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Conserved domains on  [gi|446944290|ref|WP_001021546|]
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MULTISPECIES: site-specific integrase [Bacillus]

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];
53-335 1.55e-44

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


:

Pssm-ID: 443999 [Multi-domain]  Cd Length: 291  Bit Score: 154.38  E-value: 1.55e-44
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446944290  53 DEPSLTKKRSERTKKLYLHDLSHFLRYIKET-IGIIKELSHNEMEIYF-YQLSKKYAATTLRRKKTVVQQFLKYVYDNNG 130
Cdd:COG4974   12 EELKREKGLSPNTIKAYRRDLRRFLRFLEELgKIPLAEITPEDIRAYLnYLRERGLSPSTINRYLAALRSFFRYAVREGL 91

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446944290 131 LSDNFSSRLKKVsvKKEELVNRDLFPEEVNEILDTLKKTNFF---MYSLFFLLTTTGLRIEEVANAKWADLVFHPSLnvy 207
Cdd:COG4974   92 LEDNPAAKVKLP--KKPRKLPRVLTEEEIEALLEALDTETPEglrDRALLLLLYATGLRVSELLGLKWSDIDLDRGT--- 166

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446944290 208 lLRVV-GKGNKTREVRIFEDVLndlchlRQLRKQKSELDASSSSAFLPKADGSHYRADYLSKYVAEKIEETNLPflryrk 286
Cdd:COG4974  167 -IRVRrGKGGKERTVPLSPEAL------EALREYLEERRPRDSDYLFPTRRGRPLSRRAIRKILKRLAKRAGIP------ 233

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|....*....
gi 446944290 287 HRITPHTCRHFFANHLMGKGVELKKIRDYLGHESIMTTERYLRERTRRQ 335
Cdd:COG4974  234 KRVTPHSLRHTFATHLLEAGVDLRTVQELLGHSSISTTQIYTHVSDEEL 282
 
Name Accession Description Interval E-value
XerD COG4974
Site-specific recombinase XerD [Replication, recombination and repair];
53-335 1.55e-44

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


Pssm-ID: 443999 [Multi-domain]  Cd Length: 291  Bit Score: 154.38  E-value: 1.55e-44
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446944290  53 DEPSLTKKRSERTKKLYLHDLSHFLRYIKET-IGIIKELSHNEMEIYF-YQLSKKYAATTLRRKKTVVQQFLKYVYDNNG 130
Cdd:COG4974   12 EELKREKGLSPNTIKAYRRDLRRFLRFLEELgKIPLAEITPEDIRAYLnYLRERGLSPSTINRYLAALRSFFRYAVREGL 91

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446944290 131 LSDNFSSRLKKVsvKKEELVNRDLFPEEVNEILDTLKKTNFF---MYSLFFLLTTTGLRIEEVANAKWADLVFHPSLnvy 207
Cdd:COG4974   92 LEDNPAAKVKLP--KKPRKLPRVLTEEEIEALLEALDTETPEglrDRALLLLLYATGLRVSELLGLKWSDIDLDRGT--- 166

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446944290 208 lLRVV-GKGNKTREVRIFEDVLndlchlRQLRKQKSELDASSSSAFLPKADGSHYRADYLSKYVAEKIEETNLPflryrk 286
Cdd:COG4974  167 -IRVRrGKGGKERTVPLSPEAL------EALREYLEERRPRDSDYLFPTRRGRPLSRRAIRKILKRLAKRAGIP------ 233

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|....*....
gi 446944290 287 HRITPHTCRHFFANHLMGKGVELKKIRDYLGHESIMTTERYLRERTRRQ 335
Cdd:COG4974  234 KRVTPHSLRHTFATHLLEAGVDLRTVQELLGHSSISTTQIYTHVSDEEL 282
DNA_BRE_C cd00397
DNA breaking-rejoining enzymes, C-terminal catalytic domain; The DNA breaking-rejoining enzyme ...
 158-328 6.59e-24

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: 96.40  E-value: 6.59e-24
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446944290 158 EVNEILDTL---KKTNFFMYSLFFLLTTTGLRIEEVANAKWADLVFHpslnVYLLRVVGKG---NKTREVRIFEDVLNDL 231
Cdd:cd00397    1 ELEKLLDAIdedKKIDLRDRAILLLLLETGLRISELLALKVKDIDLD----NGTIRVRGKKtkgGKERTVPLPKELAEEL 76

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446944290 232 chLRQLRKQKSELDASSSSAFLPKADGSHYRADYLSKYVAEKIEETNLPflryRKHRITPHTCRHFFANHLMGKGVELKK 311
Cdd:cd00397   77 --KEYLKERRDKRGPLLKSLYLNKLFGTKLGERLSRRTLRRIFKKAGIE----AGRKITPHSLRHTFATNLLENGVDIKV 150

                        170
                 ....*....|....*..
gi 446944290 312 IRDYLGHESIMTTERYL 328
Cdd:cd00397  151 VQKLLGHSSISTTQRYL 167
xerC PRK00236
site-specific tyrosine recombinase XerC; Reviewed
 59-327 7.08e-23

site-specific tyrosine recombinase XerC; Reviewed


Pssm-ID: 234698 [Multi-domain]  Cd Length: 297  Bit Score: 96.76  E-value: 7.08e-23
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446944290  59 KKRSERTKKLYLHDLSHFLRYIKETIGI-IKELSHNEMEIYFYQLSKK-YAATTLRRKKTVVQQFLKYVYDNNGLSDNFS 136
Cdd:PRK00236  21 RGLSPHTLRAYRRDLRAFLAFLEEHGISsLQDLDAADLRSFLARRRRQgLSARSLARRLSALRSFYRWLVRRGLLKANPA 100

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446944290 137 SRLKkvSVKKEELVNRDLFPEEVNEILDTLKKTNFFM---YSLFFLLTTTGLRIEEVANAKWADLvfhpSLNVYLLRVVG 213
Cdd:PRK00236 101 AGLR--APKIPKRLPKPLDVDQAKRLLDAIDEDDPLAlrdRAILELLYGSGLRLSELVGLDIDDL----DLASGTLRVLG 174

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446944290 214 KGNKTREVRIFEDVLNDLCHLRQLRkqksELDASSSSA-FLpkadGSHYRAdyLSKYVAEKIeetnlpFLRYRKH----- 287
Cdd:PRK00236 175 KGNKERTVPLGRAAREALEAYLALR----PLFLPDDDAlFL----GARGGR--LSPRVVQRR------VKKLGKKaglps 238

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|
gi 446944290 288 RITPHTCRHFFANHLMGKGVELKKIRDYLGHESIMTTERY 327
Cdd:PRK00236 239 HITPHKLRHSFATHLLESGGDLRAVQELLGHASLSTTQIY 278
recomb_XerD TIGR02225
tyrosine recombinase XerD; The phage integrase family describes a number of recombinases with ...
 59-327 1.01e-22

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: 96.11  E-value: 1.01e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446944290   59 KKRSERTKKLYLHDLSHFLRYIKETIGIIKELSHNEMEIYFYQLSK-KYAATTLRRKKTVVQQFLKYVYDNNGLSDNFSS 137
Cdd:TIGR02225  11 RGLSQNTLEAYRRDLEKFLEFLEERGIDLEEVDRGDIVDFLAELKEaGLSARSIARALSALRSFYRFLLREGIREDDPSA 90

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446944290  138 RLK--KVSVKKEELvnrdLFPEEVNEILDTLKKTNFFM---YSLFFLLTTTGLRIEEVANAKWADLvfhpSLNVYLLRVV 212
Cdd:TIGR02225  91 LIEppKVARKLPKV----LTVEEVEALLAAPDVDTPLGlrdRAMLELLYATGLRVSELVGLRLEDV----NLDEGFVRVR 162

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446944290  213 GKGNKTREVRIFEDVLNDL-CHLRQLRKQKSELDASSSSA-FLPKadgshyRADYLS-----KYVAEKIEETNLpflryr 285
Cdd:TIGR02225 163 GKGNKERLVPLGEEAIEALeRYLKEARPLLLKKKVKESDAlFLNR------RGGPLSrqgvwKILKEYAKRAGI------ 230

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|..
gi 446944290  286 KHRITPHTCRHFFANHLMGKGVELKKIRDYLGHESIMTTERY 327
Cdd:TIGR02225 231 EKPISPHTLRHSFATHLLENGADLRVVQELLGHADISTTQIY 272
Phage_integrase pfam00589
Phage integrase family; Members of this family cleave DNA substrates by a series of staggered ...
 154-329 6.70e-17

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: 76.97  E-value: 6.70e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446944290  154 LFPEEVNEILDTLKKTNFFMY--SLFFLLTTTGLRIEEVANAKWADLvfhpSLNVYLLRV-VGKGNKTREVRIFEDVlnd 230
Cdd:pfam00589   2 LTEDEVERLLDAAETGPLSIRdkALLELLYATGLRISELCSLRWSDI----DFENGVIRVhRGKGNKERTVPLSDAA--- 74

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446944290  231 lCHLRQLRKQKSELDASSSSAFLPKADGSHyradyLSKYVAEKIeetnlpFLRYRKH-----RITPHTCRHFFANHLMGK 305
Cdd:pfam00589  75 -LELLKEWLSKRLLEAPKSDYLFASKRGKP-----LSRQTVRKI------FKRAGKEaglelPLHPHMLRHSFATHLLEA 142

                         170       180
                  ....*....|....*....|....
gi 446944290  306 GVELKKIRDYLGHESIMTTERYLR 329
Cdd:pfam00589 143 GVDLRVVQKLLGHSSISTTQIYTH 166
 
Name Accession Description Interval E-value
XerD COG4974
Site-specific recombinase XerD [Replication, recombination and repair];
53-335 1.55e-44

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


Pssm-ID: 443999 [Multi-domain]  Cd Length: 291  Bit Score: 154.38  E-value: 1.55e-44
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446944290  53 DEPSLTKKRSERTKKLYLHDLSHFLRYIKET-IGIIKELSHNEMEIYF-YQLSKKYAATTLRRKKTVVQQFLKYVYDNNG 130
Cdd:COG4974   12 EELKREKGLSPNTIKAYRRDLRRFLRFLEELgKIPLAEITPEDIRAYLnYLRERGLSPSTINRYLAALRSFFRYAVREGL 91

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446944290 131 LSDNFSSRLKKVsvKKEELVNRDLFPEEVNEILDTLKKTNFF---MYSLFFLLTTTGLRIEEVANAKWADLVFHPSLnvy 207
Cdd:COG4974   92 LEDNPAAKVKLP--KKPRKLPRVLTEEEIEALLEALDTETPEglrDRALLLLLYATGLRVSELLGLKWSDIDLDRGT--- 166

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446944290 208 lLRVV-GKGNKTREVRIFEDVLndlchlRQLRKQKSELDASSSSAFLPKADGSHYRADYLSKYVAEKIEETNLPflryrk 286
Cdd:COG4974  167 -IRVRrGKGGKERTVPLSPEAL------EALREYLEERRPRDSDYLFPTRRGRPLSRRAIRKILKRLAKRAGIP------ 233

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|....*....
gi 446944290 287 HRITPHTCRHFFANHLMGKGVELKKIRDYLGHESIMTTERYLRERTRRQ 335
Cdd:COG4974  234 KRVTPHSLRHTFATHLLEAGVDLRTVQELLGHSSISTTQIYTHVSDEEL 282
XerC COG4973
Site-specific recombinase XerC [Replication, recombination and repair];
59-340 2.31e-33

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


Pssm-ID: 443998 [Multi-domain]  Cd Length: 287  Bit Score: 124.69  E-value: 2.31e-33
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446944290  59 KKRSERTKKLYLHDLSHFLRYIKETIGIIKELSHNEMEIYFYQLSKK-YAATTLRRKKTVVQQFLKYVYDNNGLSDNFSS 137
Cdd:COG4973   18 RRLSPKTLEAYRRDLRRLIPLLGDADLPLEELTPADVRRFLARLHRRgLSPRTLNRRLSALRSFFNWAVREGLLEANPAA 97

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446944290 138 RLKKVSVKKEELvnRDLFPEEVNEILDTLKKT--NFFMYSLFFLLTTTGLRIEEVANAKWADLVFHPSLnvylLRVVGKG 215
Cdd:COG4973   98 GVKAPKAPRKLP--RALTVDELAQLLDALADDplAVRDRAIVELLYSTGLRLGELVGLDWEDVDLDAGE----VRVRGKT 171

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446944290 216 NKTREVRIFEDVLNdlcHLRQLRKQKSELDASSSSAFLPKADGSHYRADYLSKYVAEKIEETNLPflryrkHRITPHTCR 295
Cdd:COG4973  172 GKSRTVPLGPKALA---ALREWLAVRPELAAPDEGALFPSRRGTRLSPRNVQKRLRRLAKKAGLP------KHVHPHDLR 242

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|....*
gi 446944290 296 HFFANHLMGKGVELKKIRDYLGHESIMTTERYLRErtRRQNLATI 340
Cdd:COG4973  243 HSFATHLLESGGDLRAVQELLGHASISTTQIYTHL--DFQHLAEV 285
DNA_BRE_C cd00397
DNA breaking-rejoining enzymes, C-terminal catalytic domain; The DNA breaking-rejoining enzyme ...
 158-328 6.59e-24

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: 96.40  E-value: 6.59e-24
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446944290 158 EVNEILDTL---KKTNFFMYSLFFLLTTTGLRIEEVANAKWADLVFHpslnVYLLRVVGKG---NKTREVRIFEDVLNDL 231
Cdd:cd00397    1 ELEKLLDAIdedKKIDLRDRAILLLLLETGLRISELLALKVKDIDLD----NGTIRVRGKKtkgGKERTVPLPKELAEEL 76

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446944290 232 chLRQLRKQKSELDASSSSAFLPKADGSHYRADYLSKYVAEKIEETNLPflryRKHRITPHTCRHFFANHLMGKGVELKK 311
Cdd:cd00397   77 --KEYLKERRDKRGPLLKSLYLNKLFGTKLGERLSRRTLRRIFKKAGIE----AGRKITPHSLRHTFATNLLENGVDIKV 150

                        170
                 ....*....|....*..
gi 446944290 312 IRDYLGHESIMTTERYL 328
Cdd:cd00397  151 VQKLLGHSSISTTQRYL 167
INT_RitC_C_like cd01182
C-terminal catalytic domain of recombinase RitC, a component of the recombinase trio; ...
 154-338 7.38e-24

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: 96.58  E-value: 7.38e-24
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446944290 154 LFPEEVNEIL---DTLKKTNFFMYSLFFLLTTTGLRIEEVANAKWADLVFHpslNVYLLRVVGKGNKTREVRIFEDVLNd 230
Cdd:cd01182    1 LTREEMKALLaapDRNTSLGRRDHALLLLLYDTGARVQELADLTIRDLRLD---DPATVRLHGKGRKERTVPLWKETVA- 76

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446944290 231 lcHLRQLRKQKSELDASSSSAFL-PKADGS----HYRADYLSKYVAEKIEETnlPFLryrKHRITPHTCRHFFANHLMGK 305
Cdd:cd01182   77 --ALKAYLQEFHLTPDPKQLFPLfPNRRGQpltrDGVAYILNKYVALASNRC--PSL---PKRITPHTLRHTKAMHLLQA 149

                        170       180       190
                 ....*....|....*....|....*....|...
gi 446944290 306 GVELKKIRDYLGHESIMTTERYLRERTRRQNLA 338
Cdd:cd01182  150 GVDLTVIRDWLGHESVETTQIYAEADLEMKREA 182
xerC PRK00236
site-specific tyrosine recombinase XerC; Reviewed
 59-327 7.08e-23

site-specific tyrosine recombinase XerC; Reviewed


Pssm-ID: 234698 [Multi-domain]  Cd Length: 297  Bit Score: 96.76  E-value: 7.08e-23
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446944290  59 KKRSERTKKLYLHDLSHFLRYIKETIGI-IKELSHNEMEIYFYQLSKK-YAATTLRRKKTVVQQFLKYVYDNNGLSDNFS 136
Cdd:PRK00236  21 RGLSPHTLRAYRRDLRAFLAFLEEHGISsLQDLDAADLRSFLARRRRQgLSARSLARRLSALRSFYRWLVRRGLLKANPA 100

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446944290 137 SRLKkvSVKKEELVNRDLFPEEVNEILDTLKKTNFFM---YSLFFLLTTTGLRIEEVANAKWADLvfhpSLNVYLLRVVG 213
Cdd:PRK00236 101 AGLR--APKIPKRLPKPLDVDQAKRLLDAIDEDDPLAlrdRAILELLYGSGLRLSELVGLDIDDL----DLASGTLRVLG 174

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446944290 214 KGNKTREVRIFEDVLNDLCHLRQLRkqksELDASSSSA-FLpkadGSHYRAdyLSKYVAEKIeetnlpFLRYRKH----- 287
Cdd:PRK00236 175 KGNKERTVPLGRAAREALEAYLALR----PLFLPDDDAlFL----GARGGR--LSPRVVQRR------VKKLGKKaglps 238

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|
gi 446944290 288 RITPHTCRHFFANHLMGKGVELKKIRDYLGHESIMTTERY 327
Cdd:PRK00236 239 HITPHKLRHSFATHLLESGGDLRAVQELLGHASLSTTQIY 278
recomb_XerD TIGR02225
tyrosine recombinase XerD; The phage integrase family describes a number of recombinases with ...
 59-327 1.01e-22

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: 96.11  E-value: 1.01e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446944290   59 KKRSERTKKLYLHDLSHFLRYIKETIGIIKELSHNEMEIYFYQLSK-KYAATTLRRKKTVVQQFLKYVYDNNGLSDNFSS 137
Cdd:TIGR02225  11 RGLSQNTLEAYRRDLEKFLEFLEERGIDLEEVDRGDIVDFLAELKEaGLSARSIARALSALRSFYRFLLREGIREDDPSA 90

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446944290  138 RLK--KVSVKKEELvnrdLFPEEVNEILDTLKKTNFFM---YSLFFLLTTTGLRIEEVANAKWADLvfhpSLNVYLLRVV 212
Cdd:TIGR02225  91 LIEppKVARKLPKV----LTVEEVEALLAAPDVDTPLGlrdRAMLELLYATGLRVSELVGLRLEDV----NLDEGFVRVR 162

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446944290  213 GKGNKTREVRIFEDVLNDL-CHLRQLRKQKSELDASSSSA-FLPKadgshyRADYLS-----KYVAEKIEETNLpflryr 285
Cdd:TIGR02225 163 GKGNKERLVPLGEEAIEALeRYLKEARPLLLKKKVKESDAlFLNR------RGGPLSrqgvwKILKEYAKRAGI------ 230

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|..
gi 446944290  286 KHRITPHTCRHFFANHLMGKGVELKKIRDYLGHESIMTTERY 327
Cdd:TIGR02225 231 EKPISPHTLRHSFATHLLENGADLRVVQELLGHADISTTQIY 272
INT_IntI_C cd01193
Integron integrase and similar protiens, C-terminal catalytic domain; Integron integrases ...
 154-329 9.80e-22

Integron integrase and similar protiens, C-terminal catalytic domain; Integron integrases mediate site-specific DNA recombination between a proximal primary site (attI) and a secondary target site (attC) found within mobile gene cassettes encoding resistance or virulence factors. Unlike other site specific recombinases, the attC sites lack sequence conservation. Integron integrase exhibits broader DNA specificity by recognizing the non-conserved attC sites. The structure shows that DNA target site recognition are not dependent on canonical DNA but on the position of two flipped-out bases that interact in cis and in trans with the integrase. Integron-integrases are present in many natural occurring mobile elements, including transposons and conjugative plasmids. Vibrio, Shewanella, Xanthomonas, and Pseudomonas species harbor chromosomal super-integrons. All integron-integrases carry large inserts unlike the TnpF ermF-like proteins also seen in this group.


Pssm-ID: 271193 [Multi-domain]  Cd Length: 176  Bit Score: 90.80  E-value: 9.80e-22
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446944290 154 LFPEEVNEILDTLkkTNFFMYSLFFLLTTTGLRIEEVANAKWADLVFHPSLnvylLRV-VGKGNKTREVRIFEDVLNDLC 232
Cdd:cd01193    6 LSPDEVRRILGAL--TELRHRLILSLLYGAGLRISELLRLRVKDIDFERGV----IRVrQGKGGKDRVVPLPEKLLEPLR 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446944290 233 HLRQLRKQKSELDASSSSAFLPKADGS-----HYRADYLSKYVAEKIEETNLpflryrKHRITPHTCRHFFANHLMGKGV 307
Cdd:cd01193   80 RYLKSARPKEELDPAEGRAGVLDPRTGverrhHISETTVQRALKKAVEQAGI------TKRVTPHTLRHSFATHLLEAGT 153

                        170       180
                 ....*....|....*....|..
gi 446944290 308 ELKKIRDYLGHESIMTTERYLR 329
Cdd:cd01193  154 DIRTIQELLGHSDLSTTMIYTH 175
INT_XerDC_C cd00798
XerD and XerC integrases, C-terminal catalytic domains; XerDC-like integrases are involved in ...
 157-327 1.56e-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: 87.18  E-value: 1.56e-20
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446944290 157 EEVNEILDTLKKTNFFMY---SLFFLLTTTGLRIEEVANAKWADLVFHPSLnvylLRVVGKGNKTREVRIFE---DVLND 230
Cdd:cd00798    2 DEVERLLDAPDTDTPLGLrdrAILELLYASGLRVSELVGLDLSDVDLDEGL----VRVTGKGNKERLVPFGSyavEALEE 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446944290 231 -LCHLRQLRKQKSELDAssssAFLPKadgshyRADYLSKYVAEKI-----EETNLPflryrKHrITPHTCRHFFANHLMG 304
Cdd:cd00798   78 yLEERRPLLLKKKPPDA----LFLNK------RGKRLSRRGVWRIlkkyaERAGLP-----KH-VSPHTLRHSFATHLLE 141

                        170       180
                 ....*....|....*....|...
gi 446944290 305 KGVELKKIRDYLGHESIMTTERY 327
Cdd:cd00798  142 GGADLRVVQELLGHASLSTTQIY 164
INT_Rci_Hp1_C cd00796
Shufflon-specific DNA recombinase Rci and Bacteriophage Hp1_like integrase, C-terminal ...
 152-329 1.37e-17

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: 1.37e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446944290 152 RDLFPEEVNEILDTLKKTNFFMYSLFFLLT-TTGLRIEEVANAKWADLVFhpslNVYLLRVVG-KGNKTREVRIfedvLN 229
Cdd:cd00796    3 RFLTEDEEARLLAALEESTNPHLRLIVLLAlYTGARRGEILSLRWDDIDL----EVGLIVLPEtKNGKPRTVPL----SD 74

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446944290 230 DLCHLRQLRKQKSELDAssssaFLPKADGSHYRADYLSKYVAEKIEETNLPFLRyrkhritPHTCRHFFANHLMGKGVEL 309
Cdd:cd00796   75 EAIAILKELKRKRGKDG-----FFVDGRFFGIPIASLRRAFKKARKRAGLEDLR-------FHDLRHTFASRLVQAGVPI 142

                        170       180
                 ....*....|....*....|
gi 446944290 310 KKIRDYLGHESIMTTERYLR 329
Cdd:cd00796  143 KTVAKILGHSSIKMTMRYAH 162
xerD PRK00283
tyrosine recombinase;
69-334 3.73e-17

tyrosine recombinase;


Pssm-ID: 234713 [Multi-domain]  Cd Length: 299  Bit Score: 80.62  E-value: 3.73e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446944290  69 YLHDLSHFLRYIKETIGIIKELSHNEMEIYFYQLSK-KYAATTLRRKKTVVQQFLKYVYDNNGLSDNFSSRLKkvSVKKE 147
Cdd:PRK00283  30 YRRDLELFAEWLAARGLSLAEATRDDLQAFLAELAEgGYKATSSARRLSALRRFFQFLLREGLREDDPSALLD--SPKLP 107

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446944290 148 ELVNRDLFPEEVNEILDTLKKTNFF---MYSLFFLLTTTGLRIEEVANAKWADLvfhpSLNVYLLRVVGKGNKTREVrif 224
Cdd:PRK00283 108 RRLPKTLSEAQVEALLDAPDIDTPLglrDRAMLELLYATGLRVSELVGLTLDDV----SLRQGVVRVTGKGNKERLV--- 180

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446944290 225 edVLNDLCH------LRQLRKQKseLDASSSSAFLPKAdgshyRADYLSKYVAEKI-----EETNLpflryRKHRITPHT 293
Cdd:PRK00283 181 --PLGEEAVyaieryLERGRPAL--LNGRSSDALFPSA-----RGGQLTRQTFWHRikhyaKRAGI-----DPKKLSPHV 246

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|....
gi 446944290 294 CRHFFANHLMGKGVELKKIRDYLGHESIMTTERY---LRERTRR 334
Cdd:PRK00283 247 LRHAFATHLLNHGADLRVVQELLGHSDISTTQIYthvATERLKE 290
Phage_integrase pfam00589
Phage integrase family; Members of this family cleave DNA substrates by a series of staggered ...
 154-329 6.70e-17

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: 76.97  E-value: 6.70e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446944290  154 LFPEEVNEILDTLKKTNFFMY--SLFFLLTTTGLRIEEVANAKWADLvfhpSLNVYLLRV-VGKGNKTREVRIFEDVlnd 230
Cdd:pfam00589   2 LTEDEVERLLDAAETGPLSIRdkALLELLYATGLRISELCSLRWSDI----DFENGVIRVhRGKGNKERTVPLSDAA--- 74

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446944290  231 lCHLRQLRKQKSELDASSSSAFLPKADGSHyradyLSKYVAEKIeetnlpFLRYRKH-----RITPHTCRHFFANHLMGK 305
Cdd:pfam00589  75 -LELLKEWLSKRLLEAPKSDYLFASKRGKP-----LSRQTVRKI------FKRAGKEaglelPLHPHMLRHSFATHLLEA 142

                         170       180
                  ....*....|....*....|....
gi 446944290  306 GVELKKIRDYLGHESIMTTERYLR 329
Cdd:pfam00589 143 GVDLRVVQKLLGHSSISTTQIYTH 166
INT_RitB_C_like cd00797
C-terminal catalytic domain of recombinase RitB, a component of the recombinase trio; ...
 173-328 4.01e-13

C-terminal catalytic domain of recombinase RitB, 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: 271178 [Multi-domain]  Cd Length: 198  Bit Score: 67.33  E-value: 4.01e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446944290 173 MYSLFFLLTTTGLRIEEVANAKWADlvFHPSLNVYLLRvVGKGNKTREVRIFEDVLNDLCHLRQLRKQKSelDASSSSAF 252
Cdd:cd00797   27 YATLFGLLYATGLRVGEALRLRLED--VDLDSGILTIR-QTKFGKSRLVPLHPSTVGALRDYLARRDRLL--PSPSSSYF 101

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446944290 253 LPKADGSHYRADYLSKYVAEKIEETNLPFLRyRKHRITPHTCRHFFANHLM------GKGVE--LKKIRDYLGHESIMTT 324
Cdd:cd00797  102 FVSQQGGRLTGGGVYRVFRRLLRRIGLRGAG-DGRGPRLHDLRHTFAVNRLtrwyreGADVErkLPVLSTYLGHVNVTDT 180


                 ....
gi 446944290 325 ERYL 328
Cdd:cd00797  181 YWYL 184
INT_ICEBs1_C_like cd01189
C-terminal catalytic domain of integrases from bacterial phages and conjugate transposons; ...
 156-327 5.22e-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: 65.66  E-value: 5.22e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446944290 156 PEEVNEILDTLKKTNFFMYSLFFLLTTTGLRIEEVANAKWADLVFhpslnvyllrvvgkgnKTREVRIFEDVLNDLCHLR 235
Cdd:cd01189    1 PEELKKLLEALKKRGDRYYLLFLLALLTGLRRGELLALTWSDIDF----------------ENGTIRINRTLVRKKKGGY 64

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446944290 236 QLRKQKSEldassssaflpkadgSHYRADYLSKYVAEKIEEtnlpFLRYRKH-------RITPHTCRHFFANHLMGKGVE 308
Cdd:cd01189   65 VIKPPKTK---------------SSIRTIPLPDELIELLKE----LKAFKKLlkkaglpRITPHDLRHTFASLLLEAGVP 125

                        170
                 ....*....|....*....
gi 446944290 309 LKKIRDYLGHESIMTTERY 327
Cdd:cd01189  126 LKVIAERLGHSDISTTLDV 144
xerS PRK05084
site-specific tyrosine recombinase XerS; Reviewed
 179-327 1.56e-10

site-specific tyrosine recombinase XerS; Reviewed


Pssm-ID: 235339 [Multi-domain]  Cd Length: 357  Bit Score: 61.47  E-value: 1.56e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446944290 179 LLTTTGLRIEEVANAKWADLVFhpslNVYLLRVVGKGNKTREVRIFEDVLNDLCHLRQLRKQKSELDASSSSAFLPKADG 258
Cdd:PRK05084 203 LILGSGLRVSELVNLDLSDLNL----KQMTIDVTRKGGKRDSVNIAPFALPYLEEYLKIRASRYKAEKQEKALFLTKYRG 278

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 446944290 259 SHYRadyLSKYVAEKIeetnlpFLRYR---KHRITPHTCRHFFANHLMGKGVELKKIRDYLGHESIMTTERY 327
Cdd:PRK05084 279 KPNR---ISARAIEKM------VAKYSeafGVRLTPHKLRHTLATRLYDATKDQVLVADQLGHTSTETTDLY 341
INT_RitA_C_like cd01188
C-terminal catalytic domain of recombinase RitA, a component of the recombinase trio; ...
 174-329 1.78e-10

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: 59.18  E-value: 1.78e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446944290 174 YSLFFLLTTTGLRIEEVANAKWADlvFHPSLNVylLRVVG-KGNKTREVRIFEDVLNDLCHLRQLRKQKSELDASSSSAF 252
Cdd:cd01188   23 YAILLLLARLGLRAGDVAGLRLDD--IDWRSGT--ITVRQkKTGRPVELPLTEPVGEALADYLRDGRPRTDSREVFLRAR 98

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 446944290 253 LPKadGSHYRADYLSKYVAEKIEETNLPflryrKHRITPHTCRHFFANHLMGKGVELKKIRDYLGHESIMTTERYLR 329
Cdd:cd01188   99 APY--RPLSSTSQISSIVRRYLRKAGIE-----PSHRGTHSLRHSLATRMLRAGTSLKVIADLLGHRSIETTAIYAK 168
integrase_gron TIGR02249
integron integrase; Members of this family are integrases associated with integrons (and ...
 58-327 6.74e-09

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: 56.25  E-value: 6.74e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446944290   58 TKKRSERTKKLYLHDLSHFLRYIKetIGIIKELSHNEMEIYFYQL--SKKYAATTLRRKKTVVQQFLKYVYDNN-GLSDN 134
Cdd:TIGR02249  11 TRHYAKRTEEAYLHWIKRFIRFHN--KRHPSTMGDTEVEAFLSDLavDGKVAASTQNQALNALLFLYKEILKTPlSLMER 88

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446944290  135 FssrlkkVSVKKEELVNRDLFPEEVNEILDTLKKTNFFMYSLfflLTTTGLRIEEVANAKWADLVFhpslnVYLLRVV-- 212
Cdd:TIGR02249  89 F------VRAKRPRKLPVVLTREEVRRLLEHLEGKYRLIAKL---LYGSGMRLMECLRLRIQDIDF-----DYGEIRIrq 154

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446944290  213 GKGNKTREVRIFEDVLNDLCHLRQLRKQKSELDASS--SSAFLPKADGSHY-RADY------------------------ 265
Cdd:TIGR02249 155 GKGGKDRTVTLPKELIPPLREQIELARAYHEADLAEgyGGVYLPHALARKYpNAPKewgwqylfpshrlsrdpesgvirr 234

                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 446944290  266 -------LSKYVAEKIEETNLPflryrKHrITPHTCRHFFANHLMGKGVELKKIRDYLGHESIMTTERY 327
Cdd:TIGR02249 235 hhinettIQRAVRRAVERAGIE-----KP-VTCHTLRHSFATHLLESGADIRTVQELLGHSDVKTTQIY 297
xerD PRK02436
site-specific tyrosine recombinase XerD;
59-329 2.39e-08

site-specific tyrosine recombinase XerD;


Pssm-ID: 235038 [Multi-domain]  Cd Length: 245  Bit Score: 54.22  E-value: 2.39e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446944290  59 KKRSERTKKLYLHDLSHFLRYIKEtigiikELSHNEMEIYFYQLSKkYAATTLRRKKTVVQQFLKYVYDNNGLSDNFssR 138
Cdd:PRK02436  12 KQLSENSQKSYRYDLQQFLQLVGE------RVSQEKLKLYQQSLAN-LKPSAQKRKISAVNQFLYFLYQKGELDSFF--K 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446944290 139 LKKVSVKKEElvnrdlfPEEVNEILDTlkkTNFFMYS-------LFFLLTTTGLRIEEVANAKWADLvfhpSLNVYLLRV 211
Cdd:PRK02436  83 LKETAKLPES-------KKEKLEILDL---SSFYQETpfpegqlIALLILELGLTPSEIAGLKVADI----DLDFQVLTI 148

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446944290 212 VGKGNKtREVRIFEDVLndlchlrqlrkqkSELDASSSSAFLPKADGSHYRADYLSKYVAEKIEETNLPFLryrkhriTP 291
Cdd:PRK02436 149 EKAGGK-RVLTLPEALL-------------PFLEAILNQTYLFEHKGKPYSRQWFFNQLKSFVKSIGYPGL-------SA 207

                        250       260       270
                 ....*....|....*....|....*....|....*...
gi 446944290 292 HTCRHFFANHLMGKGVELKKIRDYLGHESIMTTERYLR 329
Cdd:PRK02436 208 QKLREQFILKQKEAGKSIYELARLLGLKSPVTLEKYYK 245
FimB COG0582
Integrase/recombinase, includes phage integrase [Replication, recombination and repair, ...
 59-331 1.54e-07

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


Pssm-ID: 440347 [Multi-domain]  Cd Length: 391  Bit Score: 52.73  E-value: 1.54e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446944290  59 KKRSERTKKLYLhdlSHFLRYIKETIG--IIKELSHNEMEIYFYQLSKKYAATTLRRKKTVVQQFLKYVYDNNGLSDNFS 136
Cdd:COG0582  112 PEWKEKTAAQVR---RTLEKHIFPVLGdrPIAEITPPDLLAVLRPIEARGAPETARRVRQRLRQVFRYAVARGLIERNPA 188

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446944290 137 SRLKKVSVKKEELVNRDLFPEEVNEILDTLK--KTNFFMYSLFFLLTTTGLRIEEVANAKWADLVFHPSlnvyLLRVVGK 214
Cdd:COG0582  189 ADLKGALPKPKVKHHPALTPEELPELLRALDayRGSPVTRLALRLLLLTGVRPGELRGARWSEIDLEAA----LWTIPAE 264

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446944290 215 GNKTREVRIfedV-LNDLChLRQLRKQKselDASSSSAFL-PkadGSHYRADYLSKYVAEKIeetnLPFLRYRkhRITPH 292
Cdd:COG0582  265 RMKTRRPHI---VpLSRQA-LEILKELK---PLTGDSEYVfP---SRRGPKKPMSENTLNKA----LRRMGYG--RFTPH 328

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|....*
gi 446944290 293 TCRHFFANHLMGKGVELKKIRDYLGHESIMTTER------YLRER 331
Cdd:COG0582  329 GFRHTASTLLNEAGFPPDVIERQLAHKDGNKVRAaynradYLEER 373
INTN1_C_like cd01185
Integrase IntN1 of Bacteroides mobilizable transposon NBU1 and similar proteins, C-terminal ...
 285-329 3.77e-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: 49.18  E-value: 3.77e-07
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*
gi 446944290 285 RKHrITPHTCRHFFANHLMGKGVELKKIRDYLGHESIMTTERYLR 329
Cdd:cd01185  112 DKH-LTFHVARHTFATLLLLKGVDIETISKLLGHSSIKTTQIYAK 155
xerC PRK01287
site-specific tyrosine recombinase XerC; Reviewed
 179-329 7.18e-07

site-specific tyrosine recombinase XerC; Reviewed


Pssm-ID: 234935 [Multi-domain]  Cd Length: 358  Bit Score: 50.51  E-value: 7.18e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446944290 179 LLTTTGLRIEEVANAKWADLVFHPSLnvyLLRVVGKGNKTREVRIFEDVLNDLCH-LRQLRKQKseLDASSSSAFLPKAD 257
Cdd:PRK01287 165 LLWSTGIRRGELARLDLYDVDASRGV---VTVRQGKGNKDRVVPVGERALAWLQRyLQDVRPQL--AVRPDSGALFVAMD 239

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 446944290 258 GSHYRADYLSKYVAEKIEETNLpflryrKHRITPHTCRHFFANHLMGKGVELKKIRDYLGHESIMTTERYLR 329
Cdd:PRK01287 240 GDGLARNTLTNMVGRYIRAAGI------EKAGACHLFRHAMATQMLENGADTRHIQAILGHAKLETTQIYTR 305
PRK15417 PRK15417
integron integrase;
62-329 1.51e-05

integron integrase;


Pssm-ID: 185315 [Multi-domain]  Cd Length: 337  Bit Score: 46.19  E-value: 1.51e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446944290  62 SERTKKLYLHDLSHFLRYikETIGIIKELSHNEMEIYFYQLS--KKYAATTLRRKKTVVQQFLKYVY--DNNGLSD---- 133
Cdd:PRK15417  30 SLRTEQAYVHWVRAFIRF--HGVRHPATLGSSEVEAFLSWLAneRKVSVSTHRQALAALLFFYGKVLctDLPWLQEigrp 107

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446944290 134 NFSSRLKKVsvkkeelvnrdLFPEEVNEILDTLKKTNFFMYSLFFlltTTGLRIEEVANAKWADLVF-HPSLNVYllrvV 212
Cdd:PRK15417 108 RPSRRLPVV-----------LTPDEVVRILGFLEGEHRLFAQLLY---GTGMRISEGLQLRVKDLDFdHGTIIVR----E 169

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446944290 213 GKGNKTREVRIFEDVLNDLchLRQLRKQKS----ELDASSSSAFLPKADGSHY-RADYLSKYV---AEKIEETNLPFLRY 284
Cdd:PRK15417 170 GKGSKDRALMLPESLAPSL--REQLSRARAwwlkDQAEGRSGVALPDALERKYpRAGHSWPWFwvfAQHTHSTDPRSGVV 247

                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 446944290 285 RKHRI----------------------TPHTCRHFFANHLMGKGVELKKIRDYLGHESIMTTERYLR 329
Cdd:PRK15417 248 RRHHMydqtfqrafkraveqagitkpaTPHTLRHSFATALLRSGYDIRTVQDLLGHSDVSTTMIYTH 314
INT_C_like_3 cd01192
Uncharacterized site-specific tyrosine recombinase, C-terminal catalytic domain; Tyrosine ...
 157-328 1.89e-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: 271192 [Multi-domain]  Cd Length: 178  Bit Score: 44.59  E-value: 1.89e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446944290 157 EEVNEILDTLKKTNFFMYSLFFLLTTTGLRIEEVANAKWADLvfhpsLNVYLLRVvgKGNKTREVRIFEdvLNDLCH--L 234
Cdd:cd01192   10 KLIKEIKLYLKKANPRNYLLFIVGINTGLRISDLLSLKVEDV-----TNKDKLSI--KEQKTGKQKTFP--LNPTLVkaL 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446944290 235 RQLRKQKSELDASSSSAFLPKADGSHYRADYLSKYVAEKIEETNLPflryrkHRITPHTCRHFFANHLMGKGVELKKIRD 314
Cdd:cd01192   81 KEYIDDLDLKRNDYLFKSLKQGPEKPISRKQAYKILKKAADDLGLN------YNIGTHSLRKTFGYHVYKQGKDIELLMK 154

                        170
                 ....*....|....
gi 446944290 315 YLGHESIMTTERYL 328
Cdd:cd01192  155 LLNHSSPSITLRYL 168
COG4342 COG4342
Phage integrase/recombinase [Mobilome: prophages, transposons];
57-190 8.44e-05

Phage integrase/recombinase [Mobilome: prophages, transposons];


Pssm-ID: 443483 [Multi-domain]  Cd Length: 278  Bit Score: 43.55  E-value: 8.44e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446944290  57 LTKKRSERTKKLYLhdlshflRYIKETIGIIKELSHNEMEIYFYqlsKKYAATTLRRkktvvqqFLKYVYDNNGLSDNFS 136
Cdd:COG4342   30 LVKRVSEKTAKDYI-------SALDRYLSILTPEDLREIELAKE---KKNLVKALRN-------LANFLVERGIISEEVA 92

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 446944290 137 SRLKKVSVKKEELVnRDLFP--EEVNEILDTLKKTNFFMYSLFFLLTTTGLRIEEV 190
Cdd:COG4342   93 EKIKEVLKVKRSGV-DLYVPtdEEIREALKYLKEKDEEVYLLYKLLLFSGLRLSEA 147
INT_tnpA_C_Tn554 cd01186
Putative Transposase A from transposon Tn554, C-terminal catalytic domain; This family ...
 154-324 2.16e-04

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: 41.63  E-value: 2.16e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446944290 154 LFPEEVNEILDT--LKKTNFfmysLFFLLTTTGLRIEEVANAKWADLVFhpSLNVylLRVVGKGNKTREVRIfedvlndl 231
Cdd:cd01186    2 LTPREVQELINAcnNLRDKF----LLALLYETGLRIGEALGLRIEDIDM--ADNQ--IELVPREDNTNEARA-------- 65

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446944290 232 chlrQLRKQKSeLDASSS--SAFLPKADGSHYRADYLSKYVAEKIEETNLP-----------FLRYRKH---RITPHTCR 295
Cdd:cd01186   66 ----KSMRERR-IPVSQDliDLYADYLTYIYCEEAEFSITVFVNVKGGNQGkamnysdvydlVRRLKKRtgiDFTPHMFR 140

                        170       180
                 ....*....|....*....|....*....
gi 446944290 296 HFFANHLMGKGVELKKIRDYLGHESIMTT 324
Cdd:cd01186  141 HTHATALIRAGWSIEVVARRLGHAHVQTT 169
INT_C_like_1 cd01184
Uncharacterized site-specific tyrosine recombinase, C-terminal catalytic domain; Tyrosine ...
 156-327 2.36e-04

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: 41.52  E-value: 2.36e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446944290 156 PEEVNEILDTLKKTNF-----FMYSLFFLLTTTGLRIEEVANAKWADLVFHPSLNVYLLRVVGKGNKT------REVRIF 224
Cdd:cd01184    3 PEELAKIFSSPLYTGCkkkdpALYWLPLIGLYTGARLNEICQLRVDDIKEEDGIWCIDINDDAEGRRLktkasrRLVPIH 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446944290 225 EDVLND--LCHLRQLRKQKSELDassssaFLPKADGSHYRADYLSKyvaekieetnlPFLRYRK-------HRITPHTCR 295
Cdd:cd01184   83 PRLIELgfLDYVEALRADGKLFL------FPEKRDKDGKYSKAASK-----------WFNRLLRklgikddERKSFHSFR 145

                        170       180       190
                 ....*....|....*....|....*....|...
gi 446944290 296 HFFANHLMGKGVELKKIRDYLGHE-SIMTTERY 327
Cdd:cd01184  146 HTFITALKRAGVPEELIAQIVGHSrGGVTHDTY 178
int PHA02601
integrase; Provisional
 154-327 3.62e-04

integrase; Provisional


Pssm-ID: 222904 [Multi-domain]  Cd Length: 333  Bit Score: 42.02  E-value: 3.62e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446944290 154 LFPEEVNEILDTLKKTNFFMYSLFFLLT-TTGLRIEEVANAKWADLVfhpslNVYLLRVVGKGNKTREVRIFEDVLNdlc 232
Cdd:PHA02601 173 LTKEEIERLLDACDGSRSPDLGLIAKIClATGARWSEAETLKRSQIS-----PYKITFVKTKGKKNRTVPISEELYK--- 244

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446944290 233 hlrqlrkqkseldassssaFLPKADGSHYRADYLSKYVAEKIEETNLPflryrKHRITpHTCRHFFANHLMGKGVELKKI 312
Cdd:PHA02601 245 -------------------MLPKRRGRLFKDAYESFERAVKRAGIDLP-----EGQAT-HVLRHTFASHFMMNGGNILVL 299

                        170
                 ....*....|....*
gi 446944290 313 RDYLGHESIMTTERY 327
Cdd:PHA02601 300 QRILGHATIEMTMAY 314
INT_C_like_2 cd01191
Uncharacterized site-specific tyrosine recombinase, C-terminal catalytic domain; Tyrosine ...
 289-341 1.23e-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: 39.33  E-value: 1.23e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 446944290 289 ITPHTCRHFFANHLMGKGVELKKIRDYLGHESIMTTERYLReRTRRQNLATID 341
Cdd:cd01191  120 VYPHSFRHRFAKNFLEKYNDIALLADLMGHESIETTRIYLR-KTASEQQEIVD 171
INT_Cre_C cd00799
C-terminal catalytic domain of Cre recombinase (also called integrase); Cre-like recombinases ...
 183-339 2.55e-03

C-terminal catalytic domain of Cre recombinase (also called integrase); Cre-like recombinases are tyrosine based site specific recombinases. They belong to the superfamily of DNA breaking-rejoining enzymes, which share the same fold in their catalytic domain and the overall reaction mechanism. The bacteriophage P1 Cre recombinase maintains the circular phage replicon in a monomeric state by catalyzing a site-specific recombination between two loxP sites. The catalytic core domain of Cre recombinase is linked to a more divergent helical N-terminal domain, which interacts primarily with the DNA major groove proximal to the crossover region.


Pssm-ID: 271180  Cd Length: 188  Bit Score: 38.43  E-value: 2.55e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446944290 183 TGLRIEEVANAKWADLVF--HPSLNVYLLRvvGKGNKTRE-VRIFEDVLNDLCHLRQLRKQKSELDASSSSAFLPKADGS 259
Cdd:cd00799   28 GALRRSELVALRVEDLTRfvDGGLLIRLRR--SKTDQDGEgEIKALPYGPETCPVRALRAWLEAAGIPSGPLFRRIRRGG 105

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446944290 260 HYRADYLS-KYVAEKIEET-NLPFLRYRkhRITPHTCRHFFANHLMGKGVELKKIRDYLGHESIMTTERYLRERTR-RQN 336
Cdd:cd00799  106 SVGTTRLSdRSVARIVKRRaALAGLDPG--DFSGHSLRRGFATEAARAGASLPEIMAQGGHKSVATVMRYIREADRfKDN 183


                 ...
gi 446944290 337 LAT 339
Cdd:cd00799  184 AAA 186
INT_P4_C cd00801
Bacteriophage P4 integrase, C-terminal catalytic domain; P4-like integrases are found in ...
 156-200 4.82e-03

Bacteriophage P4 integrase, C-terminal catalytic domain; P4-like integrases are found in temperate bacteriophages, integrative plasmids, pathogenicity and symbiosis islands, and other mobile genetic elements. The P4 integrase mediates integrative and excisive site-specific recombination between two sites, called attachment sites, located on the phage genome and the bacterial chromosome. The phage attachment site is often found adjacent to the integrase gene, while the host attachment sites are typically situated near tRNA genes. 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: 271182 [Multi-domain]  Cd Length: 180  Bit Score: 37.63  E-value: 4.82e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
gi 446944290 156 PEEVNEILDTLKKTN--FFMYSLFFLLTTTGLRIEEVANAKWADLVF 200
Cdd:cd00801    2 PDELPELWRALDTANlsPPTKLALRLLLLTGQRIGELARARWSEIDL 48
Phage_int_SAM_1 pfam02899
Phage integrase, N-terminal SAM-like domain;
56-124 9.77e-03

Phage integrase, N-terminal SAM-like domain;


Pssm-ID: 427047 [Multi-domain]  Cd Length: 83  Bit Score: 34.93  E-value: 9.77e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446944290   56 SLTKKRSERTKKLYLHDLSHFLRYIKETIGIIKELSHNEMEIYFYQLSKK-YAATTLRRKKTVVQQFLKY 124
Cdd:pfam02899   9 SLERGLSPHTLRAYRRDLLAFLKFLSEGGSSLEQITTSDVRAFLAELRAQgLSASSLARRLSALRSFYQF 78
 
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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