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Conserved domains on  [gi|1221422972|ref|WP_089600850|]
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MULTISPECIES: site-specific integrase [Enterobacteriaceae]

Protein Classification

site-specific integrase( domain architecture ID 10457031)

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

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

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
Phage_integrase pfam00589
Phage integrase family; Members of this family cleave DNA substrates by a series of staggered ...
 42-233 5.82e-42

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: 141.30  E-value: 5.82e-42
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1221422972  42 YLLAPEVSALLHYVPD----LHRKMLLATLWNTGARINEALALNRSDFSLAPPYPFVQLatLKQRTEkatrtagrapags 117
Cdd:pfam00589   1 RLTEDEVERLLDAAETgplsIRDKALLELLYATGLRISELCSLRWSDIDFENGVIRVHR--GKGNKE------------- 65

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1221422972 118 qphRIVPLSDpQYVSQLEMMVATLkipLERKNKKTGRMEKARIWTITDRTVRTWLSEAVEAAAADgvtfsVPVTPHTFRH 197
Cdd:pfam00589  66 ---RTVPLSD-AALELLKEWLSKR---LLEAPKSDYLFASKRGKPLSRQTVRKIFKRAGKEAGLE-----LPLHPHMLRH 133

                         170       180       190
                  ....*....|....*....|....*....|....*.
gi 1221422972 198 SYAMHMLYAGIPLKVLQSLMGHKSISSTEVYTKVFA 233
Cdd:pfam00589 134 SFATHLLEAGVDLRVVQKLLGHSSISTTQIYTHVAD 169
 
Name Accession Description Interval E-value
Phage_integrase pfam00589
Phage integrase family; Members of this family cleave DNA substrates by a series of staggered ...
 42-233 5.82e-42

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: 141.30  E-value: 5.82e-42
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1221422972  42 YLLAPEVSALLHYVPD----LHRKMLLATLWNTGARINEALALNRSDFSLAPPYPFVQLatLKQRTEkatrtagrapags 117
Cdd:pfam00589   1 RLTEDEVERLLDAAETgplsIRDKALLELLYATGLRISELCSLRWSDIDFENGVIRVHR--GKGNKE------------- 65

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1221422972 118 qphRIVPLSDpQYVSQLEMMVATLkipLERKNKKTGRMEKARIWTITDRTVRTWLSEAVEAAAADgvtfsVPVTPHTFRH 197
Cdd:pfam00589  66 ---RTVPLSD-AALELLKEWLSKR---LLEAPKSDYLFASKRGKPLSRQTVRKIFKRAGKEAGLE-----LPLHPHMLRH 133

                         170       180       190
                  ....*....|....*....|....*....|....*.
gi 1221422972 198 SYAMHMLYAGIPLKVLQSLMGHKSISSTEVYTKVFA 233
Cdd:pfam00589 134 SFATHLLEAGVDLRVVQKLLGHSSISTTQIYTHVAD 169
XerD COG4974
Site-specific recombinase XerD [Replication, recombination and repair];
39-231 1.37e-28

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


Pssm-ID: 443999 [Multi-domain]  Cd Length: 291  Bit Score: 110.08  E-value: 1.37e-28
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1221422972  39 LPKYLLAPEVSALLHYVPD-----LHRKMLLATLWNTGARINEALALNRSDFSLAPPYPFVqlatlkqRTEKatrtagra 113
Cdd:COG4974   109 LPRVLTEEEIEALLEALDTetpegLRDRALLLLLYATGLRVSELLGLKWSDIDLDRGTIRV-------RRGK-------- 173

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1221422972 114 paGSQPhRIVPLSDPqyvsqlemmvaTLKIpLERKNKKTGRMEKARIWT------ITDRTVRTWLSEAVEAAaadGVTfs 187
Cdd:COG4974   174 --GGKE-RTVPLSPE-----------ALEA-LREYLEERRPRDSDYLFPtrrgrpLSRRAIRKILKRLAKRA---GIP-- 233

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....
gi 1221422972 188 VPVTPHTFRHSYAMHMLYAGIPLKVLQSLMGHKSISSTEVYTKV 231
Cdd:COG4974   234 KRVTPHSLRHTFATHLLEAGVDLRTVQELLGHSSISTTQIYTHV 277
DNA_BRE_C cd00397
DNA breaking-rejoining enzymes, C-terminal catalytic domain; The DNA breaking-rejoining enzyme ...
 56-229 1.59e-26

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: 101.40  E-value: 1.59e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1221422972  56 PDLHRKMLLATLWNTGARINEALALNRSDFSLAPPYpfvqlATLKQRTEKATRTagrapagsqphRIVPLSDPQYVSQLE 135
Cdd:cd00397    15 IDLRDRAILLLLLETGLRISELLALKVKDIDLDNGT-----IRVRGKKTKGGKE-----------RTVPLPKELAEELKE 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1221422972 136 MMvaTLKIPLERKNKKTGRMEKARIWTITDRTVRTWLSEAVEAAaadGVTFSVPVTPHTFRHSYAMHMLYAGIPLKVLQS 215
Cdd:cd00397    79 YL--KERRDKRGPLLKSLYLNKLFGTKLGERLSRRTLRRIFKKA---GIEAGRKITPHSLRHTFATNLLENGVDIKVVQK 153

                         170
                  ....*....|....
gi 1221422972 216 LMGHKSISSTEVYT 229
Cdd:cd00397   154 LLGHSSISTTQRYL 167
recomb_XerD TIGR02225
tyrosine recombinase XerD; The phage integrase family describes a number of recombinases with ...
 39-231 3.91e-20

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: 87.25  E-value: 3.91e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1221422972  39 LPKYLLAPEVSALLHYVP-----DLHRKMLLATLWNTGARINEALALNRSDFSLappypfvqlatlkqrTEKATRTAGRa 113
Cdd:TIGR02225 101 LPKVLTVEEVEALLAAPDvdtplGLRDRAMLELLYATGLRVSELVGLRLEDVNL---------------DEGFVRVRGK- 164

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1221422972 114 paGSQpHRIVPLSDP------QYVSQLEMMVATLKIPLERK---NKKTGRMEKARIWTItdrtvrtwLSEAVEAAaadgv 184
Cdd:TIGR02225 165 --GNK-ERLVPLGEEaiealeRYLKEARPLLLKKKVKESDAlflNRRGGPLSRQGVWKI--------LKEYAKRA----- 228

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*..
gi 1221422972 185 TFSVPVTPHTFRHSYAMHMLYAGIPLKVLQSLMGHKSISSTEVYTKV 231
Cdd:TIGR02225 229 GIEKPISPHTLRHSFATHLLENGADLRVVQELLGHADISTTQIYTHV 275
xerC PRK00236
site-specific tyrosine recombinase XerC; Reviewed
 39-231 3.08e-16

site-specific tyrosine recombinase XerC; Reviewed


Pssm-ID: 234698 [Multi-domain]  Cd Length: 297  Bit Score: 76.35  E-value: 3.08e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1221422972  39 LPKYLLAPEVSALLhYVPDLHRKM------LLATLWNTGARINEALALNRSDFSLAppypfvqLATL-------KQRTEK 105
Cdd:PRK00236  112 LPKPLDVDQAKRLL-DAIDEDDPLalrdraILELLYGSGLRLSELVGLDIDDLDLA-------SGTLrvlgkgnKERTVP 183

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1221422972 106 ATRTAGRAPAGSQPHRIVPLSDPQyvsqlemmvatlkiPLERkNKKTGRmekariwtITDRTVRTWLSEAVEAAAADGVt 185
Cdd:PRK00236  184 LGRAAREALEAYLALRPLFLPDDD--------------ALFL-GARGGR--------LSPRVVQRRVKKLGKKAGLPSH- 239

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*.
gi 1221422972 186 fsvpVTPHTFRHSYAMHMLYAGIPLKVLQSLMGHKSISSTEVYTKV 231
Cdd:PRK00236  240 ----ITPHKLRHSFATHLLESGGDLRAVQELLGHASLSTTQIYTHV 281
recomb_GmtY NF040693
gamma-mobile-trio recombinase GmtY; GmtY (gamma-mobile-trio system tyrosine recombinase) is a ...
 191-238 1.69e-05

gamma-mobile-trio recombinase GmtY; GmtY (gamma-mobile-trio system tyrosine recombinase) is a putative integrase regularly found associated with two other proteins of unknown function, in a cassette found sporadically in various Gamma-proteobacteria. Members of this family include VPA1270, found in pathogenicity island 6 of Vibrio parahaemolyticus RIMD2210633.


Pssm-ID: 468657 [Multi-domain]  Cd Length: 441  Bit Score: 45.30  E-value: 1.69e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 1221422972 191 TPHTFRHSYAMHMLYAGIPLKVLQSLMGHKSISSTEVYTKVFALDVAA 238
Cdd:NF040693  392 TPHGHRHAYGRRLRNAGVDPLEIQKAMHHKSPESQLVYTQPTAAEVRA 439
 
Name Accession Description Interval E-value
Phage_integrase pfam00589
Phage integrase family; Members of this family cleave DNA substrates by a series of staggered ...
 42-233 5.82e-42

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: 141.30  E-value: 5.82e-42
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1221422972  42 YLLAPEVSALLHYVPD----LHRKMLLATLWNTGARINEALALNRSDFSLAPPYPFVQLatLKQRTEkatrtagrapags 117
Cdd:pfam00589   1 RLTEDEVERLLDAAETgplsIRDKALLELLYATGLRISELCSLRWSDIDFENGVIRVHR--GKGNKE------------- 65

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1221422972 118 qphRIVPLSDpQYVSQLEMMVATLkipLERKNKKTGRMEKARIWTITDRTVRTWLSEAVEAAAADgvtfsVPVTPHTFRH 197
Cdd:pfam00589  66 ---RTVPLSD-AALELLKEWLSKR---LLEAPKSDYLFASKRGKPLSRQTVRKIFKRAGKEAGLE-----LPLHPHMLRH 133

                         170       180       190
                  ....*....|....*....|....*....|....*.
gi 1221422972 198 SYAMHMLYAGIPLKVLQSLMGHKSISSTEVYTKVFA 233
Cdd:pfam00589 134 SFATHLLEAGVDLRVVQKLLGHSSISTTQIYTHVAD 169
XerD COG4974
Site-specific recombinase XerD [Replication, recombination and repair];
39-231 1.37e-28

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


Pssm-ID: 443999 [Multi-domain]  Cd Length: 291  Bit Score: 110.08  E-value: 1.37e-28
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1221422972  39 LPKYLLAPEVSALLHYVPD-----LHRKMLLATLWNTGARINEALALNRSDFSLAPPYPFVqlatlkqRTEKatrtagra 113
Cdd:COG4974   109 LPRVLTEEEIEALLEALDTetpegLRDRALLLLLYATGLRVSELLGLKWSDIDLDRGTIRV-------RRGK-------- 173

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1221422972 114 paGSQPhRIVPLSDPqyvsqlemmvaTLKIpLERKNKKTGRMEKARIWT------ITDRTVRTWLSEAVEAAaadGVTfs 187
Cdd:COG4974   174 --GGKE-RTVPLSPE-----------ALEA-LREYLEERRPRDSDYLFPtrrgrpLSRRAIRKILKRLAKRA---GIP-- 233

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....
gi 1221422972 188 VPVTPHTFRHSYAMHMLYAGIPLKVLQSLMGHKSISSTEVYTKV 231
Cdd:COG4974   234 KRVTPHSLRHTFATHLLEAGVDLRTVQELLGHSSISTTQIYTHV 277
DNA_BRE_C cd00397
DNA breaking-rejoining enzymes, C-terminal catalytic domain; The DNA breaking-rejoining enzyme ...
 56-229 1.59e-26

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: 101.40  E-value: 1.59e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1221422972  56 PDLHRKMLLATLWNTGARINEALALNRSDFSLAPPYpfvqlATLKQRTEKATRTagrapagsqphRIVPLSDPQYVSQLE 135
Cdd:cd00397    15 IDLRDRAILLLLLETGLRISELLALKVKDIDLDNGT-----IRVRGKKTKGGKE-----------RTVPLPKELAEELKE 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1221422972 136 MMvaTLKIPLERKNKKTGRMEKARIWTITDRTVRTWLSEAVEAAaadGVTFSVPVTPHTFRHSYAMHMLYAGIPLKVLQS 215
Cdd:cd00397    79 YL--KERRDKRGPLLKSLYLNKLFGTKLGERLSRRTLRRIFKKA---GIEAGRKITPHSLRHTFATNLLENGVDIKVVQK 153

                         170
                  ....*....|....
gi 1221422972 216 LMGHKSISSTEVYT 229
Cdd:cd00397   154 LLGHSSISTTQRYL 167
INT_IntI_C cd01193
Integron integrase and similar protiens, C-terminal catalytic domain; Integron integrases ...
 39-231 3.02e-24

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: 95.42  E-value: 3.02e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1221422972  39 LPKYLLAPEVSALLHYVPDLHRKMLLATLWNTGARINEALALNRSDFSLAPpypfvqlATLKQRTEKATRtagrapagsq 118
Cdd:cd01193     2 LPVVLSPDEVRRILGALTELRHRLILSLLYGAGLRISELLRLRVKDIDFER-------GVIRVRQGKGGK---------- 64

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1221422972 119 pHRIVPLSDpQYVSQLEMMVATLKIPLER---------KNKKTGRMEKARIwtiTDRTVRTWLSEAVEAAaadGVTfsVP 189
Cdd:cd01193    65 -DRVVPLPE-KLLEPLRRYLKSARPKEELdpaegragvLDPRTGVERRHHI---SETTVQRALKKAVEQA---GIT--KR 134

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|..
gi 1221422972 190 VTPHTFRHSYAMHMLYAGIPLKVLQSLMGHKSISSTEVYTKV 231
Cdd:cd01193   135 VTPHTLRHSFATHLLEAGTDIRTIQELLGHSDLSTTMIYTHV 176
INT_RitC_C_like cd01182
C-terminal catalytic domain of recombinase RitC, a component of the recombinase trio; ...
 43-231 3.59e-20

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: 85.02  E-value: 3.59e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1221422972  43 LLAPEVSALLHyVPDLHRK------MLLATLWNTGARINEALALNRSDFSLAPPyPFVQLatlkqrTEKATRTagrapag 116
Cdd:cd01182     1 LTREEMKALLA-APDRNTSlgrrdhALLLLLYDTGARVQELADLTIRDLRLDDP-ATVRL------HGKGRKE------- 65

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1221422972 117 sqphRIVPLSdPQYVSQLEMMVA---TLKIPLE----RKNKKTGRMEKARIWTItdrtvrtwLSEAVEAAAADGVTFSVP 189
Cdd:cd01182    66 ----RTVPLW-KETVAALKAYLQefhLTPDPKQlfplFPNRRGQPLTRDGVAYI--------LNKYVALASNRCPSLPKR 132

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|..
gi 1221422972 190 VTPHTFRHSYAMHMLYAGIPLKVLQSLMGHKSISSTEVYTKV 231
Cdd:cd01182   133 ITPHTLRHTKAMHLLQAGVDLTVIRDWLGHESVETTQIYAEA 174
recomb_XerD TIGR02225
tyrosine recombinase XerD; The phage integrase family describes a number of recombinases with ...
 39-231 3.91e-20

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: 87.25  E-value: 3.91e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1221422972  39 LPKYLLAPEVSALLHYVP-----DLHRKMLLATLWNTGARINEALALNRSDFSLappypfvqlatlkqrTEKATRTAGRa 113
Cdd:TIGR02225 101 LPKVLTVEEVEALLAAPDvdtplGLRDRAMLELLYATGLRVSELVGLRLEDVNL---------------DEGFVRVRGK- 164

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1221422972 114 paGSQpHRIVPLSDP------QYVSQLEMMVATLKIPLERK---NKKTGRMEKARIWTItdrtvrtwLSEAVEAAaadgv 184
Cdd:TIGR02225 165 --GNK-ERLVPLGEEaiealeRYLKEARPLLLKKKVKESDAlflNRRGGPLSRQGVWKI--------LKEYAKRA----- 228

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*..
gi 1221422972 185 TFSVPVTPHTFRHSYAMHMLYAGIPLKVLQSLMGHKSISSTEVYTKV 231
Cdd:TIGR02225 229 GIEKPISPHTLRHSFATHLLENGADLRVVQELLGHADISTTQIYTHV 275
INT_XerDC_C cd00798
XerD and XerC integrases, C-terminal catalytic domains; XerDC-like integrases are involved in ...
 63-231 5.58e-20

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: 84.10  E-value: 5.58e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1221422972  63 LLATLWNTGARINEALALNRSDFSLAPPYPFVqlaTLKQRTEkatrtagrapagsqphRIVPLSDP------QY--VSQL 134
Cdd:cd00798    24 ILELLYASGLRVSELVGLDLSDVDLDEGLVRV---TGKGNKE----------------RLVPFGSYavealeEYleERRP 84

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1221422972 135 EMMVATLKIPLERkNKKTGRmekariwtITDRTVRTWLSEAVEAAAADGvtfsvPVTPHTFRHSYAMHMLYAGIPLKVLQ 214
Cdd:cd00798    85 LLLKKKPPDALFL-NKRGKR--------LSRRGVWRILKKYAERAGLPK-----HVSPHTLRHSFATHLLEGGADLRVVQ 150

                         170
                  ....*....|....*..
gi 1221422972 215 SLMGHKSISSTEVYTKV 231
Cdd:cd00798   151 ELLGHASLSTTQIYTHV 167
XerC COG4973
Site-specific recombinase XerC [Replication, recombination and repair];
39-231 4.36e-19

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


Pssm-ID: 443998 [Multi-domain]  Cd Length: 287  Bit Score: 84.24  E-value: 4.36e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1221422972  39 LPKYLLAPEVSALLHYVPD----LHRKMLLATLWNTGARINEALALNRSDFSLAPPYpfvqlATLKQRTEKatrtagrap 114
Cdd:COG4973   108 LPRALTVDELAQLLDALADdplaVRDRAIVELLYSTGLRLGELVGLDWEDVDLDAGE-----VRVRGKTGK--------- 173

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1221422972 115 agsqpHRIVPLSDpqyvsqleMMVATLKIPLERKNKKTGRMEKA-----RIWTITDRTVRTWLSEAVEAAAadgvtFSVP 189
Cdd:COG4973   174 -----SRTVPLGP--------KALAALREWLAVRPELAAPDEGAlfpsrRGTRLSPRNVQKRLRRLAKKAG-----LPKH 235

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|..
gi 1221422972 190 VTPHTFRHSYAMHMLYAGIPLKVLQSLMGHKSISSTEVYTKV 231
Cdd:COG4973   236 VHPHDLRHSFATHLLESGGDLRAVQELLGHASISTTQIYTHL 277
INT_Rci_Hp1_C cd00796
Shufflon-specific DNA recombinase Rci and Bacteriophage Hp1_like integrase, C-terminal ...
 41-229 3.84e-18

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: 78.91  E-value: 3.84e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1221422972  41 KYLLAPEVSALLHYVPDLHRKMLLATLW---NTGARINEALALNRSDFSLAppypfvqlatLKQRTEKATRTAGRapags 117
Cdd:cd00796     3 RFLTEDEEARLLAALEESTNPHLRLIVLlalYTGARRGEILSLRWDDIDLE----------VGLIVLPETKNGKP----- 67

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1221422972 118 qphRIVPLSDPqYVSQLEMmvatlkipLERKNKKTGRMEKARIWTITDRTVRTWLSEAVEAAaadGVTFsvpVTPHTFRH 197
Cdd:cd00796    68 ---RTVPLSDE-AIAILKE--------LKRKRGKDGFFVDGRFFGIPIASLRRAFKKARKRA---GLED---LRFHDLRH 129

                         170       180       190
                  ....*....|....*....|....*....|..
gi 1221422972 198 SYAMHMLYAGIPLKVLQSLMGHKSISSTEVYT 229
Cdd:cd00796   130 TFASRLVQAGVPIKTVAKILGHSSIKMTMRYA 161
xerC PRK00236
site-specific tyrosine recombinase XerC; Reviewed
 39-231 3.08e-16

site-specific tyrosine recombinase XerC; Reviewed


Pssm-ID: 234698 [Multi-domain]  Cd Length: 297  Bit Score: 76.35  E-value: 3.08e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1221422972  39 LPKYLLAPEVSALLhYVPDLHRKM------LLATLWNTGARINEALALNRSDFSLAppypfvqLATL-------KQRTEK 105
Cdd:PRK00236  112 LPKPLDVDQAKRLL-DAIDEDDPLalrdraILELLYGSGLRLSELVGLDIDDLDLA-------SGTLrvlgkgnKERTVP 183

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1221422972 106 ATRTAGRAPAGSQPHRIVPLSDPQyvsqlemmvatlkiPLERkNKKTGRmekariwtITDRTVRTWLSEAVEAAAADGVt 185
Cdd:PRK00236  184 LGRAAREALEAYLALRPLFLPDDD--------------ALFL-GARGGR--------LSPRVVQRRVKKLGKKAGLPSH- 239

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*.
gi 1221422972 186 fsvpVTPHTFRHSYAMHMLYAGIPLKVLQSLMGHKSISSTEVYTKV 231
Cdd:PRK00236  240 ----ITPHKLRHSFATHLLESGGDLRAVQELLGHASLSTTQIYTHV 281
INT_ICEBs1_C_like cd01189
C-terminal catalytic domain of integrases from bacterial phages and conjugate transposons; ...
 47-230 3.48e-14

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: 67.97  E-value: 3.48e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1221422972  47 EVSALLHYVP--DLHRKMLLATLWNTGARINEALALNRSDFSLAPPYPFV----QLATLKQRTEKATRTagrapagSQPH 120
Cdd:cd01189     3 ELKKLLEALKkrGDRYYLLFLLALLTGLRRGELLALTWSDIDFENGTIRInrtlVRKKKGGYVIKPPKT-------KSSI 75

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1221422972 121 RIVPLSDpQYVSQLEMMVATLKIpLERKNKKtgrmekariwtitdrtvrtwlseaveaaaadgvtfsvPVTPHTFRHSYA 200
Cdd:cd01189    76 RTIPLPD-ELIELLKELKAFKKL-LKKAGLP-------------------------------------RITPHDLRHTFA 116

                         170       180       190
                  ....*....|....*....|....*....|.
gi 1221422972 201 MHMLYAGIPLKVLQSLMGHKSISST-EVYTK 230
Cdd:cd01189   117 SLLLEAGVPLKVIAERLGHSDISTTlDVYAH 147
xerD PRK00283
tyrosine recombinase;
39-243 8.94e-14

tyrosine recombinase;


Pssm-ID: 234713 [Multi-domain]  Cd Length: 299  Bit Score: 69.45  E-value: 8.94e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1221422972  39 LPKYLLAPEVSALLHYVP-----DLHRKMLLATLWNTGARINEALALNRSDFSLappypfvqlatlkqrTEKATRTAGRa 113
Cdd:PRK00283  110 LPKTLSEAQVEALLDAPDidtplGLRDRAMLELLYATGLRVSELVGLTLDDVSL---------------RQGVVRVTGK- 173

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1221422972 114 paGSQpHRIVPLSdpqyvsqlEMMVATLKIPLERK---------------NKKTGRMEKARIWTItdrtvrtwlseaVEA 178
Cdd:PRK00283  174 --GNK-ERLVPLG--------EEAVYAIERYLERGrpallngrssdalfpSARGGQLTRQTFWHR------------IKH 230

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1221422972 179 AAADGVTFSVPVTPHTFRHSYAMHMLYAGIPLKVLQSLMGHKSISSTEVYTKVfaldvaARHRVQ 243
Cdd:PRK00283  231 YAKRAGIDPKKLSPHVLRHAFATHLLNHGADLRVVQELLGHSDISTTQIYTHV------ATERLK 289
INTN1_C_like cd01185
Integrase IntN1 of Bacteroides mobilizable transposon NBU1 and similar proteins, C-terminal ...
 189-232 3.91e-12

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: 62.67  E-value: 3.91e-12
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 1221422972 189 PVTPHTFRHSYAMHMLYAGIPLKVLQSLMGHKSISSTEVYTKVF 232
Cdd:cd01185   114 HLTFHVARHTFATLLLLKGVDIETISKLLGHSSIKTTQIYAKIV 157
integrase_gron TIGR02249
integron integrase; Members of this family are integrases associated with integrons (and ...
 149-231 6.88e-12

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: 64.34  E-value: 6.88e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1221422972 149 NKKTGRMEKARIW-TITDRTVRtwlsEAVEAAAADGvtfsvPVTPHTFRHSYAMHMLYAGIPLKVLQSLMGHKSISSTEV 227
Cdd:TIGR02249 226 DPESGVIRRHHINeTTIQRAVR----RAVERAGIEK-----PVTCHTLRHSFATHLLESGADIRTVQELLGHSDVKTTQI 296


                  ....
gi 1221422972 228 YTKV 231
Cdd:TIGR02249 297 YTHV 300
INT_tnpA_C_Tn554 cd01186
Putative Transposase A from transposon Tn554, C-terminal catalytic domain; This family ...
 43-225 2.03e-11

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: 61.28  E-value: 2.03e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1221422972  43 LLAPEVSALLHYVPDLHRKMLLATLWNTGARINEALALNRSDFSLAPPYpfvqlATLKQRTEKATrtAGRAPAGSQphRI 122
Cdd:cd01186     2 LTPREVQELINACNNLRDKFLLALLYETGLRIGEALGLRIEDIDMADNQ-----IELVPREDNTN--EARAKSMRE--RR 72

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1221422972 123 VPLSD------PQYVSQLEMMVATLKIPLeRKNKKTGRMEKARIWTITDRTVRTWLSEAveaaaadgvtfSVPVTPHTFR 196
Cdd:cd01186    73 IPVSQdlidlyADYLTYIYCEEAEFSITV-FVNVKGGNQGKAMNYSDVYDLVRRLKKRT-----------GIDFTPHMFR 140

                         170       180
                  ....*....|....*....|....*....
gi 1221422972 197 HSYAMHMLYAGIPLKVLQSLMGHKSISST 225
Cdd:cd01186   141 HTHATALIRAGWSIEVVARRLGHAHVQTT 169
INT_RitA_C_like cd01188
C-terminal catalytic domain of recombinase RitA, a component of the recombinase trio; ...
 166-231 4.05e-08

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: 51.86  E-value: 4.05e-08
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1221422972 166 RTVRTWLSEAveaaaadGVTFSVpVTPHTFRHSYAMHMLYAGIPLKVLQSLMGHKSISSTEVYTKV 231
Cdd:cd01188   112 SIVRRYLRKA-------GIEPSH-RGTHSLRHSLATRMLRAGTSLKVIADLLGHRSIETTAIYAKI 169
xerC PRK01287
site-specific tyrosine recombinase XerC; Reviewed
 162-231 8.26e-08

site-specific tyrosine recombinase XerC; Reviewed


Pssm-ID: 234935 [Multi-domain]  Cd Length: 358  Bit Score: 52.44  E-value: 8.26e-08
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1221422972 162 TITDRTVRTWLSEAVEAAAAdgvtfsvpvtPHTFRHSYAMHMLYAGIPLKVLQSLMGHKSISSTEVYTKV 231
Cdd:PRK01287  247 TLTNMVGRYIRAAGIEKAGA----------CHLFRHAMATQMLENGADTRHIQAILGHAKLETTQIYTRV 306
PRK15417 PRK15417
integron integrase;
39-234 1.06e-07

integron integrase;


Pssm-ID: 185315 [Multi-domain]  Cd Length: 337  Bit Score: 51.97  E-value: 1.06e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1221422972  39 LPKYLLAPEVSALLHYVPDLHRkMLLATLWNTGARINEALALNRSDFSLappypfvQLATLKQRTEKATRT-AGRAPAGS 117
Cdd:PRK15417  113 LPVVLTPDEVVRILGFLEGEHR-LFAQLLYGTGMRISEGLQLRVKDLDF-------DHGTIIVREGKGSKDrALMLPESL 184

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1221422972 118 QPHRIVPLSDPQ--YVSQLEMMVATLKIP--LERKNKKTG------------------RMEKARIWTITDRTVRTWLSEA 175
Cdd:PRK15417  185 APSLREQLSRARawWLKDQAEGRSGVALPdaLERKYPRAGhswpwfwvfaqhthstdpRSGVVRRHHMYDQTFQRAFKRA 264

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1221422972 176 VEAAaadGVTfsVPVTPHTFRHSYAMHMLYAGIPLKVLQSLMGHKSISSTEVYTKVFAL 234
Cdd:PRK15417  265 VEQA---GIT--KPATPHTLRHSFATALLRSGYDIRTVQDLLGHSDVSTTMIYTHVLKV 318
INT_C_like_1 cd01184
Uncharacterized site-specific tyrosine recombinase, C-terminal catalytic domain; Tyrosine ...
 70-230 2.59e-06

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


Pssm-ID: 271184 [Multi-domain]  Cd Length: 180  Bit Score: 46.53  E-value: 2.59e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1221422972  70 TGARINEALALNRSDFSLAPPYPFVQLATlkQRTEKATRT-AGRapagsqphRIVPLSD-------PQYVSQLEmmvATL 141
Cdd:cd01184    35 TGARLNEICQLRVDDIKEEDGIWCIDIND--DAEGRRLKTkASR--------RLVPIHPrlielgfLDYVEALR---ADG 101

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1221422972 142 KIPLER-KNKKTGRMEKAriwtitdrtVRTWLSEAVEAA---AADGVTFsvpvtpHTFRHSYAMHMLYAGIPLKVLQSLM 217
Cdd:cd01184   102 KLFLFPeKRDKDGKYSKA---------ASKWFNRLLRKLgikDDERKSF------HSFRHTFITALKRAGVPEELIAQIV 166

                         170
                  ....*....|....
gi 1221422972 218 GHK-SISSTEVYTK 230
Cdd:cd01184   167 GHSrGGVTHDTYGK 180
xerS PRK05084
site-specific tyrosine recombinase XerS; Reviewed
 186-231 1.33e-05

site-specific tyrosine recombinase XerS; Reviewed


Pssm-ID: 235339 [Multi-domain]  Cd Length: 357  Bit Score: 45.68  E-value: 1.33e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 1221422972 186 FSVPVTPHTFRHSYAMHMLYAGIPLKVLQSLMGHKSISSTEVYTKV 231
Cdd:PRK05084  299 FGVRLTPHKLRHTLATRLYDATKDQVLVADQLGHTSTETTDLYTHI 344
recomb_GmtY NF040693
gamma-mobile-trio recombinase GmtY; GmtY (gamma-mobile-trio system tyrosine recombinase) is a ...
 191-238 1.69e-05

gamma-mobile-trio recombinase GmtY; GmtY (gamma-mobile-trio system tyrosine recombinase) is a putative integrase regularly found associated with two other proteins of unknown function, in a cassette found sporadically in various Gamma-proteobacteria. Members of this family include VPA1270, found in pathogenicity island 6 of Vibrio parahaemolyticus RIMD2210633.


Pssm-ID: 468657 [Multi-domain]  Cd Length: 441  Bit Score: 45.30  E-value: 1.69e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 1221422972 191 TPHTFRHSYAMHMLYAGIPLKVLQSLMGHKSISSTEVYTKVFALDVAA 238
Cdd:NF040693  392 TPHGHRHAYGRRLRNAGVDPLEIQKAMHHKSPESQLVYTQPTAAEVRA 439
FimB COG0582
Integrase/recombinase, includes phage integrase [Replication, recombination and repair, ...
 37-235 9.31e-05

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


Pssm-ID: 440347 [Multi-domain]  Cd Length: 391  Bit Score: 43.10  E-value: 9.31e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1221422972  37 DELPKyLLApevsALLHYVPDLHRKMLLATLWNTGARINEALALNRSDFSLappypfvqlatlkqrtEKA--TRTAGRAP 114
Cdd:COG0582   209 EELPE-LLR----ALDAYRGSPVTRLALRLLLLTGVRPGELRGARWSEIDL----------------EAAlwTIPAERMK 267

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1221422972 115 AGSQphRIVPLSDPqyvsqlemMVATLKiplERKnKKTGRME------KARIWTITDRTVRTWLSEAveaaaadGVTfsv 188
Cdd:COG0582   268 TRRP--HIVPLSRQ--------ALEILK---ELK-PLTGDSEyvfpsrRGPKKPMSENTLNKALRRM-------GYG--- 323

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*...
gi 1221422972 189 PVTPHTFRHSYAMHMLYAGIPLKVLQSLMGHKSISSTE-VYTKVFALD 235
Cdd:COG0582   324 RFTPHGFRHTASTLLNEAGFPPDVIERQLAHKDGNKVRaAYNRADYLE 371
INT_C_like_2 cd01191
Uncharacterized site-specific tyrosine recombinase, C-terminal catalytic domain; Tyrosine ...
 190-228 9.67e-05

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


Pssm-ID: 271191  Cd Length: 176  Bit Score: 42.03  E-value: 9.67e-05
                          10        20        30
                  ....*....|....*....|....*....|....*....
gi 1221422972 190 VTPHTFRHSYAMHMLYAGIPLKVLQSLMGHKSISSTEVY 228
Cdd:cd01191   120 VYPHSFRHRFAKNFLEKYNDIALLADLMGHESIETTRIY 158
INT_tnpB_C_Tn554 cd01187
Putative Transposase B from transposon Tn554, C-terminal catalytic domain; This family ...
 137-228 4.20e-04

Putative Transposase B from transposon Tn554, C-terminal catalytic domain; This family includes putative Transposase B from transposon Tn554. It 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: 271187 [Multi-domain]  Cd Length: 142  Bit Score: 39.72  E-value: 4.20e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1221422972 137 MVATLKIPLerkNKKTGRMEKARIWTITDrtvrtwLSEAVEAAAADGVTFSVpvTPHTFRHSYAMHMLYAGIPLKVLQSL 216
Cdd:cd01187    60 GGKQLDIPI---SKKVAELIKTINWTLNE------LSELKNISDDHGERFRF--HTHRFRHTVATRLANSGMGILVLQQL 128

                          90
                  ....*....|..
gi 1221422972 217 MGHKSISSTEVY 228
Cdd:cd01187   129 LGHSSPEMTLRY 140
PRK09870 PRK09870
tyrosine recombinase; Provisional
 178-229 1.93e-03

tyrosine recombinase; Provisional


Pssm-ID: 182125  Cd Length: 200  Bit Score: 38.38  E-value: 1.93e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1221422972 178 AAAADGVTFSVPVTPHTFRHSYAMHMLYAGIPLKVLQSLMGHKSISSTEVYT 229
Cdd:PRK09870  126 STSGGNAGLSLEIHPHMLRHSCGFALANMGIDTRLIQDYLGHRNIRHTVWYT 177
INT_C_like_4 cd01194
Uncharacterized site-specific tyrosine recombinase, C-terminal catalytic domain; Tyrosine ...
 147-228 3.21e-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: 271194 [Multi-domain]  Cd Length: 174  Bit Score: 37.35  E-value: 3.21e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1221422972 147 RKNKKTGRMekariwtiTDRTVRTWLSEAVEAAAADgvtfSVPVTPHTFRHSYAMHMLYAGIPLKVLQSLMGHKSISSTE 226
Cdd:cd01194   103 SNNSKGQRL--------TTRSIRRIIKKYLRKAGLD----DDRLTAHSLRHTAGTLALKAGKSLREVQQLLRHSDPNTTM 170


                  ..
gi 1221422972 227 VY 228
Cdd:cd01194   171 IY 172
int PHA02601
integrase; Provisional
 30-235 3.31e-03

integrase; Provisional


Pssm-ID: 222904 [Multi-domain]  Cd Length: 333  Bit Score: 38.17  E-value: 3.31e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1221422972  30 RQMA-LVQDELPKYLLAPEVSALlhyvPDLHR--KMLLATlwntGARINEALALNRSDFSlapPY--PFVQLATLKQRTe 104
Cdd:PHA02601  168 PELAfLTKEEIERLLDACDGSRS----PDLGLiaKICLAT----GARWSEAETLKRSQIS---PYkiTFVKTKGKKNRT- 235

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1221422972 105 katrtagrapagsqphriVPLSDPQYvsqlemmvatlkiplERKNKKTGRM-----EKARiwtitdRTVRTWLSEAVEAA 179
Cdd:PHA02601  236 ------------------VPISEELY---------------KMLPKRRGRLfkdayESFE------RAVKRAGIDLPEGQ 276

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1221422972 180 AAdgvtfsvpvtpHTFRHSYAMHMLYAGIPLKVLQSLMGHKSISSTEVYTKvFALD 235
Cdd:PHA02601  277 AT-----------HVLRHTFASHFMMNGGNILVLQRILGHATIEMTMAYAH-FAPD 320
 
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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