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Conserved domains on  [gi|489830937|ref|WP_003734674|]
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MULTISPECIES: site-specific integrase [Listeria]

Protein Classification

tyrosine-type recombinase/integrase( domain architecture ID 11471964)

tyrosine-type recombinase/integrase cleaves DNA substrates by a series of staggered cuts, during which the protein becomes covalently linked to the DNA through a catalytic tyrosine residue at the carboxy end of the alignment.

Gene Ontology:  GO:0009009|GO:0006310
PubMed:  10047575|9278480

Graphical summary

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List of domain hits

Name Accession Description Interval E-value
XerD COG4974
Site-specific recombinase XerD [Replication, recombination and repair];
58-354 3.88e-48

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


:

Pssm-ID: 443999 [Multi-domain]  Cd Length: 291  Bit Score: 164.78  E-value: 3.88e-48
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489830937  58 NFKEFYTLFMKTFKDGKS-SQSTINLYDLAYNQFVDYFDE--KIKLNSIDAVQYQQFINHLSVD-YAISTVDTRHRKIRA 133
Cdd:COG4974    2 TLADLLEAFLEELKREKGlSPNTIKAYRRDLRRFLRFLEElgKIPLAEITPEDIRAYLNYLRERgLSPSTINRYLAALRS 81
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489830937 134 IFNKAVHLGYMKKNPTigAHISGQDVAKNKAQFMETDKVHLLLEELAKFHSIS---RAVIFLAVQTGMRFEEIIALTKKD 210
Cdd:COG4974   82 FFRYAVREGLLEDNPA--AKVKLPKKPRKLPRVLTEEEIEALLEALDTETPEGlrdRALLLLLYATGLRVSELLGLKWSD 159
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489830937 211 INFTKRSITVNkawdykytntfiDTKTKKSRVIYIDNSTAQYLHSYLNWHTDYMKEHaiknplmlLFITYHNKPVDNASC 290
Cdd:COG4974  160 IDLDRGTIRVR------------RGKGGKERTVPLSPEALEALREYLEERRPRDSDY--------LFPTRRGRPLSRRAI 219
                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 489830937 291 NKALKKICSTIN-SEPVTLHKLRHTHTGLCVEAGMDIIYVADRLGHDDINTTLKYYSHLSSNLRQ 354
Cdd:COG4974  220 RKILKRLAKRAGiPKRVTPHSLRHTFATHLLEAGVDLRTVQELLGHSSISTTQIYTHVSDEELRE 284
 
Name Accession Description Interval E-value
XerD COG4974
Site-specific recombinase XerD [Replication, recombination and repair];
58-354 3.88e-48

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


Pssm-ID: 443999 [Multi-domain]  Cd Length: 291  Bit Score: 164.78  E-value: 3.88e-48
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489830937  58 NFKEFYTLFMKTFKDGKS-SQSTINLYDLAYNQFVDYFDE--KIKLNSIDAVQYQQFINHLSVD-YAISTVDTRHRKIRA 133
Cdd:COG4974    2 TLADLLEAFLEELKREKGlSPNTIKAYRRDLRRFLRFLEElgKIPLAEITPEDIRAYLNYLRERgLSPSTINRYLAALRS 81
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489830937 134 IFNKAVHLGYMKKNPTigAHISGQDVAKNKAQFMETDKVHLLLEELAKFHSIS---RAVIFLAVQTGMRFEEIIALTKKD 210
Cdd:COG4974   82 FFRYAVREGLLEDNPA--AKVKLPKKPRKLPRVLTEEEIEALLEALDTETPEGlrdRALLLLLYATGLRVSELLGLKWSD 159
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489830937 211 INFTKRSITVNkawdykytntfiDTKTKKSRVIYIDNSTAQYLHSYLNWHTDYMKEHaiknplmlLFITYHNKPVDNASC 290
Cdd:COG4974  160 IDLDRGTIRVR------------RGKGGKERTVPLSPEALEALREYLEERRPRDSDY--------LFPTRRGRPLSRRAI 219
                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 489830937 291 NKALKKICSTIN-SEPVTLHKLRHTHTGLCVEAGMDIIYVADRLGHDDINTTLKYYSHLSSNLRQ 354
Cdd:COG4974  220 RKILKRLAKRAGiPKRVTPHSLRHTFATHLLEAGVDLRTVQELLGHSSISTTQIYTHVSDEELRE 284
INT_ICEBs1_C_like cd01189
C-terminal catalytic domain of integrases from bacterial phages and conjugate transposons; ...
170-347 1.52e-38

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: 134.99  E-value: 1.52e-38
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489830937 170 DKVHLLLEELAKFHSISRAVIFLAVQTGMRFEEIIALTKKDINFTKRSITVNKAWDYKYTNTFI--DTKTKKS-RVIYID 246
Cdd:cd01189    2 EELKKLLEALKKRGDRYYLLFLLALLTGLRRGELLALTWSDIDFENGTIRINRTLVRKKKGGYVikPPKTKSSiRTIPLP 81
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489830937 247 NSTAQYLhsylnwhtdymKEHaiknplmllfityhnkpvdnascnKALKKICSTINSEPVTLHKLRHTHTGLCVEAGMDI 326
Cdd:cd01189   82 DELIELL-----------KEL------------------------KAFKKLLKKAGLPRITPHDLRHTFASLLLEAGVPL 126
                        170       180
                 ....*....|....*....|.
gi 489830937 327 IYVADRLGHDDINTTLKYYSH 347
Cdd:cd01189  127 KVIAERLGHSDISTTLDVYAH 147
Phage_integrase pfam00589
Phage integrase family; Members of this family cleave DNA substrates by a series of staggered ...
166-349 2.76e-16

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: 75.82  E-value: 2.76e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489830937  166 FMETDKVHLLLEELAKF-HSI-SRAVIFLAVQTGMRFEEIIALTKKDINFTKRSITVNKawdykytntfidTKTKKSRVI 243
Cdd:pfam00589   1 RLTEDEVERLLDAAETGpLSIrDKALLELLYATGLRISELCSLRWSDIDFENGVIRVHR------------GKGNKERTV 68
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489830937  244 YIDNSTAQYLHSYLNwhtdymKEHAIKNPLMLLFITYHNKPVDNASCNKALKKICSTINSE-PVTLHKLRHTHTGLCVEA 322
Cdd:pfam00589  69 PLSDAALELLKEWLS------KRLLEAPKSDYLFASKRGKPLSRQTVRKIFKRAGKEAGLElPLHPHMLRHSFATHLLEA 142
                         170       180
                  ....*....|....*....|....*..
gi 489830937  323 GMDIIYVADRLGHDDINTTlKYYSHLS 349
Cdd:pfam00589 143 GVDLRVVQKLLGHSSISTT-QIYTHVA 168
xerC PRK00236
site-specific tyrosine recombinase XerC; Reviewed
76-350 1.01e-09

site-specific tyrosine recombinase XerC; Reviewed


Pssm-ID: 234698 [Multi-domain]  Cd Length: 297  Bit Score: 59.01  E-value: 1.01e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489830937  76 SQSTINLY--DLAynQFVDYFDEK--IKLNSIDAVQYQQFINHLSVDYAISTvdTRHRK---IRAIFNKAVHLGYMKKNP 148
Cdd:PRK00236  24 SPHTLRAYrrDLR--AFLAFLEEHgiSSLQDLDAADLRSFLARRRRQGLSAR--SLARRlsaLRSFYRWLVRRGLLKANP 99
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489830937 149 TIGahISGQDVAKNKAQFMETDKVHLLLEELAKFHSIS---RAVIFLAVQTGMRFEEIIALTKKDINFTKRSITVnkawd 225
Cdd:PRK00236 100 AAG--LRAPKIPKRLPKPLDVDQAKRLLDAIDEDDPLAlrdRAILELLYGSGLRLSELVGLDIDDLDLASGTLRV----- 172
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489830937 226 ykytntfidT-KTKKSRVIYIDNSTAQYLHSYLNwHTDYMKEHaiKNPlmlLFITYHNKPVDNASCNKALKKICSTIN-S 303
Cdd:PRK00236 173 ---------LgKGNKERTVPLGRAAREALEAYLA-LRPLFLPD--DDA---LFLGARGGRLSPRVVQRRVKKLGKKAGlP 237
                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|
gi 489830937 304 EPVTLHKLRH---THTglcVEAGMDIIYVADRLGHDDINTTlKYYSHLSS 350
Cdd:PRK00236 238 SHITPHKLRHsfaTHL---LESGGDLRAVQELLGHASLSTT-QIYTHVDF 283
integrase_gron TIGR02249
integron integrase; Members of this family are integrases associated with integrons (and ...
177-347 3.91e-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: 45.08  E-value: 3.91e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489830937  177 EELAKFHSISRAVIFLAVQ----TGMRFEEIIALTKKDINFTKRSITVnkaWDykytntfidTKTKKSRVIYIDNSTAQY 252
Cdd:TIGR02249 105 EEVRRLLEHLEGKYRLIAKllygSGMRLMECLRLRIQDIDFDYGEIRI---RQ---------GKGGKDRTVTLPKELIPP 172
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489830937  253 LHSYL----NWHTDYMKE--------HAIKN---------PLMLLFITY-----------HNKPVDNASCNKALKKICST 300
Cdd:TIGR02249 173 LREQIelarAYHEADLAEgyggvylpHALARkypnapkewGWQYLFPSHrlsrdpesgviRRHHINETTIQRAVRRAVER 252
                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*...
gi 489830937  301 INSE-PVTLHKLRHTHTGLCVEAGMDIIYVADRLGHDDINTTlKYYSH 347
Cdd:TIGR02249 253 AGIEkPVTCHTLRHSFATHLLESGADIRTVQELLGHSDVKTT-QIYTH 299
 
Name Accession Description Interval E-value
XerD COG4974
Site-specific recombinase XerD [Replication, recombination and repair];
58-354 3.88e-48

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


Pssm-ID: 443999 [Multi-domain]  Cd Length: 291  Bit Score: 164.78  E-value: 3.88e-48
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489830937  58 NFKEFYTLFMKTFKDGKS-SQSTINLYDLAYNQFVDYFDE--KIKLNSIDAVQYQQFINHLSVD-YAISTVDTRHRKIRA 133
Cdd:COG4974    2 TLADLLEAFLEELKREKGlSPNTIKAYRRDLRRFLRFLEElgKIPLAEITPEDIRAYLNYLRERgLSPSTINRYLAALRS 81
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489830937 134 IFNKAVHLGYMKKNPTigAHISGQDVAKNKAQFMETDKVHLLLEELAKFHSIS---RAVIFLAVQTGMRFEEIIALTKKD 210
Cdd:COG4974   82 FFRYAVREGLLEDNPA--AKVKLPKKPRKLPRVLTEEEIEALLEALDTETPEGlrdRALLLLLYATGLRVSELLGLKWSD 159
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489830937 211 INFTKRSITVNkawdykytntfiDTKTKKSRVIYIDNSTAQYLHSYLNWHTDYMKEHaiknplmlLFITYHNKPVDNASC 290
Cdd:COG4974  160 IDLDRGTIRVR------------RGKGGKERTVPLSPEALEALREYLEERRPRDSDY--------LFPTRRGRPLSRRAI 219
                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 489830937 291 NKALKKICSTIN-SEPVTLHKLRHTHTGLCVEAGMDIIYVADRLGHDDINTTLKYYSHLSSNLRQ 354
Cdd:COG4974  220 RKILKRLAKRAGiPKRVTPHSLRHTFATHLLEAGVDLRTVQELLGHSSISTTQIYTHVSDEELRE 284
INT_ICEBs1_C_like cd01189
C-terminal catalytic domain of integrases from bacterial phages and conjugate transposons; ...
170-347 1.52e-38

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: 134.99  E-value: 1.52e-38
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489830937 170 DKVHLLLEELAKFHSISRAVIFLAVQTGMRFEEIIALTKKDINFTKRSITVNKAWDYKYTNTFI--DTKTKKS-RVIYID 246
Cdd:cd01189    2 EELKKLLEALKKRGDRYYLLFLLALLTGLRRGELLALTWSDIDFENGTIRINRTLVRKKKGGYVikPPKTKSSiRTIPLP 81
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489830937 247 NSTAQYLhsylnwhtdymKEHaiknplmllfityhnkpvdnascnKALKKICSTINSEPVTLHKLRHTHTGLCVEAGMDI 326
Cdd:cd01189   82 DELIELL-----------KEL------------------------KAFKKLLKKAGLPRITPHDLRHTFASLLLEAGVPL 126
                        170       180
                 ....*....|....*....|.
gi 489830937 327 IYVADRLGHDDINTTLKYYSH 347
Cdd:cd01189  127 KVIAERLGHSDISTTLDVYAH 147
XerC COG4973
Site-specific recombinase XerC [Replication, recombination and repair];
66-355 4.78e-36

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


Pssm-ID: 443998 [Multi-domain]  Cd Length: 287  Bit Score: 132.78  E-value: 4.78e-36
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489830937  66 FMKTFKDGKSSQSTINLYDLAYNQFVDYFDEK-IKLNSIDAVQYQQFINHLS-VDYAISTVDTRHRKIRAIFNKAVHLGY 143
Cdd:COG4973   11 YLEHLRERRLSPKTLEAYRRDLRRLIPLLGDAdLPLEELTPADVRRFLARLHrRGLSPRTLNRRLSALRSFFNWAVREGL 90
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489830937 144 MKKNPTIGahISGQDVAKNKAQFMETDKVHLLLEELAK--FHSISRAVIFLAVQTGMRFEEIIALTKKDINFTKRSITVN 221
Cdd:COG4973   91 LEANPAAG--VKAPKAPRKLPRALTVDELAQLLDALADdpLAVRDRAIVELLYSTGLRLGELVGLDWEDVDLDAGEVRVR 168
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489830937 222 kawdykytntfidTKTKKSRVIYIDNSTAQYLHSYLNW--HTDYMKEHAiknplmlLFITYHNKPVDNASCNKALKKICS 299
Cdd:COG4973  169 -------------GKTGKSRTVPLGPKALAALREWLAVrpELAAPDEGA-------LFPSRRGTRLSPRNVQKRLRRLAK 228
                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 489830937 300 TIN-SEPVTLHKLRHTHTGLCVEAGMDIIYVADRLGHDDINTTLKyYSHLSsnlRQH 355
Cdd:COG4973  229 KAGlPKHVHPHDLRHSFATHLLESGGDLRAVQELLGHASISTTQI-YTHLD---FQH 281
DNA_BRE_C cd00397
DNA breaking-rejoining enzymes, C-terminal catalytic domain; The DNA breaking-rejoining enzyme ...
187-344 1.40e-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: 104.10  E-value: 1.40e-26
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489830937 187 RAVIFLAVQTGMRFEEIIALTKKDINFTKRSITVNKAWdykytntfidTKTKKSRVIYIDNSTAQYLHSYLNWHTDYMKE 266
Cdd:cd00397   20 RAILLLLLETGLRISELLALKVKDIDLDNGTIRVRGKK----------TKGGKERTVPLPKELAEELKEYLKERRDKRGP 89
                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 489830937 267 HAIKNPLMLLFITYHNKPVDNASCNKALKKICSTINsEPVTLHKLRHTHTGLCVEAGMDIIYVADRLGHDDINTTLKY 344
Cdd:cd00397   90 LLKSLYLNKLFGTKLGERLSRRTLRRIFKKAGIEAG-RKITPHSLRHTFATNLLENGVDIKVVQKLLGHSSISTTQRY 166
FimB COG0582
Integrase/recombinase, includes phage integrase [Replication, recombination and repair, ...
39-347 3.76e-22

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


Pssm-ID: 440347 [Multi-domain]  Cd Length: 391  Bit Score: 96.65  E-value: 3.76e-22
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489830937  39 KASKLLKQVQHDSSSLKEWnFKEFYTLFMKTFKDGKSSQ--STINLYDLAYNqfvdyfdEKIKLNSIDAVQYQQFINHLS 116
Cdd:COG0582   84 RKAAKAAAAAAAANTFEEV-AEEWLEEKKPEWKEKTAAQvrRTLEKHIFPVL-------GDRPIAEITPPDLLAVLRPIE 155
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489830937 117 VDYAISTVDTRHRKIRAIFNKAVHLGYMKKNPTIGAHISGQDVAKNKAQFMETDKVHLLLEEL--AKFHSISRAVIFLAV 194
Cdd:COG0582  156 ARGAPETARRVRQRLRQVFRYAVARGLIERNPAADLKGALPKPKVKHHPALTPEELPELLRALdaYRGSPVTRLALRLLL 235
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489830937 195 QTGMRFEEIIALTKKDINFTKRSITVNKAwdykytntfiDTKTKKSRVIYIDNSTAQYLHSylnwhtdyMKEHAIKNPLM 274
Cdd:COG0582  236 LTGVRPGELRGARWSEIDLEAALWTIPAE----------RMKTRRPHIVPLSRQALEILKE--------LKPLTGDSEYV 297
                        250       260       270       280       290       300       310
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 489830937 275 LLFITYHNKPVDNASCNKALKKIcstiNSEPVTLHKLRHTHTGLCVEAGMDIIYVADRLGHDDINTTLKYYSH 347
Cdd:COG0582  298 FPSRRGPKKPMSENTLNKALRRM----GYGRFTPHGFRHTASTLLNEAGFPPDVIERQLAHKDGNKVRAAYNR 366
Phage_integrase pfam00589
Phage integrase family; Members of this family cleave DNA substrates by a series of staggered ...
166-349 2.76e-16

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: 75.82  E-value: 2.76e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489830937  166 FMETDKVHLLLEELAKF-HSI-SRAVIFLAVQTGMRFEEIIALTKKDINFTKRSITVNKawdykytntfidTKTKKSRVI 243
Cdd:pfam00589   1 RLTEDEVERLLDAAETGpLSIrDKALLELLYATGLRISELCSLRWSDIDFENGVIRVHR------------GKGNKERTV 68
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489830937  244 YIDNSTAQYLHSYLNwhtdymKEHAIKNPLMLLFITYHNKPVDNASCNKALKKICSTINSE-PVTLHKLRHTHTGLCVEA 322
Cdd:pfam00589  69 PLSDAALELLKEWLS------KRLLEAPKSDYLFASKRGKPLSRQTVRKIFKRAGKEAGLElPLHPHMLRHSFATHLLEA 142
                         170       180
                  ....*....|....*....|....*..
gi 489830937  323 GMDIIYVADRLGHDDINTTlKYYSHLS 349
Cdd:pfam00589 143 GVDLRVVQKLLGHSSISTT-QIYTHVA 168
INT_Rci_Hp1_C cd00796
Shufflon-specific DNA recombinase Rci and Bacteriophage Hp1_like integrase, C-terminal ...
164-345 4.31e-16

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: 75.06  E-value: 4.31e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489830937 164 AQFMETDKVHLLLEELAKFHSI-SRAVIFLAVQTGMRFEEIIALTKKDINFTKRSItvnkawdykytnTFIDTKTKKSRV 242
Cdd:cd00796    2 DRFLTEDEEARLLAALEESTNPhLRLIVLLALYTGARRGEILSLRWDDIDLEVGLI------------VLPETKNGKPRT 69
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489830937 243 IYIdNSTAQYLhsylnwhtdyMKEHAIKNPLMLLFITYHNKPVDNASCNKALKKICSTINSEPVTLHKLRHTHTGLCVEA 322
Cdd:cd00796   70 VPL-SDEAIAI----------LKELKRKRGKDGFFVDGRFFGIPIASLRRAFKKARKRAGLEDLRFHDLRHTFASRLVQA 138
                        170       180
                 ....*....|....*....|...
gi 489830937 323 GMDIIYVADRLGHDDINTTLKYY 345
Cdd:cd00796  139 GVPIKTVAKILGHSSIKMTMRYA 161
INT_RitC_C_like cd01182
C-terminal catalytic domain of recombinase RitC, a component of the recombinase trio; ...
187-344 1.46e-14

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: 71.54  E-value: 1.46e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489830937 187 RAVIFLAVQTGMRFEEIIALTKKDINFTKRSitvnkawdykytNTFIDTKTKKSRVIYIDNSTAQYLHSYLNWHTDYMKE 266
Cdd:cd01182   24 HALLLLLYDTGARVQELADLTIRDLRLDDPA------------TVRLHGKGRKERTVPLWKETVAALKAYLQEFHLTPDP 91
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489830937 267 haikNPLMLLFITYHNKP--VDNAS--CNKALKKICSTINSEP--VTLHKLRHTHTGLCVEAGMDIIYVADRLGHDDINT 340
Cdd:cd01182   92 ----KQLFPLFPNRRGQPltRDGVAyiLNKYVALASNRCPSLPkrITPHTLRHTKAMHLLQAGVDLTVIRDWLGHESVET 167

                 ....
gi 489830937 341 TLKY 344
Cdd:cd01182  168 TQIY 171
INT_XerDC_C cd00798
XerD and XerC integrases, C-terminal catalytic domains; XerDC-like integrases are involved in ...
187-349 1.81e-13

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: 67.92  E-value: 1.81e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489830937 187 RAVIFLAVQTGMRFEEIIALTKKDINFTKRSITVnkawdykytntfidT-KTKKSRVIYIDNSTAQYLHSYLNWHTDYMK 265
Cdd:cd00798   22 RAILELLYASGLRVSELVGLDLSDVDLDEGLVRV--------------TgKGNKERLVPFGSYAVEALEEYLEERRPLLL 87
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489830937 266 EhaiKNPLMLLFITYHNKPVDNASCNKALKKICSTIN-SEPVTLHKLRH---THtglCVEAGMDIIYVADRLGHDDINTT 341
Cdd:cd00798   88 K---KKPPDALFLNKRGKRLSRRGVWRILKKYAERAGlPKHVSPHTLRHsfaTH---LLEGGADLRVVQELLGHASLSTT 161

                 ....*...
gi 489830937 342 lKYYSHLS 349
Cdd:cd00798  162 -QIYTHVS 168
INT_C_like_4 cd01194
Uncharacterized site-specific tyrosine recombinase, C-terminal catalytic domain; Tyrosine ...
187-345 6.31e-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: 60.85  E-value: 6.31e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489830937 187 RAVIFLAVQTGMRFEEIIALTKKDINftkrsitvnkaWDYKYTNTFIDTK--TKKSRVIYIDNSTAQYLHSYLNWHtdym 264
Cdd:cd01194   25 RAIISLMVTEGLRTVEIVRADVGDLR-----------QEGEGTILYVQGKgkTSKDDFVYLRPDVLKALQAYLKAR---- 89
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489830937 265 KEHAIKNPLmllFITYHN----KPVDNASCN----KALKKIcsTINSEPVTLHKLRHTHTGLCVEAGMDIIYVADRLGHD 336
Cdd:cd01194   90 GKLDFEEPL---FTSLSNnskgQRLTTRSIRriikKYLRKA--GLDDDRLTAHSLRHTAGTLALKAGKSLREVQQLLRHS 164

                 ....*....
gi 489830937 337 DINTTLKYY 345
Cdd:cd01194  165 DPNTTMIYA 173
INT_IntI_C cd01193
Integron integrase and similar protiens, C-terminal catalytic domain; Integron integrases ...
166-344 7.43e-11

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: 60.37  E-value: 7.43e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489830937 166 FMETDKVHLLLEELAKfhSISRAVIFLAVQTGMRFEEIIALTKKDINFTKRSITVNkawdykytntfiDTKTKKSRVIYI 245
Cdd:cd01193    5 VLSPDEVRRILGALTE--LRHRLILSLLYGAGLRISELLRLRVKDIDFERGVIRVR------------QGKGGKDRVVPL 70
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489830937 246 DNSTAQYLHSYLNWHTDYMKEHA---IKNPLMLLFITYHNKPVDNASCNKALKKICSTIN-SEPVTLHKLRH---THTgl 318
Cdd:cd01193   71 PEKLLEPLRRYLKSARPKEELDPaegRAGVLDPRTGVERRHHISETTVQRALKKAVEQAGiTKRVTPHTLRHsfaTHL-- 148
                        170       180
                 ....*....|....*....|....*.
gi 489830937 319 cVEAGMDIIYVADRLGHDDINTTLKY 344
Cdd:cd01193  149 -LEAGTDIRTIQELLGHSDLSTTMIY 173
INT_RitA_C_like cd01188
C-terminal catalytic domain of recombinase RitA, a component of the recombinase trio; ...
187-354 2.66e-10

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


Pssm-ID: 271188 [Multi-domain]  Cd Length: 179  Bit Score: 58.79  E-value: 2.66e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489830937 187 RAVIFLAVQTGMRFEEIIALTKKDINFTKRSITVnkawdykytntfIDTKTKKSRVIYIDNSTAQYLHSYL-NWHTdymk 265
Cdd:cd01188   23 YAILLLLARLGLRAGDVAGLRLDDIDWRSGTITV------------RQKKTGRPVELPLTEPVGEALADYLrDGRP---- 86
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489830937 266 ehaiKNPLMLLFITY---HNKPVDNASCNKALKKICSTINSEPVTL--HKLRHTHTGLCVEAGMDIIYVADRLGHDDINT 340
Cdd:cd01188   87 ----RTDSREVFLRArapYRPLSSTSQISSIVRRYLRKAGIEPSHRgtHSLRHSLATRMLRAGTSLKVIADLLGHRSIET 162
                        170
                 ....*....|....
gi 489830937 341 TLKYYSHLSSNLRQ 354
Cdd:cd01188  163 TAIYAKIDVDDLRE 176
xerC PRK00236
site-specific tyrosine recombinase XerC; Reviewed
76-350 1.01e-09

site-specific tyrosine recombinase XerC; Reviewed


Pssm-ID: 234698 [Multi-domain]  Cd Length: 297  Bit Score: 59.01  E-value: 1.01e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489830937  76 SQSTINLY--DLAynQFVDYFDEK--IKLNSIDAVQYQQFINHLSVDYAISTvdTRHRK---IRAIFNKAVHLGYMKKNP 148
Cdd:PRK00236  24 SPHTLRAYrrDLR--AFLAFLEEHgiSSLQDLDAADLRSFLARRRRQGLSAR--SLARRlsaLRSFYRWLVRRGLLKANP 99
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489830937 149 TIGahISGQDVAKNKAQFMETDKVHLLLEELAKFHSIS---RAVIFLAVQTGMRFEEIIALTKKDINFTKRSITVnkawd 225
Cdd:PRK00236 100 AAG--LRAPKIPKRLPKPLDVDQAKRLLDAIDEDDPLAlrdRAILELLYGSGLRLSELVGLDIDDLDLASGTLRV----- 172
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489830937 226 ykytntfidT-KTKKSRVIYIDNSTAQYLHSYLNwHTDYMKEHaiKNPlmlLFITYHNKPVDNASCNKALKKICSTIN-S 303
Cdd:PRK00236 173 ---------LgKGNKERTVPLGRAAREALEAYLA-LRPLFLPD--DDA---LFLGARGGRLSPRVVQRRVKKLGKKAGlP 237
                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|
gi 489830937 304 EPVTLHKLRH---THTglcVEAGMDIIYVADRLGHDDINTTlKYYSHLSS 350
Cdd:PRK00236 238 SHITPHKLRHsfaTHL---LESGGDLRAVQELLGHASLSTT-QIYTHVDF 283
int PHA02601
integrase; Provisional
1-349 2.92e-09

integrase; Provisional


Pssm-ID: 222904 [Multi-domain]  Cd Length: 333  Bit Score: 57.82  E-value: 2.92e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489830937   1 MKIKKLANGKYCVRLRIK-VDGEWKEKRLTDTSETNLMYKASKllkqvqhDSSSLKEWNFK------------EFYTLFM 67
Cdd:PHA02601   1 MAVRKLKDGKWLCEIYPNgRDGKRIRKRFATKGEALAFENYTM-------AEVDDKEWVGEkedrrrlsellqIWWDLHG 73
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489830937  68 KTFKDGKSSQSTI-----NLYD-----LAYNQFVDYFDEKIKlnsidavqyQQFINHLSVDYAISTVDTRHRKIRAIFNK 137
Cdd:PHA02601  74 QTLEDGKARLAKLlilckGLGDpiaseFTAKDFADYRARRLS---------GEFKVNKGRPIKPATVNRELAYLSAVFNE 144
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489830937 138 AVHLG-YMKKNPTIGahISGQDVAKNKAQFMETDKVHLLLEELAKFHSISRAVI-FLAVQTGMRFEEIIALTKKDINftk 215
Cdd:PHA02601 145 LIKLGkWSGPNPLDG--IRPFKEAEPELAFLTKEEIERLLDACDGSRSPDLGLIaKICLATGARWSEAETLKRSQIS--- 219
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489830937 216 rsitvnkawdyKYTNTFIDTKTKKSRVIYIdnstAQYLHSYLNWHTDYmkehaiknplmlLFityhnkPVDNASCNKALK 295
Cdd:PHA02601 220 -----------PYKITFVKTKGKKNRTVPI----SEELYKMLPKRRGR------------LF------KDAYESFERAVK 266
                        330       340       350       360       370
                 ....*....|....*....|....*....|....*....|....*....|....
gi 489830937 296 KICSTINSEPVTlHKLRHTHTGLCVEAGMDIIYVADRLGHDDINTTLKyYSHLS 349
Cdd:PHA02601 267 RAGIDLPEGQAT-HVLRHTFASHFMMNGGNILVLQRILGHATIEMTMA-YAHFA 318
INT_tnpA_C_Tn554 cd01186
Putative Transposase A from transposon Tn554, C-terminal catalytic domain; This family ...
187-349 8.07e-09

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: 54.73  E-value: 8.07e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489830937 187 RAVIFLAVQTGMRFEEIIALTKKDINFTKRSITVnkawdykyTNTFIDT-----KTKKSRVIYIDNSTAQYLHSYLNWHT 261
Cdd:cd01186   20 KFLLALLYETGLRIGEALGLRIEDIDMADNQIEL--------VPREDNTnearaKSMRERRIPVSQDLIDLYADYLTYIY 91
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489830937 262 DYMKEHAIKnplmlLFITYHNKPVDNASCNKALKKICSTI---NSEPVTLHKLRHTHTGLCVEAGMDIIYVADRLGHDDI 338
Cdd:cd01186   92 CEEAEFSIT-----VFVNVKGGNQGKAMNYSDVYDLVRRLkkrTGIDFTPHMFRHTHATALIRAGWSIEVVARRLGHAHV 166
                        170
                 ....*....|.
gi 489830937 339 NTTLKYYSHLS 349
Cdd:cd01186  167 QTTLNTYGHLS 177
xerS PRK05084
site-specific tyrosine recombinase XerS; Reviewed
188-349 2.97e-08

site-specific tyrosine recombinase XerS; Reviewed


Pssm-ID: 235339 [Multi-domain]  Cd Length: 357  Bit Score: 54.92  E-value: 2.97e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489830937 188 AVIFLAVQTGMRFEEIIALTKKDINFTKRSITVNKawdykytntfidtKTKKSRVIYIDNSTAQYLHSYLNWHTDymKEH 267
Cdd:PRK05084 199 AIIALILGSGLRVSELVNLDLSDLNLKQMTIDVTR-------------KGGKRDSVNIAPFALPYLEEYLKIRAS--RYK 263
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489830937 268 AIKNPLmLLFIT-YHNKP--VDNASCNKALKKIcSTINSEPVTLHKLRHTHTGLCVEAGMDIIYVADRLGHDDINTTLkY 344
Cdd:PRK05084 264 AEKQEK-ALFLTkYRGKPnrISARAIEKMVAKY-SEAFGVRLTPHKLRHTLATRLYDATKDQVLVADQLGHTSTETTD-L 340

                 ....*
gi 489830937 345 YSHLS 349
Cdd:PRK05084 341 YTHIV 345
INTN1_C_like cd01185
Integrase IntN1 of Bacteroides mobilizable transposon NBU1 and similar proteins, C-terminal ...
196-344 4.95e-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: 51.88  E-value: 4.95e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489830937 196 TGMRFEEIIALTKKDInftkrsITVNKAWDYKYtntfIDTKTKKSRVIYIDNSTAQYLHSYLNWHTDymkehaiknplML 275
Cdd:cd01185   30 TGLRFSDLKNLTWKNI------VEASGRTWIRY----RRKKTGKPVTVPLLPVAREILEKYKDDRSE-----------GK 88
                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489830937 276 LFityhnKPVDNASCNKALKKICSTIN-SEPVTLHKLRHTHTGLCVEAGMDIIYVADRLGHDDINTTLKY 344
Cdd:cd01185   89 LF-----PVLSNQKINRYLKEIAKIAGiDKHLTFHVARHTFATLLLLKGVDIETISKLLGHSSIKTTQIY 153
Phage_int_SAM_5 pfam13102
Phage integrase SAM-like domain; A family of uncharacterized proteins found by clustering ...
58-154 9.54e-07

Phage integrase SAM-like domain; A family of uncharacterized proteins found by clustering human gut metagenomic sequences. This family appears related to the N-terminal domain of phage integrases.


Pssm-ID: 463787 [Multi-domain]  Cd Length: 99  Bit Score: 46.83  E-value: 9.54e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489830937   58 NFKEFYTLFMKTFKDgKSSQSTINLYDLAYNQFVDY-FDEKIKLNSIDAVQYQQFINHLSVDYAIS--TVDTRHRKIRAI 134
Cdd:pfam13102   1 DFLDYFKEYIEELKK-KGSKGTARNYKSTLKHLKKFlKKKDITFEEITVDFLEKFEEYLKKKKGLSenTISKYFRTLRAV 79
                          90       100
                  ....*....|....*....|
gi 489830937  135 FNKAVHLGYMKKNPTIGAHI 154
Cdd:pfam13102  80 LNKAIKEGIIKKNPYPKYKI 99
INT_P4_C cd00801
Bacteriophage P4 integrase, C-terminal catalytic domain; P4-like integrases are found in ...
176-347 2.91e-06

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: 47.26  E-value: 2.91e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489830937 176 LEELAKF---------HSISRAVIFLAVQTGMRFEEIIALTKKDINFTKRSITVNKAwdykytntfiDTKTKKSRVIYId 246
Cdd:cd00801    2 PDELPELwraldtanlSPPTKLALRLLLLTGQRIGELARARWSEIDLEEKTWTIPAE----------RTKNKRPHRVPL- 70
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489830937 247 nstaqylhsylnwhTDYMKE-----HAIKNPLMLLFI--TYHNKPVDNASCNKALKKICSTinSEPVTLHKLRHTHTGLC 319
Cdd:cd00801   71 --------------SDQALEileelKEFTGDSGYLFPsrRKKKKPISENTINKALKRLGYK--GKEFTPHDLRRTFSTLL 134
                        170       180
                 ....*....|....*....|....*....
gi 489830937 320 VEAGMDiIYVADR-LGHDDINTTLKYYSH 347
Cdd:cd00801  135 NELGID-PEVIERlLNHVLGGVVRAAYNR 162
integrase_gron TIGR02249
integron integrase; Members of this family are integrases associated with integrons (and ...
177-347 3.91e-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: 45.08  E-value: 3.91e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489830937  177 EELAKFHSISRAVIFLAVQ----TGMRFEEIIALTKKDINFTKRSITVnkaWDykytntfidTKTKKSRVIYIDNSTAQY 252
Cdd:TIGR02249 105 EEVRRLLEHLEGKYRLIAKllygSGMRLMECLRLRIQDIDFDYGEIRI---RQ---------GKGGKDRTVTLPKELIPP 172
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489830937  253 LHSYL----NWHTDYMKE--------HAIKN---------PLMLLFITY-----------HNKPVDNASCNKALKKICST 300
Cdd:TIGR02249 173 LREQIelarAYHEADLAEgyggvylpHALARkypnapkewGWQYLFPSHrlsrdpesgviRRHHINETTIQRAVRRAVER 252
                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*...
gi 489830937  301 INSE-PVTLHKLRHTHTGLCVEAGMDIIYVADRLGHDDINTTlKYYSH 347
Cdd:TIGR02249 253 AGIEkPVTCHTLRHSFATHLLESGADIRTVQELLGHSDVKTT-QIYTH 299
xerD PRK02436
site-specific tyrosine recombinase XerD;
83-345 5.18e-05

site-specific tyrosine recombinase XerD;


Pssm-ID: 235038 [Multi-domain]  Cd Length: 245  Bit Score: 44.21  E-value: 5.18e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489830937  83 YDLayNQFVDYFDEKIKLNSIdaVQYQQFINHLSVDyaistvdTRHRKIRAIfNKAVHLGYMKKnptigaHISGQDVAKN 162
Cdd:PRK02436  24 YDL--QQFLQLVGERVSQEKL--KLYQQSLANLKPS-------AQKRKISAV-NQFLYFLYQKG------ELDSFFKLKE 85
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489830937 163 KAQFMETDKVHLLLEELAKF-----HSISRAVIFLAVQTGMRFEEIIALTKKDINFTKRSITVNKAwdykytntfidtKT 237
Cdd:PRK02436  86 TAKLPESKKEKLEILDLSSFyqetpFPEGQLIALLILELGLTPSEIAGLKVADIDLDFQVLTIEKA------------GG 153
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489830937 238 KksRVIYIDNSTAQYLHSYLNwhTDYMKEHaiknplmllfityHNKPVDNASCNKALKKICSTINSEPVTLHKLRHTHTG 317
Cdd:PRK02436 154 K--RVLTLPEALLPFLEAILN--QTYLFEH-------------KGKPYSRQWFFNQLKSFVKSIGYPGLSAQKLREQFIL 216
                        250       260
                 ....*....|....*....|....*...
gi 489830937 318 LCVEAGMDIIYVADRLGHDDINTTLKYY 345
Cdd:PRK02436 217 KQKEAGKSIYELARLLGLKSPVTLEKYY 244
INT_C_like_3 cd01192
Uncharacterized site-specific tyrosine recombinase, C-terminal catalytic domain; Tyrosine ...
169-344 5.48e-05

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


Pssm-ID: 271192 [Multi-domain]  Cd Length: 178  Bit Score: 43.43  E-value: 5.48e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489830937 169 TDKVHLLLEELAKFHSISRAVIFLAVQTGMRFEEIIALTKKDI-NFTKRSItvnkawdykytntfIDTKTKKSRVIYIDN 247
Cdd:cd01192    9 KKLIKEIKLYLKKANPRNYLLFIVGINTGLRISDLLSLKVEDVtNKDKLSI--------------KEQKTGKQKTFPLNP 74
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489830937 248 STAQYLHSYLNW----HTDYMKEHAIKNPlmllfityhNKPVDNASCNKALKKICSTIN-SEPVTLHKLRHTHTGLCVEA 322
Cdd:cd01192   75 TLVKALKEYIDDldlkRNDYLFKSLKQGP---------EKPISRKQAYKILKKAADDLGlNYNIGTHSLRKTFGYHVYKQ 145
                        170       180
                 ....*....|....*....|..
gi 489830937 323 GMDIIYVADRLGHDDINTTLKY 344
Cdd:cd01192  146 GKDIELLMKLLNHSSPSITLRY 167
xerC PRK01287
site-specific tyrosine recombinase XerC; Reviewed
187-349 8.49e-05

site-specific tyrosine recombinase XerC; Reviewed


Pssm-ID: 234935 [Multi-domain]  Cd Length: 358  Bit Score: 44.35  E-value: 8.49e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489830937 187 RAVIFLAVQTGMRFEEIIALTKKDINFTKRSITVNKAwdykytntfidtKTKKSRVIYIDnstaqylHSYLNWHTDYMKE 266
Cdd:PRK01287 160 RALLELLWSTGIRRGELARLDLYDVDASRGVVTVRQG------------KGNKDRVVPVG-------ERALAWLQRYLQD 220
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489830937 267 H----AIKNPLMLLFITYHNKPVD-NASCNKALKKICSTINSEPVTLHKLRHTHTGLCVEAGMDIIYVADRLGHDDINTT 341
Cdd:PRK01287 221 VrpqlAVRPDSGALFVAMDGDGLArNTLTNMVGRYIRAAGIEKAGACHLFRHAMATQMLENGADTRHIQAILGHAKLETT 300

                 ....*...
gi 489830937 342 lKYYSHLS 349
Cdd:PRK01287 301 -QIYTRVS 307
INT_RitB_C_like cd00797
C-terminal catalytic domain of recombinase RitB, a component of the recombinase trio; ...
186-359 8.88e-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: 43.06  E-value: 8.88e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489830937 186 SRAVIFLAVqTGMRFEEIIALTKKDINFTKRSITVNkawdykytntfiDTKTKKSRVIYIDNSTAQYLHSYLnwHTdyMK 265
Cdd:cd00797   28 ATLFGLLYA-TGLRVGEALRLRLEDVDLDSGILTIR------------QTKFGKSRLVPLHPSTVGALRDYL--AR--RD 90
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489830937 266 EHAIKNPLMLLFITYHNKPVDNASCNKALKKICSTINSEPVT------LHKLRHT---HTGL-CVEAGMDII----YVAD 331
Cdd:cd00797   91 RLLPSPSSSYFFVSQQGGRLTGGGVYRVFRRLLRRIGLRGAGdgrgprLHDLRHTfavNRLTrWYREGADVErklpVLST 170
                        170       180
                 ....*....|....*....|....*...
gi 489830937 332 RLGHDDINTTlKYYSHLSSNLRQHNQSK 359
Cdd:cd00797  171 YLGHVNVTDT-YWYLTATPELMELASLR 197
PRK15417 PRK15417
integron integrase;
303-348 3.74e-04

integron integrase;


Pssm-ID: 185315 [Multi-domain]  Cd Length: 337  Bit Score: 41.96  E-value: 3.74e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*.
gi 489830937 303 SEPVTLHKLRHTHTGLCVEAGMDIIYVADRLGHDDINTTLkYYSHL 348
Cdd:PRK15417 271 TKPATPHTLRHSFATALLRSGYDIRTVQDLLGHSDVSTTM-IYTHV 315
 
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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