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Conserved domains on  [gi|1499531606|gb|RMR79646|]
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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
SCOP:  4002347

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 ...
 20-170 4.24e-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: 4.24e-34
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1499531606  20 WLAVFEMFYYTGIRLNALICLRYADIDLGQRLIRVRGETEKTHREFMIPIPDGLMPHLKLLMEIAHKvGFAPTDQIFNVN 99
Cdd:cd00397    19 DRAILLLLLETGLRISELLALKVKDIDLDNGTIRVRGKKTKGGKERTVPLPKELAEELKEYLKERRD-KRGPLLKSLYLN 97

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1499531606 100 RFSGHYSRSQMNSDQVEAMYKKLTAMTGVRMTPHRFRHTIASEMMRQPErNIHITKNLLNHSNIATTMEYI 170
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 ...
 20-170 4.24e-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: 4.24e-34
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1499531606  20 WLAVFEMFYYTGIRLNALICLRYADIDLGQRLIRVRGETEKTHREFMIPIPDGLMPHLKLLMEIAHKvGFAPTDQIFNVN 99
Cdd:cd00397    19 DRAILLLLLETGLRISELLALKVKDIDLDNGTIRVRGKKTKGGKERTVPLPKELAEELKEYLKERRD-KRGPLLKSLYLN 97

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1499531606 100 RFSGHYSRSQMNSDQVEAMYKKLTAMTGVRMTPHRFRHTIASEMMRQPErNIHITKNLLNHSNIATTMEYI 170
Cdd:cd00397    98 KLFGTKLGERLSRRTLRRIFKKAGIEAGRKITPHSLRHTFATNLLENGV-DIKVVQKLLGHSSISTTQRYL 167
XerC COG4973
Site-specific recombinase XerC [Replication, recombination and repair];
17-181 3.23e-29

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


Pssm-ID: 443998 [Multi-domain]  Cd Length: 287  Bit Score: 113.90  E-value: 3.23e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1499531606  17 AWFWLAVFEMFYYTGIRLNALICLRYADIDLGQRLIRVRGeteKTHREFMIPIPDGLMPHLKLLMEIAHKVGFAPTDQIF 96
Cdd:COG4973   130 AVRDRAIVELLYSTGLRLGELVGLDWEDVDLDAGEVRVRG---KTGKSRTVPLGPKALAALREWLAVRPELAAPDEGALF 206

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1499531606  97 NVNRfsGHysrsQMNSDQVEAMYKKLTAMTGV--RMTPHRFRHTIASeMMRQPERNIHITKNLLNHSNIATTMEYIEPDY 174
Cdd:COG4973   207 PSRR--GT----RLSPRNVQKRLRRLAKKAGLpkHVHPHDLRHSFAT-HLLESGGDLRAVQELLGHASISTTQIYTHLDF 279


                  ....*..
gi 1499531606 175 DVMREVM 181
Cdd:COG4973   280 QHLAEVY 286
xerS PRK05084
site-specific tyrosine recombinase XerS; Reviewed
 21-185 3.05e-21

site-specific tyrosine recombinase XerS; Reviewed


Pssm-ID: 235339 [Multi-domain]  Cd Length: 357  Bit Score: 93.44  E-value: 3.05e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1499531606  21 LAVFEMFYYTGIRLNALICLRYADIDLGQRLIRVrgeTEKTHREFMIPIPDGLMPHLKLLMEIAHKVGFAP-TDQIFNVN 99
Cdd:PRK05084  198 LAIIALILGSGLRVSELVNLDLSDLNLKQMTIDV---TRKGGKRDSVNIAPFALPYLEEYLKIRASRYKAEkQEKALFLT 274

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1499531606 100 RFSGHYSRSQMNSdqVEAMYKKLTAMTGVRMTPHRFRHTIASEMMRQpERNIHITKNLLNHSNIATTMEYIEPDYDVMRE 179
Cdd:PRK05084  275 KYRGKPNRISARA--IEKMVAKYSEAFGVRLTPHKLRHTLATRLYDA-TKDQVLVADQLGHTSTETTDLYTHIVNDEQKE 351


                  ....*.
gi 1499531606 180 VMNERG 185
Cdd:PRK05084  352 ALDRLE 357
Phage_integrase pfam00589
Phage integrase family; Members of this family cleave DNA substrates by a series of staggered ...
 21-174 2.38e-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: 2.38e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1499531606  21 LAVFEMFYYTGIRLNALICLRYADIDLGQRLIRVrgETEKTHREFMIPIPDGLMPHLKLLMEIaHKVGFAPTDQIFnVNR 100
Cdd:pfam00589  24 KALLELLYATGLRISELCSLRWSDIDFENGVIRV--HRGKGNKERTVPLSDAALELLKEWLSK-RLLEAPKSDYLF-ASK 99

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1499531606 101 FsghysRSQMNSDQVEAMYKKLTAMTGV--RMTPHRFRHTIASEMMRQpERNIHITKNLLNHSNIATTMEYIEPDY 174
Cdd:pfam00589 100 R-----GKPLSRQTVRKIFKRAGKEAGLelPLHPHMLRHSFATHLLEA-GVDLRVVQKLLGHSSISTTQIYTHVAD 169
recomb_XerD TIGR02225
tyrosine recombinase XerD; The phage integrase family describes a number of recombinases with ...
 22-166 8.68e-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: 59.13  E-value: 8.68e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1499531606  22 AVFEMFYYTGIRLNALICLRYADIDLGQRLIRVRGeteKTHREFMIPIPDGLMPHLKLLMEIAHKVGFA----PTDQIFn 97
Cdd:TIGR02225 129 AMLELLYATGLRVSELVGLRLEDVNLDEGFVRVRG---KGNKERLVPLGEEAIEALERYLKEARPLLLKkkvkESDALF- 204

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1499531606  98 VNRFSGHYSRSQmnsdqVEAMYKKLTAMTGV--RMTPHRFRHTIASEMMrQPERNIHITKNLLNHSNIATT 166
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 ...
 20-170 4.24e-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: 4.24e-34
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1499531606  20 WLAVFEMFYYTGIRLNALICLRYADIDLGQRLIRVRGETEKTHREFMIPIPDGLMPHLKLLMEIAHKvGFAPTDQIFNVN 99
Cdd:cd00397    19 DRAILLLLLETGLRISELLALKVKDIDLDNGTIRVRGKKTKGGKERTVPLPKELAEELKEYLKERRD-KRGPLLKSLYLN 97

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1499531606 100 RFSGHYSRSQMNSDQVEAMYKKLTAMTGVRMTPHRFRHTIASEMMRQPErNIHITKNLLNHSNIATTMEYI 170
Cdd:cd00397    98 KLFGTKLGERLSRRTLRRIFKKAGIEAGRKITPHSLRHTFATNLLENGV-DIKVVQKLLGHSSISTTQRYL 167
XerC COG4973
Site-specific recombinase XerC [Replication, recombination and repair];
17-181 3.23e-29

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


Pssm-ID: 443998 [Multi-domain]  Cd Length: 287  Bit Score: 113.90  E-value: 3.23e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1499531606  17 AWFWLAVFEMFYYTGIRLNALICLRYADIDLGQRLIRVRGeteKTHREFMIPIPDGLMPHLKLLMEIAHKVGFAPTDQIF 96
Cdd:COG4973   130 AVRDRAIVELLYSTGLRLGELVGLDWEDVDLDAGEVRVRG---KTGKSRTVPLGPKALAALREWLAVRPELAAPDEGALF 206

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1499531606  97 NVNRfsGHysrsQMNSDQVEAMYKKLTAMTGV--RMTPHRFRHTIASeMMRQPERNIHITKNLLNHSNIATTMEYIEPDY 174
Cdd:COG4973   207 PSRR--GT----RLSPRNVQKRLRRLAKKAGLpkHVHPHDLRHSFAT-HLLESGGDLRAVQELLGHASISTTQIYTHLDF 279


                  ....*..
gi 1499531606 175 DVMREVM 181
Cdd:COG4973   280 QHLAEVY 286
XerD COG4974
Site-specific recombinase XerD [Replication, recombination and repair];
22-183 2.82e-27

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


Pssm-ID: 443999 [Multi-domain]  Cd Length: 291  Bit Score: 108.93  E-value: 2.82e-27
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1499531606  22 AVFEMFYYTGIRLNALICLRYADIDLGQRLIRVRGetEKTHREFMIPIPDGLMPHLKLLMEIAHKvgfAPTDQIFnVNRF 101
Cdd:COG4974   137 ALLLLLYATGLRVSELLGLKWSDIDLDRGTIRVRR--GKGGKERTVPLSPEALEALREYLEERRP---RDSDYLF-PTRR 210

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1499531606 102 SGHYSRSQMNSdqveaMYKKLTAMTGV--RMTPHRFRHTIASEMMRQpERNIHITKNLLNHSNIATTMEYIEPDYDVMRE 179
Cdd:COG4974   211 GRPLSRRAIRK-----ILKRLAKRAGIpkRVTPHSLRHTFATHLLEA-GVDLRTVQELLGHSSISTTQIYTHVSDEELRE 284


                  ....
gi 1499531606 180 VMNE 183
Cdd:COG4974   285 AVEK 288
xerS PRK05084
site-specific tyrosine recombinase XerS; Reviewed
 21-185 3.05e-21

site-specific tyrosine recombinase XerS; Reviewed


Pssm-ID: 235339 [Multi-domain]  Cd Length: 357  Bit Score: 93.44  E-value: 3.05e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1499531606  21 LAVFEMFYYTGIRLNALICLRYADIDLGQRLIRVrgeTEKTHREFMIPIPDGLMPHLKLLMEIAHKVGFAP-TDQIFNVN 99
Cdd:PRK05084  198 LAIIALILGSGLRVSELVNLDLSDLNLKQMTIDV---TRKGGKRDSVNIAPFALPYLEEYLKIRASRYKAEkQEKALFLT 274

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1499531606 100 RFSGHYSRSQMNSdqVEAMYKKLTAMTGVRMTPHRFRHTIASEMMRQpERNIHITKNLLNHSNIATTMEYIEPDYDVMRE 179
Cdd:PRK05084  275 KYRGKPNRISARA--IEKMVAKYSEAFGVRLTPHKLRHTLATRLYDA-TKDQVLVADQLGHTSTETTDLYTHIVNDEQKE 351


                  ....*.
gi 1499531606 180 VMNERG 185
Cdd:PRK05084  352 ALDRLE 357
Phage_integrase pfam00589
Phage integrase family; Members of this family cleave DNA substrates by a series of staggered ...
 21-174 2.38e-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: 2.38e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1499531606  21 LAVFEMFYYTGIRLNALICLRYADIDLGQRLIRVrgETEKTHREFMIPIPDGLMPHLKLLMEIaHKVGFAPTDQIFnVNR 100
Cdd:pfam00589  24 KALLELLYATGLRISELCSLRWSDIDFENGVIRV--HRGKGNKERTVPLSDAALELLKEWLSK-RLLEAPKSDYLF-ASK 99

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1499531606 101 FsghysRSQMNSDQVEAMYKKLTAMTGV--RMTPHRFRHTIASEMMRQpERNIHITKNLLNHSNIATTMEYIEPDY 174
Cdd:pfam00589 100 R-----GKPLSRQTVRKIFKRAGKEAGLelPLHPHMLRHSFATHLLEA-GVDLRVVQKLLGHSSISTTQIYTHVAD 169
INT_IntI_C cd01193
Integron integrase and similar protiens, C-terminal catalytic domain; Integron integrases ...
 22-169 3.82e-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: 3.82e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1499531606  22 AVFEMFYYTGIRLNALICLRYADIDLGQRLIRVRGetEKTHREFMIPIPDGLMPHLK--LLMEIAHKVGFAPTDQIFNVN 99
Cdd:cd01193    25 LILSLLYGAGLRISELLRLRVKDIDFERGVIRVRQ--GKGGKDRVVPLPEKLLEPLRryLKSARPKEELDPAEGRAGVLD 102

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1499531606 100 RFSGHYSRSQMNSDQVEAMYKKLTAMTGV--RMTPHRFRHTIASEMMRQpERNIHITKNLLNHSNIATTMEY 169
Cdd:cd01193   103 PRTGVERRHHISETTVQRALKKAVEQAGItkRVTPHTLRHSFATHLLEA-GTDIRTIQELLGHSDLSTTMIY 173
INT_XerDC_C cd00798
XerD and XerC integrases, C-terminal catalytic domains; XerDC-like integrases are involved in ...
 22-166 3.83e-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: 3.83e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1499531606  22 AVFEMFYYTGIRLNALICLRYADIDLGQRLIRVRGeteKTHREFMIPIPDGLMPHLKLLMEIAHK--VGFAPTDQIFnVN 99
Cdd:cd00798    23 AILELLYASGLRVSELVGLDLSDVDLDEGLVRVTG---KGNKERLVPFGSYAVEALEEYLEERRPllLKKKPPDALF-LN 98

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1499531606 100 RFSGHYSRsqmnsDQVEAMYKKLTAMTGV--RMTPHRFRHTIASEMMrqpER--NIHITKNLLNHSNIATT 166
Cdd:cd00798    99 KRGKRLSR-----RGVWRILKKYAERAGLpkHVSPHTLRHSFATHLL---EGgaDLRVVQELLGHASLSTT 161
INT_Rci_Hp1_C cd00796
Shufflon-specific DNA recombinase Rci and Bacteriophage Hp1_like integrase, C-terminal ...
 16-169 4.61e-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: 4.61e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1499531606  16 PAWFWLAVFEmfYYTGIRLNALICLRYADIDLGQRLIRVRGETEKTHREfmIPIPDGLMPHLKLLMEIAHKVGFAPTDQI 95
Cdd:cd00796    23 PHLRLIVLLA--LYTGARRGEILSLRWDDIDLEVGLIVLPETKNGKPRT--VPLSDEAIAILKELKRKRGKDGFFVDGRF 98

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1499531606  96 FnvnrfsgHYSRSQMNSDqVEAMYKKLtAMTGVRmtPHRFRHTIASEMMRQPERNIHITKnLLNHSNIATTMEY 169
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; ...
 21-180 6.09e-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: 6.09e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1499531606  21 LAVFEMFYYTGIRLNALICLRYADIDLGQRLIRVRGEteKTHREFMIPIPDglmphlkllmeiahKVGFA---------- 90
Cdd:cd01188    23 YAILLLLARLGLRAGDVAGLRLDDIDWRSGTITVRQK--KTGRPVELPLTE--------------PVGEAladylrdgrp 86

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1499531606  91 --PTDQIF-NVNRFSGHYSrsqmNSDQVEAMYKKLTAMTGV---RMTPHRFRHTIASEMMRQpERNIHITKNLLNHSNIA 164
Cdd:cd01188    87 rtDSREVFlRARAPYRPLS----STSQISSIVRRYLRKAGIepsHRGTHSLRHSLATRMLRA-GTSLKVIADLLGHRSIE 161

                         170
                  ....*....|....*.
gi 1499531606 165 TTMEYIEPDYDVMREV 180
Cdd:cd01188   162 TTAIYAKIDVDDLREV 177
INT_tnpA_C_Tn554 cd01186
Putative Transposase A from transposon Tn554, C-terminal catalytic domain; This family ...
 23-180 1.38e-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: 62.82  E-value: 1.38e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1499531606  23 VFEMFYYTGIRLNALICLRYADIDLGQRLIRVR-------GETEKTHREFMIPIPDGLMphlKLLME-IAHKVGFAPTDQ 94
Cdd:cd01186    22 LLALLYETGLRIGEALGLRIEDIDMADNQIELVpredntnEARAKSMRERRIPVSQDLI---DLYADyLTYIYCEEAEFS 98

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1499531606  95 IFNVNRFSGHYSRSQMNSDQVEAMYKKLTAMTGVRMTPHRFRHTIASEMMRQpERNIHITKNLLNHSNIATTME-YIEPD 173
Cdd:cd01186    99 ITVFVNVKGGNQGKAMNYSDVYDLVRRLKKRTGIDFTPHMFRHTHATALIRA-GWSIEVVARRLGHAHVQTTLNtYGHLS 177


                  ....*..
gi 1499531606 174 YDVMREV 180
Cdd:cd01186   178 EEDIRRE 184
INTN1_C_like cd01185
Integrase IntN1 of Bacteroides mobilizable transposon NBU1 and similar proteins, C-terminal ...
 23-171 9.13e-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: 9.13e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1499531606  23 VFEMFYYTGIRLNALICLRYADIDLGQRLIRVRGETEKTHREFMIPIPDGLMphlKLLMEIahkVGFAPTDQIFNVnrfs 102
Cdd:cd01185    23 MFLFSCYTGLRFSDLKNLTWKNIVEASGRTWIRYRRKKTGKPVTVPLLPVAR---EILEKY---KDDRSEGKLFPV---- 92

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1499531606 103 ghYSRSQMNsdqvEAMyKKLTAMTGVR--MTPHRFRHTIASEMMRQpERNIHITKNLLNHSNIATTMEYIE 171
Cdd:cd01185    93 --LSNQKIN----RYL-KEIAKIAGIDkhLTFHVARHTFATLLLLK-GVDIETISKLLGHSSIKTTQIYAK 155
FimB COG0582
Integrase/recombinase, includes phage integrase [Replication, recombination and repair, ...
 22-183 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 1499531606  22 AVFEMFYYTGIRLNALICLRYADIDLGQRLIRVRGETEKTHREFMIPIPDGLMPHLKLLMEIAHKVGFaptdqifnVnrF 101
Cdd:COG0582   229 LALRLLLLTGVRPGELRGARWSEIDLEAALWTIPAERMKTRRPHIVPLSRQALEILKELKPLTGDSEY--------V--F 298

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1499531606 102 SGHYSRSQMNSDQveAMYKKLTAMTGVRMTPHRFRHTIASEMMRQPErNIHITKNLLNHSNIATTME-YIEPDY-DVMRE 179
Cdd:COG0582   299 PSRRGPKKPMSEN--TLNKALRRMGYGRFTPHGFRHTASTLLNEAGF-PPDVIERQLAHKDGNKVRAaYNRADYlEERRE 375


                  ....
gi 1499531606 180 VMNE 183
Cdd:COG0582   376 MMQW 379
INT_RitC_C_like cd01182
C-terminal catalytic domain of recombinase RitC, a component of the recombinase trio; ...
 28-182 5.75e-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: 5.75e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1499531606  28 YYTGIRLNALICLRYADIDLG-QRLIRVRGeteKTHREFMIPIPDGLMPHLKLLMEIAHKvgfAPTDQIFNVNRFSGHys 106
Cdd:cd01182    31 YDTGARVQELADLTIRDLRLDdPATVRLHG---KGRKERTVPLWKETVAALKAYLQEFHL---TPDPKQLFPLFPNRR-- 102

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1499531606 107 RSQMNSDQVEAMYKK----LTAMTGV---RMTPHRFRHTIASEMMrQPERNIHITKNLLNHSNIATTMEYIEPDYDVMRE 179
Cdd:cd01182   103 GQPLTRDGVAYILNKyvalASNRCPSlpkRITPHTLRHTKAMHLL-QAGVDLTVIRDWLGHESVETTQIYAEADLEMKRE 181


                  ...
gi 1499531606 180 VMN 182
Cdd:cd01182   182 ALE 184
xerC PRK00236
site-specific tyrosine recombinase XerC; Reviewed
 22-166 5.77e-10

site-specific tyrosine recombinase XerC; Reviewed


Pssm-ID: 234698 [Multi-domain]  Cd Length: 297  Bit Score: 59.40  E-value: 5.77e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1499531606  22 AVFEMFYYTGIRLNALICLRYADIDLGQRLIRVRGeteKTHREFMIPIpdgLMPHLKLLME-IAHKVGFAPTDQ-IFnVN 99
Cdd:PRK00236  140 AILELLYGSGLRLSELVGLDIDDLDLASGTLRVLG---KGNKERTVPL---GRAAREALEAyLALRPLFLPDDDaLF-LG 212

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1499531606 100 RFSGHysrsqMNSDQVEAMYKKLTAMTGV--RMTPHRFRHTIASEMMrqpER--NIHITKNLLNHSNIATT 166
Cdd:PRK00236  213 ARGGR-----LSPRVVQRRVKKLGKKAGLpsHITPHKLRHSFATHLL---ESggDLRAVQELLGHASLSTT 275
recomb_XerD TIGR02225
tyrosine recombinase XerD; The phage integrase family describes a number of recombinases with ...
 22-166 8.68e-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: 59.13  E-value: 8.68e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1499531606  22 AVFEMFYYTGIRLNALICLRYADIDLGQRLIRVRGeteKTHREFMIPIPDGLMPHLKLLMEIAHKVGFA----PTDQIFn 97
Cdd:TIGR02225 129 AMLELLYATGLRVSELVGLRLEDVNLDEGFVRVRG---KGNKERLVPLGEEAIEALERYLKEARPLLLKkkvkESDALF- 204

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1499531606  98 VNRFSGHYSRSQmnsdqVEAMYKKLTAMTGV--RMTPHRFRHTIASEMMrQPERNIHITKNLLNHSNIATT 166
Cdd:TIGR02225 205 LNRRGGPLSRQG-----VWKILKEYAKRAGIekPISPHTLRHSFATHLL-ENGADLRVVQELLGHADISTT 269
INT_ICEBs1_C_like cd01189
C-terminal catalytic domain of integrases from bacterial phages and conjugate transposons; ...
 20-169 8.94e-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: 8.94e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1499531606  20 WLAVFEMFYYTGIRLNALICLRYADIDLGQRLIRVRGE---------------TEKTHREfmIPIPDGLMPHLKLLMeia 84
Cdd:cd01189    18 YYLLFLLALLTGLRRGELLALTWSDIDFENGTIRINRTlvrkkkggyvikppkTKSSIRT--IPLPDELIELLKELK--- 92

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1499531606  85 hkvgfaptdqifnvnrfsghysrsqmnsdqveaMYKKLTAMTGV-RMTPHRFRHTIASEMMRQPErNIHITKNLLNHSNI 163
Cdd:cd01189    93 ---------------------------------AFKKLLKKAGLpRITPHDLRHTFASLLLEAGV-PLKVIAERLGHSDI 138


                  ....*.
gi 1499531606 164 ATTMEY 169
Cdd:cd01189   139 STTLDV 144
INT_P4_C cd00801
Bacteriophage P4 integrase, C-terminal catalytic domain; P4-like integrases are found in ...
 29-183 4.15e-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: 4.15e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1499531606  29 YTGIRLNALICLRYADIDLGQRLIRVRGETEKTHREFMIPIPDGLMPHLKLLMEIAhkvgfAPTDQIFnvnrFSGHYSRS 108
Cdd:cd00801    30 LTGQRIGELARARWSEIDLEEKTWTIPAERTKNKRPHRVPLSDQALEILEELKEFT-----GDSGYLF----PSRRKKKK 100

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1499531606 109 QMNSDQVEAMYKKLTAmTGVRMTPHRFRHTIASEMMRQpERNIHITKNLLNHSNIATTME-YIEPDY-DVMREVMNE 183
Cdd:cd00801   101 PISENTINKALKRLGY-KGKEFTPHDLRRTFSTLLNEL-GIDPEVIERLLNHVLGGVVRAaYNRYDYlEERREALQA 175
INT_C_like_3 cd01192
Uncharacterized site-specific tyrosine recombinase, C-terminal catalytic domain; Tyrosine ...
 30-170 1.48e-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: 48.06  E-value: 1.48e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1499531606  30 TGIRLNALICLRYADIDLGQRL-IRVRgeteKTHREFMIPIPDGLmphLKLLMEIAHKVGFAPTDQIFN--VNRFSGHYS 106
Cdd:cd01192    36 TGLRISDLLSLKVEDVTNKDKLsIKEQ----KTGKQKTFPLNPTL---VKALKEYIDDLDLKRNDYLFKslKQGPEKPIS 108

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1499531606 107 RSQMNSdqveaMYKKLTAMTGVR--MTPHRFRHTIASeMMRQPERNIHITKNLLNHSNIATTMEYI 170
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; ...
 16-181 5.66e-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: 5.66e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1499531606  16 PAWFWLAVFEMFYYTGIRLNALICLRYADIDLGQRLIRVRGetEKTHREFMIPIPDGLMPHLKLLMEIAHKVGFAPTDQI 95
Cdd:cd00797    23 RPLTYATLFGLLYATGLRVGEALRLRLEDVDLDSGILTIRQ--TKFGKSRLVPLHPSTVGALRDYLARRDRLLPSPSSSY 100

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1499531606  96 FNVNRFSGHYSRSqmnsdQVEAMYKKLTAMTGVRMTP-------HRFRHTIA-SEMMR------QPERNIHITKNLLNHS 161
Cdd:cd00797   101 FFVSQQGGRLTGG-----GVYRVFRRLLRRIGLRGAGdgrgprlHDLRHTFAvNRLTRwyregaDVERKLPVLSTYLGHV 175

                         170       180
                  ....*....|....*....|
gi 1499531606 162 NIATTMEYIEPDYDVMREVM 181
Cdd:cd00797   176 NVTDTYWYLTATPELMELAS 195
INT_C_like_5 cd01195
Uncharacterized site-specific tyrosine recombinase, C-terminal catalytic domain; Tyrosine ...
 7-170 1.40e-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: 1.40e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1499531606   7 ATGNRTEitpawfwlAVFEMFYYTGIRLNALICLRYADIDLGQRLIRVRGETeKTHREfMIPIPDGLMPHLKllmeiAHK 86
Cdd:cd01195    17 AKGKRDE--------ALVRLLLDNALRRSEAVALDVEDLEKEHRRLRILGKG-KKQRE-VVTLPPTTREALA-----AWL 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1499531606  87 VGFAPTDQIFNVNRFSGHYSRsQMNSDQVEAMYKKLTAMTGV--RMTPHRFRHTIASEMMRQPERNIHITKNLLNHSNIA 164
Cdd:cd01195    82 AARGEAEGPLFVSLDRASRGR-RLSPQAVYRIVRRLAERIGLgkRLSPHGLRHSAITLALDAGAGLIRKVQDFSRHADLR 160


                  ....*.
gi 1499531606 165 TTMEYI 170
Cdd:cd01195   161 TLQVYD 166
INT_C_like_4 cd01194
Uncharacterized site-specific tyrosine recombinase, C-terminal catalytic domain; Tyrosine ...
 22-169 3.12e-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: 3.12e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1499531606  22 AVFEMFYYTGIRLNALICLRYADID--LGQRLIRVRGETEKTHREFMIPIPDGLMPHLKLLMEiahKVGFAPTDQIFNvn 99
Cdd:cd01194    26 AIISLMVTEGLRTVEIVRADVGDLRqeGEGTILYVQGKGKTSKDDFVYLRPDVLKALQAYLKA---RGKLDFEEPLFT-- 100

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1499531606 100 RFSGHYSRSQMNSDQVEAMYKKLTAMTGV---RMTPHRFRHTIASeMMRQPERNIHITKNLLNHSNIATTMEY 169
Cdd:cd01194   101 SLSNNSKGQRLTTRSIRRIIKKYLRKAGLdddRLTAHSLRHTAGT-LALKAGKSLREVQQLLRHSDPNTTMIY 172
PRK15417 PRK15417
integron integrase;
25-169 4.98e-05

integron integrase;


Pssm-ID: 185315 [Multi-domain]  Cd Length: 337  Bit Score: 44.65  E-value: 4.98e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1499531606  25 EMFYYTGIRLNALICLRYADIDLGQRLIRVRGETEKTHREFMIPipDGLMPHLKLLMEIAH----------KVGFAPTDQ 94
Cdd:PRK15417  138 QLLYGTGMRISEGLQLRVKDLDFDHGTIIVREGKGSKDRALMLP--ESLAPSLREQLSRARawwlkdqaegRSGVALPDA 215

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1499531606  95 I---------------------FNVNRFSGHYSRSQMNSDQVEAMYKKLTAMTGVR--MTPHRFRHTIASEMMRQPeRNI 151
Cdd:PRK15417  216 LerkypraghswpwfwvfaqhtHSTDPRSGVVRRHHMYDQTFQRAFKRAVEQAGITkpATPHTLRHSFATALLRSG-YDI 294

                         170
                  ....*....|....*...
gi 1499531606 152 HITKNLLNHSNIATTMEY 169
Cdd:PRK15417  295 RTVQDLLGHSDVSTTMIY 312
INT_tnpB_C_Tn554 cd01187
Putative Transposase B from transposon Tn554, C-terminal catalytic domain; This family ...
 21-170 5.27e-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: 5.27e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1499531606  21 LAVFEMFYYTGIRLNALICLRY----ADIDLGQRLIRVRGETEKTHREFMIPIPDGLmphlkllmeiahkvgfapTDQIF 96
Cdd:cd01187    16 IPVVQAAVFTGARASELATLKFgclhAQTSDDGTFLYWLKWENKGGKQLDIPISKKV------------------AELIK 77

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1499531606  97 NVNRFSGHYSRSQMNSDQVEAMYkkltamtgvRMTPHRFRHTIASEMMRQPERnIHITKNLLNHSNIATTMEYI 170
Cdd:cd01187    78 TINWTLNELSELKNISDDHGERF---------RFHTHRFRHTVATRLANSGMG-ILVLQQLLGHSSPEMTLRYA 141
INT_Lambda_C cd00800
C-terminal catalytic domain of Lambda integrase, a tyrosine-based site-specific recombinase; ...
 16-171 5.14e-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: 5.14e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1499531606  16 PAWFWLAvFEMFYYTGIRLNALICLRYADIDLGQRLIrvrgETEKTHREFMIPipdgLMPHLKLLMEIAHKVGFAPTDQI 95
Cdd:cd00800    11 PPLLRLA-MELALLTGQRQGDLLRLKWSDITDGGLLV----EQSKTGKKLLIP----WTPSLRALVDRIRALPRKRSEYL 81

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1499531606  96 FNvNRFSGHYSRSQMNSDQVEAMYKKLTAMTGVRMTPHRFRHTIASEMMRQpeRNIHITKNLLNHSNIATTMEYIE 171
Cdd:cd00800    82 IN-SRKGGPLSYDTLKSAWRRARKAAGLKGETEGFTFHDLRAKAATDYAEQ--GGSTDAQALLGHKSDAMTERYTR 154
xerD PRK00283
tyrosine recombinase;
22-166 6.50e-04

tyrosine recombinase;


Pssm-ID: 234713 [Multi-domain]  Cd Length: 299  Bit Score: 40.95  E-value: 6.50e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1499531606  22 AVFEMFYYTGIRLNALICLRYADIDLGQRLIRVRGeteKTHREFMIPIpdGLMPH--LKLLMEIAHK--VGFAPTDQIFn 97
Cdd:PRK00283  138 AMLELLYATGLRVSELVGLTLDDVSLRQGVVRVTG---KGNKERLVPL--GEEAVyaIERYLERGRPalLNGRSSDALF- 211

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1499531606  98 VNRFSGHYSRSqmnsdQVEAMYKKLTAMTGV---RMTPHRFRHTIASemmrqperniHITKN---------LLNHSNIAT 165
Cdd:PRK00283  212 PSARGGQLTRQ-----TFWHRIKHYAKRAGIdpkKLSPHVLRHAFAT----------HLLNHgadlrvvqeLLGHSDIST 276


                  .
gi 1499531606 166 T 166
Cdd:PRK00283  277 T 277
INT_C_like_1 cd01184
Uncharacterized site-specific tyrosine recombinase, C-terminal catalytic domain; Tyrosine ...
 14-145 2.59e-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: 2.59e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1499531606  14 ITPAWFWLAVFEMfyYTGIRLNALICLRYADIDLGQRL--IRVRGETE----KTH---RefMIPIPDGLMpHLKLLMEIA 84
Cdd:cd01184    21 KDPALYWLPLIGL--YTGARLNEICQLRVDDIKEEDGIwcIDINDDAEgrrlKTKasrR--LVPIHPRLI-ELGFLDYVE 95

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1499531606  85 HKVG----FAPTDQIFNVNRFSGHYSRsQMNSDQveamyKKLTAMTGVRMTPHRFRHTIASEMMR 145
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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