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Conserved domains on  [gi|1717609965|gb|TWP81253|]
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site-specific recombinase [Escherichia coli]

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 3.59e-27

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


:

Pssm-ID: 443999 [Multi-domain]  Cd Length: 291  Bit Score: 105.85  E-value: 3.59e-27
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1717609965  42 PAYLLAPEVSALLFYMPD-----QRHHMLFATLWNTGMRIGEARMLTPESFDLDgvRPFVRILSEKvrarrgrppKDEVR 116
Cdd:COG4974   110 PRVLTEEEIEALLEALDTetpegLRDRALLLLLYATGLRVSELLGLKWSDIDLD--RGTIRVRRGK---------GGKER 178

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1717609965 117 LVPLTDISyVRQMESWMITTRPRRREPLW------AVTDETMRNWLKQAVRRAEadgvhFSIPVTPHTFRHSYIMHMLYH 190
Cdd:COG4974   179 TVPLSPEA-LEALREYLEERRPRDSDYLFptrrgrPLSRRAIRKILKRLAKRAG-----IPKRVTPHSLRHTFATHLLEA 252

                         170       180
                  ....*....|....*....|....*
gi 1717609965 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 3.59e-27

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


Pssm-ID: 443999 [Multi-domain]  Cd Length: 291  Bit Score: 105.85  E-value: 3.59e-27
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1717609965  42 PAYLLAPEVSALLFYMPD-----QRHHMLFATLWNTGMRIGEARMLTPESFDLDgvRPFVRILSEKvrarrgrppKDEVR 116
Cdd:COG4974   110 PRVLTEEEIEALLEALDTetpegLRDRALLLLLYATGLRVSELLGLKWSDIDLD--RGTIRVRRGK---------GGKER 178

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1717609965 117 LVPLTDISyVRQMESWMITTRPRRREPLW------AVTDETMRNWLKQAVRRAEadgvhFSIPVTPHTFRHSYIMHMLYH 190
Cdd:COG4974   179 TVPLSPEA-LEALREYLEERRPRDSDYLFptrrgrPLSRRAIRKILKRLAKRAG-----IPKRVTPHSLRHTFATHLLEA 252

                         170       180
                  ....*....|....*....|....*
gi 1717609965 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 2.12e-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: 2.12e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1717609965  44 YLLAPEVSALLFYMPDQ----RHHMLFATLWNTGMRIGEARMLTPESFDLDGVRPFVRILsekvraRRGRPpkdevRLVP 119
Cdd:pfam00589   1 RLTEDEVERLLDAAETGplsiRDKALLELLYATGLRISELCSLRWSDIDFENGVIRVHRG------KGNKE-----RTVP 69

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1717609965 120 LTDiSYVRQMESWMITTRP-----------RRREPLwavTDETMRNWLKQAVRRAEADGvhfsiPVTPHTFRHSYIMHML 188
Cdd:pfam00589  70 LSD-AALELLKEWLSKRLLeapksdylfasKRGKPL---SRQTVRKIFKRAGKEAGLEL-----PLHPHMLRHSFATHLL 140

                         170       180
                  ....*....|....*....|....*....
gi 1717609965 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 3.74e-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: 92.16  E-value: 3.74e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1717609965  57 MPDQRHHMLFATLWNTGMRIGEARMLTPESFDLDGVRpfVRILSEKVRARRGRppkdEVRLVPLTDISYVRQMESWMITT 136
Cdd:cd00397    14 KIDLRDRAILLLLLETGLRISELLALKVKDIDLDNGT--IRVRGKKTKGGKER----TVPLPKELAEELKEYLKERRDKR 87

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1717609965 137 RPRRREPLWAVTDETMR------NWLKQAVRRAeadGVHFSIPVTPHTFRHSYIMHMLYHRQPRKVIQALAGHRDPRSME 210
Cdd:cd00397    88 GPLLKSLYLNKLFGTKLgerlsrRTLRRIFKKA---GIEAGRKITPHSLRHTFATNLLENGVDIKVVQKLLGHSSISTTQ 164


                  ...
gi 1717609965 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 1.92e-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: 62.60  E-value: 1.92e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1717609965  42 PAYLLAPEVSALLFYmPD------QRHHMLFATLWNTGMRIGEARMLTPESFDLDgvRPFVRIlsekvrarRGRPPKDev 115
Cdd:TIGR02225 102 PKVLTVEEVEALLAA-PDvdtplgLRDRAMLELLYATGLRVSELVGLRLEDVNLD--EGFVRV--------RGKGNKE-- 168

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1717609965 116 RLVPLTDISyVRQMESWMITTRP----------------RRREPLwavTDETMRNWLKQAVRRAeadgvhfSI--PVTPH 177
Cdd:TIGR02225 169 RLVPLGEEA-IEALERYLKEARPlllkkkvkesdalflnRRGGPL---SRQGVWKILKEYAKRA-------GIekPISPH 237

                         170       180       190
                  ....*....|....*....|....*....|....*...
gi 1717609965 178 TFRHSYIMHMLYHRQPRKVIQALAGHRDPRSMEVYTRV 215
Cdd:TIGR02225 238 TLRHSFATHLLENGADLRVVQELLGHADISTTQIYTHV 275
xerD PRK00283
tyrosine recombinase;
42-215 3.51e-08

tyrosine recombinase;


Pssm-ID: 234713 [Multi-domain]  Cd Length: 299  Bit Score: 52.89  E-value: 3.51e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1717609965  42 PAYLLAPEVSALLFYmPDQ------RHHMLFATLWNTGMRIGEARMLTPESFDLDGvrPFVRIlsekvrarRGRPPKDev 115
Cdd:PRK00283  111 PKTLSEAQVEALLDA-PDIdtplglRDRAMLELLYATGLRVSELVGLTLDDVSLRQ--GVVRV--------TGKGNKE-- 177

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1717609965 116 RLVPLTDISyVRQMESWMITTRP--------------RRREPLwavTDETMRNWLKQAVRRAEADGVHfsipVTPHTFRH 181
Cdd:PRK00283  178 RLVPLGEEA-VYAIERYLERGRPallngrssdalfpsARGGQL---TRQTFWHRIKHYAKRAGIDPKK----LSPHVLRH 249

                         170       180       190
                  ....*....|....*....|....*....|....
gi 1717609965 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 3.59e-27

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


Pssm-ID: 443999 [Multi-domain]  Cd Length: 291  Bit Score: 105.85  E-value: 3.59e-27
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1717609965  42 PAYLLAPEVSALLFYMPD-----QRHHMLFATLWNTGMRIGEARMLTPESFDLDgvRPFVRILSEKvrarrgrppKDEVR 116
Cdd:COG4974   110 PRVLTEEEIEALLEALDTetpegLRDRALLLLLYATGLRVSELLGLKWSDIDLD--RGTIRVRRGK---------GGKER 178

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1717609965 117 LVPLTDISyVRQMESWMITTRPRRREPLW------AVTDETMRNWLKQAVRRAEadgvhFSIPVTPHTFRHSYIMHMLYH 190
Cdd:COG4974   179 TVPLSPEA-LEALREYLEERRPRDSDYLFptrrgrPLSRRAIRKILKRLAKRAG-----IPKRVTPHSLRHTFATHLLEA 252

                         170       180
                  ....*....|....*....|....*
gi 1717609965 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 2.12e-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: 2.12e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1717609965  44 YLLAPEVSALLFYMPDQ----RHHMLFATLWNTGMRIGEARMLTPESFDLDGVRPFVRILsekvraRRGRPpkdevRLVP 119
Cdd:pfam00589   1 RLTEDEVERLLDAAETGplsiRDKALLELLYATGLRISELCSLRWSDIDFENGVIRVHRG------KGNKE-----RTVP 69

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1717609965 120 LTDiSYVRQMESWMITTRP-----------RRREPLwavTDETMRNWLKQAVRRAEADGvhfsiPVTPHTFRHSYIMHML 188
Cdd:pfam00589  70 LSD-AALELLKEWLSKRLLeapksdylfasKRGKPL---SRQTVRKIFKRAGKEAGLEL-----PLHPHMLRHSFATHLL 140

                         170       180
                  ....*....|....*....|....*....
gi 1717609965 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 3.74e-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: 92.16  E-value: 3.74e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1717609965  57 MPDQRHHMLFATLWNTGMRIGEARMLTPESFDLDGVRpfVRILSEKVRARRGRppkdEVRLVPLTDISYVRQMESWMITT 136
Cdd:cd00397    14 KIDLRDRAILLLLLETGLRISELLALKVKDIDLDNGT--IRVRGKKTKGGKER----TVPLPKELAEELKEYLKERRDKR 87

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1717609965 137 RPRRREPLWAVTDETMR------NWLKQAVRRAeadGVHFSIPVTPHTFRHSYIMHMLYHRQPRKVIQALAGHRDPRSME 210
Cdd:cd00397    88 GPLLKSLYLNKLFGTKLgerlsrRTLRRIFKKA---GIEAGRKITPHSLRHTFATNLLENGVDIKVVQKLLGHSSISTTQ 164


                  ...
gi 1717609965 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 5.24e-22

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: 89.26  E-value: 5.24e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1717609965  42 PAYLLAPEVSALLFYMPDQRHHMLFATLWNTGMRIGEARMLTPEsfDLDGVRPFVRIlsekvraRRGRPPKDevRLVPLT 121
Cdd:cd01193     3 PVVLSPDEVRRILGALTELRHRLILSLLYGAGLRISELLRLRVK--DIDFERGVIRV-------RQGKGGKD--RVVPLP 71

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1717609965 122 DiSYVRQMESWMITTRP--------------------RRREPLwavTDETMRNWLKQAVRRAeadGVHfsIPVTPHTFRH 181
Cdd:cd01193    72 E-KLLEPLRRYLKSARPkeeldpaegragvldprtgvERRHHI---SETTVQRALKKAVEQA---GIT--KRVTPHTLRH 142

                         170       180       190
                  ....*....|....*....|....*....|....
gi 1717609965 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 3.53e-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: 70.28  E-value: 3.53e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1717609965  49 EVSALLFYMP--DQRHHMLFATLWNTGMRIGEARMLTPESFDLDGVRPFVR--ILSEKVRARRGRPPK--DEVRLVPLTD 122
Cdd:cd01189     3 ELKKLLEALKkrGDRYYLLFLLALLTGLRRGELLALTWSDIDFENGTIRINrtLVRKKKGGYVIKPPKtkSSIRTIPLPD 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1717609965 123 iSYVRQMESWMittrprrreplwavtdetmrnWLKQAVRRAEADgvhfsiPVTPHTFRHSYIMHMLYHRQPRKVIQALAG 202
Cdd:cd01189    83 -ELIELLKELK---------------------AFKKLLKKAGLP------RITPHDLRHTFASLLLEAGVPLKVIAERLG 134

                         170
                  ....*....|..
gi 1717609965 203 HRDPRS-MEVYT 213
Cdd:cd01189   135 HSDISTtLDVYA 146
XerC COG4973
Site-specific recombinase XerC [Replication, recombination and repair];
42-215 8.09e-14

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


Pssm-ID: 443998 [Multi-domain]  Cd Length: 287  Bit Score: 69.22  E-value: 8.09e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1717609965  42 PAYLLAPEVSALLFYMPD----QRHHMLFATLWNTGMRIGEARMLTPESFDLDgvRPFVRilsekVRARRGRPpkdevRL 117
Cdd:COG4973   109 PRALTVDELAQLLDALADdplaVRDRAIVELLYSTGLRLGELVGLDWEDVDLD--AGEVR-----VRGKTGKS-----RT 176

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1717609965 118 VPLTD--ISYVRQMESWMITTRPRRREPLWA------VTDETMRNWLKQAVRRAEadgvhFSIPVTPHTFRHSYIMHMLY 189
Cdd:COG4973   177 VPLGPkaLAALREWLAVRPELAAPDEGALFPsrrgtrLSPRNVQKRLRRLAKKAG-----LPKHVHPHDLRHSFATHLLE 251

                         170       180
                  ....*....|....*....|....*.
gi 1717609965 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 9.24e-14

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: 67.30  E-value: 9.24e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1717609965  45 LLAPEVSALLfYMPD------QRHHMLFATLWNTGMRIGEARMLTPESFDLDGVrPFVRIlsekvrarRGRPPKDevRLV 118
Cdd:cd01182     1 LTREEMKALL-AAPDrntslgRRDHALLLLLYDTGARVQELADLTIRDLRLDDP-ATVRL--------HGKGRKE--RTV 68

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1717609965 119 PLTDiSYVRQMESWMittRPRRREPLWAVTDETMRN-------------WLKQAVRRAEADGVHFSIPVTPHTFRHSYIM 185
Cdd:cd01182    69 PLWK-ETVAALKAYL---QEFHLTPDPKQLFPLFPNrrgqpltrdgvayILNKYVALASNRCPSLPKRITPHTLRHTKAM 144

                         170       180       190
                  ....*....|....*....|....*....|
gi 1717609965 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 4.14e-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: 4.14e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1717609965  44 YLLAPEVSALLFYMPDQRHHMLFATLW---NTGMRIGEARMLTPESFDLDGVRPFvrilseKVRARRGRPpkdevRLVPL 120
Cdd:cd00796     4 FLTEDEEARLLAALEESTNPHLRLIVLlalYTGARRGEILSLRWDDIDLEVGLIV------LPETKNGKP-----RTVPL 72

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1717609965 121 TDIsyVRQMESWMITTRPRRREPLWAVTDETMRNWLKQAVRRA-EADGVHFsipVTPHTFRHSYIMHMLYHRQPRKVIQA 199
Cdd:cd00796    73 SDE--AIAILKELKRKRGKDGFFVDGRFFGIPIASLRRAFKKArKRAGLED---LRFHDLRHTFASRLVQAGVPIKTVAK 147

                         170
                  ....*....|....*
gi 1717609965 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 1.92e-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: 62.60  E-value: 1.92e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1717609965  42 PAYLLAPEVSALLFYmPD------QRHHMLFATLWNTGMRIGEARMLTPESFDLDgvRPFVRIlsekvrarRGRPPKDev 115
Cdd:TIGR02225 102 PKVLTVEEVEALLAA-PDvdtplgLRDRAMLELLYATGLRVSELVGLRLEDVNLD--EGFVRV--------RGKGNKE-- 168

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1717609965 116 RLVPLTDISyVRQMESWMITTRP----------------RRREPLwavTDETMRNWLKQAVRRAeadgvhfSI--PVTPH 177
Cdd:TIGR02225 169 RLVPLGEEA-IEALERYLKEARPlllkkkvkesdalflnRRGGPL---SRQGVWKILKEYAKRA-------GIekPISPH 237

                         170       180       190
                  ....*....|....*....|....*....|....*...
gi 1717609965 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 1.65e-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: 58.29  E-value: 1.65e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1717609965  49 EVSALLfYMPDQ------RHHMLFATLWNTGMRIGEARMLTPESFDLDgvRPFVRIlsekvrarRGRPPKDevRLVPLTD 122
Cdd:cd00798     3 EVERLL-DAPDTdtplglRDRAILELLYASGLRVSELVGLDLSDVDLD--EGLVRV--------TGKGNKE--RLVPFGS 69

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1717609965 123 ISyVRQMESWMITTRP--RRREPLWAV---------TDETMRNWLKQAVRRAEADGvhfsiPVTPHTFRHSYIMHMLYHR 191
Cdd:cd00798    70 YA-VEALEEYLEERRPllLKKKPPDALflnkrgkrlSRRGVWRILKKYAERAGLPK-----HVSPHTLRHSFATHLLEGG 143

                         170       180
                  ....*....|....*....|....
gi 1717609965 192 QPRKVIQALAGHRDPRSMEVYTRV 215
Cdd:cd00798   144 ADLRVVQELLGHASLSTTQIYTHV 167
integrase_gron TIGR02249
integron integrase; Members of this family are integrases associated with integrons (and ...
 46-215 1.13e-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: 54.71  E-value: 1.13e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1717609965  46 LAPEVSALLFYMPDQRHHMLFATLWNTGMRIGEARMLTPESFDLDgvrpfvrilSEKVRARRGRPPKDevRLVPLTDISY 125
Cdd:TIGR02249 102 LTREEVRRLLEHLEGKYRLIAKLLYGSGMRLMECLRLRIQDIDFD---------YGEIRIRQGKGGKD--RTVTLPKELI 170

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1717609965 126 ---VRQMES----------------WMITTRPRR-----REPLWA---------------------VTDETMRNWLKQAV 160
Cdd:TIGR02249 171 pplREQIELarayheadlaegyggvYLPHALARKypnapKEWGWQylfpshrlsrdpesgvirrhhINETTIQRAVRRAV 250

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1717609965 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 3.17e-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: 52.03  E-value: 3.17e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1717609965  45 LLAPEVSALLFYMPDQRHHMLFATLWNTGMRIGEARMLTPESFDLDGvrPFVRILSEKVRARRGRPPKDEVRLVP----- 119
Cdd:cd01186     2 LTPREVQELINACNNLRDKFLLALLYETGLRIGEALGLRIEDIDMAD--NQIELVPREDNTNEARAKSMRERRIPvsqdl 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1717609965 120 -------LTDISYVRQMESWMITTRPRRREPLWAVTDETMRNWLKQAVRRAeadgvhfSIPVTPHTFRHSYIMHMLYHRQ 192
Cdd:cd01186    80 idlyadyLTYIYCEEAEFSITVFVNVKGGNQGKAMNYSDVYDLVRRLKKRT-------GIDFTPHMFRHTHATALIRAGW 152

                         170       180
                  ....*....|....*....|....*....
gi 1717609965 193 PRKVIQALAGHRDPR-SMEVYTRVFALDM 220
Cdd:cd01186   153 SIEVVARRLGHAHVQtTLNTYGHLSEEDI 181
xerD PRK00283
tyrosine recombinase;
42-215 3.51e-08

tyrosine recombinase;


Pssm-ID: 234713 [Multi-domain]  Cd Length: 299  Bit Score: 52.89  E-value: 3.51e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1717609965  42 PAYLLAPEVSALLFYmPDQ------RHHMLFATLWNTGMRIGEARMLTPESFDLDGvrPFVRIlsekvrarRGRPPKDev 115
Cdd:PRK00283  111 PKTLSEAQVEALLDA-PDIdtplglRDRAMLELLYATGLRVSELVGLTLDDVSLRQ--GVVRV--------TGKGNKE-- 177

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1717609965 116 RLVPLTDISyVRQMESWMITTRP--------------RRREPLwavTDETMRNWLKQAVRRAEADGVHfsipVTPHTFRH 181
Cdd:PRK00283  178 RLVPLGEEA-VYAIERYLERGRPallngrssdalfpsARGGQL---TRQTFWHRIKHYAKRAGIDPKK----LSPHVLRH 249

                         170       180       190
                  ....*....|....*....|....*....|....
gi 1717609965 182 SYIMHMLYHRQPRKVIQALAGHRDPRSMEVYTRV 215
Cdd:PRK00283  250 AFATHLLNHGADLRVVQELLGHSDISTTQIYTHV 283
xerC PRK01287
site-specific tyrosine recombinase XerC; Reviewed
 61-215 1.47e-07

site-specific tyrosine recombinase XerC; Reviewed


Pssm-ID: 234935 [Multi-domain]  Cd Length: 358  Bit Score: 51.29  E-value: 1.47e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1717609965  61 RHHMLFATLWNTGMRIGEARMLtpESFDLDGVRPFVRIlsekvraRRGRPPKDEVRLVPLTDISYVRQmesWMITTRPR- 139
Cdd:PRK01287  158 RDRALLELLWSTGIRRGELARL--DLYDVDASRGVVTV-------RQGKGNKDRVVPVGERALAWLQR---YLQDVRPQl 225

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1717609965 140 ----RREPLWAVTDET--MRNWLKQAVRRA-EADGVhfSIPVTPHTFRHSYIMHMLYHRQPRKVIQALAGHRDPRSMEVY 212
Cdd:PRK01287  226 avrpDSGALFVAMDGDglARNTLTNMVGRYiRAAGI--EKAGACHLFRHAMATQMLENGADTRHIQAILGHAKLETTQIY 303


                  ...
gi 1717609965 213 TRV 215
Cdd:PRK01287  304 TRV 306
FimB COG0582
Integrase/recombinase, includes phage integrase [Replication, recombination and repair, ...
 72-219 2.13e-07

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


Pssm-ID: 440347 [Multi-domain]  Cd Length: 391  Bit Score: 50.81  E-value: 2.13e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1717609965  72 TGMRIGEARMLTPESFDLDgvRPFVRILSEKVRARRgrppkdeVRLVPLTD--ISYVRQMesWMITTR-----PRRREPL 144
Cdd:COG0582   237 TGVRPGELRGARWSEIDLE--AALWTIPAERMKTRR-------PHIVPLSRqaLEILKEL--KPLTGDseyvfPSRRGPK 305

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1717609965 145 WAVTDETMRnwlkQAVRRAEADgvhfsiPVTPHTFRHSYIMHMLYHRQPRKVIQALAGHRDPRSME-VYTRVFALD 219
Cdd:COG0582   306 KPMSENTLN----KALRRMGYG------RFTPHGFRHTASTLLNEAGFPPDVIERQLAHKDGNKVRaAYNRADYLE 371
INT_RitA_C_like cd01188
C-terminal catalytic domain of recombinase RitA, a component of the recombinase trio; ...
 64-225 2.16e-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: 49.55  E-value: 2.16e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1717609965  64 MLFATLwntGMRIGEARMLTPESFDLDGVRPFVRilsekvRARRGRPpkdevRLVPLTD------ISYVRQmeswmitTR 137
Cdd:cd01188    27 LLLARL---GLRAGDVAGLRLDDIDWRSGTITVR------QKKTGRP-----VELPLTEpvgealADYLRD-------GR 85

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1717609965 138 PRRREPLWAVTDETMRNWL----------KQAVRRAEADGVHFSipvtPHTFRHSYIMHMLYHRQPRKVIQALAGHRDPR 207
Cdd:cd01188    86 PRTDSREVFLRARAPYRPLsstsqissivRRYLRKAGIEPSHRG----THSLRHSLATRMLRAGTSLKVIADLLGHRSIE 161

                         170
                  ....*....|....*...
gi 1717609965 208 SMEVYTRVfALDMAATLA 225
Cdd:cd01188   162 TTAIYAKI-DVDDLREVA 178
INT_C_like_1 cd01184
Uncharacterized site-specific tyrosine recombinase, C-terminal catalytic domain; Tyrosine ...
 72-206 5.57e-07

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: 48.46  E-value: 5.57e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1717609965  72 TGMRIGEARMLTPESFDLDGVRPFVRILSEKvrARRGRPPKDEVRLVPLTD-------ISYVRQMESwmitTRPRRREPL 144
Cdd:cd01184    35 TGARLNEICQLRVDDIKEEDGIWCIDINDDA--EGRRLKTKASRRLVPIHPrlielgfLDYVEALRA----DGKLFLFPE 108

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1717609965 145 WAVTDET----MRNWLKQAVRRAE---ADGVHFsipvtpHTFRHSYIMHMLYHRQPRKVIQALAGHRDP 206
Cdd:cd01184   109 KRDKDGKyskaASKWFNRLLRKLGikdDERKSF------HSFRHTFITALKRAGVPEELIAQIVGHSRG 171
INTN1_C_like cd01185
Integrase IntN1 of Bacteroides mobilizable transposon NBU1 and similar proteins, C-terminal ...
 65-216 2.14e-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: 46.49  E-value: 2.14e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1717609965  65 LFATLwnTGMRIGEARMLTPESFDLDGVRPFVRILSEKVrarrgrppKDEVRlVPLTDIsyVRQ-MESWMITTRPRRREP 143
Cdd:cd01185    25 LFSCY--TGLRFSDLKNLTWKNIVEASGRTWIRYRRKKT--------GKPVT-VPLLPV--AREiLEKYKDDRSEGKLFP 91

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1717609965 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 7.25e-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: 45.15  E-value: 7.25e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1717609965  61 RHHMLFATLWNTGMRIGEARMLtpesfDLDGVRPFVRILsekVRARRGRPPKDEVRLVPLTdisyvRQMESWMITTRPRR 140
Cdd:cd01195    21 RDEALVRLLLDNALRRSEAVAL-----DVEDLEKEHRRL---RILGKGKKQREVVTLPPTT-----REALAAWLAARGEA 87

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1717609965 141 REPLWAVTDETMR------NWLKQAVRR-AEADGVHFSIpvTPHTFRHSYIMHMLYHRQP--RKViQALAGHRDPRSMEV 211
Cdd:cd01195    88 EGPLFVSLDRASRgrrlspQAVYRIVRRlAERIGLGKRL--SPHGLRHSAITLALDAGAGliRKV-QDFSRHADLRTLQV 164


                  ...
gi 1717609965 212 YTR 214
Cdd:cd01195   165 YDD 167
PRK15417 PRK15417
integron integrase;
42-218 1.03e-05

integron integrase;


Pssm-ID: 185315 [Multi-domain]  Cd Length: 337  Bit Score: 45.81  E-value: 1.03e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1717609965  42 PAYLLAPEVSALLFYMpdQRHHMLFATL-WNTGMRIGEARMLTPESFDLDGVRPFVR------------------ILSEK 102
Cdd:PRK15417  114 PVVLTPDEVVRILGFL--EGEHRLFAQLlYGTGMRISEGLQLRVKDLDFDHGTIIVRegkgskdralmlpeslapSLREQ 191

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1717609965 103 VRARRGRPPKDE------VRLVPLTDISYVRQMESW---------MITTRPR----RREPLWavtDETMRNWLKQAVRRA 163
Cdd:PRK15417  192 LSRARAWWLKDQaegrsgVALPDALERKYPRAGHSWpwfwvfaqhTHSTDPRsgvvRRHHMY---DQTFQRAFKRAVEQA 268

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1717609965 164 eadGVhfSIPVTPHTFRHSYIMHMLYHRQPRKVIQALAGHRDPRSMEVYTRVFAL 218
Cdd:PRK15417  269 ---GI--TKPATPHTLRHSFATALLRSGYDIRTVQDLLGHSDVSTTMIYTHVLKV 318
xerC PRK00236
site-specific tyrosine recombinase XerC; Reviewed
 42-215 1.28e-05

site-specific tyrosine recombinase XerC; Reviewed


Pssm-ID: 234698 [Multi-domain]  Cd Length: 297  Bit Score: 45.15  E-value: 1.28e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1717609965  42 PAYLLAPEVSALLFYMPD-----QRHHMLFATLWNTGMRIGEARMLTPESFDLDgvRPFVRILsekvrarrGRPPKDevR 116
Cdd:PRK00236  113 PKPLDVDQAKRLLDAIDEddplaLRDRAILELLYGSGLRLSELVGLDIDDLDLA--SGTLRVL--------GKGNKE--R 180

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1717609965 117 LVPLTDisYVRQ-MESWmITTRP------------RRREPLWA-VTDETMRNWLKQAvrraeadgvHFSIPVTPHTFRHS 182
Cdd:PRK00236  181 TVPLGR--AAREaLEAY-LALRPlflpdddalflgARGGRLSPrVVQRRVKKLGKKA---------GLPSHITPHKLRHS 248

                         170       180       190
                  ....*....|....*....|....*....|...
gi 1717609965 183 YIMHMLYHRQPRKVIQALAGHRDPRSMEVYTRV 215
Cdd:PRK00236  249 FATHLLESGGDLRAVQELLGHASLSTTQIYTHV 281
INT_C_like_6 cd01196
Uncharacterized site-specific tyrosine recombinase, C-terminal catalytic domain; Tyrosine ...
 161-214 3.87e-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: 37.07  E-value: 3.87e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1717609965 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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