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Conserved domains on  [gi|1608038057|gb|QBX10055|]
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integrase [Streptococcus satellite phage Javan408]

Protein Classification

site-specific integrase( domain architecture ID 10630464)

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

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

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];
71-372 1.57e-47

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


:

Pssm-ID: 443999 [Multi-domain]  Cd Length: 291  Bit Score: 163.24  E-value: 1.57e-47
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1608038057  71 KELAELWLKSY--EMTVKPQTFIATKRMLHNHL--MPVFGDIKLDKLSVSYIQGFINDLSKEFVhfgTVHSIN------K 140
Cdd:COG4974     4 ADLLEAFLEELkrEKGLSPNTIKAYRRDLRRFLrfLEELGKIPLAEITPEDIRAYLNYLRERGL---SPSTINrylaalR 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1608038057 141 RVLQYGVSLQLIPFNPARDVILPKVVKPEnkaIKFIDYNDLKALMSYMEKLSNKKYSyyfDYVLYSILLATGCRFGEAVA 220
Cdd:COG4974    81 SFFRYAVREGLLEDNPAAKVKLPKKPRKL---PRVLTEEEIEALLEALDTETPEGLR---DRALLLLLYATGLRVSELLG 154

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1608038057 221 LTWSDIDFENATIDInknynrlvdivgtPKSKAG-YRVISIDQKTINLLRLYKNRQRQLFSEVssevpsvVFATPT-RKY 298
Cdd:COG4974   155 LKWSDIDLDRGTIRV-------------RRGKGGkERTVPLSPEALEALREYLEERRPRDSDY-------LFPTRRgRPL 214

                         250       260       270       280       290       300       310
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1608038057 299 QNTAIRQgSLDRRLKEIGCP-RFTFHAFRHTHASLLLNAGISYKELQYRLGHATLAMTMdIYSHLSKDKEKEAVS 372
Cdd:COG4974   215 SRRAIRK-ILKRLAKRAGIPkRVTPHSLRHTFATHLLEAGVDLRTVQELLGHSSISTTQ-IYTHVSDEELREAVE 287
 
Name Accession Description Interval E-value
XerD COG4974
Site-specific recombinase XerD [Replication, recombination and repair];
71-372 1.57e-47

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


Pssm-ID: 443999 [Multi-domain]  Cd Length: 291  Bit Score: 163.24  E-value: 1.57e-47
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1608038057  71 KELAELWLKSY--EMTVKPQTFIATKRMLHNHL--MPVFGDIKLDKLSVSYIQGFINDLSKEFVhfgTVHSIN------K 140
Cdd:COG4974     4 ADLLEAFLEELkrEKGLSPNTIKAYRRDLRRFLrfLEELGKIPLAEITPEDIRAYLNYLRERGL---SPSTINrylaalR 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1608038057 141 RVLQYGVSLQLIPFNPARDVILPKVVKPEnkaIKFIDYNDLKALMSYMEKLSNKKYSyyfDYVLYSILLATGCRFGEAVA 220
Cdd:COG4974    81 SFFRYAVREGLLEDNPAAKVKLPKKPRKL---PRVLTEEEIEALLEALDTETPEGLR---DRALLLLLYATGLRVSELLG 154

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1608038057 221 LTWSDIDFENATIDInknynrlvdivgtPKSKAG-YRVISIDQKTINLLRLYKNRQRQLFSEVssevpsvVFATPT-RKY 298
Cdd:COG4974   155 LKWSDIDLDRGTIRV-------------RRGKGGkERTVPLSPEALEALREYLEERRPRDSDY-------LFPTRRgRPL 214

                         250       260       270       280       290       300       310
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1608038057 299 QNTAIRQgSLDRRLKEIGCP-RFTFHAFRHTHASLLLNAGISYKELQYRLGHATLAMTMdIYSHLSKDKEKEAVS 372
Cdd:COG4974   215 SRRAIRK-ILKRLAKRAGIPkRVTPHSLRHTFATHLLEAGVDLRTVQELLGHSSISTTQ-IYTHVSDEELREAVE 287
INT_ICEBs1_C_like cd01189
C-terminal catalytic domain of integrases from bacterial phages and conjugate transposons; ...
 179-361 4.37e-45

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: 151.94  E-value: 4.37e-45
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1608038057 179 NDLKALMSYMEKLSNKkysyyfDYVLYSILLATGCRFGEAVALTWSDIDFENATIDINKNYNRLVD---IVGTPKSKAGY 255
Cdd:cd01189     2 EELKKLLEALKKRGDR------YYLLFLLALLTGLRRGELLALTWSDIDFENGTIRINRTLVRKKKggyVIKPPKTKSSI 75

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1608038057 256 RVISIDQKTINLLRLYKNrqrqlfsevssevpsvvfatptrkyqntairqgsLDRRLKEIGCPRFTFHAFRHTHASLLLN 335
Cdd:cd01189    76 RTIPLPDELIELLKELKA----------------------------------FKKLLKKAGLPRITPHDLRHTFASLLLE 121

                         170       180
                  ....*....|....*....|....*.
gi 1608038057 336 AGISYKELQYRLGHATLAMTMDIYSH 361
Cdd:cd01189   122 AGVPLKVIAERLGHSDISTTLDVYAH 147
Phage_integrase pfam00589
Phage integrase family; Members of this family cleave DNA substrates by a series of staggered ...
 175-364 8.27e-21

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: 88.53  E-value: 8.27e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1608038057 175 FIDYNDLKALMSYMEKLSNKKYsyyfDYVLYSILLATGCRFGEAVALTWSDIDFENATIdinknynrLVDIVGTPKSkag 254
Cdd:pfam00589   1 RLTEDEVERLLDAAETGPLSIR----DKALLELLYATGLRISELCSLRWSDIDFENGVI--------RVHRGKGNKE--- 65

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1608038057 255 yRVISIdqkTINLLRLYKNR-QRQLFSEVSSEVpsvVFATpTRKYQntaIRQGSLDRRLKEIG-----CPRFTFHAFRHT 328
Cdd:pfam00589  66 -RTVPL---SDAALELLKEWlSKRLLEAPKSDY---LFAS-KRGKP---LSRQTVRKIFKRAGkeaglELPLHPHMLRHS 134

                         170       180       190
                  ....*....|....*....|....*....|....*.
gi 1608038057 329 HASLLLNAGISYKELQYRLGHATLAMTMdIYSHLSK 364
Cdd:pfam00589 135 FATHLLEAGVDLRVVQKLLGHSSISTTQ-IYTHVAD 169
xerC PRK00236
site-specific tyrosine recombinase XerC; Reviewed
 151-377 1.78e-13

site-specific tyrosine recombinase XerC; Reviewed


Pssm-ID: 234698 [Multi-domain]  Cd Length: 297  Bit Score: 70.18  E-value: 1.78e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1608038057 151 LIPFNPARDVILPKVVK--PenkaiKFIDYNDLKALMsymEKLSNKKYSYYFDYVLYSILLATGCRFGEAVALTWSDIDF 228
Cdd:PRK00236   94 LLKANPAAGLRAPKIPKrlP-----KPLDVDQAKRLL---DAIDEDDPLALRDRAILELLYGSGLRLSELVGLDIDDLDL 165

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1608038057 229 ENATidinknynrlVDIVGtpK-SKAgyRVISIDQKTINLLRLYKNRQRQLFSEvssevPSVVFatptRKYQNTAIRQGS 307
Cdd:PRK00236  166 ASGT----------LRVLG--KgNKE--RTVPLGRAAREALEAYLALRPLFLPD-----DDALF----LGARGGRLSPRV 222

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1608038057 308 LDRRLKEIG-----CPRFTFHAFRHTHASLLLNAGISYKELQYRLGHATLAMTmDIYSHLSKDKEKEAvsyYEKA 377
Cdd:PRK00236  223 VQRRVKKLGkkaglPSHITPHKLRHSFATHLLESGGDLRAVQELLGHASLSTT-QIYTHVDFQHLAEV---YDAA 293
recomb_XerD TIGR02225
tyrosine recombinase XerD; The phage integrase family describes a number of recombinases with ...
 107-369 8.56e-13

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: 67.99  E-value: 8.56e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1608038057 107 DIKLDKLSVSYIQGFINDLSKEfvHFGTVhSINKRV------LQYGVSLQLIPFNPARDVILPKVVKPENKAIKfIDynD 180
Cdd:TIGR02225  36 GIDLEEVDRGDIVDFLAELKEA--GLSAR-SIARALsalrsfYRFLLREGIREDDPSALIEPPKVARKLPKVLT-VE--E 109

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1608038057 181 LKALMSYMEKLSNKKYSyyfDYVLYSILLATGCRFGEAVALTWSDIDFENatidinknynRLVDIVGtpksKAGY-RVIS 259
Cdd:TIGR02225 110 VEALLAAPDVDTPLGLR---DRAMLELLYATGLRVSELVGLRLEDVNLDE----------GFVRVRG----KGNKeRLVP 172

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1608038057 260 IDQKTINLLRLYKNRQRQLFSEVSSEVPSVVFATPTRKYQNtaiRQGsLDRRLKEIG-----CPRFTFHAFRHTHASLLL 334
Cdd:TIGR02225 173 LGEEAIEALERYLKEARPLLLKKKVKESDALFLNRRGGPLS---RQG-VWKILKEYAkragiEKPISPHTLRHSFATHLL 248

                         250       260       270
                  ....*....|....*....|....*....|....*
gi 1608038057 335 NAGISYKELQYRLGHATLAMTmDIYSHLSKDKEKE 369
Cdd:TIGR02225 249 ENGADLRVVQELLGHADISTT-QIYTHVARERLKE 282
 
Name Accession Description Interval E-value
XerD COG4974
Site-specific recombinase XerD [Replication, recombination and repair];
71-372 1.57e-47

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


Pssm-ID: 443999 [Multi-domain]  Cd Length: 291  Bit Score: 163.24  E-value: 1.57e-47
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1608038057  71 KELAELWLKSY--EMTVKPQTFIATKRMLHNHL--MPVFGDIKLDKLSVSYIQGFINDLSKEFVhfgTVHSIN------K 140
Cdd:COG4974     4 ADLLEAFLEELkrEKGLSPNTIKAYRRDLRRFLrfLEELGKIPLAEITPEDIRAYLNYLRERGL---SPSTINrylaalR 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1608038057 141 RVLQYGVSLQLIPFNPARDVILPKVVKPEnkaIKFIDYNDLKALMSYMEKLSNKKYSyyfDYVLYSILLATGCRFGEAVA 220
Cdd:COG4974    81 SFFRYAVREGLLEDNPAAKVKLPKKPRKL---PRVLTEEEIEALLEALDTETPEGLR---DRALLLLLYATGLRVSELLG 154

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1608038057 221 LTWSDIDFENATIDInknynrlvdivgtPKSKAG-YRVISIDQKTINLLRLYKNRQRQLFSEVssevpsvVFATPT-RKY 298
Cdd:COG4974   155 LKWSDIDLDRGTIRV-------------RRGKGGkERTVPLSPEALEALREYLEERRPRDSDY-------LFPTRRgRPL 214

                         250       260       270       280       290       300       310
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1608038057 299 QNTAIRQgSLDRRLKEIGCP-RFTFHAFRHTHASLLLNAGISYKELQYRLGHATLAMTMdIYSHLSKDKEKEAVS 372
Cdd:COG4974   215 SRRAIRK-ILKRLAKRAGIPkRVTPHSLRHTFATHLLEAGVDLRTVQELLGHSSISTTQ-IYTHVSDEELREAVE 287
INT_ICEBs1_C_like cd01189
C-terminal catalytic domain of integrases from bacterial phages and conjugate transposons; ...
 179-361 4.37e-45

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: 151.94  E-value: 4.37e-45
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1608038057 179 NDLKALMSYMEKLSNKkysyyfDYVLYSILLATGCRFGEAVALTWSDIDFENATIDINKNYNRLVD---IVGTPKSKAGY 255
Cdd:cd01189     2 EELKKLLEALKKRGDR------YYLLFLLALLTGLRRGELLALTWSDIDFENGTIRINRTLVRKKKggyVIKPPKTKSSI 75

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1608038057 256 RVISIDQKTINLLRLYKNrqrqlfsevssevpsvvfatptrkyqntairqgsLDRRLKEIGCPRFTFHAFRHTHASLLLN 335
Cdd:cd01189    76 RTIPLPDELIELLKELKA----------------------------------FKKLLKKAGLPRITPHDLRHTFASLLLE 121

                         170       180
                  ....*....|....*....|....*.
gi 1608038057 336 AGISYKELQYRLGHATLAMTMDIYSH 361
Cdd:cd01189   122 AGVPLKVIAERLGHSDISTTLDVYAH 147
FimB COG0582
Integrase/recombinase, includes phage integrase [Replication, recombination and repair, ...
 71-361 4.33e-43

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


Pssm-ID: 440347 [Multi-domain]  Cd Length: 391  Bit Score: 154.43  E-value: 4.33e-43
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1608038057  71 KELAELWLKSYEMTVKPQTFIATKRMLHNHLMPVFGDIKLDKLSVSYIQGFINDL----SKEFVHfgTVHSINKRVLQYG 146
Cdd:COG0582   100 EEVAEEWLEEKKPEWKEKTAAQVRRTLEKHIFPVLGDRPIAEITPPDLLAVLRPIeargAPETAR--RVRQRLRQVFRYA 177

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1608038057 147 VSLQLIPFNPARDV--ILPKVVKPENKAIkfiDYNDLKALMSYMEKlsnkkYSYYFDYVLY-SILLATGCRFGEAVALTW 223
Cdd:COG0582   178 VARGLIERNPAADLkgALPKPKVKHHPAL---TPEELPELLRALDA-----YRGSPVTRLAlRLLLLTGVRPGELRGARW 249

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1608038057 224 SDIDFENATIDINKNynrlvdivgtpKSKAG-YRVISIDQKTINLLRLYKNRQRqlfsevSSEVpsvVFatPTRKYQNTA 302
Cdd:COG0582   250 SEIDLEAALWTIPAE-----------RMKTRrPHIVPLSRQALEILKELKPLTG------DSEY---VF--PSRRGPKKP 307

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1608038057 303 IRQGSLDRRLKEIGCPRFTFHAFRHTHASLLLNAGISYKELQYRLGHATLAMTMDIYSH 361
Cdd:COG0582   308 MSENTLNKALRRMGYGRFTPHGFRHTASTLLNEAGFPPDVIERQLAHKDGNKVRAAYNR 366
XerC COG4973
Site-specific recombinase XerC [Replication, recombination and repair];
71-370 1.05e-41

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


Pssm-ID: 443998 [Multi-domain]  Cd Length: 287  Bit Score: 147.80  E-value: 1.05e-41
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1608038057  71 KELAELWLKSYEM-TVKPQTFIATKRMLhNHLMPVFGD--IKLDKLSVSYIQGFINDLSKEFVHFGTV---HSINKRVLQ 144
Cdd:COG4973     5 AEALEAYLEHLRErRLSPKTLEAYRRDL-RRLIPLLGDadLPLEELTPADVRRFLARLHRRGLSPRTLnrrLSALRSFFN 83

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1608038057 145 YGVSLQLIPFNPARDVILPKVVKPENKAIkfiDYNDLKALMSYMEKlsnkKYSYYFDYVLYSILLATGCRFGEAVALTWS 224
Cdd:COG4973    84 WAVREGLLEANPAAGVKAPKAPRKLPRAL---TVDELAQLLDALAD----DPLAVRDRAIVELLYSTGLRLGELVGLDWE 156

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1608038057 225 DIDFENATIDInknynrlvdivgTPKSKAGyRVISIDQKTINLLRLYKNRQRQLfsEVSSEVPsvVFATPTRK-YQNTAI 303
Cdd:COG4973   157 DVDLDAGEVRV------------RGKTGKS-RTVPLGPKALAALREWLAVRPEL--AAPDEGA--LFPSRRGTrLSPRNV 219

                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1608038057 304 RQgSLDRRLKEIGCP-RFTFHAFRHTHASLLLNAGISYKELQYRLGHATLAMTMdIYSHLSKDKEKEA 370
Cdd:COG4973   220 QK-RLRRLAKKAGLPkHVHPHDLRHSFATHLLESGGDLRAVQELLGHASISTTQ-IYTHLDFQHLAEV 285
DNA_BRE_C cd00397
DNA breaking-rejoining enzymes, C-terminal catalytic domain; The DNA breaking-rejoining enzyme ...
 180-359 1.31e-27

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: 106.80  E-value: 1.31e-27
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1608038057 180 DLKALMSYMEKLsnkKYSYYFDYVLYSILLATGCRFGEAVALTWSDIDFENATIDINknynrlvdivGTPKSKAGYRVIS 259
Cdd:cd00397     1 ELEKLLDAIDED---KKIDLRDRAILLLLLETGLRISELLALKVKDIDLDNGTIRVR----------GKKTKGGKERTVP 67

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1608038057 260 IDQKTINLLRLYKNRQRQLFSEVSSEVPSVVFATPTRKYQNT--AIRQgsLDRRLKEIGCPRFTFHAFRHTHASLLLNAG 337
Cdd:cd00397    68 LPKELAEELKEYLKERRDKRGPLLKSLYLNKLFGTKLGERLSrrTLRR--IFKKAGIEAGRKITPHSLRHTFATNLLENG 145

                         170       180
                  ....*....|....*....|..
gi 1608038057 338 ISYKELQYRLGHATLAMTMdIY 359
Cdd:cd00397   146 VDIKVVQKLLGHSSISTTQ-RY 166
INT_tnpA_C_Tn554 cd01186
Putative Transposase A from transposon Tn554, C-terminal catalytic domain; This family ...
 201-370 2.11e-21

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: 90.55  E-value: 2.11e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1608038057 201 DYVLYSILLATGCRFGEAVALTWSDIDFENATIDINknyNRLVDIVGTPKSKAGYRVISIDQktiNLLRLYKNRQRQLFS 280
Cdd:cd01186    19 DKFLLALLYETGLRIGEALGLRIEDIDMADNQIELV---PREDNTNEARAKSMRERRIPVSQ---DLIDLYADYLTYIYC 92

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1608038057 281 EVSSEvPSVVFATPTRKYQNTAIRQGSLD---RRLKEIGCPRFTFHAFRHTHASLLLNAGISYKELQYRLGHATLAMTMD 357
Cdd:cd01186    93 EEAEF-SITVFVNVKGGNQGKAMNYSDVYdlvRRLKKRTGIDFTPHMFRHTHATALIRAGWSIEVVARRLGHAHVQTTLN 171

                         170
                  ....*....|...
gi 1608038057 358 IYSHLSKDKEKEA 370
Cdd:cd01186   172 TYGHLSEEDIRRE 184
Phage_integrase pfam00589
Phage integrase family; Members of this family cleave DNA substrates by a series of staggered ...
 175-364 8.27e-21

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: 88.53  E-value: 8.27e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1608038057 175 FIDYNDLKALMSYMEKLSNKKYsyyfDYVLYSILLATGCRFGEAVALTWSDIDFENATIdinknynrLVDIVGTPKSkag 254
Cdd:pfam00589   1 RLTEDEVERLLDAAETGPLSIR----DKALLELLYATGLRISELCSLRWSDIDFENGVI--------RVHRGKGNKE--- 65

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1608038057 255 yRVISIdqkTINLLRLYKNR-QRQLFSEVSSEVpsvVFATpTRKYQntaIRQGSLDRRLKEIG-----CPRFTFHAFRHT 328
Cdd:pfam00589  66 -RTVPL---SDAALELLKEWlSKRLLEAPKSDY---LFAS-KRGKP---LSRQTVRKIFKRAGkeaglELPLHPHMLRHS 134

                         170       180       190
                  ....*....|....*....|....*....|....*.
gi 1608038057 329 HASLLLNAGISYKELQYRLGHATLAMTMdIYSHLSK 364
Cdd:pfam00589 135 FATHLLEAGVDLRVVQKLLGHSSISTTQ-IYTHVAD 169
INT_Rci_Hp1_C cd00796
Shufflon-specific DNA recombinase Rci and Bacteriophage Hp1_like integrase, C-terminal ...
 180-361 1.14e-20

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: 87.77  E-value: 1.14e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1608038057 180 DLKALMSYMEKLSNKKYsyyfdYVLYSILLATGCRFGEAVALTWSDIDFENATIDInknynrlvdivgtPKSKAGY-RVI 258
Cdd:cd00796     9 EEARLLAALEESTNPHL-----RLIVLLALYTGARRGEILSLRWDDIDLEVGLIVL-------------PETKNGKpRTV 70

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1608038057 259 SIDQKTINLLRLYKnrqrqlfsevsSEVPSVVFATPTRKYQntaIRQGSLDRR----LKEIGCPRFTFHAFRHTHASLLL 334
Cdd:cd00796    71 PLSDEAIAILKELK-----------RKRGKDGFFVDGRFFG---IPIASLRRAfkkaRKRAGLEDLRFHDLRHTFASRLV 136

                         170       180
                  ....*....|....*....|....*..
gi 1608038057 335 NAGISYKELQYRLGHATLAMTMdIYSH 361
Cdd:cd00796   137 QAGVPIKTVAKILGHSSIKMTM-RYAH 162
xerC PRK00236
site-specific tyrosine recombinase XerC; Reviewed
 151-377 1.78e-13

site-specific tyrosine recombinase XerC; Reviewed


Pssm-ID: 234698 [Multi-domain]  Cd Length: 297  Bit Score: 70.18  E-value: 1.78e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1608038057 151 LIPFNPARDVILPKVVK--PenkaiKFIDYNDLKALMsymEKLSNKKYSYYFDYVLYSILLATGCRFGEAVALTWSDIDF 228
Cdd:PRK00236   94 LLKANPAAGLRAPKIPKrlP-----KPLDVDQAKRLL---DAIDEDDPLALRDRAILELLYGSGLRLSELVGLDIDDLDL 165

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1608038057 229 ENATidinknynrlVDIVGtpK-SKAgyRVISIDQKTINLLRLYKNRQRQLFSEvssevPSVVFatptRKYQNTAIRQGS 307
Cdd:PRK00236  166 ASGT----------LRVLG--KgNKE--RTVPLGRAAREALEAYLALRPLFLPD-----DDALF----LGARGGRLSPRV 222

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1608038057 308 LDRRLKEIG-----CPRFTFHAFRHTHASLLLNAGISYKELQYRLGHATLAMTmDIYSHLSKDKEKEAvsyYEKA 377
Cdd:PRK00236  223 VQRRVKKLGkkaglPSHITPHKLRHSFATHLLESGGDLRAVQELLGHASLSTT-QIYTHVDFQHLAEV---YDAA 293
INT_IntI_C cd01193
Integron integrase and similar protiens, C-terminal catalytic domain; Integron integrases ...
 201-362 7.46e-13

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: 66.14  E-value: 7.46e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1608038057 201 DYVLYSILLATGCRFGEAVALTWSDIDFENATIDINKnynrlvdivgtpkSKAG-YRVISIDQKTINLLRLYKNRQRQLF 279
Cdd:cd01193    23 HRLILSLLYGAGLRISELLRLRVKDIDFERGVIRVRQ-------------GKGGkDRVVPLPEKLLEPLRRYLKSARPKE 89

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1608038057 280 SEVSSEVPSVVFATPTRKYQNTAIRQGSLDRRLKEIG-----CPRFTFHAFRHTHASLLLNAGISYKELQYRLGHATLAM 354
Cdd:cd01193    90 ELDPAEGRAGVLDPRTGVERRHHISETTVQRALKKAVeqagiTKRVTPHTLRHSFATHLLEAGTDIRTIQELLGHSDLST 169


                  ....*...
gi 1608038057 355 TMdIYSHL 362
Cdd:cd01193   170 TM-IYTHV 176
recomb_XerD TIGR02225
tyrosine recombinase XerD; The phage integrase family describes a number of recombinases with ...
 107-369 8.56e-13

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: 67.99  E-value: 8.56e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1608038057 107 DIKLDKLSVSYIQGFINDLSKEfvHFGTVhSINKRV------LQYGVSLQLIPFNPARDVILPKVVKPENKAIKfIDynD 180
Cdd:TIGR02225  36 GIDLEEVDRGDIVDFLAELKEA--GLSAR-SIARALsalrsfYRFLLREGIREDDPSALIEPPKVARKLPKVLT-VE--E 109

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1608038057 181 LKALMSYMEKLSNKKYSyyfDYVLYSILLATGCRFGEAVALTWSDIDFENatidinknynRLVDIVGtpksKAGY-RVIS 259
Cdd:TIGR02225 110 VEALLAAPDVDTPLGLR---DRAMLELLYATGLRVSELVGLRLEDVNLDE----------GFVRVRG----KGNKeRLVP 172

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1608038057 260 IDQKTINLLRLYKNRQRQLFSEVSSEVPSVVFATPTRKYQNtaiRQGsLDRRLKEIG-----CPRFTFHAFRHTHASLLL 334
Cdd:TIGR02225 173 LGEEAIEALERYLKEARPLLLKKKVKESDALFLNRRGGPLS---RQG-VWKILKEYAkragiEKPISPHTLRHSFATHLL 248

                         250       260       270
                  ....*....|....*....|....*....|....*
gi 1608038057 335 NAGISYKELQYRLGHATLAMTmDIYSHLSKDKEKE 369
Cdd:TIGR02225 249 ENGADLRVVQELLGHADISTT-QIYTHVARERLKE 282
INT_C_like_1 cd01184
Uncharacterized site-specific tyrosine recombinase, C-terminal catalytic domain; Tyrosine ...
 180-361 1.17e-12

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: 65.79  E-value: 1.17e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1608038057 180 DLKALMSYM-EKLSNKKYSYYFDyvLYSILLATGCRFGEAVALTWSDIDFENAT--IDIN--KNYNRLvdivgtpKSKAG 254
Cdd:cd01184     5 ELAKIFSSPlYTGCKKKDPALYW--LPLIGLYTGARLNEICQLRVDDIKEEDGIwcIDINddAEGRRL-------KTKAS 75

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1608038057 255 YRVISIDQKTINL--LRLYKNRQRQlfsevsSEVPSVVFATPTRKYQNTAIRQ--GSLDRRLKEIGCPRFTFHAFRHTHA 330
Cdd:cd01184    76 RRLVPIHPRLIELgfLDYVEALRAD------GKLFLFPEKRDKDGKYSKAASKwfNRLLRKLGIKDDERKSFHSFRHTFI 149

                         170       180       190
                  ....*....|....*....|....*....|.
gi 1608038057 331 SLLLNAGISYKELQYRLGHATLAMTMDIYSH 361
Cdd:cd01184   150 TALKRAGVPEELIAQIVGHSRGGVTHDTYGK 180
INT_XerDC_C cd00798
XerD and XerC integrases, C-terminal catalytic domains; XerDC-like integrases are involved in ...
 203-366 2.03e-12

XerD and XerC integrases, C-terminal catalytic domains; XerDC-like integrases are involved in the site-specific integration and excision of lysogenic bacteriophage genomes, transposition of conjugative transposons, termination of chromosomal replication, and stable plasmid inheritance. They share the same fold in their catalytic domain containing six conserved active site residues and the overall reaction mechanism with the DNA breaking-rejoining enzyme superfamily. In Escherichia coli, the Xer site-specific recombination system acts to convert dimeric chromosomes, which are formed by homologous recombination to monomers. Two related recombinases, XerC and XerD, bind cooperatively to a recombination site present in the E. coli chromosome. Each recombinase catalyzes the exchange of one pair of DNA strand in a reaction that proceeds through a Holliday junction intermediate. These enzymes can bridge two different and well-separated DNA sequences called arm- and core-sites. The C-terminal domain binds, cleaves, and re-ligates DNA strands at the core-sites, while the N-terminal domain is largely responsible for high-affinity binding to the arm-type sites.


Pssm-ID: 271179 [Multi-domain]  Cd Length: 172  Bit Score: 64.84  E-value: 2.03e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1608038057 203 VLYSillaTGCRFGEAVALTWSDIDFENatidinknynRLVDIVGtpK-SKAgyRVISIDQKTINLLRLYKNRQRQLFse 281
Cdd:cd00798    27 LLYA----SGLRVSELVGLDLSDVDLDE----------GLVRVTG--KgNKE--RLVPFGSYAVEALEEYLEERRPLL-- 86

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1608038057 282 VSSEVPSVVFATptrkYQNTAIRQGSLDRRLKEIG-----CPRFTFHAFRHTHASLLLNAGISYKELQYRLGHATLAMTm 356
Cdd:cd00798    87 LKKKPPDALFLN----KRGKRLSRRGVWRILKKYAeraglPKHVSPHTLRHSFATHLLEGGADLRVVQELLGHASLSTT- 161

                         170
                  ....*....|
gi 1608038057 357 DIYSHLSKDK 366
Cdd:cd00798   162 QIYTHVSFER 171
INT_RitA_C_like cd01188
C-terminal catalytic domain of recombinase RitA, a component of the recombinase trio; ...
 201-359 2.63e-12

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: 64.57  E-value: 2.63e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1608038057 201 DYVLYSILLATGCRFGEAVALTWSDIDFENATIDI----NKNYNRLvdivgtPKSKA-GYRVISidqktinLLRL--YKN 273
Cdd:cd01188    22 DYAILLLLARLGLRAGDVAGLRLDDIDWRSGTITVrqkkTGRPVEL------PLTEPvGEALAD-------YLRDgrPRT 88

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1608038057 274 RQRQLFSEVSsevpsvvfaTPTRKYQNTAIRQGSLDRRLKEIG--CPRFTFHAFRHTHASLLLNAGISYKELQYRLGHAT 351
Cdd:cd01188    89 DSREVFLRAR---------APYRPLSSTSQISSIVRRYLRKAGiePSHRGTHSLRHSLATRMLRAGTSLKVIADLLGHRS 159


                  ....*...
gi 1608038057 352 LAMTMdIY 359
Cdd:cd01188   160 IETTA-IY 166
Phage_int_SAM_3 pfam14659
Phage integrase, N-terminal SAM-like domain; This domain is found in a variety of phage ...
 71-125 6.69e-12

Phage integrase, N-terminal SAM-like domain; This domain is found in a variety of phage integrase proteins.


Pssm-ID: 464243 [Multi-domain]  Cd Length: 55  Bit Score: 59.87  E-value: 6.69e-12
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1608038057  71 KELAELWLKSYEMTVKPQTFIATKRMLHNHLMPVFGDIKLDKLSVSYIQGFINDL 125
Cdd:pfam14659   1 EEFYEIWLEDYKPRVKPSTYATYKRIIKNHILPYFGNMKLSKITPADIQKFQNKL 55
INT_C_like_4 cd01194
Uncharacterized site-specific tyrosine recombinase, C-terminal catalytic domain; Tyrosine ...
 198-361 7.19e-11

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: 60.47  E-value: 7.19e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1608038057 198 YYFDYVLYSILLATGCRFGEAVALTWSDIDFENATIDINknynrlvdIVGTPK-SKAGYrvISIDQKTINLLRLY-KNRQ 275
Cdd:cd01194    21 GLRDRAIISLMVTEGLRTVEIVRADVGDLRQEGEGTILY--------VQGKGKtSKDDF--VYLRPDVLKALQAYlKARG 90

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1608038057 276 RQLFSEvssevPsvVFATPTRKYQNTAIRQGSLDRRLKE------IGCPRFTFHAFRHTHASLLLNAGISYKELQYRLGH 349
Cdd:cd01194    91 KLDFEE-----P--LFTSLSNNSKGQRLTTRSIRRIIKKylrkagLDDDRLTAHSLRHTAGTLALKAGKSLREVQQLLRH 163

                         170
                  ....*....|..
gi 1608038057 350 ATLAMTMdIYSH 361
Cdd:cd01194   164 SDPNTTM-IYAH 174
INT_P4_C cd00801
Bacteriophage P4 integrase, C-terminal catalytic domain; P4-like integrases are found in ...
 208-361 4.43e-10

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: 58.44  E-value: 4.43e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1608038057 208 LLATGCRFGEAVALTWSDIDFENATIDInknynrlvdIVGTPKSKAGYRV-ISiDQ--KTINLLRLYKNRQRQLFsevss 284
Cdd:cd00801    28 LLLTGQRIGELARARWSEIDLEEKTWTI---------PAERTKNKRPHRVpLS-DQalEILEELKEFTGDSGYLF----- 92

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1608038057 285 evpsvvfatPTRKYQNTAIRQGSLDRRLKEIG--CPRFTFHAFRHTHASLLLNAGISYK--ELQyrLGHATLAMTMDIYS 360
Cdd:cd00801    93 ---------PSRRKKKKPISENTINKALKRLGykGKEFTPHDLRRTFSTLLNELGIDPEviERL--LNHVLGGVVRAAYN 161


                  .
gi 1608038057 361 H 361
Cdd:cd00801   162 R 162
xerS PRK05084
site-specific tyrosine recombinase XerS; Reviewed
 169-371 2.01e-09

site-specific tyrosine recombinase XerS; Reviewed


Pssm-ID: 235339 [Multi-domain]  Cd Length: 357  Bit Score: 58.39  E-value: 2.01e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1608038057 169 ENKAIKFIDYNDLKalmsYMEKLSNKKYSYYF-----DYVLYSILLATGCRFGEAVALTWSDIDFENATID-INKNYNRl 242
Cdd:PRK05084  164 GDEDYEFLDFIDNE----YEQKLSNRALSSFKknkerDLAIIALILGSGLRVSELVNLDLSDLNLKQMTIDvTRKGGKR- 238

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1608038057 243 vDIVGTPKSKAGY--RVISIDQKTINllrlYKNRQRQLFSEVSSEVPsvvfatptRKYQNTAIrQGSLDRRLKEIGCPRf 320
Cdd:PRK05084  239 -DSVNIAPFALPYleEYLKIRASRYK----AEKQEKALFLTKYRGKP--------NRISARAI-EKMVAKYSEAFGVRL- 303

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1608038057 321 TFHAFRHTHASLLLNAGISYKELQYRLGHATLAMTmDIYSHLSKDKEKEAV 371
Cdd:PRK05084  304 TPHKLRHTLATRLYDATKDQVLVADQLGHTSTETT-DLYTHIVNDEQKEAL 353
INTN1_C_like cd01185
Integrase IntN1 of Bacteroides mobilizable transposon NBU1 and similar proteins, C-terminal ...
 180-366 1.08e-08

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: 53.81  E-value: 1.08e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1608038057 180 DLKALMSYmeKLSNKKYsyyFDYVLYSILLA--TGCRFGEAVALTWSDIDFENATIDINKNynrlvdivgTPKSKAGYRV 257
Cdd:cd01185     2 ELKRLMAL--ELSDTSR---LELVRDMFLFScyTGLRFSDLKNLTWKNIVEASGRTWIRYR---------RKKTGKPVTV 67

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1608038057 258 IsIDQKTINLLRLYKNRQRqlfsevssevPSVVFATPTRKYQNtairqgsldRRLKEI----GCPRF-TFHAFRHTHASL 332
Cdd:cd01185    68 P-LLPVAREILEKYKDDRS----------EGKLFPVLSNQKIN---------RYLKEIakiaGIDKHlTFHVARHTFATL 127

                         170       180       190
                  ....*....|....*....|....*....|....
gi 1608038057 333 LLNAGISYKELQYRLGHATLAMTMdIYSHLSKDK 366
Cdd:cd01185   128 LLLKGVDIETISKLLGHSSIKTTQ-IYAKIVDSK 160
INT_RitC_C_like cd01182
C-terminal catalytic domain of recombinase RitC, a component of the recombinase trio; ...
 201-371 3.14e-08

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: 53.05  E-value: 3.14e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1608038057 201 DYVLYSILLATGCRFGEAVALTWSDIDFENatidinknyNRLVDIVGtpK-SKagYRVISIDQKTINLLRLYknrQRQLF 279
Cdd:cd01182    23 DHALLLLLYDTGARVQELADLTIRDLRLDD---------PATVRLHG--KgRK--ERTVPLWKETVAALKAY---LQEFH 86

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1608038057 280 SEVSSEVPSVVFatpTRKYQNTAIRQGS---LDRRLKEI--GCPRF----TFHAFRHTHASLLLNAGISYKELQYRLGHA 350
Cdd:cd01182    87 LTPDPKQLFPLF---PNRRGQPLTRDGVayiLNKYVALAsnRCPSLpkriTPHTLRHTKAMHLLQAGVDLTVIRDWLGHE 163

                         170       180
                  ....*....|....*....|.
gi 1608038057 351 TLAMTMdIYSHLSKDKEKEAV 371
Cdd:cd01182   164 SVETTQ-IYAEADLEMKREAL 183
xerC PRK01287
site-specific tyrosine recombinase XerC; Reviewed
 151-363 3.95e-06

site-specific tyrosine recombinase XerC; Reviewed


Pssm-ID: 234935 [Multi-domain]  Cd Length: 358  Bit Score: 48.20  E-value: 3.95e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1608038057 151 LIPFNPARDVILPKVVKPENKAIKFIDynDLKALMSYMEK-----LSNKkysyyfdyVLYSILLATGCRFGEAVALTWSD 225
Cdd:PRK01287  114 HILYNPAEDLELPKEEKRLPRQILSEA--ETEQVLASPDLttlqgLRDR--------ALLELLWSTGIRRGELARLDLYD 183

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1608038057 226 IDFENATIDI-----NKNynrlvdivgtpkskagyRVISIDQKTINLLRLYKNRQR-QLFSEVSSEVpsvVFAT--PTRK 297
Cdd:PRK01287  184 VDASRGVVTVrqgkgNKD-----------------RVVPVGERALAWLQRYLQDVRpQLAVRPDSGA---LFVAmdGDGL 243

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1608038057 298 YQNT-------AIRQGSLDrrlKEIGCprftfHAFRHTHASLLLNAGISYKELQYRLGHATLAMTmDIYSHLS 363
Cdd:PRK01287  244 ARNTltnmvgrYIRAAGIE---KAGAC-----HLFRHAMATQMLENGADTRHIQAILGHAKLETT-QIYTRVS 307
INT_RitB_C_like cd00797
C-terminal catalytic domain of recombinase RitB, a component of the recombinase trio; ...
 202-330 4.87e-06

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: 46.92  E-value: 4.87e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1608038057 202 YVLYSILLATGCRFGEAVALTWSDIDFENATIDINKNYNRlvdivgtpKSkagyRVISIDQKTINLLRLYKNRQRQLFSE 281
Cdd:cd00797    28 ATLFGLLYATGLRVGEALRLRLEDVDLDSGILTIRQTKFG--------KS----RLVPLHPSTVGALRDYLARRDRLLPS 95

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1608038057 282 VSSEvpsVVFATPTRK-YQNTAIRQGSLdRRLKEIGC--------PRftFHAFRHTHA 330
Cdd:cd00797    96 PSSS---YFFVSQQGGrLTGGGVYRVFR-RLLRRIGLrgagdgrgPR--LHDLRHTFA 147
int PHA02601
integrase; Provisional
 155-372 9.10e-06

integrase; Provisional


Pssm-ID: 222904 [Multi-domain]  Cd Length: 333  Bit Score: 47.03  E-value: 9.10e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1608038057 155 NPARDVilpKVVKPENKAIKFIDYNDLKALMSYMEKLSNKkysyyfDYVLYSIL-LATGCRFGEAVALTWSDIDFENATI 233
Cdd:PHA02601  155 NPLDGI---RPFKEAEPELAFLTKEEIERLLDACDGSRSP------DLGLIAKIcLATGARWSEAETLKRSQISPYKITF 225

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1608038057 234 DINKN-YNRLVdivgtPKSKAGYRVISidqktinllrlykNRQRQLFSevssevpsvvfatPTRKYQNTAIRQGSLDrrL 312
Cdd:PHA02601  226 VKTKGkKNRTV-----PISEELYKMLP-------------KRRGRLFK-------------DAYESFERAVKRAGID--L 272

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1608038057 313 KEIGCPrftfHAFRHTHASLLLNAGISYKELQYRLGHATLAMTMdIYSHLSKDKEKEAVS 372
Cdd:PHA02601  273 PEGQAT----HVLRHTFASHFMMNGGNILVLQRILGHATIEMTM-AYAHFAPDHLEDAVS 327
integrase_gron TIGR02249
integron integrase; Members of this family are integrases associated with integrons (and ...
 202-361 1.34e-05

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: 46.62  E-value: 1.34e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1608038057 202 YVLYSILLATGCRFGEAVALTWSDIDFENATIDINK---NYNRLVDIvgtPKSKAGYRvisidQKTINLLRLYKNR-QRQ 277
Cdd:TIGR02249 119 RLIAKLLYGSGMRLMECLRLRIQDIDFDYGEIRIRQgkgGKDRTVTL---PKELIPPL-----REQIELARAYHEAdLAE 190

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1608038057 278 LFSEV------SSEVPSV--------VFATPT-----------RKYQNTAIRQGSLDRRLKEIGCPR-FTFHAFRHTHAS 331
Cdd:TIGR02249 191 GYGGVylphalARKYPNApkewgwqyLFPSHRlsrdpesgvirRHHINETTIQRAVRRAVERAGIEKpVTCHTLRHSFAT 270

                         170       180       190
                  ....*....|....*....|....*....|
gi 1608038057 332 LLLNAGISYKELQYRLGHATLAMTMdIYSH 361
Cdd:TIGR02249 271 HLLESGADIRTVQELLGHSDVKTTQ-IYTH 299
INT_tnpB_C_Tn554 cd01187
Putative Transposase B from transposon Tn554, C-terminal catalytic domain; This family ...
 319-356 3.48e-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: 43.19  E-value: 3.48e-05
                          10        20        30
                  ....*....|....*....|....*....|....*...
gi 1608038057 319 RFTFHAFRHTHASLLLNAGISYKELQYRLGHATLAMTM 356
Cdd:cd01187   101 RFHTHRFRHTVATRLANSGMGILVLQQLLGHSSPEMTL 138
PRK15417 PRK15417
integron integrase;
305-364 5.74e-03

integron integrase;


Pssm-ID: 185315 [Multi-domain]  Cd Length: 337  Bit Score: 38.49  E-value: 5.74e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1608038057 305 QGSLDRRLKEIGCPR-FTFHAFRHTHASLLLNAGISYKELQYRLGHATLAMTMdIYSHLSK 364
Cdd:PRK15417  258 QRAFKRAVEQAGITKpATPHTLRHSFATALLRSGYDIRTVQDLLGHSDVSTTM-IYTHVLK 317
 
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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