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Conserved domains on  [gi|553680614|gb|ESD97291|]
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site-specific recombinase, phage integrase family, partial [Escherichia coli 908616]

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];
42-215 4.67e-27

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


:

Pssm-ID: 443999 [Multi-domain]  Cd Length: 291  Bit Score: 105.08  E-value: 4.67e-27
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 553680614  42 PAYLLAPEVSALLFYMPD-----QRHHMLFATLWNTGMRIGEARMLTPESFDLNgvRPFVRILSEKvrarrgrppKDEVR 116
Cdd:COG4974  110 PRVLTEEEIEALLEALDTetpegLRDRALLLLLYATGLRVSELLGLKWSDIDLD--RGTIRVRRGK---------GGKER 178

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 553680614 117 LVPLTDISyVRQMESWMITTRPRRREPLW------AVTDETMRNWLKQAVRRAEadgvhFSIPVTPHTFRHSYIMHMLYH 190
Cdd:COG4974  179 TVPLSPEA-LEALREYLEERRPRDSDYLFptrrgrPLSRRAIRKILKRLAKRAG-----IPKRVTPHSLRHTFATHLLEA 252

                        170       180
                 ....*....|....*....|....*
gi 553680614 191 RQPRKVIQALAGHRDPRSMEVYTRV 215
Cdd:COG4974  253 GVDLRTVQELLGHSSISTTQIYTHV 277
 
Name Accession Description Interval E-value
XerD COG4974
Site-specific recombinase XerD [Replication, recombination and repair];
42-215 4.67e-27

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


Pssm-ID: 443999 [Multi-domain]  Cd Length: 291  Bit Score: 105.08  E-value: 4.67e-27
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 553680614  42 PAYLLAPEVSALLFYMPD-----QRHHMLFATLWNTGMRIGEARMLTPESFDLNgvRPFVRILSEKvrarrgrppKDEVR 116
Cdd:COG4974  110 PRVLTEEEIEALLEALDTetpegLRDRALLLLLYATGLRVSELLGLKWSDIDLD--RGTIRVRRGK---------GGKER 178

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 553680614 117 LVPLTDISyVRQMESWMITTRPRRREPLW------AVTDETMRNWLKQAVRRAEadgvhFSIPVTPHTFRHSYIMHMLYH 190
Cdd:COG4974  179 TVPLSPEA-LEALREYLEERRPRDSDYLFptrrgrPLSRRAIRKILKRLAKRAG-----IPKRVTPHSLRHTFATHLLEA 252

                        170       180
                 ....*....|....*....|....*
gi 553680614 191 RQPRKVIQALAGHRDPRSMEVYTRV 215
Cdd:COG4974  253 GVDLRTVQELLGHSSISTTQIYTHV 277
Phage_integrase pfam00589
Phage integrase family; Members of this family cleave DNA substrates by a series of staggered ...
 44-217 1.57e-23

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: 92.77  E-value: 1.57e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 553680614   44 YLLAPEVSALLFYMPDQ----RHHMLFATLWNTGMRIGEARMLTPESFDLNGVRPFVRILsekvraRRGRPpkdevRLVP 119
Cdd:pfam00589   1 RLTEDEVERLLDAAETGplsiRDKALLELLYATGLRISELCSLRWSDIDFENGVIRVHRG------KGNKE-----RTVP 69

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 553680614  120 LTDiSYVRQMESWMITTRP-----------RRREPLwavTDETMRNWLKQAVRRAEADGvhfsiPVTPHTFRHSYIMHML 188
Cdd:pfam00589  70 LSD-AALELLKEWLSKRLLeapksdylfasKRGKPL---SRQTVRKIFKRAGKEAGLEL-----PLHPHMLRHSFATHLL 140

                         170       180
                  ....*....|....*....|....*....
gi 553680614  189 YHRQPRKVIQALAGHRDPRSMEVYTRVFA 217
Cdd:pfam00589 141 EAGVDLRVVQKLLGHSSISTTQIYTHVAD 169
DNA_BRE_C cd00397
DNA breaking-rejoining enzymes, C-terminal catalytic domain; The DNA breaking-rejoining enzyme ...
 57-213 4.49e-23

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: 91.39  E-value: 4.49e-23
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 553680614  57 MPDQRHHMLFATLWNTGMRIGEARMLTPESFDLNGVRpfVRILSEKVRARRGRppkdEVRLVPLTDISYVRQMESWMITT 136
Cdd:cd00397   14 KIDLRDRAILLLLLETGLRISELLALKVKDIDLDNGT--IRVRGKKTKGGKER----TVPLPKELAEELKEYLKERRDKR 87

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 553680614 137 RPRRREPLWAVTDETMR------NWLKQAVRRAeadGVHFSIPVTPHTFRHSYIMHMLYHRQPRKVIQALAGHRDPRSME 210
Cdd:cd00397   88 GPLLKSLYLNKLFGTKLgerlsrRTLRRIFKKA---GIEAGRKITPHSLRHTFATNLLENGVDIKVVQKLLGHSSISTTQ 164


                 ...
gi 553680614 211 VYT 213
Cdd:cd00397  165 RYL 167
recomb_XerD TIGR02225
tyrosine recombinase XerD; The phage integrase family describes a number of recombinases with ...
 42-215 4.07e-11

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: 61.06  E-value: 4.07e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 553680614   42 PAYLLAPEVSALLFYmPD------QRHHMLFATLWNTGMRIGEARMLTPESFDLNgvRPFVRIlsekvrarRGRPPKDev 115
Cdd:TIGR02225 102 PKVLTVEEVEALLAA-PDvdtplgLRDRAMLELLYATGLRVSELVGLRLEDVNLD--EGFVRV--------RGKGNKE-- 168

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 553680614  116 RLVPLTDISyVRQMESWMITTRP----------------RRREPLwavTDETMRNWLKQAVRRAeadgvhfSI--PVTPH 177
Cdd:TIGR02225 169 RLVPLGEEA-IEALERYLKEARPlllkkkvkesdalflnRRGGPL---SRQGVWKILKEYAKRA-------GIekPISPH 237

                         170       180       190
                  ....*....|....*....|....*....|....*...
gi 553680614  178 TFRHSYIMHMLYHRQPRKVIQALAGHRDPRSMEVYTRV 215
Cdd:TIGR02225 238 TLRHSFATHLLENGADLRVVQELLGHADISTTQIYTHV 275
xerD PRK00283
tyrosine recombinase;
42-215 1.56e-08

tyrosine recombinase;


Pssm-ID: 234713 [Multi-domain]  Cd Length: 299  Bit Score: 53.66  E-value: 1.56e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 553680614  42 PAYLLAPEVSALLFYmPDQ------RHHMLFATLWNTGMRIGEARMLTPESFDLNGvrPFVRIlsekvrarRGRPPKDev 115
Cdd:PRK00283 111 PKTLSEAQVEALLDA-PDIdtplglRDRAMLELLYATGLRVSELVGLTLDDVSLRQ--GVVRV--------TGKGNKE-- 177

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 553680614 116 RLVPLTDISyVRQMESWMITTRP--------------RRREPLwavTDETMRNWLKQAVRRAEADGVHfsipVTPHTFRH 181
Cdd:PRK00283 178 RLVPLGEEA-VYAIERYLERGRPallngrssdalfpsARGGQL---TRQTFWHRIKHYAKRAGIDPKK----LSPHVLRH 249

                        170       180       190
                 ....*....|....*....|....*....|....
gi 553680614 182 SYIMHMLYHRQPRKVIQALAGHRDPRSMEVYTRV 215
Cdd:PRK00283 250 AFATHLLNHGADLRVVQELLGHSDISTTQIYTHV 283
 
Name Accession Description Interval E-value
XerD COG4974
Site-specific recombinase XerD [Replication, recombination and repair];
42-215 4.67e-27

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


Pssm-ID: 443999 [Multi-domain]  Cd Length: 291  Bit Score: 105.08  E-value: 4.67e-27
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 553680614  42 PAYLLAPEVSALLFYMPD-----QRHHMLFATLWNTGMRIGEARMLTPESFDLNgvRPFVRILSEKvrarrgrppKDEVR 116
Cdd:COG4974  110 PRVLTEEEIEALLEALDTetpegLRDRALLLLLYATGLRVSELLGLKWSDIDLD--RGTIRVRRGK---------GGKER 178

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 553680614 117 LVPLTDISyVRQMESWMITTRPRRREPLW------AVTDETMRNWLKQAVRRAEadgvhFSIPVTPHTFRHSYIMHMLYH 190
Cdd:COG4974  179 TVPLSPEA-LEALREYLEERRPRDSDYLFptrrgrPLSRRAIRKILKRLAKRAG-----IPKRVTPHSLRHTFATHLLEA 252

                        170       180
                 ....*....|....*....|....*
gi 553680614 191 RQPRKVIQALAGHRDPRSMEVYTRV 215
Cdd:COG4974  253 GVDLRTVQELLGHSSISTTQIYTHV 277
Phage_integrase pfam00589
Phage integrase family; Members of this family cleave DNA substrates by a series of staggered ...
 44-217 1.57e-23

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: 92.77  E-value: 1.57e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 553680614   44 YLLAPEVSALLFYMPDQ----RHHMLFATLWNTGMRIGEARMLTPESFDLNGVRPFVRILsekvraRRGRPpkdevRLVP 119
Cdd:pfam00589   1 RLTEDEVERLLDAAETGplsiRDKALLELLYATGLRISELCSLRWSDIDFENGVIRVHRG------KGNKE-----RTVP 69

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 553680614  120 LTDiSYVRQMESWMITTRP-----------RRREPLwavTDETMRNWLKQAVRRAEADGvhfsiPVTPHTFRHSYIMHML 188
Cdd:pfam00589  70 LSD-AALELLKEWLSKRLLeapksdylfasKRGKPL---SRQTVRKIFKRAGKEAGLEL-----PLHPHMLRHSFATHLL 140

                         170       180
                  ....*....|....*....|....*....
gi 553680614  189 YHRQPRKVIQALAGHRDPRSMEVYTRVFA 217
Cdd:pfam00589 141 EAGVDLRVVQKLLGHSSISTTQIYTHVAD 169
DNA_BRE_C cd00397
DNA breaking-rejoining enzymes, C-terminal catalytic domain; The DNA breaking-rejoining enzyme ...
 57-213 4.49e-23

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: 91.39  E-value: 4.49e-23
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 553680614  57 MPDQRHHMLFATLWNTGMRIGEARMLTPESFDLNGVRpfVRILSEKVRARRGRppkdEVRLVPLTDISYVRQMESWMITT 136
Cdd:cd00397   14 KIDLRDRAILLLLLETGLRISELLALKVKDIDLDNGT--IRVRGKKTKGGKER----TVPLPKELAEELKEYLKERRDKR 87

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 553680614 137 RPRRREPLWAVTDETMR------NWLKQAVRRAeadGVHFSIPVTPHTFRHSYIMHMLYHRQPRKVIQALAGHRDPRSME 210
Cdd:cd00397   88 GPLLKSLYLNKLFGTKLgerlsrRTLRRIFKKA---GIEAGRKITPHSLRHTFATNLLENGVDIKVVQKLLGHSSISTTQ 164


                 ...
gi 553680614 211 VYT 213
Cdd:cd00397  165 RYL 167
INT_IntI_C cd01193
Integron integrase and similar protiens, C-terminal catalytic domain; Integron integrases ...
 42-215 2.06e-21

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: 87.33  E-value: 2.06e-21
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 553680614  42 PAYLLAPEVSALLFYMPDQRHHMLFATLWNTGMRIGEARMLTPEsfDLNGVRPFVRIlsekvraRRGRPPKDevRLVPLT 121
Cdd:cd01193    3 PVVLSPDEVRRILGALTELRHRLILSLLYGAGLRISELLRLRVK--DIDFERGVIRV-------RQGKGGKD--RVVPLP 71

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 553680614 122 DiSYVRQMESWMITTRP--------------------RRREPLwavTDETMRNWLKQAVRRAeadGVHfsIPVTPHTFRH 181
Cdd:cd01193   72 E-KLLEPLRRYLKSARPkeeldpaegragvldprtgvERRHHI---SETTVQRALKKAVEQA---GIT--KRVTPHTLRH 142

                        170       180       190
                 ....*....|....*....|....*....|....
gi 553680614 182 SYIMHMLYHRQPRKVIQALAGHRDPRSMEVYTRV 215
Cdd:cd01193  143 SFATHLLEAGTDIRTIQELLGHSDLSTTMIYTHV 176
INT_ICEBs1_C_like cd01189
C-terminal catalytic domain of integrases from bacterial phages and conjugate transposons; ...
 49-213 4.14e-15

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: 69.90  E-value: 4.14e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 553680614  49 EVSALLFYMP--DQRHHMLFATLWNTGMRIGEARMLTPESFDLNGVRPFVR--ILSEKVRARRGRPPK--DEVRLVPLTD 122
Cdd:cd01189    3 ELKKLLEALKkrGDRYYLLFLLALLTGLRRGELLALTWSDIDFENGTIRINrtLVRKKKGGYVIKPPKtkSSIRTIPLPD 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 553680614 123 iSYVRQMESWMittrprrreplwavtdetmrnWLKQAVRRAEADgvhfsiPVTPHTFRHSYIMHMLYHRQPRKVIQALAG 202
Cdd:cd01189   83 -ELIELLKELK---------------------AFKKLLKKAGLP------RITPHDLRHTFASLLLEAGVPLKVIAERLG 134

                        170
                 ....*....|..
gi 553680614 203 HRDPRS-MEVYT 213
Cdd:cd01189  135 HSDISTtLDVYA 146
XerC COG4973
Site-specific recombinase XerC [Replication, recombination and repair];
42-215 1.84e-13

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


Pssm-ID: 443998 [Multi-domain]  Cd Length: 287  Bit Score: 67.68  E-value: 1.84e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 553680614  42 PAYLLAPEVSALLFYMPD----QRHHMLFATLWNTGMRIGEARMLTPESFDLNgvRPFVRilsekVRARRGRPpkdevRL 117
Cdd:COG4973  109 PRALTVDELAQLLDALADdplaVRDRAIVELLYSTGLRLGELVGLDWEDVDLD--AGEVR-----VRGKTGKS-----RT 176

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 553680614 118 VPLTD--ISYVRQMESWMITTRPRRREPLWA------VTDETMRNWLKQAVRRAEadgvhFSIPVTPHTFRHSYIMHMLY 189
Cdd:COG4973  177 VPLGPkaLAALREWLAVRPELAAPDEGALFPsrrgtrLSPRNVQKRLRRLAKKAG-----LPKHVHPHDLRHSFATHLLE 251

                        170       180
                 ....*....|....*....|....*.
gi 553680614 190 HRQPRKVIQALAGHRDPRSMEVYTRV 215
Cdd:COG4973  252 SGGDLRAVQELLGHASISTTQIYTHL 277
INT_RitC_C_like cd01182
C-terminal catalytic domain of recombinase RitC, a component of the recombinase trio; ...
 45-215 2.44e-13

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: 65.76  E-value: 2.44e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 553680614  45 LLAPEVSALLfYMPD------QRHHMLFATLWNTGMRIGEARMLTPESFDLnGVRPFVRIlsekvrarRGRPPKDevRLV 118
Cdd:cd01182    1 LTREEMKALL-AAPDrntslgRRDHALLLLLYDTGARVQELADLTIRDLRL-DDPATVRL--------HGKGRKE--RTV 68

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 553680614 119 PLTDiSYVRQMESWMittRPRRREPLWAVTDETMRN-------------WLKQAVRRAEADGVHFSIPVTPHTFRHSYIM 185
Cdd:cd01182   69 PLWK-ETVAALKAYL---QEFHLTPDPKQLFPLFPNrrgqpltrdgvayILNKYVALASNRCPSLPKRITPHTLRHTKAM 144

                        170       180       190
                 ....*....|....*....|....*....|
gi 553680614 186 HMLYHRQPRKVIQALAGHRDPRSMEVYTRV 215
Cdd:cd01182  145 HLLQAGVDLTVIRDWLGHESVETTQIYAEA 174
INT_Rci_Hp1_C cd00796
Shufflon-specific DNA recombinase Rci and Bacteriophage Hp1_like integrase, C-terminal ...
 44-214 3.13e-12

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: 62.34  E-value: 3.13e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 553680614  44 YLLAPEVSALLFYMPDQRHHMLFATLW---NTGMRIGEARMLTPESFDLNGVRPFvrilseKVRARRGRPpkdevRLVPL 120
Cdd:cd00796    4 FLTEDEEARLLAALEESTNPHLRLIVLlalYTGARRGEILSLRWDDIDLEVGLIV------LPETKNGKP-----RTVPL 72

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 553680614 121 TDIsyVRQMESWMITTRPRRREPLWAVTDETMRNWLKQAVRRA-EADGVHFsipVTPHTFRHSYIMHMLYHRQPRKVIQA 199
Cdd:cd00796   73 SDE--AIAILKELKRKRGKDGFFVDGRFFGIPIASLRRAFKKArKRAGLED---LRFHDLRHTFASRLVQAGVPIKTVAK 147

                        170
                 ....*....|....*
gi 553680614 200 LAGHRDPRSMEVYTR 214
Cdd:cd00796  148 ILGHSSIKMTMRYAH 162
recomb_XerD TIGR02225
tyrosine recombinase XerD; The phage integrase family describes a number of recombinases with ...
 42-215 4.07e-11

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: 61.06  E-value: 4.07e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 553680614   42 PAYLLAPEVSALLFYmPD------QRHHMLFATLWNTGMRIGEARMLTPESFDLNgvRPFVRIlsekvrarRGRPPKDev 115
Cdd:TIGR02225 102 PKVLTVEEVEALLAA-PDvdtplgLRDRAMLELLYATGLRVSELVGLRLEDVNLD--EGFVRV--------RGKGNKE-- 168

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 553680614  116 RLVPLTDISyVRQMESWMITTRP----------------RRREPLwavTDETMRNWLKQAVRRAeadgvhfSI--PVTPH 177
Cdd:TIGR02225 169 RLVPLGEEA-IEALERYLKEARPlllkkkvkesdalflnRRGGPL---SRQGVWKILKEYAKRA-------GIekPISPH 237

                         170       180       190
                  ....*....|....*....|....*....|....*...
gi 553680614  178 TFRHSYIMHMLYHRQPRKVIQALAGHRDPRSMEVYTRV 215
Cdd:TIGR02225 238 TLRHSFATHLLENGADLRVVQELLGHADISTTQIYTHV 275
INT_XerDC_C cd00798
XerD and XerC integrases, C-terminal catalytic domains; XerDC-like integrases are involved in ...
 49-215 2.69e-10

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: 57.14  E-value: 2.69e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 553680614  49 EVSALLfYMPDQ------RHHMLFATLWNTGMRIGEARMLTPESFDLNgvRPFVRIlsekvrarRGRPPKDevRLVPLTD 122
Cdd:cd00798    3 EVERLL-DAPDTdtplglRDRAILELLYASGLRVSELVGLDLSDVDLD--EGLVRV--------TGKGNKE--RLVPFGS 69

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 553680614 123 ISyVRQMESWMITTRP--RRREPLWAV---------TDETMRNWLKQAVRRAEADGvhfsiPVTPHTFRHSYIMHMLYHR 191
Cdd:cd00798   70 YA-VEALEEYLEERRPllLKKKPPDALflnkrgkrlSRRGVWRILKKYAERAGLPK-----HVSPHTLRHSFATHLLEGG 143

                        170       180
                 ....*....|....*....|....
gi 553680614 192 QPRKVIQALAGHRDPRSMEVYTRV 215
Cdd:cd00798  144 ADLRVVQELLGHASLSTTQIYTHV 167
xerD PRK00283
tyrosine recombinase;
42-215 1.56e-08

tyrosine recombinase;


Pssm-ID: 234713 [Multi-domain]  Cd Length: 299  Bit Score: 53.66  E-value: 1.56e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 553680614  42 PAYLLAPEVSALLFYmPDQ------RHHMLFATLWNTGMRIGEARMLTPESFDLNGvrPFVRIlsekvrarRGRPPKDev 115
Cdd:PRK00283 111 PKTLSEAQVEALLDA-PDIdtplglRDRAMLELLYATGLRVSELVGLTLDDVSLRQ--GVVRV--------TGKGNKE-- 177

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 553680614 116 RLVPLTDISyVRQMESWMITTRP--------------RRREPLwavTDETMRNWLKQAVRRAEADGVHfsipVTPHTFRH 181
Cdd:PRK00283 178 RLVPLGEEA-VYAIERYLERGRPallngrssdalfpsARGGQL---TRQTFWHRIKHYAKRAGIDPKK----LSPHVLRH 249

                        170       180       190
                 ....*....|....*....|....*....|....
gi 553680614 182 SYIMHMLYHRQPRKVIQALAGHRDPRSMEVYTRV 215
Cdd:PRK00283 250 AFATHLLNHGADLRVVQELLGHSDISTTQIYTHV 283
integrase_gron TIGR02249
integron integrase; Members of this family are integrases associated with integrons (and ...
 46-215 2.44e-08

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: 53.17  E-value: 2.44e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 553680614   46 LAPEVSALLFYMPDQRHHMLFATLWNTGMRIGEARMLTPESFDlngvrpFVRilsEKVRARRGRPPKDevRLVPLTDISY 125
Cdd:TIGR02249 102 LTREEVRRLLEHLEGKYRLIAKLLYGSGMRLMECLRLRIQDID------FDY---GEIRIRQGKGGKD--RTVTLPKELI 170

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 553680614  126 ---VRQMES----------------WMITTRPRR-----REPLWA---------------------VTDETMRNWLKQAV 160
Cdd:TIGR02249 171 pplREQIELarayheadlaegyggvYLPHALARKypnapKEWGWQylfpshrlsrdpesgvirrhhINETTIQRAVRRAV 250

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 553680614  161 RRAeadgvHFSIPVTPHTFRHSYIMHMLYHRQPRKVIQALAGHRDPRSMEVYTRV 215
Cdd:TIGR02249 251 ERA-----GIEKPVTCHTLRHSFATHLLESGADIRTVQELLGHSDVKTTQIYTHV 300
INT_tnpA_C_Tn554 cd01186
Putative Transposase A from transposon Tn554, C-terminal catalytic domain; This family ...
 45-220 8.33e-08

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: 50.49  E-value: 8.33e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 553680614  45 LLAPEVSALLFYMPDQRHHMLFATLWNTGMRIGEARMLTPESFDLNGvrPFVRILSEKVRARRGRPPKDEVRLVP----- 119
Cdd:cd01186    2 LTPREVQELINACNNLRDKFLLALLYETGLRIGEALGLRIEDIDMAD--NQIELVPREDNTNEARAKSMRERRIPvsqdl 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 553680614 120 -------LTDISYVRQMESWMITTRPRRREPLWAVTDETMRNWLKQAVRRAeadgvhfSIPVTPHTFRHSYIMHMLYHRQ 192
Cdd:cd01186   80 idlyadyLTYIYCEEAEFSITVFVNVKGGNQGKAMNYSDVYDLVRRLKKRT-------GIDFTPHMFRHTHATALIRAGW 152

                        170       180
                 ....*....|....*....|....*....
gi 553680614 193 PRKVIQALAGHRDPR-SMEVYTRVFALDM 220
Cdd:cd01186  153 SIEVVARRLGHAHVQtTLNTYGHLSEEDI 181
INT_RitA_C_like cd01188
C-terminal catalytic domain of recombinase RitA, a component of the recombinase trio; ...
 64-225 1.47e-07

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: 49.93  E-value: 1.47e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 553680614  64 MLFATLwntGMRIGEARMLTPESFDLNGVRPFVRilsekvRARRGRPpkdevRLVPLTD------ISYVRQmeswmitTR 137
Cdd:cd01188   27 LLLARL---GLRAGDVAGLRLDDIDWRSGTITVR------QKKTGRP-----VELPLTEpvgealADYLRD-------GR 85

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 553680614 138 PRRREPLWAVTDETMRNWL----------KQAVRRAEADGVHFSipvtPHTFRHSYIMHMLYHRQPRKVIQALAGHRDPR 207
Cdd:cd01188   86 PRTDSREVFLRARAPYRPLsstsqissivRRYLRKAGIEPSHRG----THSLRHSLATRMLRAGTSLKVIADLLGHRSIE 161

                        170
                 ....*....|....*...
gi 553680614 208 SMEVYTRVfALDMAATLA 225
Cdd:cd01188  162 TTAIYAKI-DVDDLREVA 178
FimB COG0582
Integrase/recombinase, includes phage integrase [Replication, recombination and repair, ...
 72-219 4.44e-07

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


Pssm-ID: 440347 [Multi-domain]  Cd Length: 391  Bit Score: 49.65  E-value: 4.44e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 553680614  72 TGMRIGEARMLTPESFDL-NGVrpfVRILSEKVRARRgrppkdeVRLVPLTD--ISYVRQMesWMITTR-----PRRREP 143
Cdd:COG0582  237 TGVRPGELRGARWSEIDLeAAL---WTIPAERMKTRR-------PHIVPLSRqaLEILKEL--KPLTGDseyvfPSRRGP 304

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 553680614 144 LWAVTDETMRnwlkQAVRRAEADgvhfsiPVTPHTFRHSYIMHMLYHRQPRKVIQALAGHRDPRSME-VYTRVFALD 219
Cdd:COG0582  305 KKPMSENTLN----KALRRMGYG------RFTPHGFRHTASTLLNEAGFPPDVIERQLAHKDGNKVRaAYNRADYLE 371
xerC PRK01287
site-specific tyrosine recombinase XerC; Reviewed
 61-215 7.16e-07

site-specific tyrosine recombinase XerC; Reviewed


Pssm-ID: 234935 [Multi-domain]  Cd Length: 358  Bit Score: 48.97  E-value: 7.16e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 553680614  61 RHHMLFATLWNTGMRIGEARMLtpESFDLNGVRPFVRIlsekvraRRGRPPKDEVRLVPLTDISYVRQmesWMITTRPR- 139
Cdd:PRK01287 158 RDRALLELLWSTGIRRGELARL--DLYDVDASRGVVTV-------RQGKGNKDRVVPVGERALAWLQR---YLQDVRPQl 225

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 553680614 140 ----RREPLWAVTDET--MRNWLKQAVRRA-EADGVhfSIPVTPHTFRHSYIMHMLYHRQPRKVIQALAGHRDPRSMEVY 212
Cdd:PRK01287 226 avrpDSGALFVAMDGDglARNTLTNMVGRYiRAAGI--EKAGACHLFRHAMATQMLENGADTRHIQAILGHAKLETTQIY 303


                 ...
gi 553680614 213 TRV 215
Cdd:PRK01287 304 TRV 306
INT_C_like_1 cd01184
Uncharacterized site-specific tyrosine recombinase, C-terminal catalytic domain; Tyrosine ...
 72-206 1.87e-06

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: 46.53  E-value: 1.87e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 553680614  72 TGMRIGEARMLTPES-FDLNGVrPFVRILSEKvrARRGRPPKDEVRLVPLTD-------ISYVRQMESwmitTRPRRREP 143
Cdd:cd01184   35 TGARLNEICQLRVDDiKEEDGI-WCIDINDDA--EGRRLKTKASRRLVPIHPrlielgfLDYVEALRA----DGKLFLFP 107

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 553680614 144 LWAVTDET----MRNWLKQAVRRAE---ADGVHFsipvtpHTFRHSYIMHMLYHRQPRKVIQALAGHRDP 206
Cdd:cd01184  108 EKRDKDGKyskaASKWFNRLLRKLGikdDERKSF------HSFRHTFITALKRAGVPEELIAQIVGHSRG 171
INTN1_C_like cd01185
Integrase IntN1 of Bacteroides mobilizable transposon NBU1 and similar proteins, C-terminal ...
 65-216 4.50e-06

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: 45.33  E-value: 4.50e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 553680614  65 LFATLwnTGMRIGEARMLTPESFDLNGVRPFVRILSEKVrarrgrppKDEVRlVPLTDIsyVRQ-MESWMITTRPRRREP 143
Cdd:cd01185   25 LFSCY--TGLRFSDLKNLTWKNIVEASGRTWIRYRRKKT--------GKPVT-VPLLPV--AREiLEKYKDDRSEGKLFP 91

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 553680614 144 LwaVTDETMRNWLKQAVRRAeadGVHFsiPVTPHTFRHSYIMHMLYHRQPRKVIQALAGHRDPRSMEVYTRVF 216
Cdd:cd01185   92 V--LSNQKINRYLKEIAKIA---GIDK--HLTFHVARHTFATLLLLKGVDIETISKLLGHSSIKTTQIYAKIV 157
INT_C_like_5 cd01195
Uncharacterized site-specific tyrosine recombinase, C-terminal catalytic domain; Tyrosine ...
 61-214 1.09e-05

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: 44.38  E-value: 1.09e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 553680614  61 RHHMLFATLWNTGMRIGEARMLtpesfDLNGVRPFVRILsekVRARRGRPPKDEVRLVPLTdisyvRQMESWMITTRPRR 140
Cdd:cd01195   21 RDEALVRLLLDNALRRSEAVAL-----DVEDLEKEHRRL---RILGKGKKQREVVTLPPTT-----REALAAWLAARGEA 87

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 553680614 141 REPLWAVTDETMR------NWLKQAVRR-AEADGVHFSIpvTPHTFRHSYIMHMLYHRQP--RKViQALAGHRDPRSMEV 211
Cdd:cd01195   88 EGPLFVSLDRASRgrrlspQAVYRIVRRlAERIGLGKRL--SPHGLRHSAITLALDAGAGliRKV-QDFSRHADLRTLQV 164


                 ...
gi 553680614 212 YTR 214
Cdd:cd01195  165 YDD 167
xerC PRK00236
site-specific tyrosine recombinase XerC; Reviewed
 42-215 1.79e-05

site-specific tyrosine recombinase XerC; Reviewed


Pssm-ID: 234698 [Multi-domain]  Cd Length: 297  Bit Score: 44.76  E-value: 1.79e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 553680614  42 PAYLLAPEVSALLFYMPD-----QRHHMLFATLWNTGMRIGEARMLTPESFDLNgvRPFVRILsekvrarrGRPPKDevR 116
Cdd:PRK00236 113 PKPLDVDQAKRLLDAIDEddplaLRDRAILELLYGSGLRLSELVGLDIDDLDLA--SGTLRVL--------GKGNKE--R 180

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 553680614 117 LVPLTDisYVRQ-MESWmITTRP------------RRREPLWA-VTDETMRNWLKQAvrraeadgvHFSIPVTPHTFRHS 182
Cdd:PRK00236 181 TVPLGR--AAREaLEAY-LALRPlflpdddalflgARGGRLSPrVVQRRVKKLGKKA---------GLPSHITPHKLRHS 248

                        170       180       190
                 ....*....|....*....|....*....|...
gi 553680614 183 YIMHMLYHRQPRKVIQALAGHRDPRSMEVYTRV 215
Cdd:PRK00236 249 FATHLLESGGDLRAVQELLGHASLSTTQIYTHV 281
PRK15417 PRK15417
integron integrase;
42-218 2.90e-05

integron integrase;


Pssm-ID: 185315 [Multi-domain]  Cd Length: 337  Bit Score: 44.27  E-value: 2.90e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 553680614  42 PAYLLAPEVSALLFYMpdQRHHMLFATL-WNTGMRIGEARMLTPESFDLNGVRPFVR------------------ILSEK 102
Cdd:PRK15417 114 PVVLTPDEVVRILGFL--EGEHRLFAQLlYGTGMRISEGLQLRVKDLDFDHGTIIVRegkgskdralmlpeslapSLREQ 191

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 553680614 103 VRARRGRPPKDE------VRLVPLTDISYVRQMESW---------MITTRPR----RREPLWavtDETMRNWLKQAVRRA 163
Cdd:PRK15417 192 LSRARAWWLKDQaegrsgVALPDALERKYPRAGHSWpwfwvfaqhTHSTDPRsgvvRRHHMY---DQTFQRAFKRAVEQA 268

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 553680614 164 eadGVhfSIPVTPHTFRHSYIMHMLYHRQPRKVIQALAGHRDPRSMEVYTRVFAL 218
Cdd:PRK15417 269 ---GI--TKPATPHTLRHSFATALLRSGYDIRTVQDLLGHSDVSTTMIYTHVLKV 318
INT_C_like_6 cd01196
Uncharacterized site-specific tyrosine recombinase, C-terminal catalytic domain; Tyrosine ...
 161-214 3.00e-03

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: 37.46  E-value: 3.00e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 553680614 161 RRAEADGVhfSIPVTPHTFRHSYIMHMLYHRQPRKVIQALAGHRDPRSMEVYTR 214
Cdd:cd01196  122 RRAIAADI--PTAIGNHSFRATGITAYLKNGGTLEDAQNMANHASTRTTQLYDR 173
 
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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