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Conserved domains on  [gi|447103897|ref|WP_001181153|]
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tyrosine-type DNA invertase IpuA [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

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List of domain hits

 Name Accession Description Interval E-value
DNA_BRE_C super family cl00213
DNA breaking-rejoining enzymes, C-terminal catalytic domain; The DNA breaking-rejoining enzyme ...
 1-184 3.73e-86

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: 252.04  E-value: 3.73e-86
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 447103897   1 MQNRKFLTHHEINLLLQSVKQKSCSSRDVCMILLAYFHGLRVSELLSLQLSDLELTTEKIYIQRIKNGFSTVHPLQKEEV 80
Cdd:cd01197    1 MKQRKYLTGKEVQALLQAACRGRTPARDYCLLLLAFRHGFRVSELCDLHLSDVDLESRRLHIRRLKNGFSTTHPLRFDER 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 447103897  81 IAITNWLNERNSLNVKhfnDNPWLFVSRTGKPLSRQRFYNIVSAAGKNAGLNIKVHPHMLRHACGYSLADNGVDTRLIQD 160
Cdd:cd01197   81 EALEAWLKERANWKGA---DTDWIFLSRRGGPLSRQQAYRIIRDLGKEAGTVTQTHPHMLRHACGYALADRGADTRLIQD 157

                        170       180
                 ....*....|....*....|....
gi 447103897 161 YLGHRNIRHTVIYTASNSMRFEKM 184
Cdd:cd01197  158 YLGHRNIRHTVIYTASNAARFANL 181
 
Name Accession Description Interval E-value
INT_FimBE_like cd01197
FimB and FimE and related proteins, integrase/recombinases; This CD includes proteins similar ...
 1-184 3.73e-86

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: 252.04  E-value: 3.73e-86
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 447103897   1 MQNRKFLTHHEINLLLQSVKQKSCSSRDVCMILLAYFHGLRVSELLSLQLSDLELTTEKIYIQRIKNGFSTVHPLQKEEV 80
Cdd:cd01197    1 MKQRKYLTGKEVQALLQAACRGRTPARDYCLLLLAFRHGFRVSELCDLHLSDVDLESRRLHIRRLKNGFSTTHPLRFDER 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 447103897  81 IAITNWLNERNSLNVKhfnDNPWLFVSRTGKPLSRQRFYNIVSAAGKNAGLNIKVHPHMLRHACGYSLADNGVDTRLIQD 160
Cdd:cd01197   81 EALEAWLKERANWKGA---DTDWIFLSRRGGPLSRQQAYRIIRDLGKEAGTVTQTHPHMLRHACGYALADRGADTRLIQD 157

                        170       180
                 ....*....|....*....|....
gi 447103897 161 YLGHRNIRHTVIYTASNSMRFEKM 184
Cdd:cd01197  158 YLGHRNIRHTVIYTASNAARFANL 181
PRK09870 PRK09870
tyrosine recombinase; Provisional
 1-194 5.93e-80

tyrosine recombinase; Provisional


Pssm-ID: 182125  Cd Length: 200  Bit Score: 237.14  E-value: 5.93e-80
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 447103897   1 MQNRKFLTHHEINLLLQSVKQKSCSSRDVCMILLAYFHGLRVSELLSLQLSDLELTTEKIYIQRIKNGFSTVHPLQKEEV 80
Cdd:PRK09870   7 NKKRNFLTHSEIESLLKAANTGPHAARNYCLTLLCFIHGFRASEICRLRISDIDLKAKCIYIHRLKKGFSTTHPLLNKEI 86

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 447103897  81 IAITNWLNERNSLnvkHFNDNPWLFVSRTGKPLSRQRFYNIVSAAGKNAGLNIKVHPHMLRHACGYSLADNGVDTRLIQD 160
Cdd:PRK09870  87 QALKNWLSIRTSY---PHAESEWVFLSRKGNPLSRQQFYHIISTSGGNAGLSLEIHPHMLRHSCGFALANMGIDTRLIQD 163

                        170       180       190
                 ....*....|....*....|....*....|....
gi 447103897 161 YLGHRNIRHTVIYTASNSMRFEKMWGRGDAKKQH 194
Cdd:PRK09870 164 YLGHRNIRHTVWYTASNAGRFYGIWDRARGRQRH 197
Phage_integrase pfam00589
Phage integrase family; Members of this family cleave DNA substrates by a series of staggered ...
 6-177 8.77e-53

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: 167.11  E-value: 8.77e-53
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 447103897    6 FLTHHEINLLLQSVKQKSCSSRDVCMILLAYFHGLRVSELLSLQLSDLELTTEKIYIQRIKNGFSTVHPLQKEEVIAITN 85
Cdd:pfam00589   1 RLTEDEVERLLDAAETGPLSIRDKALLELLYATGLRISELCSLRWSDIDFENGVIRVHRGKGNKERTVPLSDAALELLKE 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 447103897   86 WLnernSLNVKHFNDNPWLFVSRTGKPLSRQRFYNIVSAAGKNAGLNIKVHPHMLRHACGYSLADNGVDTRLIQDYLGHR 165
Cdd:pfam00589  81 WL----SKRLLEAPKSDYLFASKRGKPLSRQTVRKIFKRAGKEAGLELPLHPHMLRHSFATHLLEAGVDLRVVQKLLGHS 156

                         170
                  ....*....|..
gi 447103897  166 NIRHTVIYTASN 177
Cdd:pfam00589 157 SISTTQIYTHVA 168
XerD COG4974
Site-specific recombinase XerD [Replication, recombination and repair];
4-174 1.99e-42

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


Pssm-ID: 443999 [Multi-domain]  Cd Length: 291  Bit Score: 144.37  E-value: 1.99e-42
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 447103897   4 RKFLTHHEINLLLQSVKQKS-CSSRDVCMILLAYFHGLRVSELLSLQLSDLELTTEKIYIQRIKNGfstvhplqKEEVIA 82
Cdd:COG4974  110 PRVLTEEEIEALLEALDTETpEGLRDRALLLLLYATGLRVSELLGLKWSDIDLDRGTIRVRRGKGG--------KERTVP 181

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 447103897  83 ITNWLNE--RNSLNVKHFNDNPWLFVSRTGKPLSRQRFYNIVSAAGKNAGLNIKVHPHMLRHACGYSLADNGVDTRLIQD 160
Cdd:COG4974  182 LSPEALEalREYLEERRPRDSDYLFPTRRGRPLSRRAIRKILKRLAKRAGIPKRVTPHSLRHTFATHLLEAGVDLRTVQE 261

                        170
                 ....*....|....
gi 447103897 161 YLGHRNIRHTVIYT 174
Cdd:COG4974  262 LLGHSSISTTQIYT 275
recomb_XerD TIGR02225
tyrosine recombinase XerD; The phage integrase family describes a number of recombinases with ...
 5-174 7.10e-35

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: 124.62  E-value: 7.10e-35
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 447103897    5 KFLTHHEINLLLQSVKQKSCSS-RDVCMILLAYFHGLRVSELLSLQLSDLELTtEKIYIQRIKNGFSTVHPLQKEEVIAI 83
Cdd:TIGR02225 103 KVLTVEEVEALLAAPDVDTPLGlRDRAMLELLYATGLRVSELVGLRLEDVNLD-EGFVRVRGKGNKERLVPLGEEAIEAL 181

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 447103897   84 TNWLNE-RNSLNVKHFNDNPWLFVSRTGKPLSRQRFYNIVSAAGKNAGLNIKVHPHMLRHACGYSLADNGVDTRLIQDYL 162
Cdd:TIGR02225 182 ERYLKEaRPLLLKKKVKESDALFLNRRGGPLSRQGVWKILKEYAKRAGIEKPISPHTLRHSFATHLLENGADLRVVQELL 261

                         170
                  ....*....|..
gi 447103897  163 GHRNIRHTVIYT 174
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 ...
 1-184 3.73e-86

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: 252.04  E-value: 3.73e-86
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 447103897   1 MQNRKFLTHHEINLLLQSVKQKSCSSRDVCMILLAYFHGLRVSELLSLQLSDLELTTEKIYIQRIKNGFSTVHPLQKEEV 80
Cdd:cd01197    1 MKQRKYLTGKEVQALLQAACRGRTPARDYCLLLLAFRHGFRVSELCDLHLSDVDLESRRLHIRRLKNGFSTTHPLRFDER 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 447103897  81 IAITNWLNERNSLNVKhfnDNPWLFVSRTGKPLSRQRFYNIVSAAGKNAGLNIKVHPHMLRHACGYSLADNGVDTRLIQD 160
Cdd:cd01197   81 EALEAWLKERANWKGA---DTDWIFLSRRGGPLSRQQAYRIIRDLGKEAGTVTQTHPHMLRHACGYALADRGADTRLIQD 157

                        170       180
                 ....*....|....*....|....
gi 447103897 161 YLGHRNIRHTVIYTASNSMRFEKM 184
Cdd:cd01197  158 YLGHRNIRHTVIYTASNAARFANL 181
PRK09870 PRK09870
tyrosine recombinase; Provisional
 1-194 5.93e-80

tyrosine recombinase; Provisional


Pssm-ID: 182125  Cd Length: 200  Bit Score: 237.14  E-value: 5.93e-80
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 447103897   1 MQNRKFLTHHEINLLLQSVKQKSCSSRDVCMILLAYFHGLRVSELLSLQLSDLELTTEKIYIQRIKNGFSTVHPLQKEEV 80
Cdd:PRK09870   7 NKKRNFLTHSEIESLLKAANTGPHAARNYCLTLLCFIHGFRASEICRLRISDIDLKAKCIYIHRLKKGFSTTHPLLNKEI 86

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 447103897  81 IAITNWLNERNSLnvkHFNDNPWLFVSRTGKPLSRQRFYNIVSAAGKNAGLNIKVHPHMLRHACGYSLADNGVDTRLIQD 160
Cdd:PRK09870  87 QALKNWLSIRTSY---PHAESEWVFLSRKGNPLSRQQFYHIISTSGGNAGLSLEIHPHMLRHSCGFALANMGIDTRLIQD 163

                        170       180       190
                 ....*....|....*....|....*....|....
gi 447103897 161 YLGHRNIRHTVIYTASNSMRFEKMWGRGDAKKQH 194
Cdd:PRK09870 164 YLGHRNIRHTVWYTASNAGRFYGIWDRARGRQRH 197
PRK09871 PRK09871
tyrosine recombinase; Provisional
 1-187 2.19e-75

tyrosine recombinase; Provisional


Pssm-ID: 182126  Cd Length: 198  Bit Score: 225.63  E-value: 2.19e-75
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 447103897   1 MQNRKFLTHHEINLLLQSVKQKSCSSRDVCMILLAYFHGLRVSELLSLQLSDLELTTEKIYIQRIKNGFSTVHPLQKEEV 80
Cdd:PRK09871   1 MSKRRYLTGKEVQAMMQAVCYGATGARDYCLILLAYRHGMRISELLDLHYQDLDLNEGRINIRRLKNGFSTVHPLRFDER 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 447103897  81 IAITNWLNERNSLnvKHFNDNPWLFVSRTGKPLSRQRFYNIVSAAGKNAGLNIKVHPHMLRHACGYSLADNGVDTRLIQD 160
Cdd:PRK09871  81 EAVERWTQERANW--KGADRTDAIFISRRGSRLSRQQAYRIIRDAGIEAGTVTQTHPHMLRHACGYELAERGADTRLIQD 158

                        170       180
                 ....*....|....*....|....*..
gi 447103897 161 YLGHRNIRHTVIYTASNSMRFEKMWGR 187
Cdd:PRK09871 159 YLGHRNIRHTVRYTASNAARFAGLWER 185
Phage_integrase pfam00589
Phage integrase family; Members of this family cleave DNA substrates by a series of staggered ...
 6-177 8.77e-53

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: 167.11  E-value: 8.77e-53
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 447103897    6 FLTHHEINLLLQSVKQKSCSSRDVCMILLAYFHGLRVSELLSLQLSDLELTTEKIYIQRIKNGFSTVHPLQKEEVIAITN 85
Cdd:pfam00589   1 RLTEDEVERLLDAAETGPLSIRDKALLELLYATGLRISELCSLRWSDIDFENGVIRVHRGKGNKERTVPLSDAALELLKE 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 447103897   86 WLnernSLNVKHFNDNPWLFVSRTGKPLSRQRFYNIVSAAGKNAGLNIKVHPHMLRHACGYSLADNGVDTRLIQDYLGHR 165
Cdd:pfam00589  81 WL----SKRLLEAPKSDYLFASKRGKPLSRQTVRKIFKRAGKEAGLELPLHPHMLRHSFATHLLEAGVDLRVVQKLLGHS 156

                         170
                  ....*....|..
gi 447103897  166 NIRHTVIYTASN 177
Cdd:pfam00589 157 SISTTQIYTHVA 168
XerD COG4974
Site-specific recombinase XerD [Replication, recombination and repair];
4-174 1.99e-42

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


Pssm-ID: 443999 [Multi-domain]  Cd Length: 291  Bit Score: 144.37  E-value: 1.99e-42
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 447103897   4 RKFLTHHEINLLLQSVKQKS-CSSRDVCMILLAYFHGLRVSELLSLQLSDLELTTEKIYIQRIKNGfstvhplqKEEVIA 82
Cdd:COG4974  110 PRVLTEEEIEALLEALDTETpEGLRDRALLLLLYATGLRVSELLGLKWSDIDLDRGTIRVRRGKGG--------KERTVP 181

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 447103897  83 ITNWLNE--RNSLNVKHFNDNPWLFVSRTGKPLSRQRFYNIVSAAGKNAGLNIKVHPHMLRHACGYSLADNGVDTRLIQD 160
Cdd:COG4974  182 LSPEALEalREYLEERRPRDSDYLFPTRRGRPLSRRAIRKILKRLAKRAGIPKRVTPHSLRHTFATHLLEAGVDLRTVQE 261

                        170
                 ....*....|....
gi 447103897 161 YLGHRNIRHTVIYT 174
Cdd:COG4974  262 LLGHSSISTTQIYT 275
XerC COG4973
Site-specific recombinase XerC [Replication, recombination and repair];
4-174 1.48e-35

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


Pssm-ID: 443998 [Multi-domain]  Cd Length: 287  Bit Score: 126.61  E-value: 1.48e-35
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 447103897   4 RKFLTHHEINLLLQSVKQKSCSSRDVCMILLAYFHGLRVSELLSLQLSDLELTTEKIYIQRiKNGFSTVHPLQKEEVIAI 83
Cdd:COG4973  109 PRALTVDELAQLLDALADDPLAVRDRAIVELLYSTGLRLGELVGLDWEDVDLDAGEVRVRG-KTGKSRTVPLGPKALAAL 187

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 447103897  84 TNWLNERNSLNVKhfnDNPWLFVSRTGKPLSRQRFYNIVSAAGKNAGLNIKVHPHMLRHACGYSLADNGVDTRLIQDYLG 163
Cdd:COG4973  188 REWLAVRPELAAP---DEGALFPSRRGTRLSPRNVQKRLRRLAKKAGLPKHVHPHDLRHSFATHLLESGGDLRAVQELLG 264

                        170
                 ....*....|.
gi 447103897 164 HRNIRHTVIYT 174
Cdd:COG4973  265 HASISTTQIYT 275
recomb_XerD TIGR02225
tyrosine recombinase XerD; The phage integrase family describes a number of recombinases with ...
 5-174 7.10e-35

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: 124.62  E-value: 7.10e-35
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 447103897    5 KFLTHHEINLLLQSVKQKSCSS-RDVCMILLAYFHGLRVSELLSLQLSDLELTtEKIYIQRIKNGFSTVHPLQKEEVIAI 83
Cdd:TIGR02225 103 KVLTVEEVEALLAAPDVDTPLGlRDRAMLELLYATGLRVSELVGLRLEDVNLD-EGFVRVRGKGNKERLVPLGEEAIEAL 181

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 447103897   84 TNWLNE-RNSLNVKHFNDNPWLFVSRTGKPLSRQRFYNIVSAAGKNAGLNIKVHPHMLRHACGYSLADNGVDTRLIQDYL 162
Cdd:TIGR02225 182 ERYLKEaRPLLLKKKVKESDALFLNRRGGPLSRQGVWKILKEYAKRAGIEKPISPHTLRHSFATHLLENGADLRVVQELL 261

                         170
                  ....*....|..
gi 447103897  163 GHRNIRHTVIYT 174
Cdd:TIGR02225 262 GHADISTTQIYT 273
DNA_BRE_C cd00397
DNA breaking-rejoining enzymes, C-terminal catalytic domain; The DNA breaking-rejoining enzyme ...
 11-174 2.84e-33

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: 117.20  E-value: 2.84e-33
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 447103897  11 EINLLLQSVKQ-KSCSSRDVCMILLAYFHGLRVSELLSLQLSDLELTTEKIYIQRIKNGFSTVH--PLQKEEVIAITNWL 87
Cdd:cd00397    1 ELEKLLDAIDEdKKIDLRDRAILLLLLETGLRISELLALKVKDIDLDNGTIRVRGKKTKGGKERtvPLPKELAEELKEYL 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 447103897  88 NERNSLNVKHF--NDNPWLFVSRTGKPLSRQRFYNIVSAAGKNAGlnIKVHPHMLRHACGYSLADNGVDTRLIQDYLGHR 165
Cdd:cd00397   81 KERRDKRGPLLksLYLNKLFGTKLGERLSRRTLRRIFKKAGIEAG--RKITPHSLRHTFATNLLENGVDIKVVQKLLGHS 158


                 ....*....
gi 447103897 166 NIRHTVIYT 174
Cdd:cd00397  159 SISTTQRYL 167
INT_XerDC_C cd00798
XerD and XerC integrases, C-terminal catalytic domains; XerDC-like integrases are involved in ...
 27-174 7.97e-32

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: 113.37  E-value: 7.97e-32
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 447103897  27 RDVCMILLAYFHGLRVSELLSLQLSDLELTTEKIYI------QRIkngfstVhPLQKEEVIAITNWLNERNSLNVKHFND 100
Cdd:cd00798   20 RDRAILELLYASGLRVSELVGLDLSDVDLDEGLVRVtgkgnkERL------V-PFGSYAVEALEEYLEERRPLLLKKKPP 92

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 447103897 101 NPwLFVSRTGKPLSRQRFYNIVSAAGKNAGLNIKVHPHMLRHACGYSLADNGVDTRLIQDYLGHRNIRHTVIYT 174
Cdd:cd00798   93 DA-LFLNKRGKRLSRRGVWRILKKYAERAGLPKHVSPHTLRHSFATHLLEGGADLRVVQELLGHASLSTTQIYT 165
recomb_XerC TIGR02224
tyrosine recombinase XerC; The phage integrase family describes a number of recombinases with ...
 5-174 1.31e-28

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: 108.46  E-value: 1.31e-28
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 447103897    5 KFLTHHEINLLLQSVKQKSCSS---RDVCMILLAYFHGLRVSELLSLQLSDLELTTEKIYI------QRIkngfstVhPL 75
Cdd:TIGR02224 105 KFLSEDEMEALLDAPEEDDEDWlalRDRAILELLYSSGLRVSELVGLDLSDLDLDFGEVRVrgkgnkERI------V-PF 177

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 447103897   76 QKEEVIAITNWLNERNSLNVKHFNDNPwLFVSRTGKPLSRQRFYNIVSAAGKNAGLNIKVHPHMLRHACGYSLADNGVDT 155
Cdd:TIGR02224 178 GPYARDALQAYLEARRSPLLASEGQDA-LFLNRRGGRLTPRGVQYRLQQLRAKAGLPKHVHPHALRHSFATHLLNNGADL 256

                         170
                  ....*....|....*....
gi 447103897  156 RLIQDYLGHRNIRHTVIYT 174
Cdd:TIGR02224 257 RAVQELLGHASLSTTQIYT 275
INT_RitC_C_like cd01182
C-terminal catalytic domain of recombinase RitC, a component of the recombinase trio; ...
 7-180 1.66e-27

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: 102.74  E-value: 1.66e-27
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 447103897   7 LTHHEINLLLQSV-KQKSCSSRDVCMILLAYFHGLRVSELLSLQLSDLELTTEKIYIQRIK-NGFSTVhPLQKEEVIAIT 84
Cdd:cd01182    1 LTREEMKALLAAPdRNTSLGRRDHALLLLLYDTGARVQELADLTIRDLRLDDPATVRLHGKgRKERTV-PLWKETVAALK 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 447103897  85 NWLNERNSLnvKHFNDNPWLFVSRTGKPLSRQRFYNIVS-----AAGKNAGLNIKVHPHMLRHACGYSLADNGVDTRLIQ 159
Cdd:cd01182   80 AYLQEFHLT--PDPKQLFPLFPNRRGQPLTRDGVAYILNkyvalASNRCPSLPKRITPHTLRHTKAMHLLQAGVDLTVIR 157

                        170       180
                 ....*....|....*....|..
gi 447103897 160 DYLGHRNIRHTVIY-TASNSMR 180
Cdd:cd01182  158 DWLGHESVETTQIYaEADLEMK 179
xerC PRK00236
site-specific tyrosine recombinase XerC; Reviewed
 5-175 2.27e-27

site-specific tyrosine recombinase XerC; Reviewed


Pssm-ID: 234698 [Multi-domain]  Cd Length: 297  Bit Score: 105.24  E-value: 2.27e-27
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 447103897   5 KFLTHHEINLLLQSVKQKS-CSSRDVCMILLAYFHGLRVSELLSLQLSDLELTTEKIYI------QRikngfsTVhPLQK 77
Cdd:PRK00236 114 KPLDVDQAKRLLDAIDEDDpLALRDRAILELLYGSGLRLSELVGLDIDDLDLASGTLRVlgkgnkER------TV-PLGR 186

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 447103897  78 EEVIAITNWLNERNSLNVKhfnDNPwLFVSRTGKPLSRQRFYNIVSAAGKNAGLNIKVHPHMLRHACGYSLADNGVDTRL 157
Cdd:PRK00236 187 AAREALEAYLALRPLFLPD---DDA-LFLGARGGRLSPRVVQRRVKKLGKKAGLPSHITPHKLRHSFATHLLESGGDLRA 262

                        170
                 ....*....|....*...
gi 447103897 158 IQDYLGHRNIRHTVIYTA 175
Cdd:PRK00236 263 VQELLGHASLSTTQIYTH 280
xerD PRK00283
tyrosine recombinase;
5-174 2.57e-26

tyrosine recombinase;


Pssm-ID: 234713 [Multi-domain]  Cd Length: 299  Bit Score: 102.58  E-value: 2.57e-26
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 447103897   5 KFLTHHEINLLLQSVKQKS-CSSRDVCMILLAYFHGLRVSELLSLQLSDLELTTEKIYI------QRIkngfstVhPLQK 77
Cdd:PRK00283 112 KTLSEAQVEALLDAPDIDTpLGLRDRAMLELLYATGLRVSELVGLTLDDVSLRQGVVRVtgkgnkERL------V-PLGE 184

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 447103897  78 EEVIAITNWL--------NERNSlnvkhfndnPWLFVSRTGKPLSRQRFYNIVSAAGKNAGLNIK-VHPHMLRHACGYSL 148
Cdd:PRK00283 185 EAVYAIERYLergrpallNGRSS---------DALFPSARGGQLTRQTFWHRIKHYAKRAGIDPKkLSPHVLRHAFATHL 255

                        170       180
                 ....*....|....*....|....*.
gi 447103897 149 ADNGVDTRLIQDYLGHRNIRHTVIYT 174
Cdd:PRK00283 256 LNHGADLRVVQELLGHSDISTTQIYT 281
INT_IntI_C cd01193
Integron integrase and similar protiens, C-terminal catalytic domain; Integron integrases ...
 5-174 1.60e-24

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


Pssm-ID: 271193 [Multi-domain]  Cd Length: 176  Bit Score: 94.65  E-value: 1.60e-24
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 447103897   5 KFLTHHEINLLLQSVKqkscSSRDVCMILLAYFHGLRVSELLSLQLSDLELTTEKIYIQRIKNGFSTVHPLQKEEVIAIT 84
Cdd:cd01193    4 VVLSPDEVRRILGALT----ELRHRLILSLLYGAGLRISELLRLRVKDIDFERGVIRVRQGKGGKDRVVPLPEKLLEPLR 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 447103897  85 NWLNERNSLNVkHFNDNPWLFV------SRTGKPLSRQRFYNIVSAAGKNAGLNIKVHPHMLRHACGYSLADNGVDTRLI 158
Cdd:cd01193   80 RYLKSARPKEE-LDPAEGRAGVldprtgVERRHHISETTVQRALKKAVEQAGITKRVTPHTLRHSFATHLLEAGTDIRTI 158

                        170
                 ....*....|....*.
gi 447103897 159 QDYLGHRNIRHTVIYT 174
Cdd:cd01193  159 QELLGHSDLSTTMIYT 174
INT_RitA_C_like cd01188
C-terminal catalytic domain of recombinase RitA, a component of the recombinase trio; ...
 11-181 1.92e-24

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: 94.62  E-value: 1.92e-24
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 447103897  11 EINLLLQSVKQ-KSCSSRDVCMILLAYFHGLRVSELLSLQLSDLELTTEKIYIQRIKNGFSTVHPLQKEEVIAITNWLNE 89
Cdd:cd01188    4 EVRRLLAAIDRlTPVGLRDYAILLLLARLGLRAGDVAGLRLDDIDWRSGTITVRQKKTGRPVELPLTEPVGEALADYLRD 83

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 447103897  90 RNSLnvkhfNDNPWLFVSRT--GKPLSRQR-FYNIVSAAGKNAGLNIKVH-PHMLRHACGYSLADNGVDTRLIQDYLGHR 165
Cdd:cd01188   84 GRPR-----TDSREVFLRARapYRPLSSTSqISSIVRRYLRKAGIEPSHRgTHSLRHSLATRMLRAGTSLKVIADLLGHR 158

                        170
                 ....*....|....*...
gi 447103897 166 NIRHTVIY--TASNSMRF 181
Cdd:cd01188  159 SIETTAIYakIDVDDLRE 176
INT_Rci_Hp1_C cd00796
Shufflon-specific DNA recombinase Rci and Bacteriophage Hp1_like integrase, C-terminal ...
 5-174 1.50e-23

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: 92.00  E-value: 1.50e-23
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 447103897   5 KFLTHHEINLLLQSVKQKScsSRDV-CMILLAYFHGLRVSELLSLQLSDLELTTEKIYIQRIKNGFSTVHPLQKEeviai 83
Cdd:cd00796    3 RFLTEDEEARLLAALEEST--NPHLrLIVLLALYTGARRGEILSLRWDDIDLEVGLIVLPETKNGKPRTVPLSDE----- 75

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 447103897  84 tnWLNERNSLNVKHFNDNPWLFVSRTGKPlsRQRFYNIVSAAGKNAGLNiKVHPHMLRHACGYSLADNGVDTRLIQDYLG 163
Cdd:cd00796   76 --AIAILKELKRKRGKDGFFVDGRFFGIP--IASLRRAFKKARKRAGLE-DLRFHDLRHTFASRLVQAGVPIKTVAKILG 150

                        170
                 ....*....|.
gi 447103897 164 HRNIRHTVIYT 174
Cdd:cd00796  151 HSSIKMTMRYA 161
xerC PRK01287
site-specific tyrosine recombinase XerC; Reviewed
 27-174 1.35e-19

site-specific tyrosine recombinase XerC; Reviewed


Pssm-ID: 234935 [Multi-domain]  Cd Length: 358  Bit Score: 85.18  E-value: 1.35e-19
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 447103897  27 RDVCMILLAYFHGLRVSELLSLQLSDLELTTEKIYIQRIKNGFSTVHPLQKEEVIAITNWLNE-RNSLNVKHfnDNPWLF 105
Cdd:PRK01287 158 RDRALLELLWSTGIRRGELARLDLYDVDASRGVVTVRQGKGNKDRVVPVGERALAWLQRYLQDvRPQLAVRP--DSGALF 235

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 447103897 106 VSRTGKPLSRQRFYNIVSAAGKNAGLNIKVHPHMLRHACGYSLADNGVDTRLIQDYLGHRNIRHTVIYT 174
Cdd:PRK01287 236 VAMDGDGLARNTLTNMVGRYIRAAGIEKAGACHLFRHAMATQMLENGADTRHIQAILGHAKLETTQIYT 304
INT_C_like_4 cd01194
Uncharacterized site-specific tyrosine recombinase, C-terminal catalytic domain; Tyrosine ...
 7-173 7.42e-16

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


Pssm-ID: 271194 [Multi-domain]  Cd Length: 174  Bit Score: 72.02  E-value: 7.42e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 447103897   7 LTHHEINLLLQSVKQKSC--SSRDVCMILLAYFHGLRVSELLSLQLSDLELTTEK--IYIQ----RIKNGFStvhPLQKE 78
Cdd:cd01194    1 LTLEQARQLLASLPIDDSiiGLRDRAIISLMVTEGLRTVEIVRADVGDLRQEGEGtiLYVQgkgkTSKDDFV---YLRPD 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 447103897  79 EVIAITNWLNERNSLnvkHFNDnPwLFVSRT----GKPLSRQRFYNIVSAAGKNAGLN-IKVHPHMLRHACGYSLADNGV 153
Cdd:cd01194   78 VLKALQAYLKARGKL---DFEE-P-LFTSLSnnskGQRLTTRSIRRIIKKYLRKAGLDdDRLTAHSLRHTAGTLALKAGK 152

                        170       180
                 ....*....|....*....|
gi 447103897 154 DTRLIQDYLGHRNIRHTVIY 173
Cdd:cd01194  153 SLREVQQLLRHSDPNTTMIY 172
INT_C_like_3 cd01192
Uncharacterized site-specific tyrosine recombinase, C-terminal catalytic domain; Tyrosine ...
 10-173 8.60e-16

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


Pssm-ID: 271192 [Multi-domain]  Cd Length: 178  Bit Score: 71.94  E-value: 8.60e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 447103897  10 HEINLLLqsvkqKSCSSRDVCMILLAYFHGLRVSELLSLQLSDLeLTTEKIYIQRIKNGFSTVHPLQKEEVIAITNWLNE 89
Cdd:cd01192   13 KEIKLYL-----KKANPRNYLLFIVGINTGLRISDLLSLKVEDV-TNKDKLSIKEQKTGKQKTFPLNPTLVKALKEYIDD 86

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 447103897  90 RNSlnvKHFNDNPWLFVSRTGKPLSRQRFYNIVSAAGKNAGLNIKVHPHMLRHACGYSLADNGVDTRLIQDYLGHRNIRH 169
Cdd:cd01192   87 LDL---KRNDYLFKSLKQGPEKPISRKQAYKILKKAADDLGLNYNIGTHSLRKTFGYHVYKQGKDIELLMKLLNHSSPSI 163


                 ....
gi 447103897 170 TVIY 173
Cdd:cd01192  164 TLRY 167
INTN1_C_like cd01185
Integrase IntN1 of Bacteroides mobilizable transposon NBU1 and similar proteins, C-terminal ...
 16-174 1.45e-14

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: 68.06  E-value: 1.45e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 447103897  16 LQSVKQKSCSSRDV--CMILLAYFHGLRVSELLSLQLSDLELTTEKIYI--QRIKNGFSTVHPLQKEeVIAItnwLNERn 91
Cdd:cd01185    6 LMALELSDTSRLELvrDMFLFSCYTGLRFSDLKNLTWKNIVEASGRTWIryRRKKTGKPVTVPLLPV-AREI---LEKY- 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 447103897  92 slnvKHFNDNPWLFvsrtgKPLSRQRFYNIVSAAGKNAGLNIKVHPHMLRHACGYSLADNGVDTRLIQDYLGHRNIRHTV 171
Cdd:cd01185   81 ----KDDRSEGKLF-----PVLSNQKINRYLKEIAKIAGIDKHLTFHVARHTFATLLLLKGVDIETISKLLGHSSIKTTQ 151


                 ...
gi 447103897 172 IYT 174
Cdd:cd01185  152 IYA 154
INT_ICEBs1_C_like cd01189
C-terminal catalytic domain of integrases from bacterial phages and conjugate transposons; ...
 11-174 4.72e-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: 66.43  E-value: 4.72e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 447103897  11 EINLLLQSVKQKScsSRDVCMILLAYFHGLRVSELLSLQLSDLELTTEKIYI----QRIKNGFSTVHPLQKEE---VIAI 83
Cdd:cd01189    3 ELKKLLEALKKRG--DRYYLLFLLALLTGLRRGELLALTWSDIDFENGTIRInrtlVRKKKGGYVIKPPKTKSsirTIPL 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 447103897  84 TNWLNERnslnvkhfndnpwlfvsrtgkpLSRQRFYNivsAAGKNAGLNiKVHPHMLRHACGYSLADNGVDTRLIQDYLG 163
Cdd:cd01189   81 PDELIEL----------------------LKELKAFK---KLLKKAGLP-RITPHDLRHTFASLLLEAGVPLKVIAERLG 134

                        170
                 ....*....|..
gi 447103897 164 HRNIRHTV-IYT 174
Cdd:cd01189  135 HSDISTTLdVYA 146
INT_C_like_5 cd01195
Uncharacterized site-specific tyrosine recombinase, C-terminal catalytic domain; Tyrosine ...
 27-173 3.35e-13

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


Pssm-ID: 271195 [Multi-domain]  Cd Length: 170  Bit Score: 64.80  E-value: 3.35e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 447103897  27 RDVCMILLAYFHGLRVSELLSLQLSDLELttEKIYIQRIKNGfstvhPLQKEEVI-------AITNWLNERNSLNvkhfn 99
Cdd:cd01195   21 RDEALVRLLLDNALRRSEAVALDVEDLEK--EHRRLRILGKG-----KKQREVVTlppttreALAAWLAARGEAE----- 88

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 447103897 100 dNPwLFVS----RTGKPLSRQRFYNIVSAAGKNAGLNIKVHPHMLRHAcGYSLADNGV--DTRLIQDYLGHRNIRHTVIY 173
Cdd:cd01195   89 -GP-LFVSldraSRGRRLSPQAVYRIVRRLAERIGLGKRLSPHGLRHS-AITLALDAGagLIRKVQDFSRHADLRTLQVY 165
INT_RitB_C_like cd00797
C-terminal catalytic domain of recombinase RitB, a component of the recombinase trio; ...
 7-173 6.26e-11

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: 59.24  E-value: 6.26e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 447103897   7 LTHHEINLLLQSVKQKSCSS--RDV---CMILLAYFHGLRVSELLSLQLSDLELTTEKIYIQRIKNGFSTVHPLQKEEVI 81
Cdd:cd00797    1 YTDAEIRRLLAAADQLPPESplRPLtyaTLFGLLYATGLRVGEALRLRLEDVDLDSGILTIRQTKFGKSRLVPLHPSTVG 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 447103897  82 AITNWLNERN--SLNVKHfndnPWLFVSRTGKPLSRQRFYNIVSAAGKNAGLNIKV-----HPHMLRHA--------CGY 146
Cdd:cd00797   81 ALRDYLARRDrlLPSPSS----SYFFVSQQGGRLTGGGVYRVFRRLLRRIGLRGAGdgrgpRLHDLRHTfavnrltrWYR 156

                        170       180
                 ....*....|....*....|....*....
gi 447103897 147 SLADngVDTRL--IQDYLGHRNIRHTVIY 173
Cdd:cd00797  157 EGAD--VERKLpvLSTYLGHVNVTDTYWY 183
INT_tnpA_C_Tn554 cd01186
Putative Transposase A from transposon Tn554, C-terminal catalytic domain; This family ...
 7-170 3.05e-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: 57.04  E-value: 3.05e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 447103897   7 LTHHEINLLLQSVKQKscssRDVCMILLAYFHGLRVSELLSLQLSDLELTTEKIYIQ-RIKNGFSTVHPLQKEEVIAI-- 83
Cdd:cd01186    2 LTPREVQELINACNNL----RDKFLLALLYETGLRIGEALGLRIEDIDMADNQIELVpREDNTNEARAKSMRERRIPVsq 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 447103897  84 ------TNWLNERNSLNVKHfndNPWLFVS----RTGKPLSRQRFYNIVSAAGKNAGlnIKVHPHMLRHACGYSLADNGV 153
Cdd:cd01186   78 dlidlyADYLTYIYCEEAEF---SITVFVNvkggNQGKAMNYSDVYDLVRRLKKRTG--IDFTPHMFRHTHATALIRAGW 152

                        170
                 ....*....|....*..
gi 447103897 154 DTRLIQDYLGHRNIRHT 170
Cdd:cd01186  153 SIEVVARRLGHAHVQTT 169
integrase_gron TIGR02249
integron integrase; Members of this family are integrases associated with integrons (and ...
 31-174 3.85e-09

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: 55.09  E-value: 3.85e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 447103897   31 MILLAYFHGLRVSELLSLQLSDLELTTEKIYIQRIKNGFSTVHPLQKE------EVIAITNWLNERN------------S 92
Cdd:TIGR02249 121 IAKLLYGSGMRLMECLRLRIQDIDFDYGEIRIRQGKGGKDRTVTLPKElipplrEQIELARAYHEADlaegyggvylphA 200

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 447103897   93 LNVKHFNDN-----PWLFVS-------RTGK----PLSRQRFYNIVSAAGKNAGLNIKVHPHMLRHACGYSLADNGVDTR 156
Cdd:TIGR02249 201 LARKYPNAPkewgwQYLFPShrlsrdpESGVirrhHINETTIQRAVRRAVERAGIEKPVTCHTLRHSFATHLLESGADIR 280

                         170
                  ....*....|....*...
gi 447103897  157 LIQDYLGHRNIRHTVIYT 174
Cdd:TIGR02249 281 TVQELLGHSDVKTTQIYT 298
xerS PRK05084
site-specific tyrosine recombinase XerS; Reviewed
 27-174 6.60e-09

site-specific tyrosine recombinase XerS; Reviewed


Pssm-ID: 235339 [Multi-domain]  Cd Length: 357  Bit Score: 54.54  E-value: 6.60e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 447103897  27 RDVCMILLAYFHGLRVSELLSLQLSDLELTTEKIYIQRiKNGfstvhplqKEEVIAITNW--------LNERNSLnVKHF 98
Cdd:PRK05084 196 RDLAIIALILGSGLRVSELVNLDLSDLNLKQMTIDVTR-KGG--------KRDSVNIAPFalpyleeyLKIRASR-YKAE 265

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 447103897  99 NDNPWLFVSR---TGKPLSR---QRFYNIVSAAgknagLNIKVHPHMLRHACGYSLADNGVDTRLIQDYLGHRNIRHTVI 172
Cdd:PRK05084 266 KQEKALFLTKyrgKPNRISAraiEKMVAKYSEA-----FGVRLTPHKLRHTLATRLYDATKDQVLVADQLGHTSTETTDL 340


                 ..
gi 447103897 173 YT 174
Cdd:PRK05084 341 YT 342
FimB COG0582
Integrase/recombinase, includes phage integrase [Replication, recombination and repair, ...
 2-166 9.07e-09

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


Pssm-ID: 440347 [Multi-domain]  Cd Length: 391  Bit Score: 54.27  E-value: 9.07e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 447103897   2 QNRKFLTHHEINLLLQSVKQKSCSSRDVCMILLAYFHGLRVSELLSLQLSDLELTTEKIYI--QRIKNGFSTVHPLQKeE 79
Cdd:COG0582  201 KHHPALTPEELPELLRALDAYRGSPVTRLALRLLLLTGVRPGELRGARWSEIDLEAALWTIpaERMKTRRPHIVPLSR-Q 279

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 447103897  80 VIAItnwLNERNSLNvkhfNDNPWLFVSRTG--KPLSRqrfyNIVSAAGKNAGLNiKVHPHMLRHACGYSLADNGVDTRL 157
Cdd:COG0582  280 ALEI---LKELKPLT----GDSEYVFPSRRGpkKPMSE----NTLNKALRRMGYG-RFTPHGFRHTASTLLNEAGFPPDV 347


                 ....*....
gi 447103897 158 IQDYLGHRN 166
Cdd:COG0582  348 IERQLAHKD 356
INT_Cre_C cd00799
C-terminal catalytic domain of Cre recombinase (also called integrase); Cre-like recombinases ...
 27-174 2.99e-08

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: 51.53  E-value: 2.99e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 447103897  27 RDVCMILLAYFHGLRVSELLSLQLSDLELTTEKIYI---------QRIKNGFSTVHPLQKEEVI-AITNWLNERNSLnvk 96
Cdd:cd00799   17 RDRALLLLGFAGALRRSELVALRVEDLTRFVDGGLLirlrrsktdQDGEGEIKALPYGPETCPVrALRAWLEAAGIP--- 93

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 447103897  97 hfnDNPwLF--VSRTGK----PLSRQRFYNIVSAAGKNAGLNIKVH-PHMLRHACGYSLADNGVDTRLIQDYLGHRNIRH 169
Cdd:cd00799   94 ---SGP-LFrrIRRGGSvgttRLSDRSVARIVKRRAALAGLDPGDFsGHSLRRGFATEAARAGASLPEIMAQGGHKSVAT 169


                 ....*
gi 447103897 170 TVIYT 174
Cdd:cd00799  170 VMRYI 174
PRK15417 PRK15417
integron integrase;
34-174 2.10e-07

integron integrase;


Pssm-ID: 185315 [Multi-domain]  Cd Length: 337  Bit Score: 50.04  E-value: 2.10e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 447103897  34 LAYFHGLRVSELLSLQLSDLELTTEKIYIQRIKNGF-------STVHPLQKEEVI-AITNWLNER----------NSLNV 95
Cdd:PRK15417 139 LLYGTGMRISEGLQLRVKDLDFDHGTIIVREGKGSKdralmlpESLAPSLREQLSrARAWWLKDQaegrsgvalpDALER 218

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 447103897  96 KHFNDN---PWLFV----SRTGKPLS---------RQRFYNIVSAAGKNAGLNIKVHPHMLRHACGYSLADNGVDTRLIQ 159
Cdd:PRK15417 219 KYPRAGhswPWFWVfaqhTHSTDPRSgvvrrhhmyDQTFQRAFKRAVEQAGITKPATPHTLRHSFATALLRSGYDIRTVQ 298

                        170
                 ....*....|....*
gi 447103897 160 DYLGHRNIRHTVIYT 174
Cdd:PRK15417 299 DLLGHSDVSTTMIYT 313
INT_P4_C cd00801
Bacteriophage P4 integrase, C-terminal catalytic domain; P4-like integrases are found in ...
 8-164 1.48e-06

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


Pssm-ID: 271182 [Multi-domain]  Cd Length: 180  Bit Score: 46.49  E-value: 1.48e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 447103897   8 THHEINLLLQSVKQKSCSSRDVCMILLAYFHGLRVSELLSLQLSDLELTTEKIYI--QRIKNGfstvhplqKEEVIAIT- 84
Cdd:cd00801    1 SPDELPELWRALDTANLSPPTKLALRLLLLTGQRIGELARARWSEIDLEEKTWTIpaERTKNK--------RPHRVPLSd 72

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 447103897  85 ---NWLNERnslnVKHFNDNPWLFVSRTGKPLSRQRfyNIVSAAGKNAGLNIKVH-PHMLRHACGYSLADNGVDTRLIQD 160
Cdd:cd00801   73 qalEILEEL----KEFTGDSGYLFPSRRKKKKPISE--NTINKALKRLGYKGKEFtPHDLRRTFSTLLNELGIDPEVIER 146


                 ....
gi 447103897 161 YLGH 164
Cdd:cd00801  147 LLNH 150
INT_C_like_1 cd01184
Uncharacterized site-specific tyrosine recombinase, C-terminal catalytic domain; Tyrosine ...
 7-165 1.34e-05

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: 43.83  E-value: 1.34e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 447103897   7 LTHHEINLLLQSVKQKSCSSRDVC---MILLAYFHGLRVSELLSLQLSD---------LELTTEKiYIQRIKNGFST--- 71
Cdd:cd01184    1 FTPEELAKIFSSPLYTGCKKKDPAlywLPLIGLYTGARLNEICQLRVDDikeedgiwcIDINDDA-EGRRLKTKASRrlv 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 447103897  72 -VHPlqkeEVIAI--TNWLNERNSLNVKHFNDNPWLFVSRTGKPLSRqRFYNIVSAAGKNAGLNIKVHPhmLRHACGYSL 148
Cdd:cd01184   80 pIHP----RLIELgfLDYVEALRADGKLFLFPEKRDKDGKYSKAASK-WFNRLLRKLGIKDDERKSFHS--FRHTFITAL 152

                        170
                 ....*....|....*..
gi 447103897 149 ADNGVDTRLIQDYLGHR 165
Cdd:cd01184  153 KRAGVPEELIAQIVGHS 169
INT_tnpB_C_Tn554 cd01187
Putative Transposase B from transposon Tn554, C-terminal catalytic domain; This family ...
 31-173 3.07e-05

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: 42.42  E-value: 3.07e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 447103897  31 MILLAYFHGLRVSELLSLQLSDLELTTEK----IYIQRIKNGFSTVH--PLQKE--EVIAITNWlnernslNVKHFNdnp 102
Cdd:cd01187   18 VVQAAVFTGARASELATLKFGCLHAQTSDdgtfLYWLKWENKGGKQLdiPISKKvaELIKTINW-------TLNELS--- 87

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 447103897 103 wLFVSRTGKPLSRQRFynivsaagknaglnikvHPHMLRHACGYSLADNGVDTRLIQDYLGHRNIRHTVIY 173
Cdd:cd01187   88 -ELKNISDDHGERFRF-----------------HTHRFRHTVATRLANSGMGILVLQQLLGHSSPEMTLRY 140
int PHA02601
integrase; Provisional
 6-173 3.99e-05

integrase; Provisional


Pssm-ID: 222904 [Multi-domain]  Cd Length: 333  Bit Score: 43.56  E-value: 3.99e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 447103897   6 FLTHHEINLLLQSVKQ-KSCSSRDVCMILLAYfhGLRVSELLSLQLSdlELTTEKIYIQRIKNGfstvhplqKEEVIAIT 84
Cdd:PHA02601 172 FLTKEEIERLLDACDGsRSPDLGLIAKICLAT--GARWSEAETLKRS--QISPYKITFVKTKGK--------KNRTVPIS 239

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 447103897  85 NWLNERNSlnvkhfndnpwlfvSRTGK--PLSRQRFYNIVSAAGknaglnIKVHP----HMLRHACGYSLADNGVDTRLI 158
Cdd:PHA02601 240 EELYKMLP--------------KRRGRlfKDAYESFERAVKRAG------IDLPEgqatHVLRHTFASHFMMNGGNILVL 299

                        170
                 ....*....|....*
gi 447103897 159 QDYLGHRNIRHTVIY 173
Cdd:PHA02601 300 QRILGHATIEMTMAY 314
INT_Lambda_C cd00800
C-terminal catalytic domain of Lambda integrase, a tyrosine-based site-specific recombinase; ...
 32-174 5.99e-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: 38.86  E-value: 5.99e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 447103897  32 ILLAYFHGLRVSELLSLQLSDleLTTEKIYIQRIKNG----FSTVHPLQkeEVIAITNWLNERNSLnvkhfndnpWLFVS 107
Cdd:cd00800   18 MELALLTGQRQGDLLRLKWSD--ITDGGLLVEQSKTGkkllIPWTPSLR--ALVDRIRALPRKRSE---------YLINS 84

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 447103897 108 RTGKPLSRQRFYNIVSAAGKNAGLNIKVHP---HMLRHACGYSLADNGVDTRlIQDYLGHRNIRHTVIYT 174
Cdd:cd00800   85 RKGGPLSYDTLKSAWRRARKAAGLKGETEGftfHDLRAKAATDYAEQGGSTD-AQALLGHKSDAMTERYT 153
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

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