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Conserved domains on  [gi|2539732461|ref|WP_295943608|]
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integrase arm-type DNA-binding domain-containing protein [uncultured Acidovorax sp.]

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, ...
2-405 2.37e-147

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


:

Pssm-ID: 440347 [Multi-domain]  Cd Length: 391  Bit Score: 423.68  E-value: 2.37e-147
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2539732461   2 ALTDTFVKNVKPAGSATgeKHADGQGLYLHVKPAG-KYWRMSYRHLGKQKTLAIGVYPAVSLAKARKRRDEARELLAEGL 80
Cdd:COG0582     1 TLTDTAKKKAKPKDKPY--KLGDGGGLLLLVGPSGgKRWRYRYRFRGKRKRLALGVYPGVSLALARARRAEARALLALGI 78
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2539732461  81 DPSAAKKAEKLATRVAAANTFEAVAREFHATQASGWSPRYAARWIERMEKDLFPYIGKLTLPAITAPVLLDALRKVEKRG 160
Cdd:COG0582    79 DPSPARKAAKAAAAAAAANTFEEVAEEWLEEKKPEWKEKTAAQVRRTLEKHIFPVLGDRPIAEITPPDLLAVLRPIEARG 158
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2539732461 161 ANETAHTLRQTAGQVFRYGVQTGRCERSPVTDLHGALKPILVKHMAAvLEPVKAGELLRAIDGYTGQPMTKAALALSALL 240
Cdd:COG0582   159 APETARRVRQRLRQVFRYAVARGLIERNPAADLKGALPKPKVKHHPA-LTPEELPELLRALDAYRGSPVTRLALRLLLLT 237
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2539732461 241 FQRPGNIRQMEWAWIDFDKALLTIPSQDMKrrlaqkiNGRPHFVPLAPQAIAILKELQPLTGHGRYVFPSLRTGERAMSD 320
Cdd:COG0582   238 GVRPGELRGARWSEIDLEAALWTIPAERMK-------TRRPHIVPLSRQALEILKELKPLTGDSEYVFPSRRGPKKPMSE 310
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2539732461 321 NTINAALRRMGFasDEMSAHGFRAMARTLMIEriHGISADVIEAQLAHGKSGPLGAAYDRAEFMEQRRKMMREWANYLDK 400
Cdd:COG0582   311 NTLNKALRRMGY--GRFTPHGFRHTASTLLNE--AGFPPDVIERQLAHKDGNKVRAAYNRADYLEERREMMQWWADYLDA 386

                  ....*
gi 2539732461 401 LRIGA 405
Cdd:COG0582   387 LRAGA 391
 
Name Accession Description Interval E-value
FimB COG0582
Integrase/recombinase, includes phage integrase [Replication, recombination and repair, ...
2-405 2.37e-147

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


Pssm-ID: 440347 [Multi-domain]  Cd Length: 391  Bit Score: 423.68  E-value: 2.37e-147
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2539732461   2 ALTDTFVKNVKPAGSATgeKHADGQGLYLHVKPAG-KYWRMSYRHLGKQKTLAIGVYPAVSLAKARKRRDEARELLAEGL 80
Cdd:COG0582     1 TLTDTAKKKAKPKDKPY--KLGDGGGLLLLVGPSGgKRWRYRYRFRGKRKRLALGVYPGVSLALARARRAEARALLALGI 78
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2539732461  81 DPSAAKKAEKLATRVAAANTFEAVAREFHATQASGWSPRYAARWIERMEKDLFPYIGKLTLPAITAPVLLDALRKVEKRG 160
Cdd:COG0582    79 DPSPARKAAKAAAAAAAANTFEEVAEEWLEEKKPEWKEKTAAQVRRTLEKHIFPVLGDRPIAEITPPDLLAVLRPIEARG 158
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2539732461 161 ANETAHTLRQTAGQVFRYGVQTGRCERSPVTDLHGALKPILVKHMAAvLEPVKAGELLRAIDGYTGQPMTKAALALSALL 240
Cdd:COG0582   159 APETARRVRQRLRQVFRYAVARGLIERNPAADLKGALPKPKVKHHPA-LTPEELPELLRALDAYRGSPVTRLALRLLLLT 237
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2539732461 241 FQRPGNIRQMEWAWIDFDKALLTIPSQDMKrrlaqkiNGRPHFVPLAPQAIAILKELQPLTGHGRYVFPSLRTGERAMSD 320
Cdd:COG0582   238 GVRPGELRGARWSEIDLEAALWTIPAERMK-------TRRPHIVPLSRQALEILKELKPLTGDSEYVFPSRRGPKKPMSE 310
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2539732461 321 NTINAALRRMGFasDEMSAHGFRAMARTLMIEriHGISADVIEAQLAHGKSGPLGAAYDRAEFMEQRRKMMREWANYLDK 400
Cdd:COG0582   311 NTLNKALRRMGY--GRFTPHGFRHTASTLLNE--AGFPPDVIERQLAHKDGNKVRAAYNRADYLEERREMMQWWADYLDA 386

                  ....*
gi 2539732461 401 LRIGA 405
Cdd:COG0582   387 LRAGA 391
PRK09692 PRK09692
integrase; Provisional
3-405 2.30e-75

integrase; Provisional


Pssm-ID: 170049 [Multi-domain]  Cd Length: 413  Bit Score: 240.31  E-value: 2.30e-75
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2539732461   3 LTDTFVKNVKPAgSATGEKHaDGQGLYLHVKPAG-KYWRMSY-RHLGKQKT-LAIGVYPAVSLAKARKRRDEARELLAEG 79
Cdd:PRK09692    8 LTDTEIKAAKPK-EADYVLY-DGDGLELLIKSSGsKIWQFRYyRPLTKTRAkKSFGPYPSVTLADARNYRAESRSLLAKQ 85
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2539732461  80 LDPSAAKKAEKLATRVAAANTFEAVAREFHATQASGWSPRYAARWIERMEKDLFPYIGKLTLPAITAPVLLDALRKVEKR 159
Cdd:PRK09692   86 IDPQEHQQEQLRSSLEAKTNTFQLVAERWWNVKKASVTEDYAEDIWRSLERDVFPAIGDISVTDIKAHTLVQAVQPVQAR 165
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2539732461 160 GANETAHTLRQTAGQVFRYGVQTGRCERSPVTDLHGALKPILVKHMAAVlEPVKAGELLRAIDGYTGQPMTKAALALSAL 239
Cdd:PRK09692  166 GALETVRRLCQRINEVMIYAQNTGLIDAVPSVNIGKAFEKPQKKNMPSI-RPDQLPQLMQTMRTASISLSTRCLFMWQLL 244
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2539732461 240 LFQRPGNIRQMEWAWIDFDKALLTIPSQDMKRRlaqkingRPHFVPLAPQAIAILKELQPLTGHGRYVFPSLRTGERAMS 319
Cdd:PRK09692  245 TITRPAEAAEARWEEIDIEAQEWKIPAARMKMN-------RDHTVPLSDEALAILEMMKPLSGNREFIFPSRIKPNQPMN 317
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2539732461 320 DNTINAALRRMGFASDEMSaHGFRAMARTLMIERihGISADVIEAQLAHGKSGPLGAAYDRAEFMEQRRKMMREWANYLD 399
Cdd:PRK09692  318 SQTVNAALKRAGLGGVLVS-HGLRSIASTALNEQ--GFPPDVIEAALAHVDKNEVRRAYNRSDYLEQRRPMMQWWADFVM 394

                  ....*.
gi 2539732461 400 KLRIGA 405
Cdd:PRK09692  395 AADSGS 400
INT_P4_C cd00801
Bacteriophage P4 integrase, C-terminal catalytic domain; P4-like integrases are found in ...
215-398 8.60e-63

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: 200.19  E-value: 8.60e-63
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2539732461 215 GELLRAIDGYTGQPMTKAALALSALLFQRPGNIRQMEWAWIDFDKALLTIPSQDMKrrlaqkiNGRPHFVPLAPQAIAIL 294
Cdd:cd00801     6 PELWRALDTANLSPPTKLALRLLLLTGQRIGELARARWSEIDLEEKTWTIPAERTK-------NKRPHRVPLSDQALEIL 78
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2539732461 295 KELQPLTGHGRYVFPSLRTGERAMSDNTINAALRRMGFASDEMSAHGFRAMARTLMIEriHGISADVIEAQLAHGKSGPL 374
Cdd:cd00801    79 EELKEFTGDSGYLFPSRRKKKKPISENTINKALKRLGYKGKEFTPHDLRRTFSTLLNE--LGIDPEVIERLLNHVLGGVV 156
                         170       180
                  ....*....|....*....|....
gi 2539732461 375 GAAYDRAEFMEQRRKMMREWANYL 398
Cdd:cd00801   157 RAAYNRYDYLEERREALQAWADYL 180
Arm-DNA-bind_3 pfam13356
Arm DNA-binding domain; This DNA-binding domain is found at the N-terminus of a wide variety ...
3-81 1.79e-27

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: 103.88  E-value: 1.79e-27
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2539732461   3 LTDTFVKNVKPagSATGEKHADGQGLYLHVKPAG-KYWRMSYRHLGKQKTLAIGVYPAVSLAKARKRRDEARELLAEGLD 81
Cdd:pfam13356   1 LTDTAIRAAKP--LPGDKKLADGGGLYLRVTPSGsKTWRFRYRFNGKRKTLALGRYPAVSLAQARKKADEARALVAQGID 78
 
Name Accession Description Interval E-value
FimB COG0582
Integrase/recombinase, includes phage integrase [Replication, recombination and repair, ...
2-405 2.37e-147

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


Pssm-ID: 440347 [Multi-domain]  Cd Length: 391  Bit Score: 423.68  E-value: 2.37e-147
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2539732461   2 ALTDTFVKNVKPAGSATgeKHADGQGLYLHVKPAG-KYWRMSYRHLGKQKTLAIGVYPAVSLAKARKRRDEARELLAEGL 80
Cdd:COG0582     1 TLTDTAKKKAKPKDKPY--KLGDGGGLLLLVGPSGgKRWRYRYRFRGKRKRLALGVYPGVSLALARARRAEARALLALGI 78
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2539732461  81 DPSAAKKAEKLATRVAAANTFEAVAREFHATQASGWSPRYAARWIERMEKDLFPYIGKLTLPAITAPVLLDALRKVEKRG 160
Cdd:COG0582    79 DPSPARKAAKAAAAAAAANTFEEVAEEWLEEKKPEWKEKTAAQVRRTLEKHIFPVLGDRPIAEITPPDLLAVLRPIEARG 158
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2539732461 161 ANETAHTLRQTAGQVFRYGVQTGRCERSPVTDLHGALKPILVKHMAAvLEPVKAGELLRAIDGYTGQPMTKAALALSALL 240
Cdd:COG0582   159 APETARRVRQRLRQVFRYAVARGLIERNPAADLKGALPKPKVKHHPA-LTPEELPELLRALDAYRGSPVTRLALRLLLLT 237
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2539732461 241 FQRPGNIRQMEWAWIDFDKALLTIPSQDMKrrlaqkiNGRPHFVPLAPQAIAILKELQPLTGHGRYVFPSLRTGERAMSD 320
Cdd:COG0582   238 GVRPGELRGARWSEIDLEAALWTIPAERMK-------TRRPHIVPLSRQALEILKELKPLTGDSEYVFPSRRGPKKPMSE 310
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2539732461 321 NTINAALRRMGFasDEMSAHGFRAMARTLMIEriHGISADVIEAQLAHGKSGPLGAAYDRAEFMEQRRKMMREWANYLDK 400
Cdd:COG0582   311 NTLNKALRRMGY--GRFTPHGFRHTASTLLNE--AGFPPDVIERQLAHKDGNKVRAAYNRADYLEERREMMQWWADYLDA 386

                  ....*
gi 2539732461 401 LRIGA 405
Cdd:COG0582   387 LRAGA 391
PRK09692 PRK09692
integrase; Provisional
3-405 2.30e-75

integrase; Provisional


Pssm-ID: 170049 [Multi-domain]  Cd Length: 413  Bit Score: 240.31  E-value: 2.30e-75
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2539732461   3 LTDTFVKNVKPAgSATGEKHaDGQGLYLHVKPAG-KYWRMSY-RHLGKQKT-LAIGVYPAVSLAKARKRRDEARELLAEG 79
Cdd:PRK09692    8 LTDTEIKAAKPK-EADYVLY-DGDGLELLIKSSGsKIWQFRYyRPLTKTRAkKSFGPYPSVTLADARNYRAESRSLLAKQ 85
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2539732461  80 LDPSAAKKAEKLATRVAAANTFEAVAREFHATQASGWSPRYAARWIERMEKDLFPYIGKLTLPAITAPVLLDALRKVEKR 159
Cdd:PRK09692   86 IDPQEHQQEQLRSSLEAKTNTFQLVAERWWNVKKASVTEDYAEDIWRSLERDVFPAIGDISVTDIKAHTLVQAVQPVQAR 165
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2539732461 160 GANETAHTLRQTAGQVFRYGVQTGRCERSPVTDLHGALKPILVKHMAAVlEPVKAGELLRAIDGYTGQPMTKAALALSAL 239
Cdd:PRK09692  166 GALETVRRLCQRINEVMIYAQNTGLIDAVPSVNIGKAFEKPQKKNMPSI-RPDQLPQLMQTMRTASISLSTRCLFMWQLL 244
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2539732461 240 LFQRPGNIRQMEWAWIDFDKALLTIPSQDMKRRlaqkingRPHFVPLAPQAIAILKELQPLTGHGRYVFPSLRTGERAMS 319
Cdd:PRK09692  245 TITRPAEAAEARWEEIDIEAQEWKIPAARMKMN-------RDHTVPLSDEALAILEMMKPLSGNREFIFPSRIKPNQPMN 317
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2539732461 320 DNTINAALRRMGFASDEMSaHGFRAMARTLMIERihGISADVIEAQLAHGKSGPLGAAYDRAEFMEQRRKMMREWANYLD 399
Cdd:PRK09692  318 SQTVNAALKRAGLGGVLVS-HGLRSIASTALNEQ--GFPPDVIEAALAHVDKNEVRRAYNRSDYLEQRRPMMQWWADFVM 394

                  ....*.
gi 2539732461 400 KLRIGA 405
Cdd:PRK09692  395 AADSGS 400
INT_P4_C cd00801
Bacteriophage P4 integrase, C-terminal catalytic domain; P4-like integrases are found in ...
215-398 8.60e-63

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: 200.19  E-value: 8.60e-63
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2539732461 215 GELLRAIDGYTGQPMTKAALALSALLFQRPGNIRQMEWAWIDFDKALLTIPSQDMKrrlaqkiNGRPHFVPLAPQAIAIL 294
Cdd:cd00801     6 PELWRALDTANLSPPTKLALRLLLLTGQRIGELARARWSEIDLEEKTWTIPAERTK-------NKRPHRVPLSDQALEIL 78
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2539732461 295 KELQPLTGHGRYVFPSLRTGERAMSDNTINAALRRMGFASDEMSAHGFRAMARTLMIEriHGISADVIEAQLAHGKSGPL 374
Cdd:cd00801    79 EELKEFTGDSGYLFPSRRKKKKPISENTINKALKRLGYKGKEFTPHDLRRTFSTLLNE--LGIDPEVIERLLNHVLGGVV 156
                         170       180
                  ....*....|....*....|....
gi 2539732461 375 GAAYDRAEFMEQRRKMMREWANYL 398
Cdd:cd00801   157 RAAYNRYDYLEERREALQAWADYL 180
Arm-DNA-bind_3 pfam13356
Arm DNA-binding domain; This DNA-binding domain is found at the N-terminus of a wide variety ...
3-81 1.79e-27

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: 103.88  E-value: 1.79e-27
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2539732461   3 LTDTFVKNVKPagSATGEKHADGQGLYLHVKPAG-KYWRMSYRHLGKQKTLAIGVYPAVSLAKARKRRDEARELLAEGLD 81
Cdd:pfam13356   1 LTDTAIRAAKP--LPGDKKLADGGGLYLRVTPSGsKTWRFRYRFNGKRKTLALGRYPAVSLAQARKKADEARALVAQGID 78
XerD COG4974
Site-specific recombinase XerD [Replication, recombination and repair];
119-368 7.76e-12

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


Pssm-ID: 443999 [Multi-domain]  Cd Length: 291  Bit Score: 65.40  E-value: 7.76e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2539732461 119 RYAARWIERMEKDL------FPYIGKLTLPAITAPVLLDALRKVEKRG-ANETAHTLRQTAGQVFRYGVQTGRCERSPVT 191
Cdd:COG4974    19 GLSPNTIKAYRRDLrrflrfLEELGKIPLAEITPEDIRAYLNYLRERGlSPSTINRYLAALRSFFRYAVREGLLEDNPAA 98
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2539732461 192 DLHgalKPILVKHMAAVLEPVKAGELLRAIDG----------------YTGQpmtkaalalsallfqRPGNIRQMEWAWI 255
Cdd:COG4974    99 KVK---LPKKPRKLPRVLTEEEIEALLEALDTetpeglrdralllllyATGL---------------RVSELLGLKWSDI 160
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2539732461 256 DFDKALLTIPsqdmkrrlAQKiNGRPHFVPLAPQAIAILKELQPLT--GHGRYVFPSLRTgeRAMSDNTINAALRRMGFA 333
Cdd:COG4974   161 DLDRGTIRVR--------RGK-GGKERTVPLSPEALEALREYLEERrpRDSDYLFPTRRG--RPLSRRAIRKILKRLAKR 229
                         250       260       270
                  ....*....|....*....|....*....|....*...
gi 2539732461 334 ---SDEMSAHGFRAMARTLMIEriHGISADVIEAQLAH 368
Cdd:COG4974   230 agiPKRVTPHSLRHTFATHLLE--AGVDLRTVQELLGH 265
Phage_integrase pfam00589
Phage integrase family; Members of this family cleave DNA substrates by a series of staggered ...
242-368 3.25e-09

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: 55.79  E-value: 3.25e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2539732461 242 QRPGNIRQMEWAWIDFDKALLTIPSqdMKrrlaqkiNGRPHFVPLAPQAIAILKELqpLTGHGR------YVFPSLRTGE 315
Cdd:pfam00589  35 LRISELCSLRWSDIDFENGVIRVHR--GK-------GNKERTVPLSDAALELLKEW--LSKRLLeapksdYLFASKRGKP 103
                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 2539732461 316 raMSDNTINAALRRMGFAS---DEMSAHGFRAMARTLMIEriHGISADVIEAQLAH 368
Cdd:pfam00589 104 --LSRQTVRKIFKRAGKEAgleLPLHPHMLRHSFATHLLE--AGVDLRVVQKLLGH 155
XerC COG4973
Site-specific recombinase XerC [Replication, recombination and repair];
102-368 7.00e-09

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


Pssm-ID: 443998 [Multi-domain]  Cd Length: 287  Bit Score: 56.51  E-value: 7.00e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2539732461 102 EAVAREFHATQASGWSPRYAARWiERMEKDLFPYIGKLTLP--AITAPVLLDALRKVEKRG-ANETAHTLRQTAGQVFRY 178
Cdd:COG4973     6 EALEAYLEHLRERRLSPKTLEAY-RRDLRRLIPLLGDADLPleELTPADVRRFLARLHRRGlSPRTLNRRLSALRSFFNW 84
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2539732461 179 GVQTGRCERSPVTDLHGAL------KPILVKHMAAVLEPVKAGEL---LRAI---DGYTGQpmtkaalalsallfqRPGN 246
Cdd:COG4973    85 AVREGLLEANPAAGVKAPKaprklpRALTVDELAQLLDALADDPLavrDRAIvelLYSTGL---------------RLGE 149
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2539732461 247 IRQMEWAWIDFDKALLTIPSQDMKRRLaqkingrphfVPLAPQAIAILKELQPL-----TGHGRYVFPSlRTGERaMSDN 321
Cdd:COG4973   150 LVGLDWEDVDLDAGEVRVRGKTGKSRT----------VPLGPKALAALREWLAVrpelaAPDEGALFPS-RRGTR-LSPR 217
                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|
gi 2539732461 322 TINAALRRMGFA---SDEMSAHGFRAMARTLMIEriHGISADVIEAQLAH 368
Cdd:COG4973   218 NVQKRLRRLAKKaglPKHVHPHDLRHSFATHLLE--SGGDLRAVQELLGH 265
INT_Rci_Hp1_C cd00796
Shufflon-specific DNA recombinase Rci and Bacteriophage Hp1_like integrase, C-terminal ...
243-368 1.93e-08

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: 53.48  E-value: 1.93e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2539732461 243 RPGNIRQMEWAWIDFDKALLTIPsqDMKrrlaqkiNGRPHFVPLAPQAIAILKELQPLTG-HGRYVFPSLRTGERAMSDN 321
Cdd:cd00796    38 RRGEILSLRWDDIDLEVGLIVLP--ETK-------NGKPRTVPLSDEAIAILKELKRKRGkDGFFVDGRFFGIPIASLRR 108
                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*..
gi 2539732461 322 TINAALRRMGFasDEMSAHGFRAMARTLMIERihGISADVIEAQLAH 368
Cdd:cd00796   109 AFKKARKRAGL--EDLRFHDLRHTFASRLVQA--GVPIKTVAKILGH 151
 
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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