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Conserved domains on  [gi|695607702|ref|WP_032605273|]
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MULTISPECIES: tyrosine-type recombinase/integrase [Staphylococcus]

Protein Classification

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];
69-366 5.45e-39

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


:

Pssm-ID: 443999 [Multi-domain]  Cd Length: 291  Bit Score: 140.51  E-value: 5.45e-39
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 695607702  69 FDKLVDEYIEWYSARRKSS--SVKALKTHTNNHL--LPYFKSMDVFNMTTQDVMKFQNTKLKDGHSGEYLKKMHVFLVSL 144
Cdd:COG4974    3 LADLLEAFLEELKREKGLSpnTIKAYRRDLRRFLrfLEELGKIPLAEITPEDIRAYLNYLRERGLSPSTINRYLAALRSF 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 695607702 145 LNHAMKFHDLKQNVASLVGNFEIEsNKRLNYWTLEQFNQFYDALATQQQ-----KLFFKLLFYSGARKGEIRALTWRDIN 219
Cdd:COG4974   83 FRYAVREGLLEDNPAAKVKLPKKP-RKLPRVLTEEEIEALLEALDTETPeglrdRALLLLLYATGLRVSELLGLKWSDID 161

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 695607702 220 YDDDFIHINKTdyhgevtapKTKAAiRDIYLPAHMMNDIKEYLKWYKETnifKDDYVLFGRFFKAYSESTIDRWFTTALK 299
Cdd:COG4974  162 LDRGTIRVRRG---------KGGKE-RTVPLSPEALEALREYLEERRPR---DSDYLFPTRRGRPLSRRAIRKILKRLAK 228

                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 695607702 300 VLDeqLPDGQTFpriviHELRHSHASMLVNHGASIMIIAQRLGHADSnEVYNRYGHLYPSTQKEIVK 366
Cdd:COG4974  229 RAG--IPKRVTP-----HSLRHTFATHLLEAGVDLRTVQELLGHSSI-STTQIYTHVSDEELREAVE 287
Arm-DNA-bind_4 pfam14657
Arm DNA-binding domain; This family includes AP2-like domains found in a variety of phage ...
 19-59 3.05e-05

Arm DNA-binding domain; This family includes AP2-like domains found in a variety of phage integrase proteins. These domains bind to Arm DNA sites.


:

Pssm-ID: 464242  Cd Length: 44  Bit Score: 40.96  E-value: 3.05e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 695607702   19 TYYFRI-KYYDKKNQRKEIKKSGFKQRKEALKKCNEIMDELE 59
Cdd:pfam14657   1 TWYFQVyGYDDITGKRKQKTKRGFKTKKEAKEAEAEFIKKIS 42
 
Name Accession Description Interval E-value
XerD COG4974
Site-specific recombinase XerD [Replication, recombination and repair];
69-366 5.45e-39

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


Pssm-ID: 443999 [Multi-domain]  Cd Length: 291  Bit Score: 140.51  E-value: 5.45e-39
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 695607702  69 FDKLVDEYIEWYSARRKSS--SVKALKTHTNNHL--LPYFKSMDVFNMTTQDVMKFQNTKLKDGHSGEYLKKMHVFLVSL 144
Cdd:COG4974    3 LADLLEAFLEELKREKGLSpnTIKAYRRDLRRFLrfLEELGKIPLAEITPEDIRAYLNYLRERGLSPSTINRYLAALRSF 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 695607702 145 LNHAMKFHDLKQNVASLVGNFEIEsNKRLNYWTLEQFNQFYDALATQQQ-----KLFFKLLFYSGARKGEIRALTWRDIN 219
Cdd:COG4974   83 FRYAVREGLLEDNPAAKVKLPKKP-RKLPRVLTEEEIEALLEALDTETPeglrdRALLLLLYATGLRVSELLGLKWSDID 161

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 695607702 220 YDDDFIHINKTdyhgevtapKTKAAiRDIYLPAHMMNDIKEYLKWYKETnifKDDYVLFGRFFKAYSESTIDRWFTTALK 299
Cdd:COG4974  162 LDRGTIRVRRG---------KGGKE-RTVPLSPEALEALREYLEERRPR---DSDYLFPTRRGRPLSRRAIRKILKRLAK 228

                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 695607702 300 VLDeqLPDGQTFpriviHELRHSHASMLVNHGASIMIIAQRLGHADSnEVYNRYGHLYPSTQKEIVK 366
Cdd:COG4974  229 RAG--IPKRVTP-----HSLRHTFATHLLEAGVDLRTVQELLGHSSI-STTQIYTHVSDEELREAVE 287
INT_ICEBs1_C_like cd01189
C-terminal catalytic domain of integrases from bacterial phages and conjugate transposons; ...
 178-355 7.18e-35

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: 124.98  E-value: 7.18e-35
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 695607702 178 LEQFNQFYDALAT--QQQKLFFKLLFYSGARKGEIRALTWRDINYDDDFIHINKT-----DYHGEVTAPKTKAAIRDIYL 250
Cdd:cd01189    1 PEELKKLLEALKKrgDRYYLLFLLALLTGLRRGELLALTWSDIDFENGTIRINRTlvrkkKGGYVIKPPKTKSSIRTIPL 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 695607702 251 PAHMMNDIKEYLKWYKetnifkddyvlfgrffkaysestidrwfttALKVLDEqlpdgqtfPRIVIHELRHSHASMLVNH 330
Cdd:cd01189   81 PDELIELLKELKAFKK------------------------------LLKKAGL--------PRITPHDLRHTFASLLLEA 122

                        170       180
                 ....*....|....*....|....*
gi 695607702 331 GASIMIIAQRLGHADSNEVYNRYGH 355
Cdd:cd01189  123 GVPLKVIAERLGHSDISTTLDVYAH 147
Phage_integrase pfam00589
Phage integrase family; Members of this family cleave DNA substrates by a series of staggered ...
 177-358 2.59e-20

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: 86.99  E-value: 2.59e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 695607702  177 TLEQFNQFYDALATQQQ----KLFFKLLFYSGARKGEIRALTWRDINYDDDFIHINKTdyhgevtapKTKAAIrdiylpA 252
Cdd:pfam00589   3 TEDEVERLLDAAETGPLsirdKALLELLYATGLRISELCSLRWSDIDFENGVIRVHRG---------KGNKER------T 67

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 695607702  253 HMMNDikEYLKWYKET------NIFKDDYVLFGRFFKAYSESTIDRWFTTALKVLDeqlpdgqTFPRIVIHELRHSHASM 326
Cdd:pfam00589  68 VPLSD--AALELLKEWlskrllEAPKSDYLFASKRGKPLSRQTVRKIFKRAGKEAG-------LELPLHPHMLRHSFATH 138

                         170       180       190
                  ....*....|....*....|....*....|..
gi 695607702  327 LVNHGASIMIIAQRLGHADSNEVyNRYGHLYP 358
Cdd:pfam00589 139 LLEAGVDLRVVQKLLGHSSISTT-QIYTHVAD 169
int PHA02601
integrase; Provisional
 34-359 3.10e-08

integrase; Provisional


Pssm-ID: 222904 [Multi-domain]  Cd Length: 333  Bit Score: 54.73  E-value: 3.10e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 695607702  34 KEIKKSgFKQRKEALKKCNEIMDELEDVGQINKLPFDKLVDEYI-EWYSarRKSSSVKALKTHTNnHLLPYFKSMD---V 109
Cdd:PHA02601  23 KRIRKR-FATKGEALAFENYTMAEVDDKEWVGEKEDRRRLSELLqIWWD--LHGQTLEDGKARLA-KLLILCKGLGdpiA 98

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 695607702 110 FNMTTQDVMKFQNTKLKDGHS---GEYLKKMHVFLVSLLNHAMkFHDLKQ-------NVASLVGNFEiESNKRLNYWTLE 179
Cdd:PHA02601  99 SEFTAKDFADYRARRLSGEFKvnkGRPIKPATVNRELAYLSAV-FNELIKlgkwsgpNPLDGIRPFK-EAEPELAFLTKE 176

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 695607702 180 QFNQFYDALATQQQK---LFFKLLFYSGARKGEIRALTWRDINydddfihinktdyHGEVTAPKTKAA-IRDIYLPAHMM 255
Cdd:PHA02601 177 EIERLLDACDGSRSPdlgLIAKICLATGARWSEAETLKRSQIS-------------PYKITFVKTKGKkNRTVPISEELY 243

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 695607702 256 NDIKEylkwyKETNIFKDDYVLFGRffkaysestidrwfttALKVLDEQLPDGQTfprivIHELRHSHASMLVNHGASIM 335
Cdd:PHA02601 244 KMLPK-----RRGRLFKDAYESFER----------------AVKRAGIDLPEGQA-----THVLRHTFASHFMMNGGNIL 297

                        330       340
                 ....*....|....*....|....
gi 695607702 336 IIAQRLGHADSNEVYnRYGHLYPS 359
Cdd:PHA02601 298 VLQRILGHATIEMTM-AYAHFAPD 320
Arm-DNA-bind_4 pfam14657
Arm DNA-binding domain; This family includes AP2-like domains found in a variety of phage ...
 19-59 3.05e-05

Arm DNA-binding domain; This family includes AP2-like domains found in a variety of phage integrase proteins. These domains bind to Arm DNA sites.


Pssm-ID: 464242  Cd Length: 44  Bit Score: 40.96  E-value: 3.05e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 695607702   19 TYYFRI-KYYDKKNQRKEIKKSGFKQRKEALKKCNEIMDELE 59
Cdd:pfam14657   1 TWYFQVyGYDDITGKRKQKTKRGFKTKKEAKEAEAEFIKKIS 42
recomb_XerD TIGR02225
tyrosine recombinase XerD; The phage integrase family describes a number of recombinases with ...
 317-366 1.41e-03

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: 39.87  E-value: 1.41e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 695607702  317 HELRHSHASMLVNHGASIMIIAQRLGHAD--SNEVYNrygHLYPSTQKEIVK 366
Cdd:TIGR02225 237 HTLRHSFATHLLENGADLRVVQELLGHADisTTQIYT---HVARERLKEVHK 285
 
Name Accession Description Interval E-value
XerD COG4974
Site-specific recombinase XerD [Replication, recombination and repair];
69-366 5.45e-39

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


Pssm-ID: 443999 [Multi-domain]  Cd Length: 291  Bit Score: 140.51  E-value: 5.45e-39
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 695607702  69 FDKLVDEYIEWYSARRKSS--SVKALKTHTNNHL--LPYFKSMDVFNMTTQDVMKFQNTKLKDGHSGEYLKKMHVFLVSL 144
Cdd:COG4974    3 LADLLEAFLEELKREKGLSpnTIKAYRRDLRRFLrfLEELGKIPLAEITPEDIRAYLNYLRERGLSPSTINRYLAALRSF 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 695607702 145 LNHAMKFHDLKQNVASLVGNFEIEsNKRLNYWTLEQFNQFYDALATQQQ-----KLFFKLLFYSGARKGEIRALTWRDIN 219
Cdd:COG4974   83 FRYAVREGLLEDNPAAKVKLPKKP-RKLPRVLTEEEIEALLEALDTETPeglrdRALLLLLYATGLRVSELLGLKWSDID 161

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 695607702 220 YDDDFIHINKTdyhgevtapKTKAAiRDIYLPAHMMNDIKEYLKWYKETnifKDDYVLFGRFFKAYSESTIDRWFTTALK 299
Cdd:COG4974  162 LDRGTIRVRRG---------KGGKE-RTVPLSPEALEALREYLEERRPR---DSDYLFPTRRGRPLSRRAIRKILKRLAK 228

                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 695607702 300 VLDeqLPDGQTFpriviHELRHSHASMLVNHGASIMIIAQRLGHADSnEVYNRYGHLYPSTQKEIVK 366
Cdd:COG4974  229 RAG--IPKRVTP-----HSLRHTFATHLLEAGVDLRTVQELLGHSSI-STTQIYTHVSDEELREAVE 287
FimB COG0582
Integrase/recombinase, includes phage integrase [Replication, recombination and repair, ...
 69-356 3.63e-36

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


Pssm-ID: 440347 [Multi-domain]  Cd Length: 391  Bit Score: 135.17  E-value: 3.63e-36
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 695607702  69 FDKLVDEYIEWYSARRKSSSVKALKTHTNNHLLPYFKSMDVFNMTTQDVMKFQNtKLKDGHSGEYLKKMHVFLVSLLNHA 148
Cdd:COG0582   99 FEEVAEEWLEEKKPEWKEKTAAQVRRTLEKHIFPVLGDRPIAEITPPDLLAVLR-PIEARGAPETARRVRQRLRQVFRYA 177

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 695607702 149 MKFHDLKQNVAS-LVGNFEIESNKRLNYWTLEQFNQFYDAL----ATQQQKLFFKLLFYSGARKGEIRALTWRDINYDDD 223
Cdd:COG0582  178 VARGLIERNPAAdLKGALPKPKVKHHPALTPEELPELLRALdayrGSPVTRLALRLLLLTGVRPGELRGARWSEIDLEAA 257

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 695607702 224 FIHINKTDyhgevtaPKTKAAIRdIYLPAHMMndikEYLKWYKETNiFKDDYVLFGRF--FKAYSESTIDRwfttALKVL 301
Cdd:COG0582  258 LWTIPAER-------MKTRRPHI-VPLSRQAL----EILKELKPLT-GDSEYVFPSRRgpKKPMSENTLNK----ALRRM 320

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 695607702 302 DeqlpdgqtFPRIVIHELRHSHASMLVNHGASIMIIAQRLGHADSNEV---YNRYGHL 356
Cdd:COG0582  321 G--------YGRFTPHGFRHTASTLLNEAGFPPDVIERQLAHKDGNKVraaYNRADYL 370
XerC COG4973
Site-specific recombinase XerC [Replication, recombination and repair];
66-356 1.28e-35

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


Pssm-ID: 443998 [Multi-domain]  Cd Length: 287  Bit Score: 131.24  E-value: 1.28e-35
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 695607702  66 KLPFDKLVDEYIEWYSARRKSSSVKALKTHTNNHLLPYF--KSMDVFNMTTQDVMKFQNTKLKDGHSGEYLKKMHVFLVS 143
Cdd:COG4973    1 KLTLAEALEAYLEHLRERRLSPKTLEAYRRDLRRLIPLLgdADLPLEELTPADVRRFLARLHRRGLSPRTLNRRLSALRS 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 695607702 144 LLNHAMKFHDLKQNVASLVGNFEIESnKRLNYWTLEQFNQFYDALAT----QQQKLFFKLLFYSGARKGEIRALTWRDIN 219
Cdd:COG4973   81 FFNWAVREGLLEANPAAGVKAPKAPR-KLPRALTVDELAQLLDALADdplaVRDRAIVELLYSTGLRLGELVGLDWEDVD 159

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 695607702 220 YDDDFIHINktdyhgevtaPKTKAAiRDIYLPAHMMNDIKEYLKWYKETNIFKDDYVLFGRFFKAYSESTIDRWFTTALK 299
Cdd:COG4973  160 LDAGEVRVR----------GKTGKS-RTVPLGPKALAALREWLAVRPELAAPDEGALFPSRRGTRLSPRNVQKRLRRLAK 228

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 695607702 300 VLDeqLPDGQTFpriviHELRHSHASMLVNHGASIMIIAQRLGHADSNEVYnRYGHL 356
Cdd:COG4973  229 KAG--LPKHVHP-----HDLRHSFATHLLESGGDLRAVQELLGHASISTTQ-IYTHL 277
INT_ICEBs1_C_like cd01189
C-terminal catalytic domain of integrases from bacterial phages and conjugate transposons; ...
 178-355 7.18e-35

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: 124.98  E-value: 7.18e-35
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 695607702 178 LEQFNQFYDALAT--QQQKLFFKLLFYSGARKGEIRALTWRDINYDDDFIHINKT-----DYHGEVTAPKTKAAIRDIYL 250
Cdd:cd01189    1 PEELKKLLEALKKrgDRYYLLFLLALLTGLRRGELLALTWSDIDFENGTIRINRTlvrkkKGGYVIKPPKTKSSIRTIPL 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 695607702 251 PAHMMNDIKEYLKWYKetnifkddyvlfgrffkaysestidrwfttALKVLDEqlpdgqtfPRIVIHELRHSHASMLVNH 330
Cdd:cd01189   81 PDELIELLKELKAFKK------------------------------LLKKAGL--------PRITPHDLRHTFASLLLEA 122

                        170       180
                 ....*....|....*....|....*
gi 695607702 331 GASIMIIAQRLGHADSNEVYNRYGH 355
Cdd:cd01189  123 GVPLKVIAERLGHSDISTTLDVYAH 147
DNA_BRE_C cd00397
DNA breaking-rejoining enzymes, C-terminal catalytic domain; The DNA breaking-rejoining enzyme ...
 194-347 1.27e-22

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: 93.31  E-value: 1.27e-22
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 695607702 194 KLFFKLLFYSGARKGEIRALTWRDINYDDDFIHINKTDYHGEVTapktkaaiRDIYLPAHMMNDIKEYLK-WYKETNIFK 272
Cdd:cd00397   20 RAILLLLLETGLRISELLALKVKDIDLDNGTIRVRGKKTKGGKE--------RTVPLPKELAEELKEYLKeRRDKRGPLL 91

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 695607702 273 DDYVLFGRFFKAYSESTIDRWFTTALKVLDEQLPdgqtfPRIVIHELRHSHASMLVNHGASIMIIAQRLGHADSN 347
Cdd:cd00397   92 KSLYLNKLFGTKLGERLSRRTLRRIFKKAGIEAG-----RKITPHSLRHTFATNLLENGVDIKVVQKLLGHSSIS 161
INT_Rci_Hp1_C cd00796
Shufflon-specific DNA recombinase Rci and Bacteriophage Hp1_like integrase, C-terminal ...
 172-355 3.62e-21

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: 88.92  E-value: 3.62e-21
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 695607702 172 RLNYWTLEQFNQFYDAL---ATQQQKLFFKLLFYSGARKGEIRALTWRDINYDDDFIHInktdyhgevtaPKTKAAiRDI 248
Cdd:cd00796    1 RDRFLTEDEEARLLAALeesTNPHLRLIVLLALYTGARRGEILSLRWDDIDLEVGLIVL-----------PETKNG-KPR 68

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 695607702 249 YLPahMMNDIKEYLKWYKETNIFKDDYVlFGRFFKaYSESTIDRWFTTALKvlDEQLPDgqtfprIVIHELRHSHASMLV 328
Cdd:cd00796   69 TVP--LSDEAIAILKELKRKRGKDGFFV-DGRFFG-IPIASLRRAFKKARK--RAGLED------LRFHDLRHTFASRLV 136

                        170       180
                 ....*....|....*....|....*..
gi 695607702 329 NHGASIMIIAQRLGHADSnEVYNRYGH 355
Cdd:cd00796  137 QAGVPIKTVAKILGHSSI-KMTMRYAH 162
Phage_integrase pfam00589
Phage integrase family; Members of this family cleave DNA substrates by a series of staggered ...
 177-358 2.59e-20

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: 86.99  E-value: 2.59e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 695607702  177 TLEQFNQFYDALATQQQ----KLFFKLLFYSGARKGEIRALTWRDINYDDDFIHINKTdyhgevtapKTKAAIrdiylpA 252
Cdd:pfam00589   3 TEDEVERLLDAAETGPLsirdKALLELLYATGLRISELCSLRWSDIDFENGVIRVHRG---------KGNKER------T 67

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 695607702  253 HMMNDikEYLKWYKET------NIFKDDYVLFGRFFKAYSESTIDRWFTTALKVLDeqlpdgqTFPRIVIHELRHSHASM 326
Cdd:pfam00589  68 VPLSD--AALELLKEWlskrllEAPKSDYLFASKRGKPLSRQTVRKIFKRAGKEAG-------LELPLHPHMLRHSFATH 138

                         170       180       190
                  ....*....|....*....|....*....|..
gi 695607702  327 LVNHGASIMIIAQRLGHADSNEVyNRYGHLYP 358
Cdd:pfam00589 139 LLEAGVDLRVVQKLLGHSSISTT-QIYTHVAD 169
INT_C_like_1 cd01184
Uncharacterized site-specific tyrosine recombinase, C-terminal catalytic domain; Tyrosine ...
 202-355 6.32e-15

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: 71.95  E-value: 6.32e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 695607702 202 YSGARKGEIRALTWRDINYDDDFIHINKTDYHGEVTApKTKAAIRDIYLPAHMMnDIK--EYLKWYKETN---IFKDDYV 276
Cdd:cd01184   34 YTGARLNEICQLRVDDIKEEDGIWCIDINDDAEGRRL-KTKASRRLVPIHPRLI-ELGflDYVEALRADGklfLFPEKRD 111

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 695607702 277 LFGRFFKAYSestidRWFTTALKVLDEQLPDGQTFpriviHELRHSHASMLVNHGASIMIIAQRLGHADSNEVYNRYGH 355
Cdd:cd01184  112 KDGKYSKAAS-----KWFNRLLRKLGIKDDERKSF-----HSFRHTFITALKRAGVPEELIAQIVGHSRGGVTHDTYGK 180
INT_P4_C cd00801
Bacteriophage P4 integrase, C-terminal catalytic domain; P4-like integrases are found in ...
 177-356 5.20e-14

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: 69.61  E-value: 5.20e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 695607702 177 TLEQFNQFYDAL----ATQQQKLFFKLLFYSGARKGEIRALTWRDINYDDDFIHInktdyHGEVTapKTKAAIRdIYLPA 252
Cdd:cd00801    1 SPDELPELWRALdtanLSPPTKLALRLLLLTGQRIGELARARWSEIDLEEKTWTI-----PAERT--KNKRPHR-VPLSD 72

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 695607702 253 HMMNDIKEYLKWYKETnifkdDYVLFGRFFKAYSEStidrwFTTALKVLDEQLPDGQTFpriVIHELRHSHASMLVNHGA 332
Cdd:cd00801   73 QALEILEELKEFTGDS-----GYLFPSRRKKKKPIS-----ENTINKALKRLGYKGKEF---TPHDLRRTFSTLLNELGI 139

                        170       180
                 ....*....|....*....|....*..
gi 695607702 333 SIMIIAQRLGHADSNEV---YNRYGHL 356
Cdd:cd00801  140 DPEVIERLLNHVLGGVVraaYNRYDYL 166
INT_tnpA_C_Tn554 cd01186
Putative Transposase A from transposon Tn554, C-terminal catalytic domain; This family ...
 177-356 1.06e-12

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: 65.90  E-value: 1.06e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 695607702 177 TLEQFNQFYDALATQQQKLFFKLLFYSGARKGEIRALTWRDINYDDDFIHI-NKTDYHGEVTAPKTKAaiRDIYLPAHMM 255
Cdd:cd01186    3 TPREVQELINACNNLRDKFLLALLYETGLRIGEALGLRIEDIDMADNQIELvPREDNTNEARAKSMRE--RRIPVSQDLI 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 695607702 256 NDIKEYLKWYKETNIFKDDYVLF----GRFFKAYSESTIDRWFTTAlkvldEQLPDGQTFPriviHELRHSHASMLVNHG 331
Cdd:cd01186   81 DLYADYLTYIYCEEAEFSITVFVnvkgGNQGKAMNYSDVYDLVRRL-----KKRTGIDFTP----HMFRHTHATALIRAG 151

                        170       180
                 ....*....|....*....|....*
gi 695607702 332 ASIMIIAQRLGHADSNEVYNRYGHL 356
Cdd:cd01186  152 WSIEVVARRLGHAHVQTTLNTYGHL 176
INT_RitA_C_like cd01188
C-terminal catalytic domain of recombinase RitA, a component of the recombinase trio; ...
 197-353 1.95e-10

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


Pssm-ID: 271188 [Multi-domain]  Cd Length: 179  Bit Score: 59.18  E-value: 1.95e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 695607702 197 FKLLFYSGARKGEIRALTWRDINYDDDFIHINKTDYHGEVTAP---KTKAAIRDIYLPAHMMNDIKEylkwyketnIFKD 273
Cdd:cd01188   26 LLLLARLGLRAGDVAGLRLDDIDWRSGTITVRQKKTGRPVELPltePVGEALADYLRDGRPRTDSRE---------VFLR 96

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 695607702 274 DYVLFGRFF--KAYSeSTIDRWFTTAlkvldeqlpdGQTFPRIVIHELRHSHASMLVNHGASIMIIAQRLGHADSNEVYn 351
Cdd:cd01188   97 ARAPYRPLSstSQIS-SIVRRYLRKA----------GIEPSHRGTHSLRHSLATRMLRAGTSLKVIADLLGHRSIETTA- 164


                 ..
gi 695607702 352 RY 353
Cdd:cd01188  165 IY 166
int PHA02601
integrase; Provisional
 34-359 3.10e-08

integrase; Provisional


Pssm-ID: 222904 [Multi-domain]  Cd Length: 333  Bit Score: 54.73  E-value: 3.10e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 695607702  34 KEIKKSgFKQRKEALKKCNEIMDELEDVGQINKLPFDKLVDEYI-EWYSarRKSSSVKALKTHTNnHLLPYFKSMD---V 109
Cdd:PHA02601  23 KRIRKR-FATKGEALAFENYTMAEVDDKEWVGEKEDRRRLSELLqIWWD--LHGQTLEDGKARLA-KLLILCKGLGdpiA 98

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 695607702 110 FNMTTQDVMKFQNTKLKDGHS---GEYLKKMHVFLVSLLNHAMkFHDLKQ-------NVASLVGNFEiESNKRLNYWTLE 179
Cdd:PHA02601  99 SEFTAKDFADYRARRLSGEFKvnkGRPIKPATVNRELAYLSAV-FNELIKlgkwsgpNPLDGIRPFK-EAEPELAFLTKE 176

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 695607702 180 QFNQFYDALATQQQK---LFFKLLFYSGARKGEIRALTWRDINydddfihinktdyHGEVTAPKTKAA-IRDIYLPAHMM 255
Cdd:PHA02601 177 EIERLLDACDGSRSPdlgLIAKICLATGARWSEAETLKRSQIS-------------PYKITFVKTKGKkNRTVPISEELY 243

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 695607702 256 NDIKEylkwyKETNIFKDDYVLFGRffkaysestidrwfttALKVLDEQLPDGQTfprivIHELRHSHASMLVNHGASIM 335
Cdd:PHA02601 244 KMLPK-----RRGRLFKDAYESFER----------------AVKRAGIDLPEGQA-----THVLRHTFASHFMMNGGNIL 297

                        330       340
                 ....*....|....*....|....
gi 695607702 336 IIAQRLGHADSNEVYnRYGHLYPS 359
Cdd:PHA02601 298 VLQRILGHATIEMTM-AYAHFAPD 320
INT_IntI_C cd01193
Integron integrase and similar protiens, C-terminal catalytic domain; Integron integrases ...
 177-345 7.66e-08

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: 51.51  E-value: 7.66e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 695607702 177 TLEQFNQFYDALATQQQKLFFKLLFYSGARKGEIRALTWRDINYDDDFIHI-----NKTdyhgevtapktkaaiRDIYLP 251
Cdd:cd01193    7 SPDEVRRILGALTELRHRLILSLLYGAGLRISELLRLRVKDIDFERGVIRVrqgkgGKD---------------RVVPLP 71

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 695607702 252 AHMMNDIKEYLKWyketniFKDDYVLF---GRFF-----------KAYSESTIDRWFTTALKVLDEQlpdgqtfPRIVIH 317
Cdd:cd01193   72 EKLLEPLRRYLKS------ARPKEELDpaeGRAGvldprtgverrHHISETTVQRALKKAVEQAGIT-------KRVTPH 138

                        170       180
                 ....*....|....*....|....*...
gi 695607702 318 ELRHSHASMLVNHGASIMIIAQRLGHAD 345
Cdd:cd01193  139 TLRHSFATHLLEAGTDIRTIQELLGHSD 166
Phage_int_SAM_3 pfam14659
Phage integrase, N-terminal SAM-like domain; This domain is found in a variety of phage ...
 71-122 5.11e-06

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: 43.30  E-value: 5.11e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 695607702   71 KLVDEYIEWYSARRKSSSVKALKTHTNNHLLPYFKSMDVFNMTTQDVMKFQN 122
Cdd:pfam14659   2 EFYEIWLEDYKPRVKPSTYATYKRIIKNHILPYFGNMKLSKITPADIQKFQN 53
INT_RitC_C_like cd01182
C-terminal catalytic domain of recombinase RitC, a component of the recombinase trio; ...
 199-362 6.88e-06

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: 46.12  E-value: 6.88e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 695607702 199 LLFYSGARKGEIRALTWRDINYDDDfihinktdYHGEVTAPKTKaaIRDIYLPAHMMNDIKEYLKWYKETNIFKDDYVLF 278
Cdd:cd01182   29 LLYDTGARVQELADLTIRDLRLDDP--------ATVRLHGKGRK--ERTVPLWKETVAALKAYLQEFHLTPDPKQLFPLF 98

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 695607702 279 grfFKAY----SESTIDRWFTTALKVLDEQLPdgqTFP-RIVIHELRHSHASMLVNHGASIMIIAQRLGHADSnEVYNRY 353
Cdd:cd01182   99 ---PNRRgqplTRDGVAYILNKYVALASNRCP---SLPkRITPHTLRHTKAMHLLQAGVDLTVIRDWLGHESV-ETTQIY 171


                 ....*....
gi 695607702 354 ghLYPSTQK 362
Cdd:cd01182  172 --AEADLEM 178
Arm-DNA-bind_4 pfam14657
Arm DNA-binding domain; This family includes AP2-like domains found in a variety of phage ...
 19-59 3.05e-05

Arm DNA-binding domain; This family includes AP2-like domains found in a variety of phage integrase proteins. These domains bind to Arm DNA sites.


Pssm-ID: 464242  Cd Length: 44  Bit Score: 40.96  E-value: 3.05e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 695607702   19 TYYFRI-KYYDKKNQRKEIKKSGFKQRKEALKKCNEIMDELE 59
Cdd:pfam14657   1 TWYFQVyGYDDITGKRKQKTKRGFKTKKEAKEAEAEFIKKIS 42
xerD PRK00283
tyrosine recombinase;
317-345 3.44e-04

tyrosine recombinase;


Pssm-ID: 234713 [Multi-domain]  Cd Length: 299  Bit Score: 42.10  E-value: 3.44e-04
                         10        20
                 ....*....|....*....|....*....
gi 695607702 317 HELRHSHASMLVNHGASIMIIAQRLGHAD 345
Cdd:PRK00283 245 HVLRHAFATHLLNHGADLRVVQELLGHSD 273
INT_XerDC_C cd00798
XerD and XerC integrases, C-terminal catalytic domains; XerDC-like integrases are involved in ...
 200-345 9.07e-04

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: 39.80  E-value: 9.07e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 695607702 200 LFY-SGARKGEIRALTWRDINYDDDFIHI----NKTdyhgevtapktkaaiRDIYLPAHMMNDIKEYLK----WYKETNi 270
Cdd:cd00798   27 LLYaSGLRVSELVGLDLSDVDLDEGLVRVtgkgNKE---------------RLVPFGSYAVEALEEYLEerrpLLLKKK- 90

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 695607702 271 fKDDYVLFGRFFKAYSESTIDRwfttALKVLDEQLPDGQtfpRIVIHELRHSHASMLVNHGASIMIIAQRLGHAD 345
Cdd:cd00798   91 -PPDALFLNKRGKRLSRRGVWR----ILKKYAERAGLPK---HVSPHTLRHSFATHLLEGGADLRVVQELLGHAS 157
INT_C_like_4 cd01194
Uncharacterized site-specific tyrosine recombinase, C-terminal catalytic domain; Tyrosine ...
 197-352 1.03e-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: 271194 [Multi-domain]  Cd Length: 174  Bit Score: 39.66  E-value: 1.03e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 695607702 197 FKLLFYSGARKGEIRALTWRDINYDDDFIHINktdYHGevtapKTKAAIRD-IYLPAHMMNDIKEYLKWYKETnifKDDY 275
Cdd:cd01194   28 ISLMVTEGLRTVEIVRADVGDLRQEGEGTILY---VQG-----KGKTSKDDfVYLRPDVLKALQAYLKARGKL---DFEE 96

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 695607702 276 VLFGRFFKAYSESTIDRwfTTALKVLDEQLPD-GQTFPRIVIHELRHSHASMLVNHGASIMIIAQRLGHADSN--EVYNR 352
Cdd:cd01194   97 PLFTSLSNNSKGQRLTT--RSIRRIIKKYLRKaGLDDDRLTAHSLRHTAGTLALKAGKSLREVQQLLRHSDPNttMIYAH 174
recomb_XerD TIGR02225
tyrosine recombinase XerD; The phage integrase family describes a number of recombinases with ...
 317-366 1.41e-03

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: 39.87  E-value: 1.41e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 695607702  317 HELRHSHASMLVNHGASIMIIAQRLGHAD--SNEVYNrygHLYPSTQKEIVK 366
Cdd:TIGR02225 237 HTLRHSFATHLLENGADLRVVQELLGHADisTTQIYT---HVARERLKEVHK 285
 
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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