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Conserved domains on  [gi|750294070|ref|WP_040576048|]
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tyrosine-type recombinase/integrase [Porphyromonas somerae]

Protein Classification

site-specific integrase( domain architecture ID 332)

tyrosine based site-specific recombinase (integrase) is involved in cleavage of a single strand of a DNA duplex by nucleophilic attack of a conserved tyrosine to give a 3' phosphotyrosyl protein-DNA adduct

CATH:  1.10.443.10
Gene Ontology:  GO:0015074|GO:0003677|GO:0006310
PubMed:  10577069|10047575|9278480
SCOP:  4002347

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
DNA_BRE_C super family cl00213
DNA breaking-rejoining enzymes, C-terminal catalytic domain; The DNA breaking-rejoining enzyme ...
 7-308 2.16e-81

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.


The actual alignment was detected with superfamily member TIGR02224:

Pssm-ID: 469662 [Multi-domain]  Cd Length: 295  Bit Score: 248.68  E-value: 2.16e-81
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 750294070    7 ERYRRYLQYERGMSELSIVAYLTDIEHWLTLeecneLEGEALEQFLCSVDTRRARKSLIKLMETPDATRSVKRRLSALRS 86
Cdd:TIGR02224   1 EAFLEYLRLERNYSPHTVRAYRRDLEAFLEF-----LEEEGGLASLAEVTAADLRSFLAELHARGLSRRSLARKLSALRS 75

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 750294070   87 LYGYLMKIEKVEHNPFKAVQVPKDGQYLPTFVNADlltrHIERLYKEAEEEptsEGKRVAWQLAFVVDLLFQTGMRRAEL 166
Cdd:TIGR02224  76 FYRFLLRRGLIDANPAAGVRAPKQPKKLPKFLSED----EMEALLDAPEED---DEDWLALRDRAILELLYSSGLRVSEL 148

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 750294070  167 LGLHLGDIDTTKGELKVLGKRNKERIIPLGPLICQKIDLYLGYRSPKVET----EVFLLNDEGKPAKADYVYKVVKEALA 242
Cdd:TIGR02224 149 VGLDLSDLDLDFGEVRVRGKGNKERIVPFGPYARDALQAYLEARRSPLLAsegqDALFLNRRGGRLTPRGVQYRLQQLRA 228

                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 750294070  243 PLPQYSRKSPHILRHSFATAMLNNGADLMSVKELLGHDSISSTAVYTHTTFEELRKMY-NAHPRSRE 308
Cdd:TIGR02224 229 KAGLPKHVHPHALRHSFATHLLNNGADLRAVQELLGHASLSTTQIYTHVDFQHLAKVYdQAHPRAKK 295
 
Name Accession Description Interval E-value
recomb_XerC TIGR02224
tyrosine recombinase XerC; The phage integrase family describes a number of recombinases with ...
 7-308 2.16e-81

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: 248.68  E-value: 2.16e-81
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 750294070    7 ERYRRYLQYERGMSELSIVAYLTDIEHWLTLeecneLEGEALEQFLCSVDTRRARKSLIKLMETPDATRSVKRRLSALRS 86
Cdd:TIGR02224   1 EAFLEYLRLERNYSPHTVRAYRRDLEAFLEF-----LEEEGGLASLAEVTAADLRSFLAELHARGLSRRSLARKLSALRS 75

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 750294070   87 LYGYLMKIEKVEHNPFKAVQVPKDGQYLPTFVNADlltrHIERLYKEAEEEptsEGKRVAWQLAFVVDLLFQTGMRRAEL 166
Cdd:TIGR02224  76 FYRFLLRRGLIDANPAAGVRAPKQPKKLPKFLSED----EMEALLDAPEED---DEDWLALRDRAILELLYSSGLRVSEL 148

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 750294070  167 LGLHLGDIDTTKGELKVLGKRNKERIIPLGPLICQKIDLYLGYRSPKVET----EVFLLNDEGKPAKADYVYKVVKEALA 242
Cdd:TIGR02224 149 VGLDLSDLDLDFGEVRVRGKGNKERIVPFGPYARDALQAYLEARRSPLLAsegqDALFLNRRGGRLTPRGVQYRLQQLRA 228

                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 750294070  243 PLPQYSRKSPHILRHSFATAMLNNGADLMSVKELLGHDSISSTAVYTHTTFEELRKMY-NAHPRSRE 308
Cdd:TIGR02224 229 KAGLPKHVHPHALRHSFATHLLNNGADLRAVQELLGHASLSTTQIYTHVDFQHLAKVYdQAHPRAKK 295
xerC PRK00236
site-specific tyrosine recombinase XerC; Reviewed
 1-305 6.52e-71

site-specific tyrosine recombinase XerC; Reviewed


Pssm-ID: 234698 [Multi-domain]  Cd Length: 297  Bit Score: 221.95  E-value: 6.52e-71
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 750294070   1 MMDGILERYRRYLQYERGMSELSIVAYLTDIEHWLTLeeCNELEGEALEQflcsVDTRRARKSLIKLMETPDATRSVKRR 80
Cdd:PRK00236   5 DLPAALEAFLEYLRVERGLSPHTLRAYRRDLRAFLAF--LEEHGISSLQD----LDAADLRSFLARRRRQGLSARSLARR 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 750294070  81 LSALRSLYGYLMKIEKVEHNPFKAVQVPKDGQYLPTFVNADlltrHIERLYKEAEEEPTSEGKRVAwqlafVVDLLFQTG 160
Cdd:PRK00236  79 LSALRSFYRWLVRRGLLKANPAAGLRAPKIPKRLPKPLDVD----QAKRLLDAIDEDDPLALRDRA-----ILELLYGSG 149

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 750294070 161 MRRAELLGLHLGDIDTTKGELKVLGKRNKERIIPLGPLICQKIDLYLGYR-SPKVETEVFLLNDEGKPAKADYVYKVVKE 239
Cdd:PRK00236 150 LRLSELVGLDIDDLDLASGTLRVLGKGNKERTVPLGRAAREALEAYLALRpLFLPDDDALFLGARGGRLSPRVVQRRVKK 229

                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 750294070 240 AL--APLPqySRKSPHILRHSFATAMLNNGADLMSVKELLGHDSISSTAVYTHTTFEELRKMYN-AHPR 305
Cdd:PRK00236 230 LGkkAGLP--SHITPHKLRHSFATHLLESGGDLRAVQELLGHASLSTTQIYTHVDFQHLAEVYDaAHPR 296
XerD COG4974
Site-specific recombinase XerD [Replication, recombination and repair];
2-303 1.82e-70

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


Pssm-ID: 443999 [Multi-domain]  Cd Length: 291  Bit Score: 220.64  E-value: 1.82e-70
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 750294070   2 MDGILERYRRYLQYERGMSELSIVAYLTDIEHWLTLeeCNELEGEALEQflcsVDTRRARKSLIKLMETPDATRSVKRRL 81
Cdd:COG4974    3 LADLLEAFLEELKREKGLSPNTIKAYRRDLRRFLRF--LEELGKIPLAE----ITPEDIRAYLNYLRERGLSPSTINRYL 76

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 750294070  82 SALRSLYGYLMKIEKVEHNPFKAVQVPKDGQYLPTFVNADlltrHIERLYKEAEEEpTSEGKRvawqLAFVVDLLFQTGM 161
Cdd:COG4974   77 AALRSFFRYAVREGLLEDNPAAKVKLPKKPRKLPRVLTEE----EIEALLEALDTE-TPEGLR----DRALLLLLYATGL 147

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 750294070 162 RRAELLGLHLGDIDTTKGELKVL-GKRNKERIIPLGPLICQKIDLYLGYRSPKVETEVFLlNDEGKPAKADYVYKVVKEA 240
Cdd:COG4974  148 RVSELLGLKWSDIDLDRGTIRVRrGKGGKERTVPLSPEALEALREYLEERRPRDSDYLFP-TRRGRPLSRRAIRKILKRL 226

                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 750294070 241 LAPLPQYSRKSPHILRHSFATAMLNNGADLMSVKELLGHDSISSTAVYTHTTFEELRKMYNAH 303
Cdd:COG4974  227 AKRAGIPKRVTPHSLRHTFATHLLEAGVDLRTVQELLGHSSISTTQIYTHVSDEELREAVEKL 289
INT_XerDC_C cd00798
XerD and XerC integrases, C-terminal catalytic domains; XerDC-like integrases are involved in ...
 155-296 1.79e-44

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: 149.97  E-value: 1.79e-44
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 750294070 155 LLFQTGMRRAELLGLHLGDIDTTKGELKVLGKRNKERIIPLGPLICQKIDLYLGYRSPKVE----TEVFLLNDEGKPAKA 230
Cdd:cd00798   27 LLYASGLRVSELVGLDLSDVDLDEGLVRVTGKGNKERLVPFGSYAVEALEEYLEERRPLLLkkkpPDALFLNKRGKRLSR 106

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 750294070 231 DYVYKVVKEALAPLPQYSRKSPHILRHSFATAMLNNGADLMSVKELLGHDSISSTAVYTHTTFEEL 296
Cdd:cd00798  107 RGVWRILKKYAERAGLPKHVSPHTLRHSFATHLLEGGADLRVVQELLGHASLSTTQIYTHVSFERL 172
Phage_integrase pfam00589
Phage integrase family; Members of this family cleave DNA substrates by a series of staggered ...
 127-293 1.02e-33

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: 121.66  E-value: 1.02e-33
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 750294070  127 IERLYKEAEEEPTSegkrvAWQLAFVvDLLFQTGMRRAELLGLHLGDIDTTKGELKVL-GKRNKERIIPLGPLICQKIDL 205
Cdd:pfam00589   7 VERLLDAAETGPLS-----IRDKALL-ELLYATGLRISELCSLRWSDIDFENGVIRVHrGKGNKERTVPLSDAALELLKE 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 750294070  206 YLGYRS-PKVETEVFLLNDEGKPAKADYVYKVVKEALAPLPQYSRKSPHILRHSFATAMLNNGADLMSVKELLGHDSISS 284
Cdd:pfam00589  81 WLSKRLlEAPKSDYLFASKRGKPLSRQTVRKIFKRAGKEAGLELPLHPHMLRHSFATHLLEAGVDLRVVQKLLGHSSIST 160


                  ....*....
gi 750294070  285 TAVYTHTTF 293
Cdd:pfam00589 161 TQIYTHVAD 169
 
Name Accession Description Interval E-value
recomb_XerC TIGR02224
tyrosine recombinase XerC; The phage integrase family describes a number of recombinases with ...
 7-308 2.16e-81

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: 248.68  E-value: 2.16e-81
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 750294070    7 ERYRRYLQYERGMSELSIVAYLTDIEHWLTLeecneLEGEALEQFLCSVDTRRARKSLIKLMETPDATRSVKRRLSALRS 86
Cdd:TIGR02224   1 EAFLEYLRLERNYSPHTVRAYRRDLEAFLEF-----LEEEGGLASLAEVTAADLRSFLAELHARGLSRRSLARKLSALRS 75

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 750294070   87 LYGYLMKIEKVEHNPFKAVQVPKDGQYLPTFVNADlltrHIERLYKEAEEEptsEGKRVAWQLAFVVDLLFQTGMRRAEL 166
Cdd:TIGR02224  76 FYRFLLRRGLIDANPAAGVRAPKQPKKLPKFLSED----EMEALLDAPEED---DEDWLALRDRAILELLYSSGLRVSEL 148

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 750294070  167 LGLHLGDIDTTKGELKVLGKRNKERIIPLGPLICQKIDLYLGYRSPKVET----EVFLLNDEGKPAKADYVYKVVKEALA 242
Cdd:TIGR02224 149 VGLDLSDLDLDFGEVRVRGKGNKERIVPFGPYARDALQAYLEARRSPLLAsegqDALFLNRRGGRLTPRGVQYRLQQLRA 228

                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 750294070  243 PLPQYSRKSPHILRHSFATAMLNNGADLMSVKELLGHDSISSTAVYTHTTFEELRKMY-NAHPRSRE 308
Cdd:TIGR02224 229 KAGLPKHVHPHALRHSFATHLLNNGADLRAVQELLGHASLSTTQIYTHVDFQHLAKVYdQAHPRAKK 295
xerC PRK00236
site-specific tyrosine recombinase XerC; Reviewed
 1-305 6.52e-71

site-specific tyrosine recombinase XerC; Reviewed


Pssm-ID: 234698 [Multi-domain]  Cd Length: 297  Bit Score: 221.95  E-value: 6.52e-71
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 750294070   1 MMDGILERYRRYLQYERGMSELSIVAYLTDIEHWLTLeeCNELEGEALEQflcsVDTRRARKSLIKLMETPDATRSVKRR 80
Cdd:PRK00236   5 DLPAALEAFLEYLRVERGLSPHTLRAYRRDLRAFLAF--LEEHGISSLQD----LDAADLRSFLARRRRQGLSARSLARR 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 750294070  81 LSALRSLYGYLMKIEKVEHNPFKAVQVPKDGQYLPTFVNADlltrHIERLYKEAEEEPTSEGKRVAwqlafVVDLLFQTG 160
Cdd:PRK00236  79 LSALRSFYRWLVRRGLLKANPAAGLRAPKIPKRLPKPLDVD----QAKRLLDAIDEDDPLALRDRA-----ILELLYGSG 149

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 750294070 161 MRRAELLGLHLGDIDTTKGELKVLGKRNKERIIPLGPLICQKIDLYLGYR-SPKVETEVFLLNDEGKPAKADYVYKVVKE 239
Cdd:PRK00236 150 LRLSELVGLDIDDLDLASGTLRVLGKGNKERTVPLGRAAREALEAYLALRpLFLPDDDALFLGARGGRLSPRVVQRRVKK 229

                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 750294070 240 AL--APLPqySRKSPHILRHSFATAMLNNGADLMSVKELLGHDSISSTAVYTHTTFEELRKMYN-AHPR 305
Cdd:PRK00236 230 LGkkAGLP--SHITPHKLRHSFATHLLESGGDLRAVQELLGHASLSTTQIYTHVDFQHLAEVYDaAHPR 296
XerD COG4974
Site-specific recombinase XerD [Replication, recombination and repair];
2-303 1.82e-70

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


Pssm-ID: 443999 [Multi-domain]  Cd Length: 291  Bit Score: 220.64  E-value: 1.82e-70
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 750294070   2 MDGILERYRRYLQYERGMSELSIVAYLTDIEHWLTLeeCNELEGEALEQflcsVDTRRARKSLIKLMETPDATRSVKRRL 81
Cdd:COG4974    3 LADLLEAFLEELKREKGLSPNTIKAYRRDLRRFLRF--LEELGKIPLAE----ITPEDIRAYLNYLRERGLSPSTINRYL 76

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 750294070  82 SALRSLYGYLMKIEKVEHNPFKAVQVPKDGQYLPTFVNADlltrHIERLYKEAEEEpTSEGKRvawqLAFVVDLLFQTGM 161
Cdd:COG4974   77 AALRSFFRYAVREGLLEDNPAAKVKLPKKPRKLPRVLTEE----EIEALLEALDTE-TPEGLR----DRALLLLLYATGL 147

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 750294070 162 RRAELLGLHLGDIDTTKGELKVL-GKRNKERIIPLGPLICQKIDLYLGYRSPKVETEVFLlNDEGKPAKADYVYKVVKEA 240
Cdd:COG4974  148 RVSELLGLKWSDIDLDRGTIRVRrGKGGKERTVPLSPEALEALREYLEERRPRDSDYLFP-TRRGRPLSRRAIRKILKRL 226

                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 750294070 241 LAPLPQYSRKSPHILRHSFATAMLNNGADLMSVKELLGHDSISSTAVYTHTTFEELRKMYNAH 303
Cdd:COG4974  227 AKRAGIPKRVTPHSLRHTFATHLLEAGVDLRTVQELLGHSSISTTQIYTHVSDEELREAVEKL 289
recomb_XerD TIGR02225
tyrosine recombinase XerD; The phage integrase family describes a number of recombinases with ...
 7-306 6.94e-63

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: 201.27  E-value: 6.94e-63
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 750294070    7 ERYRRYLQYERGMSELSIVAYLTDIE---HWLTLEECNELEGEA--LEQFLcsvDTRRARKSliklmetpdATRSVKRRL 81
Cdd:TIGR02225   1 EQFLDYLWVERGLSQNTLEAYRRDLEkflEFLEERGIDLEEVDRgdIVDFL---AELKEAGL---------SARSIARAL 68

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 750294070   82 SALRSLYGYLMKIEKVEHNPFKAVQVPKDGQYLPtfvnaDLLT-RHIERLYkEAEEEPTSEGKRvawqLAFVVDLLFQTG 160
Cdd:TIGR02225  69 SALRSFYRFLLREGIREDDPSALIEPPKVARKLP-----KVLTvEEVEALL-AAPDVDTPLGLR----DRAMLELLYATG 138

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 750294070  161 MRRAELLGLHLGDIDTTKGELKVLGKRNKERIIPLGPLICQKIDLYLGYRSP-------KVETEVFLlNDEGKPAKADYV 233
Cdd:TIGR02225 139 LRVSELVGLRLEDVNLDEGFVRVRGKGNKERLVPLGEEAIEALERYLKEARPlllkkkvKESDALFL-NRRGGPLSRQGV 217

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 750294070  234 YKVVKEalaplpqYSRK-------SPHILRHSFATAMLNNGADLMSVKELLGHDSISSTAVYTHTTFEELRKMYNA-HPR 305
Cdd:TIGR02225 218 WKILKE-------YAKRagiekpiSPHTLRHSFATHLLENGADLRVVQELLGHADISTTQIYTHVARERLKEVHKKhHPR 290


                  .
gi 750294070  306 S 306
Cdd:TIGR02225 291 A 291
XerC COG4973
Site-specific recombinase XerC [Replication, recombination and repair];
6-300 3.84e-61

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


Pssm-ID: 443998 [Multi-domain]  Cd Length: 287  Bit Score: 196.72  E-value: 3.84e-61
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 750294070   6 LERYRRYLQyERGMSELSIVAYLTDIEHWLTLEECNELEgealeqfLCSVDTRRARKSLIKLMETPDATRSVKRRLSALR 85
Cdd:COG4973    8 LEAYLEHLR-ERRLSPKTLEAYRRDLRRLIPLLGDADLP-------LEELTPADVRRFLARLHRRGLSPRTLNRRLSALR 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 750294070  86 SLYGYLMKIEKVEHNPFKAVQVPKDGQYLPTFVNADLLTRHIERLykeaeeeptsEGKRVAWQLAFVVDLLFQTGMRRAE 165
Cdd:COG4973   80 SFFNWAVREGLLEANPAAGVKAPKAPRKLPRALTVDELAQLLDAL----------ADDPLAVRDRAIVELLYSTGLRLGE 149

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 750294070 166 LLGLHLGDIDTTKGELKVLGKRNKERIIPLGPLICQKIDLYLGYRSPKVETE---VFLlNDEGKPAKADYVYKVVKEALA 242
Cdd:COG4973  150 LVGLDWEDVDLDAGEVRVRGKTGKSRTVPLGPKALAALREWLAVRPELAAPDegaLFP-SRRGTRLSPRNVQKRLRRLAK 228

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 750294070 243 PLPQYSRKSPHILRHSFATAMLNNGADLMSVKELLGHDSISSTAVYTHTTFEELRKMY 300
Cdd:COG4973  229 KAGLPKHVHPHDLRHSFATHLLESGGDLRAVQELLGHASISTTQIYTHLDFQHLAEVY 286
xerD PRK00283
tyrosine recombinase;
1-306 3.37e-52

tyrosine recombinase;


Pssm-ID: 234713 [Multi-domain]  Cd Length: 299  Bit Score: 173.84  E-value: 3.37e-52
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 750294070   1 MMDGILERYRRYLQYERGMSELSIVAYLTDIEHWltleeCNELEGEALEqfLCSVDTRRARKSLIKLMETPDATRSVKRR 80
Cdd:PRK00283   4 ADRALIEQFLDALWVERGLAENTLSSYRRDLELF-----AEWLAARGLS--LAEATRDDLQAFLAELAEGGYKATSSARR 76

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 750294070  81 LSALRSLYGYLMKIEKVEHNPFKAVQVPKDGQYLPTfvnaDLLTRHIERLYkEAEEEPTSEGKRvawqLAFVVDLLFQTG 160
Cdd:PRK00283  77 LSALRRFFQFLLREGLREDDPSALLDSPKLPRRLPK----TLSEAQVEALL-DAPDIDTPLGLR----DRAMLELLYATG 147

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 750294070 161 MRRAELLGLHLGDIDTTKGELKVLGKRNKERIIPLGPLICQKIDLYLGYRSP----KVETEVFLLNDEGKPAKADYVYKV 236
Cdd:PRK00283 148 LRVSELVGLTLDDVSLRQGVVRVTGKGNKERLVPLGEEAVYAIERYLERGRPallnGRSSDALFPSARGGQLTRQTFWHR 227

                        250       260       270       280       290       300       310
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 750294070 237 VKEA--LAPLPQySRKSPHILRHSFATAMLNNGADLMSVKELLGHDSISSTAVYTHTTFEELRKMYN-AHPRS 306
Cdd:PRK00283 228 IKHYakRAGIDP-KKLSPHVLRHAFATHLLNHGADLRVVQELLGHSDISTTQIYTHVATERLKELHAqHHPRA 299
INT_XerDC_C cd00798
XerD and XerC integrases, C-terminal catalytic domains; XerDC-like integrases are involved in ...
 155-296 1.79e-44

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: 149.97  E-value: 1.79e-44
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 750294070 155 LLFQTGMRRAELLGLHLGDIDTTKGELKVLGKRNKERIIPLGPLICQKIDLYLGYRSPKVE----TEVFLLNDEGKPAKA 230
Cdd:cd00798   27 LLYASGLRVSELVGLDLSDVDLDEGLVRVTGKGNKERLVPFGSYAVEALEEYLEERRPLLLkkkpPDALFLNKRGKRLSR 106

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 750294070 231 DYVYKVVKEALAPLPQYSRKSPHILRHSFATAMLNNGADLMSVKELLGHDSISSTAVYTHTTFEEL 296
Cdd:cd00798  107 RGVWRILKKYAERAGLPKHVSPHTLRHSFATHLLEGGADLRVVQELLGHASLSTTQIYTHVSFERL 172
Phage_integrase pfam00589
Phage integrase family; Members of this family cleave DNA substrates by a series of staggered ...
 127-293 1.02e-33

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: 121.66  E-value: 1.02e-33
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 750294070  127 IERLYKEAEEEPTSegkrvAWQLAFVvDLLFQTGMRRAELLGLHLGDIDTTKGELKVL-GKRNKERIIPLGPLICQKIDL 205
Cdd:pfam00589   7 VERLLDAAETGPLS-----IRDKALL-ELLYATGLRISELCSLRWSDIDFENGVIRVHrGKGNKERTVPLSDAALELLKE 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 750294070  206 YLGYRS-PKVETEVFLLNDEGKPAKADYVYKVVKEALAPLPQYSRKSPHILRHSFATAMLNNGADLMSVKELLGHDSISS 284
Cdd:pfam00589  81 WLSKRLlEAPKSDYLFASKRGKPLSRQTVRKIFKRAGKEAGLELPLHPHMLRHSFATHLLEAGVDLRVVQKLLGHSSIST 160


                  ....*....
gi 750294070  285 TAVYTHTTF 293
Cdd:pfam00589 161 TQIYTHVAD 169
xerC PRK01287
site-specific tyrosine recombinase XerC; Reviewed
 71-320 5.43e-31

site-specific tyrosine recombinase XerC; Reviewed


Pssm-ID: 234935 [Multi-domain]  Cd Length: 358  Bit Score: 119.47  E-value: 5.43e-31
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 750294070  71 PDATRSVKRRLSALRSLYGYLMKIEKVEHNPFKAVQVPKDGQYLPTFVNADLLTRHIerlyKEAEEEPTSEGKRvawQLA 150
Cdd:PRK01287  89 PLSTRTQRTQLSPLRVWFRWLLKRHHILYNPAEDLELPKEEKRLPRQILSEAETEQV----LASPDLTTLQGLR---DRA 161

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 750294070 151 fVVDLLFQTGMRRAELLGLHLGDIDTTKGELKVL-GKRNKERIIPLGPLICQKIDLYLGYRSPKV----ETEVFLLNDEG 225
Cdd:PRK01287 162 -LLELLWSTGIRRGELARLDLYDVDASRGVVTVRqGKGNKDRVVPVGERALAWLQRYLQDVRPQLavrpDSGALFVAMDG 240

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 750294070 226 KPAKADYVYKVVKEALAPLPQYSRKSPHILRHSFATAMLNNGADLMSVKELLGHDSISSTAVYTHTTFEELRKMYNA-HP 304
Cdd:PRK01287 241 DGLARNTLTNMVGRYIRAAGIEKAGACHLFRHAMATQMLENGADTRHIQAILGHAKLETTQIYTRVSIGHLQAVHAStHP 320

                        250
                 ....*....|....*.
gi 750294070 305 RSRESSKERRTNHEDE 320
Cdd:PRK01287 321 AERKADEKLRDADEVG 336
DNA_BRE_C cd00397
DNA breaking-rejoining enzymes, C-terminal catalytic domain; The DNA breaking-rejoining enzyme ...
 127-289 1.68e-30

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: 113.34  E-value: 1.68e-30
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 750294070 127 IERLYKEAEEEptsegKRVAWQLAFVVDLLFQTGMRRAELLGLHLGDIDTTKGELKVLG---KRNKERIIPLGPLICQKI 203
Cdd:cd00397    2 LEKLLDAIDED-----KKIDLRDRAILLLLLETGLRISELLALKVKDIDLDNGTIRVRGkktKGGKERTVPLPKELAEEL 76

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 750294070 204 DLYLGYRSPKV-------ETEVFLLNDEGKPAKADYVYKVVKEALAPLpqYSRKSPHILRHSFATAMLNNGADLMSVKEL 276
Cdd:cd00397   77 KEYLKERRDKRgpllkslYLNKLFGTKLGERLSRRTLRRIFKKAGIEA--GRKITPHSLRHTFATNLLENGVDIKVVQKL 154

                        170
                 ....*....|...
gi 750294070 277 LGHDSISSTAVYT 289
Cdd:cd00397  155 LGHSSISTTQRYL 167
INT_IntI_C cd01193
Integron integrase and similar protiens, C-terminal catalytic domain; Integron integrases ...
 155-290 2.61e-24

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: 97.35  E-value: 2.61e-24
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 750294070 155 LLFQTGMRRAELLGLHLGDIDTTKGELKV-LGKRNKERIIPLGPLICQKIDLYLgyRSPKVETEVFLLN----------- 222
Cdd:cd01193   29 LLYGAGLRISELLRLRVKDIDFERGVIRVrQGKGGKDRVVPLPEKLLEPLRRYL--KSARPKEELDPAEgragvldprtg 106

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 750294070 223 -DEGKPAKADYVYKVVKEALAPLPQYSRKSPHILRHSFATAMLNNGADLMSVKELLGHDSISSTAVYTH 290
Cdd:cd01193  107 vERRHHISETTVQRALKKAVEQAGITKRVTPHTLRHSFATHLLEAGTDIRTIQELLGHSDLSTTMIYTH 175
xerS PRK05084
site-specific tyrosine recombinase XerS; Reviewed
 12-298 1.42e-20

site-specific tyrosine recombinase XerS; Reviewed


Pssm-ID: 235339 [Multi-domain]  Cd Length: 357  Bit Score: 90.75  E-value: 1.42e-20
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 750294070  12 YLQYERG--MSELSIVAYLTDIE---HWL--------------TLEECNELEGEALEQFlcsVDTRRARKSLI-KLMETP 71
Cdd:PRK05084  24 YYQSKLAtpYSPTTLYEYLTEYRrffNWLiseglsdaskikdiPLSTLENLTKKDVEAF---ILYLRERPLLNgHSTKKG 100

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 750294070  72 DATRSVKRRLSALRSLYGYLMKI-EKVEHNPF------KAVQVPKDGQYLPTfvNADLLTrhiERLYKEAE--------- 135
Cdd:PRK05084 101 NSQTTINRTLSALKSLFKYLTEEaENEDGEPYfyrnvmKKIELKKKKETLAA--RAHNLK---QKLFLGDEdyefldfid 175

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 750294070 136 ---EEPTSEGKRVAWQ------LAfVVDLLFQTGMRRAELLGLHLGDIDTTKGELKVLGKRNKERIIPLGPLICQKIDLY 206
Cdd:PRK05084 176 neyEQKLSNRALSSFKknkerdLA-IIALILGSGLRVSELVNLDLSDLNLKQMTIDVTRKGGKRDSVNIAPFALPYLEEY 254

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 750294070 207 LG-----YRSPKVETEVFLLNDEGKPAK--ADYVYKVVKealaplpQYS-----RKSPHILRHSFATAMLNNGADLMSVK 274
Cdd:PRK05084 255 LKirasrYKAEKQEKALFLTKYRGKPNRisARAIEKMVA-------KYSeafgvRLTPHKLRHTLATRLYDATKDQVLVA 327

                        330       340
                 ....*....|....*....|....
gi 750294070 275 ELLGHDSISSTAVYTHTTFEELRK 298
Cdd:PRK05084 328 DQLGHTSTETTDLYTHIVNDEQKE 351
INT_RitA_C_like cd01188
C-terminal catalytic domain of recombinase RitA, a component of the recombinase trio; ...
 155-299 3.37e-19

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: 83.45  E-value: 3.37e-19
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 750294070 155 LLFQTGMRRAELLGLHLGDIDTTKGELKVLG-KRNKERIIPLGPLICQKIDLYLGYRSPKVET-EVFL--LNDEGKPAKA 230
Cdd:cd01188   28 LLARLGLRAGDVAGLRLDDIDWRSGTITVRQkKTGRPVELPLTEPVGEALADYLRDGRPRTDSrEVFLraRAPYRPLSST 107

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 750294070 231 DYVYKVVKEALAPLP-QYSRKSPHILRHSFATAMLNNGADLMSVKELLGHDSISSTAVYTHTTFEELRKM 299
Cdd:cd01188  108 SQISSIVRRYLRKAGiEPSHRGTHSLRHSLATRMLRAGTSLKVIADLLGHRSIETTAIYAKIDVDDLREV 177
INT_ICEBs1_C_like cd01189
C-terminal catalytic domain of integrases from bacterial phages and conjugate transposons; ...
 127-290 3.98e-19

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: 82.22  E-value: 3.98e-19
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 750294070 127 IERLYKEAEEEPTsegkrvawQLAFVVDLLFQTGMRRAELLGLHLGDIDTTKGELKV---LGKRNKE------------- 190
Cdd:cd01189    4 LKKLLEALKKRGD--------RYYLLFLLALLTGLRRGELLALTWSDIDFENGTIRInrtLVRKKKGgyvikppktkssi 75

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 750294070 191 RIIPLGPLICQKIDLYLGYRspkvetevfllndegkpakadyvyKVVKEALAPlpqysRKSPHILRHSFATAMLNNGADL 270
Cdd:cd01189   76 RTIPLPDELIELLKELKAFK------------------------KLLKKAGLP-----RITPHDLRHTFASLLLEAGVPL 126

                        170       180
                 ....*....|....*....|.
gi 750294070 271 MSVKELLGHDSISSTA-VYTH 290
Cdd:cd01189  127 KVIAERLGHSDISTTLdVYAH 147
INT_RitC_C_like cd01182
C-terminal catalytic domain of recombinase RitC, a component of the recombinase trio; ...
 139-298 5.06e-19

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: 83.10  E-value: 5.06e-19
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 750294070 139 TSEGKRVAWQLAFvvdlLFQTGMRRAELLGLHLGDID-TTKGELKVLGKRNKERIIPLGP----LICQKIDLYLGYRSPK 213
Cdd:cd01182   17 TSLGRRDHALLLL----LYDTGARVQELADLTIRDLRlDDPATVRLHGKGRKERTVPLWKetvaALKAYLQEFHLTPDPK 92

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 750294070 214 VETEVFLlNDEGKPAKADYVY----KVVKEALAPLPQYSRK-SPHILRHSFATAMLNNGADLMSVKELLGHDSISSTAVY 288
Cdd:cd01182   93 QLFPLFP-NRRGQPLTRDGVAyilnKYVALASNRCPSLPKRiTPHTLRHTKAMHLLQAGVDLTVIRDWLGHESVETTQIY 171

                        170
                 ....*....|
gi 750294070 289 THTTFEELRK 298
Cdd:cd01182  172 AEADLEMKRE 181
INT_RitB_C_like cd00797
C-terminal catalytic domain of recombinase RitB, a component of the recombinase trio; ...
 127-299 1.29e-18

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: 82.35  E-value: 1.29e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 750294070 127 IERLYKEAEEEPTSEGKRvAWQLAFVVDLLFQTGMRRAELLGLHLGDIDTTKGELKV-LGKRNKERIIPLGPLICQKIDL 205
Cdd:cd00797    6 IRRLLAAADQLPPESPLR-PLTYATLFGLLYATGLRVGEALRLRLEDVDLDSGILTIrQTKFGKSRLVPLHPSTVGALRD 84

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 750294070 206 YLGYR---SPKVETEVFLLNDEGKPAKADYVYKVVKEAL--APLPQYSRKS---PHILRHSFATAML----NNGAD---- 269
Cdd:cd00797   85 YLARRdrlLPSPSSSYFFVSQQGGRLTGGGVYRVFRRLLrrIGLRGAGDGRgprLHDLRHTFAVNRLtrwyREGADverk 164

                        170       180       190
                 ....*....|....*....|....*....|
gi 750294070 270 LMSVKELLGHDSISSTAVYTHTTfEELRKM 299
Cdd:cd00797  165 LPVLSTYLGHVNVTDTYWYLTAT-PELMEL 193
INTN1_C_like cd01185
Integrase IntN1 of Bacteroides mobilizable transposon NBU1 and similar proteins, C-terminal ...
 126-296 2.98e-17

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: 77.69  E-value: 2.98e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 750294070 126 HIERLYKeAEEEPTSEGKRVawQLAFvvdlLFQ--TGMRRAELLGLHLGDIDTTKGELKVLGKRNK---ERIIPLGPLIC 200
Cdd:cd01185    2 ELKRLMA-LELSDTSRLELV--RDMF----LFScyTGLRFSDLKNLTWKNIVEASGRTWIRYRRKKtgkPVTVPLLPVAR 74

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 750294070 201 QKIDLYLGYRSPKVeteVFllndegKPAKADYVYKVVKEALAPLPQYSRKSPHILRHSFATAMLNNGADLMSVKELLGHD 280
Cdd:cd01185   75 EILEKYKDDRSEGK---LF------PVLSNQKINRYLKEIAKIAGIDKHLTFHVARHTFATLLLLKGVDIETISKLLGHS 145

                        170
                 ....*....|....*.
gi 750294070 281 SISSTAVYTHTTFEEL 296
Cdd:cd01185  146 SIKTTQIYAKIVDSKK 161
INT_Rci_Hp1_C cd00796
Shufflon-specific DNA recombinase Rci and Bacteriophage Hp1_like integrase, C-terminal ...
 122-290 1.38e-16

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


Pssm-ID: 271177 [Multi-domain]  Cd Length: 162  Bit Score: 75.83  E-value: 1.38e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 750294070 122 LLTRHIERLYKEAEEeptSEGKRVAWQLAFVVDllfqTGMRRAELLGLHLGDIDTTKGeLKVLG--KRNKERIIPLGPLI 199
Cdd:cd00796    5 LTEDEEARLLAALEE---STNPHLRLIVLLALY----TGARRGEILSLRWDDIDLEVG-LIVLPetKNGKPRTVPLSDEA 76

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 750294070 200 CQKIDLYLgyrsPKVETEVFLLNDEGKPAKADYVYKVVKEAL--APLPQYSrksPHILRHSFATAMLNNGADLMSVKELL 277
Cdd:cd00796   77 IAILKELK----RKRGKDGFFVDGRFFGIPIASLRRAFKKARkrAGLEDLR---FHDLRHTFASRLVQAGVPIKTVAKIL 149

                        170
                 ....*....|...
gi 750294070 278 GHDSISSTAVYTH 290
Cdd:cd00796  150 GHSSIKMTMRYAH 162
INT_C_like_4 cd01194
Uncharacterized site-specific tyrosine recombinase, C-terminal catalytic domain; Tyrosine ...
 152-290 5.64e-16

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: 74.33  E-value: 5.64e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 750294070 152 VVDLLFQTGMRRAELLGLHLGDIDTTKGE--LKVLGKR--NKERIIPLGPLICQKIDLYLGYRSP-KVETEVFLL---ND 223
Cdd:cd01194   27 IISLMVTEGLRTVEIVRADVGDLRQEGEGtiLYVQGKGktSKDDFVYLRPDVLKALQAYLKARGKlDFEEPLFTSlsnNS 106

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 750294070 224 EGKPAKADYVYKVVKEALAPLPQYSRK-SPHILRHSFATAMLNNGADLMSVKELLGHDSISSTAVYTH 290
Cdd:cd01194  107 KGQRLTTRSIRRIIKKYLRKAGLDDDRlTAHSLRHTAGTLALKAGKSLREVQQLLRHSDPNTTMIYAH 174
INT_C_like_5 cd01195
Uncharacterized site-specific tyrosine recombinase, C-terminal catalytic domain; Tyrosine ...
 152-290 1.23e-13

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


Pssm-ID: 271195 [Multi-domain]  Cd Length: 170  Bit Score: 67.88  E-value: 1.23e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 750294070 152 VVDLLFQTGMRRAELLGLHLGDIDTTKGELKVLGKRNKER-IIPLGPLICQKIDLYLGYRSPKvETEVFL---LNDEGKP 227
Cdd:cd01195   25 LVRLLLDNALRRSEAVALDVEDLEKEHRRLRILGKGKKQReVVTLPPTTREALAAWLAARGEA-EGPLFVsldRASRGRR 103

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 750294070 228 AKADYVYKVVKEALAPLPQYSRKSPHILRHSFATAMLNNGADLMS-VKELLGHDSISSTAVYTH 290
Cdd:cd01195  104 LSPQAVYRIVRRLAERIGLGKRLSPHGLRHSAITLALDAGAGLIRkVQDFSRHADLRTLQVYDD 167
INT_FimBE_like cd01197
FimB and FimE and related proteins, integrase/recombinases; This CD includes proteins similar ...
 122-299 3.95e-13

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: 66.76  E-value: 3.95e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 750294070 122 LLTRHIERLYKEAEEEPTSEGKRVAWQLAFVvdllfqTGMRRAELLGLHLGDIDTTKGELKVlgKRNKERIIPLGPLICQ 201
Cdd:cd01197    7 LTGKEVQALLQAACRGRTPARDYCLLLLAFR------HGFRVSELCDLHLSDVDLESRRLHI--RRLKNGFSTTHPLRFD 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 750294070 202 K---IDLYLGYRS--PKVETEVFLLNDEGKPAKADYVYKVVKEA--LAPLPQYSRksPHILRHSFATAMLNNGADLMSVK 274
Cdd:cd01197   79 EreaLEAWLKERAnwKGADTDWIFLSRRGGPLSRQQAYRIIRDLgkEAGTVTQTH--PHMLRHACGYALADRGADTRLIQ 156

                        170       180
                 ....*....|....*....|....*
gi 750294070 275 ELLGHDSISSTAVYTHTTFEELRKM 299
Cdd:cd01197  157 DYLGHRNIRHTVIYTASNAARFANL 181
INT_tnpA_C_Tn554 cd01186
Putative Transposase A from transposon Tn554, C-terminal catalytic domain; This family ...
 150-298 7.95e-13

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


Pssm-ID: 271186 [Multi-domain]  Cd Length: 184  Bit Score: 65.90  E-value: 7.95e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 750294070 150 AFVVDLLFQTGMRRAELLGLHLGDIDTTKGELKVLGKRN----------KERIIPLGPLIcqkIDLYLGY----RSPKVE 215
Cdd:cd01186   20 KFLLALLYETGLRIGEALGLRIEDIDMADNQIELVPREDntnearaksmRERRIPVSQDL---IDLYADYltyiYCEEAE 96

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 750294070 216 TEVFLL-----NDEGKPAKADYVYKVVKealaplpQYSRK-----SPHILRHSFATAMLNNGADLMSVKELLGHDSISST 285
Cdd:cd01186   97 FSITVFvnvkgGNQGKAMNYSDVYDLVR-------RLKKRtgidfTPHMFRHTHATALIRAGWSIEVVARRLGHAHVQTT 169

                        170
                 ....*....|....
gi 750294070 286 -AVYTHTTFEELRK 298
Cdd:cd01186  170 lNTYGHLSEEDIRR 183
integrase_gron TIGR02249
integron integrase; Members of this family are integrases associated with integrons (and ...
 155-290 9.71e-13

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: 67.80  E-value: 9.71e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 750294070  155 LLFQTGMRRAELLGLHLGDIDTTKGELKVL-GKRNKERIIPL-----GPLICQ--KIDLYLGYRSPKVETEVFL---LND 223
Cdd:TIGR02249 124 LLYGSGMRLMECLRLRIQDIDFDYGEIRIRqGKGGKDRTVTLpkeliPPLREQieLARAYHEADLAEGYGGVYLphaLAR 203

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 750294070  224 EGKPAKAD----YVYKVVKEALAP--------------LPQYSRKS-----------PHILRHSFATAMLNNGADLMSVK 274
Cdd:TIGR02249 204 KYPNAPKEwgwqYLFPSHRLSRDPesgvirrhhinettIQRAVRRAveragiekpvtCHTLRHSFATHLLESGADIRTVQ 283

                         170
                  ....*....|....*.
gi 750294070  275 ELLGHDSISSTAVYTH 290
Cdd:TIGR02249 284 ELLGHSDVKTTQIYTH 299
PRK09871 PRK09871
tyrosine recombinase; Provisional
 122-289 3.31e-10

tyrosine recombinase; Provisional


Pssm-ID: 182126  Cd Length: 198  Bit Score: 58.84  E-value: 3.31e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 750294070 122 LLTRHIERLYKEAEEEPTSEGKRVAWQLAFvvdllfQTGMRRAELLGLHLGDIDTTKGELKVLGKRNK-ERIIPLGPLIC 200
Cdd:PRK09871   7 LTGKEVQAMMQAVCYGATGARDYCLILLAY------RHGMRISELLDLHYQDLDLNEGRINIRRLKNGfSTVHPLRFDER 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 750294070 201 QKIDLYLGYRSP---KVETEVFLLNDEGKPAKADYVYKVVKEALAPLPQYSRKSPHILRHSFATAMLNNGADLMSVKELL 277
Cdd:PRK09871  81 EAVERWTQERANwkgADRTDAIFISRRGSRLSRQQAYRIIRDAGIEAGTVTQTHPHMLRHACGYELAERGADTRLIQDYL 160

                        170
                 ....*....|..
gi 750294070 278 GHDSISSTAVYT 289
Cdd:PRK09871 161 GHRNIRHTVRYT 172
Phage_int_SAM_1 pfam02899
Phage integrase, N-terminal SAM-like domain;
6-93 5.38e-10

Phage integrase, N-terminal SAM-like domain;


Pssm-ID: 427047 [Multi-domain]  Cd Length: 83  Bit Score: 55.34  E-value: 5.38e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 750294070    6 LERYRRYLQYERGMSELSIVAYLTDIEHWLT-LEEcnelEGEALEQflcsVDTRRARKSLIKLMETPDATRSVKRRLSAL 84
Cdd:pfam02899   1 IDQFLEYLSLERGLSPHTLRAYRRDLLAFLKfLSE----GGSSLEQ----ITTSDVRAFLAELRAQGLSASSLARRLSAL 72


                  ....*....
gi 750294070   85 RSLYGYLMK 93
Cdd:pfam02899  73 RSFYQFLIR 81
INT_tnpB_C_Tn554 cd01187
Putative Transposase B from transposon Tn554, C-terminal catalytic domain; This family ...
 148-290 9.56e-10

Putative Transposase B from transposon Tn554, C-terminal catalytic domain; This family includes putative Transposase B from transposon Tn554. It 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: 271187 [Multi-domain]  Cd Length: 142  Bit Score: 56.28  E-value: 9.56e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 750294070 148 QLAFVVDLLFQTGMRRAELLGLHLGDIDTTKGE-------LKVLGKRNKERIIPLGPLICQKIDLYLGYrspkvetevfL 220
Cdd:cd01187   14 QPIPVVQAAVFTGARASELATLKFGCLHAQTSDdgtflywLKWENKGGKQLDIPISKKVAELIKTINWT----------L 83

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 750294070 221 LNDEGKPAKADYVYKVvkealaplpqySRKSPHILRHSFATAMLNNGADLMSVKELLGHDSISSTAVYTH 290
Cdd:cd01187   84 NELSELKNISDDHGER-----------FRFHTHRFRHTVATRLANSGMGILVLQQLLGHSSPEMTLRYAL 142
PRK15417 PRK15417
integron integrase;
251-290 3.30e-09

integron integrase;


Pssm-ID: 185315 [Multi-domain]  Cd Length: 337  Bit Score: 57.36  E-value: 3.30e-09
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|
gi 750294070 251 SPHILRHSFATAMLNNGADLMSVKELLGHDSISSTAVYTH 290
Cdd:PRK15417 275 TPHTLRHSFATALLRSGYDIRTVQDLLGHSDVSTTMIYTH 314
FimB COG0582
Integrase/recombinase, includes phage integrase [Replication, recombination and repair, ...
 64-298 3.37e-09

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


Pssm-ID: 440347 [Multi-domain]  Cd Length: 391  Bit Score: 57.36  E-value: 3.37e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 750294070  64 LIKLMETPDATRSVKRRLSALRSLYGYLMKIEKVEHNPFKAVqvpkDGQYLPTFVNAD--LLTRHIERLYKEAEEEPTSE 141
Cdd:COG0582  150 VLRPIEARGAPETARRVRQRLRQVFRYAVARGLIERNPAADL----KGALPKPKVKHHpaLTPEELPELLRALDAYRGSP 225

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 750294070 142 GKRVAWQLAFVvdllfqTGMRRAELLGLHLGDIDTTKGELKVLG---KRNKERIIPLGPlicQKIDLyLGYRSPKVETEV 218
Cdd:COG0582  226 VTRLALRLLLL------TGVRPGELRGARWSEIDLEAALWTIPAermKTRRPHIVPLSR---QALEI-LKELKPLTGDSE 295

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 750294070 219 FLL---NDEGKPAKADYVYKVVKEAlaplpQYSRKSPHILRHSFATAMLNNGADLMSVKELLGHDSISST-AVYTHTTFE 294
Cdd:COG0582  296 YVFpsrRGPKKPMSENTLNKALRRM-----GYGRFTPHGFRHTASTLLNEAGFPPDVIERQLAHKDGNKVrAAYNRADYL 370


                 ....
gi 750294070 295 ELRK 298
Cdd:COG0582  371 EERR 374
PRK09870 PRK09870
tyrosine recombinase; Provisional
 119-289 6.05e-09

tyrosine recombinase; Provisional


Pssm-ID: 182125  Cd Length: 200  Bit Score: 54.94  E-value: 6.05e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 750294070 119 NADLLTRH------IERLYKEAEEEPTSEGKRVAWQLAFVvdllfqTGMRRAELLGLHLGDIDTTKGELKVlgKRNKERI 192
Cdd:PRK09870   4 KADNKKRNflthseIESLLKAANTGPHAARNYCLTLLCFI------HGFRASEICRLRISDIDLKAKCIYI--HRLKKGF 75

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 750294070 193 IPLGPLICQKIDL---YLGYRS--PKVETEVFLLNDEGKPAKADYVYKVVKEA--LAPLPQYSRksPHILRHSFATAMLN 265
Cdd:PRK09870  76 STTHPLLNKEIQAlknWLSIRTsyPHAESEWVFLSRKGNPLSRQQFYHIISTSggNAGLSLEIH--PHMLRHSCGFALAN 153

                        170       180
                 ....*....|....*....|....
gi 750294070 266 NGADLMSVKELLGHDSISSTAVYT 289
Cdd:PRK09870 154 MGIDTRLIQDYLGHRNIRHTVWYT 177
int PHA02601
integrase; Provisional
 75-290 2.48e-08

integrase; Provisional


Pssm-ID: 222904 [Multi-domain]  Cd Length: 333  Bit Score: 54.73  E-value: 2.48e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 750294070  75 RSVKRRLSALRSLYGYLMKIEKVE-HNPFKAVQVPKDGQYLPTFvnadLLTRHIERLYKEAEEEPTSEgkrvawqLAFVV 153
Cdd:PHA02601 129 ATVNRELAYLSAVFNELIKLGKWSgPNPLDGIRPFKEAEPELAF----LTKEEIERLLDACDGSRSPD-------LGLIA 197

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 750294070 154 DLLFQTGMRRAELLGLHLGDIDTTKGE-LKVLGKRNkeRIIPLGPlicqkiDLYlgYRSPKVETEVFllndegKPAKADY 232
Cdd:PHA02601 198 KICLATGARWSEAETLKRSQISPYKITfVKTKGKKN--RTVPISE------ELY--KMLPKRRGRLF------KDAYESF 261

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 750294070 233 vYKVVKEALAPLPQysRKSPHILRHSFATAMLNNGADLMSVKELLGHDSISSTAVYTH 290
Cdd:PHA02601 262 -ERAVKRAGIDLPE--GQATHVLRHTFASHFMMNGGNILVLQRILGHATIEMTMAYAH 316
INT_C_like_1 cd01184
Uncharacterized site-specific tyrosine recombinase, C-terminal catalytic domain; Tyrosine ...
 159-290 3.15e-06

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: 46.92  E-value: 3.15e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 750294070 159 TGMRRAELLGLHLGDI-------------DTTKGELKVLGKRnkeRIIPLGPLIcqkIDL----YLGYRSPKVETEVFLL 221
Cdd:cd01184   35 TGARLNEICQLRVDDIkeedgiwcidindDAEGRRLKTKASR---RLVPIHPRL---IELgfldYVEALRADGKLFLFPE 108

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 750294070 222 NDEGKPAKADYVYKVVKEAL--APLPQYSRKSPHILRHSFATAMLNNGADLMSVKELLGH-DSISSTAVYTH 290
Cdd:cd01184  109 KRDKDGKYSKAASKWFNRLLrkLGIKDDERKSFHSFRHTFITALKRAGVPEELIAQIVGHsRGGVTHDTYGK 180
INT_P4_C cd00801
Bacteriophage P4 integrase, C-terminal catalytic domain; P4-like integrases are found in ...
 155-302 7.08e-06

Bacteriophage P4 integrase, C-terminal catalytic domain; P4-like integrases are found in temperate bacteriophages, integrative plasmids, pathogenicity and symbiosis islands, and other mobile genetic elements. The P4 integrase mediates integrative and excisive site-specific recombination between two sites, called attachment sites, located on the phage genome and the bacterial chromosome. The phage attachment site is often found adjacent to the integrase gene, while the host attachment sites are typically situated near tRNA genes. This family belongs to the superfamily of DNA breaking-rejoining enzymes, which share the same fold in their catalytic domain and the overall reaction mechanism. The catalytic domain contains six conserved active site residues. Their overall reaction mechanism involves cleavage of a single strand of a DNA duplex by nucleophilic attack of a conserved tyrosine to give a 3' phosphotyrosyl protein-DNA adduct. In the second rejoining step, a terminal 5' hydroxyl attacks the covalent adduct to release the enzyme and generate duplex DNA.


Pssm-ID: 271182 [Multi-domain]  Cd Length: 180  Bit Score: 45.72  E-value: 7.08e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 750294070 155 LLFQTGMRRAELLGLHLGDIDTTKGELKVLGKRNK---ERIIPLGPLIcqkIDLYLGYRSPKVETE-VFllnDEGKPAKA 230
Cdd:cd00801   27 LLLLTGQRIGELARARWSEIDLEEKTWTIPAERTKnkrPHRVPLSDQA---LEILEELKEFTGDSGyLF---PSRRKKKK 100

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 750294070 231 DYVYKVVKEALAPLPQYSRK-SPHILRHSFATAMLNNGADLMSVKELLGH-DSISSTAVYTHTTF-EELRKMYNA 302
Cdd:cd00801  101 PISENTINKALKRLGYKGKEfTPHDLRRTFSTLLNELGIDPEVIERLLNHvLGGVVRAAYNRYDYlEERREALQA 175
INT_Cre_C cd00799
C-terminal catalytic domain of Cre recombinase (also called integrase); Cre-like recombinases ...
 157-289 6.74e-05

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: 43.06  E-value: 6.74e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 750294070 157 FQTGMRRAELLGLHLGDI-DTTKGELKVLGKRNK--------ERIIPLGPLICqKIDLYLGYRSPKVETEVFLL------ 221
Cdd:cd00799   26 FAGALRRSELVALRVEDLtRFVDGGLLIRLRRSKtdqdgegeIKALPYGPETC-PVRALRAWLEAAGIPSGPLFrrirrg 104

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 750294070 222 -NDEGKPAKADYVYKVVKE-ALAPLPQYSRKSPHILRHSFATAMLNNGADLMSVKELLGHDSISSTAVYT 289
Cdd:cd00799  105 gSVGTTRLSDRSVARIVKRrAALAGLDPGDFSGHSLRRGFATEAARAGASLPEIMAQGGHKSVATVMRYI 174
Phage_int_SAM_4 pfam13495
Phage integrase, N-terminal SAM-like domain;
5-95 2.08e-03

Phage integrase, N-terminal SAM-like domain;


Pssm-ID: 463898 [Multi-domain]  Cd Length: 83  Bit Score: 36.44  E-value: 2.08e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 750294070    5 ILERYRRYLQYeRGMSELSIVAYLTDIEH---WLTLEECNELEGEALEQFLCSVdtRRARKSliklmetpdATRSVKRRL 81
Cdd:pfam13495   1 LLERFREALRL-RGYAERTIKAYLRWIRRflrFHDKKHPEELTEEDIEAYLSHL--ANERNV---------SASTQNQAL 68

                          90
                  ....*....|....
gi 750294070   82 SALRSLYGYLMKIE 95
Cdd:pfam13495  69 NALSFFYRWVLERE 82
INT_C_like_2 cd01191
Uncharacterized site-specific tyrosine recombinase, C-terminal catalytic domain; Tyrosine ...
 151-301 4.97e-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: 271191  Cd Length: 176  Bit Score: 37.40  E-value: 4.97e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 750294070 151 FVVDLLFQTGMRRAELLGLHLGDIDTtkGELKVLGKRNKERIIPLgPLICQKIDLYLgYRSPKVETEVFLLNDEGKPAKA 230
Cdd:cd01191   24 FVVRFLAATGARVSELIKIKVEHVEL--GYFDIYSKGGKLRRLYI-PKKLRNEALEW-LKSTNRKSGYIFLNRFGERITT 99

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 750294070 231 DYVYKVVKealaplpQYSRKS--------PHILRHSFATAMLNNGADLMSVKELLGHDSISSTAVYTHTTFEELRKMYN 301
Cdd:cd01191  100 RGIAQQLK-------NYARKYglnpkvvyPHSFRHRFAKNFLEKYNDIALLADLMGHESIETTRIYLRKTASEQQEIVD 171
INT_Lambda_C cd00800
C-terminal catalytic domain of Lambda integrase, a tyrosine-based site-specific recombinase; ...
 144-289 9.67e-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: 36.17  E-value: 9.67e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 750294070 144 RVAWQLAFVvdllfqTGMRRAELLGLHLGDIdTTKGELKVLGKRNKERIIPLGPLICQKIDLylgYRSPKVETEVFLLND 223
Cdd:cd00800   15 RLAMELALL------TGQRQGDLLRLKWSDI-TDGGLLVEQSKTGKKLLIPWTPSLRALVDR---IRALPRKRSEYLINS 84

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 750294070 224 E-GKPAKADYVYKVVKEALAPLPQYSRKSP---HILRHSFATAMLNNGADLMSVKeLLGHDSISSTAVYT 289
Cdd:cd00800   85 RkGGPLSYDTLKSAWRRARKAAGLKGETEGftfHDLRAKAATDYAEQGGSTDAQA-LLGHKSDAMTERYT 153
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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