLRAGTSLKVIADLLGHRSI 160


                 ....*..
gi 499653598 288 KSAMRYV 294
Cdd:cd01188  161 ETTAIYA 167
INT_XerDC_C cd00798
XerD and XerC integrases, C-terminal catalytic domains; XerDC-like integrases are involved in ...
 135-278 3.44e-04

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: 40.57  E-value: 3.44e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499653598 135 ACRDRALILLGFWRGFRSDELCRVQIEHVQAHAGngitLYLPRSKGDREnlgqtyqapallKLCPVQAY-IEWITEAALV 213
Cdd:cd00798   18 GLRDRAILELLYASGLRVSELVGLDLSDVDLDEG----LVRVTGKGNKE------------RLVPFGSYaVEALEEYLEE 81

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 499653598 214 RGPVFRAVDRWG----NLSEEGLHANSVIPLLRQALERAGISaERYTSHSLRRGFATwaH--QSGWDLKSL 278
Cdd:cd00798   82 RRPLLLKKKPPDalflNKRGKRLSRRGVWRILKKYAERAGLP-KHVSPHTLRHSFAT--HllEGGADLRVV 149
PRK09870 PRK09870
tyrosine recombinase; Provisional
 135-302 7.11e-04

tyrosine recombinase; Provisional


Pssm-ID: 182125  Cd Length: 200  Bit Score: 39.92  E-value: 7.11e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499653598 135 ACRDRALILLGFWRGFRSDELCRVQIEHVQAHAGngiTLYLPRSKGdrenlGQTYQAPALLKlcPVQAYIEWITeaalVR 214
Cdd:PRK09870  31 AARNYCLTLLCFIHGFRASEICRLRISDIDLKAK---CIYIHRLKK-----GFSTTHPLLNK--EIQALKNWLS----IR 96

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499653598 215 GPVFRAVDRWGNLSEEG--LHANSVIPLLRQALERAGISAERYtSHSLRR--GFATwaHQSGWDLKSLMSYVGWKDMKSA 290
Cdd:PRK09870  97 TSYPHAESEWVFLSRKGnpLSRQQFYHIISTSGGNAGLSLEIH-PHMLRHscGFAL--ANMGIDTRLIQDYLGHRNIRHT 173

                        170
                 ....*....|....
gi 499653598 291 MRYV--EASPFHGM 302
Cdd:PRK09870 174 VWYTasNAGRFYGI 187
xerC PRK00236
site-specific tyrosine recombinase XerC; Reviewed
 6-278 7.54e-04

site-specific tyrosine recombinase XerC; Reviewed


Pssm-ID: 234698 [Multi-domain]  Cd Length: 297  Bit Score: 40.52  E-value: 7.54e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499653598   6 RYLQAATR--DNTRRSYRAAIEHF----ESAWGGFLPA-TADSVARYLVA-HAGVLSVNTLKLRLSAL---AQWHNSQG- 73
Cdd:PRK00236  15 EYLRVERGlsPHTLRAYRRDLRAFlaflEEHGISSLQDlDAADLRSFLARrRRQGLSARSLARRLSALrsfYRWLVRRGl 94

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499653598  74 -FADPtkspvvrkvFKGIRAlhPAQEK-QAEPLqlrDLEQTVAWLEQEmkdareQQDRPLLLRacrDRALILLGFWRGFR 151
Cdd:PRK00236  95 lKANP---------AAGLRA--PKIPKrLPKPL---DVDQAKRLLDAI------DEDDPLALR---DRAILELLYGSGLR 151

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499653598 152 SDELCRVQIEHVQAHAGngiTLYLpRSKGDREN----LGQTYQApallklcpVQAYIEWITEAALVRGPVFRAVdRWGNL 227
Cdd:PRK00236 152 LSELVGLDIDDLDLASG---TLRV-LGKGNKERtvplGRAAREA--------LEAYLALRPLFLPDDDALFLGA-RGGRL 218

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|...
gi 499653598 228 SeeglhANSVIPLLRQALERAGISaERYTSHSLRRGFATwaH--QSGWDLKSL 278
Cdd:PRK00236 219 S-----PRVVQRRVKKLGKKAGLP-SHITPHKLRHSFAT--HllESGGDLRAV 263
INT_FimBE_like cd01197
FimB and FimE and related proteins, integrase/recombinases; This CD includes proteins similar ...
 137-298 2.47e-03

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: 38.26  E-value: 2.47e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499653598 137 RDRALILLGFWRGFRSDELCRVQIEHVQAHAGngiTLYLPRSKGdrenlGQTYQAPalLKLCPVQAYIEWITEAALVRGp 216
Cdd:cd01197   27 RDYCLLLLAFRHGFRVSELCDLHLSDVDLESR---RLHIRRLKN-----GFSTTHP--LRFDEREALEAWLKERANWKG- 95

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499653598 217 vfrAVDRWGNLSEEG--LHANSVIPLLRQALERAGISAERYtSHSLRR--GFATwaHQSGWDLKSLMSYVGWKDMKSAMR 292
Cdd:cd01197   96 ---ADTDWIFLSRRGgpLSRQQAYRIIRDLGKEAGTVTQTH-PHMLRHacGYAL--ADRGADTRLIQDYLGHRNIRHTVI 169


                 ....*.
gi 499653598 293 YVEASP 298
Cdd:cd01197  170 YTASNA 175
FimB COG0582
Integrase/recombinase, includes phage integrase [Replication, recombination and repair, ...
 241-274 5.53e-03

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


Pssm-ID: 440347 [Multi-domain]  Cd Length: 391  Bit Score: 38.10  E-value: 5.53e-03
                         10        20        30
                 ....*....|....*....|....*....|....
gi 499653598 241 LRQALERAGIsaERYTSHSLRRGFATWAHQSGWD 274
Cdd:COG0582  313 LNKALRRMGY--GRFTPHGFRHTASTLLNEAGFP 344
 
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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