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Conserved domains on  [gi|970931799|gb|KUG43220|]
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putative phage integrase [Pseudomonas savastanoi pv. fraxini]

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

Graphical summary

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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 ...
 21-171 4.61e-34

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: 123.74  E-value: 4.61e-34
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 970931799  21 WLAVFEMFYYTGIRLNALICLRYADIDLGQRLIRVRGETEKTHREFMIPIPDGLMPHLKLLMEIAHKvGFAPTDQIFNVN 100
Cdd:cd00397   19 DRAILLLLLETGLRISELLALKVKDIDLDNGTIRVRGKKTKGGKERTVPLPKELAEELKEYLKERRD-KRGPLLKSLYLN 97

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 970931799 101 RFSGHYSRSQMNSDQVEAMYKKLTAMTGVRMTPHRFRHTIASEMMRQPErNIHITKNLLNHSNIATTMEYI 171
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 ...
 21-171 4.61e-34

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: 123.74  E-value: 4.61e-34
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 970931799  21 WLAVFEMFYYTGIRLNALICLRYADIDLGQRLIRVRGETEKTHREFMIPIPDGLMPHLKLLMEIAHKvGFAPTDQIFNVN 100
Cdd:cd00397   19 DRAILLLLLETGLRISELLALKVKDIDLDNGTIRVRGKKTKGGKERTVPLPKELAEELKEYLKERRD-KRGPLLKSLYLN 97

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 970931799 101 RFSGHYSRSQMNSDQVEAMYKKLTAMTGVRMTPHRFRHTIASEMMRQPErNIHITKNLLNHSNIATTMEYI 171
Cdd:cd00397   98 KLFGTKLGERLSRRTLRRIFKKAGIEAGRKITPHSLRHTFATNLLENGV-DIKVVQKLLGHSSISTTQRYL 167
XerC COG4973
Site-specific recombinase XerC [Replication, recombination and repair];
18-182 3.72e-29

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


Pssm-ID: 443998 [Multi-domain]  Cd Length: 287  Bit Score: 113.90  E-value: 3.72e-29
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 970931799  18 AWFWLAVFEMFYYTGIRLNALICLRYADIDLGQRLIRVRGeteKTHREFMIPIPDGLMPHLKLLMEIAHKVGFAPTDQIF 97
Cdd:COG4973  130 AVRDRAIVELLYSTGLRLGELVGLDWEDVDLDAGEVRVRG---KTGKSRTVPLGPKALAALREWLAVRPELAAPDEGALF 206

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 970931799  98 NVNRfsGHysrsQMNSDQVEAMYKKLTAMTGV--RMTPHRFRHTIASeMMRQPERNIHITKNLLNHSNIATTMEYIEPDY 175
Cdd:COG4973  207 PSRR--GT----RLSPRNVQKRLRRLAKKAGLpkHVHPHDLRHSFAT-HLLESGGDLRAVQELLGHASISTTQIYTHLDF 279


                 ....*..
gi 970931799 176 DVMREVM 182
Cdd:COG4973  280 QHLAEVY 286
xerS PRK05084
site-specific tyrosine recombinase XerS; Reviewed
 22-186 3.24e-21

site-specific tyrosine recombinase XerS; Reviewed


Pssm-ID: 235339 [Multi-domain]  Cd Length: 357  Bit Score: 93.44  E-value: 3.24e-21
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 970931799  22 LAVFEMFYYTGIRLNALICLRYADIDLGQRLIRVrgeTEKTHREFMIPIPDGLMPHLKLLMEIAHKVGFAP-TDQIFNVN 100
Cdd:PRK05084 198 LAIIALILGSGLRVSELVNLDLSDLNLKQMTIDV---TRKGGKRDSVNIAPFALPYLEEYLKIRASRYKAEkQEKALFLT 274

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 970931799 101 RFSGHYSRSQMNSdqVEAMYKKLTAMTGVRMTPHRFRHTIASEMMRQpERNIHITKNLLNHSNIATTMEYIEPDYDVMRE 180
Cdd:PRK05084 275 KYRGKPNRISARA--IEKMVAKYSEAFGVRLTPHKLRHTLATRLYDA-TKDQVLVADQLGHTSTETTDLYTHIVNDEQKE 351


                 ....*.
gi 970931799 181 VMNERG 186
Cdd:PRK05084 352 ALDRLE 357
Phage_integrase pfam00589
Phage integrase family; Members of this family cleave DNA substrates by a series of staggered ...
 22-175 2.63e-18

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: 81.21  E-value: 2.63e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 970931799   22 LAVFEMFYYTGIRLNALICLRYADIDLGQRLIRVrgETEKTHREFMIPIPDGLMPHLKLLMEIaHKVGFAPTDQIFnVNR 101
Cdd:pfam00589  24 KALLELLYATGLRISELCSLRWSDIDFENGVIRV--HRGKGNKERTVPLSDAALELLKEWLSK-RLLEAPKSDYLF-ASK 99

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 970931799  102 FsghysRSQMNSDQVEAMYKKLTAMTGV--RMTPHRFRHTIASEMMRQpERNIHITKNLLNHSNIATTMEYIEPDY 175
Cdd:pfam00589 100 R-----GKPLSRQTVRKIFKRAGKEAGLelPLHPHMLRHSFATHLLEA-GVDLRVVQKLLGHSSISTTQIYTHVAD 169
recomb_XerD TIGR02225
tyrosine recombinase XerD; The phage integrase family describes a number of recombinases with ...
 23-167 9.22e-10

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: 58.75  E-value: 9.22e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 970931799   23 AVFEMFYYTGIRLNALICLRYADIDLGQRLIRVRGeteKTHREFMIPIPDGLMPHLKLLMEIAHKVGFA----PTDQIFn 98
Cdd:TIGR02225 129 AMLELLYATGLRVSELVGLRLEDVNLDEGFVRVRG---KGNKERLVPLGEEAIEALERYLKEARPLLLKkkvkESDALF- 204

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 970931799   99 VNRFSGHYSRSQmnsdqVEAMYKKLTAMTGV--RMTPHRFRHTIASEMMrQPERNIHITKNLLNHSNIATT 167
Cdd:TIGR02225 205 LNRRGGPLSRQG-----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 ...
 21-171 4.61e-34

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: 123.74  E-value: 4.61e-34
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 970931799  21 WLAVFEMFYYTGIRLNALICLRYADIDLGQRLIRVRGETEKTHREFMIPIPDGLMPHLKLLMEIAHKvGFAPTDQIFNVN 100
Cdd:cd00397   19 DRAILLLLLETGLRISELLALKVKDIDLDNGTIRVRGKKTKGGKERTVPLPKELAEELKEYLKERRD-KRGPLLKSLYLN 97

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 970931799 101 RFSGHYSRSQMNSDQVEAMYKKLTAMTGVRMTPHRFRHTIASEMMRQPErNIHITKNLLNHSNIATTMEYI 171
Cdd:cd00397   98 KLFGTKLGERLSRRTLRRIFKKAGIEAGRKITPHSLRHTFATNLLENGV-DIKVVQKLLGHSSISTTQRYL 167
XerC COG4973
Site-specific recombinase XerC [Replication, recombination and repair];
18-182 3.72e-29

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


Pssm-ID: 443998 [Multi-domain]  Cd Length: 287  Bit Score: 113.90  E-value: 3.72e-29
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 970931799  18 AWFWLAVFEMFYYTGIRLNALICLRYADIDLGQRLIRVRGeteKTHREFMIPIPDGLMPHLKLLMEIAHKVGFAPTDQIF 97
Cdd:COG4973  130 AVRDRAIVELLYSTGLRLGELVGLDWEDVDLDAGEVRVRG---KTGKSRTVPLGPKALAALREWLAVRPELAAPDEGALF 206

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 970931799  98 NVNRfsGHysrsQMNSDQVEAMYKKLTAMTGV--RMTPHRFRHTIASeMMRQPERNIHITKNLLNHSNIATTMEYIEPDY 175
Cdd:COG4973  207 PSRR--GT----RLSPRNVQKRLRRLAKKAGLpkHVHPHDLRHSFAT-HLLESGGDLRAVQELLGHASISTTQIYTHLDF 279


                 ....*..
gi 970931799 176 DVMREVM 182
Cdd:COG4973  280 QHLAEVY 286
XerD COG4974
Site-specific recombinase XerD [Replication, recombination and repair];
23-184 3.18e-27

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


Pssm-ID: 443999 [Multi-domain]  Cd Length: 291  Bit Score: 108.93  E-value: 3.18e-27
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 970931799  23 AVFEMFYYTGIRLNALICLRYADIDLGQRLIRVRGetEKTHREFMIPIPDGLMPHLKLLMEIAHKvgfAPTDQIFnVNRF 102
Cdd:COG4974  137 ALLLLLYATGLRVSELLGLKWSDIDLDRGTIRVRR--GKGGKERTVPLSPEALEALREYLEERRP---RDSDYLF-PTRR 210

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 970931799 103 SGHYSRSQMNSdqveaMYKKLTAMTGV--RMTPHRFRHTIASEMMRQpERNIHITKNLLNHSNIATTMEYIEPDYDVMRE 180
Cdd:COG4974  211 GRPLSRRAIRK-----ILKRLAKRAGIpkRVTPHSLRHTFATHLLEA-GVDLRTVQELLGHSSISTTQIYTHVSDEELRE 284


                 ....
gi 970931799 181 VMNE 184
Cdd:COG4974  285 AVEK 288
xerS PRK05084
site-specific tyrosine recombinase XerS; Reviewed
 22-186 3.24e-21

site-specific tyrosine recombinase XerS; Reviewed


Pssm-ID: 235339 [Multi-domain]  Cd Length: 357  Bit Score: 93.44  E-value: 3.24e-21
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 970931799  22 LAVFEMFYYTGIRLNALICLRYADIDLGQRLIRVrgeTEKTHREFMIPIPDGLMPHLKLLMEIAHKVGFAP-TDQIFNVN 100
Cdd:PRK05084 198 LAIIALILGSGLRVSELVNLDLSDLNLKQMTIDV---TRKGGKRDSVNIAPFALPYLEEYLKIRASRYKAEkQEKALFLT 274

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 970931799 101 RFSGHYSRSQMNSdqVEAMYKKLTAMTGVRMTPHRFRHTIASEMMRQpERNIHITKNLLNHSNIATTMEYIEPDYDVMRE 180
Cdd:PRK05084 275 KYRGKPNRISARA--IEKMVAKYSEAFGVRLTPHKLRHTLATRLYDA-TKDQVLVADQLGHTSTETTDLYTHIVNDEQKE 351


                 ....*.
gi 970931799 181 VMNERG 186
Cdd:PRK05084 352 ALDRLE 357
Phage_integrase pfam00589
Phage integrase family; Members of this family cleave DNA substrates by a series of staggered ...
 22-175 2.63e-18

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: 81.21  E-value: 2.63e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 970931799   22 LAVFEMFYYTGIRLNALICLRYADIDLGQRLIRVrgETEKTHREFMIPIPDGLMPHLKLLMEIaHKVGFAPTDQIFnVNR 101
Cdd:pfam00589  24 KALLELLYATGLRISELCSLRWSDIDFENGVIRV--HRGKGNKERTVPLSDAALELLKEWLSK-RLLEAPKSDYLF-ASK 99

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 970931799  102 FsghysRSQMNSDQVEAMYKKLTAMTGV--RMTPHRFRHTIASEMMRQpERNIHITKNLLNHSNIATTMEYIEPDY 175
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 ...
 23-167 4.01e-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: 69.46  E-value: 4.01e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 970931799  23 AVFEMFYYTGIRLNALICLRYADIDLGQRLIRVRGeteKTHREFMIPIPDGLMPHLKLLMEIAHK--VGFAPTDQIFnVN 100
Cdd:cd00798   23 AILELLYASGLRVSELVGLDLSDVDLDEGLVRVTG---KGNKERLVPFGSYAVEALEEYLEERRPllLKKKPPDALF-LN 98

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 970931799 101 RFSGHYSRsqmnsDQVEAMYKKLTAMTGV--RMTPHRFRHTIASEMMrqpER--NIHITKNLLNHSNIATT 167
Cdd:cd00798   99 KRGKRLSR-----RGVWRILKKYAERAGLpkHVSPHTLRHSFATHLL---EGgaDLRVVQELLGHASLSTT 161
INT_IntI_C cd01193
Integron integrase and similar protiens, C-terminal catalytic domain; Integron integrases ...
 23-170 4.08e-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: 69.61  E-value: 4.08e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 970931799  23 AVFEMFYYTGIRLNALICLRYADIDLGQRLIRVRGetEKTHREFMIPIPDGLMPHLK--LLMEIAHKVGFAPTDQIFNVN 100
Cdd:cd01193   25 LILSLLYGAGLRISELLRLRVKDIDFERGVIRVRQ--GKGGKDRVVPLPEKLLEPLRryLKSARPKEELDPAEGRAGVLD 102

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 970931799 101 RFSGHYSRSQMNSDQVEAMYKKLTAMTGV--RMTPHRFRHTIASEMMRQpERNIHITKNLLNHSNIATTMEY 170
Cdd:cd01193  103 PRTGVERRHHISETTVQRALKKAVEQAGItkRVTPHTLRHSFATHLLEA-GTDIRTIQELLGHSDLSTTMIY 173
INT_Rci_Hp1_C cd00796
Shufflon-specific DNA recombinase Rci and Bacteriophage Hp1_like integrase, C-terminal ...
 17-170 4.73e-13

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: 66.20  E-value: 4.73e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 970931799  17 PAWFWLAVFEmfYYTGIRLNALICLRYADIDLGQRLIRVRGETEKTHREfmIPIPDGLMPHLKLLMEIAHKVGFAPTDQI 96
Cdd:cd00796   23 PHLRLIVLLA--LYTGARRGEILSLRWDDIDLEVGLIVLPETKNGKPRT--VPLSDEAIAILKELKRKRGKDGFFVDGRF 98

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 970931799  97 FnvnrfsgHYSRSQMNSDqVEAMYKKLtAMTGVRmtPHRFRHTIASEMMRQPERNIHITKnLLNHSNIATTMEY 170
Cdd:cd00796   99 F-------GIPIASLRRA-FKKARKRA-GLEDLR--FHDLRHTFASRLVQAGVPIKTVAK-ILGHSSIKMTMRY 160
INT_RitA_C_like cd01188
C-terminal catalytic domain of recombinase RitA, a component of the recombinase trio; ...
 22-181 6.62e-12

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: 63.41  E-value: 6.62e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 970931799  22 LAVFEMFYYTGIRLNALICLRYADIDLGQRLIRVRGEteKTHREFMIPIPDglmphlkllmeiahKVGFA---------- 91
Cdd:cd01188   23 YAILLLLARLGLRAGDVAGLRLDDIDWRSGTITVRQK--KTGRPVELPLTE--------------PVGEAladylrdgrp 86

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 970931799  92 --PTDQIF-NVNRFSGHYSrsqmNSDQVEAMYKKLTAMTGV---RMTPHRFRHTIASEMMRQpERNIHITKNLLNHSNIA 165
Cdd:cd01188   87 rtDSREVFlRARAPYRPLS----STSQISSIVRRYLRKAGIepsHRGTHSLRHSLATRMLRA-GTSLKVIADLLGHRSIE 161

                        170
                 ....*....|....*.
gi 970931799 166 TTMEYIEPDYDVMREV 181
Cdd:cd01188  162 TTAIYAKIDVDDLREV 177
INT_tnpA_C_Tn554 cd01186
Putative Transposase A from transposon Tn554, C-terminal catalytic domain; This family ...
 24-181 1.44e-11

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: 62.43  E-value: 1.44e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 970931799  24 VFEMFYYTGIRLNALICLRYADIDLGQRLIRVR-------GETEKTHREFMIPIPDGLMphlKLLME-IAHKVGFAPTDQ 95
Cdd:cd01186   22 LLALLYETGLRIGEALGLRIEDIDMADNQIELVpredntnEARAKSMRERRIPVSQDLI---DLYADyLTYIYCEEAEFS 98

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 970931799  96 IFNVNRFSGHYSRSQMNSDQVEAMYKKLTAMTGVRMTPHRFRHTIASEMMRQpERNIHITKNLLNHSNIATTME-YIEPD 174
Cdd:cd01186   99 ITVFVNVKGGNQGKAMNYSDVYDLVRRLKKRTGIDFTPHMFRHTHATALIRA-GWSIEVVARRLGHAHVQTTLNtYGHLS 177


                 ....*..
gi 970931799 175 YDVMREV 181
Cdd:cd01186  178 EEDIRRE 184
INTN1_C_like cd01185
Integrase IntN1 of Bacteroides mobilizable transposon NBU1 and similar proteins, C-terminal ...
 24-172 9.63e-11

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


Pssm-ID: 271185 [Multi-domain]  Cd Length: 161  Bit Score: 59.59  E-value: 9.63e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 970931799  24 VFEMFYYTGIRLNALICLRYADIDLGQRLIRVRGETEKTHREFMIPIPDGLMphlKLLMEIahkVGFAPTDQIFNVnrfs 103
Cdd:cd01185   23 MFLFSCYTGLRFSDLKNLTWKNIVEASGRTWIRYRRKKTGKPVTVPLLPVAR---EILEKY---KDDRSEGKLFPV---- 92

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 970931799 104 ghYSRSQMNsdqvEAMyKKLTAMTGVR--MTPHRFRHTIASEMMRQpERNIHITKNLLNHSNIATTMEYIE 172
Cdd:cd01185   93 --LSNQKIN----RYL-KEIAKIAGIDkhLTFHVARHTFATLLLLK-GVDIETISKLLGHSSIKTTQIYAK 155
FimB COG0582
Integrase/recombinase, includes phage integrase [Replication, recombination and repair, ...
 23-184 1.20e-10

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


Pssm-ID: 440347 [Multi-domain]  Cd Length: 391  Bit Score: 62.36  E-value: 1.20e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 970931799  23 AVFEMFYYTGIRLNALICLRYADIDLGQRLIRVRGETEKTHREFMIPIPDGLMPHLKLLMEIAHKVGFaptdqifnVnrF 102
Cdd:COG0582  229 LALRLLLLTGVRPGELRGARWSEIDLEAALWTIPAERMKTRRPHIVPLSRQALEILKELKPLTGDSEY--------V--F 298

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 970931799 103 SGHYSRSQMNSDQveAMYKKLTAMTGVRMTPHRFRHTIASEMMRQPErNIHITKNLLNHSNIATTME-YIEPDY-DVMRE 180
Cdd:COG0582  299 PSRRGPKKPMSEN--TLNKALRRMGYGRFTPHGFRHTASTLLNEAGF-PPDVIERQLAHKDGNKVRAaYNRADYlEERRE 375


                 ....
gi 970931799 181 VMNE 184
Cdd:COG0582  376 MMQW 379
INT_RitC_C_like cd01182
C-terminal catalytic domain of recombinase RitC, a component of the recombinase trio; ...
 29-183 5.83e-10

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: 58.06  E-value: 5.83e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 970931799  29 YYTGIRLNALICLRYADIDLG-QRLIRVRGeteKTHREFMIPIPDGLMPHLKLLMEIAHKvgfAPTDQIFNVNRFSGHys 107
Cdd:cd01182   31 YDTGARVQELADLTIRDLRLDdPATVRLHG---KGRKERTVPLWKETVAALKAYLQEFHL---TPDPKQLFPLFPNRR-- 102

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 970931799 108 RSQMNSDQVEAMYKK----LTAMTGV---RMTPHRFRHTIASEMMrQPERNIHITKNLLNHSNIATTMEYIEPDYDVMRE 180
Cdd:cd01182  103 GQPLTRDGVAYILNKyvalASNRCPSlpkRITPHTLRHTKAMHLL-QAGVDLTVIRDWLGHESVETTQIYAEADLEMKRE 181


                 ...
gi 970931799 181 VMN 183
Cdd:cd01182  182 ALE 184
xerC PRK00236
site-specific tyrosine recombinase XerC; Reviewed
 23-167 6.13e-10

site-specific tyrosine recombinase XerC; Reviewed


Pssm-ID: 234698 [Multi-domain]  Cd Length: 297  Bit Score: 59.40  E-value: 6.13e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 970931799  23 AVFEMFYYTGIRLNALICLRYADIDLGQRLIRVRGeteKTHREFMIPIpdgLMPHLKLLME-IAHKVGFAPTDQ-IFnVN 100
Cdd:PRK00236 140 AILELLYGSGLRLSELVGLDIDDLDLASGTLRVLG---KGNKERTVPL---GRAAREALEAyLALRPLFLPDDDaLF-LG 212

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 970931799 101 RFSGHysrsqMNSDQVEAMYKKLTAMTGV--RMTPHRFRHTIASEMMrqpER--NIHITKNLLNHSNIATT 167
Cdd:PRK00236 213 ARGGR-----LSPRVVQRRVKKLGKKAGLpsHITPHKLRHSFATHLL---ESggDLRAVQELLGHASLSTT 275
recomb_XerD TIGR02225
tyrosine recombinase XerD; The phage integrase family describes a number of recombinases with ...
 23-167 9.22e-10

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: 58.75  E-value: 9.22e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 970931799   23 AVFEMFYYTGIRLNALICLRYADIDLGQRLIRVRGeteKTHREFMIPIPDGLMPHLKLLMEIAHKVGFA----PTDQIFn 98
Cdd:TIGR02225 129 AMLELLYATGLRVSELVGLRLEDVNLDEGFVRVRG---KGNKERLVPLGEEAIEALERYLKEARPLLLKkkvkESDALF- 204

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 970931799   99 VNRFSGHYSRSQmnsdqVEAMYKKLTAMTGV--RMTPHRFRHTIASEMMrQPERNIHITKNLLNHSNIATT 167
Cdd:TIGR02225 205 LNRRGGPLSRQG-----VWKILKEYAKRAGIekPISPHTLRHSFATHLL-ENGADLRVVQELLGHADISTT 269
INT_ICEBs1_C_like cd01189
C-terminal catalytic domain of integrases from bacterial phages and conjugate transposons; ...
 21-170 9.33e-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: 56.41  E-value: 9.33e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 970931799  21 WLAVFEMFYYTGIRLNALICLRYADIDLGQRLIRVRGE---------------TEKTHREfmIPIPDGLMPHLKLLMeia 85
Cdd:cd01189   18 YYLLFLLALLTGLRRGELLALTWSDIDFENGTIRINRTlvrkkkggyvikppkTKSSIRT--IPLPDELIELLKELK--- 92

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 970931799  86 hkvgfaptdqifnvnrfsghysrsqmnsdqveaMYKKLTAMTGV-RMTPHRFRHTIASEMMRQPErNIHITKNLLNHSNI 164
Cdd:cd01189   93 ---------------------------------AFKKLLKKAGLpRITPHDLRHTFASLLLEAGV-PLKVIAERLGHSDI 138


                 ....*.
gi 970931799 165 ATTMEY 170
Cdd:cd01189  139 STTLDV 144
INT_P4_C cd00801
Bacteriophage P4 integrase, C-terminal catalytic domain; P4-like integrases are found in ...
 30-184 4.17e-07

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: 49.58  E-value: 4.17e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 970931799  30 YTGIRLNALICLRYADIDLGQRLIRVRGETEKTHREFMIPIPDGLMPHLKLLMEIAhkvgfAPTDQIFnvnrFSGHYSRS 109
Cdd:cd00801   30 LTGQRIGELARARWSEIDLEEKTWTIPAERTKNKRPHRVPLSDQALEILEELKEFT-----GDSGYLF----PSRRKKKK 100

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 970931799 110 QMNSDQVEAMYKKLTAmTGVRMTPHRFRHTIASEMMRQpERNIHITKNLLNHSNIATTME-YIEPDY-DVMREVMNE 184
Cdd:cd00801  101 PISENTINKALKRLGY-KGKEFTPHDLRRTFSTLLNEL-GIDPEVIERLLNHVLGGVVRAaYNRYDYlEERREALQA 175
INT_C_like_3 cd01192
Uncharacterized site-specific tyrosine recombinase, C-terminal catalytic domain; Tyrosine ...
 31-171 1.56e-06

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


Pssm-ID: 271192 [Multi-domain]  Cd Length: 178  Bit Score: 47.67  E-value: 1.56e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 970931799  31 TGIRLNALICLRYADIDLGQRL-IRVRgeteKTHREFMIPIPDGLmphLKLLMEIAHKVGFAPTDQIFN--VNRFSGHYS 107
Cdd:cd01192   36 TGLRISDLLSLKVEDVTNKDKLsIKEQ----KTGKQKTFPLNPTL---VKALKEYIDDLDLKRNDYLFKslKQGPEKPIS 108

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 970931799 108 RSQMNSdqveaMYKKLTAMTGVR--MTPHRFRHTIASeMMRQPERNIHITKNLLNHSNIATTMEYI 171
Cdd:cd01192  109 RKQAYK-----ILKKAADDLGLNynIGTHSLRKTFGY-HVYKQGKDIELLMKLLNHSSPSITLRYL 168
INT_RitB_C_like cd00797
C-terminal catalytic domain of recombinase RitB, a component of the recombinase trio; ...
 17-182 6.07e-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: 46.53  E-value: 6.07e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 970931799  17 PAWFWLAVFEMFYYTGIRLNALICLRYADIDLGQRLIRVRGetEKTHREFMIPIPDGLMPHLKLLMEIAHKVGFAPTDQI 96
Cdd:cd00797   23 RPLTYATLFGLLYATGLRVGEALRLRLEDVDLDSGILTIRQ--TKFGKSRLVPLHPSTVGALRDYLARRDRLLPSPSSSY 100

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 970931799  97 FNVNRFSGHYSRSqmnsdQVEAMYKKLTAMTGVRMTP-------HRFRHTIA-SEMMR------QPERNIHITKNLLNHS 162
Cdd:cd00797  101 FFVSQQGGRLTGG-----GVYRVFRRLLRRIGLRGAGdgrgprlHDLRHTFAvNRLTRwyregaDVERKLPVLSTYLGHV 175

                        170       180
                 ....*....|....*....|
gi 970931799 163 NIATTMEYIEPDYDVMREVM 182
Cdd:cd00797  176 NVTDTYWYLTATPELMELAS 195
INT_C_like_5 cd01195
Uncharacterized site-specific tyrosine recombinase, C-terminal catalytic domain; Tyrosine ...
 8-171 1.47e-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: 271195 [Multi-domain]  Cd Length: 170  Bit Score: 44.77  E-value: 1.47e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 970931799   8 ATGNRTEitpawfwlAVFEMFYYTGIRLNALICLRYADIDLGQRLIRVRGETeKTHREfMIPIPDGLMPHLKllmeiAHK 87
Cdd:cd01195   17 AKGKRDE--------ALVRLLLDNALRRSEAVALDVEDLEKEHRRLRILGKG-KKQRE-VVTLPPTTREALA-----AWL 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 970931799  88 VGFAPTDQIFNVNRFSGHYSRsQMNSDQVEAMYKKLTAMTGV--RMTPHRFRHTIASEMMRQPERNIHITKNLLNHSNIA 165
Cdd:cd01195   82 AARGEAEGPLFVSLDRASRGR-RLSPQAVYRIVRRLAERIGLgkRLSPHGLRHSAITLALDAGAGLIRKVQDFSRHADLR 160


                 ....*.
gi 970931799 166 TTMEYI 171
Cdd:cd01195  161 TLQVYD 166
INT_C_like_4 cd01194
Uncharacterized site-specific tyrosine recombinase, C-terminal catalytic domain; Tyrosine ...
 23-170 3.22e-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: 271194 [Multi-domain]  Cd Length: 174  Bit Score: 43.90  E-value: 3.22e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 970931799  23 AVFEMFYYTGIRLNALICLRYADID--LGQRLIRVRGETEKTHREFMIPIPDGLMPHLKLLMEiahKVGFAPTDQIFNvn 100
Cdd:cd01194   26 AIISLMVTEGLRTVEIVRADVGDLRqeGEGTILYVQGKGKTSKDDFVYLRPDVLKALQAYLKA---RGKLDFEEPLFT-- 100

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 970931799 101 RFSGHYSRSQMNSDQVEAMYKKLTAMTGV---RMTPHRFRHTIASeMMRQPERNIHITKNLLNHSNIATTMEY 170
Cdd:cd01194  101 SLSNNSKGQRLTTRSIRRIIKKYLRKAGLdddRLTAHSLRHTAGT-LALKAGKSLREVQQLLRHSDPNTTMIY 172
PRK15417 PRK15417
integron integrase;
26-170 4.96e-05

integron integrase;


Pssm-ID: 185315 [Multi-domain]  Cd Length: 337  Bit Score: 44.65  E-value: 4.96e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 970931799  26 EMFYYTGIRLNALICLRYADIDLGQRLIRVRGETEKTHREFMIPipDGLMPHLKLLMEIAH----------KVGFAPTDQ 95
Cdd:PRK15417 138 QLLYGTGMRISEGLQLRVKDLDFDHGTIIVREGKGSKDRALMLP--ESLAPSLREQLSRARawwlkdqaegRSGVALPDA 215

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 970931799  96 I---------------------FNVNRFSGHYSRSQMNSDQVEAMYKKLTAMTGVR--MTPHRFRHTIASEMMRQPeRNI 152
Cdd:PRK15417 216 LerkypraghswpwfwvfaqhtHSTDPRSGVVRRHHMYDQTFQRAFKRAVEQAGITkpATPHTLRHSFATALLRSG-YDI 294

                        170
                 ....*....|....*...
gi 970931799 153 HITKNLLNHSNIATTMEY 170
Cdd:PRK15417 295 RTVQDLLGHSDVSTTMIY 312
INT_tnpB_C_Tn554 cd01187
Putative Transposase B from transposon Tn554, C-terminal catalytic domain; This family ...
 22-171 5.60e-05

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


Pssm-ID: 271187 [Multi-domain]  Cd Length: 142  Bit Score: 42.80  E-value: 5.60e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 970931799  22 LAVFEMFYYTGIRLNALICLRY----ADIDLGQRLIRVRGETEKTHREFMIPIPDGLmphlkllmeiahkvgfapTDQIF 97
Cdd:cd01187   16 IPVVQAAVFTGARASELATLKFgclhAQTSDDGTFLYWLKWENKGGKQLDIPISKKV------------------AELIK 77

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 970931799  98 NVNRFSGHYSRSQMNSDQVEAMYkkltamtgvRMTPHRFRHTIASEMMRQPERnIHITKNLLNHSNIATTMEYI 171
Cdd:cd01187   78 TINWTLNELSELKNISDDHGERF---------RFHTHRFRHTVATRLANSGMG-ILVLQQLLGHSSPEMTLRYA 141
INT_Lambda_C cd00800
C-terminal catalytic domain of Lambda integrase, a tyrosine-based site-specific recombinase; ...
 17-172 5.16e-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: 5.16e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 970931799  17 PAWFWLAvFEMFYYTGIRLNALICLRYADIDLGQRLIrvrgETEKTHREFMIPipdgLMPHLKLLMEIAHKVGFAPTDQI 96
Cdd:cd00800   11 PPLLRLA-MELALLTGQRQGDLLRLKWSDITDGGLLV----EQSKTGKKLLIP----WTPSLRALVDRIRALPRKRSEYL 81

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 970931799  97 FNvNRFSGHYSRSQMNSDQVEAMYKKLTAMTGVRMTPHRFRHTIASEMMRQpeRNIHITKNLLNHSNIATTMEYIE 172
Cdd:cd00800   82 IN-SRKGGPLSYDTLKSAWRRARKAAGLKGETEGFTFHDLRAKAATDYAEQ--GGSTDAQALLGHKSDAMTERYTR 154
xerD PRK00283
tyrosine recombinase;
23-167 7.39e-04

tyrosine recombinase;


Pssm-ID: 234713 [Multi-domain]  Cd Length: 299  Bit Score: 40.95  E-value: 7.39e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 970931799  23 AVFEMFYYTGIRLNALICLRYADIDLGQRLIRVRGeteKTHREFMIPIpdGLMPH--LKLLMEIAHK--VGFAPTDQIFn 98
Cdd:PRK00283 138 AMLELLYATGLRVSELVGLTLDDVSLRQGVVRVTG---KGNKERLVPL--GEEAVyaIERYLERGRPalLNGRSSDALF- 211

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 970931799  99 VNRFSGHYSRSqmnsdQVEAMYKKLTAMTGV---RMTPHRFRHTIASemmrqperniHITKN---------LLNHSNIAT 166
Cdd:PRK00283 212 PSARGGQLTRQ-----TFWHRIKHYAKRAGIdpkKLSPHVLRHAFAT----------HLLNHgadlrvvqeLLGHSDIST 276


                 .
gi 970931799 167 T 167
Cdd:PRK00283 277 T 277
INT_C_like_1 cd01184
Uncharacterized site-specific tyrosine recombinase, C-terminal catalytic domain; Tyrosine ...
 15-146 2.55e-03

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: 38.44  E-value: 2.55e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 970931799  15 ITPAWFWLAVFEMfyYTGIRLNALICLRYADIDLGQRL--IRVRGETE----KTH---RefMIPIPDGLMpHLKLLMEIA 85
Cdd:cd01184   21 KDPALYWLPLIGL--YTGARLNEICQLRVDDIKEEDGIwcIDINDDAEgrrlKTKasrR--LVPIHPRLI-ELGFLDYVE 95

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 970931799  86 HKVG----FAPTDQIFNVNRFSGHYSRsQMNSDQveamyKKLTAMTGVRMTPHRFRHTIASEMMR 146
Cdd:cd01184   96 ALRAdgklFLFPEKRDKDGKYSKAASK-WFNRLL-----RKLGIKDDERKSFHSFRHTFITALKR 154
 
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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