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Conserved domains on  [gi|501562005|ref|WP_012566477|]
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site-specific integrase [Rhodospirillum centenum]

Protein Classification

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

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

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

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
XerD COG4974
Site-specific recombinase XerD [Replication, recombination and repair];
121-424 8.98e-46

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


:

Pssm-ID: 443999 [Multi-domain]  Cd Length: 291  Bit Score: 160.16  E-value: 8.98e-46
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501562005 121 TVRDAVASYLATLQNAR-----TRKEFDTEAKAHI--LPALGGIDLSKLTSGRITKWLEgiansppRLRTKTKAAerrta 193
Cdd:COG4974    2 TLADLLEAFLEELKREKglspnTIKAYRRDLRRFLrfLEELGKIPLAEITPEDIRAYLN-------YLRERGLSP----- 69

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501562005 194 dvdmsdpdvirrrrHTANHQLKILKAALNHAYRGKRVETDSAWATVRPFKGvsEARVRWLAQDEAVRLVNASAPD----- 268
Cdd:COG4974   70 --------------STINRYLAALRSFFRYAVREGLLEDNPAAKVKLPKKP--RKLPRVLTEEEIEALLEALDTEtpegl 133

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501562005 269 -LRAMVRGALLTGCRYEELARLRVQEIDLLNGSVYVRLSKSGKPRHVVLTEEGVAFFRDH--TAGRTADDLVFTRANGEP 345
Cdd:COG4974  134 rDRALLLLLYATGLRVSELLGLKWSDIDLDRGTIRVRRGKGGKERTVPLSPEALEALREYleERRPRDSDYLFPTRRGRP 213

                        250       260       270       280       290       300       310
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 501562005 346 WGKSHQHRPIKDACAAAKIKPAISFHILRHTHASWLAQRGVSMQVIAAQLGHSDTRITERhYAHLSPSHHAAAVRAALP 424
Cdd:COG4974  214 LSRRAIRKILKRLAKRAGIPKRVTPHSLRHTFATHLLEAGVDLRTVQELLGHSSISTTQI-YTHVSDEELREAVEKLHP 291
 
Name Accession Description Interval E-value
XerD COG4974
Site-specific recombinase XerD [Replication, recombination and repair];
121-424 8.98e-46

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


Pssm-ID: 443999 [Multi-domain]  Cd Length: 291  Bit Score: 160.16  E-value: 8.98e-46
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501562005 121 TVRDAVASYLATLQNAR-----TRKEFDTEAKAHI--LPALGGIDLSKLTSGRITKWLEgiansppRLRTKTKAAerrta 193
Cdd:COG4974    2 TLADLLEAFLEELKREKglspnTIKAYRRDLRRFLrfLEELGKIPLAEITPEDIRAYLN-------YLRERGLSP----- 69

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501562005 194 dvdmsdpdvirrrrHTANHQLKILKAALNHAYRGKRVETDSAWATVRPFKGvsEARVRWLAQDEAVRLVNASAPD----- 268
Cdd:COG4974   70 --------------STINRYLAALRSFFRYAVREGLLEDNPAAKVKLPKKP--RKLPRVLTEEEIEALLEALDTEtpegl 133

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501562005 269 -LRAMVRGALLTGCRYEELARLRVQEIDLLNGSVYVRLSKSGKPRHVVLTEEGVAFFRDH--TAGRTADDLVFTRANGEP 345
Cdd:COG4974  134 rDRALLLLLYATGLRVSELLGLKWSDIDLDRGTIRVRRGKGGKERTVPLSPEALEALREYleERRPRDSDYLFPTRRGRP 213

                        250       260       270       280       290       300       310
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 501562005 346 WGKSHQHRPIKDACAAAKIKPAISFHILRHTHASWLAQRGVSMQVIAAQLGHSDTRITERhYAHLSPSHHAAAVRAALP 424
Cdd:COG4974  214 LSRRAIRKILKRLAKRAGIPKRVTPHSLRHTFATHLLEAGVDLRTVQELLGHSSISTTQI-YTHVSDEELREAVEKLHP 291
INT_Rci_Hp1_C cd00796
Shufflon-specific DNA recombinase Rci and Bacteriophage Hp1_like integrase, C-terminal ...
 249-409 6.99e-30

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: 113.58  E-value: 6.99e-30
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501562005 249 RVRWLAQDEAVRLVNA----SAPDLRAMVRGALLTGCRYEELARLRVQEIDLLNGSVYVRLSKSGKPRHVVLTEEGVAFF 324
Cdd:cd00796    1 RDRFLTEDEEARLLAAleesTNPHLRLIVLLALYTGARRGEILSLRWDDIDLEVGLIVLPETKNGKPRTVPLSDEAIAIL 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501562005 325 RDHTAGRTADDLVFTRangePWGKSHQH---RPIKDACAAAKIkPAISFHILRHTHASWLAQRGVSMQVIAAQLGHSDTR 401
Cdd:cd00796   81 KELKRKRGKDGFFVDG----RFFGIPIAslrRAFKKARKRAGL-EDLRFHDLRHTFASRLVQAGVPIKTVAKILGHSSIK 155


                 ....*...
gi 501562005 402 ITERhYAH 409
Cdd:cd00796  156 MTMR-YAH 162
Phage_integrase pfam00589
Phage integrase family; Members of this family cleave DNA substrates by a series of staggered ...
 252-412 1.32e-26

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: 105.09  E-value: 1.32e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501562005  252 WLAQDEAVRLVNASAPD-----LRAMVRGALLTGCRYEELARLRVQEIDLLNGSVYVRLSKSGKPRHVVLTEEGVAFFRD 326
Cdd:pfam00589   1 RLTEDEVERLLDAAETGplsirDKALLELLYATGLRISELCSLRWSDIDFENGVIRVHRGKGNKERTVPLSDAALELLKE 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501562005  327 HTAGRTA----DDLVFTRANGEPWGKSHQHRPIKDACAAAKIKPAISFHILRHTHASWLAQRGVSMQVIAAQLGHSDTRI 402
Cdd:pfam00589  81 WLSKRLLeapkSDYLFASKRGKPLSRQTVRKIFKRAGKEAGLELPLHPHMLRHSFATHLLEAGVDLRVVQKLLGHSSIST 160

                         170
                  ....*....|
gi 501562005  403 TeRHYAHLSP 412
Cdd:pfam00589 161 T-QIYTHVAD 169
int PHA02601
integrase; Provisional
 209-420 4.16e-13

integrase; Provisional


Pssm-ID: 222904 [Multi-domain]  Cd Length: 333  Bit Score: 70.14  E-value: 4.16e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501562005 209 TANHQLKILKAALNHAYRGKRVETDSAWATVRPFKgVSEARVRWLAQDEAVRLVNASA----PDLRAMVRGALLTGCRYE 284
Cdd:PHA02601 130 TVNRELAYLSAVFNELIKLGKWSGPNPLDGIRPFK-EAEPELAFLTKEEIERLLDACDgsrsPDLGLIAKICLATGARWS 208

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501562005 285 ELARLRVQEIdlLNGSVYVRLSKSGKPRHVVLTEEgVAFFRDHTAGRtaddlVFTRANGEpwgkshQHRPIKdacaAAKI 364
Cdd:PHA02601 209 EAETLKRSQI--SPYKITFVKTKGKKNRTVPISEE-LYKMLPKRRGR-----LFKDAYES------FERAVK----RAGI 270

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 501562005 365 K--PAISFHILRHTHASWLAQRGVSMQVIAAQLGHSDTRITERhYAHLSPSHHAAAVR 420
Cdd:PHA02601 271 DlpEGQATHVLRHTFASHFMMNGGNILVLQRILGHATIEMTMA-YAHFAPDHLEDAVS 327
integrase_gron TIGR02249
integron integrase; Members of this family are integrases associated with integrons (and ...
 253-426 3.00e-11

integron integrase; Members of this family are integrases associated with integrons (and super-integrons), which are systems for incorporating and expressing cassettes of laterally transferred DNA. Incorporation occurs at an attI site. A super-integron, as in Vibrio sp., may include over 100 cassettes. This family belongs to the phage integrase family (pfam00589) that also includes recombinases XerC (TIGR02224) and XerD (TIGR02225), which are bacterial housekeeping proteins. Within this family of integron integrases, some are designated by class, e.g. IntI4, a class 4 integron integrase from Vibrio cholerae N16961. [DNA metabolism, DNA replication, recombination, and repair, Mobile and extrachromosomal element functions, Other]


Pssm-ID: 131303 [Multi-domain]  Cd Length: 315  Bit Score: 64.34  E-value: 3.00e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501562005  253 LAQDEAVRLVNASAPDLRAMVRgaLLTGC--RYEELARLRVQEIDLLNGSVYVRLSKSGKPRHVVLTEEGVA-------- 322
Cdd:TIGR02249 102 LTREEVRRLLEHLEGKYRLIAK--LLYGSgmRLMECLRLRIQDIDFDYGEIRIRQGKGGKDRTVTLPKELIPplreqiel 179

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501562005  323 ----FFRDHTAGR------TADDLVFTRANGE-PW---------------GKSHQH--------RPIKDACAAAKIKPAI 368
Cdd:TIGR02249 180 arayHEADLAEGYggvylpHALARKYPNAPKEwGWqylfpshrlsrdpesGVIRRHhinettiqRAVRRAVERAGIEKPV 259

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 501562005  369 SFHILRHTHASWLAQRGVSMQVIAAQLGHSDTRITERhYAHLSpSHHAAAVRAALPNL 426
Cdd:TIGR02249 260 TCHTLRHSFATHLLESGADIRTVQELLGHSDVKTTQI-YTHVL-NRGASGVLSPLDRL 315
 
Name Accession Description Interval E-value
XerD COG4974
Site-specific recombinase XerD [Replication, recombination and repair];
121-424 8.98e-46

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


Pssm-ID: 443999 [Multi-domain]  Cd Length: 291  Bit Score: 160.16  E-value: 8.98e-46
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501562005 121 TVRDAVASYLATLQNAR-----TRKEFDTEAKAHI--LPALGGIDLSKLTSGRITKWLEgiansppRLRTKTKAAerrta 193
Cdd:COG4974    2 TLADLLEAFLEELKREKglspnTIKAYRRDLRRFLrfLEELGKIPLAEITPEDIRAYLN-------YLRERGLSP----- 69

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501562005 194 dvdmsdpdvirrrrHTANHQLKILKAALNHAYRGKRVETDSAWATVRPFKGvsEARVRWLAQDEAVRLVNASAPD----- 268
Cdd:COG4974   70 --------------STINRYLAALRSFFRYAVREGLLEDNPAAKVKLPKKP--RKLPRVLTEEEIEALLEALDTEtpegl 133

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501562005 269 -LRAMVRGALLTGCRYEELARLRVQEIDLLNGSVYVRLSKSGKPRHVVLTEEGVAFFRDH--TAGRTADDLVFTRANGEP 345
Cdd:COG4974  134 rDRALLLLLYATGLRVSELLGLKWSDIDLDRGTIRVRRGKGGKERTVPLSPEALEALREYleERRPRDSDYLFPTRRGRP 213

                        250       260       270       280       290       300       310
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 501562005 346 WGKSHQHRPIKDACAAAKIKPAISFHILRHTHASWLAQRGVSMQVIAAQLGHSDTRITERhYAHLSPSHHAAAVRAALP 424
Cdd:COG4974  214 LSRRAIRKILKRLAKRAGIPKRVTPHSLRHTFATHLLEAGVDLRTVQELLGHSSISTTQI-YTHVSDEELREAVEKLHP 291
XerC COG4973
Site-specific recombinase XerC [Replication, recombination and repair];
121-420 1.15e-32

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


Pssm-ID: 443998 [Multi-domain]  Cd Length: 287  Bit Score: 125.07  E-value: 1.15e-32
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501562005 121 TVRDAVASYLATLQN----ARTRKEFDTEAKAHIlPALGG--IDLSKLTSGRITKWLEgiansppRLRTKTKAAerrtad 194
Cdd:COG4973    3 TLAEALEAYLEHLRErrlsPKTLEAYRRDLRRLI-PLLGDadLPLEELTPADVRRFLA-------RLHRRGLSP------ 68

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501562005 195 vdmsdpdvirrrrHTANHQLKILKAALNHAYRGKRVETDSAwATVRPFKgVSEARVRWLAQDEAVRLVNASAPD-----L 269
Cdd:COG4973   69 -------------RTLNRRLSALRSFFNWAVREGLLEANPA-AGVKAPK-APRKLPRALTVDELAQLLDALADDplavrD 133

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501562005 270 RAMVRGALLTGCRYEELARLRVQEIDLLNGSVYVRlSKSGKPRHVVLTEEGVAFFRDHTAGRTA-----DDLVFTRANGE 344
Cdd:COG4973  134 RAIVELLYSTGLRLGELVGLDWEDVDLDAGEVRVR-GKTGKSRTVPLGPKALAALREWLAVRPElaapdEGALFPSRRGT 212

                        250       260       270       280       290       300       310
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 501562005 345 PWGKSH-QHRpIKDACAAAKIKPAISFHILRHTHASWLAQRGVSMQVIAAQLGHSDTRITERhYAHLSPSHHAAAVR 420
Cdd:COG4973  213 RLSPRNvQKR-LRRLAKKAGLPKHVHPHDLRHSFATHLLESGGDLRAVQELLGHASISTTQI-YTHLDFQHLAEVYR 287
INT_Rci_Hp1_C cd00796
Shufflon-specific DNA recombinase Rci and Bacteriophage Hp1_like integrase, C-terminal ...
 249-409 6.99e-30

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: 113.58  E-value: 6.99e-30
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501562005 249 RVRWLAQDEAVRLVNA----SAPDLRAMVRGALLTGCRYEELARLRVQEIDLLNGSVYVRLSKSGKPRHVVLTEEGVAFF 324
Cdd:cd00796    1 RDRFLTEDEEARLLAAleesTNPHLRLIVLLALYTGARRGEILSLRWDDIDLEVGLIVLPETKNGKPRTVPLSDEAIAIL 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501562005 325 RDHTAGRTADDLVFTRangePWGKSHQH---RPIKDACAAAKIkPAISFHILRHTHASWLAQRGVSMQVIAAQLGHSDTR 401
Cdd:cd00796   81 KELKRKRGKDGFFVDG----RFFGIPIAslrRAFKKARKRAGL-EDLRFHDLRHTFASRLVQAGVPIKTVAKILGHSSIK 155


                 ....*...
gi 501562005 402 ITERhYAH 409
Cdd:cd00796  156 MTMR-YAH 162
FimB COG0582
Integrase/recombinase, includes phage integrase [Replication, recombination and repair, ...
 12-409 4.00e-28

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


Pssm-ID: 440347 [Multi-domain]  Cd Length: 391  Bit Score: 114.75  E-value: 4.00e-28
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501562005  12 TKAKRAKLAPRPKPYWREIDRGrhvGYYRGSASGSWIAR-RFLGGGKYQERRLGMADDIRDADGIEVLSFEQAQAAARIW 90
Cdd:COG0582    3 TDTAKKKAKPKDKPYKLGDGGG---LLLLVGPSGGKRWRyRYRFRGKRKRLALGVYPGVSLALARARRAEARALLALGID 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501562005  91 FEDCARADLEAERRREAEaagepvhqggpwTVRDAVASYLATLQN---ARTRKEFDTEAKAHILPALGGIDLSKLTSGRI 167
Cdd:COG0582   80 PSPARKAAKAAAAAAAAN------------TFEEVAEEWLEEKKPewkEKTAAQVRRTLEKHIFPVLGDRPIAEITPPDL 147

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501562005 168 TKWLEGIANspprlrtktkaaerrtadvdmsdpdviRRRRHTANHQLKILKAALNHAYRGKRVETDSAWATVRPFKGVSE 247
Cdd:COG0582  148 LAVLRPIEA---------------------------RGAPETARRVRQRLRQVFRYAVARGLIERNPAADLKGALPKPKV 200

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501562005 248 ARVRWLAQDEAVRLVNA-----SAPDLRAMVRGALLTGCRYEELARLRVQEIDLLNGSVYVR--LSKSGKPRHVVLTEEG 320
Cdd:COG0582  201 KHHPALTPEELPELLRAldayrGSPVTRLALRLLLLTGVRPGELRGARWSEIDLEAALWTIPaeRMKTRRPHIVPLSRQA 280

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501562005 321 VAFFRDHTAGRTADDLVFTRANGepwgkshQHRPIKDACAAAKIK----PAISFHILRHTHASWLAQRGVSMQVIAAQLG 396
Cdd:COG0582  281 LEILKELKPLTGDSEYVFPSRRG-------PKKPMSENTLNKALRrmgyGRFTPHGFRHTASTLLNEAGFPPDVIERQLA 353

                        410
                 ....*....|...
gi 501562005 397 HSDTRITERHYAH 409
Cdd:COG0582  354 HKDGNKVRAAYNR 366
Phage_integrase pfam00589
Phage integrase family; Members of this family cleave DNA substrates by a series of staggered ...
 252-412 1.32e-26

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: 105.09  E-value: 1.32e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501562005  252 WLAQDEAVRLVNASAPD-----LRAMVRGALLTGCRYEELARLRVQEIDLLNGSVYVRLSKSGKPRHVVLTEEGVAFFRD 326
Cdd:pfam00589   1 RLTEDEVERLLDAAETGplsirDKALLELLYATGLRISELCSLRWSDIDFENGVIRVHRGKGNKERTVPLSDAALELLKE 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501562005  327 HTAGRTA----DDLVFTRANGEPWGKSHQHRPIKDACAAAKIKPAISFHILRHTHASWLAQRGVSMQVIAAQLGHSDTRI 402
Cdd:pfam00589  81 WLSKRLLeapkSDYLFASKRGKPLSRQTVRKIFKRAGKEAGLELPLHPHMLRHSFATHLLEAGVDLRVVQKLLGHSSIST 160

                         170
                  ....*....|
gi 501562005  403 TeRHYAHLSP 412
Cdd:pfam00589 161 T-QIYTHVAD 169
INT_ICEBs1_C_like cd01189
C-terminal catalytic domain of integrases from bacterial phages and conjugate transposons; ...
 269-409 2.82e-23

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: 95.32  E-value: 2.82e-23
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501562005 269 LRAMVRGALLTGCRYEELARLRVQEIDLLNGSVYVR--LSKSGKPRHVVLTEEGVAFFRD-HTAGRTADDLvftrangep 345
Cdd:cd01189   18 YYLLFLLALLTGLRRGELLALTWSDIDFENGTIRINrtLVRKKKGGYVIKPPKTKSSIRTiPLPDELIELL--------- 88

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 501562005 346 wgksHQHRPIKDACAAAKIkPAISFHILRHTHASWLAQRGVSMQVIAAQLGHSDTRITERHYAH 409
Cdd:cd01189   89 ----KELKAFKKLLKKAGL-PRITPHDLRHTFASLLLEAGVPLKVIAERLGHSDISTTLDVYAH 147
DNA_BRE_C cd00397
DNA breaking-rejoining enzymes, C-terminal catalytic domain; The DNA breaking-rejoining enzyme ...
 270-405 1.07e-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: 94.08  E-value: 1.07e-22
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501562005 270 RAMVRGALLTGCRYEELARLRVQEIDLLNGSVYVR--LSKSGKPRHVVLTEEGVAFFRD------HTAGRTADDLVFTRA 341
Cdd:cd00397   20 RAILLLLLETGLRISELLALKVKDIDLDNGTIRVRgkKTKGGKERTVPLPKELAEELKEylkerrDKRGPLLKSLYLNKL 99

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 501562005 342 NGEPWGKSHQHRPIKDACAAAKIKPA--ISFHILRHTHASWLAQRGVSMQVIAAQLGHSDTRITER 405
Cdd:cd00397  100 FGTKLGERLSRRTLRRIFKKAGIEAGrkITPHSLRHTFATNLLENGVDIKVVQKLLGHSSISTTQR 165
INTN1_C_like cd01185
Integrase IntN1 of Bacteroides mobilizable transposon NBU1 and similar proteins, C-terminal ...
 256-413 6.75e-16

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: 74.99  E-value: 6.75e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501562005 256 DEAVRLVNA--SAPDLRAMVRGALL----TGCRYEELARLRVQEIDLLNGSVYVRL--SKSGKPRHVVLTEEGVAFFRDH 327
Cdd:cd01185    1 EELKRLMALelSDTSRLELVRDMFLfscyTGLRFSDLKNLTWKNIVEASGRTWIRYrrKKTGKPVTVPLLPVAREILEKY 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501562005 328 TAGRTaDDLVFTRANgepwgKSHQHRPIKDACAAAKIKPAISFHILRHTHASWLAQRGVSMQVIAAQLGHSDTRITErHY 407
Cdd:cd01185   81 KDDRS-EGKLFPVLS-----NQKINRYLKEIAKIAGIDKHLTFHVARHTFATLLLLKGVDIETISKLLGHSSIKTTQ-IY 153


                 ....*.
gi 501562005 408 AHLSPS 413
Cdd:cd01185  154 AKIVDS 159
INT_IntI_C cd01193
Integron integrase and similar protiens, C-terminal catalytic domain; Integron integrases ...
 253-410 3.47e-15

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: 73.08  E-value: 3.47e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501562005 253 LAQDEAVRLVNAsAPDLRAMVRGALLTGC--RYEELARLRVQEIDLLNGSVYVRLSKSGKPRHVVLTEEGVAFFRDHTAG 330
Cdd:cd01193    6 LSPDEVRRILGA-LTELRHRLILSLLYGAglRISELLRLRVKDIDFERGVIRVRQGKGGKDRVVPLPEKLLEPLRRYLKS 84

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501562005 331 RTADDLVFTRANGEPW-----GKSHQH--------RPIKDACAAAKIKPAISFHILRHTHASWLAQRGVSMQVIAAQLGH 397
Cdd:cd01193   85 ARPKEELDPAEGRAGVldprtGVERRHhisettvqRALKKAVEQAGITKRVTPHTLRHSFATHLLEAGTDIRTIQELLGH 164

                        170
                 ....*....|...
gi 501562005 398 SDTRITErHYAHL 410
Cdd:cd01193  165 SDLSTTM-IYTHV 176
INT_RitA_C_like cd01188
C-terminal catalytic domain of recombinase RitA, a component of the recombinase trio; ...
 256-403 1.29e-14

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: 71.50  E-value: 1.29e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501562005 256 DEAVRLVNASAPDL------RAMVRGALLTGCRYEELARLRVQEIDLLNGSVYVRLSKSGKPRHVVLTE---EGVAFFRD 326
Cdd:cd01188    3 DEVRRLLAAIDRLTpvglrdYAILLLLARLGLRAGDVAGLRLDDIDWRSGTITVRQKKTGRPVELPLTEpvgEALADYLR 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501562005 327 HTAGRTADDLVFTRAN---GEPWGKSHQHRPIKDACAAAKIKPAI-SFHILRHTHASWLAQRGVSMQVIAAQLGHSDTRI 402
Cdd:cd01188   83 DGRPRTDSREVFLRARapyRPLSSTSQISSIVRRYLRKAGIEPSHrGTHSLRHSLATRMLRAGTSLKVIADLLGHRSIET 162


                 .
gi 501562005 403 T 403
Cdd:cd01188  163 T 163
int PHA02601
integrase; Provisional
 209-420 4.16e-13

integrase; Provisional


Pssm-ID: 222904 [Multi-domain]  Cd Length: 333  Bit Score: 70.14  E-value: 4.16e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501562005 209 TANHQLKILKAALNHAYRGKRVETDSAWATVRPFKgVSEARVRWLAQDEAVRLVNASA----PDLRAMVRGALLTGCRYE 284
Cdd:PHA02601 130 TVNRELAYLSAVFNELIKLGKWSGPNPLDGIRPFK-EAEPELAFLTKEEIERLLDACDgsrsPDLGLIAKICLATGARWS 208

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501562005 285 ELARLRVQEIdlLNGSVYVRLSKSGKPRHVVLTEEgVAFFRDHTAGRtaddlVFTRANGEpwgkshQHRPIKdacaAAKI 364
Cdd:PHA02601 209 EAETLKRSQI--SPYKITFVKTKGKKNRTVPISEE-LYKMLPKRRGR-----LFKDAYES------FERAVK----RAGI 270

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 501562005 365 K--PAISFHILRHTHASWLAQRGVSMQVIAAQLGHSDTRITERhYAHLSPSHHAAAVR 420
Cdd:PHA02601 271 DlpEGQATHVLRHTFASHFMMNGGNILVLQRILGHATIEMTMA-YAHFAPDHLEDAVS 327
INT_P4_C cd00801
Bacteriophage P4 integrase, C-terminal catalytic domain; P4-like integrases are found in ...
 267-409 4.36e-13

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: 67.30  E-value: 4.36e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501562005 267 PDLRAMVRGALLTGCRYEELARLRVQEIDLLNG--SVYVRLSKSGKPrHVV-LTEEGVAFFRDHTAGRTADDLVFTrang 343
Cdd:cd00801   19 PPTKLALRLLLLTGQRIGELARARWSEIDLEEKtwTIPAERTKNKRP-HRVpLSDQALEILEELKEFTGDSGYLFP---- 93

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501562005 344 ePWGKSHQHRPIKDACAAAK----IKPAISFHILRHTHASWLAQRGVSMQVIAAQLGHSDTRITERHYAH 409
Cdd:cd00801   94 -SRRKKKKPISENTINKALKrlgyKGKEFTPHDLRRTFSTLLNELGIDPEVIERLLNHVLGGVVRAAYNR 162
INT_XerDC_C cd00798
XerD and XerC integrases, C-terminal catalytic domains; XerDC-like integrases are involved in ...
 255-414 2.27e-12

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


Pssm-ID: 271179 [Multi-domain]  Cd Length: 172  Bit Score: 64.84  E-value: 2.27e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501562005 255 QDEAVRLVNASAPDLRAMVR-GALL-----TGCRYEELARLRVQEIDLLNGSVYVRlSKSGKPRHVVLTEEGV------- 321
Cdd:cd00798    1 VDEVERLLDAPDTDTPLGLRdRAILellyaSGLRVSELVGLDLSDVDLDEGLVRVT-GKGNKERLVPFGSYAVealeeyl 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501562005 322 AFFRDHTAGRTADDLVFTRANGEPWGKSHQHRPIKDACAAAKIKPAISFHILRHTHASWLAQRGVSMQVIAAQLGHSDTR 401
Cdd:cd00798   80 EERRPLLLKKKPPDALFLNKRGKRLSRRGVWRILKKYAERAGLPKHVSPHTLRHSFATHLLEGGADLRVVQELLGHASLS 159

                        170
                 ....*....|...
gi 501562005 402 ITERhYAHLSPSH 414
Cdd:cd00798  160 TTQI-YTHVSFER 171
integrase_gron TIGR02249
integron integrase; Members of this family are integrases associated with integrons (and ...
 253-426 3.00e-11

integron integrase; Members of this family are integrases associated with integrons (and super-integrons), which are systems for incorporating and expressing cassettes of laterally transferred DNA. Incorporation occurs at an attI site. A super-integron, as in Vibrio sp., may include over 100 cassettes. This family belongs to the phage integrase family (pfam00589) that also includes recombinases XerC (TIGR02224) and XerD (TIGR02225), which are bacterial housekeeping proteins. Within this family of integron integrases, some are designated by class, e.g. IntI4, a class 4 integron integrase from Vibrio cholerae N16961. [DNA metabolism, DNA replication, recombination, and repair, Mobile and extrachromosomal element functions, Other]


Pssm-ID: 131303 [Multi-domain]  Cd Length: 315  Bit Score: 64.34  E-value: 3.00e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501562005  253 LAQDEAVRLVNASAPDLRAMVRgaLLTGC--RYEELARLRVQEIDLLNGSVYVRLSKSGKPRHVVLTEEGVA-------- 322
Cdd:TIGR02249 102 LTREEVRRLLEHLEGKYRLIAK--LLYGSgmRLMECLRLRIQDIDFDYGEIRIRQGKGGKDRTVTLPKELIPplreqiel 179

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501562005  323 ----FFRDHTAGR------TADDLVFTRANGE-PW---------------GKSHQH--------RPIKDACAAAKIKPAI 368
Cdd:TIGR02249 180 arayHEADLAEGYggvylpHALARKYPNAPKEwGWqylfpshrlsrdpesGVIRRHhinettiqRAVRRAVERAGIEKPV 259

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 501562005  369 SFHILRHTHASWLAQRGVSMQVIAAQLGHSDTRITERhYAHLSpSHHAAAVRAALPNL 426
Cdd:TIGR02249 260 TCHTLRHSFATHLLESGADIRTVQELLGHSDVKTTQI-YTHVL-NRGASGVLSPLDRL 315
recomb_XerD TIGR02225
tyrosine recombinase XerD; The phage integrase family describes a number of recombinases with ...
 253-424 3.01e-11

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: 63.75  E-value: 3.01e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501562005  253 LAQDEAVRLVNASAPDLRAMVRG-ALL-----TGCRYEELARLRVQEIDLLNGSVYVRlSKSGKPRHVVLTEEGVAF--- 323
Cdd:TIGR02225 105 LTVEEVEALLAAPDVDTPLGLRDrAMLellyaTGLRVSELVGLRLEDVNLDEGFVRVR-GKGNKERLVPLGEEAIEAler 183

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501562005  324 ----FRDHTAGRTA--DDLVFTRANGEPWGKSHQHRPIKDACAAAKIKPAISFHILRHTHASWLAQRGVSMQVIAAQLGH 397
Cdd:TIGR02225 184 ylkeARPLLLKKKVkeSDALFLNRRGGPLSRQGVWKILKEYAKRAGIEKPISPHTLRHSFATHLLENGADLRVVQELLGH 263

                         170       180       190
                  ....*....|....*....|....*....|
gi 501562005  398 SD---TRIterhYAHLSPSHHAAAVRAALP 424
Cdd:TIGR02225 264 ADistTQI----YTHVARERLKEVHKKHHP 289
INT_C_like_1 cd01184
Uncharacterized site-specific tyrosine recombinase, C-terminal catalytic domain; Tyrosine ...
 253-409 3.32e-11

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: 61.94  E-value: 3.32e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501562005 253 LAQDEAVRLVNASA--------PDLRAMVRGALLTGCRYEELARLRVQEIDLLNGSVYVRL-----SKSGK--------P 311
Cdd:cd01184    1 FTPEELAKIFSSPLytgckkkdPALYWLPLIGLYTGARLNEICQLRVDDIKEEDGIWCIDInddaeGRRLKtkasrrlvP 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501562005 312 RHVVLTEEGvafFRDHTAGRTADDLVF----TRANGEPWGKSHQhRPIKDACAAAKIKPA--ISFHILRHTHASWLAQRG 385
Cdd:cd01184   81 IHPRLIELG---FLDYVEALRADGKLFlfpeKRDKDGKYSKAAS-KWFNRLLRKLGIKDDerKSFHSFRHTFITALKRAG 156

                        170       180
                 ....*....|....*....|....
gi 501562005 386 VSMQVIAAQLGHSDTRITERHYAH 409
Cdd:cd01184  157 VPEELIAQIVGHSRGGVTHDTYGK 180
PRK09870 PRK09870
tyrosine recombinase; Provisional
 251-403 9.09e-10

tyrosine recombinase; Provisional


Pssm-ID: 182125  Cd Length: 200  Bit Score: 58.03  E-value: 9.09e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501562005 251 RWLAQDEAVRLVNASAPDLRAmVRGALLT------GCRYEELARLRVQEIDLLNGSVYV-RLSKSGKPRHVVLTEEgVAF 323
Cdd:PRK09870  11 NFLTHSEIESLLKAANTGPHA-ARNYCLTllcfihGFRASEICRLRISDIDLKAKCIYIhRLKKGFSTTHPLLNKE-IQA 88

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501562005 324 FRDHTAGRT-----ADDLVFTRANGEPWGKSHQHRPIKDACAAAKIKPAISFHILRHTHASWLAQRGVSMQVIAAQLGHS 398
Cdd:PRK09870  89 LKNWLSIRTsyphaESEWVFLSRKGNPLSRQQFYHIISTSGGNAGLSLEIHPHMLRHSCGFALANMGIDTRLIQDYLGHR 168


                 ....*
gi 501562005 399 DTRIT 403
Cdd:PRK09870 169 NIRHT 173
INT_tnpA_C_Tn554 cd01186
Putative Transposase A from transposon Tn554, C-terminal catalytic domain; This family ...
 253-411 1.27e-09

Putative Transposase A from transposon Tn554, C-terminal catalytic domain; This family includes putative Transposase A from transposon Tn554. It belongs to a DNA breaking-rejoining enzyme superfamily. The catalytic domain contains six conserved active site residues. The recombination reaction involves cleavage of a single strand of a DNA duplex by nucleophilic attack of a conserved tyrosine to give a 3' phosphotyrosyl protein-DNA adduct. In the second rejoining step, a terminal 5' hydroxyl attacks the covalent adduct to release the enzyme and generate duplex DNA. Many DNA breaking-rejoining enzymes also have N-terminal domains, which show little sequence or structure similarity.


Pssm-ID: 271186 [Multi-domain]  Cd Length: 184  Bit Score: 57.43  E-value: 1.27e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501562005 253 LAQDEAVRLVNASApDLRAMVRGALL--TGCRYEELARLRVQEIDLLNGSVYVR---------LSKSGKPRHVVLTEEGV 321
Cdd:cd01186    2 LTPREVQELINACN-NLRDKFLLALLyeTGLRIGEALGLRIEDIDMADNQIELVpredntneaRAKSMRERRIPVSQDLI 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501562005 322 AFFRD-----HTAGRTADDLVFTRANGEPWGKSHQHRPIKDACAAAKIKPAISF--HILRHTHASWLAQRGVSMQVIAAQ 394
Cdd:cd01186   81 DLYADyltyiYCEEAEFSITVFVNVKGGNQGKAMNYSDVYDLVRRLKKRTGIDFtpHMFRHTHATALIRAGWSIEVVARR 160

                        170
                 ....*....|....*..
gi 501562005 395 LGHSDTRITERHYAHLS 411
Cdd:cd01186  161 LGHAHVQTTLNTYGHLS 177
INT_RitC_C_like cd01182
C-terminal catalytic domain of recombinase RitC, a component of the recombinase trio; ...
 255-411 1.49e-09

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: 57.29  E-value: 1.49e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501562005 255 QDEAVRLVnASAPDL--------RAMVRGALLTGCRYEELARLRVQEIDLLNGSVYVRLSKSGKPRHVVLTEEGVAFFRD 326
Cdd:cd01182    2 TREEMKAL-LAAPDRntslgrrdHALLLLLYDTGARVQELADLTIRDLRLDDPATVRLHGKGRKERTVPLWKETVAALKA 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501562005 327 HTAGRTADDL------VFTRANGEPWGKSHQHRPIKDACAAAK-----IKPAISFHILRHTHASWLAQRGVSMQVIAAQL 395
Cdd:cd01182   81 YLQEFHLTPDpkqlfpLFPNRRGQPLTRDGVAYILNKYVALASnrcpsLPKRITPHTLRHTKAMHLLQAGVDLTVIRDWL 160

                        170
                 ....*....|....*.
gi 501562005 396 GHSDTRITErHYAHLS 411
Cdd:cd01182  161 GHESVETTQ-IYAEAD 175
INT_C_like_4 cd01194
Uncharacterized site-specific tyrosine recombinase, C-terminal catalytic domain; Tyrosine ...
 270-409 2.17e-09

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: 56.61  E-value: 2.17e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501562005 270 RAMVRGALLTGCRYEELARLRVQEIDLLNGSVYVRLS---KSGKPRHVVLTEEGVAFFRDHTAGR---TADDLVFT---- 339
Cdd:cd01194   25 RAIISLMVTEGLRTVEIVRADVGDLRQEGEGTILYVQgkgKTSKDDFVYLRPDVLKALQAYLKARgklDFEEPLFTslsn 104

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 501562005 340 RANGEPWGKSHQHRPIKDACAAAKIKPA-ISFHILRHTHASWLAQRGVSMQVIAAQLGHSDTRITERhYAH 409
Cdd:cd01194  105 NSKGQRLTTRSIRRIIKKYLRKAGLDDDrLTAHSLRHTAGTLALKAGKSLREVQQLLRHSDPNTTMI-YAH 174
recomb_XerC TIGR02224
tyrosine recombinase XerC; The phage integrase family describes a number of recombinases with ...
 236-424 8.09e-09

tyrosine recombinase XerC; 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 XerC, one of two closely related chromosomal proteins along with XerD (TIGR02225). 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 homologs of XerC on other replicons, the chomosomal copy was preferred for building this model. This model does not detect all XerC, as some apparent XerC examples score in the gray zone between trusted (450) and noise (410) cutoffs, along with some XerD examples. XerC and XerD interact with cell division protein FtsK. [DNA metabolism, DNA replication, recombination, and repair]


Pssm-ID: 274042 [Multi-domain]  Cd Length: 295  Bit Score: 56.46  E-value: 8.09e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501562005  236 WATVRPFKGVSEARV-----RWLAQDEAVRLVNASAPDL--------RAMVrgALL--TGCRYEELARLRVQEIDLLNGS 300
Cdd:TIGR02224  85 LIDANPAAGVRAPKQpkklpKFLSEDEMEALLDAPEEDDedwlalrdRAIL--ELLysSGLRVSELVGLDLSDLDLDFGE 162

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501562005  301 VYVRlSKSGKPRHVVLTEEGVAF-------FRDHTAGRTADDLVFTRANGEPWGKSHQHRPIKDACAAAKIKPAISFHIL 373
Cdd:TIGR02224 163 VRVR-GKGNKERIVPFGPYARDAlqayleaRRSPLLASEGQDALFLNRRGGRLTPRGVQYRLQQLRAKAGLPKHVHPHAL 241

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|.
gi 501562005  374 RHTHASWLAQRGVSMQVIAAQLGHSDTRITERhYAHLSPSHHAAAVRAALP 424
Cdd:TIGR02224 242 RHSFATHLLNNGADLRAVQELLGHASLSTTQI-YTHVDFQHLAKVYDQAHP 291
xerD PRK00283
tyrosine recombinase;
253-415 1.85e-08

tyrosine recombinase;


Pssm-ID: 234713 [Multi-domain]  Cd Length: 299  Bit Score: 55.58  E-value: 1.85e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501562005 253 LAQDEAVRLVNASAPD------LRAMVRgaLL--TGCRYEELARLRVQEIDLLNGSVYVRlSKSGKPRHVVLTEEGVA-- 322
Cdd:PRK00283 114 LSEAQVEALLDAPDIDtplglrDRAMLE--LLyaTGLRVSELVGLTLDDVSLRQGVVRVT-GKGNKERLVPLGEEAVYai 190

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501562005 323 -----FFRDHTAGRTADDLVFTRANGEPWGKSHQHRPIKDACAAAKIKPA-ISFHILRHTHASWLAQRGVSMQVIAAQLG 396
Cdd:PRK00283 191 eryleRGRPALLNGRSSDALFPSARGGQLTRQTFWHRIKHYAKRAGIDPKkLSPHVLRHAFATHLLNHGADLRVVQELLG 270

                        170       180
                 ....*....|....*....|....*.
gi 501562005 397 HSD-------TRITERHYAHLSPSHH 415
Cdd:PRK00283 271 HSDisttqiyTHVATERLKELHAQHH 296
INT_C_like_3 cd01192
Uncharacterized site-specific tyrosine recombinase, C-terminal catalytic domain; Tyrosine ...
 279-407 2.44e-08

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: 53.45  E-value: 2.44e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501562005 279 TGCRYEELARLRVQEIdLLNGSVYVRLSKSGKPRHVVLTEEGVAFFRDHTAGRTADDlvftRANGEPWGKSHQHRPI--- 355
Cdd:cd01192   36 TGLRISDLLSLKVEDV-TNKDKLSIKEQKTGKQKTFPLNPTLVKALKEYIDDLDLKR----NDYLFKSLKQGPEKPIsrk 110

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 501562005 356 ------KDACAAAKIKPAISFHILRHTHASWLAQRGVSMQVIAAQLGHSDTRITeRHY 407
Cdd:cd01192  111 qaykilKKAADDLGLNYNIGTHSLRKTFGYHVYKQGKDIELLMKLLNHSSPSIT-LRY 167
PRK09871 PRK09871
tyrosine recombinase; Provisional
 280-408 7.90e-07

tyrosine recombinase; Provisional


Pssm-ID: 182126  Cd Length: 198  Bit Score: 49.60  E-value: 7.90e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501562005 280 GCRYEELARLRVQEIDLLNGSVYVRLSKSG-KPRHVVLTEEGVA---FFRDHTAGRTAD--DLVFTRANGEPWGKSHQHR 353
Cdd:PRK09871  39 GMRISELLDLHYQDLDLNEGRINIRRLKNGfSTVHPLRFDEREAverWTQERANWKGADrtDAIFISRRGSRLSRQQAYR 118

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 501562005 354 PIKDACAAAKIKPAISFHILRHTHASWLAQRGVSMQVIAAQLGHSDTRITERHYA 408
Cdd:PRK09871 119 IIRDAGIEAGTVTQTHPHMLRHACGYELAERGADTRLIQDYLGHRNIRHTVRYTA 173
xerC PRK01287
site-specific tyrosine recombinase XerC; Reviewed
 270-414 1.15e-06

site-specific tyrosine recombinase XerC; Reviewed


Pssm-ID: 234935 [Multi-domain]  Cd Length: 358  Bit Score: 50.51  E-value: 1.15e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501562005 270 RAMVRGALLTGCRYEELARLRVQEIDLLNGSVYVRLSKSGKPRHVVLTEEGVAFF-------RDHTAGRTADDLVFTRAN 342
Cdd:PRK01287 160 RALLELLWSTGIRRGELARLDLYDVDASRGVVTVRQGKGNKDRVVPVGERALAWLqrylqdvRPQLAVRPDSGALFVAMD 239

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 501562005 343 GEPWGKSHQHRPIKDACAAAKIKPAISFHILRHTHASWLAQRGVSMQVIAAQLGHSDTRITERhYAHLSPSH 414
Cdd:PRK01287 240 GDGLARNTLTNMVGRYIRAAGIEKAGACHLFRHAMATQMLENGADTRHIQAILGHAKLETTQI-YTRVSIGH 310
INT_FimBE_like cd01197
FimB and FimE and related proteins, integrase/recombinases; This CD includes proteins similar ...
 257-408 9.08e-06

FimB and FimE and related proteins, integrase/recombinases; This CD includes proteins similar to E.coli FimE and FimB and Proteus mirabilis MrpI. FimB and FimE are the regulatory proteins during expression of type 1 fimbriae in Escherichia coli. The fimB and fimE proteins direct the phase switch into the 'on' and 'off' position. MrpI is the regulatory protein of proteus mirabilis fimbriae expression. This family belongs to the integrase/recombinase superfamily.


Pssm-ID: 271197 [Multi-domain]  Cd Length: 181  Bit Score: 45.96  E-value: 9.08e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501562005 257 EAVRLVNASAPDlRAMVRGALLTGCRYEELARLRVQEIDLLNGSVYVRLSKSG-KPRHVVLTEEGVAF-----FRDHTAG 330
Cdd:cd01197   17 QAACRGRTPARD-YCLLLLAFRHGFRVSELCDLHLSDVDLESRRLHIRRLKNGfSTTHPLRFDEREALeawlkERANWKG 95

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 501562005 331 RTADDLVFTRANGePWGKSHQHRPIKDACAAAKIKPAISFHILRHTHASWLAQRGVSMQVIAAQLGHSDTRITERHYA 408
Cdd:cd01197   96 ADTDWIFLSRRGG-PLSRQQAYRIIRDLGKEAGTVTQTHPHMLRHACGYALADRGADTRLIQDYLGHRNIRHTVIYTA 172
xerC PRK00236
site-specific tyrosine recombinase XerC; Reviewed
 121-425 1.55e-04

site-specific tyrosine recombinase XerC; Reviewed


Pssm-ID: 234698 [Multi-domain]  Cd Length: 297  Bit Score: 43.60  E-value: 1.55e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501562005 121 TVRDAVASYLATLQNAR-----TRKEF--DTEAKAHILPALGGIDLSKLTSGRITKWLEgiansppRLRTKTKAAerRTa 193
Cdd:PRK00236   5 DLPAALEAFLEYLRVERglsphTLRAYrrDLRAFLAFLEEHGISSLQDLDAADLRSFLA-------RRRRQGLSA--RS- 74

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501562005 194 dvdmsdpdvIRRRrhtanhqLKILKAALNHAYRGKRVETDsawatvrPFKGVSEARV-----RWLAQDEAVRLVNASAPD 268
Cdd:PRK00236  75 ---------LARR-------LSALRSFYRWLVRRGLLKAN-------PAAGLRAPKIpkrlpKPLDVDQAKRLLDAIDED 131

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501562005 269 ----LR--AMVrgALLTGC--RYEELARLRVQEIDLLNGSVYVrLSKSGKPRHVVLTEEGV----AFFRDHTAGRTADDL 336
Cdd:PRK00236 132 dplaLRdrAIL--ELLYGSglRLSELVGLDIDDLDLASGTLRV-LGKGNKERTVPLGRAARealeAYLALRPLFLPDDDA 208

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501562005 337 VFTRANGEPWGKSHQHRPIKDACAAAKIKPAISFHILRHTHASWLAQRGVSMQVIAAQLGHSDTRITERhYAHLSPSHHA 416
Cdd:PRK00236 209 LFLGARGGRLSPRVVQRRVKKLGKKAGLPSHITPHKLRHSFATHLLESGGDLRAVQELLGHASLSTTQI-YTHVDFQHLA 287


                 ....*....
gi 501562005 417 AAVRAALPN 425
Cdd:PRK00236 288 EVYDAAHPR 296
xerS PRK05084
site-specific tyrosine recombinase XerS; Reviewed
 276-411 4.07e-04

site-specific tyrosine recombinase XerS; Reviewed


Pssm-ID: 235339 [Multi-domain]  Cd Length: 357  Bit Score: 42.21  E-value: 4.07e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501562005 276 ALL--TGCRYEELARLRVQEIDLLNGSVYVrLSKSGKPRHVVLTEEGVAFFRDHTAGRTA-------DDLVF-TRANGEP 345
Cdd:PRK05084 202 ALIlgSGLRVSELVNLDLSDLNLKQMTIDV-TRKGGKRDSVNIAPFALPYLEEYLKIRASrykaekqEKALFlTKYRGKP 280

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 501562005 346 wgKSHQHRPIKDACA--AAKIKPAISFHILRHTHASWLAQRGVSMQVIAAQLGHSDTRITERhYAHLS 411
Cdd:PRK05084 281 --NRISARAIEKMVAkySEAFGVRLTPHKLRHTLATRLYDATKDQVLVADQLGHTSTETTDL-YTHIV 345
INT_RitB_C_like cd00797
C-terminal catalytic domain of recombinase RitB, a component of the recombinase trio; ...
 279-412 7.39e-04

C-terminal catalytic domain of recombinase RitB, a component of the recombinase trio; Recombinases belonging to the RitA (also known as pAE1 due to its presence in the deletion prone region of plasmid pAE1 of Alcaligenes eutrophus H1), RitB, and RitC families are associated in a complex referred to as a Recombinase in Trio (RIT) element. These RIT elements consist of three adjacent and unidirectional overlapping genes, one from each family (ritABC in order of transcription). All three integrases contain a catalytic motif, suggesting that they are all active enzymes. However, their specific roles are not yet fully understood. All three families belong to the superfamily of DNA breaking-rejoining enzymes, which share the same fold in their catalytic domain and the overall reaction mechanism.


Pssm-ID: 271178 [Multi-domain]  Cd Length: 198  Bit Score: 40.75  E-value: 7.39e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501562005 279 TGCRYEELARLRVQEIDLLNGSVYVRLSKSGKPRHVVLTEEGVAFFRDHTAGRTA------DDLVFTRANGEPWGKSHQH 352
Cdd:cd00797   37 TGLRVGEALRLRLEDVDLDSGILTIRQTKFGKSRLVPLHPSTVGALRDYLARRDRllpspsSSYFFVSQQGGRLTGGGVY 116

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 501562005 353 RPIKDACAAAKIKPAIS-----FHILRHTHA-----SWlAQRGVSMQ----VIAAQLGHSDTRITErHYAHLSP 412
Cdd:cd00797  117 RVFRRLLRRIGLRGAGDgrgprLHDLRHTFAvnrltRW-YREGADVErklpVLSTYLGHVNVTDTY-WYLTATP 188
INT_Cre_C cd00799
C-terminal catalytic domain of Cre recombinase (also called integrase); Cre-like recombinases ...
 270-405 2.43e-03

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


Pssm-ID: 271180  Cd Length: 188  Bit Score: 38.82  E-value: 2.43e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501562005 270 RAMVRGALLTGCRYEELARLRVQEI-DLLNGSVYVRLSKS-----GKPRHVVLTEEGV-------------------AFF 324
Cdd:cd00799   19 RALLLLGFAGALRRSELVALRVEDLtRFVDGGLLIRLRRSktdqdGEGEIKALPYGPEtcpvralrawleaagipsgPLF 98

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501562005 325 RDHTAGRtaddlvftRANGEPWGKSHQHRPIKDACAAAKIKPA-ISFHILRHTHASWLAQRGVSMQVIAAQLGHSDTRIT 403
Cdd:cd00799   99 RRIRRGG--------SVGTTRLSDRSVARIVKRRAALAGLDPGdFSGHSLRRGFATEAARAGASLPEIMAQGGHKSVATV 170


                 ..
gi 501562005 404 ER 405
Cdd:cd00799  171 MR 172
INT_Lambda_C cd00800
C-terminal catalytic domain of Lambda integrase, a tyrosine-based site-specific recombinase; ...
 264-407 3.36e-03

C-terminal catalytic domain of Lambda integrase, a tyrosine-based site-specific recombinase; Lambda-type integrases catalyze site-specific integration and excision of temperate bacteriophages and other mobile genetic elements to and from the bacterial host chromosome. They are tyrosine-based site-specific recombinase and belong to the superfamily of DNA breaking-rejoining enzymes, which share the same fold in their catalytic domain and the overall reaction mechanism. The phage lambda integrase can bridge two different and well-separated DNA sequences called arm- and core-sites. The C-terminal domain binds, cleaves and re-ligates DNA strands at the core-sites, while the N-terminal domain is largely responsible for high-affinity binding to the arm-type sites.


Pssm-ID: 271181 [Multi-domain]  Cd Length: 161  Bit Score: 38.09  E-value: 3.36e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501562005 264 ASAPDLRAMVRGALLTGCRYEELARLRVQEIDllNGSVYVRLSKSGKPRHVVLT---EEGVAFFRDHTAGRTADDLVFTR 340
Cdd:cd00800    9 EAPPLLRLAMELALLTGQRQGDLLRLKWSDIT--DGGLLVEQSKTGKKLLIPWTpslRALVDRIRALPRKRSEYLINSRK 86

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501562005 341 anGEPWGKSHQHRPIKDACAAAKIKPAIS---FHILRHTHASWLAQRGVSMQvIAAQLGHSDTRITERHY 407
Cdd:cd00800   87 --GGPLSYDTLKSAWRRARKAAGLKGETEgftFHDLRAKAATDYAEQGGSTD-AQALLGHKSDAMTERYT 153
INT_C_like_6 cd01196
Uncharacterized site-specific tyrosine recombinase, C-terminal catalytic domain; Tyrosine ...
 270-404 5.03e-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: 271196  Cd Length: 183  Bit Score: 37.84  E-value: 5.03e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501562005 270 RAMVRGALLTGCRYEELARLRVQEIDLLNGSVYVRLSKSGKPRHVVLTEEGV-AFFRDH-TAGRTADD----LVFTRANG 343
Cdd:cd01196   23 RALIALMVYSFARIGAVLAMRVEDVYDQGRRLWVRLAEKGGKQHEMPCHHDLeEYLRAYlEAAEIEEDpkgpLFRTTRGG 102

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 501562005 344 ------EPWGKSHQHRPIKDACAAAKIKPAISFHILRHTHASWLAQRGVSMQVIAAQLGHSDTRITE 404
Cdd:cd01196  103 trklthNPLTQANAYRMVRRRAIAADIPTAIGNHSFRATGITAYLKNGGTLEDAQNMANHASTRTTQ 169
 
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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