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Conserved domains on  [gi|1499404721|gb|RMQ62705|]
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hypothetical protein ALQ01_03933, partial [Pseudomonas savastanoi pv. glycinea]

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 ...
 90-240 4.91e-33

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


:

Pssm-ID: 271175 [Multi-domain]  Cd Length: 167  Bit Score: 122.20  E-value: 4.91e-33
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1499404721  90 WLAVFEMFYYTGIRLNALICLRYADIDMGERLIKVRGETEKTHREFMIPIPDRLMPHLKQLMDiAHRVGFSPTDQIFNVN 169
Cdd:cd00397    19 DRAILLLLLETGLRISELLALKVKDIDLDNGTIRVRGKKTKGGKERTVPLPKELAEELKEYLK-ERRDKRGPLLKSLYLN 97

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1499404721 170 RFSGHYSRSQMNSDQVEAMYKKLTAMTGVRMTPHRFRHTIASEMMRQPErNIHITKSLLNHSNITTTMEYI 240
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 ...
 90-240 4.91e-33

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


Pssm-ID: 271175 [Multi-domain]  Cd Length: 167  Bit Score: 122.20  E-value: 4.91e-33
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1499404721  90 WLAVFEMFYYTGIRLNALICLRYADIDMGERLIKVRGETEKTHREFMIPIPDRLMPHLKQLMDiAHRVGFSPTDQIFNVN 169
Cdd:cd00397    19 DRAILLLLLETGLRISELLALKVKDIDLDNGTIRVRGKKTKGGKERTVPLPKELAEELKEYLK-ERRDKRGPLLKSLYLN 97

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1499404721 170 RFSGHYSRSQMNSDQVEAMYKKLTAMTGVRMTPHRFRHTIASEMMRQPErNIHITKSLLNHSNITTTMEYI 240
Cdd:cd00397    98 KLFGTKLGERLSRRTLRRIFKKAGIEAGRKITPHSLRHTFATNLLENGV-DIKVVQKLLGHSSISTTQRYL 167
XerC COG4973
Site-specific recombinase XerC [Replication, recombination and repair];
17-251 3.66e-32

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


Pssm-ID: 443998 [Multi-domain]  Cd Length: 287  Bit Score: 123.53  E-value: 3.66e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1499404721  17 RRRAASPGYRYAMEHGLVElkVNPLKetRVIPTKRPK---KTINTDAIVRarnWLNILVQEERAtakraeitpaWFWLAV 93
Cdd:COG4973    74 RLSALRSFFNWAVREGLLE--ANPAA--GVKAPKAPRklpRALTVDELAQ---LLDALADDPLA----------VRDRAI 136

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1499404721  94 FEMFYYTGIRLNALICLRYADIDMGERLIKVRGeteKTHREFMIPIPDRLMPHLKQLMDIAHRVGFSPTDQIFNVNRfsG 173
Cdd:COG4973   137 VELLYSTGLRLGELVGLDWEDVDLDAGEVRVRG---KTGKSRTVPLGPKALAALREWLAVRPELAAPDEGALFPSRR--G 211

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1499404721 174 HysrsQMNSDQVEAMYKKLTAMTGV--RMTPHRFRHTIASeMMRQPERNIHITKSLLNHSNITTTMEYIEPDYDVMREVM 251
Cdd:COG4973   212 T----RLSPRNVQKRLRRLAKKAGLpkHVHPHDLRHSFAT-HLLESGGDLRAVQELLGHASISTTQIYTHLDFQHLAEVY 286
xerS PRK05084
site-specific tyrosine recombinase XerS; Reviewed
 91-255 7.64e-21

site-specific tyrosine recombinase XerS; Reviewed


Pssm-ID: 235339 [Multi-domain]  Cd Length: 357  Bit Score: 93.06  E-value: 7.64e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1499404721  91 LAVFEMFYYTGIRLNALICLRYADIDMGERLIKVrgeTEKTHREFMIPIPDRLMPHLKQLMDI-AHRVGFSPTDQIFNVN 169
Cdd:PRK05084  198 LAIIALILGSGLRVSELVNLDLSDLNLKQMTIDV---TRKGGKRDSVNIAPFALPYLEEYLKIrASRYKAEKQEKALFLT 274

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1499404721 170 RFSGHYSRSQMNSdqVEAMYKKLTAMTGVRMTPHRFRHTIASEMMRQpERNIHITKSLLNHSNITTTMEYIEPDYDVMRE 249
Cdd:PRK05084  275 KYRGKPNRISARA--IEKMVAKYSEAFGVRLTPHKLRHTLATRLYDA-TKDQVLVADQLGHTSTETTDLYTHIVNDEQKE 351


                  ....*.
gi 1499404721 250 VMNERG 255
Cdd:PRK05084  352 ALDRLE 357
Phage_integrase pfam00589
Phage integrase family; Members of this family cleave DNA substrates by a series of staggered ...
 91-244 8.36e-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: 80.44  E-value: 8.36e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1499404721  91 LAVFEMFYYTGIRLNALICLRYADIDMGERLIKVrgETEKTHREFMIPIPDRLMPHLKQLMDIaHRVGFSPTDQIFnVNR 170
Cdd:pfam00589  24 KALLELLYATGLRISELCSLRWSDIDFENGVIRV--HRGKGNKERTVPLSDAALELLKEWLSK-RLLEAPKSDYLF-ASK 99

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1499404721 171 FsghysRSQMNSDQVEAMYKKLTAMTGV--RMTPHRFRHTIASEMMRQpERNIHITKSLLNHSNITTTMEYIEPDY 244
Cdd:pfam00589 100 R-----GKPLSRQTVRKIFKRAGKEAGLelPLHPHMLRHSFATHLLEA-GVDLRVVQKLLGHSSISTTQIYTHVAD 169
recomb_XerD TIGR02225
tyrosine recombinase XerD; The phage integrase family describes a number of recombinases with ...
 92-236 6.17e-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: 59.90  E-value: 6.17e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1499404721  92 AVFEMFYYTGIRLNALICLRYADIDMGERLIKVRGeteKTHREFMIPIPDRLMPHLKQLMDIAhRVGFS-----PTDQIF 166
Cdd:TIGR02225 129 AMLELLYATGLRVSELVGLRLEDVNLDEGFVRVRG---KGNKERLVPLGEEAIEALERYLKEA-RPLLLkkkvkESDALF 204

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1499404721 167 nVNRFSGHYSRSQmnsdqVEAMYKKLTAMTGV--RMTPHRFRHTIASEMMrQPERNIHITKSLLNHSNITTT 236
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 ...
 90-240 4.91e-33

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


Pssm-ID: 271175 [Multi-domain]  Cd Length: 167  Bit Score: 122.20  E-value: 4.91e-33
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1499404721  90 WLAVFEMFYYTGIRLNALICLRYADIDMGERLIKVRGETEKTHREFMIPIPDRLMPHLKQLMDiAHRVGFSPTDQIFNVN 169
Cdd:cd00397    19 DRAILLLLLETGLRISELLALKVKDIDLDNGTIRVRGKKTKGGKERTVPLPKELAEELKEYLK-ERRDKRGPLLKSLYLN 97

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1499404721 170 RFSGHYSRSQMNSDQVEAMYKKLTAMTGVRMTPHRFRHTIASEMMRQPErNIHITKSLLNHSNITTTMEYI 240
Cdd:cd00397    98 KLFGTKLGERLSRRTLRRIFKKAGIEAGRKITPHSLRHTFATNLLENGV-DIKVVQKLLGHSSISTTQRYL 167
XerC COG4973
Site-specific recombinase XerC [Replication, recombination and repair];
17-251 3.66e-32

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


Pssm-ID: 443998 [Multi-domain]  Cd Length: 287  Bit Score: 123.53  E-value: 3.66e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1499404721  17 RRRAASPGYRYAMEHGLVElkVNPLKetRVIPTKRPK---KTINTDAIVRarnWLNILVQEERAtakraeitpaWFWLAV 93
Cdd:COG4973    74 RLSALRSFFNWAVREGLLE--ANPAA--GVKAPKAPRklpRALTVDELAQ---LLDALADDPLA----------VRDRAI 136

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1499404721  94 FEMFYYTGIRLNALICLRYADIDMGERLIKVRGeteKTHREFMIPIPDRLMPHLKQLMDIAHRVGFSPTDQIFNVNRfsG 173
Cdd:COG4973   137 VELLYSTGLRLGELVGLDWEDVDLDAGEVRVRG---KTGKSRTVPLGPKALAALREWLAVRPELAAPDEGALFPSRR--G 211

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1499404721 174 HysrsQMNSDQVEAMYKKLTAMTGV--RMTPHRFRHTIASeMMRQPERNIHITKSLLNHSNITTTMEYIEPDYDVMREVM 251
Cdd:COG4973   212 T----RLSPRNVQKRLRRLAKKAGLpkHVHPHDLRHSFAT-HLLESGGDLRAVQELLGHASISTTQIYTHLDFQHLAEVY 286
XerD COG4974
Site-specific recombinase XerD [Replication, recombination and repair];
25-253 1.89e-29

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


Pssm-ID: 443999 [Multi-domain]  Cd Length: 291  Bit Score: 116.25  E-value: 1.89e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1499404721  25 YRYAMEHGLVElkVNPLKETRVIPTKRPK-KTINTDAIVRARNWLNilvqEERATAKRaeitpawfWLAVFEMFYYTGIR 103
Cdd:COG4974    83 FRYAVREGLLE--DNPAAKVKLPKKPRKLpRVLTEEEIEALLEALD----TETPEGLR--------DRALLLLLYATGLR 148

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1499404721 104 LNALICLRYADIDMGERLIKVRGetEKTHREFMIPIPDRLMPHLKQLMDIAHRvgfSPTDQIFnVNRFSGHYSRSQMNSd 183
Cdd:COG4974   149 VSELLGLKWSDIDLDRGTIRVRR--GKGGKERTVPLSPEALEALREYLEERRP---RDSDYLF-PTRRGRPLSRRAIRK- 221

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1499404721 184 qveaMYKKLTAMTGV--RMTPHRFRHTIASEMMRQpERNIHITKSLLNHSNITTTMEYIEPDYDVMREVMNE 253
Cdd:COG4974   222 ----ILKRLAKRAGIpkRVTPHSLRHTFATHLLEA-GVDLRTVQELLGHSSISTTQIYTHVSDEELREAVEK 288
xerS PRK05084
site-specific tyrosine recombinase XerS; Reviewed
 91-255 7.64e-21

site-specific tyrosine recombinase XerS; Reviewed


Pssm-ID: 235339 [Multi-domain]  Cd Length: 357  Bit Score: 93.06  E-value: 7.64e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1499404721  91 LAVFEMFYYTGIRLNALICLRYADIDMGERLIKVrgeTEKTHREFMIPIPDRLMPHLKQLMDI-AHRVGFSPTDQIFNVN 169
Cdd:PRK05084  198 LAIIALILGSGLRVSELVNLDLSDLNLKQMTIDV---TRKGGKRDSVNIAPFALPYLEEYLKIrASRYKAEKQEKALFLT 274

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1499404721 170 RFSGHYSRSQMNSdqVEAMYKKLTAMTGVRMTPHRFRHTIASEMMRQpERNIHITKSLLNHSNITTTMEYIEPDYDVMRE 249
Cdd:PRK05084  275 KYRGKPNRISARA--IEKMVAKYSEAFGVRLTPHKLRHTLATRLYDA-TKDQVLVADQLGHTSTETTDLYTHIVNDEQKE 351


                  ....*.
gi 1499404721 250 VMNERG 255
Cdd:PRK05084  352 ALDRLE 357
Phage_integrase pfam00589
Phage integrase family; Members of this family cleave DNA substrates by a series of staggered ...
 91-244 8.36e-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: 80.44  E-value: 8.36e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1499404721  91 LAVFEMFYYTGIRLNALICLRYADIDMGERLIKVrgETEKTHREFMIPIPDRLMPHLKQLMDIaHRVGFSPTDQIFnVNR 170
Cdd:pfam00589  24 KALLELLYATGLRISELCSLRWSDIDFENGVIRV--HRGKGNKERTVPLSDAALELLKEWLSK-RLLEAPKSDYLF-ASK 99

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1499404721 171 FsghysRSQMNSDQVEAMYKKLTAMTGV--RMTPHRFRHTIASEMMRQpERNIHITKSLLNHSNITTTMEYIEPDY 244
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 ...
 92-236 8.45e-15

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: 71.77  E-value: 8.45e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1499404721  92 AVFEMFYYTGIRLNALICLRYADIDMGERLIKVRGeteKTHREFMIPIPDRLMPHLKQLMDIAHR--VGFSPTDQIFnVN 169
Cdd:cd00798    23 AILELLYASGLRVSELVGLDLSDVDLDEGLVRVTG---KGNKERLVPFGSYAVEALEEYLEERRPllLKKKPPDALF-LN 98

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1499404721 170 RFSGHYSRsqmnsDQVEAMYKKLTAMTGV--RMTPHRFRHTIASEMMrqpER--NIHITKSLLNHSNITTT 236
Cdd:cd00798    99 KRGKRLSR-----RGVWRILKKYAERAGLpkHVSPHTLRHSFATHLL---EGgaDLRVVQELLGHASLSTT 161
INT_IntI_C cd01193
Integron integrase and similar protiens, C-terminal catalytic domain; Integron integrases ...
 92-239 8.24e-13

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: 66.53  E-value: 8.24e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1499404721  92 AVFEMFYYTGIRLNALICLRYADIDMGERLIKVRGetEKTHREFMIPIPDRLMPHLKQLMDIAHRVG--FSPTDQIFNVN 169
Cdd:cd01193    25 LILSLLYGAGLRISELLRLRVKDIDFERGVIRVRQ--GKGGKDRVVPLPEKLLEPLRRYLKSARPKEelDPAEGRAGVLD 102

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1499404721 170 RFSGHYSRSQMNSDQVEAMYKKLTAMTGV--RMTPHRFRHTIASEMMRQpERNIHITKSLLNHSNITTTMEY 239
Cdd:cd01193   103 PRTGVERRHHISETTVQRALKKAVEQAGItkRVTPHTLRHSFATHLLEA-GTDIRTIQELLGHSDLSTTMIY 173
xerC PRK00236
site-specific tyrosine recombinase XerC; Reviewed
 25-236 3.65e-12

site-specific tyrosine recombinase XerC; Reviewed


Pssm-ID: 234698 [Multi-domain]  Cd Length: 297  Bit Score: 66.72  E-value: 3.65e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1499404721  25 YRYAMEHGLveLKVNPLKETRViPtKRPK---KTINTDAIVRArnwLNILVQEEratakraeitpaWFWL---AVFEMFY 98
Cdd:PRK00236   86 YRWLVRRGL--LKANPAAGLRA-P-KIPKrlpKPLDVDQAKRL---LDAIDEDD------------PLALrdrAILELLY 146

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1499404721  99 YTGIRLNALICLRYADIDMGERLIKVRGeteKTHREFMIPipdrLMPHLKQLMD--IAHRVGFSPTDQ-IFnVNRFSGHy 175
Cdd:PRK00236  147 GSGLRLSELVGLDIDDLDLASGTLRVLG---KGNKERTVP----LGRAAREALEayLALRPLFLPDDDaLF-LGARGGR- 217

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1499404721 176 srsqMNSDQVEAMYKKLTAMTGV--RMTPHRFRHTIASEMMrqpER--NIHITKSLLNHSNITTT 236
Cdd:PRK00236  218 ----LSPRVVQRRVKKLGKKAGLpsHITPHKLRHSFATHLL---ESggDLRAVQELLGHASLSTT 275
INT_RitA_C_like cd01188
C-terminal catalytic domain of recombinase RitA, a component of the recombinase trio; ...
 91-250 4.03e-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: 64.57  E-value: 4.03e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1499404721  91 LAVFEMFYYTGIRLNALICLRYADIDMGERLIKVRGEteKTHREFMIPIPDrlmPHLKQLMD-IAHRVGFSPTDQIF-NV 168
Cdd:cd01188    23 YAILLLLARLGLRAGDVAGLRLDDIDWRSGTITVRQK--KTGRPVELPLTE---PVGEALADyLRDGRPRTDSREVFlRA 97

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1499404721 169 NRFSGHYSrsqmNSDQVEAMYKKLTAMTGV---RMTPHRFRHTIASEMMRQpERNIHITKSLLNHSNITTTMEYIEPDYD 245
Cdd:cd01188    98 RAPYRPLS----STSQISSIVRRYLRKAGIepsHRGTHSLRHSLATRMLRA-GTSLKVIADLLGHRSIETTAIYAKIDVD 172


                  ....*
gi 1499404721 246 VMREV 250
Cdd:cd01188   173 DLREV 177
FimB COG0582
Integrase/recombinase, includes phage integrase [Replication, recombination and repair, ...
 25-253 6.61e-12

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


Pssm-ID: 440347 [Multi-domain]  Cd Length: 391  Bit Score: 66.60  E-value: 6.61e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1499404721  25 YRYAMEHGLVElkVNPLKETRVIPTKRPKKtiNTDAIVRARnwLNILVQEERATAKRAEITPAWFWLAvfemfyYTGIRL 104
Cdd:COG0582   174 FRYAVARGLIE--RNPAADLKGALPKPKVK--HHPALTPEE--LPELLRALDAYRGSPVTRLALRLLL------LTGVRP 241

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1499404721 105 NALICLRYADIDMGERLIKVRGETEKTHREFMIPIPDRLMPHLKQLMDIAHRVGFsptdqifnVnrFSGHYSRSQMNSDQ 184
Cdd:COG0582   242 GELRGARWSEIDLEAALWTIPAERMKTRRPHIVPLSRQALEILKELKPLTGDSEY--------V--FPSRRGPKKPMSEN 311

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1499404721 185 veAMYKKLTAMTGVRMTPHRFRHTIASEMMRQPErNIHITKSLLNHSNITTTME-YIEPDY-DVMREVMNE 253
Cdd:COG0582   312 --TLNKALRRMGYGRFTPHGFRHTASTLLNEAGF-PPDVIERQLAHKDGNKVRAaYNRADYlEERREMMQW 379
INTN1_C_like cd01185
Integrase IntN1 of Bacteroides mobilizable transposon NBU1 and similar proteins, C-terminal ...
 93-241 1.24e-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: 62.67  E-value: 1.24e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1499404721  93 VFEMFYYTGIRLNALICLRYADIDMGERLIKVRGETEKTHREFMIPIPdrlmPHLKQLmdIAHRVGFSPTDQIFNVnrfs 172
Cdd:cd01185    23 MFLFSCYTGLRFSDLKNLTWKNIVEASGRTWIRYRRKKTGKPVTVPLL----PVAREI--LEKYKDDRSEGKLFPV---- 92

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1499404721 173 ghYSRSQMNsdqvEAMyKKLTAMTGVR--MTPHRFRHTIASEMMRQpERNIHITKSLLNHSNITTTMEYIE 241
Cdd:cd01185    93 --LSNQKIN----RYL-KEIAKIAGIDkhLTFHVARHTFATLLLLK-GVDIETISKLLGHSSIKTTQIYAK 155
INT_Rci_Hp1_C cd00796
Shufflon-specific DNA recombinase Rci and Bacteriophage Hp1_like integrase, C-terminal ...
 86-239 8.87e-11

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: 60.03  E-value: 8.87e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1499404721  86 PAWFWLAVFEmfYYTGIRLNALICLRYADIDMgERLIKVRGETeKTHREFMIPIPDRLMPHLKQLMDIAHRVGFSPTDQI 165
Cdd:cd00796    23 PHLRLIVLLA--LYTGARRGEILSLRWDDIDL-EVGLIVLPET-KNGKPRTVPLSDEAIAILKELKRKRGKDGFFVDGRF 98

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1499404721 166 FnvnrfsgHYSRSQMNSDqVEAMYKKLtAMTGVRmtPHRFRHTIASEMMRQPERNIHITKsLLNHSNITTTMEY 239
Cdd:cd00796    99 F-------GIPIASLRRA-FKKARKRA-GLEDLR--FHDLRHTFASRLVQAGVPIKTVAK-ILGHSSIKMTMRY 160
INT_tnpA_C_Tn554 cd01186
Putative Transposase A from transposon Tn554, C-terminal catalytic domain; This family ...
 93-250 9.55e-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: 60.51  E-value: 9.55e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1499404721  93 VFEMFYYTGIRLNALICLRYADIDMGERLIKVR-------GETEKTHREFMIPIPDRLMphlKQLMD-IAHRVGFSPTDQ 164
Cdd:cd01186    22 LLALLYETGLRIGEALGLRIEDIDMADNQIELVpredntnEARAKSMRERRIPVSQDLI---DLYADyLTYIYCEEAEFS 98

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1499404721 165 IFNVNRFSGHYSRSQMNSDQVEAMYKKLTAMTGVRMTPHRFRHTIASEMMRQpERNIHITKSLLNHSNITTTME-YIEPD 243
Cdd:cd01186    99 ITVFVNVKGGNQGKAMNYSDVYDLVRRLKKRTGIDFTPHMFRHTHATALIRA-GWSIEVVARRLGHAHVQTTLNtYGHLS 177


                  ....*..
gi 1499404721 244 YDVMREV 250
Cdd:cd01186   178 EEDIRRE 184
INT_ICEBs1_C_like cd01189
C-terminal catalytic domain of integrases from bacterial phages and conjugate transposons; ...
 90-239 2.82e-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: 58.34  E-value: 2.82e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1499404721  90 WLAVFEMFYYTGIRLNALICLRYADIDMGERLIKVRGE---------------TEKTHREfmIPIPDRLMPHLKQLMdia 154
Cdd:cd01189    18 YYLLFLLALLTGLRRGELLALTWSDIDFENGTIRINRTlvrkkkggyvikppkTKSSIRT--IPLPDELIELLKELK--- 92

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1499404721 155 hrvgfsptdqifnvnrfsghysrsqmnsdqveaMYKKLTAMTGV-RMTPHRFRHTIASEMMRQPErNIHITKSLLNHSNI 233
Cdd:cd01189    93 ---------------------------------AFKKLLKKAGLpRITPHDLRHTFASLLLEAGV-PLKVIAERLGHSDI 138


                  ....*.
gi 1499404721 234 TTTMEY 239
Cdd:cd01189   139 STTLDV 144
recomb_XerD TIGR02225
tyrosine recombinase XerD; The phage integrase family describes a number of recombinases with ...
 92-236 6.17e-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: 59.90  E-value: 6.17e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1499404721  92 AVFEMFYYTGIRLNALICLRYADIDMGERLIKVRGeteKTHREFMIPIPDRLMPHLKQLMDIAhRVGFS-----PTDQIF 166
Cdd:TIGR02225 129 AMLELLYATGLRVSELVGLRLEDVNLDEGFVRVRG---KGNKERLVPLGEEAIEALERYLKEA-RPLLLkkkvkESDALF 204

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1499404721 167 nVNRFSGHYSRSQmnsdqVEAMYKKLTAMTGV--RMTPHRFRHTIASEMMrQPERNIHITKSLLNHSNITTT 236
Cdd:TIGR02225 205 -LNRRGGPLSRQG-----VWKILKEYAKRAGIekPISPHTLRHSFATHLL-ENGADLRVVQELLGHADISTT 269
INT_RitC_C_like cd01182
C-terminal catalytic domain of recombinase RitC, a component of the recombinase trio; ...
 98-252 3.04e-09

C-terminal catalytic domain of recombinase RitC, a component of the recombinase trio; Recombinases belonging to the RitA (also known as pAE1 due to its presence in the deletion prone region of plasmid pAE1 of Alcaligenes eutrophus H1), RitB, and RitC families are associated in a complex referred to as a Recombinase in Trio (RIT) element. These RIT elements consist of three adjacent and unidirectional overlapping genes, one from each family (ritABC in order of transcription). All three integrases contain a catalytic motif, suggesting that they are all active enzymes. However, their specific roles are not yet fully understood. All three families belong to the superfamily of DNA breaking-rejoining enzymes, which share the same fold in their catalytic domain and the overall reaction mechanism.


Pssm-ID: 271183 [Multi-domain]  Cd Length: 186  Bit Score: 56.13  E-value: 3.04e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1499404721  98 YYTGIRLNALICLRYADIDMGE-RLIKVRGeteKTHREFMIPIPDRLMPHLKQLMDIAHRvgfSPTDQIFNVNRFSGHys 176
Cdd:cd01182    31 YDTGARVQELADLTIRDLRLDDpATVRLHG---KGRKERTVPLWKETVAALKAYLQEFHL---TPDPKQLFPLFPNRR-- 102

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1499404721 177 RSQMNSDQVEAMYKK----LTAMTGV---RMTPHRFRHTIASEMMrQPERNIHITKSLLNHSNITTTMEYIEPDYDVMRE 249
Cdd:cd01182   103 GQPLTRDGVAYILNKyvalASNRCPSlpkRITPHTLRHTKAMHLL-QAGVDLTVIRDWLGHESVETTQIYAEADLEMKRE 181


                  ...
gi 1499404721 250 VMN 252
Cdd:cd01182   182 ALE 184
INT_P4_C cd00801
Bacteriophage P4 integrase, C-terminal catalytic domain; P4-like integrases are found in ...
 99-253 1.28e-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: 51.50  E-value: 1.28e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1499404721  99 YTGIRLNALICLRYADIDMGERLIKVRGETEKTHREFMIPIPDRLMPHLKQLMDIAHRVGFsptdqIFnvnrFSGHYSRS 178
Cdd:cd00801    30 LTGQRIGELARARWSEIDLEEKTWTIPAERTKNKRPHRVPLSDQALEILEELKEFTGDSGY-----LF----PSRRKKKK 100

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1499404721 179 QMNSDQVEAMYKKLTAmTGVRMTPHRFRHTIASEMMRQpERNIHITKSLLNHSNITTTME-YIEPDY-DVMREVMNE 253
Cdd:cd00801   101 PISENTINKALKRLGY-KGKEFTPHDLRRTFSTLLNEL-GIDPEVIERLLNHVLGGVVRAaYNRYDYlEERREALQA 175
INT_RitB_C_like cd00797
C-terminal catalytic domain of recombinase RitB, a component of the recombinase trio; ...
 86-251 1.45e-05

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: 45.76  E-value: 1.45e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1499404721  86 PAWFWLAVFEMFYYTGIRLNALICLRYADIDMGERLIKVRGetEKTHREFMIPIPDRLMPHLKQLMDIAHRVGFSPTDQI 165
Cdd:cd00797    23 RPLTYATLFGLLYATGLRVGEALRLRLEDVDLDSGILTIRQ--TKFGKSRLVPLHPSTVGALRDYLARRDRLLPSPSSSY 100

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1499404721 166 FNVNRFSGHYSRSqmnsdQVEAMYKKLTAMTGVRMTP-------HRFRHTIA-SEMMR------QPERNIHITKSLLNHS 231
Cdd:cd00797   101 FFVSQQGGRLTGG-----GVYRVFRRLLRRIGLRGAGdgrgprlHDLRHTFAvNRLTRwyregaDVERKLPVLSTYLGHV 175

                         170       180
                  ....*....|....*....|
gi 1499404721 232 NITTTMEYIEPDYDVMREVM 251
Cdd:cd00797   176 NVTDTYWYLTATPELMELAS 195
INT_C_like_5 cd01195
Uncharacterized site-specific tyrosine recombinase, C-terminal catalytic domain; Tyrosine ...
 91-240 1.90e-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: 1.90e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1499404721  91 LAVFEMFYYTGIRLNALICLRYADIDMGERLIKVRGETEKTHREFMIPipdrlmPHLKQLMDiAHRVGFSPTDQIFNVNR 170
Cdd:cd01195    23 EALVRLLLDNALRRSEAVALDVEDLEKEHRRLRILGKGKKQREVVTLP------PTTREALA-AWLAARGEAEGPLFVSL 95

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1499404721 171 FSGHYSRsQMNSDQVEAMYKKLTAMTGV--RMTPHRFRHTIASEMMRQPERNIHITKSLLNHSNITTTMEYI 240
Cdd:cd01195    96 DRASRGR-RLSPQAVYRIVRRLAERIGLgkRLSPHGLRHSAITLALDAGAGLIRKVQDFSRHADLRTLQVYD 166
INT_tnpB_C_Tn554 cd01187
Putative Transposase B from transposon Tn554, C-terminal catalytic domain; This family ...
 91-240 2.92e-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: 43.57  E-value: 2.92e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1499404721  91 LAVFEMFYYTGIRLNALICLRY----ADIDMGERLIKVRGETEKTHREFMIPIPDRLmphlkqlmdiahrvgfspTDQIF 166
Cdd:cd01187    16 IPVVQAAVFTGARASELATLKFgclhAQTSDDGTFLYWLKWENKGGKQLDIPISKKV------------------AELIK 77

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1499404721 167 NVNRFSGHYSRSQMNSDQVEAMYkkltamtgvRMTPHRFRHTIASEMMRQPERnIHITKSLLNHSNITTTMEYI 240
Cdd:cd01187    78 TINWTLNELSELKNISDDHGERF---------RFHTHRFRHTVATRLANSGMG-ILVLQQLLGHSSPEMTLRYA 141
PRK15417 PRK15417
integron integrase;
95-239 3.87e-05

integron integrase;


Pssm-ID: 185315 [Multi-domain]  Cd Length: 337  Bit Score: 45.42  E-value: 3.87e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1499404721  95 EMFYYTGIRLNALICLRYADIDMGERLIKVRGETEKTHREFMIPipDRLMPHLKQLMDIAH------------------- 155
Cdd:PRK15417  138 QLLYGTGMRISEGLQLRVKDLDFDHGTIIVREGKGSKDRALMLP--ESLAPSLREQLSRARawwlkdqaegrsgvalpda 215

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1499404721 156 ------RVGFS-PTDQIF-----NVNRFSGHYSRSQMNSDQVEAMYKKLTAMTGVR--MTPHRFRHTIASEMMRQpERNI 221
Cdd:PRK15417  216 lerkypRAGHSwPWFWVFaqhthSTDPRSGVVRRHHMYDQTFQRAFKRAVEQAGITkpATPHTLRHSFATALLRS-GYDI 294

                         170
                  ....*....|....*...
gi 1499404721 222 HITKSLLNHSNITTTMEY 239
Cdd:PRK15417  295 RTVQDLLGHSDVSTTMIY 312
INT_C_like_3 cd01192
Uncharacterized site-specific tyrosine recombinase, C-terminal catalytic domain; Tyrosine ...
 100-240 5.42e-05

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


Pssm-ID: 271192 [Multi-domain]  Cd Length: 178  Bit Score: 43.82  E-value: 5.42e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1499404721 100 TGIRLNALICLRYADIDMGERL-IKVRgeteKTHREFMIPIPDRLmphLKQLMDIAHRVGFSPTDQIFN--VNRFSGHYS 176
Cdd:cd01192    36 TGLRISDLLSLKVEDVTNKDKLsIKEQ----KTGKQKTFPLNPTL---VKALKEYIDDLDLKRNDYLFKslKQGPEKPIS 108

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1499404721 177 RSQMNSdqveaMYKKLTAMTGVR--MTPHRFRHTIASeMMRQPERNIHITKSLLNHSNITTTMEYI 240
Cdd:cd01192   109 RKQAYK-----ILKKAADDLGLNynIGTHSLRKTFGY-HVYKQGKDIELLMKLLNHSSPSITLRYL 168
INT_C_like_4 cd01194
Uncharacterized site-specific tyrosine recombinase, C-terminal catalytic domain; Tyrosine ...
 92-239 6.27e-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: 43.52  E-value: 6.27e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1499404721  92 AVFEMFYYTGIRLNALICLRYADID--MGERLIKVRGETEKTHREFMIPIPDRLMPHLKQLMDiahRVGFSPTDQIFNvn 169
Cdd:cd01194    26 AIISLMVTEGLRTVEIVRADVGDLRqeGEGTILYVQGKGKTSKDDFVYLRPDVLKALQAYLKA---RGKLDFEEPLFT-- 100

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1499404721 170 RFSGHYSRSQMNSDQVEAMYKKLTAMTGV---RMTPHRFRHTIASeMMRQPERNIHITKSLLNHSNITTTMEY 239
Cdd:cd01194   101 SLSNNSKGQRLTTRSIRRIIKKYLRKAGLdddRLTAHSLRHTAGT-LALKAGKSLREVQQLLRHSDPNTTMIY 172
INT_Lambda_C cd00800
C-terminal catalytic domain of Lambda integrase, a tyrosine-based site-specific recombinase; ...
 86-241 2.95e-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: 41.17  E-value: 2.95e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1499404721  86 PAWFWLAvFEMFYYTGIRLNALICLRYADIDMGERLIkvrgETEKTHREFMIPIPDRLMPHLKQLMDIAHRVGFSptdqI 165
Cdd:cd00800    11 PPLLRLA-MELALLTGQRQGDLLRLKWSDITDGGLLV----EQSKTGKKLLIPWTPSLRALVDRIRALPRKRSEY----L 81

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1499404721 166 FNvNRFSGHYSRSQMNSDQVEAMYKKLTAMTGVRMTPHRFRHTIASEMMRQpeRNIHITKSLLNHSNITTTMEYIE 241
Cdd:cd00800    82 IN-SRKGGPLSYDTLKSAWRRARKAAGLKGETEGFTFHDLRAKAATDYAEQ--GGSTDAQALLGHKSDAMTERYTR 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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