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Conserved domains on  [gi|1877302362|dbj|BBQ60651|]
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hypothetical protein WP2S18E08_06340 [Escherichia coli]

Protein Classification

site-specific integrase( domain architecture ID 10092426)

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
INT_P4_C cd00801
Bacteriophage P4 integrase, C-terminal catalytic domain; P4-like integrases are found in ...
 48-234 1.33e-54

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: 173.61  E-value: 1.33e-54
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1877302362  48 TLEELRFLMEHFaEATNVGLLMQHLIRFCIYTGgQRPFEMIASQWCDVDFQQKTLLVTADVSKNKREHLIPLTESALQEL 127
Cdd:cd00801     1 SPDELPELWRAL-DTANLSPPTKLALRLLLLTG-QRIGELARARWSEIDLEEKTWTIPAERTKNKRPHRVPLSDQALEIL 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1877302362 128 SCVQELTKEksSPYIFPLSTNGKRPVRTDSLARAImyfRAFNPDFKIFTARDLRRTCKTLMGEAGISKEIRDRIQNHALN 207
Cdd:cd00801    79 EELKEFTGD--SGYLFPSRRKKKKPISENTINKAL---KRLGYKGKEFTPHDLRRTFSTLLNELGIDPEVIERLLNHVLG 153

                         170       180
                  ....*....|....*....|....*..
gi 1877302362 208 DVSSKHYDRYDYLPEKRRALEIWEDRV 234
Cdd:cd00801   154 GVVRAAYNRYDYLEERREALQAWADYL 180
 
Name Accession Description Interval E-value
INT_P4_C cd00801
Bacteriophage P4 integrase, C-terminal catalytic domain; P4-like integrases are found in ...
 48-234 1.33e-54

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: 173.61  E-value: 1.33e-54
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1877302362  48 TLEELRFLMEHFaEATNVGLLMQHLIRFCIYTGgQRPFEMIASQWCDVDFQQKTLLVTADVSKNKREHLIPLTESALQEL 127
Cdd:cd00801     1 SPDELPELWRAL-DTANLSPPTKLALRLLLLTG-QRIGELARARWSEIDLEEKTWTIPAERTKNKRPHRVPLSDQALEIL 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1877302362 128 SCVQELTKEksSPYIFPLSTNGKRPVRTDSLARAImyfRAFNPDFKIFTARDLRRTCKTLMGEAGISKEIRDRIQNHALN 207
Cdd:cd00801    79 EELKEFTGD--SGYLFPSRRKKKKPISENTINKAL---KRLGYKGKEFTPHDLRRTFSTLLNELGIDPEVIERLLNHVLG 153

                         170       180
                  ....*....|....*....|....*..
gi 1877302362 208 DVSSKHYDRYDYLPEKRRALEIWEDRV 234
Cdd:cd00801   154 GVVRAAYNRYDYLEERREALQAWADYL 180
FimB COG0582
Integrase/recombinase, includes phage integrase [Replication, recombination and repair, ...
 25-234 4.67e-44

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


Pssm-ID: 440347 [Multi-domain]  Cd Length: 391  Bit Score: 152.89  E-value: 4.67e-44
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1877302362  25 LEANPVSVIPKQSSAEKVG-DTWLTLEELRFLMEHFaEATNVGLLMQHLIRFCIYTGgQRPFEMIASQWCDVDFQQKTLL 103
Cdd:COG0582   183 IERNPAADLKGALPKPKVKhHPALTPEELPELLRAL-DAYRGSPVTRLALRLLLLTG-VRPGELRGARWSEIDLEAALWT 260

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1877302362 104 VTADVSKNKREHLIPLTESALQELSCVQELTKekSSPYIFPLSTNGKRPVRTDSLARAI--MyfrafnpDFKIFTARDLR 181
Cdd:COG0582   261 IPAERMKTRRPHIVPLSRQALEILKELKPLTG--DSEYVFPSRRGPKKPMSENTLNKALrrM-------GYGRFTPHGFR 331

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1877302362 182 RTCKTLMGEAGISKEIRDRIQNHALNDVSSKHYDRYDYLPEKRRALEIWEDRV 234
Cdd:COG0582   332 HTASTLLNEAGFPPDVIERQLAHKDGNKVRAAYNRADYLEERREMMQWWADYL 384
PRK09692 PRK09692
integrase; Provisional
 83-235 8.10e-13

integrase; Provisional


Pssm-ID: 170049 [Multi-domain]  Cd Length: 413  Bit Score: 67.36  E-value: 8.10e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1877302362  83 RPFEMIASQWCDVDFQQKTLLVTADVSKNKREHLIPLTESALQELSCVQELTKEKSspYIFPLSTNGKRPVRTDSLARAI 162
Cdd:PRK09692  248 RPAEAAEARWEEIDIEAQEWKIPAARMKMNRDHTVPLSDEALAILEMMKPLSGNRE--FIFPSRIKPNQPMNSQTVNAAL 325

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1877302362 163 MyfRA-FNpdfKIFTARDLRRTCKTLMGEAGISKEIRDRIQNHALNDVSSKHYDRYDYLPEKRRALEIWEDRVN 235
Cdd:PRK09692  326 K--RAgLG---GVLVSHGLRSIASTALNEQGFPPDVIEAALAHVDKNEVRRAYNRSDYLEQRRPMMQWWADFVM 394
Phage_integrase pfam00589
Phage integrase family; Members of this family cleave DNA substrates by a series of staggered ...
 46-194 5.07e-10

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: 56.94  E-value: 5.07e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1877302362  46 WLTLEELRFLMeHFAEATNVGLLMQHLIRFCIYTGgQRPFEMIASQWCDVDFQQKTLLVtaDVSKNKREHLIPLTE---S 122
Cdd:pfam00589   1 RLTEDEVERLL-DAAETGPLSIRDKALLELLYATG-LRISELCSLRWSDIDFENGVIRV--HRGKGNKERTVPLSDaalE 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1877302362 123 ALQELSCVQELTKEKSSpYIFPlSTNGKRpvrtdslaraiMYFRAFNPDFK----------IFTARDLRRTCKTLMGEAG 192
Cdd:pfam00589  77 LLKEWLSKRLLEAPKSD-YLFA-SKRGKP-----------LSRQTVRKIFKragkeaglelPLHPHMLRHSFATHLLEAG 143


                  ..
gi 1877302362 193 IS 194
Cdd:pfam00589 144 VD 145
 
Name Accession Description Interval E-value
INT_P4_C cd00801
Bacteriophage P4 integrase, C-terminal catalytic domain; P4-like integrases are found in ...
 48-234 1.33e-54

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: 173.61  E-value: 1.33e-54
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1877302362  48 TLEELRFLMEHFaEATNVGLLMQHLIRFCIYTGgQRPFEMIASQWCDVDFQQKTLLVTADVSKNKREHLIPLTESALQEL 127
Cdd:cd00801     1 SPDELPELWRAL-DTANLSPPTKLALRLLLLTG-QRIGELARARWSEIDLEEKTWTIPAERTKNKRPHRVPLSDQALEIL 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1877302362 128 SCVQELTKEksSPYIFPLSTNGKRPVRTDSLARAImyfRAFNPDFKIFTARDLRRTCKTLMGEAGISKEIRDRIQNHALN 207
Cdd:cd00801    79 EELKEFTGD--SGYLFPSRRKKKKPISENTINKAL---KRLGYKGKEFTPHDLRRTFSTLLNELGIDPEVIERLLNHVLG 153

                         170       180
                  ....*....|....*....|....*..
gi 1877302362 208 DVSSKHYDRYDYLPEKRRALEIWEDRV 234
Cdd:cd00801   154 GVVRAAYNRYDYLEERREALQAWADYL 180
FimB COG0582
Integrase/recombinase, includes phage integrase [Replication, recombination and repair, ...
 25-234 4.67e-44

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


Pssm-ID: 440347 [Multi-domain]  Cd Length: 391  Bit Score: 152.89  E-value: 4.67e-44
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1877302362  25 LEANPVSVIPKQSSAEKVG-DTWLTLEELRFLMEHFaEATNVGLLMQHLIRFCIYTGgQRPFEMIASQWCDVDFQQKTLL 103
Cdd:COG0582   183 IERNPAADLKGALPKPKVKhHPALTPEELPELLRAL-DAYRGSPVTRLALRLLLLTG-VRPGELRGARWSEIDLEAALWT 260

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1877302362 104 VTADVSKNKREHLIPLTESALQELSCVQELTKekSSPYIFPLSTNGKRPVRTDSLARAI--MyfrafnpDFKIFTARDLR 181
Cdd:COG0582   261 IPAERMKTRRPHIVPLSRQALEILKELKPLTG--DSEYVFPSRRGPKKPMSENTLNKALrrM-------GYGRFTPHGFR 331

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1877302362 182 RTCKTLMGEAGISKEIRDRIQNHALNDVSSKHYDRYDYLPEKRRALEIWEDRV 234
Cdd:COG0582   332 HTASTLLNEAGFPPDVIERQLAHKDGNKVRAAYNRADYLEERREMMQWWADYL 384
XerD COG4974
Site-specific recombinase XerD [Replication, recombination and repair];
25-226 8.19e-21

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


Pssm-ID: 443999 [Multi-domain]  Cd Length: 291  Bit Score: 88.90  E-value: 8.19e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1877302362  25 LEANPVSVIPKQSSAEKVgDTWLTLEELRFLMEHFAEATNVGLLMQHLIRFCIYTGgQRPFEMIASQWCDVDFQQKTLLV 104
Cdd:COG4974    92 LEDNPAAKVKLPKKPRKL-PRVLTEEEIEALLEALDTETPEGLRDRALLLLLYATG-LRVSELLGLKWSDIDLDRGTIRV 169

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1877302362 105 TAdvSKNKREHLIPLTESALQELSCVQELTKEKSSPYIFPlSTNGkRPVRTDSLARAI-MYFRAFNPDFKIfTARDLRRT 183
Cdd:COG4974   170 RR--GKGGKERTVPLSPEALEALREYLEERRPRDSDYLFP-TRRG-RPLSRRAIRKILkRLAKRAGIPKRV-TPHSLRHT 244

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....
gi 1877302362 184 CKTLMGEAGISKEIRDRIQNHAlnDVSS-KHYDRYDylPEKRRA 226
Cdd:COG4974   245 FATHLLEAGVDLRTVQELLGHS--SISTtQIYTHVS--DEELRE 284
XerC COG4973
Site-specific recombinase XerC [Replication, recombination and repair];
25-219 1.58e-13

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


Pssm-ID: 443998 [Multi-domain]  Cd Length: 287  Bit Score: 68.45  E-value: 1.58e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1877302362  25 LEANPVSVI--PKQssaEKVGDTWLTLEELRFLMEHFAEATnVGLLMQHLIRFCIYTGgQRPFEMIASQWCDVDFQQKTL 102
Cdd:COG4973    91 LEANPAAGVkaPKA---PRKLPRALTVDELAQLLDALADDP-LAVRDRAIVELLYSTG-LRLGELVGLDWEDVDLDAGEV 165

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1877302362 103 LVTAdvsKNKREHLIPLTESALQELSC---VQELTKEKSSPYIFPlSTNGKRpVRTDSLARAI-MYFRAFNPDfKIFTAR 178
Cdd:COG4973   166 RVRG---KTGKSRTVPLGPKALAALREwlaVRPELAAPDEGALFP-SRRGTR-LSPRNVQKRLrRLAKKAGLP-KHVHPH 239

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|..
gi 1877302362 179 DLRRTCKTLMGEAGISKEIRDRIQNHAlnDVSS-KHYDRYDY 219
Cdd:COG4973   240 DLRHSFATHLLESGGDLRAVQELLGHA--SISTtQIYTHLDF 279
INT_Rci_Hp1_C cd00796
Shufflon-specific DNA recombinase Rci and Bacteriophage Hp1_like integrase, C-terminal ...
 44-217 7.44e-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: 64.66  E-value: 7.44e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1877302362  44 DTWLTLEELRFLMEHFAEATNvgllmQHL---IRFCIYTGgQRPFEMIASQWCDVDFQQKTllVTADVSKNKREHLIPLT 120
Cdd:cd00796     2 DRFLTEDEEARLLAALEESTN-----PHLrliVLLALYTG-ARRGEILSLRWDDIDLEVGL--IVLPETKNGKPRTVPLS 73

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1877302362 121 ESALQELscvQELTKEKSSPYIFPlsTNGKRPVRTDSLARAIMyfRAFN----PDFKIftaRDLRRTCKTLMGEAGIS-K 195
Cdd:cd00796    74 DEAIAIL---KELKRKRGKDGFFV--DGRFFGIPIASLRRAFK--KARKraglEDLRF---HDLRHTFASRLVQAGVPiK 143

                         170       180
                  ....*....|....*....|..
gi 1877302362 196 EIRdRIQNHAlndvSSKHYDRY 217
Cdd:cd00796   144 TVA-KILGHS----SIKMTMRY 160
PRK09692 PRK09692
integrase; Provisional
 83-235 8.10e-13

integrase; Provisional


Pssm-ID: 170049 [Multi-domain]  Cd Length: 413  Bit Score: 67.36  E-value: 8.10e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1877302362  83 RPFEMIASQWCDVDFQQKTLLVTADVSKNKREHLIPLTESALQELSCVQELTKEKSspYIFPLSTNGKRPVRTDSLARAI 162
Cdd:PRK09692  248 RPAEAAEARWEEIDIEAQEWKIPAARMKMNRDHTVPLSDEALAILEMMKPLSGNRE--FIFPSRIKPNQPMNSQTVNAAL 325

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1877302362 163 MyfRA-FNpdfKIFTARDLRRTCKTLMGEAGISKEIRDRIQNHALNDVSSKHYDRYDYLPEKRRALEIWEDRVN 235
Cdd:PRK09692  326 K--RAgLG---GVLVSHGLRSIASTALNEQGFPPDVIEAALAHVDKNEVRRAYNRSDYLEQRRPMMQWWADFVM 394
Phage_integrase pfam00589
Phage integrase family; Members of this family cleave DNA substrates by a series of staggered ...
 46-194 5.07e-10

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: 56.94  E-value: 5.07e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1877302362  46 WLTLEELRFLMeHFAEATNVGLLMQHLIRFCIYTGgQRPFEMIASQWCDVDFQQKTLLVtaDVSKNKREHLIPLTE---S 122
Cdd:pfam00589   1 RLTEDEVERLL-DAAETGPLSIRDKALLELLYATG-LRISELCSLRWSDIDFENGVIRV--HRGKGNKERTVPLSDaalE 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1877302362 123 ALQELSCVQELTKEKSSpYIFPlSTNGKRpvrtdslaraiMYFRAFNPDFK----------IFTARDLRRTCKTLMGEAG 192
Cdd:pfam00589  77 LLKEWLSKRLLEAPKSD-YLFA-SKRGKP-----------LSRQTVRKIFKragkeaglelPLHPHMLRHSFATHLLEAG 143


                  ..
gi 1877302362 193 IS 194
Cdd:pfam00589 144 VD 145
DNA_BRE_C cd00397
DNA breaking-rejoining enzymes, C-terminal catalytic domain; The DNA breaking-rejoining enzyme ...
 51-218 8.19e-10

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: 56.33  E-value: 8.19e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1877302362  51 ELRFLMEHFAEATNVGLLMQHLIRFCIYTGGqRPFEMIASQWCDVDFQQKTLLVTADVSKNKREHLIPLTESALQELscv 130
Cdd:cd00397     1 ELEKLLDAIDEDKKIDLRDRAILLLLLETGL-RISELLALKVKDIDLDNGTIRVRGKKTKGGKERTVPLPKELAEEL--- 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1877302362 131 QELTKE---------KSSPYIFPLSTNGKRPVRTDSLARAIMyfRAFNPDFKIFTARDLRRTCKTLMGEAGIS-KEIRDR 200
Cdd:cd00397    77 KEYLKErrdkrgpllKSLYLNKLFGTKLGERLSRRTLRRIFK--KAGIEAGRKITPHSLRHTFATNLLENGVDiKVVQKL 154

                         170
                  ....*....|....*...
gi 1877302362 201 iqnhaLNDVSSKHYDRYD 218
Cdd:cd00397   155 -----LGHSSISTTQRYL 167
INT_ICEBs1_C_like cd01189
C-terminal catalytic domain of integrases from bacterial phages and conjugate transposons; ...
 49-200 1.22e-06

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: 46.78  E-value: 1.22e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1877302362  49 LEELRFLMEHFAEAtnvGLLMQHLIRFCIYTGgQRPFEMIASQWCDVDFQQKTLLVTADVSKNKREHLipltesalqels 128
Cdd:cd01189     1 PEELKKLLEALKKR---GDRYYLLFLLALLTG-LRRGELLALTWSDIDFENGTIRINRTLVRKKKGGY------------ 64

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1877302362 129 cVQELTKEKSSPYIFPLStngkrpvrtDSLARAIMYFRAFNPDFK-----IFTARDLRRTCKTLMGEAGIS-KEIRDR 200
Cdd:cd01189    65 -VIKPPKTKSSIRTIPLP---------DELIELLKELKAFKKLLKkaglpRITPHDLRHTFASLLLEAGVPlKVIAER 132
Phage_integr_3 pfam16795
Archaeal phage integrase; catalyzes cleavage and ligation of DNA.
 135-214 2.03e-03

Archaeal phage integrase; catalyzes cleavage and ligation of DNA.


Pssm-ID: 407057  Cd Length: 162  Bit Score: 37.75  E-value: 2.03e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1877302362 135 KEKSSPYIFPLSTNGKRPVRTDSLARAIMYFRAfnPDFKIFTARDLRRTCKTLMGEAGISKEIRDRIQNHALNDVSSKHY 214
Cdd:pfam16795  68 GSKKAFYAYHPTDFAERLERLELTEEAVKDFEA--KKGRAVKAKYIRKWVATKLAELGVPLEVIDFIQGRKPSSVLTQHY 145
INT_RitA_C_like cd01188
C-terminal catalytic domain of recombinase RitA, a component of the recombinase trio; ...
 48-199 5.50e-03

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: 36.84  E-value: 5.50e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1877302362  48 TLEELRFLMEHFAEATNVGLlMQHLIRFCIYTGGQRPFEMIASQWCDVDFQQKTLLVTAdvSKNKREHLIPLTESALQEL 127
Cdd:cd01188     1 SPDEVRRLLAAIDRLTPVGL-RDYAILLLLARLGLRAGDVAGLRLDDIDWRSGTITVRQ--KKTGRPVELPLTEPVGEAL 77

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1877302362 128 SCVQELTKEKS-SPYIFPLSTNGKRP-VRTDSLARAI-MYFRAFNPDFKIFTARDLRRTCKTLMGEAGIS-KEIRD 199
Cdd:cd01188    78 ADYLRDGRPRTdSREVFLRARAPYRPlSSTSQISSIVrRYLRKAGIEPSHRGTHSLRHSLATRMLRAGTSlKVIAD 153
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

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