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Conserved domains on  [gi|1025816214|gb|ANC66333|]
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putative site-specific recombinase [Actinobacillus pleuropneumoniae]

Protein Classification

similar to tyrosine recombinase XerD( domain architecture ID 11471964)

protein similar to tyrosine recombinase XerD

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];
4-298 3.22e-40

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


:

Pssm-ID: 443999 [Multi-domain]  Cd Length: 291  Bit Score: 141.67  E-value: 3.22e-40
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1025816214   4 TTFDMLLSKFFLY----RHLRIDTIKSYEKAVRQLQKNCS---LQYPDEISELLILQWRKRVVGQSIIEVTWNSYIRQLK 76
Cdd:COG4974     1 LTLADLLEAFLEElkreKGLSPNTIKAYRRDLRRFLRFLEelgKIPLAEITPEDIRAYLNYLRERGLSPSTINRYLAALR 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1025816214  77 TIFKFGIEKQLLpfTKNPFDGL-FIREGKKKRKVYTSSDLKKLSFGITESKHLPPILRplwftkTIIMTFRYTAIRRSQL 155
Cdd:COG4974    81 SFFRYAVREGLL--EDNPAAKVkLPKKPRKLPRVLTEEEIEALLEALDTETPEGLRDR------ALLLLLYATGLRVSEL 152

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1025816214 156 NKLRIKDVDLLNQVIHIPSEinKNHEYHILPISttlyPYLKKLLTELSKLNQPVESQLfninLFSNavkRKGEKMTNNQV 235
Cdd:COG4974   153 LGLKWSDIDLDRGTIRVRRG--KGGKERTVPLS----PEALEALREYLEERRPRDSDY----LFPT---RRGRPLSRRAI 219

                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1025816214 236 SYIFKVISKYTGIIS--SPHRFRHTAATNLMKKPENLYIAKQLLGHKDVKVTLSYIEDNIDSIRE 298
Cdd:COG4974   220 RKILKRLAKRAGIPKrvTPHSLRHTFATHLLEAGVDLRTVQELLGHSSISTTQIYTHVSDEELRE 284
 
Name Accession Description Interval E-value
XerD COG4974
Site-specific recombinase XerD [Replication, recombination and repair];
4-298 3.22e-40

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


Pssm-ID: 443999 [Multi-domain]  Cd Length: 291  Bit Score: 141.67  E-value: 3.22e-40
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1025816214   4 TTFDMLLSKFFLY----RHLRIDTIKSYEKAVRQLQKNCS---LQYPDEISELLILQWRKRVVGQSIIEVTWNSYIRQLK 76
Cdd:COG4974     1 LTLADLLEAFLEElkreKGLSPNTIKAYRRDLRRFLRFLEelgKIPLAEITPEDIRAYLNYLRERGLSPSTINRYLAALR 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1025816214  77 TIFKFGIEKQLLpfTKNPFDGL-FIREGKKKRKVYTSSDLKKLSFGITESKHLPPILRplwftkTIIMTFRYTAIRRSQL 155
Cdd:COG4974    81 SFFRYAVREGLL--EDNPAAKVkLPKKPRKLPRVLTEEEIEALLEALDTETPEGLRDR------ALLLLLYATGLRVSEL 152

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1025816214 156 NKLRIKDVDLLNQVIHIPSEinKNHEYHILPISttlyPYLKKLLTELSKLNQPVESQLfninLFSNavkRKGEKMTNNQV 235
Cdd:COG4974   153 LGLKWSDIDLDRGTIRVRRG--KGGKERTVPLS----PEALEALREYLEERRPRDSDY----LFPT---RRGRPLSRRAI 219

                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1025816214 236 SYIFKVISKYTGIIS--SPHRFRHTAATNLMKKPENLYIAKQLLGHKDVKVTLSYIEDNIDSIRE 298
Cdd:COG4974   220 RKILKRLAKRAGIPKrvTPHSLRHTFATHLLEAGVDLRTVQELLGHSSISTTQIYTHVSDEELRE 284
DNA_BRE_C cd00397
DNA breaking-rejoining enzymes, C-terminal catalytic domain; The DNA breaking-rejoining enzyme ...
 139-289 5.07e-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: 101.02  E-value: 5.07e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1025816214 139 KTIIMTFRYTAIRRSQLNKLRIKDVDLLNQVIHIPSEINKNHEYHILPISTTLYPYLKKLLTELSKLNQPVESQLFNINL 218
Cdd:cd00397    20 RAILLLLLETGLRISELLALKVKDIDLDNGTIRVRGKKTKGGKERTVPLPKELAEELKEYLKERRDKRGPLLKSLYLNKL 99

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1025816214 219 FSNavkRKGEKMTNNQVSYIFKVISKYTGIISSPHRFRHTAATNLMKKPENLYIAKQLLGHKDVKVTLSYI 289
Cdd:cd00397   100 FGT---KLGERLSRRTLRRIFKKAGIEAGRKITPHSLRHTFATNLLENGVDIKVVQKLLGHSSISTTQRYL 167
Phage_integrase pfam00589
Phage integrase family; Members of this family cleave DNA substrates by a series of staggered ...
 138-292 5.88e-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: 76.59  E-value: 5.88e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1025816214 138 TKTIIMTFRYTAIRRSQLNKLRIKDVDLLNQVIHIPseINKNHEYHILPISTTLYPYLKKLLTELSKLNQPVESqlfnin 217
Cdd:pfam00589  23 DKALLELLYATGLRISELCSLRWSDIDFENGVIRVH--RGKGNKERTVPLSDAALELLKEWLSKRLLEAPKSDY------ 94

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1025816214 218 LFsnaVKRKGEKMTNNQVSYIFKVISKYTGIIS--SPHRFRHTAATNLMKKPENLYIAKQLLGHKDVKVTLSYIEDN 292
Cdd:pfam00589  95 LF---ASKRGKPLSRQTVRKIFKRAGKEAGLELplHPHMLRHSFATHLLEAGVDLRVVQKLLGHSSISTTQIYTHVA 168
xerS PRK05084
site-specific tyrosine recombinase XerS; Reviewed
 141-298 4.98e-10

site-specific tyrosine recombinase XerS; Reviewed


Pssm-ID: 235339 [Multi-domain]  Cd Length: 357  Bit Score: 59.55  E-value: 4.98e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1025816214 141 IIMTFRYTAIRRSQLNKLRIKDVDLLNQVIHIpseINKNHEYHILPISTTLYPYLKKLLTELSKLNQPVESQlfnINLFS 220
Cdd:PRK05084  200 IIALILGSGLRVSELVNLDLSDLNLKQMTIDV---TRKGGKRDSVNIAPFALPYLEEYLKIRASRYKAEKQE---KALFL 273

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1025816214 221 NAVKRKGEKMTNNQvsyIFKVISKYT---GIISSPHRFRHTAATNLMKKPENLYIAKQLLGHKDVKVTLSYIEDNIDSIR 297
Cdd:PRK05084  274 TKYRGKPNRISARA---IEKMVAKYSeafGVRLTPHKLRHTLATRLYDATKDQVLVADQLGHTSTETTDLYTHIVNDEQK 350


                  .
gi 1025816214 298 E 298
Cdd:PRK05084  351 E 351
recomb_XerD TIGR02225
tyrosine recombinase XerD; The phage integrase family describes a number of recombinases with ...
 17-285 2.41e-08

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: 54.12  E-value: 2.41e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1025816214  17 RHLRIDTIKSYEKAVRQLQKNCSLQ--YPDEISELLI---LQWRKRvvgQSIIEVTWNSYIRQLKTIFKFGIEKQLLPFt 91
Cdd:TIGR02225  11 RGLSQNTLEAYRRDLEKFLEFLEERgiDLEEVDRGDIvdfLAELKE---AGLSARSIARALSALRSFYRFLLREGIRED- 86

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1025816214  92 kNPfdGLFIREGKKKR---KVYTSSDLKKLsfgiteskhL--PPILRPLWFTKTIIMTFRY-TAIRRSQLNKLRIKDVDL 165
Cdd:TIGR02225  87 -DP--SALIEPPKVARklpKVLTVEEVEAL---------LaaPDVDTPLGLRDRAMLELLYaTGLRVSELVGLRLEDVNL 154

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1025816214 166 LNQVIHIPSEINKNHeyhILPISTTLYPYLKKLLTE----LSKLNQPVESQLFninlfsnaVKRKGEKMTNNQVSYIFKV 241
Cdd:TIGR02225 155 DEGFVRVRGKGNKER---LVPLGEEAIEALERYLKEarplLLKKKVKESDALF--------LNRRGGPLSRQGVWKILKE 223

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|....*.
gi 1025816214 242 ISKYTGIIS--SPHRFRHTAATNLMKKPENLYIAKQLLGHKDVKVT 285
Cdd:TIGR02225 224 YAKRAGIEKpiSPHTLRHSFATHLLENGADLRVVQELLGHADISTT 269
 
Name Accession Description Interval E-value
XerD COG4974
Site-specific recombinase XerD [Replication, recombination and repair];
4-298 3.22e-40

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


Pssm-ID: 443999 [Multi-domain]  Cd Length: 291  Bit Score: 141.67  E-value: 3.22e-40
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1025816214   4 TTFDMLLSKFFLY----RHLRIDTIKSYEKAVRQLQKNCS---LQYPDEISELLILQWRKRVVGQSIIEVTWNSYIRQLK 76
Cdd:COG4974     1 LTLADLLEAFLEElkreKGLSPNTIKAYRRDLRRFLRFLEelgKIPLAEITPEDIRAYLNYLRERGLSPSTINRYLAALR 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1025816214  77 TIFKFGIEKQLLpfTKNPFDGL-FIREGKKKRKVYTSSDLKKLSFGITESKHLPPILRplwftkTIIMTFRYTAIRRSQL 155
Cdd:COG4974    81 SFFRYAVREGLL--EDNPAAKVkLPKKPRKLPRVLTEEEIEALLEALDTETPEGLRDR------ALLLLLYATGLRVSEL 152

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1025816214 156 NKLRIKDVDLLNQVIHIPSEinKNHEYHILPISttlyPYLKKLLTELSKLNQPVESQLfninLFSNavkRKGEKMTNNQV 235
Cdd:COG4974   153 LGLKWSDIDLDRGTIRVRRG--KGGKERTVPLS----PEALEALREYLEERRPRDSDY----LFPT---RRGRPLSRRAI 219

                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1025816214 236 SYIFKVISKYTGIIS--SPHRFRHTAATNLMKKPENLYIAKQLLGHKDVKVTLSYIEDNIDSIRE 298
Cdd:COG4974   220 RKILKRLAKRAGIPKrvTPHSLRHTFATHLLEAGVDLRTVQELLGHSSISTTQIYTHVSDEELRE 284
XerC COG4973
Site-specific recombinase XerC [Replication, recombination and repair];
3-288 1.89e-30

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


Pssm-ID: 443998 [Multi-domain]  Cd Length: 287  Bit Score: 115.83  E-value: 1.89e-30
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1025816214   3 RTTFDMLLSKFFLY---RHLRIDTIKSYEKAVRQLQKNCSLQ--YPDEISELLILQWRKRVVGQSIIEVTWNSYIRQLKT 77
Cdd:COG4973     1 KLTLAEALEAYLEHlreRRLSPKTLEAYRRDLRRLIPLLGDAdlPLEELTPADVRRFLARLHRRGLSPRTLNRRLSALRS 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1025816214  78 IFKFGIEKQLLPftKNPFDGL-FIREGKKKRKVYTSSDLKKLsFGITESKHLPPILRPlwftktIIMTFRYTAIRRSQLN 156
Cdd:COG4973    81 FFNWAVREGLLE--ANPAAGVkAPKAPRKLPRALTVDELAQL-LDALADDPLAVRDRA------IVELLYSTGLRLGELV 151

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1025816214 157 KLRIKDVDLLNQVIHIPSeinKNHEYHILPISTTLYPYLKKLLTELSKLNQPVESQLFninlfsnaVKRKGEKMTNNQVS 236
Cdd:COG4973   152 GLDWEDVDLDAGEVRVRG---KTGKSRTVPLGPKALAALREWLAVRPELAAPDEGALF--------PSRRGTRLSPRNVQ 220

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1025816214 237 YIFKVISKYTGI--ISSPHRFRHTAATNLMKKPENLYIAKQLLGHKDVKVTLSY 288
Cdd:COG4973   221 KRLRRLAKKAGLpkHVHPHDLRHSFATHLLESGGDLRAVQELLGHASISTTQIY 274
DNA_BRE_C cd00397
DNA breaking-rejoining enzymes, C-terminal catalytic domain; The DNA breaking-rejoining enzyme ...
 139-289 5.07e-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: 101.02  E-value: 5.07e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1025816214 139 KTIIMTFRYTAIRRSQLNKLRIKDVDLLNQVIHIPSEINKNHEYHILPISTTLYPYLKKLLTELSKLNQPVESQLFNINL 218
Cdd:cd00397    20 RAILLLLLETGLRISELLALKVKDIDLDNGTIRVRGKKTKGGKERTVPLPKELAEELKEYLKERRDKRGPLLKSLYLNKL 99

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1025816214 219 FSNavkRKGEKMTNNQVSYIFKVISKYTGIISSPHRFRHTAATNLMKKPENLYIAKQLLGHKDVKVTLSYI 289
Cdd:cd00397   100 FGT---KLGERLSRRTLRRIFKKAGIEAGRKITPHSLRHTFATNLLENGVDIKVVQKLLGHSSISTTQRYL 167
FimB COG0582
Integrase/recombinase, includes phage integrase [Replication, recombination and repair, ...
 44-285 6.53e-19

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


Pssm-ID: 440347 [Multi-domain]  Cd Length: 391  Bit Score: 85.86  E-value: 6.53e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1025816214  44 DEISELLILQWRKRVVGQSIIEvTWNSYIRQLKTIFKFGIEKQLLPFtkNPFDGL---FIREGKKKRKVYTSSDLKKLsF 120
Cdd:COG0582   140 AEITPPDLLAVLRPIEARGAPE-TARRVRQRLRQVFRYAVARGLIER--NPAADLkgaLPKPKVKHHPALTPEELPEL-L 215

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1025816214 121 GITESKHLPPILRPLWftKTIIMTFrytaIRRSQLNKLRIKDVDLLNQVIHIPSEINKNHEYHILPISTTLYPYLKKL-- 198
Cdd:COG0582   216 RALDAYRGSPVTRLAL--RLLLLTG----VRPGELRGARWSEIDLEAALWTIPAERMKTRRPHIVPLSRQALEILKELkp 289

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1025816214 199 LTELSKLnqpvesqlfninLFSNAvKRKGEKMTNNQVSYIFKVIsKYTGIisSPHRFRHTAATNLMKKPENLYIAKQLLG 278
Cdd:COG0582   290 LTGDSEY------------VFPSR-RGPKKPMSENTLNKALRRM-GYGRF--TPHGFRHTASTLLNEAGFPPDVIERQLA 353


                  ....*..
gi 1025816214 279 HKDVKVT 285
Cdd:COG0582   354 HKDGNKV 360
Phage_integrase pfam00589
Phage integrase family; Members of this family cleave DNA substrates by a series of staggered ...
 138-292 5.88e-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: 76.59  E-value: 5.88e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1025816214 138 TKTIIMTFRYTAIRRSQLNKLRIKDVDLLNQVIHIPseINKNHEYHILPISTTLYPYLKKLLTELSKLNQPVESqlfnin 217
Cdd:pfam00589  23 DKALLELLYATGLRISELCSLRWSDIDFENGVIRVH--RGKGNKERTVPLSDAALELLKEWLSKRLLEAPKSDY------ 94

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1025816214 218 LFsnaVKRKGEKMTNNQVSYIFKVISKYTGIIS--SPHRFRHTAATNLMKKPENLYIAKQLLGHKDVKVTLSYIEDN 292
Cdd:pfam00589  95 LF---ASKRGKPLSRQTVRKIFKRAGKEAGLELplHPHMLRHSFATHLLEAGVDLRVVQKLLGHSSISTTQIYTHVA 168
INT_IntI_C cd01193
Integron integrase and similar protiens, C-terminal catalytic domain; Integron integrases ...
 138-288 2.15e-14

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: 70.00  E-value: 2.15e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1025816214 138 TKTIIMTFRYTAIRRSQLNKLRIKDVDLLNQVIHIpsEINKNHEYHILPISTTLYPYLKKLLTELSKLNQPVESQLFNIN 217
Cdd:cd01193    23 HRLILSLLYGAGLRISELLRLRVKDIDFERGVIRV--RQGKGGKDRVVPLPEKLLEPLRRYLKSARPKEELDPAEGRAGV 100

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1025816214 218 LFSNAVKRKGEKMTNNQVSYIFKVISKYTGIIS--SPHRFRHTAATNLMKKPENLYIAKQLLGHKDVKVTLSY 288
Cdd:cd01193   101 LDPRTGVERRHHISETTVQRALKKAVEQAGITKrvTPHTLRHSFATHLLEAGTDIRTIQELLGHSDLSTTMIY 173
INT_Rci_Hp1_C cd00796
Shufflon-specific DNA recombinase Rci and Bacteriophage Hp1_like integrase, C-terminal ...
 111-288 3.26e-14

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: 68.89  E-value: 3.26e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1025816214 111 TSSDLKKLSFGITESKhlppilRPLWftKTIIMTFRYTAIRRSQLNKLRIKDVDLLNQVIHIPseINKNHEYHILPISTT 190
Cdd:cd00796     6 TEDEEARLLAALEEST------NPHL--RLIVLLALYTGARRGEILSLRWDDIDLEVGLIVLP--ETKNGKPRTVPLSDE 75

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1025816214 191 LYPYLKKLLTELSKLNQPVesqlfninlfsnavKRKGEKMTNNQVSYIFKVISKYTGIIS-SPHRFRHTAATNLMKKPEN 269
Cdd:cd00796    76 AIAILKELKRKRGKDGFFV--------------DGRFFGIPIASLRRAFKKARKRAGLEDlRFHDLRHTFASRLVQAGVP 141

                         170
                  ....*....|....*....
gi 1025816214 270 LYIAKQLLGHKDVKVTLSY 288
Cdd:cd00796   142 IKTVAKILGHSSIKMTMRY 160
INT_P4_C cd00801
Bacteriophage P4 integrase, C-terminal catalytic domain; P4-like integrases are found in ...
 113-285 4.02e-13

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: 66.52  E-value: 4.02e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1025816214 113 SDLKKLSFGITESKHLPPILRPLWFTktiiMtfrYTAIRRSQLNKLRIKDVDLLNQVIHIPSEINKNHEYHILPISttly 192
Cdd:cd00801     3 DELPELWRALDTANLSPPTKLALRLL----L---LTGQRIGELARARWSEIDLEEKTWTIPAERTKNKRPHRVPLS---- 71

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1025816214 193 PYLKKLLTELSKLNQpvESQLfninLFSnAVKRKGEKMTNNQVSYIFKVISkYTGIISSPHRFRHTAATNLmkkPENLY- 271
Cdd:cd00801    72 DQALEILEELKEFTG--DSGY----LFP-SRRKKKKPISENTINKALKRLG-YKGKEFTPHDLRRTFSTLL---NELGId 140

                         170
                  ....*....|....*.
gi 1025816214 272 --IAKQLLGHKDVKVT 285
Cdd:cd00801   141 peVIERLLNHVLGGVV 156
INT_RitC_C_like cd01182
C-terminal catalytic domain of recombinase RitC, a component of the recombinase trio; ...
 140-298 4.66e-12

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: 63.45  E-value: 4.66e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1025816214 140 TIIMTFRY-TAIRRSQLNKLRIKDVDLLNQ-VIHIpseINKNHEYHILPISTTLYPYLKKLLTELSKLnqPVESQLFNin 217
Cdd:cd01182    24 HALLLLLYdTGARVQELADLTIRDLRLDDPaTVRL---HGKGRKERTVPLWKETVAALKAYLQEFHLT--PDPKQLFP-- 96

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1025816214 218 LFSNavkRKGEKMTNNQVSYIfkvISKYTGIIS----------SPHRFRHTAATNLMKKPENL-YIAKqLLGHKDVKVTL 286
Cdd:cd01182    97 LFPN---RRGQPLTRDGVAYI---LNKYVALASnrcpslpkriTPHTLRHTKAMHLLQAGVDLtVIRD-WLGHESVETTQ 169

                         170
                  ....*....|..
gi 1025816214 287 SYIEDNIDSIRE 298
Cdd:cd01182   170 IYAEADLEMKRE 181
INT_tnpA_C_Tn554 cd01186
Putative Transposase A from transposon Tn554, C-terminal catalytic domain; This family ...
 139-298 2.00e-10

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: 58.97  E-value: 2.00e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1025816214 139 KTIIMTFRYTAIRRSQLNKLRIKDVDLLNQVIHI-PSEINKNHEYHIL------PISTTL---YP-YLKKLLTELSKlnq 207
Cdd:cd01186    20 KFLLALLYETGLRIGEALGLRIEDIDMADNQIELvPREDNTNEARAKSmrerriPVSQDLidlYAdYLTYIYCEEAE--- 96

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1025816214 208 pvesqlFNINLFSNaVKRK--GEKMTNNQVSYIFKVISKYTGIISSPHRFRHTAATNLMKKPENLYIAKQLLGHKDVKVT 285
Cdd:cd01186    97 ------FSITVFVN-VKGGnqGKAMNYSDVYDLVRRLKKRTGIDFTPHMFRHTHATALIRAGWSIEVVARRLGHAHVQTT 169

                         170
                  ....*....|....
gi 1025816214 286 LS-YIEDNIDSIRE 298
Cdd:cd01186   170 LNtYGHLSEEDIRR 183
xerS PRK05084
site-specific tyrosine recombinase XerS; Reviewed
 141-298 4.98e-10

site-specific tyrosine recombinase XerS; Reviewed


Pssm-ID: 235339 [Multi-domain]  Cd Length: 357  Bit Score: 59.55  E-value: 4.98e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1025816214 141 IIMTFRYTAIRRSQLNKLRIKDVDLLNQVIHIpseINKNHEYHILPISTTLYPYLKKLLTELSKLNQPVESQlfnINLFS 220
Cdd:PRK05084  200 IIALILGSGLRVSELVNLDLSDLNLKQMTIDV---TRKGGKRDSVNIAPFALPYLEEYLKIRASRYKAEKQE---KALFL 273

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1025816214 221 NAVKRKGEKMTNNQvsyIFKVISKYT---GIISSPHRFRHTAATNLMKKPENLYIAKQLLGHKDVKVTLSYIEDNIDSIR 297
Cdd:PRK05084  274 TKYRGKPNRISARA---IEKMVAKYSeafGVRLTPHKLRHTLATRLYDATKDQVLVADQLGHTSTETTDLYTHIVNDEQK 350


                  .
gi 1025816214 298 E 298
Cdd:PRK05084  351 E 351
recomb_XerD TIGR02225
tyrosine recombinase XerD; The phage integrase family describes a number of recombinases with ...
 17-285 2.41e-08

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: 54.12  E-value: 2.41e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1025816214  17 RHLRIDTIKSYEKAVRQLQKNCSLQ--YPDEISELLI---LQWRKRvvgQSIIEVTWNSYIRQLKTIFKFGIEKQLLPFt 91
Cdd:TIGR02225  11 RGLSQNTLEAYRRDLEKFLEFLEERgiDLEEVDRGDIvdfLAELKE---AGLSARSIARALSALRSFYRFLLREGIRED- 86

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1025816214  92 kNPfdGLFIREGKKKR---KVYTSSDLKKLsfgiteskhL--PPILRPLWFTKTIIMTFRY-TAIRRSQLNKLRIKDVDL 165
Cdd:TIGR02225  87 -DP--SALIEPPKVARklpKVLTVEEVEAL---------LaaPDVDTPLGLRDRAMLELLYaTGLRVSELVGLRLEDVNL 154

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1025816214 166 LNQVIHIPSEINKNHeyhILPISTTLYPYLKKLLTE----LSKLNQPVESQLFninlfsnaVKRKGEKMTNNQVSYIFKV 241
Cdd:TIGR02225 155 DEGFVRVRGKGNKER---LVPLGEEAIEALERYLKEarplLLKKKVKESDALF--------LNRRGGPLSRQGVWKILKE 223

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|....*.
gi 1025816214 242 ISKYTGIIS--SPHRFRHTAATNLMKKPENLYIAKQLLGHKDVKVT 285
Cdd:TIGR02225 224 YAKRAGIEKpiSPHTLRHSFATHLLENGADLRVVQELLGHADISTT 269
INT_ICEBs1_C_like cd01189
C-terminal catalytic domain of integrases from bacterial phages and conjugate transposons; ...
 147-288 3.26e-08

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: 51.79  E-value: 3.26e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1025816214 147 YTAIRRSQLNKLRIKDVDLLNQVIHIPSEINKNHEYHIlpisttlypYLKKLLTELSK----LNQPVESQLFNINLFSNA 222
Cdd:cd01189    27 LTGLRRGELLALTWSDIDFENGTIRINRTLVRKKKGGY---------VIKPPKTKSSIrtipLPDELIELLKELKAFKKL 97

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1025816214 223 VKRKGEKMTnnqvsyifkviskytgiisSPHRFRHTAATNLMKKPENLYIAKQLLGHKDVKVTLSY 288
Cdd:cd01189    98 LKKAGLPRI-------------------TPHDLRHTFASLLLEAGVPLKVIAERLGHSDISTTLDV 144
INT_XerDC_C cd00798
XerD and XerC integrases, C-terminal catalytic domains; XerDC-like integrases are involved in ...
 148-288 6.91e-08

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: 51.36  E-value: 6.91e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1025816214 148 TAIRRSQLNKLRIKDVDLLNQVIHIpseINKNHEYHILPISTT----LYPYLKKLLTELSKLNQPVEsqlfninLFSNav 223
Cdd:cd00798    31 SGLRVSELVGLDLSDVDLDEGLVRV---TGKGNKERLVPFGSYaveaLEEYLEERRPLLLKKKPPDA-------LFLN-- 98

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1025816214 224 kRKGEKMTNNQVSYIFKVISKYTGIIS--SPHRFRHTAATNLMkkpEN---LYIAKQLLGHKDVKVTLSY 288
Cdd:cd00798    99 -KRGKRLSRRGVWRILKKYAERAGLPKhvSPHTLRHSFATHLL---EGgadLRVVQELLGHASLSTTQIY 164
INTN1_C_like cd01185
Integrase IntN1 of Bacteroides mobilizable transposon NBU1 and similar proteins, C-terminal ...
 147-290 1.45e-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: 50.34  E-value: 1.45e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1025816214 147 YTAIRRSQLNKLRIKDVDLLNQVIHIPSEINKNHEYHILPisttLYPYLKKLLTELSklNQPVESQLFNInlfsnavkrk 226
Cdd:cd01185    29 YTGLRFSDLKNLTWKNIVEASGRTWIRYRRKKTGKPVTVP----LLPVAREILEKYK--DDRSEGKLFPV---------- 92

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1025816214 227 gekMTNNQVSYIFKVISKYTGI---ISSpHRFRHTAATNLMKKPENLYIAKQLLGHKDVKVTLSYIE 290
Cdd:cd01185    93 ---LSNQKINRYLKEIAKIAGIdkhLTF-HVARHTFATLLLLKGVDIETISKLLGHSSIKTTQIYAK 155
INT_C_like_5 cd01195
Uncharacterized site-specific tyrosine recombinase, C-terminal catalytic domain; Tyrosine ...
 131-289 7.71e-07

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


Pssm-ID: 271195 [Multi-domain]  Cd Length: 170  Bit Score: 48.24  E-value: 7.71e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1025816214 131 ILRPLWftktiimtfrYTAIRRSQLNKLRIKDVDLLNQVIHIPSEINKNHEyhILPISTTLYPYLKKLLTELSKLNQPve 210
Cdd:cd01195    25 LVRLLL----------DNALRRSEAVALDVEDLEKEHRRLRILGKGKKQRE--VVTLPPTTREALAAWLAARGEAEGP-- 90

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1025816214 211 sqlfninLFSNAVKR-KGEKMTNNQVSYIFKVISKYTGIIS--SPHRFRHTAATNLMKKPE-NLYIAKQLLGHKDVKVTL 286
Cdd:cd01195    91 -------LFVSLDRAsRGRRLSPQAVYRIVRRLAERIGLGKrlSPHGLRHSAITLALDAGAgLIRKVQDFSRHADLRTLQ 163


                  ...
gi 1025816214 287 SYI 289
Cdd:cd01195   164 VYD 166
INT_RitA_C_like cd01188
C-terminal catalytic domain of recombinase RitA, a component of the recombinase trio; ...
 150-298 9.20e-07

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


Pssm-ID: 271188 [Multi-domain]  Cd Length: 179  Bit Score: 48.01  E-value: 9.20e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1025816214 150 IRRSQLNKLRIKDVDLLNQVIHIPSEinKNHEYHILPIsttLYPYLKKLLTELSKLNQPVESQLfninLFSNAvKRKGEK 229
Cdd:cd01188    34 LRAGDVAGLRLDDIDWRSGTITVRQK--KTGRPVELPL---TEPVGEALADYLRDGRPRTDSRE----VFLRA-RAPYRP 103

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1025816214 230 MTNN-QVSYIFKVISKYTGIISS---PHRFRHTAATNLMKKPENLYIAKQLLGHKDVKVTLSYIEDNIDSIRE 298
Cdd:cd01188   104 LSSTsQISSIVRRYLRKAGIEPShrgTHSLRHSLATRMLRAGTSLKVIADLLGHRSIETTAIYAKIDVDDLRE 176
INT_C_like_4 cd01194
Uncharacterized site-specific tyrosine recombinase, C-terminal catalytic domain; Tyrosine ...
 224-288 3.33e-06

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


Pssm-ID: 271194 [Multi-domain]  Cd Length: 174  Bit Score: 46.60  E-value: 3.33e-06
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1025816214 224 KRKGEKMTNNQVSYIFKVISKYTGIIS---SPHRFRHTAATNLMKKPENLYIAKQLLGHKDVKVTLSY 288
Cdd:cd01194   105 NSKGQRLTTRSIRRIIKKYLRKAGLDDdrlTAHSLRHTAGTLALKAGKSLREVQQLLRHSDPNTTMIY 172
INT_FimBE_like cd01197
FimB and FimE and related proteins, integrase/recombinases; This CD includes proteins similar ...
 105-292 3.65e-06

FimB and FimE and related proteins, integrase/recombinases; This CD includes proteins similar to E.coli FimE and FimB and Proteus mirabilis MrpI. FimB and FimE are the regulatory proteins during expression of type 1 fimbriae in Escherichia coli. The fimB and fimE proteins direct the phase switch into the 'on' and 'off' position. MrpI is the regulatory protein of proteus mirabilis fimbriae expression. This family belongs to the integrase/recombinase superfamily.


Pssm-ID: 271197 [Multi-domain]  Cd Length: 181  Bit Score: 46.35  E-value: 3.65e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1025816214 105 KKRKVYTSSDLKKLSFGITESKHlPPILRPLwftktIIMTFRYtAIRRSQLNKLRIKDVDLLNQVIHIPSEinKNHEYHI 184
Cdd:cd01197     2 KQRKYLTGKEVQALLQAACRGRT-PARDYCL-----LLLAFRH-GFRVSELCDLHLSDVDLESRRLHIRRL--KNGFSTT 72

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1025816214 185 LPISTTLYPYLKKLLTELSKLnQPVESQLFNINlfsnavkRKGEKMTNNQVSYIFKVISKYTGII--SSPHRFRHTAATN 262
Cdd:cd01197    73 HPLRFDEREALEAWLKERANW-KGADTDWIFLS-------RRGGPLSRQQAYRIIRDLGKEAGTVtqTHPHMLRHACGYA 144

                         170       180       190
                  ....*....|....*....|....*....|
gi 1025816214 263 LMKKPENLYIAKQLLGHKDVKVTLSYIEDN 292
Cdd:cd01197   145 LADRGADTRLIQDYLGHRNIRHTVIYTASN 174
INT_RitB_C_like cd00797
C-terminal catalytic domain of recombinase RitB, a component of the recombinase trio; ...
 110-290 3.25e-05

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: 43.83  E-value: 3.25e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1025816214 110 YTSSDLKKLsfgITESKHLPPI--LRPlWFTKTIIMTFRYTAIRRSQLNKLRIKDVDLLNQVIHIPSeiNKNHEYHILPI 187
Cdd:cd00797     1 YTDAEIRRL---LAAADQLPPEspLRP-LTYATLFGLLYATGLRVGEALRLRLEDVDLDSGILTIRQ--TKFGKSRLVPL 74

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1025816214 188 STTLYPYLKKLL-TELSKLNQPVESQLFninlfsnaVKRKGEKMTNNQVSYIFKVISKYTGIISSP-------HRFRHTA 259
Cdd:cd00797    75 HPSTVGALRDYLaRRDRLLPSPSSSYFF--------VSQQGGRLTGGGVYRVFRRLLRRIGLRGAGdgrgprlHDLRHTF 146

                         170       180       190
                  ....*....|....*....|....*....|....*....
gi 1025816214 260 ATNLMKK-------PEN-LYIAKQLLGHKDVKVTLSYIE 290
Cdd:cd00797   147 AVNRLTRwyregadVERkLPVLSTYLGHVNVTDTYWYLT 185
INT_tnpB_C_Tn554 cd01187
Putative Transposase B from transposon Tn554, C-terminal catalytic domain; This family ...
 233-289 6.55e-05

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: 42.03  E-value: 6.55e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1025816214 233 NQVSYIFKVISKYTGII-SSPHRFRHTAATNLMKKPENLYIAKQLLGHKDVKVTLSYI 289
Cdd:cd01187    84 NELSELKNISDDHGERFrFHTHRFRHTVATRLANSGMGILVLQQLLGHSSPEMTLRYA 141
INT_C_like_1 cd01184
Uncharacterized site-specific tyrosine recombinase, C-terminal catalytic domain; Tyrosine ...
 147-285 6.34e-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: 39.98  E-value: 6.34e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1025816214 147 YTAIRRSQLNKLRIKDVDLLNQVIHIpsEINKNHEYhilpisttlypylKKLLTELSKLNQPVESQLFNINL-------- 218
Cdd:cd01184    34 YTGARLNEICQLRVDDIKEEDGIWCI--DINDDAEG-------------RRLKTKASRRLVPIHPRLIELGFldyvealr 98

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1025816214 219 -----FSNAVKRKGEKMTNNQVSYIFKVISKYTGIISSP----HRFRHTAATNLMKKPENLYIAKQLLGHKDVKVT 285
Cdd:cd01184    99 adgklFLFPEKRDKDGKYSKAASKWFNRLLRKLGIKDDErksfHSFRHTFITALKRAGVPEELIAQIVGHSRGGVT 174
integrase_gron TIGR02249
integron integrase; Members of this family are integrases associated with integrons (and ...
 251-288 1.13e-03

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: 40.07  E-value: 1.13e-03
                          10        20        30
                  ....*....|....*....|....*....|....*...
gi 1025816214 251 SPHRFRHTAATNLMKKPENLYIAKQLLGHKDVKVTLSY 288
Cdd:TIGR02249 260 TCHTLRHSFATHLLESGADIRTVQELLGHSDVKTTQIY 297
xerC PRK01287
site-specific tyrosine recombinase XerC; Reviewed
 148-288 1.37e-03

site-specific tyrosine recombinase XerC; Reviewed


Pssm-ID: 234935 [Multi-domain]  Cd Length: 358  Bit Score: 39.73  E-value: 1.37e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1025816214 148 TAIRRSQLNKLRIKDVDLLNQVIHIPSeiNKNHEYHILPISTTLYPYLKKLLTELS-KLNQPVESQLFNINLFSNAVKRK 226
Cdd:PRK01287  169 TGIRRGELARLDLYDVDASRGVVTVRQ--GKGNKDRVVPVGERALAWLQRYLQDVRpQLAVRPDSGALFVAMDGDGLARN 246

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1025816214 227 GekMTNNQVSYIFKVISKYTGiisSPHRFRHTAATNLMKKPENLYIAKQLLGHKDVKVTLSY 288
Cdd:PRK01287  247 T--LTNMVGRYIRAAGIEKAG---ACHLFRHAMATQMLENGADTRHIQAILGHAKLETTQIY 303
int PHA02601
integrase; Provisional
 219-288 1.73e-03

integrase; Provisional


Pssm-ID: 222904 [Multi-domain]  Cd Length: 333  Bit Score: 39.33  E-value: 1.73e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1025816214 219 FSNAVKRKGEKMTNNQvsyifkviskytgiisSPHRFRHTAATNLMKKPENLYIAKQLLGHKDVKVTLSY 288
Cdd:PHA02601  261 FERAVKRAGIDLPEGQ----------------ATHVLRHTFASHFMMNGGNILVLQRILGHATIEMTMAY 314
INT_C_like_3 cd01192
Uncharacterized site-specific tyrosine recombinase, C-terminal catalytic domain; Tyrosine ...
 148-289 2.18e-03

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


Pssm-ID: 271192 [Multi-domain]  Cd Length: 178  Bit Score: 38.43  E-value: 2.18e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1025816214 148 TAIRRSQLNKLRIKDVdLLNQVIHIPSeiNKNHEYHILPISTTLYPYLKKLLTELSKLNQPvesqlfniNLFSNAVKRKG 227
Cdd:cd01192    36 TGLRISDLLSLKVEDV-TNKDKLSIKE--QKTGKQKTFPLNPTLVKALKEYIDDLDLKRND--------YLFKSLKQGPE 104

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1025816214 228 EKMTNNQVSYIFKVISKYTGI---ISSpHRFRHTAATNLMKKPENLYIAKQLLGHKDVKVTLSYI 289
Cdd:cd01192   105 KPISRKQAYKILKKAADDLGLnynIGT-HSLRKTFGYHVYKQGKDIELLMKLLNHSSPSITLRYL 168
xerD PRK00283
tyrosine recombinase;
218-285 2.24e-03

tyrosine recombinase;


Pssm-ID: 234713 [Multi-domain]  Cd Length: 299  Bit Score: 39.02  E-value: 2.24e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1025816214 218 LFSNAvkrKGEKMTNNQVSYIFKVISKYTGIIS---SPHRFRHTAATNLMKKPENLYIAKQLLGHKDVKVT 285
Cdd:PRK00283  210 LFPSA---RGGQLTRQTFWHRIKHYAKRAGIDPkklSPHVLRHAFATHLLNHGADLRVVQELLGHSDISTT 277
PRK09870 PRK09870
tyrosine recombinase; Provisional
 150-292 2.42e-03

tyrosine recombinase; Provisional


Pssm-ID: 182125  Cd Length: 200  Bit Score: 38.38  E-value: 2.42e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1025816214 150 IRRSQLNKLRIKDVDLLNQVIHIpseinknheYHILPISTTLYPYLKKLLTELSK-LNQPVESQLFNIN-LFsnaVKRKG 227
Cdd:PRK09870   46 FRASEICRLRISDIDLKAKCIYI---------HRLKKGFSTTHPLLNKEIQALKNwLSIRTSYPHAESEwVF---LSRKG 113

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1025816214 228 EKMTNNQVSYIFKVISKYTG--IISSPHRFRHTAATNLMKKPENLYIAKQLLGHKDVKVTLSYIEDN 292
Cdd:PRK09870  114 NPLSRQQFYHIISTSGGNAGlsLEIHPHMLRHSCGFALANMGIDTRLIQDYLGHRNIRHTVWYTASN 180
xerC PRK00236
site-specific tyrosine recombinase XerC; Reviewed
 225-285 3.45e-03

site-specific tyrosine recombinase XerC; Reviewed


Pssm-ID: 234698 [Multi-domain]  Cd Length: 297  Bit Score: 38.60  E-value: 3.45e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1025816214 225 RKGEKMTNNQVSYIFKVISKYTGIIS--SPHRFRHTAATNLMKKPENLYIAKQLLGHKDVKVT 285
Cdd:PRK00236  213 ARGGRLSPRVVQRRVKKLGKKAGLPShiTPHKLRHSFATHLLESGGDLRAVQELLGHASLSTT 275
PRK15417 PRK15417
integron integrase;
220-288 7.30e-03

integron integrase;


Pssm-ID: 185315 [Multi-domain]  Cd Length: 337  Bit Score: 37.72  E-value: 7.30e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1025816214 220 SNAVKRkgEKMTNNQVSYIFKVISKYTGII--SSPHRFRHTAATNLMKKPENLYIAKQLLGHKDVKVTLSY 288
Cdd:PRK15417  244 SGVVRR--HHMYDQTFQRAFKRAVEQAGITkpATPHTLRHSFATALLRSGYDIRTVQDLLGHSDVSTTMIY 312
 
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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