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Conserved domains on  [gi|1339709323|ref|WP_103597515|]
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tyrosine recombinase XerS, partial [Bacillus thuringiensis]

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 ...
 1-217 2.14e-102

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 PRK05084:

Pssm-ID: 469662 [Multi-domain]  Cd Length: 357  Bit Score: 300.30  E-value: 2.14e-102
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1339709323   1 HKEKVDAAARADDVANMIFNEKDDVAFLQFLANDYGEMLkdiSPKKYSFFQRDKERDIAIISLILGTGLRVSEVVSLTIS 80
Cdd:PRK05084  144 KKKKETLAARAHNLKQKLFLGDEDYEFLDFIDNEYEQKL---SNRALSSFKKNKERDLAIIALILGSGLRVSELVNLDLS 220

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1339709323  81 SINFRQGKVKVTRKGNKRSSILATHSCLDDVQEYIKVRLSKYNCPQDEDLLFVTNYKGKYTQLTVRAIQKLCDKYSSAFD 160
Cdd:PRK05084  221 DLNLKQMTIDVTRKGGKRDSVNIAPFALPYLEEYLKIRASRYKAEKQEKALFLTKYRGKPNRISARAIEKMVAKYSEAFG 300

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1339709323 161 EKRSPHKLRHTYATNHYKENKDLVLLRDQLGHTSVEVTSIYTNINNEKKREAVDRLE 217
Cdd:PRK05084  301 VRLTPHKLRHTLATRLYDATKDQVLVADQLGHTSTETTDLYTHIVNDEQKEALDRLE 357
 
Name Accession Description Interval E-value
xerS PRK05084
site-specific tyrosine recombinase XerS; Reviewed
 1-217 2.14e-102

site-specific tyrosine recombinase XerS; Reviewed


Pssm-ID: 235339 [Multi-domain]  Cd Length: 357  Bit Score: 300.30  E-value: 2.14e-102
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1339709323   1 HKEKVDAAARADDVANMIFNEKDDVAFLQFLANDYGEMLkdiSPKKYSFFQRDKERDIAIISLILGTGLRVSEVVSLTIS 80
Cdd:PRK05084  144 KKKKETLAARAHNLKQKLFLGDEDYEFLDFIDNEYEQKL---SNRALSSFKKNKERDLAIIALILGSGLRVSELVNLDLS 220

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1339709323  81 SINFRQGKVKVTRKGNKRSSILATHSCLDDVQEYIKVRLSKYNCPQDEDLLFVTNYKGKYTQLTVRAIQKLCDKYSSAFD 160
Cdd:PRK05084  221 DLNLKQMTIDVTRKGGKRDSVNIAPFALPYLEEYLKIRASRYKAEKQEKALFLTKYRGKPNRISARAIEKMVAKYSEAFG 300

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1339709323 161 EKRSPHKLRHTYATNHYKENKDLVLLRDQLGHTSVEVTSIYTNINNEKKREAVDRLE 217
Cdd:PRK05084  301 VRLTPHKLRHTLATRLYDATKDQVLVADQLGHTSTETTDLYTHIVNDEQKEALDRLE 357
XerD COG4974
Site-specific recombinase XerD [Replication, recombination and repair];
56-217 5.87e-39

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


Pssm-ID: 443999 [Multi-domain]  Cd Length: 291  Bit Score: 135.89  E-value: 5.87e-39
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1339709323  56 RDIAIISLILGTGLRVSEVVSLTISSINFRQGKVKVTR-KGNKRSSILATHSCLDDVQEYIKVRLskyncPQDEDLLFVt 134
Cdd:COG4974   134 RDRALLLLLYATGLRVSELLGLKWSDIDLDRGTIRVRRgKGGKERTVPLSPEALEALREYLEERR-----PRDSDYLFP- 207

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1339709323 135 NYKGKytQLTVRAIQKLCDKYSSA--FDEKRSPHKLRHTYATNHYKENKDLVLLRDQLGHTSVEVTSIYTNINNEKKREA 212
Cdd:COG4974   208 TRRGR--PLSRRAIRKILKRLAKRagIPKRVTPHSLRHTFATHLLEAGVDLRTVQELLGHSSISTTQIYTHVSDEELREA 285


                  ....*
gi 1339709323 213 VDRLE 217
Cdd:COG4974   286 VEKLH 290
DNA_BRE_C cd00397
DNA breaking-rejoining enzymes, C-terminal catalytic domain; The DNA breaking-rejoining enzyme ...
 56-202 7.41e-32

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: 114.11  E-value: 7.41e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1339709323  56 RDIAIISLILGTGLRVSEVVSLTISSINFRQGKVKVTRKGNKRSS---ILATHSCLDDVQEYIKVRLSKYNCPQDEDLLF 132
Cdd:cd00397    18 RDRAILLLLLETGLRISELLALKVKDIDLDNGTIRVRGKKTKGGKertVPLPKELAEELKEYLKERRDKRGPLLKSLYLN 97

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1339709323 133 VTNYKGKYTQLTVRAIQKLCDKYSSAFDEKRSPHKLRHTYATNHYKENKDLVLLRDQLGHTSVEVTSIYT 202
Cdd:cd00397    98 KLFGTKLGERLSRRTLRRIFKKAGIEAGRKITPHSLRHTFATNLLENGVDIKVVQKLLGHSSISTTQRYL 167
recomb_XerD TIGR02225
tyrosine recombinase XerD; The phage integrase family describes a number of recombinases with ...
 56-211 2.15e-27

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: 105.36  E-value: 2.15e-27
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1339709323  56 RDIAIISLILGTGLRVSEVVSLTISSINFRQGKVKVTRKGNKRSSILATHSCLDDVQEYIKVR---LSKYNCPQdEDLLF 132
Cdd:TIGR02225 126 RDRAMLELLYATGLRVSELVGLRLEDVNLDEGFVRVRGKGNKERLVPLGEEAIEALERYLKEArplLLKKKVKE-SDALF 204

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1339709323 133 VTNYKGKYTQLTV-RAIQKLCDKysSAFDEKRSPHKLRHTYATnHYKENK-DLVLLRDQLGHTSVEVTSIYTNINNEKKR 210
Cdd:TIGR02225 205 LNRRGGPLSRQGVwKILKEYAKR--AGIEKPISPHTLRHSFAT-HLLENGaDLRVVQELLGHADISTTQIYTHVARERLK 281


                  .
gi 1339709323 211 E 211
Cdd:TIGR02225 282 E 282
Phage_integrase pfam00589
Phage integrase family; Members of this family cleave DNA substrates by a series of staggered ...
 53-205 3.68e-22

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: 88.92  E-value: 3.68e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1339709323  53 DKERDIAIISLILGTGLRVSEVVSLTISSINFRQGKVKVTRKGNKRSSILAThscLDDVQEYIKVRLSKYNCPQDE-DLL 131
Cdd:pfam00589  19 LSIRDKALLELLYATGLRISELCSLRWSDIDFENGVIRVHRGKGNKERTVPL---SDAALELLKEWLSKRLLEAPKsDYL 95

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1339709323 132 FVtNYKGKytQLTVRAIQKLCDK--YSSAFDEKRSPHKLRHTYATNHYKENKDLVLLRDQLGHTSVEVTSIYTNIN 205
Cdd:pfam00589  96 FA-SKRGK--PLSRQTVRKIFKRagKEAGLELPLHPHMLRHSFATHLLEAGVDLRVVQKLLGHSSISTTQIYTHVA 168
 
Name Accession Description Interval E-value
xerS PRK05084
site-specific tyrosine recombinase XerS; Reviewed
 1-217 2.14e-102

site-specific tyrosine recombinase XerS; Reviewed


Pssm-ID: 235339 [Multi-domain]  Cd Length: 357  Bit Score: 300.30  E-value: 2.14e-102
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1339709323   1 HKEKVDAAARADDVANMIFNEKDDVAFLQFLANDYGEMLkdiSPKKYSFFQRDKERDIAIISLILGTGLRVSEVVSLTIS 80
Cdd:PRK05084  144 KKKKETLAARAHNLKQKLFLGDEDYEFLDFIDNEYEQKL---SNRALSSFKKNKERDLAIIALILGSGLRVSELVNLDLS 220

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1339709323  81 SINFRQGKVKVTRKGNKRSSILATHSCLDDVQEYIKVRLSKYNCPQDEDLLFVTNYKGKYTQLTVRAIQKLCDKYSSAFD 160
Cdd:PRK05084  221 DLNLKQMTIDVTRKGGKRDSVNIAPFALPYLEEYLKIRASRYKAEKQEKALFLTKYRGKPNRISARAIEKMVAKYSEAFG 300

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1339709323 161 EKRSPHKLRHTYATNHYKENKDLVLLRDQLGHTSVEVTSIYTNINNEKKREAVDRLE 217
Cdd:PRK05084  301 VRLTPHKLRHTLATRLYDATKDQVLVADQLGHTSTETTDLYTHIVNDEQKEALDRLE 357
XerD COG4974
Site-specific recombinase XerD [Replication, recombination and repair];
56-217 5.87e-39

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


Pssm-ID: 443999 [Multi-domain]  Cd Length: 291  Bit Score: 135.89  E-value: 5.87e-39
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1339709323  56 RDIAIISLILGTGLRVSEVVSLTISSINFRQGKVKVTR-KGNKRSSILATHSCLDDVQEYIKVRLskyncPQDEDLLFVt 134
Cdd:COG4974   134 RDRALLLLLYATGLRVSELLGLKWSDIDLDRGTIRVRRgKGGKERTVPLSPEALEALREYLEERR-----PRDSDYLFP- 207

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1339709323 135 NYKGKytQLTVRAIQKLCDKYSSA--FDEKRSPHKLRHTYATNHYKENKDLVLLRDQLGHTSVEVTSIYTNINNEKKREA 212
Cdd:COG4974   208 TRRGR--PLSRRAIRKILKRLAKRagIPKRVTPHSLRHTFATHLLEAGVDLRTVQELLGHSSISTTQIYTHVSDEELREA 285


                  ....*
gi 1339709323 213 VDRLE 217
Cdd:COG4974   286 VEKLH 290
xerC PRK00236
site-specific tyrosine recombinase XerC; Reviewed
 54-215 6.95e-34

site-specific tyrosine recombinase XerC; Reviewed


Pssm-ID: 234698 [Multi-domain]  Cd Length: 297  Bit Score: 122.57  E-value: 6.95e-34
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1339709323  54 KERDIAIISLILGTGLRVSEVVSLTISSINFRQGKVKVTRKGNKRSSILATHSCLDDVQEYIKVRLSKyncPQDEDLLFV 133
Cdd:PRK00236  135 ALRDRAILELLYGSGLRLSELVGLDIDDLDLASGTLRVLGKGNKERTVPLGRAAREALEAYLALRPLF---LPDDDALFL 211

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1339709323 134 tNYKGKytQLTVRAIQKLCDKY--SSAFDEKRSPHKLRHTYATNHYKENKDLVLLRDQLGHTSVEVTSIYTNINNEKKRE 211
Cdd:PRK00236  212 -GARGG--RLSPRVVQRRVKKLgkKAGLPSHITPHKLRHSFATHLLESGGDLRAVQELLGHASLSTTQIYTHVDFQHLAE 288


                  ....
gi 1339709323 212 AVDR 215
Cdd:PRK00236  289 VYDA 292
DNA_BRE_C cd00397
DNA breaking-rejoining enzymes, C-terminal catalytic domain; The DNA breaking-rejoining enzyme ...
 56-202 7.41e-32

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: 114.11  E-value: 7.41e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1339709323  56 RDIAIISLILGTGLRVSEVVSLTISSINFRQGKVKVTRKGNKRSS---ILATHSCLDDVQEYIKVRLSKYNCPQDEDLLF 132
Cdd:cd00397    18 RDRAILLLLLETGLRISELLALKVKDIDLDNGTIRVRGKKTKGGKertVPLPKELAEELKEYLKERRDKRGPLLKSLYLN 97

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1339709323 133 VTNYKGKYTQLTVRAIQKLCDKYSSAFDEKRSPHKLRHTYATNHYKENKDLVLLRDQLGHTSVEVTSIYT 202
Cdd:cd00397    98 KLFGTKLGERLSRRTLRRIFKKAGIEAGRKITPHSLRHTFATNLLENGVDIKVVQKLLGHSSISTTQRYL 167
XerC COG4973
Site-specific recombinase XerC [Replication, recombination and repair];
56-212 4.97e-31

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


Pssm-ID: 443998 [Multi-domain]  Cd Length: 287  Bit Score: 115.06  E-value: 4.97e-31
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1339709323  56 RDIAIISLILGTGLRVSEVVSLTISSINFRQGKVKVTRKGNKRSSILATHSCLDDVQEYIKVRlsKYNCPQDEDLLFVTn 135
Cdd:COG4973   132 RDRAIVELLYSTGLRLGELVGLDWEDVDLDAGEVRVRGKTGKSRTVPLGPKALAALREWLAVR--PELAAPDEGALFPS- 208

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1339709323 136 YKGkyTQLTVRAIQKLCDKYSSA--FDEKRSPHKLRHTYATNHYKENKDLVLLRDQLGHTSVEVTSIYTNINNEKKREA 212
Cdd:COG4973   209 RRG--TRLSPRNVQKRLRRLAKKagLPKHVHPHDLRHSFATHLLESGGDLRAVQELLGHASISTTQIYTHLDFQHLAEV 285
INT_XerDC_C cd00798
XerD and XerC integrases, C-terminal catalytic domains; XerDC-like integrases are involved in ...
 56-208 5.50e-31

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: 111.83  E-value: 5.50e-31
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1339709323  56 RDIAIISLILGTGLRVSEVVSLTISSINFRQGKVKVTRKGNKRSSILATHSCLDDVQEYIKVRLSKYNCPQDEDLLFVtN 135
Cdd:cd00798    20 RDRAILELLYASGLRVSELVGLDLSDVDLDEGLVRVTGKGNKERLVPFGSYAVEALEEYLEERRPLLLKKKPPDALFL-N 98

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1339709323 136 YKGKYtqLTVRAIQKLCDKY--SSAFDEKRSPHKLRHTYATnHYKENK-DLVLLRDQLGHTSVEVTSIYTNINNEK 208
Cdd:cd00798    99 KRGKR--LSRRGVWRILKKYaeRAGLPKHVSPHTLRHSFAT-HLLEGGaDLRVVQELLGHASLSTTQIYTHVSFER 171
INT_RitC_C_like cd01182
C-terminal catalytic domain of recombinase RitC, a component of the recombinase trio; ...
 56-216 1.31e-29

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: 108.52  E-value: 1.31e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1339709323  56 RDIAIISLILGTGLRVSEVVSLTISSINF-RQGKVKVTRKGNKRSSILATHSCLDDVQEYIKVRLSKyncPQDEDL--LF 132
Cdd:cd01182    22 RDHALLLLLYDTGARVQELADLTIRDLRLdDPATVRLHGKGRKERTVPLWKETVAALKAYLQEFHLT---PDPKQLfpLF 98

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1339709323 133 VTNYKGKytqLTVRAIQKLCDKY-------SSAFDEKRSPHKLRHTYATNHYKENKDLVLLRDQLGHTSVEVTSIYTNIN 205
Cdd:cd01182    99 PNRRGQP---LTRDGVAYILNKYvalasnrCPSLPKRITPHTLRHTKAMHLLQAGVDLTVIRDWLGHESVETTQIYAEAD 175

                         170
                  ....*....|.
gi 1339709323 206 NEKKREAVDRL 216
Cdd:cd01182   176 LEMKREALEKA 186
recomb_XerD TIGR02225
tyrosine recombinase XerD; The phage integrase family describes a number of recombinases with ...
 56-211 2.15e-27

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: 105.36  E-value: 2.15e-27
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1339709323  56 RDIAIISLILGTGLRVSEVVSLTISSINFRQGKVKVTRKGNKRSSILATHSCLDDVQEYIKVR---LSKYNCPQdEDLLF 132
Cdd:TIGR02225 126 RDRAMLELLYATGLRVSELVGLRLEDVNLDEGFVRVRGKGNKERLVPLGEEAIEALERYLKEArplLLKKKVKE-SDALF 204

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1339709323 133 VTNYKGKYTQLTV-RAIQKLCDKysSAFDEKRSPHKLRHTYATnHYKENK-DLVLLRDQLGHTSVEVTSIYTNINNEKKR 210
Cdd:TIGR02225 205 LNRRGGPLSRQGVwKILKEYAKR--AGIEKPISPHTLRHSFAT-HLLENGaDLRVVQELLGHADISTTQIYTHVARERLK 281


                  .
gi 1339709323 211 E 211
Cdd:TIGR02225 282 E 282
Phage_integrase pfam00589
Phage integrase family; Members of this family cleave DNA substrates by a series of staggered ...
 53-205 3.68e-22

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: 88.92  E-value: 3.68e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1339709323  53 DKERDIAIISLILGTGLRVSEVVSLTISSINFRQGKVKVTRKGNKRSSILAThscLDDVQEYIKVRLSKYNCPQDE-DLL 131
Cdd:pfam00589  19 LSIRDKALLELLYATGLRISELCSLRWSDIDFENGVIRVHRGKGNKERTVPL---SDAALELLKEWLSKRLLEAPKsDYL 95

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1339709323 132 FVtNYKGKytQLTVRAIQKLCDK--YSSAFDEKRSPHKLRHTYATNHYKENKDLVLLRDQLGHTSVEVTSIYTNIN 205
Cdd:pfam00589  96 FA-SKRGK--PLSRQTVRKIFKRagKEAGLELPLHPHMLRHSFATHLLEAGVDLRVVQKLLGHSSISTTQIYTHVA 168
INT_RitA_C_like cd01188
C-terminal catalytic domain of recombinase RitA, a component of the recombinase trio; ...
 56-211 5.36e-21

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: 86.14  E-value: 5.36e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1339709323  56 RDIAIISLILGTGLRVSEVVSLTISSINFRQGKVKVTRKGNKRSSILAThscLDDVQE----YIKVRLSKYncpqDEDLL 131
Cdd:cd01188    21 RDYAILLLLARLGLRAGDVAGLRLDDIDWRSGTITVRQKKTGRPVELPL---TEPVGEaladYLRDGRPRT----DSREV 93

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1339709323 132 FVTnYKGKYTQLTV-RAIQKLCDKYSSAF---DEKRSPHKLRHTYATNHYKENKDLVLLRDQLGHTSVEVTSIYTNINNE 207
Cdd:cd01188    94 FLR-ARAPYRPLSStSQISSIVRRYLRKAgiePSHRGTHSLRHSLATRMLRAGTSLKVIADLLGHRSIETTAIYAKIDVD 172


                  ....
gi 1339709323 208 KKRE 211
Cdd:cd01188   173 DLRE 176
xerD PRK00283
tyrosine recombinase;
56-216 6.83e-21

tyrosine recombinase;


Pssm-ID: 234713 [Multi-domain]  Cd Length: 299  Bit Score: 88.33  E-value: 6.83e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1339709323  56 RDIAIISLILGTGLRVSEVVSLTISSINFRQGKVKVTRKGNKRS----SILATHSclddVQEYIKVRLSKYNCPQDEDLL 131
Cdd:PRK00283  135 RDRAMLELLYATGLRVSELVGLTLDDVSLRQGVVRVTGKGNKERlvplGEEAVYA----IERYLERGRPALLNGRSSDAL 210

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1339709323 132 FVTNYKGKYTQLTVRAIQKLCDKYSSAFDEKRSPHKLRHTYATnHYKENK-DLVLLRDQLGHTSVEVTSIYTNInnekkr 210
Cdd:PRK00283  211 FPSARGGQLTRQTFWHRIKHYAKRAGIDPKKLSPHVLRHAFAT-HLLNHGaDLRVVQELLGHSDISTTQIYTHV------ 283


                  ....*.
gi 1339709323 211 eAVDRL 216
Cdd:PRK00283  284 -ATERL 288
INT_IntI_C cd01193
Integron integrase and similar protiens, C-terminal catalytic domain; Integron integrases ...
 56-204 3.02e-19

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


Pssm-ID: 271193 [Multi-domain]  Cd Length: 176  Bit Score: 81.17  E-value: 3.02e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1339709323  56 RDIAIISLILGTGLRVSEVVSLTISSINFRQGKVKVTR-KGNKRSSILATHSCLDDVQEYIKVRLSKYNCPQDEDLLFVT 134
Cdd:cd01193    22 RHRLILSLLYGAGLRISELLRLRVKDIDFERGVIRVRQgKGGKDRVVPLPEKLLEPLRRYLKSARPKEELDPAEGRAGVL 101

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1339709323 135 NYKGKY---TQLTVRAIQKLCDKY--SSAFDEKRSPHKLRHTYATNHYKENKDLVLLRDQLGHTSVEVTSIYTNI 204
Cdd:cd01193   102 DPRTGVerrHHISETTVQRALKKAveQAGITKRVTPHTLRHSFATHLLEAGTDIRTIQELLGHSDLSTTMIYTHV 176
INT_C_like_4 cd01194
Uncharacterized site-specific tyrosine recombinase, C-terminal catalytic domain; Tyrosine ...
 56-201 2.80e-15

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: 70.87  E-value: 2.80e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1339709323  56 RDIAIISLILGTGLRVSEVVSLTISSINFR--------QGKvkvtRKGNKRSSILATHSCLDDVQEYIKVRLSKyncpQD 127
Cdd:cd01194    23 RDRAIISLMVTEGLRTVEIVRADVGDLRQEgegtilyvQGK----GKTSKDDFVYLRPDVLKALQAYLKARGKL----DF 94

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1339709323 128 EDLLFVT---NYKGKytQLTVRAIQKLCDKYSSA--FDEKR-SPHKLRHTYATNHYKENKDLVLLRDQLGHTSVEVTSIY 201
Cdd:cd01194    95 EEPLFTSlsnNSKGQ--RLTTRSIRRIIKKYLRKagLDDDRlTAHSLRHTAGTLALKAGKSLREVQQLLRHSDPNTTMIY 172
xerC PRK01287
site-specific tyrosine recombinase XerC; Reviewed
 56-204 5.97e-15

site-specific tyrosine recombinase XerC; Reviewed


Pssm-ID: 234935 [Multi-domain]  Cd Length: 358  Bit Score: 72.47  E-value: 5.97e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1339709323  56 RDIAIISLILGTGLRVSEVVSLTISSINFRQGKVKVTR-KGNKRSSILATHSCLDDVQEYIK-VR---LSKYNCPQdedl 130
Cdd:PRK01287  158 RDRALLELLWSTGIRRGELARLDLYDVDASRGVVTVRQgKGNKDRVVPVGERALAWLQRYLQdVRpqlAVRPDSGA---- 233

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1339709323 131 LFVTNY-----KGKYTQLTVRAIQklcdkySSAFDEKRSPHKLRHTYATNHYKENKDLVLLRDQLGHTSVEVTSIYTNI 204
Cdd:PRK01287  234 LFVAMDgdglaRNTLTNMVGRYIR------AAGIEKAGACHLFRHAMATQMLENGADTRHIQAILGHAKLETTQIYTRV 306
INT_Rci_Hp1_C cd00796
Shufflon-specific DNA recombinase Rci and Bacteriophage Hp1_like integrase, C-terminal ...
 59-203 4.15e-14

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: 67.35  E-value: 4.15e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1339709323  59 AIISLILGTGLRVSEVVSLTISSINFRQGKV--KVTRKGNKRssilaTHSCLDDVQEYIKVRLSKYncpqDEDLLFVTNY 136
Cdd:cd00796    27 LIVLLALYTGARRGEILSLRWDDIDLEVGLIvlPETKNGKPR-----TVPLSDEAIAILKELKRKR----GKDGFFVDGR 97

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1339709323 137 KGKYTQLTV-RAIQKLCDKyssAFDEKRSPHKLRHTYATNHYKENKDLVLLRDQLGHTSVEVTSIYTN 203
Cdd:cd00796    98 FFGIPIASLrRAFKKARKR---AGLEDLRFHDLRHTFASRLVQAGVPIKTVAKILGHSSIKMTMRYAH 162
INT_ICEBs1_C_like cd01189
C-terminal catalytic domain of integrases from bacterial phages and conjugate transposons; ...
 50-202 7.77e-14

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


Pssm-ID: 271189 [Multi-domain]  Cd Length: 147  Bit Score: 66.04  E-value: 7.77e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1339709323  50 FQRDKERDIAIISLILGTGLRVSEVVSLTISSINFRQGKVKVTR------KGNKRSSILATHSCLDDVQ--EYIKVRLSK 121
Cdd:cd01189    11 LKKRGDRYYLLFLLALLTGLRRGELLALTWSDIDFENGTIRINRtlvrkkKGGYVIKPPKTKSSIRTIPlpDELIELLKE 90

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1339709323 122 YncpqdedllfvtnykgkytqltvRAIQKLCDKyssAFDEKRSPHKLRHTYATNHYKENKDLVLLRDQLGHTSVEVT-SI 200
Cdd:cd01189    91 L-----------------------KAFKKLLKK---AGLPRITPHDLRHTFASLLLEAGVPLKVIAERLGHSDISTTlDV 144


                  ..
gi 1339709323 201 YT 202
Cdd:cd01189   145 YA 146
INT_C_like_3 cd01192
Uncharacterized site-specific tyrosine recombinase, C-terminal catalytic domain; Tyrosine ...
 47-207 1.85e-12

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


Pssm-ID: 271192 [Multi-domain]  Cd Length: 178  Bit Score: 63.08  E-value: 1.85e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1339709323  47 YSFFQRDKERDIAIISLILGTGLRVSEVVSLTISSInFRQGKVKVT-RKGNKRSSILATHSCLDDVQEYIKVRlskynCP 125
Cdd:cd01192    16 KLYLKKANPRNYLLFIVGINTGLRISDLLSLKVEDV-TNKDKLSIKeQKTGKQKTFPLNPTLVKALKEYIDDL-----DL 89

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1339709323 126 QDEDLLFVTNYKGKYTQLTV----RAIQKLCDKYSSAfdEKRSPHKLRHTYATNHYKENKDLVLLRDQLGHTSVEVTSIY 201
Cdd:cd01192    90 KRNDYLFKSLKQGPEKPISRkqayKILKKAADDLGLN--YNIGTHSLRKTFGYHVYKQGKDIELLMKLLNHSSPSITLRY 167


                  ....*.
gi 1339709323 202 TNINNE 207
Cdd:cd01192   168 LGIDQE 173
INT_FimBE_like cd01197
FimB and FimE and related proteins, integrase/recombinases; This CD includes proteins similar ...
 52-208 1.07e-11

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: 61.37  E-value: 1.07e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1339709323  52 RDKERDIAIISLILGTGLRVSEVVSLTISSINFRQGKVKVTRKGNKRSSilaTHSCLDD----VQEYIKVRLSKYncPQD 127
Cdd:cd01197    23 RTPARDYCLLLLAFRHGFRVSELCDLHLSDVDLESRRLHIRRLKNGFST---THPLRFDereaLEAWLKERANWK--GAD 97

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1339709323 128 EDLLFVTNYKGKYTQLTV-RAIQKLCDKysSAFDEKRSPHKLRHTYATNHYKENKDLVLLRDQLGHTSVEVTSIYTNINN 206
Cdd:cd01197    98 TDWIFLSRRGGPLSRQQAyRIIRDLGKE--AGTVTQTHPHMLRHACGYALADRGADTRLIQDYLGHRNIRHTVIYTASNA 175


                  ..
gi 1339709323 207 EK 208
Cdd:cd01197   176 AR 177
INT_RitB_C_like cd00797
C-terminal catalytic domain of recombinase RitB, a component of the recombinase trio; ...
 61-216 3.00e-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: 60.40  E-value: 3.00e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1339709323  61 ISLILGTGLRVSEVVSLTISSINFRQGKVKVTRKGNKRSSILATHSCLDDV-QEYIKVRLSKYNCPQDEdLLFVTNYKGK 139
Cdd:cd00797    31 FGLLYATGLRVGEALRLRLEDVDLDSGILTIRQTKFGKSRLVPLHPSTVGAlRDYLARRDRLLPSPSSS-YFFVSQQGGR 109

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1339709323 140 YTQLTV-RAIQKLCDK--YSSAFDeKRSP--HKLRHTYATNH----YKENKDLV----LLRDQLGHTSVEVTSIYTNINN 206
Cdd:cd00797   110 LTGGGVyRVFRRLLRRigLRGAGD-GRGPrlHDLRHTFAVNRltrwYREGADVErklpVLSTYLGHVNVTDTYWYLTATP 188

                         170
                  ....*....|
gi 1339709323 207 EKKREAVDRL 216
Cdd:cd00797   189 ELMELASLRL 198
INT_C_like_5 cd01195
Uncharacterized site-specific tyrosine recombinase, C-terminal catalytic domain; Tyrosine ...
 56-201 3.50e-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: 56.71  E-value: 3.50e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1339709323  56 RDIAIISLILGTGLRVSEVVSLTISSINFRQGKVKVTRKGNK-RSSILATHSCLDDVQEYIKVRLSKyncpqdEDLLFVT 134
Cdd:cd01195    21 RDEALVRLLLDNALRRSEAVALDVEDLEKEHRRLRILGKGKKqREVVTLPPTTREALAAWLAARGEA------EGPLFVS 94

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1339709323 135 NYKGKYT-QLTVRAIQKLCDKYSSA--FDEKRSPHKLRHTYATNHYKENKDLV-LLRDQLGHTSVEVTSIY 201
Cdd:cd01195    95 LDRASRGrRLSPQAVYRIVRRLAERigLGKRLSPHGLRHSAITLALDAGAGLIrKVQDFSRHADLRTLQVY 165
INTN1_C_like cd01185
Integrase IntN1 of Bacteroides mobilizable transposon NBU1 and similar proteins, C-terminal ...
 52-209 8.78e-10

Integrase IntN1 of Bacteroides mobilizable transposon NBU1 and similar proteins, C-terminal catalytic domain; IntN1 is a tyrosine recombinase for the integration and excision of Bacteroides mobilizable transposon NBU1 from the host chromosome. IntN1 does not require strict homology between the recombining sites seen with other tyrosine recombinases. This family belongs to the superfamily of DNA breaking-rejoining enzymes, which share the same fold in their catalytic domain and the overall reaction mechanism. The catalytic domain contains six conserved active site residues. Their overall reaction mechanism involves cleavage of a single strand of a DNA duplex by nucleophilic attack of a conserved tyrosine to give a 3' phosphotyrosyl protein-DNA adduct. In the second rejoining step, a terminal 5' hydroxyl attacks the covalent adduct to release the enzyme and generate duplex DNA.


Pssm-ID: 271185 [Multi-domain]  Cd Length: 161  Bit Score: 55.35  E-value: 8.78e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1339709323  52 RDKERDIAIISLIlgTGLRVSEVVSLTISSINFRQGK---VKVTRKGNKRSSILathscLDDVQEYIkvrLSKYNCPQDE 128
Cdd:cd01185    17 LELVRDMFLFSCY--TGLRFSDLKNLTWKNIVEASGRtwiRYRRKKTGKPVTVP-----LLPVAREI---LEKYKDDRSE 86

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1339709323 129 DLLFvTNYKGKYTQLTVRAIQKLCDKyssafDEKRSPHKLRHTYATNHYKENKDLVLLRDQLGHTSVEVTSIYTNINNEK 208
Cdd:cd01185    87 GKLF-PVLSNQKINRYLKEIAKIAGI-----DKHLTFHVARHTFATLLLLKGVDIETISKLLGHSSIKTTQIYAKIVDSK 160


                  .
gi 1339709323 209 K 209
Cdd:cd01185   161 K 161
INT_C_like_2 cd01191
Uncharacterized site-specific tyrosine recombinase, C-terminal catalytic domain; Tyrosine ...
 42-216 1.11e-09

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


Pssm-ID: 271191  Cd Length: 176  Bit Score: 55.51  E-value: 1.11e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1339709323  42 ISPKKYSFFQRDKERD-----IAIISLILGTGLRVSEVVSLTISSINFrqGKVKVTRKGNKRSSILATHSCLDDVQEYIK 116
Cdd:cd01191     2 ISNADYNFLKKCLKKDgnlewYFVVRFLAATGARVSELIKIKVEHVEL--GYFDIYSKGGKLRRLYIPKKLRNEALEWLK 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1339709323 117 VRlskyncPQDEDLLFVTNYkGKytQLTVRAIQKLCDKYSSAFDEKRS---PHKLRHTYATNHYKENKDLVLLRDQLGHT 193
Cdd:cd01191    80 ST------NRKSGYIFLNRF-GE--RITTRGIAQQLKNYARKYGLNPKvvyPHSFRHRFAKNFLEKYNDIALLADLMGHE 150

                         170       180
                  ....*....|....*....|...
gi 1339709323 194 SVEVTSIYTNINNEKKREAVDRL 216
Cdd:cd01191   151 SIETTRIYLRKTASEQQEIVDKI 173
INT_tnpA_C_Tn554 cd01186
Putative Transposase A from transposon Tn554, C-terminal catalytic domain; This family ...
 56-212 5.03e-09

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: 53.96  E-value: 5.03e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1339709323  56 RDIAIISLILGTGLRVSEVVSLTISSINFRQGKVKVTRKGN----------KRSSILATHSCLDDVQEYIkvrLSKYNCP 125
Cdd:cd01186    18 RDKFLLALLYETGLRIGEALGLRIEDIDMADNQIELVPREDntnearaksmRERRIPVSQDLIDLYADYL---TYIYCEE 94

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1339709323 126 QDEDLLFVTNYKGK--YTQLTVRAIQKLCDKYSSAFDEKRSPHKLRHTYATNHYKENKDLVLLRDQLGHTSVEVT-SIYT 202
Cdd:cd01186    95 AEFSITVFVNVKGGnqGKAMNYSDVYDLVRRLKKRTGIDFTPHMFRHTHATALIRAGWSIEVVARRLGHAHVQTTlNTYG 174

                         170
                  ....*....|
gi 1339709323 203 NINNEKKREA 212
Cdd:cd01186   175 HLSEEDIRRE 184
integrase_gron TIGR02249
integron integrase; Members of this family are integrases associated with integrons (and ...
 60-206 8.13e-07

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


Pssm-ID: 131303 [Multi-domain]  Cd Length: 315  Bit Score: 48.54  E-value: 8.13e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1339709323  60 IISLILGTGLRVSEVVSLTISSINFRQGKVKVTR-KGNK-RSSILAthsclDDVQEYIKVRLSKYNCPQDEDLlfVTNYK 137
Cdd:TIGR02249 121 IAKLLYGSGMRLMECLRLRIQDIDFDYGEIRIRQgKGGKdRTVTLP-----KELIPPLREQIELARAYHEADL--AEGYG 193

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1339709323 138 GKYTQltvraiQKLCDKYSSAFDE----------KRS------------------------------------PHKLRHT 171
Cdd:TIGR02249 194 GVYLP------HALARKYPNAPKEwgwqylfpshRLSrdpesgvirrhhinettiqravrraveragiekpvtCHTLRHS 267

                         170       180       190
                  ....*....|....*....|....*....|....*
gi 1339709323 172 YATNHYKENKDLVLLRDQLGHTSVEVTSIYTNINN 206
Cdd:TIGR02249 268 FATHLLESGADIRTVQELLGHSDVKTTQIYTHVLN 302
PRK09871 PRK09871
tyrosine recombinase; Provisional
 55-205 1.66e-06

tyrosine recombinase; Provisional


Pssm-ID: 182126  Cd Length: 198  Bit Score: 46.90  E-value: 1.66e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1339709323  55 ERDIAIISLILGTGLRVSEVVSLTISSINFRQGKVKVTRKGNKRSSIlatHSCLDDVQEYI----KVRLSkYNCPQDEDL 130
Cdd:PRK09871   26 ARDYCLILLAYRHGMRISELLDLHYQDLDLNEGRINIRRLKNGFSTV---HPLRFDEREAVerwtQERAN-WKGADRTDA 101

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1339709323 131 LFVTNYKGKYT-QLTVRAIQKLCDKYSSAfdEKRSPHKLRHTYATNHYKENKDLVLLRDQLGHTSVEVTSIYTNIN 205
Cdd:PRK09871  102 IFISRRGSRLSrQQAYRIIRDAGIEAGTV--TQTHPHMLRHACGYELAERGADTRLIQDYLGHRNIRHTVRYTASN 175
PRK15417 PRK15417
integron integrase;
63-204 2.53e-06

integron integrase;


Pssm-ID: 185315 [Multi-domain]  Cd Length: 337  Bit Score: 47.35  E-value: 2.53e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1339709323  63 LILGTGLRVSEVVSLTISSINFRQGKVKVTR-KGNKRSSILATHSCLDDVQEYIKVRLSKYNCPQDE--------DLL-- 131
Cdd:PRK15417  139 LLYGTGMRISEGLQLRVKDLDFDHGTIIVREgKGSKDRALMLPESLAPSLREQLSRARAWWLKDQAEgrsgvalpDALer 218

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1339709323 132 --------------------------FVTNYKGKYTQLTVRAIQKLCDKysSAFDEKRSPHKLRHTYATNHYKENKDLVL 185
Cdd:PRK15417  219 kypraghswpwfwvfaqhthstdprsGVVRRHHMYDQTFQRAFKRAVEQ--AGITKPATPHTLRHSFATALLRSGYDIRT 296

                         170
                  ....*....|....*....
gi 1339709323 186 LRDQLGHTSVEVTSIYTNI 204
Cdd:PRK15417  297 VQDLLGHSDVSTTMIYTHV 315
INT_C_like_6 cd01196
Uncharacterized site-specific tyrosine recombinase, C-terminal catalytic domain; Tyrosine ...
 56-213 4.39e-05

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


Pssm-ID: 271196  Cd Length: 183  Bit Score: 42.47  E-value: 4.39e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1339709323  56 RDIAIISLILGTGLRVSEVVSLTISSInFRQGK---VKVTRKGNKRSSILATHscldDVQEYIKVRLSKYNCPQDEDLLF 132
Cdd:cd01196    21 RDRALIALMVYSFARIGAVLAMRVEDV-YDQGRrlwVRLAEKGGKQHEMPCHH----DLEEYLRAYLEAAEIEEDPKGPL 95

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1339709323 133 VTNYKGKYTQLTVRAIQKlcdkySSAFDEKR------------SPHKLRHTYATNHYKENKDLVLLRDQLGHTSVEVTSI 200
Cdd:cd01196    96 FRTTRGGTRKLTHNPLTQ-----ANAYRMVRrraiaadiptaiGNHSFRATGITAYLKNGGTLEDAQNMANHASTRTTQL 170

                         170
                  ....*....|...
gi 1339709323 201 YTNINNEKKREAV 213
Cdd:cd01196   171 YDRRSDKITLDEV 183
int PHA02601
integrase; Provisional
 53-201 6.79e-05

integrase; Provisional


Pssm-ID: 222904 [Multi-domain]  Cd Length: 333  Bit Score: 42.79  E-value: 6.79e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1339709323  53 DKERDIAIISLI-LGTGLRVSEVVSLTISSI-NFRQGKVKVtrKGNKRSSILAThsclddvQEYIKVRlskyncPQDEDL 130
Cdd:PHA02601  188 SRSPDLGLIAKIcLATGARWSEAETLKRSQIsPYKITFVKT--KGKKNRTVPIS-------EELYKML------PKRRGR 252

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1339709323 131 LFVTNYkGKYTQLTVRAIQKLcdkyssafDEKRSPHKLRHTYATnHYKENK-DLVLLRDQLGHTSVEVTSIY 201
Cdd:PHA02601  253 LFKDAY-ESFERAVKRAGIDL--------PEGQATHVLRHTFAS-HFMMNGgNILVLQRILGHATIEMTMAY 314
INT_tnpB_C_Tn554 cd01187
Putative Transposase B from transposon Tn554, C-terminal catalytic domain; This family ...
 51-201 1.51e-04

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


Pssm-ID: 271187 [Multi-domain]  Cd Length: 142  Bit Score: 40.49  E-value: 1.51e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1339709323  51 QRDKERD-IAIISLILGTGLRVSEVVSLtisSINFRQGKVKVTRKGNKRSSILATHSC------LDDVQEYIKvrlsKYN 123
Cdd:cd01187     8 ALDLLPQpIPVVQAAVFTGARASELATL---KFGCLHAQTSDDGTFLYWLKWENKGGKqldipiSKKVAELIK----TIN 80

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1339709323 124 cpqdedllfvtnykgkYTQLTVRAIQKLCDKYSSAFDEKrsPHKLRHTYATNHYKENKDLVLLRDQLGHTSVEVTSIY 201
Cdd:cd01187    81 ----------------WTLNELSELKNISDDHGERFRFH--THRFRHTVATRLANSGMGILVLQQLLGHSSPEMTLRY 140
PRK09870 PRK09870
tyrosine recombinase; Provisional
 68-220 1.09e-03

tyrosine recombinase; Provisional


Pssm-ID: 182125  Cd Length: 200  Bit Score: 38.77  E-value: 1.09e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1339709323  68 GLRVSEVVSLTISSINFRQGKVKVTRKGNKRSSilaTHSCLDD----VQEYIKVRLSkYNCPQDEDLLFVTNYKGKYTQL 143
Cdd:PRK09870   45 GFRASEICRLRISDIDLKAKCIYIHRLKKGFST---THPLLNKeiqaLKNWLSIRTS-YPHAESEWVFLSRKGNPLSRQQ 120

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1339709323 144 TVRAIQKLCDKYSSAFDEKrsPHKLRHTYATNHYKENKDLVLLRDQLGHTSVEVTSIYTNINNEKKREAVDRLERRQ 220
Cdd:PRK09870  121 FYHIISTSGGNAGLSLEIH--PHMLRHSCGFALANMGIDTRLIQDYLGHRNIRHTVWYTASNAGRFYGIWDRARGRQ 195
INT_Lambda_C cd00800
C-terminal catalytic domain of Lambda integrase, a tyrosine-based site-specific recombinase; ...
 59-202 9.54e-03

C-terminal catalytic domain of Lambda integrase, a tyrosine-based site-specific recombinase; Lambda-type integrases catalyze site-specific integration and excision of temperate bacteriophages and other mobile genetic elements to and from the bacterial host chromosome. They are tyrosine-based site-specific recombinase and belong to the superfamily of DNA breaking-rejoining enzymes, which share the same fold in their catalytic domain and the overall reaction mechanism. The phage lambda integrase can bridge two different and well-separated DNA sequences called arm- and core-sites. The C-terminal domain binds, cleaves and re-ligates DNA strands at the core-sites, while the N-terminal domain is largely responsible for high-affinity binding to the arm-type sites.


Pssm-ID: 271181 [Multi-domain]  Cd Length: 161  Bit Score: 35.40  E-value: 9.54e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1339709323  59 AIISLILGTGLRVSEVVSLTISSI-----NFRQGkvkvtrKGNKRSSILATHS---CLDDVQEYiKVRLSKYncpqdedl 130
Cdd:cd00800    16 LAMELALLTGQRQGDLLRLKWSDItdgglLVEQS------KTGKKLLIPWTPSlraLVDRIRAL-PRKRSEY-------- 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1339709323 131 LFVTNYKGKYTQLTV-----RAIQKLCDKYSSA---FdekrspHKLRHTYATnhykENKDLVLLRDQ---LGHTSVEVTS 199
Cdd:cd00800    81 LINSRKGGPLSYDTLksawrRARKAAGLKGETEgftF------HDLRAKAAT----DYAEQGGSTDAqalLGHKSDAMTE 150


                  ...
gi 1339709323 200 IYT 202
Cdd:cd00800   151 RYT 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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