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Conserved domains on  [gi|447068466|ref|WP_001145722|]
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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];
64-348 7.32e-45

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


:

Pssm-ID: 443999 [Multi-domain]  Cd Length: 291  Bit Score: 155.15  E-value: 7.32e-45
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 447068466  64 FFNRLKNE-NLSARSIEKRTTEYNTHIK--ERFGNIPIGKITTTQCTAFRNYLLnDAGLSVGYARSVWAGFKAVINYAKK 140
Cdd:COG4974   10 FLEELKREkGLSPNTIKAYRRDLRRFLRflEELGKIPLAEITPEDIRAYLNYLR-ERGLSPSTINRYLAALRSFFRYAVR 88

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 447068466 141 HYKLLYDPTLSVTPIPRTKPQAKFITREEFDEKVEQITNDTS-----RQLTKLLFYSGLRIGEALALQWKDydkikgeid 215
Cdd:COG4974   89 EGLLEDNPAAKVKLPKKPRKLPRVLTEEEIEALLEALDTETPeglrdRALLLLLYATGLRVSELLGLKWSD--------- 159

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 447068466 216 vnkkINLSNREIEYNLKKESSKGIIPVPKLIREMLKNMYNESSKRykyfDENY-FIFGGLEPIRYVTYSYHFKSVF---- 290
Cdd:COG4974  160 ----IDLDRGTIRVRRGKGGKERTVPLSPEALEALREYLEERRPR----DSDYlFPTRRGRPLSRRAIRKILKRLAkrag 231

                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 447068466 291 --PNLKIHHLRHSYASYLINNGVDMYLLMELMRHSNITeTIQTYSHLYTDKKHQAMNIFD 348
Cdd:COG4974  232 ipKRVTPHSLRHTFATHLLEAGVDLRTVQELLGHSSIS-TTQIYTHVSDEELREAVEKLH 290
Arm-DNA-bind_4 pfam14657
Arm DNA-binding domain; This family includes AP2-like domains found in a variety of phage ...
 11-51 7.84e-08

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: 47.90  E-value: 7.84e-08
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 447068466   11 KWYFSIR-YKDVYGNNKRKMKRGFERKKDAKLAESEFIQNVK 51
Cdd:pfam14657   1 TWYFQVYgYDDITGKRKQKTKRGFKTKKEAKEAEAEFIKKIS 42
 
Name Accession Description Interval E-value
XerD COG4974
Site-specific recombinase XerD [Replication, recombination and repair];
64-348 7.32e-45

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


Pssm-ID: 443999 [Multi-domain]  Cd Length: 291  Bit Score: 155.15  E-value: 7.32e-45
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 447068466  64 FFNRLKNE-NLSARSIEKRTTEYNTHIK--ERFGNIPIGKITTTQCTAFRNYLLnDAGLSVGYARSVWAGFKAVINYAKK 140
Cdd:COG4974   10 FLEELKREkGLSPNTIKAYRRDLRRFLRflEELGKIPLAEITPEDIRAYLNYLR-ERGLSPSTINRYLAALRSFFRYAVR 88

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 447068466 141 HYKLLYDPTLSVTPIPRTKPQAKFITREEFDEKVEQITNDTS-----RQLTKLLFYSGLRIGEALALQWKDydkikgeid 215
Cdd:COG4974   89 EGLLEDNPAAKVKLPKKPRKLPRVLTEEEIEALLEALDTETPeglrdRALLLLLYATGLRVSELLGLKWSD--------- 159

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 447068466 216 vnkkINLSNREIEYNLKKESSKGIIPVPKLIREMLKNMYNESSKRykyfDENY-FIFGGLEPIRYVTYSYHFKSVF---- 290
Cdd:COG4974  160 ----IDLDRGTIRVRRGKGGKERTVPLSPEALEALREYLEERRPR----DSDYlFPTRRGRPLSRRAIRKILKRLAkrag 231

                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 447068466 291 --PNLKIHHLRHSYASYLINNGVDMYLLMELMRHSNITeTIQTYSHLYTDKKHQAMNIFD 348
Cdd:COG4974  232 ipKRVTPHSLRHTFATHLLEAGVDLRTVQELLGHSSIS-TTQIYTHVSDEELREAVEKLH 290
INT_ICEBs1_C_like cd01189
C-terminal catalytic domain of integrases from bacterial phages and conjugate transposons; ...
 167-334 5.72e-30

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: 111.88  E-value: 5.72e-30
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 447068466 167 REEFDE--KVEQITNDTSRQLTKLLFYSGLRIGEALALQWKDYDKIKGEIDVNK--KINLSNREIEYNLKKESSKGIIPV 242
Cdd:cd01189    1 PEELKKllEALKKRGDRYYLLFLLALLTGLRRGELLALTWSDIDFENGTIRINRtlVRKKKGGYVIKPPKTKSSIRTIPL 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 447068466 243 PKLIREMLKNMynessKRYKYFDENYfifgGLEPIRyvtysyhfksvfpnlkIHHLRHSYASYLINNGVDMYLLMELMRH 322
Cdd:cd01189   81 PDELIELLKEL-----KAFKKLLKKA----GLPRIT----------------PHDLRHTFASLLLEAGVPLKVIAERLGH 135

                        170
                 ....*....|..
gi 447068466 323 SNITETIQTYSH 334
Cdd:cd01189  136 SDISTTLDVYAH 147
Phage_integrase pfam00589
Phage integrase family; Members of this family cleave DNA substrates by a series of staggered ...
 182-336 7.04e-17

Phage integrase family; Members of this family cleave DNA substrates by a series of staggered cuts, during which the protein becomes covalently linked to the DNA through a catalytic tyrosine residue at the carboxy end of the alignment. The catalytic site residues in CRE recombinase are Arg-173, His-289, Arg-292 and Tyr-324.


Pssm-ID: 395471 [Multi-domain]  Cd Length: 169  Bit Score: 76.97  E-value: 7.04e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 447068466  182 SRQLTKLLFYSGLRIGEALALQWKDydkikgeidvnkkINLSNREIEYNLKKESSKGIIPVPKLIREMLKNMYnesSKRY 261
Cdd:pfam00589  23 DKALLELLYATGLRISELCSLRWSD-------------IDFENGVIRVHRGKGNKERTVPLSDAALELLKEWL---SKRL 86

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 447068466  262 KYFDENYFIFGGL--EPIRYVTYSYHFKSVFPNLKI------HHLRHSYASYLINNGVDMYLLMELMRHSNITETiQTYS 333
Cdd:pfam00589  87 LEAPKSDYLFASKrgKPLSRQTVRKIFKRAGKEAGLelplhpHMLRHSFATHLLEAGVDLRVVQKLLGHSSISTT-QIYT 165


                  ...
gi 447068466  334 HLY 336
Cdd:pfam00589 166 HVA 168
xerC PRK00236
site-specific tyrosine recombinase XerC; Reviewed
 64-341 6.04e-09

site-specific tyrosine recombinase XerC; Reviewed


Pssm-ID: 234698 [Multi-domain]  Cd Length: 297  Bit Score: 56.32  E-value: 6.04e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 447068466  64 FFNRLKNE-NLSARSIEkrttEYNTHIK------ERFGNIPIGKITTTQctaFRNYL--LNDAGLSvgyARSV---WAGF 131
Cdd:PRK00236  13 FLEYLRVErGLSPHTLR----AYRRDLRaflaflEEHGISSLQDLDAAD---LRSFLarRRRQGLS---ARSLarrLSAL 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 447068466 132 KAVINYAKKHYKLLYDPTLSV-TP-IPRTKPqaKFITREEFDEKVEQITNDT---SRQLTKL-LFY-SGLRIGEALALQW 204
Cdd:PRK00236  83 RSFYRWLVRRGLLKANPAAGLrAPkIPKRLP--KPLDVDQAKRLLDAIDEDDplaLRDRAILeLLYgSGLRLSELVGLDI 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 447068466 205 KDYDKIKGEIDVNKKINlsnreieynlkKESskgIIPVPKLIREMLKNmYNESSKRYKYFDENYFI--FGG-LEP--IRY 279
Cdd:PRK00236 161 DDLDLASGTLRVLGKGN-----------KER---TVPLGRAAREALEA-YLALRPLFLPDDDALFLgaRGGrLSPrvVQR 225

                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 447068466 280 VTYSY-HFKSVFPNLKIHHLRHSYASYLINNGVDMYLLMELMRHSNITETiQTYSHLytDKKH 341
Cdd:PRK00236 226 RVKKLgKKAGLPSHITPHKLRHSFATHLLESGGDLRAVQELLGHASLSTT-QIYTHV--DFQH 285
Arm-DNA-bind_4 pfam14657
Arm DNA-binding domain; This family includes AP2-like domains found in a variety of phage ...
 11-51 7.84e-08

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: 47.90  E-value: 7.84e-08
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 447068466   11 KWYFSIR-YKDVYGNNKRKMKRGFERKKDAKLAESEFIQNVK 51
Cdd:pfam14657   1 TWYFQVYgYDDITGKRKQKTKRGFKTKKEAKEAEAEFIKKIS 42
 
Name Accession Description Interval E-value
XerD COG4974
Site-specific recombinase XerD [Replication, recombination and repair];
64-348 7.32e-45

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


Pssm-ID: 443999 [Multi-domain]  Cd Length: 291  Bit Score: 155.15  E-value: 7.32e-45
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 447068466  64 FFNRLKNE-NLSARSIEKRTTEYNTHIK--ERFGNIPIGKITTTQCTAFRNYLLnDAGLSVGYARSVWAGFKAVINYAKK 140
Cdd:COG4974   10 FLEELKREkGLSPNTIKAYRRDLRRFLRflEELGKIPLAEITPEDIRAYLNYLR-ERGLSPSTINRYLAALRSFFRYAVR 88

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 447068466 141 HYKLLYDPTLSVTPIPRTKPQAKFITREEFDEKVEQITNDTS-----RQLTKLLFYSGLRIGEALALQWKDydkikgeid 215
Cdd:COG4974   89 EGLLEDNPAAKVKLPKKPRKLPRVLTEEEIEALLEALDTETPeglrdRALLLLLYATGLRVSELLGLKWSD--------- 159

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 447068466 216 vnkkINLSNREIEYNLKKESSKGIIPVPKLIREMLKNMYNESSKRykyfDENY-FIFGGLEPIRYVTYSYHFKSVF---- 290
Cdd:COG4974  160 ----IDLDRGTIRVRRGKGGKERTVPLSPEALEALREYLEERRPR----DSDYlFPTRRGRPLSRRAIRKILKRLAkrag 231

                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 447068466 291 --PNLKIHHLRHSYASYLINNGVDMYLLMELMRHSNITeTIQTYSHLYTDKKHQAMNIFD 348
Cdd:COG4974  232 ipKRVTPHSLRHTFATHLLEAGVDLRTVQELLGHSSIS-TTQIYTHVSDEELREAVEKLH 290
XerC COG4973
Site-specific recombinase XerC [Replication, recombination and repair];
64-343 5.13e-30

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


Pssm-ID: 443998 [Multi-domain]  Cd Length: 287  Bit Score: 115.83  E-value: 5.13e-30
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 447068466  64 FFNRLKNENLSARSIEKRTTEYNTHIKE-RFGNIPIGKITTTQctaFRNYL--LNDAGLSVGYARSVWAGFKAVINYAKK 140
Cdd:COG4973   11 YLEHLRERRLSPKTLEAYRRDLRRLIPLlGDADLPLEELTPAD---VRRFLarLHRRGLSPRTLNRRLSALRSFFNWAVR 87

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 447068466 141 HYKLLYDPTLSVTPIPRTKPQAKFITREEFDEKVEQITNDTS----RQLTKLLFYSGLRIGEALALQWKDYDKIKGEIDV 216
Cdd:COG4973   88 EGLLEANPAAGVKAPKAPRKLPRALTVDELAQLLDALADDPLavrdRAIVELLYSTGLRLGELVGLDWEDVDLDAGEVRV 167

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 447068466 217 nkkinlsnreieynLKKESSKGIIPVPKLIREMLKNmYNESSKRYKYFDENY-FIFGGLEPIRYVTYSYHFKS------V 289
Cdd:COG4973  168 --------------RGKTGKSRTVPLGPKALAALRE-WLAVRPELAAPDEGAlFPSRRGTRLSPRNVQKRLRRlakkagL 232

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|....
gi 447068466 290 FPNLKIHHLRHSYASYLINNGVDMYLLMELMRHSNITeTIQTYSHLytDKKHQA 343
Cdd:COG4973  233 PKHVHPHDLRHSFATHLLESGGDLRAVQELLGHASIS-TTQIYTHL--DFQHLA 283
INT_ICEBs1_C_like cd01189
C-terminal catalytic domain of integrases from bacterial phages and conjugate transposons; ...
 167-334 5.72e-30

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: 111.88  E-value: 5.72e-30
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 447068466 167 REEFDE--KVEQITNDTSRQLTKLLFYSGLRIGEALALQWKDYDKIKGEIDVNK--KINLSNREIEYNLKKESSKGIIPV 242
Cdd:cd01189    1 PEELKKllEALKKRGDRYYLLFLLALLTGLRRGELLALTWSDIDFENGTIRINRtlVRKKKGGYVIKPPKTKSSIRTIPL 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 447068466 243 PKLIREMLKNMynessKRYKYFDENYfifgGLEPIRyvtysyhfksvfpnlkIHHLRHSYASYLINNGVDMYLLMELMRH 322
Cdd:cd01189   81 PDELIELLKEL-----KAFKKLLKKA----GLPRIT----------------PHDLRHTFASLLLEAGVPLKVIAERLGH 135

                        170
                 ....*....|..
gi 447068466 323 SNITETIQTYSH 334
Cdd:cd01189  136 SDISTTLDVYAH 147
FimB COG0582
Integrase/recombinase, includes phage integrase [Replication, recombination and repair, ...
 69-345 3.44e-22

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


Pssm-ID: 440347 [Multi-domain]  Cd Length: 391  Bit Score: 96.26  E-value: 3.44e-22
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 447068466  69 KNENLSARSIEKRTTEYNTHIKERFGNIPIGKITTTQCTAFRNYLLNDAGLSVgyARSVWAGFKAVINYAKKHYKLLYDP 148
Cdd:COG0582  110 KKPEWKEKTAAQVRRTLEKHIFPVLGDRPIAEITPPDLLAVLRPIEARGAPET--ARRVRQRLRQVFRYAVARGLIERNP 187

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 447068466 149 TLSVT---PIPRTKPQAkFITREEFDEKVEQITNDTSRQLTK----LLFYSGLRIGEALALQWKDydkikgeidvnkkIN 221
Cdd:COG0582  188 AADLKgalPKPKVKHHP-ALTPEELPELLRALDAYRGSPVTRlalrLLLLTGVRPGELRGARWSE-------------ID 253

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 447068466 222 LSNREIEYNlkKESSKG----IIPVPKLIREMLKNMYnESSKRYKYfdenyfIF----GGLEPIRYVTYSYHFKSV-FPN 292
Cdd:COG0582  254 LEAALWTIP--AERMKTrrphIVPLSRQALEILKELK-PLTGDSEY------VFpsrrGPKKPMSENTLNKALRRMgYGR 324

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|....
gi 447068466 293 LKIHHLRHSYASYLINNGVDMYLLMELMRHSNITETIQTYSH-LYTDKKHQAMN 345
Cdd:COG0582  325 FTPHGFRHTASTLLNEAGFPPDVIERQLAHKDGNKVRAAYNRaDYLEERREMMQ 378
DNA_BRE_C cd00397
DNA breaking-rejoining enzymes, C-terminal catalytic domain; The DNA breaking-rejoining enzyme ...
 185-332 6.25e-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: 88.31  E-value: 6.25e-21
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 447068466 185 LTKLLFYSGLRIGEALALQWKDYDKIKGEIDVNKKInlsnreieynlKKESSKGIIPVPKLIREMLKNMYNESSKRYKYF 264
Cdd:cd00397   22 ILLLLLETGLRISELLALKVKDIDLDNGTIRVRGKK-----------TKGGKERTVPLPKELAEELKEYLKERRDKRGPL 90

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 447068466 265 DENYFIFGGLEPIRYVTYSYH---------FKSVFPNLKIHHLRHSYASYLINNGVDMYLLMELMRHSNITeTIQTY 332
Cdd:cd00397   91 LKSLYLNKLFGTKLGERLSRRtlrrifkkaGIEAGRKITPHSLRHTFATNLLENGVDIKVVQKLLGHSSIS-TTQRY 166
INT_Rci_Hp1_C cd00796
Shufflon-specific DNA recombinase Rci and Bacteriophage Hp1_like integrase, C-terminal ...
 161-334 1.68e-20

Shufflon-specific DNA recombinase Rci and Bacteriophage Hp1_like integrase, C-terminal catalytic domain; Rci protein is a tyrosine recombinase specifically involved in Shufflon type of DNA rearrangement in bacteria. The shufflon of plasmid R64 consists of four invertible DNA segments which are separated and flanked by seven 19-bp repeat sequences. RCI recombinase facilitates the site-specific recombination between any inverted repeats results in an inversion of the DNA segment(s) either independently or in groups. HP1 integrase promotes site-specific recombination of the HP1 genome into that of Haemophilus influenza. Bacteriophage Hp1_like integrases are tyrosine based site specific recombinases. They belong to the superfamily of DNA breaking-rejoining enzymes, which share the same fold in their catalytic domain and the overall reaction mechanism. The catalytic domain contains six conserved active site residues. Their overall reaction mechanism is essentially identical and involves cleavage of a single strand of a DNA duplex by nucleophilic attack of a conserved tyrosine to give a 3' phosphotyrosyl protein-DNA adduct. In the second rejoining step, a terminal 5' hydroxyl attacks the covalent adduct to release the enzyme and generate duplex DNA.


Pssm-ID: 271177 [Multi-domain]  Cd Length: 162  Bit Score: 87.00  E-value: 1.68e-20
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 447068466 161 QAKFITREEFDEKVEQITNDTSRQL---TKLLFYSGLRIGEALALQWKDydkikgeidvnkkINLSNREIEynlkKESSK 237
Cdd:cd00796    1 RDRFLTEDEEARLLAALEESTNPHLrliVLLALYTGARRGEILSLRWDD-------------IDLEVGLIV----LPETK 63

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 447068466 238 G----IIPVPKLIREMLKNMYNESSKRYKYFdenyfiFGGLEPIRYVTYSYHFKSVF-----PNLKIHHLRHSYASYLIN 308
Cdd:cd00796   64 NgkprTVPLSDEAIAILKELKRKRGKDGFFV------DGRFFGIPIASLRRAFKKARkraglEDLRFHDLRHTFASRLVQ 137

                        170       180
                 ....*....|....*....|....*.
gi 447068466 309 NGVDMYLLMELMRHSNItETIQTYSH 334
Cdd:cd00796  138 AGVPIKTVAKILGHSSI-KMTMRYAH 162
Phage_integrase pfam00589
Phage integrase family; Members of this family cleave DNA substrates by a series of staggered ...
 182-336 7.04e-17

Phage integrase family; Members of this family cleave DNA substrates by a series of staggered cuts, during which the protein becomes covalently linked to the DNA through a catalytic tyrosine residue at the carboxy end of the alignment. The catalytic site residues in CRE recombinase are Arg-173, His-289, Arg-292 and Tyr-324.


Pssm-ID: 395471 [Multi-domain]  Cd Length: 169  Bit Score: 76.97  E-value: 7.04e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 447068466  182 SRQLTKLLFYSGLRIGEALALQWKDydkikgeidvnkkINLSNREIEYNLKKESSKGIIPVPKLIREMLKNMYnesSKRY 261
Cdd:pfam00589  23 DKALLELLYATGLRISELCSLRWSD-------------IDFENGVIRVHRGKGNKERTVPLSDAALELLKEWL---SKRL 86

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 447068466  262 KYFDENYFIFGGL--EPIRYVTYSYHFKSVFPNLKI------HHLRHSYASYLINNGVDMYLLMELMRHSNITETiQTYS 333
Cdd:pfam00589  87 LEAPKSDYLFASKrgKPLSRQTVRKIFKRAGKEAGLelplhpHMLRHSFATHLLEAGVDLRVVQKLLGHSSISTT-QIYT 165


                  ...
gi 447068466  334 HLY 336
Cdd:pfam00589 166 HVA 168
INT_IntI_C cd01193
Integron integrase and similar protiens, C-terminal catalytic domain; Integron integrases ...
 163-335 5.44e-14

Integron integrase and similar protiens, C-terminal catalytic domain; Integron integrases mediate site-specific DNA recombination between a proximal primary site (attI) and a secondary target site (attC) found within mobile gene cassettes encoding resistance or virulence factors. Unlike other site specific recombinases, the attC sites lack sequence conservation. Integron integrase exhibits broader DNA specificity by recognizing the non-conserved attC sites. The structure shows that DNA target site recognition are not dependent on canonical DNA but on the position of two flipped-out bases that interact in cis and in trans with the integrase. Integron-integrases are present in many natural occurring mobile elements, including transposons and conjugative plasmids. Vibrio, Shewanella, Xanthomonas, and Pseudomonas species harbor chromosomal super-integrons. All integron-integrases carry large inserts unlike the TnpF ermF-like proteins also seen in this group.


Pssm-ID: 271193 [Multi-domain]  Cd Length: 176  Bit Score: 69.23  E-value: 5.44e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 447068466 163 KFITREEFDEKVEQITNDTSRQLTKLLFYSGLRIGEALALQWKDYDKIKGEIDVnkkinlsnreieynlkkESSKG---- 238
Cdd:cd01193    4 VVLSPDEVRRILGALTELRHRLILSLLYGAGLRISELLRLRVKDIDFERGVIRV-----------------RQGKGgkdr 66

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 447068466 239 IIPVPKLIREMLKNmYNESSKRYKYFDENYFIFGGLEPIRYVTYSYHF--KSVFPNLK-------------IHHLRHSYA 303
Cdd:cd01193   67 VVPLPEKLLEPLRR-YLKSARPKEELDPAEGRAGVLDPRTGVERRHHIseTTVQRALKkaveqagitkrvtPHTLRHSFA 145

                        170       180       190
                 ....*....|....*....|....*....|..
gi 447068466 304 SYLINNGVDMYLLMELMRHSNItETIQTYSHL 335
Cdd:cd01193  146 THLLEAGTDIRTIQELLGHSDL-STTMIYTHV 176
INTN1_C_like cd01185
Integrase IntN1 of Bacteroides mobilizable transposon NBU1 and similar proteins, C-terminal ...
 177-340 7.64e-13

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: 65.75  E-value: 7.64e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 447068466 177 ITNDTSRQLTKLLF----YSGLRIGEALALQWKDYDKIKGeidvnkkinlsNREIEYNLKKESSKGIIPVPKLIREMLKn 252
Cdd:cd01185   11 LSDTSRLELVRDMFlfscYTGLRFSDLKNLTWKNIVEASG-----------RTWIRYRRKKTGKPVTVPLLPVAREILE- 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 447068466 253 mynesskRYKYFDENYFIFGGLEpirYVTYSYHFKSVFPNLKIH-----HL-RHSYASYLINNGVDMYLLMELMRHSNIT 326
Cdd:cd01185   79 -------KYKDDRSEGKLFPVLS---NQKINRYLKEIAKIAGIDkhltfHVaRHTFATLLLLKGVDIETISKLLGHSSIK 148

                        170
                 ....*....|....
gi 447068466 327 ETiQTYSHLYTDKK 340
Cdd:cd01185  149 TT-QIYAKIVDSKK 161
INT_tnpA_C_Tn554 cd01186
Putative Transposase A from transposon Tn554, C-terminal catalytic domain; This family ...
 165-335 1.93e-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: 65.13  E-value: 1.93e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 447068466 165 ITREEFDEKVEQITNDTSRQLTKLLFYSGLRIGEALALQWKDYDKIKGEIDVNKKINLSNREIeynlKKESSKGIIPVPK 244
Cdd:cd01186    2 LTPREVQELINACNNLRDKFLLALLYETGLRIGEALGLRIEDIDMADNQIELVPREDNTNEAR----AKSMRERRIPVSQ 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 447068466 245 LIREMLKNMYNESSKRYKYFDENYF--IFGG--LEPIRYVTYSYHFKSVFPNLKI----HHLRHSYASYLINNGVDMYLL 316
Cdd:cd01186   78 DLIDLYADYLTYIYCEEAEFSITVFvnVKGGnqGKAMNYSDVYDLVRRLKKRTGIdftpHMFRHTHATALIRAGWSIEVV 157

                        170
                 ....*....|....*....
gi 447068466 317 MELMRHSNITETIQTYSHL 335
Cdd:cd01186  158 ARRLGHAHVQTTLNTYGHL 176
INT_XerDC_C cd00798
XerD and XerC integrases, C-terminal catalytic domains; XerDC-like integrases are involved in ...
 189-341 7.61e-11

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: 60.22  E-value: 7.61e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 447068466 189 LFY-SGLRIGEALALQWKDYDKIKGEIDVNKKINlsnreieynlkKESskgIIPVPKLIREMLKNMYNESSKRYKYFDEN 267
Cdd:cd00798   27 LLYaSGLRVSELVGLDLSDVDLDEGLVRVTGKGN-----------KER---LVPFGSYAVEALEEYLEERRPLLLKKKPP 92

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 447068466 268 YFIF-----GGLEP-------IRYVTYSYHFKSVFPnlkiHHLRHSYASYLINNGVDMYLLMELMRHSNITETiQTYSHL 335
Cdd:cd00798   93 DALFlnkrgKRLSRrgvwrilKKYAERAGLPKHVSP----HTLRHSFATHLLEGGADLRVVQELLGHASLSTT-QIYTHV 167


                 ....*.
gi 447068466 336 ytDKKH 341
Cdd:cd00798  168 --SFER 171
INT_C_like_1 cd01184
Uncharacterized site-specific tyrosine recombinase, C-terminal catalytic domain; Tyrosine ...
 191-334 2.73e-10

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: 58.86  E-value: 2.73e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 447068466 191 YSGLRIGEALALQWKDYDKIKGeIDVnkkINLSNREIEYNLKKESSKGIIPVPK-LIR----EMLKNMynESSKRYKYFD 265
Cdd:cd01184   34 YTGARLNEICQLRVDDIKEEDG-IWC---IDINDDAEGRRLKTKASRRLVPIHPrLIElgflDYVEAL--RADGKLFLFP 107

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 447068466 266 ENYFIFGGlepiRYVTYSYHFKSVFPNLKIHH--------LRHSYASYLINNGVDMYLLMELMRHSNITETIQTYSH 334
Cdd:cd01184  108 EKRDKDGK----YSKAASKWFNRLLRKLGIKDderksfhsFRHTFITALKRAGVPEELIAQIVGHSRGGVTHDTYGK 180
xerC PRK00236
site-specific tyrosine recombinase XerC; Reviewed
 64-341 6.04e-09

site-specific tyrosine recombinase XerC; Reviewed


Pssm-ID: 234698 [Multi-domain]  Cd Length: 297  Bit Score: 56.32  E-value: 6.04e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 447068466  64 FFNRLKNE-NLSARSIEkrttEYNTHIK------ERFGNIPIGKITTTQctaFRNYL--LNDAGLSvgyARSV---WAGF 131
Cdd:PRK00236  13 FLEYLRVErGLSPHTLR----AYRRDLRaflaflEEHGISSLQDLDAAD---LRSFLarRRRQGLS---ARSLarrLSAL 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 447068466 132 KAVINYAKKHYKLLYDPTLSV-TP-IPRTKPqaKFITREEFDEKVEQITNDT---SRQLTKL-LFY-SGLRIGEALALQW 204
Cdd:PRK00236  83 RSFYRWLVRRGLLKANPAAGLrAPkIPKRLP--KPLDVDQAKRLLDAIDEDDplaLRDRAILeLLYgSGLRLSELVGLDI 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 447068466 205 KDYDKIKGEIDVNKKINlsnreieynlkKESskgIIPVPKLIREMLKNmYNESSKRYKYFDENYFI--FGG-LEP--IRY 279
Cdd:PRK00236 161 DDLDLASGTLRVLGKGN-----------KER---TVPLGRAAREALEA-YLALRPLFLPDDDALFLgaRGGrLSPrvVQR 225

                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 447068466 280 VTYSY-HFKSVFPNLKIHHLRHSYASYLINNGVDMYLLMELMRHSNITETiQTYSHLytDKKH 341
Cdd:PRK00236 226 RVKKLgKKAGLPSHITPHKLRHSFATHLLESGGDLRAVQELLGHASLSTT-QIYTHV--DFQH 285
Arm-DNA-bind_4 pfam14657
Arm DNA-binding domain; This family includes AP2-like domains found in a variety of phage ...
 11-51 7.84e-08

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: 47.90  E-value: 7.84e-08
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 447068466   11 KWYFSIR-YKDVYGNNKRKMKRGFERKKDAKLAESEFIQNVK 51
Cdd:pfam14657   1 TWYFQVYgYDDITGKRKQKTKRGFKTKKEAKEAEAEFIKKIS 42
int PHA02601
integrase; Provisional
 1-343 2.00e-07

integrase; Provisional


Pssm-ID: 222904 [Multi-domain]  Cd Length: 333  Bit Score: 52.04  E-value: 2.00e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 447068466   1 MPVYKDDNtGKWYFSIRykdVYGNNKRKMKRGFERKKDAKLAESefiqnvkygysdnqpfeYIFFNRLKNENLSARSIEK 80
Cdd:PHA02601   1 MAVRKLKD-GKWLCEIY---PNGRDGKRIRKRFATKGEALAFEN-----------------YTMAEVDDKEWVGEKEDRR 59

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 447068466  81 RTTEY-----------NTHIKERF----------GNIPIGKITTTQCTAFRNYLLNDaGLSVGYARSV--------WAGF 131
Cdd:PHA02601  60 RLSELlqiwwdlhgqtLEDGKARLakllilckglGDPIASEFTAKDFADYRARRLSG-EFKVNKGRPIkpatvnreLAYL 138

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 447068466 132 KAVINYAKKHYKL-LYDPTLSVTPIPRTKPQAKFITREEFDEKVEQITNDTSRQLT---KLLFYSGLRIGEALALqwkdy 207
Cdd:PHA02601 139 SAVFNELIKLGKWsGPNPLDGIRPFKEAEPELAFLTKEEIERLLDACDGSRSPDLGliaKICLATGARWSEAETL----- 213

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 447068466 208 dkikgeidvnKKINLSNREIEYNLKKESSKGIIPVPKLIREMLknmyneSSKRYKYFDENYFIFGglepiRYVtysyhfK 287
Cdd:PHA02601 214 ----------KRSQISPYKITFVKTKGKKNRTVPISEELYKML------PKRRGRLFKDAYESFE-----RAV------K 266

                        330       340       350       360       370       380
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 447068466 288 SVFPNL----KIHHLRHSYASYLINNGVDMYLLMELMRHSNITETIQtYSHLYTDKKHQA 343
Cdd:PHA02601 267 RAGIDLpegqATHVLRHTFASHFMMNGGNILVLQRILGHATIEMTMA-YAHFAPDHLEDA 325
xerD PRK00283
tyrosine recombinase;
296-338 2.86e-06

tyrosine recombinase;


Pssm-ID: 234713 [Multi-domain]  Cd Length: 299  Bit Score: 48.26  E-value: 2.86e-06
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|...
gi 447068466 296 HHLRHSYASYLINNGVDMYLLMELMRHSNITETiQTYSHLYTD 338
Cdd:PRK00283 245 HVLRHAFATHLLNHGADLRVVQELLGHSDISTT-QIYTHVATE 286
INT_P4_C cd00801
Bacteriophage P4 integrase, C-terminal catalytic domain; P4-like integrases are found in ...
 179-344 3.64e-04

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: 40.72  E-value: 3.64e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 447068466 179 NDTSRQLTKLLFYSGLRIGEALALQWKDYDKIKGEIDVNKKINLSNREIeynlkkesskgIIPVPKLIREMLKNmyness 258
Cdd:cd00801   18 SPPTKLALRLLLLTGQRIGELARARWSEIDLEEKTWTIPAERTKNKRPH-----------RVPLSDQALEILEE------ 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 447068466 259 kRYKYFDENYFIFGGL----EPIRYVTYSYHFKSVFPNLKI---HHLRHSYASYLINNGVDMYLLMELMRHSNITETIQT 331
Cdd:cd00801   81 -LKEFTGDSGYLFPSRrkkkKPISENTINKALKRLGYKGKEftpHDLRRTFSTLLNELGIDPEVIERLLNHVLGGVVRAA 159

                        170
                 ....*....|....
gi 447068466 332 YSH-LYTDKKHQAM 344
Cdd:cd00801  160 YNRyDYLEERREAL 173
xerS PRK05084
site-specific tyrosine recombinase XerS; Reviewed
 188-345 1.45e-03

site-specific tyrosine recombinase XerS; Reviewed


Pssm-ID: 235339 [Multi-domain]  Cd Length: 357  Bit Score: 40.29  E-value: 1.45e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 447068466 188 LLFYSGLRIGEALALQWKDYDKIKGEIDVNKKINlsnreieynlKKESskgiIPVPKLIREMLKNMYNESSKRYKYfDEN 267
Cdd:PRK05084 203 LILGSGLRVSELVNLDLSDLNLKQMTIDVTRKGG----------KRDS----VNIAPFALPYLEEYLKIRASRYKA-EKQ 267

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 447068466 268 YFIF------GGLEPIRYVT-------YSYHFKSvfpNLKIHHLRHSYASYLINNGVDMYLLMELMRHSNiTETIQTYSH 334
Cdd:PRK05084 268 EKALfltkyrGKPNRISARAiekmvakYSEAFGV---RLTPHKLRHTLATRLYDATKDQVLVADQLGHTS-TETTDLYTH 343

                        170
                 ....*....|.
gi 447068466 335 LYTDKKHQAMN 345
Cdd:PRK05084 344 IVNDEQKEALD 354
Phage_int_SAM_3 pfam14659
Phage integrase, N-terminal SAM-like domain; This domain is found in a variety of phage ...
 60-113 1.68e-03

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: 35.98  E-value: 1.68e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 447068466   60 FEYIFFNRLKNeNLSARSIEKRTTEYNTHIKERFGNIPIGKITTTQCTAFRNYL 113
Cdd:pfam14659   3 FYEIWLEDYKP-RVKPSTYATYKRIIKNHILPYFGNMKLSKITPADIQKFQNKL 55
INT_RitC_C_like cd01182
C-terminal catalytic domain of recombinase RitC, a component of the recombinase trio; ...
 165-345 3.53e-03

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: 38.03  E-value: 3.53e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 447068466 165 ITREEFDEKVEQITNDTS---RQLTKLLF-Y-SGLRIGEALALQWKDYDkikgeIDVNKKINLSnreieynlkkesSKG- 238
Cdd:cd01182    1 LTREEMKALLAAPDRNTSlgrRDHALLLLlYdTGARVQELADLTIRDLR-----LDDPATVRLH------------GKGr 63

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 447068466 239 ---IIPVPKLIREMLKNMYNESSKRYKYFDENY-FIFGGLEP-----IRYV--TYSYHFKSVFPNLK----IHHLRHSYA 303
Cdd:cd01182   64 kerTVPLWKETVAALKAYLQEFHLTPDPKQLFPlFPNRRGQPltrdgVAYIlnKYVALASNRCPSLPkritPHTLRHTKA 143

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|..
gi 447068466 304 SYLINNGVDMYLLMELMRHSNItETIQTYSHLYTDKKHQAMN 345
Cdd:cd01182  144 MHLLQAGVDLTVIRDWLGHESV-ETTQIYAEADLEMKREALE 184
INT_C_like_3 cd01192
Uncharacterized site-specific tyrosine recombinase, C-terminal catalytic domain; Tyrosine ...
 192-328 6.60e-03

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


Pssm-ID: 271192 [Multi-domain]  Cd Length: 178  Bit Score: 37.27  E-value: 6.60e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 447068466 192 SGLRIGEALALQWKDydkikgeidVNKKINLSNREieynlKKESSKGIIPVPKLIREMLKNMYNESSKRYKYFDENYFIF 271
Cdd:cd01192   36 TGLRISDLLSLKVED---------VTNKDKLSIKE-----QKTGKQKTFPLNPTLVKALKEYIDDLDLKRNDYLFKSLKQ 101

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 447068466 272 GGLEPIRYVTYSYHFKSVFPNLKI------HHLRHSYASYLINNGVDMYLLMELMRHSNITET 328
Cdd:cd01192  102 GPEKPISRKQAYKILKKAADDLGLnynigtHSLRKTFGYHVYKQGKDIELLMKLLNHSSPSIT 164
 
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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