NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|446747453|ref|WP_000824709|]
View 

tyrosine-type DNA invertase [Escherichia coli]

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

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

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 ...
 2-179 6.14e-82

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 cd01197:

Pssm-ID: 469662 [Multi-domain]  Cd Length: 181  Bit Score: 240.87  E-value: 6.14e-82
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446747453   2 KRKYLTSDEVYKLLDYIYKNRHNHRDYCMVSMAFIHGLRVSELIELKLTDYESISRKIYIHRLKGGLSTTHPLLDFESKA 81
Cdd:cd01197    3 QRKYLTGKEVQALLQAACRGRTPARDYCLLLLAFRHGFRVSELCDLHLSDVDLESRRLHIRRLKNGFSTTHPLRFDEREA 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446747453  82 LEMWLNERRYLKGNRTPWMFLSRHGGSLSRQRFYQLLKNYGEKAQLSLSIHPHMLRHACGYNLAELGNDTRLIQDYLGHR 161
Cdd:cd01197   83 LEAWLKERANWKGADTDWIFLSRRGGPLSRQQAYRIIRDLGKEAGTVTQTHPHMLRHACGYALADRGADTRLIQDYLGHR 162

                        170
                 ....*....|....*...
gi 446747453 162 SIRHTVLYTAANAERFNR 179
Cdd:cd01197  163 NIRHTVIYTASNAARFAN 180
 
Name Accession Description Interval E-value
INT_FimBE_like cd01197
FimB and FimE and related proteins, integrase/recombinases; This CD includes proteins similar ...
 2-179 6.14e-82

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: 240.87  E-value: 6.14e-82
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446747453   2 KRKYLTSDEVYKLLDYIYKNRHNHRDYCMVSMAFIHGLRVSELIELKLTDYESISRKIYIHRLKGGLSTTHPLLDFESKA 81
Cdd:cd01197    3 QRKYLTGKEVQALLQAACRGRTPARDYCLLLLAFRHGFRVSELCDLHLSDVDLESRRLHIRRLKNGFSTTHPLRFDEREA 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446747453  82 LEMWLNERRYLKGNRTPWMFLSRHGGSLSRQRFYQLLKNYGEKAQLSLSIHPHMLRHACGYNLAELGNDTRLIQDYLGHR 161
Cdd:cd01197   83 LEAWLKERANWKGADTDWIFLSRRGGPLSRQQAYRIIRDLGKEAGTVTQTHPHMLRHACGYALADRGADTRLIQDYLGHR 162

                        170
                 ....*....|....*...
gi 446747453 162 SIRHTVLYTAANAERFNR 179
Cdd:cd01197  163 NIRHTVIYTASNAARFAN 180
PRK09870 PRK09870
tyrosine recombinase; Provisional
 2-181 1.43e-70

tyrosine recombinase; Provisional


Pssm-ID: 182125  Cd Length: 200  Bit Score: 212.88  E-value: 1.43e-70
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446747453   2 KRKYLTSDEVYKLLDYIYKNRHNHRDYCMVSMAFIHGLRVSELIELKLTDYESISRKIYIHRLKGGLSTTHPLLDFESKA 81
Cdd:PRK09870   9 KRNFLTHSEIESLLKAANTGPHAARNYCLTLLCFIHGFRASEICRLRISDIDLKAKCIYIHRLKKGFSTTHPLLNKEIQA 88

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446747453  82 LEMWLNERRYLKGNRTPWMFLSRHGGSLSRQRFYQLLKNYGEKAQLSLSIHPHMLRHACGYNLAELGNDTRLIQDYLGHR 161
Cdd:PRK09870  89 LKNWLSIRTSYPHAESEWVFLSRKGNPLSRQQFYHIISTSGGNAGLSLEIHPHMLRHSCGFALANMGIDTRLIQDYLGHR 168

                        170       180
                 ....*....|....*....|
gi 446747453 162 SIRHTVLYTAANAERFNRAW 181
Cdd:PRK09870 169 NIRHTVWYTASNAGRFYGIW 188
Phage_integrase pfam00589
Phage integrase family; Members of this family cleave DNA substrates by a series of staggered ...
 5-174 1.69e-45

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: 147.85  E-value: 1.69e-45
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446747453    5 YLTSDEVYKLLDYIYKNRHNHRDYCMVSMAFIHGLRVSELIELKLTDYESISRKIYIHRLKGGLSTTHPLLDFESKALEM 84
Cdd:pfam00589   1 RLTEDEVERLLDAAETGPLSIRDKALLELLYATGLRISELCSLRWSDIDFENGVIRVHRGKGNKERTVPLSDAALELLKE 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446747453   85 WLnERRYLKGNRTPWMFLSRHGGSLSRQRFYQLLKNYGEKAQLSLSIHPHMLRHACGYNLAELGNDTRLIQDYLGHRSIR 164
Cdd:pfam00589  81 WL-SKRLLEAPKSDYLFASKRGKPLSRQTVRKIFKRAGKEAGLELPLHPHMLRHSFATHLLEAGVDLRVVQKLLGHSSIS 159

                         170
                  ....*....|
gi 446747453  165 HTVLYTAANA 174
Cdd:pfam00589 160 TTQIYTHVAD 169
XerD COG4974
Site-specific recombinase XerD [Replication, recombination and repair];
2-180 1.53e-34

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


Pssm-ID: 443999 [Multi-domain]  Cd Length: 291  Bit Score: 123.57  E-value: 1.53e-34
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446747453   2 KRKYLTSDEVYKLLDYIYKNRHNH-RDYCMVSMAFIHGLRVSELIELKLTDYESISRKIYIHRLKGGLSTTHPLLDFESK 80
Cdd:COG4974  109 LPRVLTEEEIEALLEALDTETPEGlRDRALLLLLYATGLRVSELLGLKWSDIDLDRGTIRVRRGKGGKERTVPLSPEALE 188

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446747453  81 ALEMWLNERRylkGNRTPWMFLSRHGGSLSRQRFYQLLKNYGEKAQLSLSIHPHMLRHACGYNLAELGNDTRLIQDYLGH 160
Cdd:COG4974  189 ALREYLEERR---PRDSDYLFPTRRGRPLSRRAIRKILKRLAKRAGIPKRVTPHSLRHTFATHLLEAGVDLRTVQELLGH 265

                        170       180
                 ....*....|....*....|
gi 446747453 161 RSIRHTVLYTAANAERFNRA 180
Cdd:COG4974  266 SSISTTQIYTHVSDEELREA 285
recomb_XerD TIGR02225
tyrosine recombinase XerD; The phage integrase family describes a number of recombinases with ...
 4-181 4.66e-34

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: 121.92  E-value: 4.66e-34
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446747453    4 KYLTSDEVYKLLDYIYKNRHNH-RDYCMVSMAFIHGLRVSELIELKLTDYESISRKIYIhRLKGGLSTTHPLLDFESKAL 82
Cdd:TIGR02225 103 KVLTVEEVEALLAAPDVDTPLGlRDRAMLELLYATGLRVSELVGLRLEDVNLDEGFVRV-RGKGNKERLVPLGEEAIEAL 181

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446747453   83 EMWLNERRYL----KGNRTPWMFLSRHGGSLSRQRFYQLLKNYGEKAQLSLSIHPHMLRHACGYNLAELGNDTRLIQDYL 158
Cdd:TIGR02225 182 ERYLKEARPLllkkKVKESDALFLNRRGGPLSRQGVWKILKEYAKRAGIEKPISPHTLRHSFATHLLENGADLRVVQELL 261

                         170       180
                  ....*....|....*....|...
gi 446747453  159 GHRSIRHTVLYTAANAERFNRAW 181
Cdd:TIGR02225 262 GHADISTTQIYTHVARERLKEVH 284
 
Name Accession Description Interval E-value
INT_FimBE_like cd01197
FimB and FimE and related proteins, integrase/recombinases; This CD includes proteins similar ...
 2-179 6.14e-82

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: 240.87  E-value: 6.14e-82
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446747453   2 KRKYLTSDEVYKLLDYIYKNRHNHRDYCMVSMAFIHGLRVSELIELKLTDYESISRKIYIHRLKGGLSTTHPLLDFESKA 81
Cdd:cd01197    3 QRKYLTGKEVQALLQAACRGRTPARDYCLLLLAFRHGFRVSELCDLHLSDVDLESRRLHIRRLKNGFSTTHPLRFDEREA 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446747453  82 LEMWLNERRYLKGNRTPWMFLSRHGGSLSRQRFYQLLKNYGEKAQLSLSIHPHMLRHACGYNLAELGNDTRLIQDYLGHR 161
Cdd:cd01197   83 LEAWLKERANWKGADTDWIFLSRRGGPLSRQQAYRIIRDLGKEAGTVTQTHPHMLRHACGYALADRGADTRLIQDYLGHR 162

                        170
                 ....*....|....*...
gi 446747453 162 SIRHTVLYTAANAERFNR 179
Cdd:cd01197  163 NIRHTVIYTASNAARFAN 180
PRK09870 PRK09870
tyrosine recombinase; Provisional
 2-181 1.43e-70

tyrosine recombinase; Provisional


Pssm-ID: 182125  Cd Length: 200  Bit Score: 212.88  E-value: 1.43e-70
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446747453   2 KRKYLTSDEVYKLLDYIYKNRHNHRDYCMVSMAFIHGLRVSELIELKLTDYESISRKIYIHRLKGGLSTTHPLLDFESKA 81
Cdd:PRK09870   9 KRNFLTHSEIESLLKAANTGPHAARNYCLTLLCFIHGFRASEICRLRISDIDLKAKCIYIHRLKKGFSTTHPLLNKEIQA 88

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446747453  82 LEMWLNERRYLKGNRTPWMFLSRHGGSLSRQRFYQLLKNYGEKAQLSLSIHPHMLRHACGYNLAELGNDTRLIQDYLGHR 161
Cdd:PRK09870  89 LKNWLSIRTSYPHAESEWVFLSRKGNPLSRQQFYHIISTSGGNAGLSLEIHPHMLRHSCGFALANMGIDTRLIQDYLGHR 168

                        170       180
                 ....*....|....*....|
gi 446747453 162 SIRHTVLYTAANAERFNRAW 181
Cdd:PRK09870 169 NIRHTVWYTASNAGRFYGIW 188
PRK09871 PRK09871
tyrosine recombinase; Provisional
 2-184 1.65e-61

tyrosine recombinase; Provisional


Pssm-ID: 182126  Cd Length: 198  Bit Score: 189.81  E-value: 1.65e-61
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446747453   2 KRKYLTSDEVYKLLDYIYKNRHNHRDYCMVSMAFIHGLRVSELIELKLTDYESISRKIYIHRLKGGLSTTHPLLDFESKA 81
Cdd:PRK09871   3 KRRYLTGKEVQAMMQAVCYGATGARDYCLILLAYRHGMRISELLDLHYQDLDLNEGRINIRRLKNGFSTVHPLRFDEREA 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446747453  82 LEMWLNERRYLKG-NRTPWMFLSRHGGSLSRQRFYQLLKNYGEKAQLSLSIHPHMLRHACGYNLAELGNDTRLIQDYLGH 160
Cdd:PRK09871  83 VERWTQERANWKGaDRTDAIFISRRGSRLSRQQAYRIIRDAGIEAGTVTQTHPHMLRHACGYELAERGADTRLIQDYLGH 162

                        170       180
                 ....*....|....*....|....
gi 446747453 161 RSIRHTVLYTAANAERFNRAWVKD 184
Cdd:PRK09871 163 RNIRHTVRYTASNAARFAGLWERN 186
Phage_integrase pfam00589
Phage integrase family; Members of this family cleave DNA substrates by a series of staggered ...
 5-174 1.69e-45

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: 147.85  E-value: 1.69e-45
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446747453    5 YLTSDEVYKLLDYIYKNRHNHRDYCMVSMAFIHGLRVSELIELKLTDYESISRKIYIHRLKGGLSTTHPLLDFESKALEM 84
Cdd:pfam00589   1 RLTEDEVERLLDAAETGPLSIRDKALLELLYATGLRISELCSLRWSDIDFENGVIRVHRGKGNKERTVPLSDAALELLKE 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446747453   85 WLnERRYLKGNRTPWMFLSRHGGSLSRQRFYQLLKNYGEKAQLSLSIHPHMLRHACGYNLAELGNDTRLIQDYLGHRSIR 164
Cdd:pfam00589  81 WL-SKRLLEAPKSDYLFASKRGKPLSRQTVRKIFKRAGKEAGLELPLHPHMLRHSFATHLLEAGVDLRVVQKLLGHSSIS 159

                         170
                  ....*....|
gi 446747453  165 HTVLYTAANA 174
Cdd:pfam00589 160 TTQIYTHVAD 169
XerD COG4974
Site-specific recombinase XerD [Replication, recombination and repair];
2-180 1.53e-34

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


Pssm-ID: 443999 [Multi-domain]  Cd Length: 291  Bit Score: 123.57  E-value: 1.53e-34
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446747453   2 KRKYLTSDEVYKLLDYIYKNRHNH-RDYCMVSMAFIHGLRVSELIELKLTDYESISRKIYIHRLKGGLSTTHPLLDFESK 80
Cdd:COG4974  109 LPRVLTEEEIEALLEALDTETPEGlRDRALLLLLYATGLRVSELLGLKWSDIDLDRGTIRVRRGKGGKERTVPLSPEALE 188

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446747453  81 ALEMWLNERRylkGNRTPWMFLSRHGGSLSRQRFYQLLKNYGEKAQLSLSIHPHMLRHACGYNLAELGNDTRLIQDYLGH 160
Cdd:COG4974  189 ALREYLEERR---PRDSDYLFPTRRGRPLSRRAIRKILKRLAKRAGIPKRVTPHSLRHTFATHLLEAGVDLRTVQELLGH 265

                        170       180
                 ....*....|....*....|
gi 446747453 161 RSIRHTVLYTAANAERFNRA 180
Cdd:COG4974  266 SSISTTQIYTHVSDEELREA 285
recomb_XerD TIGR02225
tyrosine recombinase XerD; The phage integrase family describes a number of recombinases with ...
 4-181 4.66e-34

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: 121.92  E-value: 4.66e-34
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446747453    4 KYLTSDEVYKLLDYIYKNRHNH-RDYCMVSMAFIHGLRVSELIELKLTDYESISRKIYIhRLKGGLSTTHPLLDFESKAL 82
Cdd:TIGR02225 103 KVLTVEEVEALLAAPDVDTPLGlRDRAMLELLYATGLRVSELVGLRLEDVNLDEGFVRV-RGKGNKERLVPLGEEAIEAL 181

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446747453   83 EMWLNERRYL----KGNRTPWMFLSRHGGSLSRQRFYQLLKNYGEKAQLSLSIHPHMLRHACGYNLAELGNDTRLIQDYL 158
Cdd:TIGR02225 182 ERYLKEARPLllkkKVKESDALFLNRRGGPLSRQGVWKILKEYAKRAGIEKPISPHTLRHSFATHLLENGADLRVVQELL 261

                         170       180
                  ....*....|....*....|...
gi 446747453  159 GHRSIRHTVLYTAANAERFNRAW 181
Cdd:TIGR02225 262 GHADISTTQIYTHVARERLKEVH 284
XerC COG4973
Site-specific recombinase XerC [Replication, recombination and repair];
3-181 4.60e-32

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


Pssm-ID: 443998 [Multi-domain]  Cd Length: 287  Bit Score: 116.98  E-value: 4.60e-32
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446747453   3 RKYLTSDEVYKLLDYIYKNRHNHRDYCMVSMAFIHGLRVSELIELKLTDYESISRKIYIHRlKGGLSTTHPLLDFESKAL 82
Cdd:COG4973  109 PRALTVDELAQLLDALADDPLAVRDRAIVELLYSTGLRLGELVGLDWEDVDLDAGEVRVRG-KTGKSRTVPLGPKALAAL 187

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446747453  83 EMWLNERRYLKGNRTPWMFLSRHGGSLSRQRFYQLLKNYGEKAQLSLSIHPHMLRHACGYNLAELGNDTRLIQDYLGHRS 162
Cdd:COG4973  188 REWLAVRPELAAPDEGALFPSRRGTRLSPRNVQKRLRRLAKKAGLPKHVHPHDLRHSFATHLLESGGDLRAVQELLGHAS 267

                        170
                 ....*....|....*....
gi 446747453 163 IRHTVLYTAANAERFNRAW 181
Cdd:COG4973  268 ISTTQIYTHLDFQHLAEVY 286
INT_XerDC_C cd00798
XerD and XerC integrases, C-terminal catalytic domains; XerDC-like integrases are involved in ...
 9-176 2.02e-26

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: 99.12  E-value: 2.02e-26
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446747453   9 DEVYKLLDYIYKN-RHNHRDYCMVSMAFIHGLRVSELIELKLTDYESISRKIYIhRLKGGLSTTHPLLDFESKALEMWLN 87
Cdd:cd00798    2 DEVERLLDAPDTDtPLGLRDRAILELLYASGLRVSELVGLDLSDVDLDEGLVRV-TGKGNKERLVPFGSYAVEALEEYLE 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446747453  88 ERRY--LKGNRTPWMFLSRHGGSLSRQRFYQLLKNYGEKAQLSLSIHPHMLRHACGYNLAELGNDTRLIQDYLGHRSIRH 165
Cdd:cd00798   81 ERRPllLKKKPPDALFLNKRGKRLSRRGVWRILKKYAERAGLPKHVSPHTLRHSFATHLLEGGADLRVVQELLGHASLST 160

                        170
                 ....*....|.
gi 446747453 166 TVLYTAANAER 176
Cdd:cd00798  161 TQIYTHVSFER 171
DNA_BRE_C cd00397
DNA breaking-rejoining enzymes, C-terminal catalytic domain; The DNA breaking-rejoining enzyme ...
 10-170 1.73e-25

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: 96.78  E-value: 1.73e-25
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446747453  10 EVYKLLDYIYKNR-HNHRDYCMVSMAFIHGLRVSELIELKLTDYESISRKIYIHRLKGGLSTTH--PLLDFESKALEMWL 86
Cdd:cd00397    1 ELEKLLDAIDEDKkIDLRDRAILLLLLETGLRISELLALKVKDIDLDNGTIRVRGKKTKGGKERtvPLPKELAEELKEYL 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446747453  87 NERR-----YLKGNRTPWMFLSRHGGSLSRQRFYQLLKNYGEKAqlSLSIHPHMLRHACGYNLAELGNDTRLIQDYLGHR 161
Cdd:cd00397   81 KERRdkrgpLLKSLYLNKLFGTKLGERLSRRTLRRIFKKAGIEA--GRKITPHSLRHTFATNLLENGVDIKVVQKLLGHS 158


                 ....*....
gi 446747453 162 SIRHTVLYT 170
Cdd:cd00397  159 SISTTQRYL 167
xerC PRK00236
site-specific tyrosine recombinase XerC; Reviewed
 4-176 9.04e-25

site-specific tyrosine recombinase XerC; Reviewed


Pssm-ID: 234698 [Multi-domain]  Cd Length: 297  Bit Score: 97.92  E-value: 9.04e-25
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446747453   4 KYLTSDEVYKLLDYIYKN-RHNHRDYCMVSMAFIHGLRVSELIELKLTDYESISRKIYIHRlKGGLSTTHPLLDFESKAL 82
Cdd:PRK00236 114 KPLDVDQAKRLLDAIDEDdPLALRDRAILELLYGSGLRLSELVGLDIDDLDLASGTLRVLG-KGNKERTVPLGRAAREAL 192

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446747453  83 EMWLNERRYLKGNRTPwMFLSRHGGSLSRQRFYQLLKNYGEKAQLSLSIHPHMLRHACGYNLAELGNDTRLIQDYLGHRS 162
Cdd:PRK00236 193 EAYLALRPLFLPDDDA-LFLGARGGRLSPRVVQRRVKKLGKKAGLPSHITPHKLRHSFATHLLESGGDLRAVQELLGHAS 271

                        170
                 ....*....|....
gi 446747453 163 IRHTVLYTAANAER 176
Cdd:PRK00236 272 LSTTQIYTHVDFQH 285
INT_RitC_C_like cd01182
C-terminal catalytic domain of recombinase RitC, a component of the recombinase trio; ...
 6-180 2.05e-24

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: 94.27  E-value: 2.05e-24
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446747453   6 LTSDEVYKLLDYIykNRHNH---RDYCMVSMAFIHGLRVSELIELKlTDYESISRKIYIH-RLKGGLSTTHPLLDFESKA 81
Cdd:cd01182    1 LTREEMKALLAAP--DRNTSlgrRDHALLLLLYDTGARVQELADLT-IRDLRLDDPATVRlHGKGRKERTVPLWKETVAA 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446747453  82 LEMWLNERRYL-KGNRTPWMFLSRHGGSLSRQRFYQLLKNYGEKAQ-----LSLSIHPHMLRHACGYNLAELGNDTRLIQ 155
Cdd:cd01182   78 LKAYLQEFHLTpDPKQLFPLFPNRRGQPLTRDGVAYILNKYVALASnrcpsLPKRITPHTLRHTKAMHLLQAGVDLTVIR 157

                        170       180
                 ....*....|....*....|....*
gi 446747453 156 DYLGHRSIRHTVLYTAANAERFNRA 180
Cdd:cd01182  158 DWLGHESVETTQIYAEADLEMKREA 182
xerD PRK00283
tyrosine recombinase;
4-181 3.91e-24

tyrosine recombinase;


Pssm-ID: 234713 [Multi-domain]  Cd Length: 299  Bit Score: 96.03  E-value: 3.91e-24
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446747453   4 KYLTSDEVYKLLDYIYKNRH-NHRDYCMVSMAFIHGLRVSELIELKLTDyesISRKIYIHRL--KGGLSTTHPLLDFESK 80
Cdd:PRK00283 112 KTLSEAQVEALLDAPDIDTPlGLRDRAMLELLYATGLRVSELVGLTLDD---VSLRQGVVRVtgKGNKERLVPLGEEAVY 188

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446747453  81 ALEMWLNERR--YLKGNRTPWMFLSRHGGSLSRQRFYQLLKNYGEKAQLSLS-IHPHMLRHACGYNLAELGNDTRLIQDY 157
Cdd:PRK00283 189 AIERYLERGRpaLLNGRSSDALFPSARGGQLTRQTFWHRIKHYAKRAGIDPKkLSPHVLRHAFATHLLNHGADLRVVQEL 268

                        170       180
                 ....*....|....*....|....
gi 446747453 158 LGHRSIRHTVLYTAANAERFNRAW 181
Cdd:PRK00283 269 LGHSDISTTQIYTHVATERLKELH 292
recomb_XerC TIGR02224
tyrosine recombinase XerC; The phage integrase family describes a number of recombinases with ...
 4-176 4.92e-23

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: 93.06  E-value: 4.92e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446747453    4 KYLTSDEVYKLLDYIYKNRHNH---RDYCMVSMAFIHGLRVSELIELKLTDYESISRKIYIHRlKGGLSTTHPLLDFESK 80
Cdd:TIGR02224 105 KFLSEDEMEALLDAPEEDDEDWlalRDRAILELLYSSGLRVSELVGLDLSDLDLDFGEVRVRG-KGNKERIVPFGPYARD 183

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446747453   81 ALEMWLNERRYLKGNRTPW--MFLSRHGGSLSRQRFYQLLKNYGEKAQLSLSIHPHMLRHACGYNLAELGNDTRLIQDYL 158
Cdd:TIGR02224 184 ALQAYLEARRSPLLASEGQdaLFLNRRGGRLTPRGVQYRLQQLRAKAGLPKHVHPHALRHSFATHLLNNGADLRAVQELL 263

                         170
                  ....*....|....*...
gi 446747453  159 GHRSIRHTVLYTAANAER 176
Cdd:TIGR02224 264 GHASLSTTQIYTHVDFQH 281
INT_RitA_C_like cd01188
C-terminal catalytic domain of recombinase RitA, a component of the recombinase trio; ...
 7-169 6.83e-22

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: 87.68  E-value: 6.83e-22
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446747453   7 TSDEVYKLLDYIYKNRHN-HRDYCMVSMAFIHGLRVSELIELKLTDYESISRKIYIHRLKGGLSTTHPLLDFESKALEMW 85
Cdd:cd01188    1 SPDEVRRLLAAIDRLTPVgLRDYAILLLLARLGLRAGDVAGLRLDDIDWRSGTITVRQKKTGRPVELPLTEPVGEALADY 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446747453  86 LNERRYLkgNRTPWMFLSRH--GGSLSRQR-FYQLLKNYGEKAQLSLSIH-PHMLRHACGYNLAELGNDTRLIQDYLGHR 161
Cdd:cd01188   81 LRDGRPR--TDSREVFLRARapYRPLSSTSqISSIVRRYLRKAGIEPSHRgTHSLRHSLATRMLRAGTSLKVIADLLGHR 158


                 ....*...
gi 446747453 162 SIRHTVLY 169
Cdd:cd01188  159 SIETTAIY 166
INT_Rci_Hp1_C cd00796
Shufflon-specific DNA recombinase Rci and Bacteriophage Hp1_like integrase, C-terminal ...
 4-170 7.20e-21

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


Pssm-ID: 271177 [Multi-domain]  Cd Length: 162  Bit Score: 84.30  E-value: 7.20e-21
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446747453   4 KYLTSDEVYKLLDYIyKNRHNHRDYCMVSMAFIHGLRVSELIELKLTDYESISRKIYIHRLKGGLSTTHPLLDFESKALE 83
Cdd:cd00796    3 RFLTEDEEARLLAAL-EESTNPHLRLIVLLALYTGARRGEILSLRWDDIDLEVGLIVLPETKNGKPRTVPLSDEAIAILK 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446747453  84 mwlnerRYLKGNRTPWMFLSRHGGSLSRQRFYQLLKNYGEKAQLSlSIHPHMLRHACGYNLAELGNDTRLIQDYLGHRSI 163
Cdd:cd00796   82 ------ELKRKRGKDGFFVDGRFFGIPIASLRRAFKKARKRAGLE-DLRFHDLRHTFASRLVQAGVPIKTVAKILGHSSI 154


                 ....*..
gi 446747453 164 RHTVLYT 170
Cdd:cd00796  155 KMTMRYA 161
INT_IntI_C cd01193
Integron integrase and similar protiens, C-terminal catalytic domain; Integron integrases ...
 6-170 1.09e-19

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: 81.55  E-value: 1.09e-19
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446747453   6 LTSDEVYKLLDyiykNRHNHRDYCMVSMAFIHGLRVSELIELKLTDYESISRKIYIHRLKGGLSTTHPLLDFESKALEMW 85
Cdd:cd01193    6 LSPDEVRRILG----ALTELRHRLILSLLYGAGLRISELLRLRVKDIDFERGVIRVRQGKGGKDRVVPLPEKLLEPLRRY 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446747453  86 LNERRYLkgnrtPWMFLS-------------RHGGSLSRQRFYQLLKNYGEKAQLSLSIHPHMLRHACGYNLAELGNDTR 152
Cdd:cd01193   82 LKSARPK-----EELDPAegragvldprtgvERRHHISETTVQRALKKAVEQAGITKRVTPHTLRHSFATHLLEAGTDIR 156

                        170
                 ....*....|....*...
gi 446747453 153 LIQDYLGHRSIRHTVLYT 170
Cdd:cd01193  157 TIQELLGHSDLSTTMIYT 174
INT_C_like_3 cd01192
Uncharacterized site-specific tyrosine recombinase, C-terminal catalytic domain; Tyrosine ...
 13-180 2.55e-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: 271192 [Multi-domain]  Cd Length: 178  Bit Score: 65.01  E-value: 2.55e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446747453  13 KLLDYIYKNRH--NHRDYCMVSMAFIHGLRVSELIELKLTDYeSISRKIYIHRLKGGLSTTHPLLDFESKALEMWLNERr 90
Cdd:cd01192   10 KLIKEIKLYLKkaNPRNYLLFIVGINTGLRISDLLSLKVEDV-TNKDKLSIKEQKTGKQKTFPLNPTLVKALKEYIDDL- 87

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446747453  91 YLKGNRTPWMFLSRH-GGSLSRQRFYQLLKNYGEKAQLSLSIHPHMLRHACGYNLAELGNDTRLIQDYLGHRSIRHTVLY 169
Cdd:cd01192   88 DLKRNDYLFKSLKQGpEKPISRKQAYKILKKAADDLGLNYNIGTHSLRKTFGYHVYKQGKDIELLMKLLNHSSPSITLRY 167

                        170
                 ....*....|.
gi 446747453 170 TAANAERFNRA 180
Cdd:cd01192  168 LGIDQEDVDKA 178
xerS PRK05084
site-specific tyrosine recombinase XerS; Reviewed
 1-170 5.35e-13

site-specific tyrosine recombinase XerS; Reviewed


Pssm-ID: 235339 [Multi-domain]  Cd Length: 357  Bit Score: 66.10  E-value: 5.35e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446747453   1 MKRKYLTSDEVYKLLDYIYKNRHNH--------------RDYCMVSMAFIHGLRVSELIELKLTDYESISRKIYIHRlKG 66
Cdd:PRK05084 157 LKQKLFLGDEDYEFLDFIDNEYEQKlsnralssfkknkeRDLAIIALILGSGLRVSELVNLDLSDLNLKQMTIDVTR-KG 235

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446747453  67 GLSTTHPLLDFESKALEMWLNER--RYLKGNRTPWMFLSRHGGSLSR--QRFYQ-LLKNYGEKAQLSLSihPHMLRHACG 141
Cdd:PRK05084 236 GKRDSVNIAPFALPYLEEYLKIRasRYKAEKQEKALFLTKYRGKPNRisARAIEkMVAKYSEAFGVRLT--PHKLRHTLA 313

                        170       180
                 ....*....|....*....|....*....
gi 446747453 142 YNLAELGNDTRLIQDYLGHRSIRHTVLYT 170
Cdd:PRK05084 314 TRLYDATKDQVLVADQLGHTSTETTDLYT 342
INT_C_like_5 cd01195
Uncharacterized site-specific tyrosine recombinase, C-terminal catalytic domain; Tyrosine ...
 7-169 1.71e-11

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: 59.79  E-value: 1.71e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446747453   7 TSDEVYKLLDYI-YKNRHNHRDYCMVSMAFIHGLRVSELIELKLTDYESISRKIYIHRlKGGLSTTHPLLDFES-KALEM 84
Cdd:cd01195    1 SREEARQRLDAAdRHTAKGKRDEALVRLLLDNALRRSEAVALDVEDLEKEHRRLRILG-KGKKQREVVTLPPTTrEALAA 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446747453  85 WLNERRYLKGnrtP-WMFLSR--HGGSLSRQRFYQLLKNYGEKAQLSLSIHPHMLRHACGYNLAELGND-TRLIQDYLGH 160
Cdd:cd01195   80 WLAARGEAEG---PlFVSLDRasRGRRLSPQAVYRIVRRLAERIGLGKRLSPHGLRHSAITLALDAGAGlIRKVQDFSRH 156


                 ....*....
gi 446747453 161 RSIRHTVLY 169
Cdd:cd01195  157 ADLRTLQVY 165
xerC PRK01287
site-specific tyrosine recombinase XerC; Reviewed
 26-170 4.88e-11

site-specific tyrosine recombinase XerC; Reviewed


Pssm-ID: 234935 [Multi-domain]  Cd Length: 358  Bit Score: 60.53  E-value: 4.88e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446747453  26 RDYCMVSMAFIHGLRVSELIELKLTDYESISRKIYIHRLKGGLSTTHPLldfESKALeMWLNerRYLKGNR--------T 97
Cdd:PRK01287 158 RDRALLELLWSTGIRRGELARLDLYDVDASRGVVTVRQGKGNKDRVVPV---GERAL-AWLQ--RYLQDVRpqlavrpdS 231

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 446747453  98 PWMFLSRHGGSLSRQRFYQLLKNYGEKAQLSLSIHPHMLRHACGYNLAELGNDTRLIQDYLGHRSIRHTVLYT 170
Cdd:PRK01287 232 GALFVAMDGDGLARNTLTNMVGRYIRAAGIEKAGACHLFRHAMATQMLENGADTRHIQAILGHAKLETTQIYT 304
INT_ICEBs1_C_like cd01189
C-terminal catalytic domain of integrases from bacterial phages and conjugate transposons; ...
 9-166 4.88e-11

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: 57.95  E-value: 4.88e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446747453   9 DEVYKLLDYIYKnrHNHRDYCMVSMAFIHGLRVSELIELKLTDYESISRKIYIHRlkgglstthplldfeskALEMWLNE 88
Cdd:cd01189    2 EELKKLLEALKK--RGDRYYLLFLLALLTGLRRGELLALTWSDIDFENGTIRINR-----------------TLVRKKKG 62

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446747453  89 RRYLK------GNRT----PWMF--LSRHggslsrQRFYQLLKNYGEKAqlslsIHPHMLRHACGYNLAELGNDTRLIQD 156
Cdd:cd01189   63 GYVIKppktksSIRTiplpDELIelLKEL------KAFKKLLKKAGLPR-----ITPHDLRHTFASLLLEAGVPLKVIAE 131

                        170
                 ....*....|
gi 446747453 157 YLGHRSIRHT 166
Cdd:cd01189  132 RLGHSDISTT 141
INT_C_like_2 cd01191
Uncharacterized site-specific tyrosine recombinase, C-terminal catalytic domain; Tyrosine ...
 8-169 8.16e-11

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: 58.20  E-value: 8.16e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446747453   8 SDEVYKLLDYIYKNRHNHRDYCMVSMAFIHGLRVSELIELKLTDYESISRKIYIhrlKGG-LSTTHPLLDFESKALEmWL 86
Cdd:cd01191    3 SNADYNFLKKCLKKDGNLEWYFVVRFLAATGARVSELIKIKVEHVELGYFDIYS---KGGkLRRLYIPKKLRNEALE-WL 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446747453  87 NERrylkGNRTPWMFLSRHGGSLSRQRFYQLLKNYGEKAQLSLS-IHPHMLRHACGYNLAELGNDTRLIQDYLGHRSIRH 165
Cdd:cd01191   79 KST----NRKSGYIFLNRFGERITTRGIAQQLKNYARKYGLNPKvVYPHSFRHRFAKNFLEKYNDIALLADLMGHESIET 154


                 ....
gi 446747453 166 TVLY 169
Cdd:cd01191  155 TRIY 158
INTN1_C_like cd01185
Integrase IntN1 of Bacteroides mobilizable transposon NBU1 and similar proteins, C-terminal ...
 9-170 7.43e-10

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: 55.35  E-value: 7.43e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446747453   9 DEVYKLLDYIYKN---RHNHRDYCMVSMaFIhGLRVSELIELKLTDYESISRKIYI--HRLKGGLSTTHPLLDfesKALE 83
Cdd:cd01185    1 EELKRLMALELSDtsrLELVRDMFLFSC-YT-GLRFSDLKNLTWKNIVEASGRTWIryRRKKTGKPVTVPLLP---VARE 75

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446747453  84 mWLNERRYLKGNRTPWMFLSRhggslsrQRFYQLLKNYGEKAQLSLSIHPHMLRHACGYNLAELGNDTRLIQDYLGHRSI 163
Cdd:cd01185   76 -ILEKYKDDRSEGKLFPVLSN-------QKINRYLKEIAKIAGIDKHLTFHVARHTFATLLLLKGVDIETISKLLGHSSI 147


                 ....*..
gi 446747453 164 RHTVLYT 170
Cdd:cd01185  148 KTTQIYA 154
INT_C_like_4 cd01194
Uncharacterized site-specific tyrosine recombinase, C-terminal catalytic domain; Tyrosine ...
 6-169 3.60e-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: 53.53  E-value: 3.60e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446747453   6 LTSDEVYKLLDYIYKNRH--NHRDYCMVSMAFIHGLRVSELIELKLTDYESISRK--IYIHRlKGGLSTTH--PLLDFES 79
Cdd:cd01194    1 LTLEQARQLLASLPIDDSiiGLRDRAIISLMVTEGLRTVEIVRADVGDLRQEGEGtiLYVQG-KGKTSKDDfvYLRPDVL 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446747453  80 KALEMWLNERRYLKgNRTPwMFLS----RHGGSLSRQRFYQLLKNYGEKAQL-SLSIHPHMLRHACGYNLAELGNDTRLI 154
Cdd:cd01194   80 KALQAYLKARGKLD-FEEP-LFTSlsnnSKGQRLTTRSIRRIIKKYLRKAGLdDDRLTAHSLRHTAGTLALKAGKSLREV 157

                        170
                 ....*....|....*
gi 446747453 155 QDYLGHRSIRHTVLY 169
Cdd:cd01194  158 QQLLRHSDPNTTMIY 172
PRK15417 PRK15417
integron integrase;
6-170 5.03e-08

integron integrase;


Pssm-ID: 185315 [Multi-domain]  Cd Length: 337  Bit Score: 51.59  E-value: 5.03e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446747453   6 LTSDEVYKLLDYIyknRHNHRDYcmVSMAFIHGLRVSELIELKLTDYESISRKIYIHRLKGGL--------STTHPLLDF 77
Cdd:PRK15417 117 LTPDEVVRILGFL---EGEHRLF--AQLLYGTGMRISEGLQLRVKDLDFDHGTIIVREGKGSKdralmlpeSLAPSLREQ 191

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446747453  78 ESKALEMWLN---------------ERRYLK-GNRTPWMFL-SRHGGS------------LSRQRFYQLLKNYGEKAQLS 128
Cdd:PRK15417 192 LSRARAWWLKdqaegrsgvalpdalERKYPRaGHSWPWFWVfAQHTHStdprsgvvrrhhMYDQTFQRAFKRAVEQAGIT 271

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|..
gi 446747453 129 LSIHPHMLRHACGYNLAELGNDTRLIQDYLGHRSIRHTVLYT 170
Cdd:PRK15417 272 KPATPHTLRHSFATALLRSGYDIRTVQDLLGHSDVSTTMIYT 313
integrase_gron TIGR02249
integron integrase; Members of this family are integrases associated with integrons (and ...
 6-170 1.30e-07

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: 50.47  E-value: 1.30e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446747453    6 LTSDEVYKLLDYIyKNRHnhrdYCMVSMAFIHGLRVSELIELKLTDYESISRKIYIHRLKGGLSTT--------HPLLDF 77
Cdd:TIGR02249 102 LTREEVRRLLEHL-EGKY----RLIAKLLYGSGMRLMECLRLRIQDIDFDYGEIRIRQGKGGKDRTvtlpkeliPPLREQ 176

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446747453   78 ESKALEMWLN---------------ERRYLKGNRTP---WMFLS-------------RHggSLSRQRFYQLLKNYGEKAQ 126
Cdd:TIGR02249 177 IELARAYHEAdlaegyggvylphalARKYPNAPKEWgwqYLFPShrlsrdpesgvirRH--HINETTIQRAVRRAVERAG 254

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....
gi 446747453  127 LSLSIHPHMLRHACGYNLAELGNDTRLIQDYLGHRSIRHTVLYT 170
Cdd:TIGR02249 255 IEKPVTCHTLRHSFATHLLESGADIRTVQELLGHSDVKTTQIYT 298
INT_tnpB_C_Tn554 cd01187
Putative Transposase B from transposon Tn554, C-terminal catalytic domain; This family ...
 24-169 8.79e-06

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: 43.57  E-value: 8.79e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446747453  24 NHRDYC-MVSMAFIHGLRVSELIELK---LTDYESISR---KIYIHRLKGGLSTTHPLLDFESKALEMW---LNERRYLK 93
Cdd:cd01187   11 LLPQPIpVVQAAVFTGARASELATLKfgcLHAQTSDDGtflYWLKWENKGGKQLDIPISKKVAELIKTInwtLNELSELK 90

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 446747453  94 GnrtpwmflsRHGGSLSRQRFyqllknygekaqlslsiHPHMLRHACGYNLAELGNDTRLIQDYLGHRSIRHTVLY 169
Cdd:cd01187   91 N---------ISDDHGERFRF-----------------HTHRFRHTVATRLANSGMGILVLQQLLGHSSPEMTLRY 140
INT_RitB_C_like cd00797
C-terminal catalytic domain of recombinase RitB, a component of the recombinase trio; ...
 28-175 1.15e-04

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


Pssm-ID: 271178 [Multi-domain]  Cd Length: 198  Bit Score: 41.14  E-value: 1.15e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446747453  28 YCMVSMAFIHGLRVSELIELKLTDYESISRKIYIHRLKGGLSTTHPLLDFESKALEMWLNERRYLKGNR-TPWMFLSRHG 106
Cdd:cd00797   28 ATLFGLLYATGLRVGEALRLRLEDVDLDSGILTIRQTKFGKSRLVPLHPSTVGALRDYLARRDRLLPSPsSSYFFVSQQG 107

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446747453 107 GSLS----RQRFYQLLKNYGEK-AQLSLSIHPHMLRHA--------CGYNLAELGNDTRLIQDYLGHRSIRHTVLYTAAN 173
Cdd:cd00797  108 GRLTgggvYRVFRRLLRRIGLRgAGDGRGPRLHDLRHTfavnrltrWYREGADVERKLPVLSTYLGHVNVTDTYWYLTAT 187


                 ..
gi 446747453 174 AE 175
Cdd:cd00797  188 PE 189
INT_Lambda_C cd00800
C-terminal catalytic domain of Lambda integrase, a tyrosine-based site-specific recombinase; ...
 33-170 1.87e-04

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: 40.02  E-value: 1.87e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446747453  33 MAFIHGLRVSELIELKLTDYESISrkIYIHRLKGGLSTTHPLLDfESKALemwLNERRYLKGNRTPWMFLSRHGGSLSRQ 112
Cdd:cd00800   20 LALLTGQRQGDLLRLKWSDITDGG--LLVEQSKTGKKLLIPWTP-SLRAL---VDRIRALPRKRSEYLINSRKGGPLSYD 93

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 446747453 113 RFYQLLKNYGEKAQLSLSIHP---HMLRHACGYNLAELGNDTRlIQDYLGHRSIRHTVLYT 170
Cdd:cd00800   94 TLKSAWRRARKAAGLKGETEGftfHDLRAKAATDYAEQGGSTD-AQALLGHKSDAMTERYT 153
FimB COG0582
Integrase/recombinase, includes phage integrase [Replication, recombination and repair, ...
 2-162 1.73e-03

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


Pssm-ID: 440347 [Multi-domain]  Cd Length: 391  Bit Score: 38.48  E-value: 1.73e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446747453   2 KRKYLTSDEVYKLLDYIYKNRHNHRDYCMVSMAFIHGLRVSELIELKLTDYESISRKIYIH--RLKGGLSTTHPLLDFes 79
Cdd:COG0582  202 HHPALTPEELPELLRALDAYRGSPVTRLALRLLLLTGVRPGELRGARWSEIDLEAALWTIPaeRMKTRRPHIVPLSRQ-- 279

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446747453  80 kALEMwLNERRYLKGNRtPWMFLSRHGGS--LSRQRFYQLLKNYGEKaqlslSIHPHMLRHACGYNLAELGNDTRLIQDY 157
Cdd:COG0582  280 -ALEI-LKELKPLTGDS-EYVFPSRRGPKkpMSENTLNKALRRMGYG-----RFTPHGFRHTASTLLNEAGFPPDVIERQ 351


                 ....*
gi 446747453 158 LGHRS 162
Cdd:COG0582  352 LAHKD 356
 
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.
Help | Disclaimer | Write to the Help Desk
NCBI | NLM | NIH