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Conserved domains on  [gi|763844138|gb|KJC03975|]
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resolvase (plasmid) [Citrobacter freundii]

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];
33-222 4.49e-23

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


:

Pssm-ID: 443999 [Multi-domain]  Cd Length: 291  Bit Score: 95.06  E-value: 4.49e-23
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 763844138  33 PPYLLAPEVALLLSYMHD-----LRERCYFETLWNCGARPNEALALTPQDFAFDAAMPYVTL-KTLKQRnrgrgrpqknD 106
Cdd:COG4974  110 PRVLTEEEIEALLEALDTetpegLRDRALLLLLYATGLRVSELLGLKWSDIDLDRGTIRVRRgKGGKER----------T 179

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 763844138 107 LPVRNVALwdadyrARMQSLIATFGIRKTDLLWPGRRRcedkvpASVSADTVARWLNRALENAardGVTFSVSPivpKTF 186
Cdd:COG4974  180 VPLSPEAL------EALREYLEERRPRDSDYLFPTRRG------RPLSRRAIRKILKRLAKRA---GIPKRVTP---HSL 241

                        170       180       190
                 ....*....|....*....|....*....|....*.
gi 763844138 187 RHSFAMHILFNRIHPKVLQALMGHKSFKSTEVYTRL 222
Cdd:COG4974  242 RHTFATHLLEAGVDLRTVQELLGHSSISTTQIYTHV 277
 
Name Accession Description Interval E-value
XerD COG4974
Site-specific recombinase XerD [Replication, recombination and repair];
33-222 4.49e-23

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


Pssm-ID: 443999 [Multi-domain]  Cd Length: 291  Bit Score: 95.06  E-value: 4.49e-23
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 763844138  33 PPYLLAPEVALLLSYMHD-----LRERCYFETLWNCGARPNEALALTPQDFAFDAAMPYVTL-KTLKQRnrgrgrpqknD 106
Cdd:COG4974  110 PRVLTEEEIEALLEALDTetpegLRDRALLLLLYATGLRVSELLGLKWSDIDLDRGTIRVRRgKGGKER----------T 179

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 763844138 107 LPVRNVALwdadyrARMQSLIATFGIRKTDLLWPGRRRcedkvpASVSADTVARWLNRALENAardGVTFSVSPivpKTF 186
Cdd:COG4974  180 VPLSPEAL------EALREYLEERRPRDSDYLFPTRRG------RPLSRRAIRKILKRLAKRA---GIPKRVTP---HSL 241

                        170       180       190
                 ....*....|....*....|....*....|....*.
gi 763844138 187 RHSFAMHILFNRIHPKVLQALMGHKSFKSTEVYTRL 222
Cdd:COG4974  242 RHTFATHLLEAGVDLRTVQELLGHSSISTTQIYTHV 277
Phage_integrase pfam00589
Phage integrase family; Members of this family cleave DNA substrates by a series of staggered ...
 35-223 1.94e-22

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: 90.46  E-value: 1.94e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 763844138   35 YLLAPEVALLLSYMHD----LRERCYFETLWNCGARPNEALALTPQDFAFDAAMPYVT-LKTLKQRNrgrgrpqkndLPV 109
Cdd:pfam00589   1 RLTEDEVERLLDAAETgplsIRDKALLELLYATGLRISELCSLRWSDIDFENGVIRVHrGKGNKERT----------VPL 70

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 763844138  110 RNVALwdadYRARMQSLIATFGIRKTDLLWPGRRRCEdkvpasVSADTVARWLNRALENAARDGvtfsvsPIVPKTFRHS 189
Cdd:pfam00589  71 SDAAL----ELLKEWLSKRLLEAPKSDYLFASKRGKP------LSRQTVRKIFKRAGKEAGLEL------PLHPHMLRHS 134

                         170       180       190
                  ....*....|....*....|....*....|....
gi 763844138  190 FAMHILFNRIHPKVLQALMGHKSFKSTEVYTRLF 223
Cdd:pfam00589 135 FATHLLEAGVDLRVVQKLLGHSSISTTQIYTHVA 168
INT_IntI_C cd01193
Integron integrase and similar protiens, C-terminal catalytic domain; Integron integrases ...
 34-222 5.62e-18

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: 78.86  E-value: 5.62e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 763844138  34 PYLLAP-EVALLLSYMHDLRERCYFETLWNCGARPNEALALTPQDFAFDAAMPYVTlktlkqrnRGRGR-------PQKN 105
Cdd:cd01193    3 PVVLSPdEVRRILGALTELRHRLILSLLYGAGLRISELLRLRVKDIDFERGVIRVR--------QGKGGkdrvvplPEKL 74

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 763844138 106 DLPVRNvaLWDAdyrARMQSLIATFGIRKTDLLWPGRRRCEDKVpasvSADTVARWLNRALENAardGVTfsvSPIVPKT 185
Cdd:cd01193   75 LEPLRR--YLKS---ARPKEELDPAEGRAGVLDPRTGVERRHHI----SETTVQRALKKAVEQA---GIT---KRVTPHT 139

                        170       180       190
                 ....*....|....*....|....*....|....*..
gi 763844138 186 FRHSFAMHILFNRIHPKVLQALMGHKSFKSTEVYTRL 222
Cdd:cd01193  140 LRHSFATHLLEAGTDIRTIQELLGHSDLSTTMIYTHV 176
recomb_XerD TIGR02225
tyrosine recombinase XerD; The phage integrase family describes a number of recombinases with ...
 33-220 1.49e-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: 62.98  E-value: 1.49e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 763844138   33 PPYLLAPEVALLLSYM-----HDLRERCYFETLWNCGARPNEALALTPQDFAFDAAMPYVTLKTLKQRNrgrgrpqkndL 107
Cdd:TIGR02225 102 PKVLTVEEVEALLAAPdvdtpLGLRDRAMLELLYATGLRVSELVGLRLEDVNLDEGFVRVRGKGNKERL----------V 171

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 763844138  108 PVRNVAL-WDADY--RARMQSLIATfgIRKTDLLWPGRRRcedkvpASVSADTVARWLNralENAARDGVTFSVSPivpK 184
Cdd:TIGR02225 172 PLGEEAIeALERYlkEARPLLLKKK--VKESDALFLNRRG------GPLSRQGVWKILK---EYAKRAGIEKPISP---H 237

                         170       180       190
                  ....*....|....*....|....*....|....*.
gi 763844138  185 TFRHSFAMHILFNRIHPKVLQALMGHKSFKSTEVYT 220
Cdd:TIGR02225 238 TLRHSFATHLLENGADLRVVQELLGHADISTTQIYT 273
xerC PRK00236
site-specific tyrosine recombinase XerC; Reviewed
 49-222 1.01e-07

site-specific tyrosine recombinase XerC; Reviewed


Pssm-ID: 234698 [Multi-domain]  Cd Length: 297  Bit Score: 51.69  E-value: 1.01e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 763844138  49 HDLRERCYFETLWNCGARPNEALALTPQDFAFDAAMPYVTLKTLKQRnrgrgrpqknDLPV-RNVALWDADYRArmqslI 127
Cdd:PRK00236 134 LALRDRAILELLYGSGLRLSELVGLDIDDLDLASGTLRVLGKGNKER----------TVPLgRAAREALEAYLA-----L 198

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 763844138 128 ATFGIRKTDLLWPGRR--RcedkvpasVSADTVARWLNRALENAardGVTFSVSPivpKTFRHSFAMHILFN----Rihp 201
Cdd:PRK00236 199 RPLFLPDDDALFLGARggR--------LSPRVVQRRVKKLGKKA---GLPSHITP---HKLRHSFATHLLESggdlR--- 261

                        170       180
                 ....*....|....*....|.
gi 763844138 202 kVLQALMGHKSFKSTEVYTRL 222
Cdd:PRK00236 262 -AVQELLGHASLSTTQIYTHV 281
 
Name Accession Description Interval E-value
XerD COG4974
Site-specific recombinase XerD [Replication, recombination and repair];
33-222 4.49e-23

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


Pssm-ID: 443999 [Multi-domain]  Cd Length: 291  Bit Score: 95.06  E-value: 4.49e-23
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 763844138  33 PPYLLAPEVALLLSYMHD-----LRERCYFETLWNCGARPNEALALTPQDFAFDAAMPYVTL-KTLKQRnrgrgrpqknD 106
Cdd:COG4974  110 PRVLTEEEIEALLEALDTetpegLRDRALLLLLYATGLRVSELLGLKWSDIDLDRGTIRVRRgKGGKER----------T 179

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 763844138 107 LPVRNVALwdadyrARMQSLIATFGIRKTDLLWPGRRRcedkvpASVSADTVARWLNRALENAardGVTFSVSPivpKTF 186
Cdd:COG4974  180 VPLSPEAL------EALREYLEERRPRDSDYLFPTRRG------RPLSRRAIRKILKRLAKRA---GIPKRVTP---HSL 241

                        170       180       190
                 ....*....|....*....|....*....|....*.
gi 763844138 187 RHSFAMHILFNRIHPKVLQALMGHKSFKSTEVYTRL 222
Cdd:COG4974  242 RHTFATHLLEAGVDLRTVQELLGHSSISTTQIYTHV 277
Phage_integrase pfam00589
Phage integrase family; Members of this family cleave DNA substrates by a series of staggered ...
 35-223 1.94e-22

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: 90.46  E-value: 1.94e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 763844138   35 YLLAPEVALLLSYMHD----LRERCYFETLWNCGARPNEALALTPQDFAFDAAMPYVT-LKTLKQRNrgrgrpqkndLPV 109
Cdd:pfam00589   1 RLTEDEVERLLDAAETgplsIRDKALLELLYATGLRISELCSLRWSDIDFENGVIRVHrGKGNKERT----------VPL 70

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 763844138  110 RNVALwdadYRARMQSLIATFGIRKTDLLWPGRRRCEdkvpasVSADTVARWLNRALENAARDGvtfsvsPIVPKTFRHS 189
Cdd:pfam00589  71 SDAAL----ELLKEWLSKRLLEAPKSDYLFASKRGKP------LSRQTVRKIFKRAGKEAGLEL------PLHPHMLRHS 134

                         170       180       190
                  ....*....|....*....|....*....|....
gi 763844138  190 FAMHILFNRIHPKVLQALMGHKSFKSTEVYTRLF 223
Cdd:pfam00589 135 FATHLLEAGVDLRVVQKLLGHSSISTTQIYTHVA 168
INT_IntI_C cd01193
Integron integrase and similar protiens, C-terminal catalytic domain; Integron integrases ...
 34-222 5.62e-18

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: 78.86  E-value: 5.62e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 763844138  34 PYLLAP-EVALLLSYMHDLRERCYFETLWNCGARPNEALALTPQDFAFDAAMPYVTlktlkqrnRGRGR-------PQKN 105
Cdd:cd01193    3 PVVLSPdEVRRILGALTELRHRLILSLLYGAGLRISELLRLRVKDIDFERGVIRVR--------QGKGGkdrvvplPEKL 74

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 763844138 106 DLPVRNvaLWDAdyrARMQSLIATFGIRKTDLLWPGRRRCEDKVpasvSADTVARWLNRALENAardGVTfsvSPIVPKT 185
Cdd:cd01193   75 LEPLRR--YLKS---ARPKEELDPAEGRAGVLDPRTGVERRHHI----SETTVQRALKKAVEQA---GIT---KRVTPHT 139

                        170       180       190
                 ....*....|....*....|....*....|....*..
gi 763844138 186 FRHSFAMHILFNRIHPKVLQALMGHKSFKSTEVYTRL 222
Cdd:cd01193  140 LRHSFATHLLEAGTDIRTIQELLGHSDLSTTMIYTHV 176
DNA_BRE_C cd00397
DNA breaking-rejoining enzymes, C-terminal catalytic domain; The DNA breaking-rejoining enzyme ...
 40-220 6.91e-18

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: 78.29  E-value: 6.91e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 763844138  40 EVALLLSYM-----HDLRERCYFETLWNCGARPNEALALTPQDFAFDaaMPYVTLKTLKQRNRGRgrpqkndlpvRNVAL 114
Cdd:cd00397    1 ELEKLLDAIdedkkIDLRDRAILLLLLETGLRISELLALKVKDIDLD--NGTIRVRGKKTKGGKE----------RTVPL 68

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 763844138 115 WDADYRARMQSLIATFGIRKTDLLWPGRRRcedKVPASVSADTVARWLNRALENAARDGVTfsvsPIVPKTFRHSFAMHI 194
Cdd:cd00397   69 PKELAEELKEYLKERRDKRGPLLKSLYLNK---LFGTKLGERLSRRTLRRIFKKAGIEAGR----KITPHSLRHTFATNL 141

                        170       180
                 ....*....|....*....|....*.
gi 763844138 195 LFNRIHPKVLQALMGHKSFKSTEVYT 220
Cdd:cd00397  142 LENGVDIKVVQKLLGHSSISTTQRYL 167
XerC COG4973
Site-specific recombinase XerC [Replication, recombination and repair];
33-222 5.11e-17

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


Pssm-ID: 443998 [Multi-domain]  Cd Length: 287  Bit Score: 78.46  E-value: 5.11e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 763844138  33 PPYLLAPEVALLLSYMHD----LRERCYFETLWNCGARPNEALALTPQDFAFDAAMPYVTLKTLKQRnrgrgrpqknDLP 108
Cdd:COG4973  109 PRALTVDELAQLLDALADdplaVRDRAIVELLYSTGLRLGELVGLDWEDVDLDAGEVRVRGKTGKSR----------TVP 178

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 763844138 109 VRNVALwdaDYRARMQSLIATFGIRKTDLLWPGRRRcedkvpASVSADTVARWLNRAlenAARDGVTfsvSPIVPKTFRH 188
Cdd:COG4973  179 LGPKAL---AALREWLAVRPELAAPDEGALFPSRRG------TRLSPRNVQKRLRRL---AKKAGLP---KHVHPHDLRH 243

                        170       180       190
                 ....*....|....*....|....*....|....
gi 763844138 189 SFAMHILFNRIHPKVLQALMGHKSFKSTEVYTRL 222
Cdd:COG4973  244 SFATHLLESGGDLRAVQELLGHASISTTQIYTHL 277
INT_ICEBs1_C_like cd01189
C-terminal catalytic domain of integrases from bacterial phages and conjugate transposons; ...
 40-220 5.49e-13

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: 64.50  E-value: 5.49e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 763844138  40 EVALLLSYM--HDLRERCYFETLWNCGARPNEALALTPQDFAFDAAMPYVTlKTLKQRNRGRGR--PQKNDLPVRNVALW 115
Cdd:cd01189    3 ELKKLLEALkkRGDRYYLLFLLALLTGLRRGELLALTWSDIDFENGTIRIN-RTLVRKKKGGYVikPPKTKSSIRTIPLP 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 763844138 116 DadyrarmqSLIatfgirktDLLwpgRRRcedkvpasvsadtvaRWLNRALENAardgvtfSVSPIVPKTFRHSFAMHIL 195
Cdd:cd01189   82 D--------ELI--------ELL---KEL---------------KAFKKLLKKA-------GLPRITPHDLRHTFASLLL 120

                        170       180
                 ....*....|....*....|....*.
gi 763844138 196 FNRIHPKVLQALMGHKSFKST-EVYT 220
Cdd:cd01189  121 EAGVPLKVIAERLGHSDISTTlDVYA 146
INT_XerDC_C cd00798
XerD and XerC integrases, C-terminal catalytic domains; XerDC-like integrases are involved in ...
 49-220 2.73e-12

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: 63.30  E-value: 2.73e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 763844138  49 HDLRERCYFETLWNCGARPNEALALTPQDFAFDAAMPYVTLKTLKQRnrgrgrpqknDLPVRNVAL-WDADYRARMQSLI 127
Cdd:cd00798   17 LGLRDRAILELLYASGLRVSELVGLDLSDVDLDEGLVRVTGKGNKER----------LVPFGSYAVeALEEYLEERRPLL 86

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 763844138 128 ATFgiRKTDLLWPGRRRcedkvpASVSADTVARWLNRALENAardGVTFSVSPivpKTFRHSFAMHILFNRIHPKVLQAL 207
Cdd:cd00798   87 LKK--KPPDALFLNKRG------KRLSRRGVWRILKKYAERA---GLPKHVSP---HTLRHSFATHLLEGGADLRVVQEL 152

                        170
                 ....*....|...
gi 763844138 208 MGHKSFKSTEVYT 220
Cdd:cd00798  153 LGHASLSTTQIYT 165
recomb_XerD TIGR02225
tyrosine recombinase XerD; The phage integrase family describes a number of recombinases with ...
 33-220 1.49e-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: 62.98  E-value: 1.49e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 763844138   33 PPYLLAPEVALLLSYM-----HDLRERCYFETLWNCGARPNEALALTPQDFAFDAAMPYVTLKTLKQRNrgrgrpqkndL 107
Cdd:TIGR02225 102 PKVLTVEEVEALLAAPdvdtpLGLRDRAMLELLYATGLRVSELVGLRLEDVNLDEGFVRVRGKGNKERL----------V 171

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 763844138  108 PVRNVAL-WDADY--RARMQSLIATfgIRKTDLLWPGRRRcedkvpASVSADTVARWLNralENAARDGVTFSVSPivpK 184
Cdd:TIGR02225 172 PLGEEAIeALERYlkEARPLLLKKK--VKESDALFLNRRG------GPLSRQGVWKILK---EYAKRAGIEKPISP---H 237

                         170       180       190
                  ....*....|....*....|....*....|....*.
gi 763844138  185 TFRHSFAMHILFNRIHPKVLQALMGHKSFKSTEVYT 220
Cdd:TIGR02225 238 TLRHSFATHLLENGADLRVVQELLGHADISTTQIYT 273
INT_RitC_C_like cd01182
C-terminal catalytic domain of recombinase RitC, a component of the recombinase trio; ...
 59-221 2.01e-10

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: 58.44  E-value: 2.01e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 763844138  59 TLWNCGARPNEALALTPQDFAFDAAmPYVTLktlkqrnRGRGRPQkndlpvRNVALWDADYRArMQSLIATFGIRKTDL- 137
Cdd:cd01182   29 LLYDTGARVQELADLTIRDLRLDDP-ATVRL-------HGKGRKE------RTVPLWKETVAA-LKAYLQEFHLTPDPKq 93

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 763844138 138 ---LWPGRRRcedkvpASVSADTVARWLNRALENAARDGVTFSVSpIVPKTFRHSFAMHILFNRIHPKVLQALMGHKSFK 214
Cdd:cd01182   94 lfpLFPNRRG------QPLTRDGVAYILNKYVALASNRCPSLPKR-ITPHTLRHTKAMHLLQAGVDLTVIRDWLGHESVE 166


                 ....*..
gi 763844138 215 STEVYTR 221
Cdd:cd01182  167 TTQIYAE 173
xerC PRK00236
site-specific tyrosine recombinase XerC; Reviewed
 49-222 1.01e-07

site-specific tyrosine recombinase XerC; Reviewed


Pssm-ID: 234698 [Multi-domain]  Cd Length: 297  Bit Score: 51.69  E-value: 1.01e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 763844138  49 HDLRERCYFETLWNCGARPNEALALTPQDFAFDAAMPYVTLKTLKQRnrgrgrpqknDLPV-RNVALWDADYRArmqslI 127
Cdd:PRK00236 134 LALRDRAILELLYGSGLRLSELVGLDIDDLDLASGTLRVLGKGNKER----------TVPLgRAAREALEAYLA-----L 198

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 763844138 128 ATFGIRKTDLLWPGRR--RcedkvpasVSADTVARWLNRALENAardGVTFSVSPivpKTFRHSFAMHILFN----Rihp 201
Cdd:PRK00236 199 RPLFLPDDDALFLGARggR--------LSPRVVQRRVKKLGKKA---GLPSHITP---HKLRHSFATHLLESggdlR--- 261

                        170       180
                 ....*....|....*....|.
gi 763844138 202 kVLQALMGHKSFKSTEVYTRL 222
Cdd:PRK00236 262 -AVQELLGHASLSTTQIYTHV 281
INT_Rci_Hp1_C cd00796
Shufflon-specific DNA recombinase Rci and Bacteriophage Hp1_like integrase, C-terminal ...
 35-221 2.71e-07

Shufflon-specific DNA recombinase Rci and Bacteriophage Hp1_like integrase, C-terminal catalytic domain; Rci protein is a tyrosine recombinase specifically involved in Shufflon type of DNA rearrangement in bacteria. The shufflon of plasmid R64 consists of four invertible DNA segments which are separated and flanked by seven 19-bp repeat sequences. RCI recombinase facilitates the site-specific recombination between any inverted repeats results in an inversion of the DNA segment(s) either independently or in groups. HP1 integrase promotes site-specific recombination of the HP1 genome into that of Haemophilus influenza. Bacteriophage Hp1_like integrases are tyrosine based site specific recombinases. They belong to the superfamily of DNA breaking-rejoining enzymes, which share the same fold in their catalytic domain and the overall reaction mechanism. The catalytic domain contains six conserved active site residues. Their overall reaction mechanism is essentially identical and involves cleavage of a single strand of a DNA duplex by nucleophilic attack of a conserved tyrosine to give a 3' phosphotyrosyl protein-DNA adduct. In the second rejoining step, a terminal 5' hydroxyl attacks the covalent adduct to release the enzyme and generate duplex DNA.


Pssm-ID: 271177 [Multi-domain]  Cd Length: 162  Bit Score: 48.86  E-value: 2.71e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 763844138  35 YLLAPEVALLLS---YMHDLRERCYFETLWNCGARPNEALALTPQDFAFDaaMPYVTLKTLKQrnrgrGRPQKndLPVRN 111
Cdd:cd00796    4 FLTEDEEARLLAaleESTNPHLRLIVLLALYTGARRGEILSLRWDDIDLE--VGLIVLPETKN-----GKPRT--VPLSD 74

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 763844138 112 VAlwdadyRARMQSLIATfgiRKTDLLWPgrrrceDKVPASVSADTVARWLNRALENAARDGVTFsvspivpKTFRHSFA 191
Cdd:cd00796   75 EA------IAILKELKRK---RGKDGFFV------DGRFFGIPIASLRRAFKKARKRAGLEDLRF-------HDLRHTFA 132

                        170       180       190
                 ....*....|....*....|....*....|
gi 763844138 192 MHILFNRIHPKVLQALMGHKSFKSTEVYTR 221
Cdd:cd00796  133 SRLVQAGVPIKTVAKILGHSSIKMTMRYAH 162
INT_C_like_1 cd01184
Uncharacterized site-specific tyrosine recombinase, C-terminal catalytic domain; Tyrosine ...
 64-221 5.18e-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: 5.18e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 763844138  64 GARPNEALALTPQDFAFDAAMPYVTLktlkqRNRGRGRPQKNDLPVRNVALWDADYRARMQSLIATFGIRKTDLLWPGRR 143
Cdd:cd01184   36 GARLNEICQLRVDDIKEEDGIWCIDI-----NDDAEGRRLKTKASRRLVPIHPRLIELGFLDYVEALRADGKLFLFPEKR 110

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 763844138 144 RCEDKvpasvSADTVARWLNRALENA---ARDGVTFSVspivpktFRHSFAMHILFNRIHPKVLQALMGHKSfkSTEVYT 220
Cdd:cd01184  111 DKDGK-----YSKAASKWFNRLLRKLgikDDERKSFHS-------FRHTFITALKRAGVPEELIAQIVGHSR--GGVTHD 176


                 .
gi 763844138 221 R 221
Cdd:cd01184  177 T 177
INTN1_C_like cd01185
Integrase IntN1 of Bacteroides mobilizable transposon NBU1 and similar proteins, C-terminal ...
 163-223 8.70e-07

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: 47.64  E-value: 8.70e-07
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 763844138 163 NRALENAARD-GVTFSVSPivpKTFRHSFAMHILFNRIHPKVLQALMGHKSFKSTEVYTRLF 223
Cdd:cd01185   99 NRYLKEIAKIaGIDKHLTF---HVARHTFATLLLLKGVDIETISKLLGHSSIKTTQIYAKIV 157
xerD PRK00283
tyrosine recombinase;
33-220 4.10e-06

tyrosine recombinase;


Pssm-ID: 234713 [Multi-domain]  Cd Length: 299  Bit Score: 46.72  E-value: 4.10e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 763844138  33 PPYLLAPEVALLLSYMH-----DLRERCYFETLWNCGARPNEALALTPQDfafdaampyVTLKTLKQRNRGRGRpqKNDL 107
Cdd:PRK00283 111 PKTLSEAQVEALLDAPDidtplGLRDRAMLELLYATGLRVSELVGLTLDD---------VSLRQGVVRVTGKGN--KERL 179

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 763844138 108 -PV-RNVALWDADY--RARMQSLiatfGIRKTDLLWPGRRRcedkvpASVSADTVARWLNRAlenAARDGVtfSVSPIVP 183
Cdd:PRK00283 180 vPLgEEAVYAIERYleRGRPALL----NGRSSDALFPSARG------GQLTRQTFWHRIKHY---AKRAGI--DPKKLSP 244

                        170       180       190
                 ....*....|....*....|....*....|....*..
gi 763844138 184 KTFRHSFAMHILFNRIHPKVLQALMGHKSFKSTEVYT 220
Cdd:PRK00283 245 HVLRHAFATHLLNHGADLRVVQELLGHSDISTTQIYT 281
xerC PRK01287
site-specific tyrosine recombinase XerC; Reviewed
 51-221 8.02e-06

site-specific tyrosine recombinase XerC; Reviewed


Pssm-ID: 234935 [Multi-domain]  Cd Length: 358  Bit Score: 46.28  E-value: 8.02e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 763844138  51 LRERCYFETLWNCGARPNEALALTPQDFafDAAMPYVTLKtlkqrnRGRGRpQKNDLPVRNVAL-WDADY--RARMQsLI 127
Cdd:PRK01287 157 LRDRALLELLWSTGIRRGELARLDLYDV--DASRGVVTVR------QGKGN-KDRVVPVGERALaWLQRYlqDVRPQ-LA 226

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 763844138 128 ATFGIRKTDLLWPGRRrcedkvpasVSADTVARWLNRALENAARDgvtfsvSPIVPKTFRHSFAMHILFNRIHPKVLQAL 207
Cdd:PRK01287 227 VRPDSGALFVAMDGDG---------LARNTLTNMVGRYIRAAGIE------KAGACHLFRHAMATQMLENGADTRHIQAI 291

                        170
                 ....*....|....
gi 763844138 208 MGHKSFKSTEVYTR 221
Cdd:PRK01287 292 LGHAKLETTQIYTR 305
INT_RitA_C_like cd01188
C-terminal catalytic domain of recombinase RitA, a component of the recombinase trio; ...
 136-234 5.72e-04

C-terminal catalytic domain of recombinase RitA, a component of the recombinase trio; Recombinases RitA (also known as pAE1), RitB, and RitC are encoded by three adjacent and overlapping genes. Collectively they are known as the Recombinase in Trio (RIT). This RitA family includes various bacterial integrases and integrases from the deletion-prone region of plasmid pAE1 of Alcaligenes eutrophus H1. All three integrases contain a catalytic motif, suggesting that they are all active enzymes. However, their specific roles are not fully understood. All three families belong to the superfamily of DNA breaking-rejoining enzymes, which share the same fold in their catalytic domain and the overall reaction mechanism. The catalytic domain contains six conserved active site residues. Their overall reaction mechanism is essentially identical and involves cleavage of a single strand of a DNA duplex by nucleophilic attack of a conserved tyrosine to give a 3' phosphotyrosyl protein-DNA adduct. In the second rejoining step, a terminal 5' hydroxyl attacks the covalent adduct to release the enzyme and generate duplex DNA.


Pssm-ID: 271188 [Multi-domain]  Cd Length: 179  Bit Score: 39.53  E-value: 5.72e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 763844138 136 DLLWPGRRRCEDK---------VPASVSADTVARWLNRALENAARDGVTFSvspivPKTFRHSFAMHILFNRIHPKVLQA 206
Cdd:cd01188   79 DYLRDGRPRTDSRevflrarapYRPLSSTSQISSIVRRYLRKAGIEPSHRG-----THSLRHSLATRMLRAGTSLKVIAD 153

                         90       100
                 ....*....|....*....|....*...
gi 763844138 207 LMGHKSFKSTEVYTRLflfDVAGQHQVS 234
Cdd:cd01188  154 LLGHRSIETTAIYAKI---DVDDLREVA 178
PRK15417 PRK15417
integron integrase;
157-229 6.25e-04

integron integrase;


Pssm-ID: 185315 [Multi-domain]  Cd Length: 337  Bit Score: 40.41  E-value: 6.25e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 763844138 157 TVARWLNRALENAardGVTfsvSPIVPKTFRHSFAMHILFNRIHPKVLQALMGHKSFKSTEVYTRLFLFDVAG 229
Cdd:PRK15417 256 TFQRAFKRAVEQA---GIT---KPATPHTLRHSFATALLRSGYDIRTVQDLLGHSDVSTTMIYTHVLKVGGAG 322
INT_C_like_2 cd01191
Uncharacterized site-specific tyrosine recombinase, C-terminal catalytic domain; Tyrosine ...
 159-221 1.18e-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: 271191  Cd Length: 176  Bit Score: 38.56  E-value: 1.18e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 763844138 159 ARWLNRALENAARD-GVTFSVspIVPKTFRHSFAMHIL--FNRIhpKVLQALMGHKSFKSTEVYTR 221
Cdd:cd01191   99 TRGIAQQLKNYARKyGLNPKV--VYPHSFRHRFAKNFLekYNDI--ALLADLMGHESIETTRIYLR 160
INT_tnpA_C_Tn554 cd01186
Putative Transposase A from transposon Tn554, C-terminal catalytic domain; This family ...
 36-216 3.26e-03

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: 37.40  E-value: 3.26e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 763844138  36 LLAPEVALLLSYMHDLRERCYFETLWNCGARPNEALALTPQDFafDAAMPYVTLKTLKQRNRG----RGRPQKNDLPVRN 111
Cdd:cd01186    2 LTPREVQELINACNNLRDKFLLALLYETGLRIGEALGLRIEDI--DMADNQIELVPREDNTNEarakSMRERRIPVSQDL 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 763844138 112 VALWDaDYRARMQSLIATFGIRKTDLLWpgrRRCEDKVPASVSADTVARWLNRalenaaRDGVTFSvspivPKTFRHSFA 191
Cdd:cd01186   80 IDLYA-DYLTYIYCEEAEFSITVFVNVK---GGNQGKAMNYSDVYDLVRRLKK------RTGIDFT-----PHMFRHTHA 144

                        170       180
                 ....*....|....*....|....*
gi 763844138 192 MHILFNRIHPKVLQALMGHKSFKST 216
Cdd:cd01186  145 TALIRAGWSIEVVARRLGHAHVQTT 169
 
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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