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Conserved domains on  [gi|15829543|ref|NP_308316|]
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integrase [Escherichia coli O157:H7 str. Sakai]

Protein Classification

tyrosine-type recombinase/integrase( domain architecture ID 11426450)

tyrosine-type recombinase/integrase is a tyrosine based site-specific recombinase (integrase) 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

Graphical summary

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List of domain hits

Name Accession Description Interval E-value
FimB COG0582
Integrase/recombinase, includes phage integrase [Replication, recombination and repair, ...
2-386 4.03e-172

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


:

Pssm-ID: 440347 [Multi-domain]  Cd Length: 391  Bit Score: 485.70  E-value: 4.03e-172
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15829543   2 PLNDMQIRRAKPEAKAYTFGDGLGLSLLIEPNGSKSWRFRYRYAGKPKMISLGVYPTITLADARSRRDEARKLVAEGKNP 81
Cdd:COG0582   1 TLTDTAKKKAKPKDKPYKLGDGGGLLLLVGPSGGKRWRYRYRFRGKRKRLALGVYPGVSLALARARRAEARALLALGIDP 80
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15829543  82 SEVRKEQKLAMQTESENAFEKIAREWHQLKSAKWSAGYASDIMEAFKNDIFPYVGTRPVGEIKPLELLNVLRKIEKRGAL 161
Cdd:COG0582  81 SPARKAAKAAAAAAAANTFEEVAEEWLEEKKPEWKEKTAAQVRRTLEKHIFPVLGDRPIAEITPPDLLAVLRPIEARGAP 160
                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15829543 162 EKMRKVRQRCSEVFRYAIATGRAEYNPAADLSSALEVHQSNHFPFLKADEIPDFLRALEGYSGSKLVQIATKLLMITGVR 241
Cdd:COG0582 161 ETARRVRQRLRQVFRYAVARGLIERNPAADLKGALPKPKVKHHPALTPEELPELLRALDAYRGSPVTRLALRLLLLTGVR 240
                       250       260       270       280       290       300       310       320
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15829543 242 TIELRAALWQEFDLDNAIWEIPAERMKMRRPHLVPLSSQAVDLLNELKIMTGNYRYVFPGRNDPNRPMSEASINQAIKRI 321
Cdd:COG0582 241 PGELRGARWSEIDLEAALWTIPAERMKTRRPHIVPLSRQALEILKELKPLTGDSEYVFPSRRGPKKPMSENTLNKALRRM 320
                       330       340       350       360       370       380
                ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 15829543 322 GYgGKVTGHGFRHTLSTILHEQGFESAWIEIQLAHVDKNSIRGTYNHAQYFSGRKSMMDWYSNLI 386
Cdd:COG0582 321 GY-GRFTPHGFRHTASTLLNEAGFPPDVIERQLAHKDGNKVRAAYNRADYLEERREMMQWWADYL 384
 
Name Accession Description Interval E-value
FimB COG0582
Integrase/recombinase, includes phage integrase [Replication, recombination and repair, ...
2-386 4.03e-172

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


Pssm-ID: 440347 [Multi-domain]  Cd Length: 391  Bit Score: 485.70  E-value: 4.03e-172
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15829543   2 PLNDMQIRRAKPEAKAYTFGDGLGLSLLIEPNGSKSWRFRYRYAGKPKMISLGVYPTITLADARSRRDEARKLVAEGKNP 81
Cdd:COG0582   1 TLTDTAKKKAKPKDKPYKLGDGGGLLLLVGPSGGKRWRYRYRFRGKRKRLALGVYPGVSLALARARRAEARALLALGIDP 80
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15829543  82 SEVRKEQKLAMQTESENAFEKIAREWHQLKSAKWSAGYASDIMEAFKNDIFPYVGTRPVGEIKPLELLNVLRKIEKRGAL 161
Cdd:COG0582  81 SPARKAAKAAAAAAAANTFEEVAEEWLEEKKPEWKEKTAAQVRRTLEKHIFPVLGDRPIAEITPPDLLAVLRPIEARGAP 160
                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15829543 162 EKMRKVRQRCSEVFRYAIATGRAEYNPAADLSSALEVHQSNHFPFLKADEIPDFLRALEGYSGSKLVQIATKLLMITGVR 241
Cdd:COG0582 161 ETARRVRQRLRQVFRYAVARGLIERNPAADLKGALPKPKVKHHPALTPEELPELLRALDAYRGSPVTRLALRLLLLTGVR 240
                       250       260       270       280       290       300       310       320
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15829543 242 TIELRAALWQEFDLDNAIWEIPAERMKMRRPHLVPLSSQAVDLLNELKIMTGNYRYVFPGRNDPNRPMSEASINQAIKRI 321
Cdd:COG0582 241 PGELRGARWSEIDLEAALWTIPAERMKTRRPHIVPLSRQALEILKELKPLTGDSEYVFPSRRGPKKPMSENTLNKALRRM 320
                       330       340       350       360       370       380
                ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 15829543 322 GYgGKVTGHGFRHTLSTILHEQGFESAWIEIQLAHVDKNSIRGTYNHAQYFSGRKSMMDWYSNLI 386
Cdd:COG0582 321 GY-GRFTPHGFRHTASTLLNEAGFPPDVIERQLAHKDGNKVRAAYNRADYLEERREMMQWWADYL 384
PRK09692 PRK09692
integrase; Provisional
2-386 1.06e-113

integrase; Provisional


Pssm-ID: 170049 [Multi-domain]  Cd Length: 413  Bit Score: 338.15  E-value: 1.06e-113
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15829543    2 PLNDMQIRRAKPEAKAYTFGDGLGLSLLIEPNGSKSWRFRY-RYAGKPKM-ISLGVYPTITLADARSRRDEARKLVAEGK 79
Cdd:PRK09692   7 PLTDTEIKAAKPKEADYVLYDGDGLELLIKSSGSKIWQFRYyRPLTKTRAkKSFGPYPSVTLADARNYRAESRSLLAKQI 86
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15829543   80 NPSEVRKEQKLAMQTESENAFEKIAREWHQLKSAKWSAGYASDIMEAFKNDIFPYVGTRPVGEIKPLELLNVLRKIEKRG 159
Cdd:PRK09692  87 DPQEHQQEQLRSSLEAKTNTFQLVAERWWNVKKASVTEDYAEDIWRSLERDVFPAIGDISVTDIKAHTLVQAVQPVQARG 166
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15829543  160 ALEKMRKVRQRCSEVFRYAIATGRAEYNPAADLSSALEVHQSNHFPFLKADEIPDFLRALEGYSgsklVQIATKLL---- 235
Cdd:PRK09692 167 ALETVRRLCQRINEVMIYAQNTGLIDAVPSVNIGKAFEKPQKKNMPSIRPDQLPQLMQTMRTAS----ISLSTRCLfmwq 242
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15829543  236 MITGVRTIELRAALWQEFDLDNAIWEIPAERMKMRRPHLVPLSSQAVDLLNELKIMTGNYRYVFPGRNDPNRPMSEASIN 315
Cdd:PRK09692 243 LLTITRPAEAAEARWEEIDIEAQEWKIPAARMKMNRDHTVPLSDEALAILEMMKPLSGNREFIFPSRIKPNQPMNSQTVN 322
                        330       340       350       360       370       380       390
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 15829543  316 QAIKRIGYGGKVTGHGFRHTLSTILHEQGFESAWIEIQLAHVDKNSIRGTYNHAQYFSGRKSMMDWYSNLI 386
Cdd:PRK09692 323 AALKRAGLGGVLVSHGLRSIASTALNEQGFPPDVIEAALAHVDKNEVRRAYNRSDYLEQRRPMMQWWADFV 393
INT_P4_C cd00801
Bacteriophage P4 integrase, C-terminal catalytic domain; P4-like integrases are found in ...
210-386 1.49e-72

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: 224.46  E-value: 1.49e-72
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15829543 210 DEIPDFLRALEGYSGSKLVQIATKLLMITGVRTIELRAALWQEFDLDNAIWEIPAERMKMRRPHLVPLSSQAVDLLNELK 289
Cdd:cd00801   3 DELPELWRALDTANLSPPTKLALRLLLLTGQRIGELARARWSEIDLEEKTWTIPAERTKNKRPHRVPLSDQALEILEELK 82
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15829543 290 IMTGNYRYVFPGRNDPNRPMSEASINQAIKRIGYGGKV-TGHGFRHTLSTILHEQGFESAWIEIQLAHVDKNSIRGTYNH 368
Cdd:cd00801  83 EFTGDSGYLFPSRRKKKKPISENTINKALKRLGYKGKEfTPHDLRRTFSTLLNELGIDPEVIERLLNHVLGGVVRAAYNR 162
                       170
                ....*....|....*...
gi 15829543 369 AQYFSGRKSMMDWYSNLI 386
Cdd:cd00801 163 YDYLEERREALQAWADYL 180
Arm-DNA-bind_3 pfam13356
Arm DNA-binding domain; This DNA-binding domain is found at the N-terminus of a wide variety ...
3-80 2.32e-31

Arm DNA-binding domain; This DNA-binding domain is found at the N-terminus of a wide variety of phage integrase proteins.


Pssm-ID: 433141 [Multi-domain]  Cd Length: 78  Bit Score: 113.89  E-value: 2.32e-31
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 15829543     3 LNDMQIRRAKPEAKAYTFGDGLGLSLLIEPNGSKSWRFRYRYAGKPKMISLGVYPTITLADARSRRDEARKLVAEGKN 80
Cdd:pfam13356   1 LTDTAIRAAKPLPGDKKLADGGGLYLRVTPSGSKTWRFRYRFNGKRKTLALGRYPAVSLAQARKKADEARALVAQGID 78
 
Name Accession Description Interval E-value
FimB COG0582
Integrase/recombinase, includes phage integrase [Replication, recombination and repair, ...
2-386 4.03e-172

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


Pssm-ID: 440347 [Multi-domain]  Cd Length: 391  Bit Score: 485.70  E-value: 4.03e-172
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15829543   2 PLNDMQIRRAKPEAKAYTFGDGLGLSLLIEPNGSKSWRFRYRYAGKPKMISLGVYPTITLADARSRRDEARKLVAEGKNP 81
Cdd:COG0582   1 TLTDTAKKKAKPKDKPYKLGDGGGLLLLVGPSGGKRWRYRYRFRGKRKRLALGVYPGVSLALARARRAEARALLALGIDP 80
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15829543  82 SEVRKEQKLAMQTESENAFEKIAREWHQLKSAKWSAGYASDIMEAFKNDIFPYVGTRPVGEIKPLELLNVLRKIEKRGAL 161
Cdd:COG0582  81 SPARKAAKAAAAAAAANTFEEVAEEWLEEKKPEWKEKTAAQVRRTLEKHIFPVLGDRPIAEITPPDLLAVLRPIEARGAP 160
                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15829543 162 EKMRKVRQRCSEVFRYAIATGRAEYNPAADLSSALEVHQSNHFPFLKADEIPDFLRALEGYSGSKLVQIATKLLMITGVR 241
Cdd:COG0582 161 ETARRVRQRLRQVFRYAVARGLIERNPAADLKGALPKPKVKHHPALTPEELPELLRALDAYRGSPVTRLALRLLLLTGVR 240
                       250       260       270       280       290       300       310       320
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15829543 242 TIELRAALWQEFDLDNAIWEIPAERMKMRRPHLVPLSSQAVDLLNELKIMTGNYRYVFPGRNDPNRPMSEASINQAIKRI 321
Cdd:COG0582 241 PGELRGARWSEIDLEAALWTIPAERMKTRRPHIVPLSRQALEILKELKPLTGDSEYVFPSRRGPKKPMSENTLNKALRRM 320
                       330       340       350       360       370       380
                ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 15829543 322 GYgGKVTGHGFRHTLSTILHEQGFESAWIEIQLAHVDKNSIRGTYNHAQYFSGRKSMMDWYSNLI 386
Cdd:COG0582 321 GY-GRFTPHGFRHTASTLLNEAGFPPDVIERQLAHKDGNKVRAAYNRADYLEERREMMQWWADYL 384
PRK09692 PRK09692
integrase; Provisional
2-386 1.06e-113

integrase; Provisional


Pssm-ID: 170049 [Multi-domain]  Cd Length: 413  Bit Score: 338.15  E-value: 1.06e-113
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15829543    2 PLNDMQIRRAKPEAKAYTFGDGLGLSLLIEPNGSKSWRFRY-RYAGKPKM-ISLGVYPTITLADARSRRDEARKLVAEGK 79
Cdd:PRK09692   7 PLTDTEIKAAKPKEADYVLYDGDGLELLIKSSGSKIWQFRYyRPLTKTRAkKSFGPYPSVTLADARNYRAESRSLLAKQI 86
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15829543   80 NPSEVRKEQKLAMQTESENAFEKIAREWHQLKSAKWSAGYASDIMEAFKNDIFPYVGTRPVGEIKPLELLNVLRKIEKRG 159
Cdd:PRK09692  87 DPQEHQQEQLRSSLEAKTNTFQLVAERWWNVKKASVTEDYAEDIWRSLERDVFPAIGDISVTDIKAHTLVQAVQPVQARG 166
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15829543  160 ALEKMRKVRQRCSEVFRYAIATGRAEYNPAADLSSALEVHQSNHFPFLKADEIPDFLRALEGYSgsklVQIATKLL---- 235
Cdd:PRK09692 167 ALETVRRLCQRINEVMIYAQNTGLIDAVPSVNIGKAFEKPQKKNMPSIRPDQLPQLMQTMRTAS----ISLSTRCLfmwq 242
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15829543  236 MITGVRTIELRAALWQEFDLDNAIWEIPAERMKMRRPHLVPLSSQAVDLLNELKIMTGNYRYVFPGRNDPNRPMSEASIN 315
Cdd:PRK09692 243 LLTITRPAEAAEARWEEIDIEAQEWKIPAARMKMNRDHTVPLSDEALAILEMMKPLSGNREFIFPSRIKPNQPMNSQTVN 322
                        330       340       350       360       370       380       390
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 15829543  316 QAIKRIGYGGKVTGHGFRHTLSTILHEQGFESAWIEIQLAHVDKNSIRGTYNHAQYFSGRKSMMDWYSNLI 386
Cdd:PRK09692 323 AALKRAGLGGVLVSHGLRSIASTALNEQGFPPDVIEAALAHVDKNEVRRAYNRSDYLEQRRPMMQWWADFV 393
INT_P4_C cd00801
Bacteriophage P4 integrase, C-terminal catalytic domain; P4-like integrases are found in ...
210-386 1.49e-72

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: 224.46  E-value: 1.49e-72
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15829543 210 DEIPDFLRALEGYSGSKLVQIATKLLMITGVRTIELRAALWQEFDLDNAIWEIPAERMKMRRPHLVPLSSQAVDLLNELK 289
Cdd:cd00801   3 DELPELWRALDTANLSPPTKLALRLLLLTGQRIGELARARWSEIDLEEKTWTIPAERTKNKRPHRVPLSDQALEILEELK 82
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15829543 290 IMTGNYRYVFPGRNDPNRPMSEASINQAIKRIGYGGKV-TGHGFRHTLSTILHEQGFESAWIEIQLAHVDKNSIRGTYNH 368
Cdd:cd00801  83 EFTGDSGYLFPSRRKKKKPISENTINKALKRLGYKGKEfTPHDLRRTFSTLLNELGIDPEVIERLLNHVLGGVVRAAYNR 162
                       170
                ....*....|....*...
gi 15829543 369 AQYFSGRKSMMDWYSNLI 386
Cdd:cd00801 163 YDYLEERREALQAWADYL 180
Arm-DNA-bind_3 pfam13356
Arm DNA-binding domain; This DNA-binding domain is found at the N-terminus of a wide variety ...
3-80 2.32e-31

Arm DNA-binding domain; This DNA-binding domain is found at the N-terminus of a wide variety of phage integrase proteins.


Pssm-ID: 433141 [Multi-domain]  Cd Length: 78  Bit Score: 113.89  E-value: 2.32e-31
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 15829543     3 LNDMQIRRAKPEAKAYTFGDGLGLSLLIEPNGSKSWRFRYRYAGKPKMISLGVYPTITLADARSRRDEARKLVAEGKN 80
Cdd:pfam13356   1 LTDTAIRAAKPLPGDKKLADGGGLYLRVTPSGSKTWRFRYRFNGKRKTLALGRYPAVSLAQARKKADEARALVAQGID 78
Phage_integrase pfam00589
Phage integrase family; Members of this family cleave DNA substrates by a series of staggered ...
206-371 5.46e-24

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: 97.39  E-value: 5.46e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15829543   206 FLKADEIPDFLRALEGYSGSKLVQIATKLLMITGVRTIELRAALWQEFDLDNAIWEIPaeRMKMRRPHLVPLSSQAVDLL 285
Cdd:pfam00589   1 RLTEDEVERLLDAAETGPLSIRDKALLELLYATGLRISELCSLRWSDIDFENGVIRVH--RGKGNKERTVPLSDAALELL 78
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15829543   286 NELkiMTGNYR------YVFPGRndPNRPMSEASINQAIKRIGYG----GKVTGHGFRHTLSTILHEQGFESAWIEIQLA 355
Cdd:pfam00589  79 KEW--LSKRLLeapksdYLFASK--RGKPLSRQTVRKIFKRAGKEagleLPLHPHMLRHSFATHLLEAGVDLRVVQKLLG 154
                         170
                  ....*....|....*.
gi 15829543   356 HVDKNSIRgTYNHAQY 371
Cdd:pfam00589 155 HSSISTTQ-IYTHVAD 169
XerD COG4974
Site-specific recombinase XerD [Replication, recombination and repair];
99-344 6.54e-20

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


Pssm-ID: 443999 [Multi-domain]  Cd Length: 291  Bit Score: 88.90  E-value: 6.54e-20
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15829543  99 AFEKIAREWhqLKSAKWSAGYASDIMEAFKNDI------FPYVGTRPVGEIKPLELLNVLRKIEKRGALEK-MRKVRQRC 171
Cdd:COG4974   2 TLADLLEAF--LEELKREKGLSPNTIKAYRRDLrrflrfLEELGKIPLAEITPEDIRAYLNYLRERGLSPStINRYLAAL 79
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15829543 172 SEVFRYAIATGRAEYNPAADLSSAlevHQSNHFP-FLKADEIPDFLRALEGYSGSKLVQIA-TKLLMITGVRTIELRAAL 249
Cdd:COG4974  80 RSFFRYAVREGLLEDNPAAKVKLP---KKPRKLPrVLTEEEIEALLEALDTETPEGLRDRAlLLLLYATGLRVSELLGLK 156
                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15829543 250 WQEFDLDNAIWEIPAErmKMRRPHLVPLSSQAVDLLNELKIMTGNY--RYVFPGRNDpnRPMSEASINQAIKRI----GY 323
Cdd:COG4974 157 WSDIDLDRGTIRVRRG--KGGKERTVPLSPEALEALREYLEERRPRdsDYLFPTRRG--RPLSRRAIRKILKRLakraGI 232
                       250       260
                ....*....|....*....|.
gi 15829543 324 GGKVTGHGFRHTLSTILHEQG 344
Cdd:COG4974 233 PKRVTPHSLRHTFATHLLEAG 253
XerC COG4973
Site-specific recombinase XerC [Replication, recombination and repair];
117-371 1.26e-17

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


Pssm-ID: 443998 [Multi-domain]  Cd Length: 287  Bit Score: 82.32  E-value: 1.26e-17
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15829543 117 AGYASDImeafkNDIFPYVG--TRPVGEIKPLELLNVLRKIEKRG-ALEKMRKVRQRCSEVFRYAIATGRAEYNPAADLS 193
Cdd:COG4973  26 EAYRRDL-----RRLIPLLGdaDLPLEELTPADVRRFLARLHRRGlSPRTLNRRLSALRSFFNWAVREGLLEANPAAGVK 100
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15829543 194 SAlevHQSNHFP-FLKADEIPDFLRALEGYSGSKLVQIATKLLMITGVRTIELRAALWQEFDLDNAIWEIpaeRMKMRRP 272
Cdd:COG4973 101 AP---KAPRKLPrALTVDELAQLLDALADDPLAVRDRAIVELLYSTGLRLGELVGLDWEDVDLDAGEVRV---RGKTGKS 174
                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15829543 273 HLVPLSSQAVDLLNELKIMTGNY-----RYVFPGRNDpnRPMSEASINQAIKRI----GYGGKVTGHGFRHTLSTILHEQ 343
Cdd:COG4973 175 RTVPLGPKALAALREWLAVRPELaapdeGALFPSRRG--TRLSPRNVQKRLRRLakkaGLPKHVHPHDLRHSFATHLLES 252
                       250       260
                ....*....|....*....|....*...
gi 15829543 344 GFESAWIEIQLAHVDKNSIRGtYNHAQY 371
Cdd:COG4973 253 GGDLRAVQELLGHASISTTQI-YTHLDF 279
DNA_BRE_C cd00397
DNA breaking-rejoining enzymes, C-terminal catalytic domain; The DNA breaking-rejoining enzyme ...
233-363 2.34e-14

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: 70.20  E-value: 2.34e-14
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15829543 233 KLLMITGVRTIELRAALWQEFDLDNAIWEIPAERMKMRRPHLVPLSSQAVDLLNEL--------KIMTGNYRYVFPGRND 304
Cdd:cd00397  24 LLLLETGLRISELLALKVKDIDLDNGTIRVRGKKTKGGKERTVPLPKELAEELKEYlkerrdkrGPLLKSLYLNKLFGTK 103
                        90       100       110       120       130       140
                ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 15829543 305 PNRPMSEASINQAIKRIG--YGGKVTGHGFRHTLSTILHEQGFESAWIEIQLAHVDKNSIR 363
Cdd:cd00397 104 LGERLSRRTLRRIFKKAGieAGRKITPHSLRHTFATNLLENGVDIKVVQKLLGHSSISTTQ 164
INT_Rci_Hp1_C cd00796
Shufflon-specific DNA recombinase Rci and Bacteriophage Hp1_like integrase, C-terminal ...
206-344 9.80e-10

Shufflon-specific DNA recombinase Rci and Bacteriophage Hp1_like integrase, C-terminal catalytic domain; Rci protein is a tyrosine recombinase specifically involved in Shufflon type of DNA rearrangement in bacteria. The shufflon of plasmid R64 consists of four invertible DNA segments which are separated and flanked by seven 19-bp repeat sequences. RCI recombinase facilitates the site-specific recombination between any inverted repeats results in an inversion of the DNA segment(s) either independently or in groups. HP1 integrase promotes site-specific recombination of the HP1 genome into that of Haemophilus influenza. Bacteriophage Hp1_like integrases are tyrosine based site specific recombinases. They belong to the superfamily of DNA breaking-rejoining enzymes, which share the same fold in their catalytic domain and the overall reaction mechanism. The catalytic domain contains six conserved active site residues. Their overall reaction mechanism is essentially identical and involves cleavage of a single strand of a DNA duplex by nucleophilic attack of a conserved tyrosine to give a 3' phosphotyrosyl protein-DNA adduct. In the second rejoining step, a terminal 5' hydroxyl attacks the covalent adduct to release the enzyme and generate duplex DNA.


Pssm-ID: 271177 [Multi-domain]  Cd Length: 162  Bit Score: 56.95  E-value: 9.80e-10
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15829543 206 FLKADEIPDFLRALEGYSGsKLVQIATKLLMITGVRTIELRAALWQEFDLDnaIWEIPAERMKMRRPHLVPLSSQAVDLL 285
Cdd:cd00796   4 FLTEDEEARLLAALEESTN-PHLRLIVLLALYTGARRGEILSLRWDDIDLE--VGLIVLPETKNGKPRTVPLSDEAIAIL 80
                        90       100       110       120       130       140
                ....*....|....*....|....*....|....*....|....*....|....*....|
gi 15829543 286 NELKIMTGNYRYVFPGRNDPNRPMS-EASINQAIKRIGYGGkVTGHGFRHTLSTILHEQG 344
Cdd:cd00796  81 KELKRKRGKDGFFVDGRFFGIPIASlRRAFKKARKRAGLED-LRFHDLRHTFASRLVQAG 139
INT_ICEBs1_C_like cd01189
C-terminal catalytic domain of integrases from bacterial phages and conjugate transposons; ...
209-368 4.22e-07

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: 49.09  E-value: 4.22e-07
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15829543 209 ADEIPDFLRALEGYSgsKLVQIATKLLMITGVRTIELRAALWQEFDLDN-------AIWEIPAERMKMRRP------HLV 275
Cdd:cd01189   1 PEELKKLLEALKKRG--DRYYLLFLLALLTGLRRGELLALTWSDIDFENgtirinrTLVRKKKGGYVIKPPktkssiRTI 78
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15829543 276 PLSSQAVDLLNELKimtgnyryvfpgrndpnrpmseaSINQAIKRIGyGGKVTGHGFRHTLSTILHEQGFESAWIEIQLA 355
Cdd:cd01189  79 PLPDELIELLKELK-----------------------AFKKLLKKAG-LPRITPHDLRHTFASLLLEAGVPLKVIAERLG 134
                       170
                ....*....|...
gi 15829543 356 HVDKNSIRGTYNH 368
Cdd:cd01189 135 HSDISTTLDVYAH 147
INTN1_C_like cd01185
Integrase IntN1 of Bacteroides mobilizable transposon NBU1 and similar proteins, C-terminal ...
238-344 5.51e-07

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: 48.80  E-value: 5.51e-07
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15829543 238 TGVRTIELRAALWQEFDLDNAIWEIPAERMKMRRPHLVPLSSQAVDLLNELKiMTGNYRYVFPGrndpnrpMSEASINQA 317
Cdd:cd01185  30 TGLRFSDLKNLTWKNIVEASGRTWIRYRRKKTGKPVTVPLLPVAREILEKYK-DDRSEGKLFPV-------LSNQKINRY 101
                        90       100       110
                ....*....|....*....|....*....|.
gi 15829543 318 IKRIGY--G--GKVTGHGFRHTLSTILHEQG 344
Cdd:cd01185 102 LKEIAKiaGidKHLTFHVARHTFATLLLLKG 132
INT_tnpA_C_Tn554 cd01186
Putative Transposase A from transposon Tn554, C-terminal catalytic domain; This family ...
234-368 3.26e-05

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: 44.33  E-value: 3.26e-05
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15829543 234 LLMITGVRTIELRAALWQEFDL-DNAIWEIP------AERMKMRRPHLVPLSSQAVDLLNELKI-----MTGNYRYVFPG 301
Cdd:cd01186  25 LLYETGLRIGEALGLRIEDIDMaDNQIELVPredntnEARAKSMRERRIPVSQDLIDLYADYLTyiyceEAEFSITVFVN 104
                        90       100       110       120       130       140       150
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 15829543 302 RNDPN--RPMSEASINQAIKRIGY--GGKVTGHGFRHTLSTILHEQGFESAWIEIQLAHVDKNSIRGTYNH 368
Cdd:cd01186 105 VKGGNqgKAMNYSDVYDLVRRLKKrtGIDFTPHMFRHTHATALIRAGWSIEVVARRLGHAHVQTTLNTYGH 175
INT_IntI_C cd01193
Integron integrase and similar protiens, C-terminal catalytic domain; Integron integrases ...
212-358 4.12e-03

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: 38.02  E-value: 4.12e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15829543 212 IPDFL-----RALEGYSGSKLVQIATKLLMITGVRTIELRAALWQEFDLDNAIWEIpaERMKMRRPHLVPLSSQAVDLLN 286
Cdd:cd01193   2 LPVVLspdevRRILGALTELRHRLILSLLYGAGLRISELLRLRVKDIDFERGVIRV--RQGKGGKDRVVPLPEKLLEPLR 79
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15829543 287 ELKIMTGNYRYVFPG---------RNDPNR--PMSEASINQAIKRI----GYGGKVTGHGFRHTLSTILHEQGFESAWIE 351
Cdd:cd01193  80 RYLKSARPKEELDPAegragvldpRTGVERrhHISETTVQRALKKAveqaGITKRVTPHTLRHSFATHLLEAGTDIRTIQ 159

                ....*..
gi 15829543 352 IQLAHVD 358
Cdd:cd01193 160 ELLGHSD 166
 
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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