NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|490989887|ref|WP_004851620|]
View 

MULTISPECIES: tyrosine-type DNA invertase [Klebsiella]

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 ...
 1-181 1.48e-88

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: 257.05  E-value: 1.48e-88
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490989887   1 MKKRKYLSKKEVQALIAASQQQDGSLRDYCMLLMCFIHGLRVSELRFLKVSDIDLSSQRIAIRRLKNGFSTIHPLQPREQ 80
Cdd:cd01197    1 MKQRKYLTGKEVQALLQAACRGRTPARDYCLLLLAFRHGFRVSELCDLHLSDVDLESRRLHIRRLKNGFSTTHPLRFDER 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490989887  81 LALSQWLVKRTSCLNADLPWLFLSRKGTPLSRQHIHVMMRNYGVQAGIAVPVHPHMLRHACGYALAEEGVDTRLIQDYLG 160
Cdd:cd01197   81 EALEAWLKERANWKGADTDWIFLSRRGGPLSRQQAYRIIRDLGKEAGTVTQTHPHMLRHACGYALADRGADTRLIQDYLG 160

                        170       180
                 ....*....|....*....|.
gi 490989887 161 HRNIQHTVLYTASNPARFSSI 181
Cdd:cd01197  161 HRNIRHTVIYTASNAARFANL 181
 
Name Accession Description Interval E-value
INT_FimBE_like cd01197
FimB and FimE and related proteins, integrase/recombinases; This CD includes proteins similar ...
 1-181 1.48e-88

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: 257.05  E-value: 1.48e-88
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490989887   1 MKKRKYLSKKEVQALIAASQQQDGSLRDYCMLLMCFIHGLRVSELRFLKVSDIDLSSQRIAIRRLKNGFSTIHPLQPREQ 80
Cdd:cd01197    1 MKQRKYLTGKEVQALLQAACRGRTPARDYCLLLLAFRHGFRVSELCDLHLSDVDLESRRLHIRRLKNGFSTTHPLRFDER 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490989887  81 LALSQWLVKRTSCLNADLPWLFLSRKGTPLSRQHIHVMMRNYGVQAGIAVPVHPHMLRHACGYALAEEGVDTRLIQDYLG 160
Cdd:cd01197   81 EALEAWLKERANWKGADTDWIFLSRRGGPLSRQQAYRIIRDLGKEAGTVTQTHPHMLRHACGYALADRGADTRLIQDYLG 160

                        170       180
                 ....*....|....*....|.
gi 490989887 161 HRNIQHTVLYTASNPARFSSI 181
Cdd:cd01197  161 HRNIRHTVIYTASNAARFANL 181
PRK09870 PRK09870
tyrosine recombinase; Provisional
 1-181 6.91e-76

tyrosine recombinase; Provisional


Pssm-ID: 182125  Cd Length: 200  Bit Score: 225.97  E-value: 6.91e-76
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490989887   1 MKKRKYLSKKEVQALIAASQQQDGSLRDYCMLLMCFIHGLRVSELRFLKVSDIDLSSQRIAIRRLKNGFSTIHPLQPREQ 80
Cdd:PRK09870   7 NKKRNFLTHSEIESLLKAANTGPHAARNYCLTLLCFIHGFRASEICRLRISDIDLKAKCIYIHRLKKGFSTTHPLLNKEI 86

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490989887  81 LALSQWLVKRTSCLNADLPWLFLSRKGTPLSRQHIHVMMRNYGVQAGIAVPVHPHMLRHACGYALAEEGVDTRLIQDYLG 160
Cdd:PRK09870  87 QALKNWLSIRTSYPHAESEWVFLSRKGNPLSRQQFYHIISTSGGNAGLSLEIHPHMLRHSCGFALANMGIDTRLIQDYLG 166

                        170       180
                 ....*....|....*....|.
gi 490989887 161 HRNIQHTVLYTASNPARFSSI 181
Cdd:PRK09870 167 HRNIRHTVWYTASNAGRFYGI 187
Phage_integrase pfam00589
Phage integrase family; Members of this family cleave DNA substrates by a series of staggered ...
 6-175 4.89e-49

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: 156.33  E-value: 4.89e-49
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490989887    6 YLSKKEVQALIAASQQQDGSLRDYCMLLMCFIHGLRVSELRFLKVSDIDLSSQRIAIRRLKNGFSTIHPLQPREQLALSQ 85
Cdd:pfam00589   1 RLTEDEVERLLDAAETGPLSIRDKALLELLYATGLRISELCSLRWSDIDFENGVIRVHRGKGNKERTVPLSDAALELLKE 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490989887   86 WLVKRTSCLNADlPWLFLSRKGTPLSRQHIHVMMRNYGVQAGIAVPVHPHMLRHACGYALAEEGVDTRLIQDYLGHRNIQ 165
Cdd:pfam00589  81 WLSKRLLEAPKS-DYLFASKRGKPLSRQTVRKIFKRAGKEAGLELPLHPHMLRHSFATHLLEAGVDLRVVQKLLGHSSIS 159

                         170
                  ....*....|
gi 490989887  166 HTVLYTASNP 175
Cdd:pfam00589 160 TTQIYTHVAD 169
XerD COG4974
Site-specific recombinase XerD [Replication, recombination and repair];
2-177 5.91e-40

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


Pssm-ID: 443999 [Multi-domain]  Cd Length: 291  Bit Score: 137.05  E-value: 5.91e-40
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490989887   2 KKRKYLSKKEVQALIAASQQQD-GSLRDYCMLLMCFIHGLRVSELRFLKVSDIDLSSQRIAIRRLKNGFSTIHPLQPREQ 80
Cdd:COG4974  108 KLPRVLTEEEIEALLEALDTETpEGLRDRALLLLLYATGLRVSELLGLKWSDIDLDRGTIRVRRGKGGKERTVPLSPEAL 187

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490989887  81 LALSQWLVKRTSclnADLPWLFLSRKGTPLSRQHIHVMMRNYGVQAGIAVPVHPHMLRHACGYALAEEGVDTRLIQDYLG 160
Cdd:COG4974  188 EALREYLEERRP---RDSDYLFPTRRGRPLSRRAIRKILKRLAKRAGIPKRVTPHSLRHTFATHLLEAGVDLRTVQELLG 264

                        170
                 ....*....|....*..
gi 490989887 161 HRNIQHTVLYTASNPAR 177
Cdd:COG4974  265 HSSISTTQIYTHVSDEE 281
recomb_XerD TIGR02225
tyrosine recombinase XerD; The phage integrase family describes a number of recombinases with ...
 5-171 1.09e-33

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: 120.76  E-value: 1.09e-33
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490989887    5 KYLSKKEVQALIAASQQQD-GSLRDYCMLLMCFIHGLRVSELRFLKVSDIDLSsQRIAIRRLKNGFSTIHPLQPREQLAL 83
Cdd:TIGR02225 103 KVLTVEEVEALLAAPDVDTpLGLRDRAMLELLYATGLRVSELVGLRLEDVNLD-EGFVRVRGKGNKERLVPLGEEAIEAL 181

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490989887   84 SQWLVKRTSCLNADL----PWLFLSRKGTPLSRQHIHVMMRNYGVQAGIAVPVHPHMLRHACGYALAEEGVDTRLIQDYL 159
Cdd:TIGR02225 182 ERYLKEARPLLLKKKvkesDALFLNRRGGPLSRQGVWKILKEYAKRAGIEKPISPHTLRHSFATHLLENGADLRVVQELL 261

                         170
                  ....*....|..
gi 490989887  160 GHRNIQHTVLYT 171
Cdd:TIGR02225 262 GHADISTTQIYT 273
 
Name Accession Description Interval E-value
INT_FimBE_like cd01197
FimB and FimE and related proteins, integrase/recombinases; This CD includes proteins similar ...
 1-181 1.48e-88

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: 257.05  E-value: 1.48e-88
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490989887   1 MKKRKYLSKKEVQALIAASQQQDGSLRDYCMLLMCFIHGLRVSELRFLKVSDIDLSSQRIAIRRLKNGFSTIHPLQPREQ 80
Cdd:cd01197    1 MKQRKYLTGKEVQALLQAACRGRTPARDYCLLLLAFRHGFRVSELCDLHLSDVDLESRRLHIRRLKNGFSTTHPLRFDER 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490989887  81 LALSQWLVKRTSCLNADLPWLFLSRKGTPLSRQHIHVMMRNYGVQAGIAVPVHPHMLRHACGYALAEEGVDTRLIQDYLG 160
Cdd:cd01197   81 EALEAWLKERANWKGADTDWIFLSRRGGPLSRQQAYRIIRDLGKEAGTVTQTHPHMLRHACGYALADRGADTRLIQDYLG 160

                        170       180
                 ....*....|....*....|.
gi 490989887 161 HRNIQHTVLYTASNPARFSSI 181
Cdd:cd01197  161 HRNIRHTVIYTASNAARFANL 181
PRK09870 PRK09870
tyrosine recombinase; Provisional
 1-181 6.91e-76

tyrosine recombinase; Provisional


Pssm-ID: 182125  Cd Length: 200  Bit Score: 225.97  E-value: 6.91e-76
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490989887   1 MKKRKYLSKKEVQALIAASQQQDGSLRDYCMLLMCFIHGLRVSELRFLKVSDIDLSSQRIAIRRLKNGFSTIHPLQPREQ 80
Cdd:PRK09870   7 NKKRNFLTHSEIESLLKAANTGPHAARNYCLTLLCFIHGFRASEICRLRISDIDLKAKCIYIHRLKKGFSTTHPLLNKEI 86

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490989887  81 LALSQWLVKRTSCLNADLPWLFLSRKGTPLSRQHIHVMMRNYGVQAGIAVPVHPHMLRHACGYALAEEGVDTRLIQDYLG 160
Cdd:PRK09870  87 QALKNWLSIRTSYPHAESEWVFLSRKGNPLSRQQFYHIISTSGGNAGLSLEIHPHMLRHSCGFALANMGIDTRLIQDYLG 166

                        170       180
                 ....*....|....*....|.
gi 490989887 161 HRNIQHTVLYTASNPARFSSI 181
Cdd:PRK09870 167 HRNIRHTVWYTASNAGRFYGI 187
PRK09871 PRK09871
tyrosine recombinase; Provisional
 1-181 2.75e-75

tyrosine recombinase; Provisional


Pssm-ID: 182126  Cd Length: 198  Bit Score: 224.09  E-value: 2.75e-75
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490989887   1 MKKRKYLSKKEVQALIAASQQQDGSLRDYCMLLMCFIHGLRVSELRFLKVSDIDLSSQRIAIRRLKNGFSTIHPLQPREQ 80
Cdd:PRK09871   1 MSKRRYLTGKEVQAMMQAVCYGATGARDYCLILLAYRHGMRISELLDLHYQDLDLNEGRINIRRLKNGFSTVHPLRFDER 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490989887  81 LALSQWLVKRTSCLNAD-LPWLFLSRKGTPLSRQHIHVMMRNYGVQAGIAVPVHPHMLRHACGYALAEEGVDTRLIQDYL 159
Cdd:PRK09871  81 EAVERWTQERANWKGADrTDAIFISRRGSRLSRQQAYRIIRDAGIEAGTVTQTHPHMLRHACGYELAERGADTRLIQDYL 160

                        170       180
                 ....*....|....*....|..
gi 490989887 160 GHRNIQHTVLYTASNPARFSSI 181
Cdd:PRK09871 161 GHRNIRHTVRYTASNAARFAGL 182
Phage_integrase pfam00589
Phage integrase family; Members of this family cleave DNA substrates by a series of staggered ...
 6-175 4.89e-49

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: 156.33  E-value: 4.89e-49
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490989887    6 YLSKKEVQALIAASQQQDGSLRDYCMLLMCFIHGLRVSELRFLKVSDIDLSSQRIAIRRLKNGFSTIHPLQPREQLALSQ 85
Cdd:pfam00589   1 RLTEDEVERLLDAAETGPLSIRDKALLELLYATGLRISELCSLRWSDIDFENGVIRVHRGKGNKERTVPLSDAALELLKE 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490989887   86 WLVKRTSCLNADlPWLFLSRKGTPLSRQHIHVMMRNYGVQAGIAVPVHPHMLRHACGYALAEEGVDTRLIQDYLGHRNIQ 165
Cdd:pfam00589  81 WLSKRLLEAPKS-DYLFASKRGKPLSRQTVRKIFKRAGKEAGLELPLHPHMLRHSFATHLLEAGVDLRVVQKLLGHSSIS 159

                         170
                  ....*....|
gi 490989887  166 HTVLYTASNP 175
Cdd:pfam00589 160 TTQIYTHVAD 169
XerD COG4974
Site-specific recombinase XerD [Replication, recombination and repair];
2-177 5.91e-40

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


Pssm-ID: 443999 [Multi-domain]  Cd Length: 291  Bit Score: 137.05  E-value: 5.91e-40
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490989887   2 KKRKYLSKKEVQALIAASQQQD-GSLRDYCMLLMCFIHGLRVSELRFLKVSDIDLSSQRIAIRRLKNGFSTIHPLQPREQ 80
Cdd:COG4974  108 KLPRVLTEEEIEALLEALDTETpEGLRDRALLLLLYATGLRVSELLGLKWSDIDLDRGTIRVRRGKGGKERTVPLSPEAL 187

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490989887  81 LALSQWLVKRTSclnADLPWLFLSRKGTPLSRQHIHVMMRNYGVQAGIAVPVHPHMLRHACGYALAEEGVDTRLIQDYLG 160
Cdd:COG4974  188 EALREYLEERRP---RDSDYLFPTRRGRPLSRRAIRKILKRLAKRAGIPKRVTPHSLRHTFATHLLEAGVDLRTVQELLG 264

                        170
                 ....*....|....*..
gi 490989887 161 HRNIQHTVLYTASNPAR 177
Cdd:COG4974  265 HSSISTTQIYTHVSDEE 281
XerC COG4973
Site-specific recombinase XerC [Replication, recombination and repair];
2-171 5.77e-36

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


Pssm-ID: 443998 [Multi-domain]  Cd Length: 287  Bit Score: 126.61  E-value: 5.77e-36
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490989887   2 KKRKYLSKKEVQALIAASQQQDGSLRDYCMLLMCFIHGLRVSELRFLKVSDIDLSSQRIAIRRlKNGFSTIHPLQPREQL 81
Cdd:COG4973  107 KLPRALTVDELAQLLDALADDPLAVRDRAIVELLYSTGLRLGELVGLDWEDVDLDAGEVRVRG-KTGKSRTVPLGPKALA 185

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490989887  82 ALSQWLVKRTSCLNADLPWLFLSRKGTPLSRQHIHVMMRNYGVQAGIAVPVHPHMLRHACGYALAEEGVDTRLIQDYLGH 161
Cdd:COG4973  186 ALREWLAVRPELAAPDEGALFPSRRGTRLSPRNVQKRLRRLAKKAGLPKHVHPHDLRHSFATHLLESGGDLRAVQELLGH 265

                        170
                 ....*....|
gi 490989887 162 RNIQHTVLYT 171
Cdd:COG4973  266 ASISTTQIYT 275
recomb_XerD TIGR02225
tyrosine recombinase XerD; The phage integrase family describes a number of recombinases with ...
 5-171 1.09e-33

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: 120.76  E-value: 1.09e-33
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490989887    5 KYLSKKEVQALIAASQQQD-GSLRDYCMLLMCFIHGLRVSELRFLKVSDIDLSsQRIAIRRLKNGFSTIHPLQPREQLAL 83
Cdd:TIGR02225 103 KVLTVEEVEALLAAPDVDTpLGLRDRAMLELLYATGLRVSELVGLRLEDVNLD-EGFVRVRGKGNKERLVPLGEEAIEAL 181

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490989887   84 SQWLVKRTSCLNADL----PWLFLSRKGTPLSRQHIHVMMRNYGVQAGIAVPVHPHMLRHACGYALAEEGVDTRLIQDYL 159
Cdd:TIGR02225 182 ERYLKEARPLLLKKKvkesDALFLNRRGGPLSRQGVWKILKEYAKRAGIEKPISPHTLRHSFATHLLENGADLRVVQELL 261

                         170
                  ....*....|..
gi 490989887  160 GHRNIQHTVLYT 171
Cdd:TIGR02225 262 GHADISTTQIYT 273
DNA_BRE_C cd00397
DNA breaking-rejoining enzymes, C-terminal catalytic domain; The DNA breaking-rejoining enzyme ...
 11-171 1.63e-28

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: 104.10  E-value: 1.63e-28
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490989887  11 EVQALIAASQQQDG-SLRDYCMLLMCFIHGLRVSELRFLKVSDIDLSSQRIAIRRLKNGFSTIH--PLQPREQLALSQWL 87
Cdd:cd00397    1 ELEKLLDAIDEDKKiDLRDRAILLLLLETGLRISELLALKVKDIDLDNGTIRVRGKKTKGGKERtvPLPKELAEELKEYL 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490989887  88 -VKRTSCLNADLPWLFLSRKGTPLSRQHIHVMMRNYGVQAGIA--VPVHPHMLRHACGYALAEEGVDTRLIQDYLGHRNI 164
Cdd:cd00397   81 kERRDKRGPLLKSLYLNKLFGTKLGERLSRRTLRRIFKKAGIEagRKITPHSLRHTFATNLLENGVDIKVVQKLLGHSSI 160


                 ....*..
gi 490989887 165 QHTVLYT 171
Cdd:cd00397  161 STTQRYL 167
INT_XerDC_C cd00798
XerD and XerC integrases, C-terminal catalytic domains; XerDC-like integrases are involved in ...
 11-171 4.89e-28

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: 102.97  E-value: 4.89e-28
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490989887  11 EVQALI-AASQQQDGSLRDYCML-LMcFIHGLRVSELRFLKVSDIDLSSQRIAIRRlKNGFSTIHPLQPREQLALSQWLV 88
Cdd:cd00798    3 EVERLLdAPDTDTPLGLRDRAILeLL-YASGLRVSELVGLDLSDVDLDEGLVRVTG-KGNKERLVPFGSYAVEALEEYLE 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490989887  89 KRTSCLNADLPW--LFLSRKGTPLSRQHIHVMMRNYGVQAGIAVPVHPHMLRHACGYALAEEGVDTRLIQDYLGHRNIQH 166
Cdd:cd00798   81 ERRPLLLKKKPPdaLFLNKRGKRLSRRGVWRILKKYAERAGLPKHVSPHTLRHSFATHLLEGGADLRVVQELLGHASLST 160


                 ....*
gi 490989887 167 TVLYT 171
Cdd:cd00798  161 TQIYT 165
INT_IntI_C cd01193
Integron integrase and similar protiens, C-terminal catalytic domain; Integron integrases ...
 7-171 3.14e-27

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: 100.81  E-value: 3.14e-27
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490989887   7 LSKKEVQALIAASQqqdgSLRDYCMLLMCFIHGLRVSELRFLKVSDIDLSSQRIAIRRLKNGFSTIHPLQPREQLALSQW 86
Cdd:cd01193    6 LSPDEVRRILGALT----ELRHRLILSLLYGAGLRISELLRLRVKDIDFERGVIRVRQGKGGKDRVVPLPEKLLEPLRRY 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490989887  87 LvkrtsCLNADLPWLFLS-------------RKGTPLSRQHIHVMMRNYGVQAGIAVPVHPHMLRHACGYALAEEGVDTR 153
Cdd:cd01193   82 L-----KSARPKEELDPAegragvldprtgvERRHHISETTVQRALKKAVEQAGITKRVTPHTLRHSFATHLLEAGTDIR 156

                        170
                 ....*....|....*...
gi 490989887 154 LIQDYLGHRNIQHTVLYT 171
Cdd:cd01193  157 TIQELLGHSDLSTTMIYT 174
recomb_XerC TIGR02224
tyrosine recombinase XerC; The phage integrase family describes a number of recombinases with ...
 5-171 1.07e-26

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: 102.30  E-value: 1.07e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490989887    5 KYLSKKEVQALIAASQQQDGS---LRDYCMLLMCFIHGLRVSELRFLKVSDIDLSSQRIAIRRlKNGFSTIHPLQPREQL 81
Cdd:TIGR02224 105 KFLSEDEMEALLDAPEEDDEDwlaLRDRAILELLYSSGLRVSELVGLDLSDLDLDFGEVRVRG-KGNKERIVPFGPYARD 183

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490989887   82 ALSQWLVKRTSCL--NADLPWLFLSRKGTPLSRQHIHVMMRNYGVQAGIAVPVHPHMLRHACGYALAEEGVDTRLIQDYL 159
Cdd:TIGR02224 184 ALQAYLEARRSPLlaSEGQDALFLNRRGGRLTPRGVQYRLQQLRAKAGLPKHVHPHALRHSFATHLLNNGADLRAVQELL 263

                         170
                  ....*....|..
gi 490989887  160 GHRNIQHTVLYT 171
Cdd:TIGR02224 264 GHASLSTTQIYT 275
INT_RitA_C_like cd01188
C-terminal catalytic domain of recombinase RitA, a component of the recombinase trio; ...
 8-170 9.06e-26

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: 97.31  E-value: 9.06e-26
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490989887   8 SKKEVQALIAASQQQD-GSLRDYCMLLMCFIHGLRVSELRFLKVSDIDLSSQRIAIRRLKNGFSTIHPLQPREQLALSQW 86
Cdd:cd01188    1 SPDEVRRLLAAIDRLTpVGLRDYAILLLLARLGLRAGDVAGLRLDDIDWRSGTITVRQKKTGRPVELPLTEPVGEALADY 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490989887  87 L-VKRTSClnaDLPWLFLSRK---GTPLSRQHIHVMMRNYGVQAGIAVPVH-PHMLRHACGYALAEEGVDTRLIQDYLGH 161
Cdd:cd01188   81 LrDGRPRT---DSREVFLRARapyRPLSSTSQISSIVRRYLRKAGIEPSHRgTHSLRHSLATRMLRAGTSLKVIADLLGH 157


                 ....*....
gi 490989887 162 RNIQHTVLY 170
Cdd:cd01188  158 RSIETTAIY 166
xerC PRK00236
site-specific tyrosine recombinase XerC; Reviewed
 5-172 1.00e-25

site-specific tyrosine recombinase XerC; Reviewed


Pssm-ID: 234698 [Multi-domain]  Cd Length: 297  Bit Score: 99.84  E-value: 1.00e-25
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490989887   5 KYLSKKEVQALIAASQQQD-GSLRDYCMLLMCFIHGLRVSELRFLKVSDIDLSSQRIAI-------RRLkngfstihPLQ 76
Cdd:PRK00236 114 KPLDVDQAKRLLDAIDEDDpLALRDRAILELLYGSGLRLSELVGLDIDDLDLASGTLRVlgkgnkeRTV--------PLG 185

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490989887  77 PREQLALSQWLVKRTSCLNADLPwLFLSRKGTPLSRQHIHVMMRNYGVQAGIAVPVHPHMLRHACGYALAEEGVDTRLIQ 156
Cdd:PRK00236 186 RAAREALEAYLALRPLFLPDDDA-LFLGARGGRLSPRVVQRRVKKLGKKAGLPSHITPHKLRHSFATHLLESGGDLRAVQ 264

                        170
                 ....*....|....*.
gi 490989887 157 DYLGHRNIQHTVLYTA 172
Cdd:PRK00236 265 ELLGHASLSTTQIYTH 280
xerD PRK00283
tyrosine recombinase;
5-171 4.77e-24

tyrosine recombinase;


Pssm-ID: 234713 [Multi-domain]  Cd Length: 299  Bit Score: 95.64  E-value: 4.77e-24
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490989887   5 KYLSKKEVQALIAASQQQDG-SLRDYCMLLMCFIHGLRVSELRFLKVSDIDLsSQRIAIRRLKNGFSTIHPLQPREQLAL 83
Cdd:PRK00283 112 KTLSEAQVEALLDAPDIDTPlGLRDRAMLELLYATGLRVSELVGLTLDDVSL-RQGVVRVTGKGNKERLVPLGEEAVYAI 190

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490989887  84 SQWLVKRTSCL--NADLPWLFLSRKGTPLSRQHIHVMMRNYGVQAGIAV-PVHPHMLRHAcgYA--LAEEGVDTRLIQDY 158
Cdd:PRK00283 191 ERYLERGRPALlnGRSSDALFPSARGGQLTRQTFWHRIKHYAKRAGIDPkKLSPHVLRHA--FAthLLNHGADLRVVQEL 268

                        170
                 ....*....|...
gi 490989887 159 LGHRNIQHTVLYT 171
Cdd:PRK00283 269 LGHSDISTTQIYT 281
INT_RitC_C_like cd01182
C-terminal catalytic domain of recombinase RitC, a component of the recombinase trio; ...
 7-171 7.09e-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: 92.73  E-value: 7.09e-24
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490989887   7 LSKKEVQALIAA-SQQQDGSLRDYCMLLMCFIHGLRVSELRFLKVSDIDLSSQR-IAIRRLKNGFSTIhPLQPREQLALS 84
Cdd:cd01182    1 LTREEMKALLAApDRNTSLGRRDHALLLLLYDTGARVQELADLTIRDLRLDDPAtVRLHGKGRKERTV-PLWKETVAALK 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490989887  85 QWLVKRTSCLN-ADLPWLFLSRKGTPLSRQHIHVMMRNYGVQA-----GIAVPVHPHMLRHACGYALAEEGVDTRLIQDY 158
Cdd:cd01182   80 AYLQEFHLTPDpKQLFPLFPNRRGQPLTRDGVAYILNKYVALAsnrcpSLPKRITPHTLRHTKAMHLLQAGVDLTVIRDW 159

                        170
                 ....*....|...
gi 490989887 159 LGHRNIQHTVLYT 171
Cdd:cd01182  160 LGHESVETTQIYA 172
INT_Rci_Hp1_C cd00796
Shufflon-specific DNA recombinase Rci and Bacteriophage Hp1_like integrase, C-terminal ...
 5-171 7.37e-22

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: 86.61  E-value: 7.37e-22
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490989887   5 KYLSKKEVQALIAASQQqDGSLRDYCMLLMCFIHGLRVSELRFLKVSDIDLSSQRIAIRRLKNGFSTIHPLQPREQLALS 84
Cdd:cd00796    3 RFLTEDEEARLLAALEE-STNPHLRLIVLLALYTGARRGEILSLRWDDIDLEVGLIVLPETKNGKPRTVPLSDEAIAILK 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490989887  85 QWLVKRtsclNADLPWLFLSRKGTPLS--RQHIHVMMRNYGVQAgiavpVHPHMLRHACGYALAEEGVDTRLIQDYLGHR 162
Cdd:cd00796   82 ELKRKR----GKDGFFVDGRFFGIPIAslRRAFKKARKRAGLED-----LRFHDLRHTFASRLVQAGVPIKTVAKILGHS 152


                 ....*....
gi 490989887 163 NIQHTVLYT 171
Cdd:cd00796  153 SIKMTMRYA 161
xerC PRK01287
site-specific tyrosine recombinase XerC; Reviewed
 4-171 6.02e-19

site-specific tyrosine recombinase XerC; Reviewed


Pssm-ID: 234935 [Multi-domain]  Cd Length: 358  Bit Score: 82.49  E-value: 6.02e-19
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490989887   4 RKYLSKKEVQALIAASQQQD-GSLRDYCMLLMCFIHGLRVSELRFLKVSDIDLSSQRIAIRRLKNGFSTIHPLQPREQLA 82
Cdd:PRK01287 134 RQILSEAETEQVLASPDLTTlQGLRDRALLELLWSTGIRRGELARLDLYDVDASRGVVTVRQGKGNKDRVVPVGERALAW 213

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490989887  83 LSQWL--VKRTSCLNADLPWLFLSRKGTPLSRQHIHVMMRNYGVQAGIAVPVHPHMLRHACGYALAEEGVDTRLIQDYLG 160
Cdd:PRK01287 214 LQRYLqdVRPQLAVRPDSGALFVAMDGDGLARNTLTNMVGRYIRAAGIEKAGACHLFRHAMATQMLENGADTRHIQAILG 293

                        170
                 ....*....|.
gi 490989887 161 HRNIQHTVLYT 171
Cdd:PRK01287 294 HAKLETTQIYT 304
INT_RitB_C_like cd00797
C-terminal catalytic domain of recombinase RitB, a component of the recombinase trio; ...
 7-175 6.38e-19

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: 80.04  E-value: 6.38e-19
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490989887   7 LSKKEVQALIAASQQ--QDGSLRD---YCMLLMCFIHGLRVSELRFLKVSDIDLSSQRIAIRRLKNGFSTIHPLQPREQL 81
Cdd:cd00797    1 YTDAEIRRLLAAADQlpPESPLRPltyATLFGLLYATGLRVGEALRLRLEDVDLDSGILTIRQTKFGKSRLVPLHPSTVG 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490989887  82 ALSQWL-VKRTSCLNADLPWLFLSRKGTPLSRQHIHVMMRNYGVQAGIAVPV-----HPHMLRHACGY----ALAEEGVD 151
Cdd:cd00797   81 ALRDYLaRRDRLLPSPSSSYFFVSQQGGRLTGGGVYRVFRRLLRRIGLRGAGdgrgpRLHDLRHTFAVnrltRWYREGAD 160

                        170       180
                 ....*....|....*....|....*...
gi 490989887 152 TR----LIQDYLGHRNIQHTVLYTASNP 175
Cdd:cd00797  161 VErklpVLSTYLGHVNVTDTYWYLTATP 188
INT_ICEBs1_C_like cd01189
C-terminal catalytic domain of integrases from bacterial phages and conjugate transposons; ...
 9-167 3.53e-14

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: 66.04  E-value: 3.53e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490989887   9 KKEVQALIAASQQQDgsLRDYCMLLMCFIHGLRVSELRFLKVSDIDLSSQRIAIRR----LKNGFSTIHPLQPREQ---L 81
Cdd:cd01189    1 PEELKKLLEALKKRG--DRYYLLFLLALLTGLRRGELLALTWSDIDFENGTIRINRtlvrKKKGGYVIKPPKTKSSirtI 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490989887  82 ALSQWLVKrtsclnadlpwLFLSRKgtplsrqHIHVMMRNYGVQagiavPVHPHMLRHACGYALAEEGVDTRLIQDYLGH 161
Cdd:cd01189   79 PLPDELIE-----------LLKELK-------AFKKLLKKAGLP-----RITPHDLRHTFASLLLEAGVPLKVIAERLGH 135


                 ....*.
gi 490989887 162 RNIQHT 167
Cdd:cd01189  136 SDISTT 141
FimB COG0582
Integrase/recombinase, includes phage integrase [Replication, recombination and repair, ...
 2-163 4.66e-13

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


Pssm-ID: 440347 [Multi-domain]  Cd Length: 391  Bit Score: 66.22  E-value: 4.66e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490989887   2 KKRKYLSKKEVQALIAASQQQDGSLRDYCMLLMCFIHGLRVSELRFLKVSDIDLSSQRIAIR--RLKNGFSTIHPLqPRE 79
Cdd:COG0582  201 KHHPALTPEELPELLRALDAYRGSPVTRLALRLLLLTGVRPGELRGARWSEIDLEAALWTIPaeRMKTRRPHIVPL-SRQ 279

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490989887  80 QLALSQWLVKRTSclnaDLPWLFLSRKG--TPLSRQHIHVMMRNYGVQagiavPVHPHMLRHACGYALAEEGVDTRLIQD 157
Cdd:COG0582  280 ALEILKELKPLTG----DSEYVFPSRRGpkKPMSENTLNKALRRMGYG-----RFTPHGFRHTASTLLNEAGFPPDVIER 350


                 ....*.
gi 490989887 158 YLGHRN 163
Cdd:COG0582  351 QLAHKD 356
INT_C_like_4 cd01194
Uncharacterized site-specific tyrosine recombinase, C-terminal catalytic domain; Tyrosine ...
 7-170 1.07e-12

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: 62.78  E-value: 1.07e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490989887   7 LSKKEVQALIAASQQQDG--SLRDYCMLLMCFIHGLRVSELRFLKVSDIDLSSQRIAI------RRLKNGFStihPLQPR 78
Cdd:cd01194    1 LTLEQARQLLASLPIDDSiiGLRDRAIISLMVTEGLRTVEIVRADVGDLRQEGEGTILyvqgkgKTSKDDFV---YLRPD 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490989887  79 EQLALSQWLVKRtSCLNADLPwLFLS----RKGTPLSRQHIHVMMRNYGVQAGI-AVPVHPHMLRHACGYALAEEGVDTR 153
Cdd:cd01194   78 VLKALQAYLKAR-GKLDFEEP-LFTSlsnnSKGQRLTTRSIRRIIKKYLRKAGLdDDRLTAHSLRHTAGTLALKAGKSLR 155

                        170
                 ....*....|....*..
gi 490989887 154 LIQDYLGHRNIQHTVLY 170
Cdd:cd01194  156 EVQQLLRHSDPNTTMIY 172
INT_C_like_3 cd01192
Uncharacterized site-specific tyrosine recombinase, C-terminal catalytic domain; Tyrosine ...
 25-170 1.83e-12

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: 62.31  E-value: 1.83e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490989887  25 SLRDYCMLLMCFIHGLRVSELRFLKVSDIDLSsQRIAIRRLKNGFSTIHPLQPREQLALSQWLVKRTSCLNADLPWLFLS 104
Cdd:cd01192   23 NPRNYLLFIVGINTGLRISDLLSLKVEDVTNK-DKLSIKEQKTGKQKTFPLNPTLVKALKEYIDDLDLKRNDYLFKSLKQ 101

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 490989887 105 RKGTPLSRQHIHVMMRNYGVQAGIAVPVHPHMLRHACGYALAEEGVDTRLIQDYLGHRNIQHTVLY 170
Cdd:cd01192  102 GPEKPISRKQAYKILKKAADDLGLNYNIGTHSLRKTFGYHVYKQGKDIELLMKLLNHSSPSITLRY 167
INTN1_C_like cd01185
Integrase IntN1 of Bacteroides mobilizable transposon NBU1 and similar proteins, C-terminal ...
 11-171 1.09e-11

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: 59.97  E-value: 1.09e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490989887  11 EVQALIAASQQQDGSLRDY--CMLLMCFIhGLRVSELRFLKVSDIDLSSQR--IAIRRLKNGFSTIHPLQPreqlALSQW 86
Cdd:cd01185    2 ELKRLMALELSDTSRLELVrdMFLFSCYT-GLRFSDLKNLTWKNIVEASGRtwIRYRRKKTGKPVTVPLLP----VAREI 76

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490989887  87 LVKRTscLNADLPWLFLsrkgtPLSRQHIHVMMRNYGVQAGIAVPVHPHMLRHACGYALAEEGVDTRLIQDYLGHRNIQH 166
Cdd:cd01185   77 LEKYK--DDRSEGKLFP-----VLSNQKINRYLKEIAKIAGIDKHLTFHVARHTFATLLLLKGVDIETISKLLGHSSIKT 149


                 ....*
gi 490989887 167 TVLYT 171
Cdd:cd01185  150 TQIYA 154
integrase_gron TIGR02249
integron integrase; Members of this family are integrases associated with integrons (and ...
 7-171 2.25e-11

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


Pssm-ID: 131303 [Multi-domain]  Cd Length: 315  Bit Score: 60.87  E-value: 2.25e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490989887    7 LSKKEVQALIaasQQQDGSLRDYCMLLmcFIHGLRVSELRFLKVSDIDLSSQRIAIRRLKNG--------FSTIHPLQPR 78
Cdd:TIGR02249 102 LTREEVRRLL---EHLEGKYRLIAKLL--YGSGMRLMECLRLRIQDIDFDYGEIRIRQGKGGkdrtvtlpKELIPPLREQ 176

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490989887   79 EQLALSQW----------------LVKRTSCLNADLPWLFL---------SRKGTpLSRQHIH-----VMMRNYGVQAGI 128
Cdd:TIGR02249 177 IELARAYHeadlaegyggvylphaLARKYPNAPKEWGWQYLfpshrlsrdPESGV-IRRHHINettiqRAVRRAVERAGI 255

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|...
gi 490989887  129 AVPVHPHMLRHACGYALAEEGVDTRLIQDYLGHRNIQHTVLYT 171
Cdd:TIGR02249 256 EKPVTCHTLRHSFATHLLESGADIRTVQELLGHSDVKTTQIYT 298
INT_C_like_5 cd01195
Uncharacterized site-specific tyrosine recombinase, C-terminal catalytic domain; Tyrosine ...
 13-170 6.27e-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: 58.25  E-value: 6.27e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490989887  13 QALIAASQQQDGSLRDYCMLLMCFIHGLRVSELRFLKVSDIDLSSQRIAIRRLKNGFSTIHPLQPREQLALSQWLVKRTS 92
Cdd:cd01195    7 QRLDAADRHTAKGKRDEALVRLLLDNALRRSEAVALDVEDLEKEHRRLRILGKGKKQREVVTLPPTTREALAAWLAARGE 86

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490989887  93 clnADLPwLFLS----RKGTPLSRQHIHVMMRNYGVQAGIAVPVHPHMLRH-ACGYALAEEGVDTRLIQDYLGHRNIQHT 167
Cdd:cd01195   87 ---AEGP-LFVSldraSRGRRLSPQAVYRIVRRLAERIGLGKRLSPHGLRHsAITLALDAGAGLIRKVQDFSRHADLRTL 162


                 ...
gi 490989887 168 VLY 170
Cdd:cd01195  163 QVY 165
xerS PRK05084
site-specific tyrosine recombinase XerS; Reviewed
 27-171 2.07e-10

site-specific tyrosine recombinase XerS; Reviewed


Pssm-ID: 235339 [Multi-domain]  Cd Length: 357  Bit Score: 58.39  E-value: 2.07e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490989887  27 RDYCMLLMCFIHGLRVSELRFLKVSDIDLSSQRIAIRRLKNGFSTIhPLQPREQLALSQWLVKRTSCLNADLP--WLFLS 104
Cdd:PRK05084 196 RDLAIIALILGSGLRVSELVNLDLSDLNLKQMTIDVTRKGGKRDSV-NIAPFALPYLEEYLKIRASRYKAEKQekALFLT 274

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490989887 105 R---KGTPLSRQHIHVMMRNYgvQAGIAVPVHPHMLRHACGYALAEEGVDTRLIQDYLGHRNIQHTVLYT 171
Cdd:PRK05084 275 KyrgKPNRISARAIEKMVAKY--SEAFGVRLTPHKLRHTLATRLYDATKDQVLVADQLGHTSTETTDLYT 342
INT_tnpA_C_Tn554 cd01186
Putative Transposase A from transposon Tn554, C-terminal catalytic domain; This family ...
 7-167 5.07e-10

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: 55.89  E-value: 5.07e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490989887   7 LSKKEVQALIAASqqqdGSLRDYCMLLMCFIHGLRVSELRFLKVSDIDLSSQRIAIR-RLKNGFSTIHPLQPREQLALSQ 85
Cdd:cd01186    2 LTPREVQELINAC----NNLRDKFLLALLYETGLRIGEALGLRIEDIDMADNQIELVpREDNTNEARAKSMRERRIPVSQ 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490989887  86 WLVK--------RTSCLNADLPWLFLSRK----GTPLSRQHIHVMMRNYGVQAGIAVpvHPHMLRHACGYALAEEGVDTR 153
Cdd:cd01186   78 DLIDlyadyltyIYCEEAEFSITVFVNVKggnqGKAMNYSDVYDLVRRLKKRTGIDF--TPHMFRHTHATALIRAGWSIE 155

                        170
                 ....*....|....
gi 490989887 154 LIQDYLGHRNIQHT 167
Cdd:cd01186  156 VVARRLGHAHVQTT 169
INT_P4_C cd00801
Bacteriophage P4 integrase, C-terminal catalytic domain; P4-like integrases are found in ...
 8-161 1.43e-09

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: 54.58  E-value: 1.43e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490989887   8 SKKEVQALIAASQQQDGSLRDYCMLLMCFIHGLRVSELRFLKVSDIDLSSQRIAI--RRLKNGfsTIHplqpreQLALSQ 85
Cdd:cd00801    1 SPDELPELWRALDTANLSPPTKLALRLLLLTGQRIGELARARWSEIDLEEKTWTIpaERTKNK--RPH------RVPLSD 72

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490989887  86 WLVK-----RTscLNADLPWLFLSRKGT--PLSRQHIHVMMRNYGvqaGIAVPVHPHMLRHACGYALAEEGVDTRLIQDY 158
Cdd:cd00801   73 QALEileelKE--FTGDSGYLFPSRRKKkkPISENTINKALKRLG---YKGKEFTPHDLRRTFSTLLNELGIDPEVIERL 147


                 ...
gi 490989887 159 LGH 161
Cdd:cd00801  148 LNH 150
PRK15417 PRK15417
integron integrase;
39-171 8.92e-09

integron integrase;


Pssm-ID: 185315 [Multi-domain]  Cd Length: 337  Bit Score: 53.51  E-value: 8.92e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490989887  39 GLRVSELRFLKVSDIDLSSQRIAIRRLKN----GFSTIHPLQP--REQLALSQ-WLVK-----RTSCLNADL-------- 98
Cdd:PRK15417 144 GMRISEGLQLRVKDLDFDHGTIIVREGKGskdrALMLPESLAPslREQLSRARaWWLKdqaegRSGVALPDAlerkypra 223

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490989887  99 ----PWLFLSRKGTPLSRQHIHVMMRNYGV-------------QAGIAVPVHPHMLRHACGYALAEEGVDTRLIQDYLGH 161
Cdd:PRK15417 224 ghswPWFWVFAQHTHSTDPRSGVVRRHHMYdqtfqrafkraveQAGITKPATPHTLRHSFATALLRSGYDIRTVQDLLGH 303

                        170
                 ....*....|
gi 490989887 162 RNIQHTVLYT 171
Cdd:PRK15417 304 SDVSTTMIYT 313
INT_C_like_2 cd01191
Uncharacterized site-specific tyrosine recombinase, C-terminal catalytic domain; Tyrosine ...
 18-173 3.41e-07

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: 47.80  E-value: 3.41e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490989887  18 ASQQQDGSLRDYCMLLMCFIHGLRVSELRFLKVSDI-----DLSSQRIAIRRLkngfstIHPLQPREQlALsQWLVKRts 92
Cdd:cd01191   12 KCLKKDGNLEWYFVVRFLAATGARVSELIKIKVEHVelgyfDIYSKGGKLRRL------YIPKKLRNE-AL-EWLKST-- 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490989887  93 clNADLPWLFLSRKGTPLSRQHIHVMMRNYGVQAGIAVPV-HPHMLRHACGYALAEEGVDTRLIQDYLGHRNIQHTVLY- 170
Cdd:cd01191   82 --NRKSGYIFLNRFGERITTRGIAQQLKNYARKYGLNPKVvYPHSFRHRFAKNFLEKYNDIALLADLMGHESIETTRIYl 159


                 ....*
gi 490989887 171 --TAS 173
Cdd:cd01191  160 rkTAS 164
INT_C_like_6 cd01196
Uncharacterized site-specific tyrosine recombinase, C-terminal catalytic domain; Tyrosine ...
 26-170 1.80e-06

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


Pssm-ID: 271196  Cd Length: 183  Bit Score: 45.93  E-value: 1.80e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490989887  26 LRDYCML-LMCFIHGlRVSELRFLKVSDIDLSSQRIAIR-RLKNGFSTIHPLQPREQLALSQWLVKRTSCLNADLPWLFL 103
Cdd:cd01196   20 LRDRALIaLMVYSFA-RIGAVLAMRVEDVYDQGRRLWVRlAEKGGKQHEMPCHHDLEEYLRAYLEAAEIEEDPKGPLFRT 98

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 490989887 104 SRKGT------PLSRQHIHVMMRNYGVQAGIAVPVHPHMLRHACGYALAEEGVDTRLIQDYLGHRNIQHTVLY 170
Cdd:cd01196   99 TRGGTrklthnPLTQANAYRMVRRRAIAADIPTAIGNHSFRATGITAYLKNGGTLEDAQNMANHASTRTTQLY 171
INT_C_like_1 cd01184
Uncharacterized site-specific tyrosine recombinase, C-terminal catalytic domain; Tyrosine ...
 7-162 5.52e-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: 44.61  E-value: 5.52e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490989887   7 LSKKEVQALIAASQQQDGSLRDYC---MLLMCFIHGLRVSELRFLKVSDI---------DLSSqRIAIRRLKNGFST--- 71
Cdd:cd01184    1 FTPEELAKIFSSPLYTGCKKKDPAlywLPLIGLYTGARLNEICQLRVDDIkeedgiwciDIND-DAEGRRLKTKASRrlv 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490989887  72 -IHPlqpreQLALSQWL--VKRTSclNADLPWLFLSRK------GTPLSRQHIHvMMRNYGVQAGIAVPVHPhmLRHACG 142
Cdd:cd01184   80 pIHP-----RLIELGFLdyVEALR--ADGKLFLFPEKRdkdgkySKAASKWFNR-LLRKLGIKDDERKSFHS--FRHTFI 149

                        170       180
                 ....*....|....*....|
gi 490989887 143 YALAEEGVDTRLIQDYLGHR 162
Cdd:cd01184  150 TALKRAGVPEELIAQIVGHS 169
INT_Lambda_C cd00800
C-terminal catalytic domain of Lambda integrase, a tyrosine-based site-specific recombinase; ...
 32-171 1.80e-05

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: 42.72  E-value: 1.80e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490989887  32 LLMCFIHGLRVSELRFLKVSDIDlsSQRIAIRRLKNGFSTIHPLQPREQLALSQwLVKRTSCLnadLPWLFLSRKGTPLS 111
Cdd:cd00800   18 MELALLTGQRQGDLLRLKWSDIT--DGGLLVEQSKTGKKLLIPWTPSLRALVDR-IRALPRKR---SEYLINSRKGGPLS 91

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 490989887 112 RQHIHVMMRNYGVQAGIAVPVHP---HMLRHACGYALAEEGVDTRlIQDYLGHRNIQHTVLYT 171
Cdd:cd00800   92 YDTLKSAWRRARKAAGLKGETEGftfHDLRAKAATDYAEQGGSTD-AQALLGHKSDAMTERYT 153
INT_Cre_C cd00799
C-terminal catalytic domain of Cre recombinase (also called integrase); Cre-like recombinases ...
 26-171 3.02e-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: 42.67  E-value: 3.02e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490989887  26 LRDYCMLLMCFIHGLRVSEL---RFLKVSDIDLSSQRIAIRRLK---NGFSTIHPLQPREQL----ALSQWLVKRtscLN 95
Cdd:cd00799   16 LRDRALLLLGFAGALRRSELvalRVEDLTRFVDGGLLIRLRRSKtdqDGEGEIKALPYGPETcpvrALRAWLEAA---GI 92

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490989887  96 ADLPwLF--LSRKG----TPLSRQHIHVMMRNYGVQAGIAVPVH-PHMLRHacGYA--LAEEGVDTRLIQDYLGHRNIQH 166
Cdd:cd00799   93 PSGP-LFrrIRRGGsvgtTRLSDRSVARIVKRRAALAGLDPGDFsGHSLRR--GFAteAARAGASLPEIMAQGGHKSVAT 169


                 ....*
gi 490989887 167 TVLYT 171
Cdd:cd00799  170 VMRYI 174
INT_tnpB_C_Tn554 cd01187
Putative Transposase B from transposon Tn554, C-terminal catalytic domain; This family ...
 133-170 1.64e-04

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: 40.11  E-value: 1.64e-04
                         10        20        30
                 ....*....|....*....|....*....|....*...
gi 490989887 133 HPHMLRHACGYALAEEGVDTRLIQDYLGHRNIQHTVLY 170
Cdd:cd01187  103 HTHRFRHTVATRLANSGMGILVLQQLLGHSSPEMTLRY 140
int PHA02601
integrase; Provisional
 6-170 3.01e-03

integrase; Provisional


Pssm-ID: 222904 [Multi-domain]  Cd Length: 333  Bit Score: 37.40  E-value: 3.01e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490989887   6 YLSKKEVQALIAASQQQDgsLRDYCMLLM-CFIHGLRVSELRFLKVSDIdlSSQRIAIRRLKNGfstihplQPReQLALS 84
Cdd:PHA02601 172 FLTKEEIERLLDACDGSR--SPDLGLIAKiCLATGARWSEAETLKRSQI--SPYKITFVKTKGK-------KNR-TVPIS 239

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490989887  85 QWLVKrtsclnadlpwlFLSRKGTPL---SRQHIHVMMRnygvQAGIAVPVH--PHMLRHACGYALAEEGVDTRLIQDYL 159
Cdd:PHA02601 240 EELYK------------MLPKRRGRLfkdAYESFERAVK----RAGIDLPEGqaTHVLRHTFASHFMMNGGNILVLQRIL 303

                        170
                 ....*....|.
gi 490989887 160 GHRNIQHTVLY 170
Cdd:PHA02601 304 GHATIEMTMAY 314
 
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