NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|1274245735|gb|PIH86481|]
View 

integrase [Pseudomonas syringae pv. actinidiae]

Protein Classification

site-specific integrase( domain architecture ID 10086937)

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:  10047575|9278480|10577069
SCOP:  4002347

Graphical summary

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

List of domain hits

 Name Accession Description Interval E-value
DNA_BRE_C cd00397
DNA breaking-rejoining enzymes, C-terminal catalytic domain; The DNA breaking-rejoining enzyme ...
 62-212 9.16e-33

DNA breaking-rejoining enzymes, C-terminal catalytic domain; The DNA breaking-rejoining enzyme superfamily includes type IB topoisomerases and tyrosine based site-specific recombinases (integrases) that share the same fold in their catalytic domain containing conserved active site residues. The best-studied members of this diverse superfamily include Human topoisomerase I, the bacteriophage lambda integrase, the bacteriophage P1 Cre recombinase, the yeast Flp recombinase, and the bacterial XerD/C recombinases. Their overall reaction mechanism is essentially identical and involves cleavage of a single strand of a DNA duplex by nucleophilic attack of a conserved tyrosine to give a 3' phosphotyrosyl protein-DNA adduct. In the second rejoining step, a terminal 5' hydroxyl attacks the covalent adduct to release the enzyme and generate duplex DNA. The enzymes differ in that topoisomerases cleave and then rejoin the same 5' and 3' termini, whereas a site-specific recombinase transfers a 5' hydroxyl generated by recombinase cleavage to a new 3' phosphate partner located in a different duplex region. Many DNA breaking-rejoining enzymes also have N-terminal domains, which show little sequence or structure similarity.


:

Pssm-ID: 271175 [Multi-domain]  Cd Length: 167  Bit Score: 121.05  E-value: 9.16e-33
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1274245735  62 WLAVFEMFYYTGIRLNALICLRYSDIDLGERLIRVRGETEKTHREFMIPIPDGLMPHLKLLMDiAHRVGLAPMDQIFNVN 141
Cdd:cd00397    19 DRAILLLLLETGLRISELLALKVKDIDLDNGTIRVRGKKTKGGKERTVPLPKELAEELKEYLK-ERRDKRGPLLKSLYLN 97

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1274245735 142 KFSGHYSRTQMNTDQVESMYKKLTAMTGVRMTPHRFRHTIASEMMRQPErNIHITKSLLNHSNIATTMEYI 212
Cdd:cd00397    98 KLFGTKLGERLSRRTLRRIFKKAGIEAGRKITPHSLRHTFATNLLENGV-DIKVVQKLLGHSSISTTQRYL 167
 
Name Accession Description Interval E-value
DNA_BRE_C cd00397
DNA breaking-rejoining enzymes, C-terminal catalytic domain; The DNA breaking-rejoining enzyme ...
 62-212 9.16e-33

DNA breaking-rejoining enzymes, C-terminal catalytic domain; The DNA breaking-rejoining enzyme superfamily includes type IB topoisomerases and tyrosine based site-specific recombinases (integrases) that share the same fold in their catalytic domain containing conserved active site residues. The best-studied members of this diverse superfamily include Human topoisomerase I, the bacteriophage lambda integrase, the bacteriophage P1 Cre recombinase, the yeast Flp recombinase, and the bacterial XerD/C recombinases. Their overall reaction mechanism is essentially identical and involves cleavage of a single strand of a DNA duplex by nucleophilic attack of a conserved tyrosine to give a 3' phosphotyrosyl protein-DNA adduct. In the second rejoining step, a terminal 5' hydroxyl attacks the covalent adduct to release the enzyme and generate duplex DNA. The enzymes differ in that topoisomerases cleave and then rejoin the same 5' and 3' termini, whereas a site-specific recombinase transfers a 5' hydroxyl generated by recombinase cleavage to a new 3' phosphate partner located in a different duplex region. Many DNA breaking-rejoining enzymes also have N-terminal domains, which show little sequence or structure similarity.


Pssm-ID: 271175 [Multi-domain]  Cd Length: 167  Bit Score: 121.05  E-value: 9.16e-33
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1274245735  62 WLAVFEMFYYTGIRLNALICLRYSDIDLGERLIRVRGETEKTHREFMIPIPDGLMPHLKLLMDiAHRVGLAPMDQIFNVN 141
Cdd:cd00397    19 DRAILLLLLETGLRISELLALKVKDIDLDNGTIRVRGKKTKGGKERTVPLPKELAEELKEYLK-ERRDKRGPLLKSLYLN 97

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1274245735 142 KFSGHYSRTQMNTDQVESMYKKLTAMTGVRMTPHRFRHTIASEMMRQPErNIHITKSLLNHSNIATTMEYI 212
Cdd:cd00397    98 KLFGTKLGERLSRRTLRRIFKKAGIEAGRKITPHSLRHTFATNLLENGV-DIKVVQKLLGHSSISTTQRYL 167
XerC COG4973
Site-specific recombinase XerC [Replication, recombination and repair];
1-223 3.11e-29

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


Pssm-ID: 443998 [Multi-domain]  Cd Length: 287  Bit Score: 115.06  E-value: 3.11e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1274245735   1 MEHGLVElkVNPLKetRVIPTKRPKKTIKTDAIVRARNWLNILVKEERATENRAeitpawfwlaVFEMFYYTGIRLNALI 80
Cdd:COG4973    86 VREGLLE--ANPAA--GVKAPKAPRKLPRALTVDELAQLLDALADDPLAVRDRA----------IVELLYSTGLRLGELV 151

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1274245735  81 CLRYSDIDLGERLIRVRGeteKTHREFMIPIPDGLMPHLKLLMDIAHRVGLAPMDQIFNvnkfsgHYSRTQMNTDQVESM 160
Cdd:COG4973   152 GLDWEDVDLDAGEVRVRG---KTGKSRTVPLGPKALAALREWLAVRPELAAPDEGALFP------SRRGTRLSPRNVQKR 222

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1274245735 161 YKKLTAMTGV--RMTPHRFRHTIASeMMRQPERNIHITKSLLNHSNIATTMEYIEPDYDVMREVM 223
Cdd:COG4973   223 LRRLAKKAGLpkHVHPHDLRHSFAT-HLLESGGDLRAVQELLGHASISTTQIYTHLDFQHLAEVY 286
xerS PRK05084
site-specific tyrosine recombinase XerS; Reviewed
 63-227 7.63e-20

site-specific tyrosine recombinase XerS; Reviewed


Pssm-ID: 235339 [Multi-domain]  Cd Length: 357  Bit Score: 89.98  E-value: 7.63e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1274245735  63 LAVFEMFYYTGIRLNALICLRYSDIDLGERLIRVrgeTEKTHREFMIPIPDGLMPHLKLLMDI-AHRVGLAPMDQIFNVN 141
Cdd:PRK05084  198 LAIIALILGSGLRVSELVNLDLSDLNLKQMTIDV---TRKGGKRDSVNIAPFALPYLEEYLKIrASRYKAEKQEKALFLT 274

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1274245735 142 KFSGHYSRTQMNTdqVESMYKKLTAMTGVRMTPHRFRHTIASEMMRQpERNIHITKSLLNHSNIATTMEYIEPDYDVMRE 221
Cdd:PRK05084  275 KYRGKPNRISARA--IEKMVAKYSEAFGVRLTPHKLRHTLATRLYDA-TKDQVLVADQLGHTSTETTDLYTHIVNDEQKE 351


                  ....*.
gi 1274245735 222 VMNERG 227
Cdd:PRK05084  352 ALDRLE 357
Phage_integrase pfam00589
Phage integrase family; Members of this family cleave DNA substrates by a series of staggered ...
 63-216 3.40e-16

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: 75.82  E-value: 3.40e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1274245735  63 LAVFEMFYYTGIRLNALICLRYSDIDLGERLIRVrgETEKTHREFMIPIPDGLMPHLKLLMDIAHRVGLAPmDQIFnVNK 142
Cdd:pfam00589  24 KALLELLYATGLRISELCSLRWSDIDFENGVIRV--HRGKGNKERTVPLSDAALELLKEWLSKRLLEAPKS-DYLF-ASK 99

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1274245735 143 FsghysRTQMNTDQVESMYKKLTAMTGV--RMTPHRFRHTIASEMMRQpERNIHITKSLLNHSNIATTMEYIEPDY 216
Cdd:pfam00589 100 R-----GKPLSRQTVRKIFKRAGKEAGLelPLHPHMLRHSFATHLLEA-GVDLRVVQKLLGHSSISTTQIYTHVAD 169
recomb_XerD TIGR02225
tyrosine recombinase XerD; The phage integrase family describes a number of recombinases with ...
 64-208 1.15e-08

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: 56.05  E-value: 1.15e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1274245735  64 AVFEMFYYTGIRLNALICLRYSDIDLGERLIRVRGeteKTHREFMIPIPD----GLMPHLK----LLMDIAHRVGlapmD 135
Cdd:TIGR02225 129 AMLELLYATGLRVSELVGLRLEDVNLDEGFVRVRG---KGNKERLVPLGEeaieALERYLKearpLLLKKKVKES----D 201

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1274245735 136 QIFnVNKFSGHYSRtQMntdqVESMYKKLTAMTGV--RMTPHRFRHTIASEMMrQPERNIHITKSLLNHSNIATT 208
Cdd:TIGR02225 202 ALF-LNRRGGPLSR-QG----VWKILKEYAKRAGIekPISPHTLRHSFATHLL-ENGADLRVVQELLGHADISTT 269
 
Name Accession Description Interval E-value
DNA_BRE_C cd00397
DNA breaking-rejoining enzymes, C-terminal catalytic domain; The DNA breaking-rejoining enzyme ...
 62-212 9.16e-33

DNA breaking-rejoining enzymes, C-terminal catalytic domain; The DNA breaking-rejoining enzyme superfamily includes type IB topoisomerases and tyrosine based site-specific recombinases (integrases) that share the same fold in their catalytic domain containing conserved active site residues. The best-studied members of this diverse superfamily include Human topoisomerase I, the bacteriophage lambda integrase, the bacteriophage P1 Cre recombinase, the yeast Flp recombinase, and the bacterial XerD/C recombinases. Their overall reaction mechanism is essentially identical and involves cleavage of a single strand of a DNA duplex by nucleophilic attack of a conserved tyrosine to give a 3' phosphotyrosyl protein-DNA adduct. In the second rejoining step, a terminal 5' hydroxyl attacks the covalent adduct to release the enzyme and generate duplex DNA. The enzymes differ in that topoisomerases cleave and then rejoin the same 5' and 3' termini, whereas a site-specific recombinase transfers a 5' hydroxyl generated by recombinase cleavage to a new 3' phosphate partner located in a different duplex region. Many DNA breaking-rejoining enzymes also have N-terminal domains, which show little sequence or structure similarity.


Pssm-ID: 271175 [Multi-domain]  Cd Length: 167  Bit Score: 121.05  E-value: 9.16e-33
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1274245735  62 WLAVFEMFYYTGIRLNALICLRYSDIDLGERLIRVRGETEKTHREFMIPIPDGLMPHLKLLMDiAHRVGLAPMDQIFNVN 141
Cdd:cd00397    19 DRAILLLLLETGLRISELLALKVKDIDLDNGTIRVRGKKTKGGKERTVPLPKELAEELKEYLK-ERRDKRGPLLKSLYLN 97

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1274245735 142 KFSGHYSRTQMNTDQVESMYKKLTAMTGVRMTPHRFRHTIASEMMRQPErNIHITKSLLNHSNIATTMEYI 212
Cdd:cd00397    98 KLFGTKLGERLSRRTLRRIFKKAGIEAGRKITPHSLRHTFATNLLENGV-DIKVVQKLLGHSSISTTQRYL 167
XerC COG4973
Site-specific recombinase XerC [Replication, recombination and repair];
1-223 3.11e-29

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


Pssm-ID: 443998 [Multi-domain]  Cd Length: 287  Bit Score: 115.06  E-value: 3.11e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1274245735   1 MEHGLVElkVNPLKetRVIPTKRPKKTIKTDAIVRARNWLNILVKEERATENRAeitpawfwlaVFEMFYYTGIRLNALI 80
Cdd:COG4973    86 VREGLLE--ANPAA--GVKAPKAPRKLPRALTVDELAQLLDALADDPLAVRDRA----------IVELLYSTGLRLGELV 151

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1274245735  81 CLRYSDIDLGERLIRVRGeteKTHREFMIPIPDGLMPHLKLLMDIAHRVGLAPMDQIFNvnkfsgHYSRTQMNTDQVESM 160
Cdd:COG4973   152 GLDWEDVDLDAGEVRVRG---KTGKSRTVPLGPKALAALREWLAVRPELAAPDEGALFP------SRRGTRLSPRNVQKR 222

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1274245735 161 YKKLTAMTGV--RMTPHRFRHTIASeMMRQPERNIHITKSLLNHSNIATTMEYIEPDYDVMREVM 223
Cdd:COG4973   223 LRRLAKKAGLpkHVHPHDLRHSFAT-HLLESGGDLRAVQELLGHASISTTQIYTHLDFQHLAEVY 286
XerD COG4974
Site-specific recombinase XerD [Replication, recombination and repair];
64-225 2.68e-25

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


Pssm-ID: 443999 [Multi-domain]  Cd Length: 291  Bit Score: 104.31  E-value: 2.68e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1274245735  64 AVFEMFYYTGIRLNALICLRYSDIDLGERLIRVRGetEKTHREFMIPIPDGLMPHLKLLMDIAHRvglAPMDQIFnVNKF 143
Cdd:COG4974   137 ALLLLLYATGLRVSELLGLKWSDIDLDRGTIRVRR--GKGGKERTVPLSPEALEALREYLEERRP---RDSDYLF-PTRR 210

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1274245735 144 SGHYSRTQMNtdqveSMYKKLTAMTGV--RMTPHRFRHTIASEMMRQpERNIHITKSLLNHSNIATTMEYIEPDYDVMRE 221
Cdd:COG4974   211 GRPLSRRAIR-----KILKRLAKRAGIpkRVTPHSLRHTFATHLLEA-GVDLRTVQELLGHSSISTTQIYTHVSDEELRE 284


                  ....
gi 1274245735 222 VMNE 225
Cdd:COG4974   285 AVEK 288
xerS PRK05084
site-specific tyrosine recombinase XerS; Reviewed
 63-227 7.63e-20

site-specific tyrosine recombinase XerS; Reviewed


Pssm-ID: 235339 [Multi-domain]  Cd Length: 357  Bit Score: 89.98  E-value: 7.63e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1274245735  63 LAVFEMFYYTGIRLNALICLRYSDIDLGERLIRVrgeTEKTHREFMIPIPDGLMPHLKLLMDI-AHRVGLAPMDQIFNVN 141
Cdd:PRK05084  198 LAIIALILGSGLRVSELVNLDLSDLNLKQMTIDV---TRKGGKRDSVNIAPFALPYLEEYLKIrASRYKAEKQEKALFLT 274

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1274245735 142 KFSGHYSRTQMNTdqVESMYKKLTAMTGVRMTPHRFRHTIASEMMRQpERNIHITKSLLNHSNIATTMEYIEPDYDVMRE 221
Cdd:PRK05084  275 KYRGKPNRISARA--IEKMVAKYSEAFGVRLTPHKLRHTLATRLYDA-TKDQVLVADQLGHTSTETTDLYTHIVNDEQKE 351


                  ....*.
gi 1274245735 222 VMNERG 227
Cdd:PRK05084  352 ALDRLE 357
Phage_integrase pfam00589
Phage integrase family; Members of this family cleave DNA substrates by a series of staggered ...
 63-216 3.40e-16

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: 75.82  E-value: 3.40e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1274245735  63 LAVFEMFYYTGIRLNALICLRYSDIDLGERLIRVrgETEKTHREFMIPIPDGLMPHLKLLMDIAHRVGLAPmDQIFnVNK 142
Cdd:pfam00589  24 KALLELLYATGLRISELCSLRWSDIDFENGVIRV--HRGKGNKERTVPLSDAALELLKEWLSKRLLEAPKS-DYLF-ASK 99

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1274245735 143 FsghysRTQMNTDQVESMYKKLTAMTGV--RMTPHRFRHTIASEMMRQpERNIHITKSLLNHSNIATTMEYIEPDY 216
Cdd:pfam00589 100 R-----GKPLSRQTVRKIFKRAGKEAGLelPLHPHMLRHSFATHLLEA-GVDLRVVQKLLGHSSISTTQIYTHVAD 169
INT_XerDC_C cd00798
XerD and XerC integrases, C-terminal catalytic domains; XerDC-like integrases are involved in ...
 64-208 4.16e-14

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: 69.85  E-value: 4.16e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1274245735  64 AVFEMFYYTGIRLNALICLRYSDIDLGERLIRVRGeteKTHREFMIPIPDGLMPHLKLLMDIAHRVGL--APMDQIFnVN 141
Cdd:cd00798    23 AILELLYASGLRVSELVGLDLSDVDLDEGLVRVTG---KGNKERLVPFGSYAVEALEEYLEERRPLLLkkKPPDALF-LN 98

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1274245735 142 KFSGhysrtQMNTDQVESMYKKLTAMTGV--RMTPHRFRHTIASEMMrqpER--NIHITKSLLNHSNIATT 208
Cdd:cd00798    99 KRGK-----RLSRRGVWRILKKYAERAGLpkHVSPHTLRHSFATHLL---EGgaDLRVVQELLGHASLSTT 161
INT_IntI_C cd01193
Integron integrase and similar protiens, C-terminal catalytic domain; Integron integrases ...
 64-211 7.22e-14

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: 69.23  E-value: 7.22e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1274245735  64 AVFEMFYYTGIRLNALICLRYSDIDLGERLIRVRGetEKTHREFMIPIPDGLMPHLKLLMDIA-HRVGLAPMDQIFNV-N 141
Cdd:cd01193    25 LILSLLYGAGLRISELLRLRVKDIDFERGVIRVRQ--GKGGKDRVVPLPEKLLEPLRRYLKSArPKEELDPAEGRAGVlD 102

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1274245735 142 KFSGHYSRTQMNTDQVESMYKKLTAMTGV--RMTPHRFRHTIASEMMRQpERNIHITKSLLNHSNIATTMEY 211
Cdd:cd01193   103 PRTGVERRHHISETTVQRALKKAVEQAGItkRVTPHTLRHSFATHLLEA-GTDIRTIQELLGHSDLSTTMIY 173
INT_tnpA_C_Tn554 cd01186
Putative Transposase A from transposon Tn554, C-terminal catalytic domain; This family ...
 65-222 9.79e-14

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: 68.98  E-value: 9.79e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1274245735  65 VFEMFYYTGIRLNALICLRYSDIDLGERLIRVR-------GETEKTHREFMIPIPDGLMphlKLLMD-IAHRVGLAPMDQ 136
Cdd:cd01186    22 LLALLYETGLRIGEALGLRIEDIDMADNQIELVpredntnEARAKSMRERRIPVSQDLI---DLYADyLTYIYCEEAEFS 98

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1274245735 137 IFNVNKFSGHYSRTQMNTDQVESMYKKLTAMTGVRMTPHRFRHTIASEMMRQpERNIHITKSLLNHSNIATTME-YIEPD 215
Cdd:cd01186    99 ITVFVNVKGGNQGKAMNYSDVYDLVRRLKKRTGIDFTPHMFRHTHATALIRA-GWSIEVVARRLGHAHVQTTLNtYGHLS 177


                  ....*..
gi 1274245735 216 YDVMREV 222
Cdd:cd01186   178 EEDIRRE 184
INT_RitA_C_like cd01188
C-terminal catalytic domain of recombinase RitA, a component of the recombinase trio; ...
 63-222 1.10e-11

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: 63.03  E-value: 1.10e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1274245735  63 LAVFEMFYYTGIRLNALICLRYSDIDLGERLIRVRGEteKTHREFMIPIPDGLmphLKLLMD-IAHRVGLAPMDQIF-NV 140
Cdd:cd01188    23 YAILLLLARLGLRAGDVAGLRLDDIDWRSGTITVRQK--KTGRPVELPLTEPV---GEALADyLRDGRPRTDSREVFlRA 97

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1274245735 141 NKFSGHYSrtqmNTDQVESMYKKLTAMTGV---RMTPHRFRHTIASEMMRQpERNIHITKSLLNHSNIATTMEYIEPDYD 217
Cdd:cd01188    98 RAPYRPLS----STSQISSIVRRYLRKAGIepsHRGTHSLRHSLATRMLRA-GTSLKVIADLLGHRSIETTAIYAKIDVD 172


                  ....*
gi 1274245735 218 VMREV 222
Cdd:cd01188   173 DLREV 177
xerC PRK00236
site-specific tyrosine recombinase XerC; Reviewed
 64-208 7.15e-11

site-specific tyrosine recombinase XerC; Reviewed


Pssm-ID: 234698 [Multi-domain]  Cd Length: 297  Bit Score: 62.48  E-value: 7.15e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1274245735  64 AVFEMFYYTGIRLNALICLRYSDIDLGERLIRVRGeteKTHREFMIPIpdgLMPHLKLLMD-IAHRVGLAPMDQ-IFnVN 141
Cdd:PRK00236  140 AILELLYGSGLRLSELVGLDIDDLDLASGTLRVLG---KGNKERTVPL---GRAAREALEAyLALRPLFLPDDDaLF-LG 212

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1274245735 142 KFSGHysrtqMNTDQVESMYKKLTAMTGV--RMTPHRFRHTIASEMMrqpER--NIHITKSLLNHSNIATT 208
Cdd:PRK00236  213 ARGGR-----LSPRVVQRRVKKLGKKAGLpsHITPHKLRHSFATHLL---ESggDLRAVQELLGHASLSTT 275
INTN1_C_like cd01185
Integrase IntN1 of Bacteroides mobilizable transposon NBU1 and similar proteins, C-terminal ...
 65-213 2.07e-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: 58.81  E-value: 2.07e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1274245735  65 VFEMFYYTGIRLNALICLRYSDIDLGERLIRVRGETEKTHREFMIPIPDGLMPHLKLLMDIAHRvglapmDQIFNVnkfs 144
Cdd:cd01185    23 MFLFSCYTGLRFSDLKNLTWKNIVEASGRTWIRYRRKKTGKPVTVPLLPVAREILEKYKDDRSE------GKLFPV---- 92

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1274245735 145 ghYSRTQMNTdqvesmY-KKLTAMTGVR--MTPHRFRHTIASEMMRQpERNIHITKSLLNHSNIATTMEYIE 213
Cdd:cd01185    93 --LSNQKINR------YlKEIAKIAGIDkhLTFHVARHTFATLLLLK-GVDIETISKLLGHSSIKTTQIYAK 155
INT_ICEBs1_C_like cd01189
C-terminal catalytic domain of integrases from bacterial phages and conjugate transposons; ...
 62-211 6.71e-10

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


Pssm-ID: 271189 [Multi-domain]  Cd Length: 147  Bit Score: 57.18  E-value: 6.71e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1274245735  62 WLAVFEMFYYTGIRLNALICLRYSDIDLGERLIRVRGE---------------TEKTHREfmIPIPDGLMPHLKLLMdia 126
Cdd:cd01189    18 YYLLFLLALLTGLRRGELLALTWSDIDFENGTIRINRTlvrkkkggyvikppkTKSSIRT--IPLPDELIELLKELK--- 92

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1274245735 127 hrvglapmdqifnvnkfsghysrtqmntdqvesMYKKLTAMTGV-RMTPHRFRHTIASEMMRQPErNIHITKSLLNHSNI 205
Cdd:cd01189    93 ---------------------------------AFKKLLKKAGLpRITPHDLRHTFASLLLEAGV-PLKVIAERLGHSDI 138


                  ....*.
gi 1274245735 206 ATTMEY 211
Cdd:cd01189   139 STTLDV 144
INT_Rci_Hp1_C cd00796
Shufflon-specific DNA recombinase Rci and Bacteriophage Hp1_like integrase, C-terminal ...
 58-211 7.37e-10

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: 57.34  E-value: 7.37e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1274245735  58 PAWFWLAVFEmfYYTGIRLNALICLRYSDIDLGERLIRVRGETEKTHREfmIPIPDGLMPHLKLLMdiahrvgLAPMDQI 137
Cdd:cd00796    23 PHLRLIVLLA--LYTGARRGEILSLRWDDIDLEVGLIVLPETKNGKPRT--VPLSDEAIAILKELK-------RKRGKDG 91

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1274245735 138 FNVNKFSGHYSRTQMNTDqvesmYKKLTAMTGV-RMTPHRFRHTIASEMMRQPERNIHITKsLLNHSNIATTMEY 211
Cdd:cd00796    92 FFVDGRFFGIPIASLRRA-----FKKARKRAGLeDLRFHDLRHTFASRLVQAGVPIKTVAK-ILGHSSIKMTMRY 160
INT_RitC_C_like cd01182
C-terminal catalytic domain of recombinase RitC, a component of the recombinase trio; ...
 70-224 2.74e-09

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: 56.13  E-value: 2.74e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1274245735  70 YYTGIRLNALICLRYSDIDLGE-RLIRVRGeteKTHREFMIPIPDGLMPHLKLLMDIAHRvglAPMDQIFNVNKFSGHys 148
Cdd:cd01182    31 YDTGARVQELADLTIRDLRLDDpATVRLHG---KGRKERTVPLWKETVAALKAYLQEFHL---TPDPKQLFPLFPNRR-- 102

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1274245735 149 RTQMNTDQVESMYKK----LTAMTGV---RMTPHRFRHTIASEMMrQPERNIHITKSLLNHSNIATTMEYIEPDYDVMRE 221
Cdd:cd01182   103 GQPLTRDGVAYILNKyvalASNRCPSlpkRITPHTLRHTKAMHLL-QAGVDLTVIRDWLGHESVETTQIYAEADLEMKRE 181


                  ...
gi 1274245735 222 VMN 224
Cdd:cd01182   182 ALE 184
FimB COG0582
Integrase/recombinase, includes phage integrase [Replication, recombination and repair, ...
 64-225 3.53e-09

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


Pssm-ID: 440347 [Multi-domain]  Cd Length: 391  Bit Score: 58.13  E-value: 3.53e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1274245735  64 AVFEMFYYTGIRLNALICLRYSDIDLGERLIRVRGETEKTHREFMIPIPDGLMPHLKLLMDIAHRVGLapmdqIF-NVNK 142
Cdd:COG0582   229 LALRLLLLTGVRPGELRGARWSEIDLEAALWTIPAERMKTRRPHIVPLSRQALEILKELKPLTGDSEY-----VFpSRRG 303

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1274245735 143 FSGHYSRTQMNtdqvesmyKKLTAMTGVRMTPHRFRHTIASEMMRQPErNIHITKSLLNHSNIATTME-YIEPDY-DVMR 220
Cdd:COG0582   304 PKKPMSENTLN--------KALRRMGYGRFTPHGFRHTASTLLNEAGF-PPDVIERQLAHKDGNKVRAaYNRADYlEERR 374


                  ....*
gi 1274245735 221 EVMNE 225
Cdd:COG0582   375 EMMQW 379
recomb_XerD TIGR02225
tyrosine recombinase XerD; The phage integrase family describes a number of recombinases with ...
 64-208 1.15e-08

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: 56.05  E-value: 1.15e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1274245735  64 AVFEMFYYTGIRLNALICLRYSDIDLGERLIRVRGeteKTHREFMIPIPD----GLMPHLK----LLMDIAHRVGlapmD 135
Cdd:TIGR02225 129 AMLELLYATGLRVSELVGLRLEDVNLDEGFVRVRG---KGNKERLVPLGEeaieALERYLKearpLLLKKKVKES----D 201

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1274245735 136 QIFnVNKFSGHYSRtQMntdqVESMYKKLTAMTGV--RMTPHRFRHTIASEMMrQPERNIHITKSLLNHSNIATT 208
Cdd:TIGR02225 202 ALF-LNRRGGPLSR-QG----VWKILKEYAKRAGIekPISPHTLRHSFATHLL-ENGADLRVVQELLGHADISTT 269
INT_C_like_4 cd01194
Uncharacterized site-specific tyrosine recombinase, C-terminal catalytic domain; Tyrosine ...
 64-211 2.99e-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: 271194 [Multi-domain]  Cd Length: 174  Bit Score: 50.07  E-value: 2.99e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1274245735  64 AVFEMFYYTGIRLNALICLRYSDID--LGERLIRVRGETEKTHREFMIPIPDGLMPHLKLLMDiahRVGLAPMDQIFNvn 141
Cdd:cd01194    26 AIISLMVTEGLRTVEIVRADVGDLRqeGEGTILYVQGKGKTSKDDFVYLRPDVLKALQAYLKA---RGKLDFEEPLFT-- 100

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1274245735 142 KFSGHYSRTQMNTDQVESMYKKLTAMTGV---RMTPHRFRHTIASeMMRQPERNIHITKSLLNHSNIATTMEY 211
Cdd:cd01194   101 SLSNNSKGQRLTTRSIRRIIKKYLRKAGLdddRLTAHSLRHTAGT-LALKAGKSLREVQQLLRHSDPNTTMIY 172
INT_P4_C cd00801
Bacteriophage P4 integrase, C-terminal catalytic domain; P4-like integrases are found in ...
 71-225 1.31e-06

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


Pssm-ID: 271182 [Multi-domain]  Cd Length: 180  Bit Score: 48.42  E-value: 1.31e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1274245735  71 YTGIRLNALICLRYSDIDLGERLIRVRGETEKTHREFMIPIPDGLMPHLKLLMDIAHRVGLapmdqIFnvnkFSGHYSRT 150
Cdd:cd00801    30 LTGQRIGELARARWSEIDLEEKTWTIPAERTKNKRPHRVPLSDQALEILEELKEFTGDSGY-----LF----PSRRKKKK 100

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1274245735 151 QMNTDQVESMYKKLTAmTGVRMTPHRFRHTIASEMMRQpERNIHITKSLLNHSNIATTME-YIEPDY-DVMREVMNE 225
Cdd:cd00801   101 PISENTINKALKRLGY-KGKEFTPHDLRRTFSTLLNEL-GIDPEVIERLLNHVLGGVVRAaYNRYDYlEERREALQA 175
INT_RitB_C_like cd00797
C-terminal catalytic domain of recombinase RitB, a component of the recombinase trio; ...
 58-223 3.94e-06

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: 47.30  E-value: 3.94e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1274245735  58 PAWFWLAVFEMFYYTGIRLNALICLRYSDIDLGERLIRVRGetEKTHREFMIPIPDGLMPHLKLLMDIAHRVGLAPMDQI 137
Cdd:cd00797    23 RPLTYATLFGLLYATGLRVGEALRLRLEDVDLDSGILTIRQ--TKFGKSRLVPLHPSTVGALRDYLARRDRLLPSPSSSY 100

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1274245735 138 FNVNKFSGHYSRtqmntDQVESMYKKLTAMTGVRMTP-------HRFRHTIA-SEMMR------QPERNIHITKSLLNHS 203
Cdd:cd00797   101 FFVSQQGGRLTG-----GGVYRVFRRLLRRIGLRGAGdgrgprlHDLRHTFAvNRLTRwyregaDVERKLPVLSTYLGHV 175

                         170       180
                  ....*....|....*....|
gi 1274245735 204 NIATTMEYIEPDYDVMREVM 223
Cdd:cd00797   176 NVTDTYWYLTATPELMELAS 195
integrase_gron TIGR02249
integron integrase; Members of this family are integrases associated with integrons (and ...
 68-211 4.21e-06

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: 48.16  E-value: 4.21e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1274245735  68 MFYYTGIRLNALICLRYSDIDLGERLIRVR-GETEKTHRefmIPIPDGLMPHLKLLMDIAHRVGLAPMDQIF-------- 138
Cdd:TIGR02249 124 LLYGSGMRLMECLRLRIQDIDFDYGEIRIRqGKGGKDRT---VTLPKELIPPLREQIELARAYHEADLAEGYggvylpha 200

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1274245735 139 -----------------------NVNKFSGHYSRTQMNTDQVESMYKKLTAMTGVR--MTPHRFRHTIASEMMRQPErNI 193
Cdd:TIGR02249 201 larkypnapkewgwqylfpshrlSRDPESGVIRRHHINETTIQRAVRRAVERAGIEkpVTCHTLRHSFATHLLESGA-DI 279

                         170
                  ....*....|....*...
gi 1274245735 194 HITKSLLNHSNIATTMEY 211
Cdd:TIGR02249 280 RTVQELLGHSDVKTTQIY 297
INT_C_like_3 cd01192
Uncharacterized site-specific tyrosine recombinase, C-terminal catalytic domain; Tyrosine ...
 72-212 1.08e-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: 271192 [Multi-domain]  Cd Length: 178  Bit Score: 45.75  E-value: 1.08e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1274245735  72 TGIRLNALICLRYSDIDLGERL-IRVRgeteKTHREFMIPIPDGLmphLKLLMDIAHRVGLAPMDQIFN--VNKFSGHYS 148
Cdd:cd01192    36 TGLRISDLLSLKVEDVTNKDKLsIKEQ----KTGKQKTFPLNPTL---VKALKEYIDDLDLKRNDYLFKslKQGPEKPIS 108

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1274245735 149 RTQMNTdqvesMYKKLTAMTGVR--MTPHRFRHTIAsEMMRQPERNIHITKSLLNHSNIATTMEYI 212
Cdd:cd01192   109 RKQAYK-----ILKKAADDLGLNynIGTHSLRKTFG-YHVYKQGKDIELLMKLLNHSSPSITLRYL 168
PRK15417 PRK15417
integron integrase;
67-211 4.31e-05

integron integrase;


Pssm-ID: 185315 [Multi-domain]  Cd Length: 337  Bit Score: 45.04  E-value: 4.31e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1274245735  67 EMFYYTGIRLNALICLRYSDIDLGERLIRVRGETEKTHREFMipIPDGLMPHLK---------LLMDIAH-RVGLAPMDQ 136
Cdd:PRK15417  138 QLLYGTGMRISEGLQLRVKDLDFDHGTIIVREGKGSKDRALM--LPESLAPSLReqlsrarawWLKDQAEgRSGVALPDA 215

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1274245735 137 I---------------------FNVNKFSGHYSRTQMNTDQVESMYKKLTAMTGVR--MTPHRFRHTIASEMMRQpERNI 193
Cdd:PRK15417  216 LerkypraghswpwfwvfaqhtHSTDPRSGVVRRHHMYDQTFQRAFKRAVEQAGITkpATPHTLRHSFATALLRS-GYDI 294

                         170
                  ....*....|....*...
gi 1274245735 194 HITKSLLNHSNIATTMEY 211
Cdd:PRK15417  295 RTVQDLLGHSDVSTTMIY 312
INT_C_like_5 cd01195
Uncharacterized site-specific tyrosine recombinase, C-terminal catalytic domain; Tyrosine ...
 63-212 1.27e-04

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: 42.46  E-value: 1.27e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1274245735  63 LAVFEMFYYTGIRLNALICLRYSDIDLGERLIRVRGETEKTHREFMIPIP--DGLMPHLKllmdiAHRVGLAPMDQIFNV 140
Cdd:cd01195    23 EALVRLLLDNALRRSEAVALDVEDLEKEHRRLRILGKGKKQREVVTLPPTtrEALAAWLA-----ARGEAEGPLFVSLDR 97

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1274245735 141 NKFSGHYSRTQmntdqVESMYKKLTAMTGV--RMTPHRFRHTIASEMMRQPERNIHITKSLLNHSNIATTMEYI 212
Cdd:cd01195    98 ASRGRRLSPQA-----VYRIVRRLAERIGLgkRLSPHGLRHSAITLALDAGAGLIRKVQDFSRHADLRTLQVYD 166
INT_tnpB_C_Tn554 cd01187
Putative Transposase B from transposon Tn554, C-terminal catalytic domain; This family ...
 63-212 5.79e-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: 39.72  E-value: 5.79e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1274245735  63 LAVFEMFYYTGIRLNALICLRY----SDIDLGERLIRVRGETEKTHREFMIPIPDGLmphlkllmdiaHRVglapmdqIF 138
Cdd:cd01187    16 IPVVQAAVFTGARASELATLKFgclhAQTSDDGTFLYWLKWENKGGKQLDIPISKKV-----------AEL-------IK 77

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1274245735 139 NVNKFSGHYSRTQMNTDQVESMYkkltamtgvRMTPHRFRHTIASEMMRQPERnIHITKSLLNHSNIATTMEYI 212
Cdd:cd01187    78 TINWTLNELSELKNISDDHGERF---------RFHTHRFRHTVATRLANSGMG-ILVLQQLLGHSSPEMTLRYA 141
INT_C_like_1 cd01184
Uncharacterized site-specific tyrosine recombinase, C-terminal catalytic domain; Tyrosine ...
 40-203 5.98e-04

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: 40.37  E-value: 5.98e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1274245735  40 LNILVKEErATENRAEITPAWFWLAVFEMfyYTGIRLNALICLRYSDIDLGERL--IRVRGETE----KTH---RefMIP 110
Cdd:cd01184     6 LAKIFSSP-LYTGCKKKDPALYWLPLIGL--YTGARLNEICQLRVDDIKEEDGIwcIDINDDAEgrrlKTKasrR--LVP 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1274245735 111 IPDGLMpHLKLL-----MDIAHRVGLAPmDQIFNVNKFSGHYSRtQMNtdqveSMYKKLTAMTGVRMTPHRFRHTIASEM 185
Cdd:cd01184    81 IHPRLI-ELGFLdyveaLRADGKLFLFP-EKRDKDGKYSKAASK-WFN-----RLLRKLGIKDDERKSFHSFRHTFITAL 152

                         170       180
                  ....*....|....*....|
gi 1274245735 186 MRQ--PERnihITKSLLNHS 203
Cdd:cd01184   153 KRAgvPEE---LIAQIVGHS 169
INT_Lambda_C cd00800
C-terminal catalytic domain of Lambda integrase, a tyrosine-based site-specific recombinase; ...
 58-213 6.53e-04

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


Pssm-ID: 271181 [Multi-domain]  Cd Length: 161  Bit Score: 40.02  E-value: 6.53e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1274245735  58 PAWFWLAvFEMFYYTGIRLNALICLRYSDIDLGERLIrvrgETEKTHREFMIPipdgLMPHLKLLMDIAHRVGLAPMDQI 137
Cdd:cd00800    11 PPLLRLA-MELALLTGQRQGDLLRLKWSDITDGGLLV----EQSKTGKKLLIP----WTPSLRALVDRIRALPRKRSEYL 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1274245735 138 FNvnkfsgHYSRTQMNTDQVESMYKKltAMT-------GVRMTPHRFRHTIASEMMRQpeRNIHITKSLLNHSNIATTME 210
Cdd:cd00800    82 IN------SRKGGPLSYDTLKSAWRR--ARKaaglkgeTEGFTFHDLRAKAATDYAEQ--GGSTDAQALLGHKSDAMTER 151


                  ...
gi 1274245735 211 YIE 213
Cdd:cd00800   152 YTR 154
xerC PRK01287
site-specific tyrosine recombinase XerC; Reviewed
 64-211 4.91e-03

site-specific tyrosine recombinase XerC; Reviewed


Pssm-ID: 234935 [Multi-domain]  Cd Length: 358  Bit Score: 38.96  E-value: 4.91e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1274245735  64 AVFEMFYYTGIRLNALICLRYSDIDLGERLIRVRgeTEKTHREFMIPIP-----------DGLMPHLKLLMD-----IAH 127
Cdd:PRK01287  161 ALLELLWSTGIRRGELARLDLYDVDASRGVVTVR--QGKGNKDRVVPVGeralawlqrylQDVRPQLAVRPDsgalfVAM 238

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1274245735 128 R-VGLAPMdqifNVNKFSGHYSRtqmntdqvESMYKKLTAMtgvrmtpHRFRHTIASEMMRQPERNIHItKSLLNHSNIA 206
Cdd:PRK01287  239 DgDGLARN----TLTNMVGRYIR--------AAGIEKAGAC-------HLFRHAMATQMLENGADTRHI-QAILGHAKLE 298


                  ....*
gi 1274245735 207 TTMEY 211
Cdd:PRK01287  299 TTQIY 303
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

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