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Conserved domains on  [gi|504293879|ref|WP_014480981|]
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MULTISPECIES: tyrosine-type recombinase/integrase [Bacillus]

Protein Classification

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

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

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

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
XerD COG4974
Site-specific recombinase XerD [Replication, recombination and repair];
38-322 3.08e-67

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


:

Pssm-ID: 443999 [Multi-domain]  Cd Length: 291  Bit Score: 212.55  E-value: 3.08e-67
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504293879  38 ELFETENYRERTINDYRKYWSEFMEVAGIQPTDNITDITEDHLRSYISTMLNvRDLSPVTINIRLGGIKSILSRMTKRGL 117
Cdd:COG4974   13 ELKREKGLSPNTIKAYRRDLRRFLRFLEELGKIPLAEITPEDIRAYLNYLRE-RGLSPSTINRYLAALRSFFRYAVREGL 91

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504293879 118 INENPAKRVTKLRVDEKTIKMLTDSQVRRFFKMIDKDTFPGFRDYVAFLIALKCGLRSNELEGLKPEDIDFDNLVIMLPG 197
Cdd:COG4974   92 LEDNPAAKVKLPKKPRKLPRVLTEEEIEALLEALDTETPEGLRDRALLLLLYATGLRVSELLGLKWSDIDLDRGTIRVRR 171

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504293879 198 AvnKNRKNRMVPMTEQVAEELRQLLTEMTEYFGTFthVFVNQYGEKIAKDHLRKRAAKYGEMADLKKECRPslHSLRHTF 277
Cdd:COG4974  172 G--KGGKERTVPLSPEALEALREYLEERRPRDSDY--LFPTRRGRPLSRRAIRKILKRLAKRAGIPKRVTP--HSLRHTF 245

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|....*
gi 504293879 278 AINYLRNGSDIRSLQKIMGHADLASTEIYLDYVDDIVIEQYRKAS 322
Cdd:COG4974  246 ATHLLEAGVDLRTVQELLGHSSISTTQIYTHVSDEELREAVEKLH 290
 
Name Accession Description Interval E-value
XerD COG4974
Site-specific recombinase XerD [Replication, recombination and repair];
38-322 3.08e-67

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


Pssm-ID: 443999 [Multi-domain]  Cd Length: 291  Bit Score: 212.55  E-value: 3.08e-67
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504293879  38 ELFETENYRERTINDYRKYWSEFMEVAGIQPTDNITDITEDHLRSYISTMLNvRDLSPVTINIRLGGIKSILSRMTKRGL 117
Cdd:COG4974   13 ELKREKGLSPNTIKAYRRDLRRFLRFLEELGKIPLAEITPEDIRAYLNYLRE-RGLSPSTINRYLAALRSFFRYAVREGL 91

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504293879 118 INENPAKRVTKLRVDEKTIKMLTDSQVRRFFKMIDKDTFPGFRDYVAFLIALKCGLRSNELEGLKPEDIDFDNLVIMLPG 197
Cdd:COG4974   92 LEDNPAAKVKLPKKPRKLPRVLTEEEIEALLEALDTETPEGLRDRALLLLLYATGLRVSELLGLKWSDIDLDRGTIRVRR 171

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504293879 198 AvnKNRKNRMVPMTEQVAEELRQLLTEMTEYFGTFthVFVNQYGEKIAKDHLRKRAAKYGEMADLKKECRPslHSLRHTF 277
Cdd:COG4974  172 G--KGGKERTVPLSPEALEALREYLEERRPRDSDY--LFPTRRGRPLSRRAIRKILKRLAKRAGIPKRVTP--HSLRHTF 245

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|....*
gi 504293879 278 AINYLRNGSDIRSLQKIMGHADLASTEIYLDYVDDIVIEQYRKAS 322
Cdd:COG4974  246 ATHLLEAGVDLRTVQELLGHSSISTTQIYTHVSDEELREAVEKLH 290
DNA_BRE_C cd00397
DNA breaking-rejoining enzymes, C-terminal catalytic domain; The DNA breaking-rejoining enzyme ...
 143-307 2.15e-39

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: 136.84  E-value: 2.15e-39
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504293879 143 QVRRFFKMIDKDTFPGFRDYVAFLIALKCGLRSNELEGLKPEDIDFDNLVIMLPGAVNKNRKNRMVPMTEQVAEELRQLL 222
Cdd:cd00397    1 ELEKLLDAIDEDKKIDLRDRAILLLLLETGLRISELLALKVKDIDLDNGTIRVRGKKTKGGKERTVPLPKELAEELKEYL 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504293879 223 TEMTEYFG------TFTHVFVNQYGEKIAKDHLRKRAAKYGEMAdlkkECRPSLHSLRHTFAINYLRNGSDIRSLQKIMG 296
Cdd:cd00397   81 KERRDKRGpllkslYLNKLFGTKLGERLSRRTLRRIFKKAGIEA----GRKITPHSLRHTFATNLLENGVDIKVVQKLLG 156

                        170
                 ....*....|.
gi 504293879 297 HADLASTEIYL 307
Cdd:cd00397  157 HSSISTTQRYL 167
xerC PRK00236
site-specific tyrosine recombinase XerC; Reviewed
 44-306 1.54e-38

site-specific tyrosine recombinase XerC; Reviewed


Pssm-ID: 234698 [Multi-domain]  Cd Length: 297  Bit Score: 138.36  E-value: 1.54e-38
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504293879  44 NYRERTINDYR---KYWSEFMEVAGIQptdNITDITEDHLRSYISTMLNvRDLSPVTINIRLGGIKSILSRMTKRGLINE 120
Cdd:PRK00236  22 GLSPHTLRAYRrdlRAFLAFLEEHGIS---SLQDLDAADLRSFLARRRR-QGLSARSLARRLSALRSFYRWLVRRGLLKA 97

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504293879 121 NPAKRVTKLRVdEKTI-KMLTDSQVRRFFKMIDKDTFPGFRDYVAFLIALKCGLRSNELEGLKPEDIDFDNLVIMLPGav 199
Cdd:PRK00236  98 NPAAGLRAPKI-PKRLpKPLDVDQAKRLLDAIDEDDPLALRDRAILELLYGSGLRLSELVGLDIDDLDLASGTLRVLG-- 174

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504293879 200 nKNRKNRMVPMTEQVAEELRQLLtEMTEYFGTFTH-VFVNQYGEKIAKDHLRKRAAKYGEMADLKKECRPslHSLRHTFA 278
Cdd:PRK00236 175 -KGNKERTVPLGRAAREALEAYL-ALRPLFLPDDDaLFLGARGGRLSPRVVQRRVKKLGKKAGLPSHITP--HKLRHSFA 250

                        250       260
                 ....*....|....*....|....*...
gi 504293879 279 INYLRNGSDIRSLQKIMGHADLASTEIY 306
Cdd:PRK00236 251 THLLESGGDLRAVQELLGHASLSTTQIY 278
recomb_XerD TIGR02225
tyrosine recombinase XerD; The phage integrase family describes a number of recombinases with ...
 49-306 2.95e-38

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: 137.33  E-value: 2.95e-38
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504293879   49 TINDYR---KYWSEFMEVAGIqptdNITDITEDHLRSYISTMLNvRDLSPVTINIRLGGIKSILSRMTKRGLINENPAKR 125
Cdd:TIGR02225  17 TLEAYRrdlEKFLEFLEERGI----DLEEVDRGDIVDFLAELKE-AGLSARSIARALSALRSFYRFLLREGIREDDPSAL 91

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504293879  126 VTKLRVDEKTIKMLTDSQVRRFFKMIDKDTFPGFRDYVAFLIALKCGLRSNELEGLKPEDIDFDNLVIMLPGavnKNRKN 205
Cdd:TIGR02225  92 IEPPKVARKLPKVLTVEEVEALLAAPDVDTPLGLRDRAMLELLYATGLRVSELVGLRLEDVNLDEGFVRVRG---KGNKE 168

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504293879  206 RMVPMTEQVAEELRQLLTEMTEYFGTFTH-----VFVNQYGEKIAKDHLRKRAAKYGEMADLKKECRPslHSLRHTFAIN 280
Cdd:TIGR02225 169 RLVPLGEEAIEALERYLKEARPLLLKKKVkesdaLFLNRRGGPLSRQGVWKILKEYAKRAGIEKPISP--HTLRHSFATH 246

                         250       260
                  ....*....|....*....|....*.
gi 504293879  281 YLRNGSDIRSLQKIMGHADLASTEIY 306
Cdd:TIGR02225 247 LLENGADLRVVQELLGHADISTTQIY 272
Phage_integrase pfam00589
Phage integrase family; Members of this family cleave DNA substrates by a series of staggered ...
 139-308 3.84e-31

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: 115.11  E-value: 3.84e-31
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504293879  139 LTDSQVRRFFKMIDKDTFPgFRDYVAFLIALKCGLRSNELEGLKPEDIDFDNLVIMLPgaVNKNRKNRMVPMTEQVAEEL 218
Cdd:pfam00589   2 LTEDEVERLLDAAETGPLS-IRDKALLELLYATGLRISELCSLRWSDIDFENGVIRVH--RGKGNKERTVPLSDAALELL 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504293879  219 RQLLTEMTEYFGTFTHVFVNQYGEKIAKDHLRKRAAKYGEMADLKKECRPslHSLRHTFAINYLRNGSDIRSLQKIMGHA 298
Cdd:pfam00589  79 KEWLSKRLLEAPKSDYLFASKRGKPLSRQTVRKIFKRAGKEAGLELPLHP--HMLRHSFATHLLEAGVDLRVVQKLLGHS 156

                         170
                  ....*....|
gi 504293879  299 DLASTEIYLD 308
Cdd:pfam00589 157 SISTTQIYTH 166
 
Name Accession Description Interval E-value
XerD COG4974
Site-specific recombinase XerD [Replication, recombination and repair];
38-322 3.08e-67

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


Pssm-ID: 443999 [Multi-domain]  Cd Length: 291  Bit Score: 212.55  E-value: 3.08e-67
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504293879  38 ELFETENYRERTINDYRKYWSEFMEVAGIQPTDNITDITEDHLRSYISTMLNvRDLSPVTINIRLGGIKSILSRMTKRGL 117
Cdd:COG4974   13 ELKREKGLSPNTIKAYRRDLRRFLRFLEELGKIPLAEITPEDIRAYLNYLRE-RGLSPSTINRYLAALRSFFRYAVREGL 91

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504293879 118 INENPAKRVTKLRVDEKTIKMLTDSQVRRFFKMIDKDTFPGFRDYVAFLIALKCGLRSNELEGLKPEDIDFDNLVIMLPG 197
Cdd:COG4974   92 LEDNPAAKVKLPKKPRKLPRVLTEEEIEALLEALDTETPEGLRDRALLLLLYATGLRVSELLGLKWSDIDLDRGTIRVRR 171

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504293879 198 AvnKNRKNRMVPMTEQVAEELRQLLTEMTEYFGTFthVFVNQYGEKIAKDHLRKRAAKYGEMADLKKECRPslHSLRHTF 277
Cdd:COG4974  172 G--KGGKERTVPLSPEALEALREYLEERRPRDSDY--LFPTRRGRPLSRRAIRKILKRLAKRAGIPKRVTP--HSLRHTF 245

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|....*
gi 504293879 278 AINYLRNGSDIRSLQKIMGHADLASTEIYLDYVDDIVIEQYRKAS 322
Cdd:COG4974  246 ATHLLEAGVDLRTVQELLGHSSISTTQIYTHVSDEELREAVEKLH 290
XerC COG4973
Site-specific recombinase XerC [Replication, recombination and repair];
26-319 8.64e-57

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


Pssm-ID: 443998 [Multi-domain]  Cd Length: 287  Bit Score: 185.55  E-value: 8.64e-57
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504293879  26 TKTVHEALGIVCELFETENYRERTINDYRKYWSEFMEVAGIQPTDnITDITEDHLRSYISTMLNvRDLSPVTINIRLGGI 105
Cdd:COG4973    1 KLTLAEALEAYLEHLRERRLSPKTLEAYRRDLRRLIPLLGDADLP-LEELTPADVRRFLARLHR-RGLSPRTLNRRLSAL 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504293879 106 KSILSRMTKRGLINENPAKRVTKLRVDEKTIKMLTDSQVRRFFKMIDKDTFpGFRDYVAFLIALKCGLRSNELEGLKPED 185
Cdd:COG4973   79 RSFFNWAVREGLLEANPAAGVKAPKAPRKLPRALTVDELAQLLDALADDPL-AVRDRAIVELLYSTGLRLGELVGLDWED 157

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504293879 186 IDFDNLVIMLPGavnKNRKNRMVPMTEQVAEELRQLLTEMTEYFGTFTH-VFVNQYGEKIAKDHLRKRAAKYGEMADLKK 264
Cdd:COG4973  158 VDLDAGEVRVRG---KTGKSRTVPLGPKALAALREWLAVRPELAAPDEGaLFPSRRGTRLSPRNVQKRLRRLAKKAGLPK 234

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 504293879 265 ECRPslHSLRHTFAINYLRNGSDIRSLQKIMGHADLASTEIYLDYVDDIVIEQYR 319
Cdd:COG4973  235 HVHP--HDLRHSFATHLLESGGDLRAVQELLGHASISTTQIYTHLDFQHLAEVYR 287
DNA_BRE_C cd00397
DNA breaking-rejoining enzymes, C-terminal catalytic domain; The DNA breaking-rejoining enzyme ...
 143-307 2.15e-39

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: 136.84  E-value: 2.15e-39
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504293879 143 QVRRFFKMIDKDTFPGFRDYVAFLIALKCGLRSNELEGLKPEDIDFDNLVIMLPGAVNKNRKNRMVPMTEQVAEELRQLL 222
Cdd:cd00397    1 ELEKLLDAIDEDKKIDLRDRAILLLLLETGLRISELLALKVKDIDLDNGTIRVRGKKTKGGKERTVPLPKELAEELKEYL 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504293879 223 TEMTEYFG------TFTHVFVNQYGEKIAKDHLRKRAAKYGEMAdlkkECRPSLHSLRHTFAINYLRNGSDIRSLQKIMG 296
Cdd:cd00397   81 KERRDKRGpllkslYLNKLFGTKLGERLSRRTLRRIFKKAGIEA----GRKITPHSLRHTFATNLLENGVDIKVVQKLLG 156

                        170
                 ....*....|.
gi 504293879 297 HADLASTEIYL 307
Cdd:cd00397  157 HSSISTTQRYL 167
xerC PRK00236
site-specific tyrosine recombinase XerC; Reviewed
 44-306 1.54e-38

site-specific tyrosine recombinase XerC; Reviewed


Pssm-ID: 234698 [Multi-domain]  Cd Length: 297  Bit Score: 138.36  E-value: 1.54e-38
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504293879  44 NYRERTINDYR---KYWSEFMEVAGIQptdNITDITEDHLRSYISTMLNvRDLSPVTINIRLGGIKSILSRMTKRGLINE 120
Cdd:PRK00236  22 GLSPHTLRAYRrdlRAFLAFLEEHGIS---SLQDLDAADLRSFLARRRR-QGLSARSLARRLSALRSFYRWLVRRGLLKA 97

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504293879 121 NPAKRVTKLRVdEKTI-KMLTDSQVRRFFKMIDKDTFPGFRDYVAFLIALKCGLRSNELEGLKPEDIDFDNLVIMLPGav 199
Cdd:PRK00236  98 NPAAGLRAPKI-PKRLpKPLDVDQAKRLLDAIDEDDPLALRDRAILELLYGSGLRLSELVGLDIDDLDLASGTLRVLG-- 174

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504293879 200 nKNRKNRMVPMTEQVAEELRQLLtEMTEYFGTFTH-VFVNQYGEKIAKDHLRKRAAKYGEMADLKKECRPslHSLRHTFA 278
Cdd:PRK00236 175 -KGNKERTVPLGRAAREALEAYL-ALRPLFLPDDDaLFLGARGGRLSPRVVQRRVKKLGKKAGLPSHITP--HKLRHSFA 250

                        250       260
                 ....*....|....*....|....*...
gi 504293879 279 INYLRNGSDIRSLQKIMGHADLASTEIY 306
Cdd:PRK00236 251 THLLESGGDLRAVQELLGHASLSTTQIY 278
recomb_XerD TIGR02225
tyrosine recombinase XerD; The phage integrase family describes a number of recombinases with ...
 49-306 2.95e-38

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: 137.33  E-value: 2.95e-38
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504293879   49 TINDYR---KYWSEFMEVAGIqptdNITDITEDHLRSYISTMLNvRDLSPVTINIRLGGIKSILSRMTKRGLINENPAKR 125
Cdd:TIGR02225  17 TLEAYRrdlEKFLEFLEERGI----DLEEVDRGDIVDFLAELKE-AGLSARSIARALSALRSFYRFLLREGIREDDPSAL 91

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504293879  126 VTKLRVDEKTIKMLTDSQVRRFFKMIDKDTFPGFRDYVAFLIALKCGLRSNELEGLKPEDIDFDNLVIMLPGavnKNRKN 205
Cdd:TIGR02225  92 IEPPKVARKLPKVLTVEEVEALLAAPDVDTPLGLRDRAMLELLYATGLRVSELVGLRLEDVNLDEGFVRVRG---KGNKE 168

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504293879  206 RMVPMTEQVAEELRQLLTEMTEYFGTFTH-----VFVNQYGEKIAKDHLRKRAAKYGEMADLKKECRPslHSLRHTFAIN 280
Cdd:TIGR02225 169 RLVPLGEEAIEALERYLKEARPLLLKKKVkesdaLFLNRRGGPLSRQGVWKILKEYAKRAGIEKPISP--HTLRHSFATH 246

                         250       260
                  ....*....|....*....|....*.
gi 504293879  281 YLRNGSDIRSLQKIMGHADLASTEIY 306
Cdd:TIGR02225 247 LLENGADLRVVQELLGHADISTTQIY 272
INT_XerDC_C cd00798
XerD and XerC integrases, C-terminal catalytic domains; XerDC-like integrases are involved in ...
 143-306 1.04e-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: 119.15  E-value: 1.04e-32
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504293879 143 QVRRFFKMIDKDTFPGFRDyvAFLIAL--KCGLRSNELEGLKPEDIDFDNLVIMLPGavnKNRKNRMVPMTEQVAEELRQ 220
Cdd:cd00798    3 EVERLLDAPDTDTPLGLRD--RAILELlyASGLRVSELVGLDLSDVDLDEGLVRVTG---KGNKERLVPFGSYAVEALEE 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504293879 221 LLTE---MTEYFGTFTHVFVNQYGEKIAKDHLRKRAAKYGEMADLKKECRPslHSLRHTFAINYLRNGSDIRSLQKIMGH 297
Cdd:cd00798   78 YLEErrpLLLKKKPPDALFLNKRGKRLSRRGVWRILKKYAERAGLPKHVSP--HTLRHSFATHLLEGGADLRVVQELLGH 155


                 ....*....
gi 504293879 298 ADLASTEIY 306
Cdd:cd00798  156 ASLSTTQIY 164
Phage_integrase pfam00589
Phage integrase family; Members of this family cleave DNA substrates by a series of staggered ...
 139-308 3.84e-31

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: 115.11  E-value: 3.84e-31
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504293879  139 LTDSQVRRFFKMIDKDTFPgFRDYVAFLIALKCGLRSNELEGLKPEDIDFDNLVIMLPgaVNKNRKNRMVPMTEQVAEEL 218
Cdd:pfam00589   2 LTEDEVERLLDAAETGPLS-IRDKALLELLYATGLRISELCSLRWSDIDFENGVIRVH--RGKGNKERTVPLSDAALELL 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504293879  219 RQLLTEMTEYFGTFTHVFVNQYGEKIAKDHLRKRAAKYGEMADLKKECRPslHSLRHTFAINYLRNGSDIRSLQKIMGHA 298
Cdd:pfam00589  79 KEWLSKRLLEAPKSDYLFASKRGKPLSRQTVRKIFKRAGKEAGLELPLHP--HMLRHSFATHLLEAGVDLRVVQKLLGHS 156

                         170
                  ....*....|
gi 504293879  299 DLASTEIYLD 308
Cdd:pfam00589 157 SISTTQIYTH 166
INT_IntI_C cd01193
Integron integrase and similar protiens, C-terminal catalytic domain; Integron integrases ...
 139-307 3.93e-29

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: 110.06  E-value: 3.93e-29
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504293879 139 LTDSQVRRFFkmidkDTFPGFRDYVAFLIALKCGLRSNELEGLKPEDIDFDNLVIMLPGAvnKNRKNRMVPMTEQVAEEL 218
Cdd:cd01193    6 LSPDEVRRIL-----GALTELRHRLILSLLYGAGLRISELLRLRVKDIDFERGVIRVRQG--KGGKDRVVPLPEKLLEPL 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504293879 219 RQLLTEMT----EYFGTFTHVFVNQYGEKIAKDHLRKRA-----AKYGEMADLKKECRPslHSLRHTFAINYLRNGSDIR 289
Cdd:cd01193   79 RRYLKSARpkeeLDPAEGRAGVLDPRTGVERRHHISETTvqralKKAVEQAGITKRVTP--HTLRHSFATHLLEAGTDIR 156

                        170
                 ....*....|....*...
gi 504293879 290 SLQKIMGHADLASTEIYL 307
Cdd:cd01193  157 TIQELLGHSDLSTTMIYT 174
xerD PRK00283
tyrosine recombinase;
49-306 1.93e-26

tyrosine recombinase;


Pssm-ID: 234713 [Multi-domain]  Cd Length: 299  Bit Score: 106.04  E-value: 1.93e-26
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504293879  49 TINDYR---KYWSEFMEVAGIqptdNITDITEDHLRSYISTMLNvRDLSPVTINIRLGGIKSiLSRMTKR-GLINENPAK 124
Cdd:PRK00283  26 TLSSYRrdlELFAEWLAARGL----SLAEATRDDLQAFLAELAE-GGYKATSSARRLSALRR-FFQFLLReGLREDDPSA 99

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504293879 125 RVTKLRVDEKTIKMLTDSQVRRFFKMIDKDTFPGFRDYvAFLIAL-KCGLRSNELEGLKPEDIDFDNLVIMLPGavnKNR 203
Cdd:PRK00283 100 LLDSPKLPRRLPKTLSEAQVEALLDAPDIDTPLGLRDR-AMLELLyATGLRVSELVGLTLDDVSLRQGVVRVTG---KGN 175

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504293879 204 KNRMVPMTEQVAEELRQLLTEMTEYF---GTFTHVFVNQYGEKIAKD---HLRKRAAKYgemADLKKEcRPSLHSLRHTF 277
Cdd:PRK00283 176 KERLVPLGEEAVYAIERYLERGRPALlngRSSDALFPSARGGQLTRQtfwHRIKHYAKR---AGIDPK-KLSPHVLRHAF 251

                        250       260
                 ....*....|....*....|....*....
gi 504293879 278 AINYLRNGSDIRSLQKIMGHADLASTEIY 306
Cdd:PRK00283 252 ATHLLNHGADLRVVQELLGHSDISTTQIY 280
xerC PRK01287
site-specific tyrosine recombinase XerC; Reviewed
 44-306 3.39e-26

site-specific tyrosine recombinase XerC; Reviewed


Pssm-ID: 234935 [Multi-domain]  Cd Length: 358  Bit Score: 106.75  E-value: 3.39e-26
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504293879  44 NYRERTINDYRKYWSEFM---EVAGI----QPTDNITDITEDHLRSYISTmlNVRDLSPVTINIRLGGIKSILSRMTKRG 116
Cdd:PRK01287  36 NWSERTLKVYTEHLYPFIlwcEERGLyyaaDVTLPVLERYQRYLYGYRKA--NGEPLSTRTQRTQLSPLRVWFRWLLKRH 113

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504293879 117 LINENPAKRVTkLRVDEKTI--KMLTDSQVRRFFKMIDKDTFPGFRDYVAFLIALKCGLRSNELEGLKPEDIDFDNLVIM 194
Cdd:PRK01287 114 HILYNPAEDLE-LPKEEKRLprQILSEAETEQVLASPDLTTLQGLRDRALLELLWSTGIRRGELARLDLYDVDASRGVVT 192

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504293879 195 LPGAvnKNRKNRMVPMTEQ----VAEELRQLLTEMTEYFGTfTHVFVNQYGEKIAKDHLRKRAAKYGEMADLKKecRPSL 270
Cdd:PRK01287 193 VRQG--KGNKDRVVPVGERalawLQRYLQDVRPQLAVRPDS-GALFVAMDGDGLARNTLTNMVGRYIRAAGIEK--AGAC 267

                        250       260       270
                 ....*....|....*....|....*....|....*.
gi 504293879 271 HSLRHTFAINYLRNGSDIRSLQKIMGHADLASTEIY 306
Cdd:PRK01287 268 HLFRHAMATQMLENGADTRHIQAILGHAKLETTQIY 303
INT_RitC_C_like cd01182
C-terminal catalytic domain of recombinase RitC, a component of the recombinase trio; ...
 139-308 1.60e-25

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: 100.82  E-value: 1.60e-25
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504293879 139 LTDSQVRRFFKMIDKDTFPGFRDYVAFLIALKCGLRSNELEGLKPEDIDFDNL-VIMLPGavnKNRKNRMVPMTEQVAEE 217
Cdd:cd01182    1 LTREEMKALLAAPDRNTSLGRRDHALLLLLYDTGARVQELADLTIRDLRLDDPaTVRLHG---KGRKERTVPLWKETVAA 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504293879 218 LRQLlteMTEYFGTFT-----HVFVNQYGEKIAKDHLRKRAAKYGEMAdlkKECRPSL------HSLRHTFAINYLRNGS 286
Cdd:cd01182   78 LKAY---LQEFHLTPDpkqlfPLFPNRRGQPLTRDGVAYILNKYVALA---SNRCPSLpkritpHTLRHTKAMHLLQAGV 151

                        170       180
                 ....*....|....*....|..
gi 504293879 287 DIRSLQKIMGHADLASTEIYLD 308
Cdd:cd01182  152 DLTVIRDWLGHESVETTQIYAE 173
INT_Rci_Hp1_C cd00796
Shufflon-specific DNA recombinase Rci and Bacteriophage Hp1_like integrase, C-terminal ...
 139-306 9.89e-24

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: 95.09  E-value: 9.89e-24
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504293879 139 LTDSQVRRFFKMIDKDTFPGFRDYVAFLIALkcGLRSNELEGLKPEDIDFDNLVIMLPGAvnKNRKNRMVPMTEQVAEEL 218
Cdd:cd00796    5 LTEDEEARLLAALEESTNPHLRLIVLLALYT--GARRGEILSLRWDDIDLEVGLIVLPET--KNGKPRTVPLSDEAIAIL 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504293879 219 RQLLTEMTEY-FGTFTHVFVNQYgekiakDHLRKRAAKYGEMADLKKeCRPslHSLRHTFAINYLRNGSDIRSLQKIMGH 297
Cdd:cd00796   81 KELKRKRGKDgFFVDGRFFGIPI------ASLRRAFKKARKRAGLED-LRF--HDLRHTFASRLVQAGVPIKTVAKILGH 151


                 ....*....
gi 504293879 298 ADLASTEIY 306
Cdd:cd00796  152 SSIKMTMRY 160
FimB COG0582
Integrase/recombinase, includes phage integrase [Replication, recombination and repair, ...
 72-304 5.60e-21

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


Pssm-ID: 440347 [Multi-domain]  Cd Length: 391  Bit Score: 92.41  E-value: 5.60e-21
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504293879  72 ITDITEDHLRSYISTMLNvrDLSPVTINIRLGGIKSILSRMTKRGLINENPAKRVTKLRVDEKTIKM--LTDSQVRRFFK 149
Cdd:COG0582  139 IAEITPPDLLAVLRPIEA--RGAPETARRVRQRLRQVFRYAVARGLIERNPAADLKGALPKPKVKHHpaLTPEELPELLR 216

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504293879 150 MIDK-DTFPGFRDYVAFLIAlkCGLRSNELEGLKPEDIDFDNLVIMLPGAVNKNRKNRMVPMTEQVAEelrqLLTEMTEY 228
Cdd:COG0582  217 ALDAyRGSPVTRLALRLLLL--TGVRPGELRGARWSEIDLEAALWTIPAERMKTRRPHIVPLSRQALE----ILKELKPL 290

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504293879 229 FGTFTHVFVNQYGEK--IAKDHLRK--RAAKYGEMadlkkecrpSLHSLRHTFAINYLRNGSDIRSLQKIMGHADLASTE 304
Cdd:COG0582  291 TGDSEYVFPSRRGPKkpMSENTLNKalRRMGYGRF---------TPHGFRHTASTLLNEAGFPPDVIERQLAHKDGNKVR 361
INT_RitA_C_like cd01188
C-terminal catalytic domain of recombinase RitA, a component of the recombinase trio; ...
 140-307 1.17e-20

C-terminal catalytic domain of recombinase RitA, a component of the recombinase trio; Recombinases RitA (also known as pAE1), RitB, and RitC are encoded by three adjacent and overlapping genes. Collectively they are known as the Recombinase in Trio (RIT). This RitA family includes various bacterial integrases and integrases from the deletion-prone region of plasmid pAE1 of Alcaligenes eutrophus H1. All three integrases contain a catalytic motif, suggesting that they are all active enzymes. However, their specific roles are not fully understood. All three families belong to the superfamily of DNA breaking-rejoining enzymes, which share the same fold in their catalytic domain and the overall reaction mechanism. The catalytic domain contains six conserved active site residues. Their overall reaction mechanism is essentially identical and involves cleavage of a single strand of a DNA duplex by nucleophilic attack of a conserved tyrosine to give a 3' phosphotyrosyl protein-DNA adduct. In the second rejoining step, a terminal 5' hydroxyl attacks the covalent adduct to release the enzyme and generate duplex DNA.


Pssm-ID: 271188 [Multi-domain]  Cd Length: 179  Bit Score: 87.30  E-value: 1.17e-20
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504293879 140 TDSQVRRFFKMIDKDTFPGFRDYVAFLIALKCGLRSNELEGLKPEDIDFDNLVIMLPGAvnKNRKNRMVPMTEQVAEELR 219
Cdd:cd01188    1 SPDEVRRLLAAIDRLTPVGLRDYAILLLLARLGLRAGDVAGLRLDDIDWRSGTITVRQK--KTGRPVELPLTEPVGEALA 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504293879 220 QLL------TEMTEYFGTFTHvfvnQYGEKIAKDHLRKRAAKYGEMADLKKECRpSLHSLRHTFAINYLRNGSDIRSLQK 293
Cdd:cd01188   79 DYLrdgrprTDSREVFLRARA----PYRPLSSTSQISSIVRRYLRKAGIEPSHR-GTHSLRHSLATRMLRAGTSLKVIAD 153

                        170
                 ....*....|....
gi 504293879 294 IMGHADLASTEIYL 307
Cdd:cd01188  154 LLGHRSIETTAIYA 167
INT_ICEBs1_C_like cd01189
C-terminal catalytic domain of integrases from bacterial phages and conjugate transposons; ...
 141-306 1.52e-19

C-terminal catalytic domain of integrases from bacterial phages and conjugate transposons; This family of tyrosine based site-specific integrases is has origins in bacterial phages and conjugate transposons. One member is the integrase from Bacillus subtilis conjugative transposon ICEBs1. ICEBs1 can be excised and transfered to various recipients in response to DNA damage or high concentrations of potential mating partners. The family belongs to the superfamily of DNA breaking-rejoining enzymes, which share the same fold in their catalytic domain and the overall reaction mechanism. The catalytic domain contains six conserved active site residues. Their overall reaction mechanism involves cleavage of a single strand of a DNA duplex by nucleophilic attack of a conserved tyrosine to give a 3' phosphotyrosyl protein-DNA adduct. In the second rejoining step, a terminal 5' hydroxyl attacks the covalent adduct to release the enzyme and generate duplex DNA.


Pssm-ID: 271189 [Multi-domain]  Cd Length: 147  Bit Score: 83.38  E-value: 1.52e-19
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504293879 141 DSQVRRFFKMIDKDtfpGFRDYVAFLIALKCGLRSNELEGLKPEDIDFDNLVIMLPGAVNKNRK-------------NRM 207
Cdd:cd01189    1 PEELKKLLEALKKR---GDRYYLLFLLALLTGLRRGELLALTWSDIDFENGTIRINRTLVRKKKggyvikppktkssIRT 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504293879 208 VPMTEQVAEELRQLLtemteyfgtfthvfvnqygekiakdHLRKRAAKYGEMadlkkecRPSLHSLRHTFAINYLRNGSD 287
Cdd:cd01189   78 IPLPDELIELLKELK-------------------------AFKKLLKKAGLP-------RITPHDLRHTFASLLLEAGVP 125

                        170       180
                 ....*....|....*....|
gi 504293879 288 IRSLQKIMGHADLAST-EIY 306
Cdd:cd01189  126 LKVIAERLGHSDISTTlDVY 145
INT_C_like_4 cd01194
Uncharacterized site-specific tyrosine recombinase, C-terminal catalytic domain; Tyrosine ...
 139-307 5.80e-19

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: 82.81  E-value: 5.80e-19
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504293879 139 LTDSQVRRFFKMIDKD-TFPGFRDYVAFLIALKCGLRSNELEGLKPEDID--FDNLVIMLPGAvNKNRKNRMVPMTEQVA 215
Cdd:cd01194    1 LTLEQARQLLASLPIDdSIIGLRDRAIISLMVTEGLRTVEIVRADVGDLRqeGEGTILYVQGK-GKTSKDDFVYLRPDVL 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504293879 216 EELRQLLT---EMTEYFGTFTHVFVNQYGEKIAKDHLRKRAAKYGEMADLKKEcRPSLHSLRHTFAINYLRNGSDIRSLQ 292
Cdd:cd01194   80 KALQAYLKargKLDFEEPLFTSLSNNSKGQRLTTRSIRRIIKKYLRKAGLDDD-RLTAHSLRHTAGTLALKAGKSLREVQ 158

                        170
                 ....*....|....*
gi 504293879 293 KIMGHADLASTEIYL 307
Cdd:cd01194  159 QLLRHSDPNTTMIYA 173
INT_RitB_C_like cd00797
C-terminal catalytic domain of recombinase RitB, a component of the recombinase trio; ...
 139-307 1.03e-15

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: 74.26  E-value: 1.03e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504293879 139 LTDSQVRRFFKMIDK----DTFPGFRDYVAFLIALKCGLRSNELEGLKPEDIDFDNLVIMLPGavNKNRKNRMVPMTEQV 214
Cdd:cd00797    1 YTDAEIRRLLAAADQlppeSPLRPLTYATLFGLLYATGLRVGEALRLRLEDVDLDSGILTIRQ--TKFGKSRLVPLHPST 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504293879 215 AEELRQLLTEM--------TEYF-----------GTFTHVFvNQYGEKIAkdhLRKRAAKYGemadlkkecrPSLHSLRH 275
Cdd:cd00797   79 VGALRDYLARRdrllpspsSSYFfvsqqggrltgGGVYRVF-RRLLRRIG---LRGAGDGRG----------PRLHDLRH 144

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|
gi 504293879 276 TFAINYL----RNGSDIRS----LQKIMGHADLASTEIYL 307
Cdd:cd00797  145 TFAVNRLtrwyREGADVERklpvLSTYLGHVNVTDTYWYL 184
int PHA02601
integrase; Provisional
 91-314 1.06e-15

integrase; Provisional


Pssm-ID: 222904 [Multi-domain]  Cd Length: 333  Bit Score: 76.69  E-value: 1.06e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504293879  91 RDLSPVTINIRLGGIKSILSRMTKRGLIN-ENPAKRVTKLRVDEKTIKMLTDSQVRRFFKMIDkdtfpGFRDYVAFLIAL 169
Cdd:PHA02601 124 RPIKPATVNRELAYLSAVFNELIKLGKWSgPNPLDGIRPFKEAEPELAFLTKEEIERLLDACD-----GSRSPDLGLIAK 198

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504293879 170 KC---GLRSNELEGLKPEDIdfdnlvimLPGAVN----KNRKNRMVPMTEQVAEELRQLLTEMteyfgtfthvFVNQYGe 242
Cdd:PHA02601 199 IClatGARWSEAETLKRSQI--------SPYKITfvktKGKKNRTVPISEELYKMLPKRRGRL----------FKDAYE- 259

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 504293879 243 kiakdhlrkRAAKYGEMADLKKECRPSLHSLRHTFAINYLRNGSDIRSLQKIMGHADLASTEIYL----DYVDDIV 314
Cdd:PHA02601 260 ---------SFERAVKRAGIDLPEGQATHVLRHTFASHFMMNGGNILVLQRILGHATIEMTMAYAhfapDHLEDAV 326
INT_P4_C cd00801
Bacteriophage P4 integrase, C-terminal catalytic domain; P4-like integrases are found in ...
 140-299 6.79e-15

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: 71.53  E-value: 6.79e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504293879 140 TDSQVRRFFKMIDKDTF-PGFRDYVAFLIALkcGLRSNELEGLKPEDIDFDNLVIMLPGAVNKNRKNRMVPMTEQVAEel 218
Cdd:cd00801    1 SPDELPELWRALDTANLsPPTKLALRLLLLT--GQRIGELARARWSEIDLEEKTWTIPAERTKNKRPHRVPLSDQALE-- 76

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504293879 219 rqLLTEMTEYFGTFTHVFVNQYGEK--IAKDHLRKRAAKYGEMADLkkecrPSLHSLRHTFAINYLRNGSDIRSLQKIMG 296
Cdd:cd00801   77 --ILEELKEFTGDSGYLFPSRRKKKkpISENTINKALKRLGYKGKE-----FTPHDLRRTFSTLLNELGIDPEVIERLLN 149


                 ...
gi 504293879 297 HAD 299
Cdd:cd00801  150 HVL 152
integrase_gron TIGR02249
integron integrase; Members of this family are integrases associated with integrons (and ...
 38-306 1.16e-14

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: 73.58  E-value: 1.16e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504293879   38 ELFETENYRERTINDYRKYWSEFMEVAGIQPTDNITDiteDHLRSYISTMLNVRDLSPVTINIRLGGI----KSILsRMT 113
Cdd:TIGR02249   7 EHMRTRHYAKRTEEAYLHWIKRFIRFHNKRHPSTMGD---TEVEAFLSDLAVDGKVAASTQNQALNALlflyKEIL-KTP 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504293879  114 KRGLINENPAKRVTKLRVdektikMLTDSQVRRFFKMIDkdtfPGFRDYVAFLIAlkCGLRSNELEGLKPEDIDFDNLVI 193
Cdd:TIGR02249  83 LSLMERFVRAKRPRKLPV------VLTREEVRRLLEHLE----GKYRLIAKLLYG--SGMRLMECLRLRIQDIDFDYGEI 150

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504293879  194 MLPGAvnKNRKNRMVPMTEQVAEELRQLLTEMTEY----------------------------------FGTFTHvFVNQ 239
Cdd:TIGR02249 151 RIRQG--KGGKDRTVTLPKELIPPLREQIELARAYheadlaegyggvylphalarkypnapkewgwqylFPSHRL-SRDP 227

                         250       260       270       280       290       300       310
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 504293879  240 YGEKIAKDHLR--------KRAAkygEMADLKKECRPslHSLRHTFAINYLRNGSDIRSLQKIMGHADLASTEIY 306
Cdd:TIGR02249 228 ESGVIRRHHINettiqravRRAV---ERAGIEKPVTC--HTLRHSFATHLLESGADIRTVQELLGHSDVKTTQIY 297
INTN1_C_like cd01185
Integrase IntN1 of Bacteroides mobilizable transposon NBU1 and similar proteins, C-terminal ...
 164-314 2.74e-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: 69.60  E-value: 2.74e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504293879 164 AFLIALKCGLRSNELEGLKPEDIDFDNLVIMLPGAVNKNRKNRMVPMTEQVaeelRQLLTEmteYFGTFTHVFVNQYgek 243
Cdd:cd01185   23 MFLFSCYTGLRFSDLKNLTWKNIVEASGRTWIRYRRKKTGKPVTVPLLPVA----REILEK---YKDDRSEGKLFPV--- 92

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 504293879 244 IAKDHLRKRAAKYGEMADLKKecRPSLHSLRHTFAINYLRNGSDIRSLQKIMGHADLASTEIYLDYVDDIV 314
Cdd:cd01185   93 LSNQKINRYLKEIAKIAGIDK--HLTFHVARHTFATLLLLKGVDIETISKLLGHSSIKTTQIYAKIVDSKK 161
INT_C_like_1 cd01184
Uncharacterized site-specific tyrosine recombinase, C-terminal catalytic domain; Tyrosine ...
 139-299 2.96e-12

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: 64.25  E-value: 2.96e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504293879 139 LTDSQVRRFFKMIDKDTFPGFRDYV--AFLIALKCGLRSNELEGLKPEDIDFDN--LVIML-PGAVNKNRKN----RMVP 209
Cdd:cd01184    1 FTPEELAKIFSSPLYTGCKKKDPALywLPLIGLYTGARLNEICQLRVDDIKEEDgiWCIDInDDAEGRRLKTkasrRLVP 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504293879 210 MT-------------EQVAEELRQLLTEMTEYFGTFTHVFVNQYGEkiakdHLRKRAAKYGEMAdlkkecrpSLHSLRHT 276
Cdd:cd01184   81 IHprlielgfldyveALRADGKLFLFPEKRDKDGKYSKAASKWFNR-----LLRKLGIKDDERK--------SFHSFRHT 147

                        170       180
                 ....*....|....*....|....
gi 504293879 277 FaINYLRN-GSDIRSLQKIMGHAD 299
Cdd:cd01184  148 F-ITALKRaGVPEELIAQIVGHSR 170
INT_C_like_5 cd01195
Uncharacterized site-specific tyrosine recombinase, C-terminal catalytic domain; Tyrosine ...
 143-311 8.92e-10

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: 57.10  E-value: 8.92e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504293879 143 QVRRFFKMIDKDTFPGFRDYVAFLIALKCGLRSNELEGLKPEDIDFDNLVIMLPGavnKNRKNR-MVPMTEQVAEELRQL 221
Cdd:cd01195    4 EARQRLDAADRHTAKGKRDEALVRLLLDNALRRSEAVALDVEDLEKEHRRLRILG---KGKKQReVVTLPPTTREALAAW 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504293879 222 LTEMTE----YFGTFTHvfvNQYGEKIAKDHLRKRAAKYGEMADLKKECRPslHSLRHTFAINYLRNG-SDIRSLQKIMG 296
Cdd:cd01195   81 LAARGEaegpLFVSLDR---ASRGRRLSPQAVYRIVRRLAERIGLGKRLSP--HGLRHSAITLALDAGaGLIRKVQDFSR 155

                        170
                 ....*....|....*
gi 504293879 297 HADLASTEIYLDYVD 311
Cdd:cd01195  156 HADLRTLQVYDDQRD 170
PRK15417 PRK15417
integron integrase;
157-306 1.23e-08

integron integrase;


Pssm-ID: 185315 [Multi-domain]  Cd Length: 337  Bit Score: 55.44  E-value: 1.23e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504293879 157 PGFRDYVAFLIA---LKCGLRSNELEGLKPEDIDFDNLVIMLPGAvnKNRKNRMVPMTEQVAEELRQLLTEMTEY----- 228
Cdd:PRK15417 126 LGFLEGEHRLFAqllYGTGMRISEGLQLRVKDLDFDHGTIIVREG--KGSKDRALMLPESLAPSLREQLSRARAWwlkdq 203

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504293879 229 -----------------------------FGTFTHVFVNQYGeKIAKDHLR----KRAAKYG-EMADLKKECRPslHSLR 274
Cdd:PRK15417 204 aegrsgvalpdalerkypraghswpwfwvFAQHTHSTDPRSG-VVRRHHMYdqtfQRAFKRAvEQAGITKPATP--HTLR 280

                        170       180       190
                 ....*....|....*....|....*....|..
gi 504293879 275 HTFAINYLRNGSDIRSLQKIMGHADLASTEIY 306
Cdd:PRK15417 281 HSFATALLRSGYDIRTVQDLLGHSDVSTTMIY 312
INT_FimBE_like cd01197
FimB and FimE and related proteins, integrase/recombinases; This CD includes proteins similar ...
 137-306 1.38e-08

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: 53.67  E-value: 1.38e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504293879 137 KMLTDSQVRRFFKMIDKDTFPGfRDYVAFLIALKCGLRSNELEGLKPEDIDFDNLVIMLPGAvnKNRKNRMVPMTEQVAE 216
Cdd:cd01197    5 KYLTGKEVQALLQAACRGRTPA-RDYCLLLLAFRHGFRVSELCDLHLSDVDLESRRLHIRRL--KNGFSTTHPLRFDERE 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504293879 217 ELRQLLTEMTEYFGTFTH-VFVNQYGEKIAKDHLRKRAAKYGEMADLKKECRPslHSLRHTFAINYLRNGSDIRSLQKIM 295
Cdd:cd01197   82 ALEAWLKERANWKGADTDwIFLSRRGGPLSRQQAYRIIRDLGKEAGTVTQTHP--HMLRHACGYALADRGADTRLIQDYL 159

                        170
                 ....*....|.
gi 504293879 296 GHADLASTEIY 306
Cdd:cd01197  160 GHRNIRHTVIY 170
INT_tnpA_C_Tn554 cd01186
Putative Transposase A from transposon Tn554, C-terminal catalytic domain; This family ...
 139-303 2.62e-08

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: 52.80  E-value: 2.62e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504293879 139 LTDSQVRRFFkmidkDTFPGFRDyvAFLIAL--KCGLRSNELEGLKPEDIDFDNLVIML-PGAVNKN--RKNRMVPMTEQ 213
Cdd:cd01186    2 LTPREVQELI-----NACNNLRD--KFLLALlyETGLRIGEALGLRIEDIDMADNQIELvPREDNTNeaRAKSMRERRIP 74

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504293879 214 VAEELRQLLTE-MTEYFG----TFTHVFVNQYGEKIAKdhlrkrAAKYGEMADLKKECRP------SLHSLRHTFAINYL 282
Cdd:cd01186   75 VSQDLIDLYADyLTYIYCeeaeFSITVFVNVKGGNQGK------AMNYSDVYDLVRRLKKrtgidfTPHMFRHTHATALI 148

                        170       180
                 ....*....|....*....|.
gi 504293879 283 RNGSDIRSLQKIMGHADLAST 303
Cdd:cd01186  149 RAGWSIEVVARRLGHAHVQTT 169
xerS PRK05084
site-specific tyrosine recombinase XerS; Reviewed
 50-312 5.64e-08

site-specific tyrosine recombinase XerS; Reviewed


Pssm-ID: 235339 [Multi-domain]  Cd Length: 357  Bit Score: 53.77  E-value: 5.64e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504293879  50 INDYRKYWSEFMEvAGIQPTDNITDI---TEDHLR-----SYISTMLNVRDL---------SPVTINIRLGGIKSI---- 108
Cdd:PRK05084  42 LTEYRRFFNWLIS-EGLSDASKIKDIplsTLENLTkkdveAFILYLRERPLLnghstkkgnSQTTINRTLSALKSLfkyl 120

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504293879 109 ------------LSR--MTKRGLINENP-----AKRVT-KLRVDEKTIKMLT----------DSQVRRFFKMiDKDtfpg 158
Cdd:PRK05084 121 teeaenedgepyFYRnvMKKIELKKKKEtlaarAHNLKqKLFLGDEDYEFLDfidneyeqklSNRALSSFKK-NKE---- 195

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504293879 159 fRDYVAFLIALKCGLRSNELEGLKPEDIDFDNLVImlpGAVNKNRKNRMVPMTEQVAEELRQLLTEMTEYFG---TFTHV 235
Cdd:PRK05084 196 -RDLAIIALILGSGLRVSELVNLDLSDLNLKQMTI---DVTRKGGKRDSVNIAPFALPYLEEYLKIRASRYKaekQEKAL 271

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504293879 236 FVNQYGEKIAKdhLRKRA-----AKYGEmaDLKKECRPslHSLRHTFAINYLRNGSDIRSLQKIMGHADLASTEIYLDYV 310
Cdd:PRK05084 272 FLTKYRGKPNR--ISARAiekmvAKYSE--AFGVRLTP--HKLRHTLATRLYDATKDQVLVADQLGHTSTETTDLYTHIV 345


                 ..
gi 504293879 311 DD 312
Cdd:PRK05084 346 ND 347
INT_C_like_3 cd01192
Uncharacterized site-specific tyrosine recombinase, C-terminal catalytic domain; Tyrosine ...
 158-307 1.79e-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: 271192 [Multi-domain]  Cd Length: 178  Bit Score: 50.37  E-value: 1.79e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504293879 158 GFRDYVAFLIALKCGLRSNELEGLKPEDIDF-DNLVIMlpgaVNKNRKNRMVPM----TEQVAEELRQLLTEMTEYFgtf 232
Cdd:cd01192   23 NPRNYLLFIVGINTGLRISDLLSLKVEDVTNkDKLSIK----EQKTGKQKTFPLnptlVKALKEYIDDLDLKRNDYL--- 95

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 504293879 233 thvfVNQYGEKIAKDHLRKRAAKYgeMADLKKEC----RPSLHSLRHTFAINYLRNGSDIRSLQKIMGHADLASTEIYL 307
Cdd:cd01192   96 ----FKSLKQGPEKPISRKQAYKI--LKKAADDLglnyNIGTHSLRKTFGYHVYKQGKDIELLMKLLNHSSPSITLRYL 168
INT_C_like_2 cd01191
Uncharacterized site-specific tyrosine recombinase, C-terminal catalytic domain; Tyrosine ...
 163-307 1.92e-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: 50.50  E-value: 1.92e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504293879 163 VAFLIAlkCGLRSNELEGLKPEDIDFDNLVIMLPGAvnknrKNRMVPMTEQVAEELRQLLTEMTEYFGtftHVFVNQYGE 242
Cdd:cd01191   26 VRFLAA--TGARVSELIKIKVEHVELGYFDIYSKGG-----KLRRLYIPKKLRNEALEWLKSTNRKSG---YIFLNRFGE 95

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 504293879 243 KIAKDHLRKRAAKYGEMADL-KKECRPslHSLRHTFAINYLRNGSDIRSLQKIMGHADLASTEIYL 307
Cdd:cd01191   96 RITTRGIAQQLKNYARKYGLnPKVVYP--HSFRHRFAKNFLEKYNDIALLADLMGHESIETTRIYL 159
INT_tnpB_C_Tn554 cd01187
Putative Transposase B from transposon Tn554, C-terminal catalytic domain; This family ...
 160-306 3.67e-07

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: 48.97  E-value: 3.67e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504293879 160 RDYVAFLIAL-KCGLRSNELEGLK----PEDIDFDNLVIMLPGAVNKNRKNRMVPMTEQVAEELRQLltemteyfgtfth 234
Cdd:cd01187   13 PQPIPVVQAAvFTGARASELATLKfgclHAQTSDDGTFLYWLKWENKGGKQLDIPISKKVAELIKTI------------- 79

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 504293879 235 vfvnqygekiaKDHLRKRAAKYGEMADLKKECRPSLHSLRHTFAINYLRNGSDIRSLQKIMGHADLASTEIY 306
Cdd:cd01187   80 -----------NWTLNELSELKNISDDHGERFRFHTHRFRHTVATRLANSGMGILVLQQLLGHSSPEMTLRY 140
INT_Lambda_C cd00800
C-terminal catalytic domain of Lambda integrase, a tyrosine-based site-specific recombinase; ...
 163-308 2.00e-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: 44.26  E-value: 2.00e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504293879 163 VAFLIALKCGLRSNELEGLKPEDIDFDNLVIMlpgaVNKNRKNRMVPMTeqvaEELRQLLTEMTEY-FGTFTHVFVNQYG 241
Cdd:cd00800   16 LAMELALLTGQRQGDLLRLKWSDITDGGLLVE----QSKTGKKLLIPWT----PSLRALVDRIRALpRKRSEYLINSRKG 87

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 504293879 242 EKIAKDHLRKRAAKYGEMADLKKEC-RPSLHSLRHTFAINYLRNGSDiRSLQKIMGHADLASTEIYLD 308
Cdd:cd00800   88 GPLSYDTLKSAWRRARKAAGLKGETeGFTFHDLRAKAATDYAEQGGS-TDAQALLGHKSDAMTERYTR 154
PRK09870 PRK09870
tyrosine recombinase; Provisional
 132-306 2.54e-05

tyrosine recombinase; Provisional


Pssm-ID: 182125  Cd Length: 200  Bit Score: 44.54  E-value: 2.54e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504293879 132 DEKTIKMLTDSQVRRFFKMIDKDTFPGfRDYVAFLIALKCGLRSNELEGLKPEDIDFDNLVIMlpgaVNKNRK--NRMVP 209
Cdd:PRK09870   6 DNKKRNFLTHSEIESLLKAANTGPHAA-RNYCLTLLCFIHGFRASEICRLRISDIDLKAKCIY----IHRLKKgfSTTHP 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504293879 210 MTEQVAEELRQLLTEMTEYFGTFTH-VFVNQYGEKIAKDHLRKRAAKYGEMADLKKECRPslHSLRHTFAINYLRNGSDI 288
Cdd:PRK09870  81 LLNKEIQALKNWLSIRTSYPHAESEwVFLSRKGNPLSRQQFYHIISTSGGNAGLSLEIHP--HMLRHSCGFALANMGIDT 158

                        170
                 ....*....|....*...
gi 504293879 289 RSLQKIMGHADLASTEIY 306
Cdd:PRK09870 159 RLIQDYLGHRNIRHTVWY 176
Phage_int_SAM_4 pfam13495
Phage integrase, N-terminal SAM-like domain;
41-117 7.23e-05

Phage integrase, N-terminal SAM-like domain;


Pssm-ID: 463898 [Multi-domain]  Cd Length: 83  Bit Score: 40.67  E-value: 7.23e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504293879   41 ETENYRERTINDYrKYW----SEFMEvagiqpTDNITDITEDHLRSYISTMLNVRDLSPVTINIRLGGIKSILSRMTKRG 116
Cdd:pfam13495  10 RLRGYAERTIKAY-LRWirrfLRFHD------KKHPEELTEEDIEAYLSHLANERNVSASTQNQALNALSFFYRWVLERE 82


                  .
gi 504293879  117 L 117
Cdd:pfam13495  83 L 83
PRK09871 PRK09871
tyrosine recombinase; Provisional
 158-306 7.14e-04

tyrosine recombinase; Provisional


Pssm-ID: 182126  Cd Length: 198  Bit Score: 39.97  E-value: 7.14e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504293879 158 GFRDYVAFLIALKCGLRSNELEGLKPEDIDFDNlvimlpGAVN----KNRKNRMVPMTEQVAEELRQLLTEMTEYFGT-- 231
Cdd:PRK09871  25 GARDYCLILLAYRHGMRISELLDLHYQDLDLNE------GRINirrlKNGFSTVHPLRFDEREAVERWTQERANWKGAdr 98

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 504293879 232 FTHVFVNQYGEKIAKDHLRKRAAKYGEMADLKKECRPslHSLRHTFAINYLRNGSDIRSLQKIMGHADLASTEIY 306
Cdd:PRK09871  99 TDAIFISRRGSRLSRQQAYRIIRDAGIEAGTVTQTHP--HMLRHACGYELAERGADTRLIQDYLGHRNIRHTVRY 171
 
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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