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Conserved domains on  [gi|593776133|ref|YP_009013928|]
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tyrosine-type recombinase/integrase [Mycobacterium phage Turbido]

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];
80-370 3.35e-37

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


:

Pssm-ID: 443999 [Multi-domain]  Cd Length: 291  Bit Score: 135.89  E-value: 3.35e-37
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 593776133  80 VEEYTKKWIAERDLAGGTKDLYTTHARKRIY--PVLGDTPVVEMTPALVRAWWAGMGKEY--PTARRHAYNVLRAVMNTA 155
Cdd:COG4974    7 LEAFLEELKREKGLSPNTIKAYRRDLRRFLRflEELGKIPLAEITPEDIRAYLNYLRERGlsPSTINRYLAALRSFFRYA 86

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 593776133 156 VEDKLLSENPCR-IEQKAVAERDVEALTPQELDIVASEVFEH------YRVAVYILAWTSLRFGELIELRRKDIDDDGET 228
Cdd:COG4974   87 VREGLLEDNPAAkVKLPKKPRKLPRVLTEEEIEALLEALDTEtpeglrDRALLLLLYATGLRVSELLGLKWSDIDLDRGT 166

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 593776133 229 mkLRVRRGaarvgekivvgntKTvRSKRPVTVPPHVAQMIREHMKDRtkmNKGPEALLVTTTQGNRLSKSAFTRSLKRGY 308
Cdd:COG4974  167 --IRVRRG-------------KG-GKERTVPLSPEALEALREYLEER---RPRDSDYLFPTRRGRPLSRRAIRKILKRLA 227

                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 593776133 309 AKLG-RTDLRIHDLRAVGATLAAQSGATTKELMVRLGHTTPRMAMKYQMASEARDEEIARKMS 370
Cdd:COG4974  228 KRAGiPKRVTPHSLRHTFATHLLEAGVDLRTVQELLGHSSISTTQIYTHVSDEELREAVEKLH 290
 
Name Accession Description Interval E-value
XerD COG4974
Site-specific recombinase XerD [Replication, recombination and repair];
80-370 3.35e-37

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


Pssm-ID: 443999 [Multi-domain]  Cd Length: 291  Bit Score: 135.89  E-value: 3.35e-37
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 593776133  80 VEEYTKKWIAERDLAGGTKDLYTTHARKRIY--PVLGDTPVVEMTPALVRAWWAGMGKEY--PTARRHAYNVLRAVMNTA 155
Cdd:COG4974    7 LEAFLEELKREKGLSPNTIKAYRRDLRRFLRflEELGKIPLAEITPEDIRAYLNYLRERGlsPSTINRYLAALRSFFRYA 86

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 593776133 156 VEDKLLSENPCR-IEQKAVAERDVEALTPQELDIVASEVFEH------YRVAVYILAWTSLRFGELIELRRKDIDDDGET 228
Cdd:COG4974   87 VREGLLEDNPAAkVKLPKKPRKLPRVLTEEEIEALLEALDTEtpeglrDRALLLLLYATGLRVSELLGLKWSDIDLDRGT 166

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 593776133 229 mkLRVRRGaarvgekivvgntKTvRSKRPVTVPPHVAQMIREHMKDRtkmNKGPEALLVTTTQGNRLSKSAFTRSLKRGY 308
Cdd:COG4974  167 --IRVRRG-------------KG-GKERTVPLSPEALEALREYLEER---RPRDSDYLFPTRRGRPLSRRAIRKILKRLA 227

                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 593776133 309 AKLG-RTDLRIHDLRAVGATLAAQSGATTKELMVRLGHTTPRMAMKYQMASEARDEEIARKMS 370
Cdd:COG4974  228 KRAGiPKRVTPHSLRHTFATHLLEAGVDLRTVQELLGHSSISTTQIYTHVSDEELREAVEKLH 290
DNA_BRE_C cd00397
DNA breaking-rejoining enzymes, C-terminal catalytic domain; The DNA breaking-rejoining enzyme ...
 197-354 2.46e-21

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: 89.85  E-value: 2.46e-21
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 593776133 197 YRVAVYILAWTSLRFGELIELRRKDIDDDGETmkLRVRRGAarvgekivvgntKTVRSKRPVTVPPHVAQMIREHMKD-R 275
Cdd:cd00397   19 DRAILLLLLETGLRISELLALKVKDIDLDNGT--IRVRGKK------------TKGGKERTVPLPKELAEELKEYLKErR 84

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 593776133 276 TKMNKGPEALLVTTTQGNRLSKSAFTRSLKRGYAKLGR---TDLRIHDLRAVGATLAAQSGATTKELMVRLGHTTPRMAM 352
Cdd:cd00397   85 DKRGPLLKSLYLNKLFGTKLGERLSRRTLRRIFKKAGIeagRKITPHSLRHTFATNLLENGVDIKVVQKLLGHSSISTTQ 164


                 ..
gi 593776133 353 KY 354
Cdd:cd00397  165 RY 166
Phage_integrase pfam00589
Phage integrase family; Members of this family cleave DNA substrates by a series of staggered ...
 196-354 3.74e-12

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: 63.88  E-value: 3.74e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 593776133  196 HYRVAVYILAWTSLRFGELIELRRKDIDDDGETMKLRVrrgaarvgekivvgnTKTvRSKRPVTVPPHVAQMIREHMKDR 275
Cdd:pfam00589  22 RDKALLELLYATGLRISELCSLRWSDIDFENGVIRVHR---------------GKG-NKERTVPLSDAALELLKEWLSKR 85

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 593776133  276 TKMNKGPEALLVTTtQGNRLSKSAFTRSLKRGYAKLGRTD-LRIHDLRAVGATLAAQSGATTKELMVRLGHTTPRMAMKY 354
Cdd:pfam00589  86 LLEAPKSDYLFASK-RGKPLSRQTVRKIFKRAGKEAGLELpLHPHMLRHSFATHLLEAGVDLRVVQKLLGHSSISTTQIY 164
 
Name Accession Description Interval E-value
XerD COG4974
Site-specific recombinase XerD [Replication, recombination and repair];
80-370 3.35e-37

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


Pssm-ID: 443999 [Multi-domain]  Cd Length: 291  Bit Score: 135.89  E-value: 3.35e-37
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 593776133  80 VEEYTKKWIAERDLAGGTKDLYTTHARKRIY--PVLGDTPVVEMTPALVRAWWAGMGKEY--PTARRHAYNVLRAVMNTA 155
Cdd:COG4974    7 LEAFLEELKREKGLSPNTIKAYRRDLRRFLRflEELGKIPLAEITPEDIRAYLNYLRERGlsPSTINRYLAALRSFFRYA 86

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 593776133 156 VEDKLLSENPCR-IEQKAVAERDVEALTPQELDIVASEVFEH------YRVAVYILAWTSLRFGELIELRRKDIDDDGET 228
Cdd:COG4974   87 VREGLLEDNPAAkVKLPKKPRKLPRVLTEEEIEALLEALDTEtpeglrDRALLLLLYATGLRVSELLGLKWSDIDLDRGT 166

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 593776133 229 mkLRVRRGaarvgekivvgntKTvRSKRPVTVPPHVAQMIREHMKDRtkmNKGPEALLVTTTQGNRLSKSAFTRSLKRGY 308
Cdd:COG4974  167 --IRVRRG-------------KG-GKERTVPLSPEALEALREYLEER---RPRDSDYLFPTRRGRPLSRRAIRKILKRLA 227

                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 593776133 309 AKLG-RTDLRIHDLRAVGATLAAQSGATTKELMVRLGHTTPRMAMKYQMASEARDEEIARKMS 370
Cdd:COG4974  228 KRAGiPKRVTPHSLRHTFATHLLEAGVDLRTVQELLGHSSISTTQIYTHVSDEELREAVEKLH 290
XerC COG4973
Site-specific recombinase XerC [Replication, recombination and repair];
77-369 1.17e-34

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


Pssm-ID: 443998 [Multi-domain]  Cd Length: 287  Bit Score: 128.93  E-value: 1.17e-34
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 593776133  77 AITVEEYTKKWIA---ERDLAGGTKDLYTTHARkRIYPVLGD--TPVVEMTPALVRAWWAGMGKEYPTAR--RHAYNVLR 149
Cdd:COG4973    1 KLTLAEALEAYLEhlrERRLSPKTLEAYRRDLR-RLIPLLGDadLPLEELTPADVRRFLARLHRRGLSPRtlNRRLSALR 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 593776133 150 AVMNTAVEDKLLSENPCR-IEQKAVAERDVEALTPQE----LDIVASEVFE-HYRVAVYILAWTSLRFGELIELRRKDID 223
Cdd:COG4973   80 SFFNWAVREGLLEANPAAgVKAPKAPRKLPRALTVDElaqlLDALADDPLAvRDRAIVELLYSTGLRLGELVGLDWEDVD 159

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 593776133 224 DDGETmkLRVRrgaarvgekivvgnTKTvRSKRPVTVPPHVAQMIREHMKDRTKMNKGPEALLVTTTQGNRLSKSAFTRS 303
Cdd:COG4973  160 LDAGE--VRVR--------------GKT-GKSRTVPLGPKALAALREWLAVRPELAAPDEGALFPSRRGTRLSPRNVQKR 222

                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 593776133 304 LKRGYAKLG-RTDLRIHDLRAVGATLAAQSGATTKELMVRLGHTTPRMAMKYqmaSEARDEEIARKM 369
Cdd:COG4973  223 LRRLAKKAGlPKHVHPHDLRHSFATHLLESGGDLRAVQELLGHASISTTQIY---THLDFQHLAEVY 286
FimB COG0582
Integrase/recombinase, includes phage integrase [Replication, recombination and repair, ...
 9-350 2.60e-26

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


Pssm-ID: 440347 [Multi-domain]  Cd Length: 391  Bit Score: 108.59  E-value: 2.60e-26
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 593776133   9 TRRGWGKLRVIGSGRIHASYMHDGVRYNAPTTYDNRMDAEAWLAREHRLIEMEQwtPPAERLAKKAASAITVEEYTKKWI 88
Cdd:COG0582   30 GPSGGKRWRYRYRFRGKRKRLALGVYPGVSLALARARRAEARALLALGIDPSPA--RKAAKAAAAAAAANTFEEVAEEWL 107

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 593776133  89 AER--DLAGGTKDLYTTHARKRIYPVLGDTPVVEMTPALVRAWWAGMGKE--YPTARRhAYNVLRAVMNTAVEDKLLSEN 164
Cdd:COG0582  108 EEKkpEWKEKTAAQVRRTLEKHIFPVLGDRPIAEITPPDLLAVLRPIEARgaPETARR-VRQRLRQVFRYAVARGLIERN 186

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 593776133 165 PC---RIEQKAVAERDVEALTPQEL-----DIVASEVFEHYRVAVYILAWTSLRFGELIELRRKDIDDDGETMKLRVRRg 236
Cdd:COG0582  187 PAadlKGALPKPKVKHHPALTPEELpellrALDAYRGSPVTRLALRLLLLTGVRPGELRGARWSEIDLEAALWTIPAER- 265

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 593776133 237 aarvgekivvgnTKTvRSKRPVTVPPHVAQMIREhMKDRTkmnkGPEALLVTTTQGNR--LSKSAFTRSLKRgyakLGRT 314
Cdd:COG0582  266 ------------MKT-RRPHIVPLSRQALEILKE-LKPLT----GDSEYVFPSRRGPKkpMSENTLNKALRR----MGYG 323

                        330       340       350
                 ....*....|....*....|....*....|....*.
gi 593776133 315 DLRIHDLRAVGATLAAQSGATTKELMVRLGHTTPRM 350
Cdd:COG0582  324 RFTPHGFRHTASTLLNEAGFPPDVIERQLAHKDGNK 359
DNA_BRE_C cd00397
DNA breaking-rejoining enzymes, C-terminal catalytic domain; The DNA breaking-rejoining enzyme ...
 197-354 2.46e-21

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: 89.85  E-value: 2.46e-21
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 593776133 197 YRVAVYILAWTSLRFGELIELRRKDIDDDGETmkLRVRRGAarvgekivvgntKTVRSKRPVTVPPHVAQMIREHMKD-R 275
Cdd:cd00397   19 DRAILLLLLETGLRISELLALKVKDIDLDNGT--IRVRGKK------------TKGGKERTVPLPKELAEELKEYLKErR 84

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 593776133 276 TKMNKGPEALLVTTTQGNRLSKSAFTRSLKRGYAKLGR---TDLRIHDLRAVGATLAAQSGATTKELMVRLGHTTPRMAM 352
Cdd:cd00397   85 DKRGPLLKSLYLNKLFGTKLGERLSRRTLRRIFKKAGIeagRKITPHSLRHTFATNLLENGVDIKVVQKLLGHSSISTTQ 164


                 ..
gi 593776133 353 KY 354
Cdd:cd00397  165 RY 166
INT_ICEBs1_C_like cd01189
C-terminal catalytic domain of integrases from bacterial phages and conjugate transposons; ...
 196-354 1.55e-20

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: 86.84  E-value: 1.55e-20
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 593776133 196 HYRVAVYILAWTSLRFGELIELRRKDIDDDGETmkLRVRRGAARVGE-KIVVGNTKTVRSKRPVTVPPHVAQMIREHMkd 274
Cdd:cd01189   17 RYYLLFLLALLTGLRRGELLALTWSDIDFENGT--IRINRTLVRKKKgGYVIKPPKTKSSIRTIPLPDELIELLKELK-- 92

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 593776133 275 rtkmnkgpeallvtttqgnrlsksAFTRSLKrgyaKLGRTDLRIHDLRAVGATLAAQSGATTKELMVRLGHTTPRMAMKY 354
Cdd:cd01189   93 ------------------------AFKKLLK----KAGLPRITPHDLRHTFASLLLEAGVPLKVIAERLGHSDISTTLDV 144
INT_Rci_Hp1_C cd00796
Shufflon-specific DNA recombinase Rci and Bacteriophage Hp1_like integrase, C-terminal ...
 181-356 4.32e-13

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: 66.58  E-value: 4.32e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 593776133 181 LTPQELD--IVASEVF--EHYRVAVYILAWTSLRFGELIELRRKDIDDDGETmklrvrrgaarvgekIVVGNTKTvrsKR 256
Cdd:cd00796    5 LTEDEEArlLAALEEStnPHLRLIVLLALYTGARRGEILSLRWDDIDLEVGL---------------IVLPETKN---GK 66

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 593776133 257 PVTVPphVAQMIREHMKDRTKmnKGPEALLVTTTQGNRLSKSAFTRSLKRGYAKLGRTDLRIHDLRAVGATLAAQSGATT 336
Cdd:cd00796   67 PRTVP--LSDEAIAILKELKR--KRGKDGFFVDGRFFGIPIASLRRAFKKARKRAGLEDLRFHDLRHTFASRLVQAGVPI 142

                        170       180
                 ....*....|....*....|
gi 593776133 337 KELMVRLGHTTPRMAMKYQM 356
Cdd:cd00796  143 KTVAKILGHSSIKMTMRYAH 162
Phage_integrase pfam00589
Phage integrase family; Members of this family cleave DNA substrates by a series of staggered ...
 196-354 3.74e-12

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: 63.88  E-value: 3.74e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 593776133  196 HYRVAVYILAWTSLRFGELIELRRKDIDDDGETMKLRVrrgaarvgekivvgnTKTvRSKRPVTVPPHVAQMIREHMKDR 275
Cdd:pfam00589  22 RDKALLELLYATGLRISELCSLRWSDIDFENGVIRVHR---------------GKG-NKERTVPLSDAALELLKEWLSKR 85

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 593776133  276 TKMNKGPEALLVTTtQGNRLSKSAFTRSLKRGYAKLGRTD-LRIHDLRAVGATLAAQSGATTKELMVRLGHTTPRMAMKY 354
Cdd:pfam00589  86 LLEAPKSDYLFASK-RGKPLSRQTVRKIFKRAGKEAGLELpLHPHMLRHSFATHLLEAGVDLRVVQKLLGHSSISTTQIY 164
INT_Lambda_C cd00800
C-terminal catalytic domain of Lambda integrase, a tyrosine-based site-specific recombinase; ...
 204-354 2.73e-07

C-terminal catalytic domain of Lambda integrase, a tyrosine-based site-specific recombinase; Lambda-type integrases catalyze site-specific integration and excision of temperate bacteriophages and other mobile genetic elements to and from the bacterial host chromosome. They are tyrosine-based site-specific recombinase and belong to the superfamily of DNA breaking-rejoining enzymes, which share the same fold in their catalytic domain and the overall reaction mechanism. The phage lambda integrase 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: 271181 [Multi-domain]  Cd Length: 161  Bit Score: 49.65  E-value: 2.73e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 593776133 204 LAW-TSLRFGELIELRRKDIDDDGetmklrvrrgaarvgekIVVGNTKTvRSKRPVTVPPHVAQMIrehmkDRTKMNKGP 282
Cdd:cd00800   20 LALlTGQRQGDLLRLKWSDITDGG-----------------LLVEQSKT-GKKLLIPWTPSLRALV-----DRIRALPRK 76

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 593776133 283 EAL-LVTTTQGNRLS----KSAFTRSLKRGYAKLGRTDLRIHDLRAVGATLAAQSGATTKELMVrLGHTTPRMAMKY 354
Cdd:cd00800   77 RSEyLINSRKGGPLSydtlKSAWRRARKAAGLKGETEGFTFHDLRAKAATDYAEQGGSTDAQAL-LGHKSDAMTERY 152
INT_C_like_4 cd01194
Uncharacterized site-specific tyrosine recombinase, C-terminal catalytic domain; Tyrosine ...
 198-354 1.36e-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: 271194 [Multi-domain]  Cd Length: 174  Bit Score: 45.06  E-value: 1.36e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 593776133 198 RVAVYILAWTSLRFGELIELRRKDIDDDGETMKLRVRrgaarvgekivvGNTKTVRSkRPVTVPPHVAQMIREHMKDRTK 277
Cdd:cd01194   25 RAIISLMVTEGLRTVEIVRADVGDLRQEGEGTILYVQ------------GKGKTSKD-DFVYLRPDVLKALQAYLKARGK 91

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 593776133 278 MNKGpEALLVTTTQ---GNRLSKSAFTRSLKRGYAKLGRTDLRI--HDLRAVGATLAAQSGATTKELMVRLGHTTPRMAM 352
Cdd:cd01194   92 LDFE-EPLFTSLSNnskGQRLTTRSIRRIIKKYLRKAGLDDDRLtaHSLRHTAGTLALKAGKSLREVQQLLRHSDPNTTM 170


                 ..
gi 593776133 353 KY 354
Cdd:cd01194  171 IY 172
INT_RitB_C_like cd00797
C-terminal catalytic domain of recombinase RitB, a component of the recombinase trio; ...
 197-334 2.84e-04

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: 41.52  E-value: 2.84e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 593776133 197 YRVAVYILAWTSLRFGELIELRRKDIDDDGETmkLRVRrgaarvgekivvgNTKTVRSkRPVTVPPHVAQMIREHMKDRT 276
Cdd:cd00797   27 YATLFGLLYATGLRVGEALRLRLEDVDLDSGI--LTIR-------------QTKFGKS-RLVPLHPSTVGALRDYLARRD 90

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 593776133 277 KMNKGP-EALLVTTTQGNRLSKSAFTRSLKRGYAKLG------RTDLRIHDLR---AVGATLA-AQSGA 334
Cdd:cd00797   91 RLLPSPsSSYFFVSQQGGRLTGGGVYRVFRRLLRRIGlrgagdGRGPRLHDLRhtfAVNRLTRwYREGA 159
Phage_int_SAM_5 pfam13102
Phage integrase SAM-like domain; A family of uncharacterized proteins found by clustering ...
 79-165 1.02e-03

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: 37.97  E-value: 1.02e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 593776133   79 TVEEYTKKWIAERDLAG--GTKDLY-TTHARKRIYPVLGDTPVVEMTPALVRAWWAGMGKEYP----TARRHaYNVLRAV 151
Cdd:pfam13102   1 DFLDYFKEYIEELKKKGskGTARNYkSTLKHLKKFLKKKDITFEEITVDFLEKFEEYLKKKKGlsenTISKY-FRTLRAV 79

                          90
                  ....*....|....
gi 593776133  152 MNTAVEDKLLSENP 165
Cdd:pfam13102  80 LNKAIKEGIIKKNP 93
INT_Cre_C cd00799
C-terminal catalytic domain of Cre recombinase (also called integrase); Cre-like recombinases ...
 206-355 1.49e-03

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


Pssm-ID: 271180  Cd Length: 188  Bit Score: 39.20  E-value: 1.49e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 593776133 206 WTSLRFGELIELRRKDI-DDDGETMKLRVRRgaarvgekivvgnTKTVRSKRPVTVPPHVAQMI---------REHMKDR 275
Cdd:cd00799   27 AGALRRSELVALRVEDLtRFVDGGLLIRLRR-------------SKTDQDGEGEIKALPYGPETcpvralrawLEAAGIP 93

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 593776133 276 TkmnkGPeaLLVTTTQGNRLSKSA-FTRSLKRGYAKLGR------TDLRIHDLRAVGATLAAQSGATTKELMVRLGHTTP 348
Cdd:cd00799   94 S----GP--LFRRIRRGGSVGTTRlSDRSVARIVKRRAAlagldpGDFSGHSLRRGFATEAARAGASLPEIMAQGGHKSV 167


                 ....*..
gi 593776133 349 RMAMKYQ 355
Cdd:cd00799  168 ATVMRYI 174
INT_C_like_5 cd01195
Uncharacterized site-specific tyrosine recombinase, C-terminal catalytic domain; Tyrosine ...
 201-355 2.24e-03

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


Pssm-ID: 271195 [Multi-domain]  Cd Length: 170  Bit Score: 38.61  E-value: 2.24e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 593776133 201 VYILAWTSLRFGELIELRRKDIDddgetmklrvrrgaARVGEKIVVGNTKTVRSkrPVTVPPHVAQMIREHMKDRTKmnk 280
Cdd:cd01195   26 VRLLLDNALRRSEAVALDVEDLE--------------KEHRRLRILGKGKKQRE--VVTLPPTTREALAAWLAARGE--- 86

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 593776133 281 gPEALLVTT----TQGNRLSKSAFTRSLKRGYAKLGRTD-LRIHDLRAVGATLAAQSGATTKELMVRLG-HTTPRMAMKY 354
Cdd:cd01195   87 -AEGPLFVSldraSRGRRLSPQAVYRIVRRLAERIGLGKrLSPHGLRHSAITLALDAGAGLIRKVQDFSrHADLRTLQVY 165


                 .
gi 593776133 355 Q 355
Cdd:cd01195  166 D 166
INTN1_C_like cd01185
Integrase IntN1 of Bacteroides mobilizable transposon NBU1 and similar proteins, C-terminal ...
 184-354 7.72e-03

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: 36.86  E-value: 7.72e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 593776133 184 QELDIVASEVFEHYRVAVYILAWTSLRFGELIELRRKDIDDDGETMKLRVRRgaarvgekivvgnTKTvrsKRPVTVP-- 261
Cdd:cd01185    7 MALELSDTSRLELVRDMFLFSCYTGLRFSDLKNLTWKNIVEASGRTWIRYRR-------------KKT---GKPVTVPll 70

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 593776133 262 PHVAQMIREHMKDRTKMNKGPEallvtttqgnrLSKSAFTRSLKRGYAKLG-RTDLRIHDLRAVGATLAAQSGATTKELM 340
Cdd:cd01185   71 PVAREILEKYKDDRSEGKLFPV-----------LSNQKINRYLKEIAKIAGiDKHLTFHVARHTFATLLLLKGVDIETIS 139

                        170
                 ....*....|....
gi 593776133 341 VRLGHTTPRMAMKY 354
Cdd:cd01185  140 KLLGHSSIKTTQIY 153
 
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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