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Conserved domains on  [gi|1873298962|ref|WP_180263288|]
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site-specific integrase, partial [Enterobacter hormaechei]

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 ...
 87-273 4.67e-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: 4.67e-54
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1873298962  87 TLEELRVVMEQFaGATNVGPLMQHLIRFCVyAGGQRPFEMIASQWSAIDWQQKTLLVIADVSKNKREHLIPLTESALQEL 166
Cdd:cd00801     1 SPDELPELWRAL-DTANLSPPTKLALRLLL-LTGQRIGELARARWSEIDLEEKTWTIPAERTKNKRPHRVPLSDQALEIL 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1873298962 167 ASVKELTKesNSPYIFPLSTNGDRPVRTDSLARSImyfRAFNPEFKVFTARDLRRTCKTLMGEAGISKEIRDRIQNHALN 246
Cdd:cd00801    79 EELKEFTG--DSGYLFPSRRKKKKPISENTINKAL---KRLGYKGKEFTPHDLRRTFSTLLNELGIDPEVIERLLNHVLG 153

                         170       180
                  ....*....|....*....|....*..
gi 1873298962 247 DVSSKHYDRYDYLPEKRRALEIWEDRV 273
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 ...
 87-273 4.67e-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: 4.67e-54
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1873298962  87 TLEELRVVMEQFaGATNVGPLMQHLIRFCVyAGGQRPFEMIASQWSAIDWQQKTLLVIADVSKNKREHLIPLTESALQEL 166
Cdd:cd00801     1 SPDELPELWRAL-DTANLSPPTKLALRLLL-LTGQRIGELARARWSEIDLEEKTWTIPAERTKNKRPHRVPLSDQALEIL 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1873298962 167 ASVKELTKesNSPYIFPLSTNGDRPVRTDSLARSImyfRAFNPEFKVFTARDLRRTCKTLMGEAGISKEIRDRIQNHALN 246
Cdd:cd00801    79 EELKEFTG--DSGYLFPSRRKKKKPISENTINKAL---KRLGYKGKEFTPHDLRRTFSTLLNELGIDPEVIERLLNHVLG 153

                         170       180
                  ....*....|....*....|....*..
gi 1873298962 247 DVSSKHYDRYDYLPEKRRALEIWEDRV 273
Cdd:cd00801   154 GVVRAAYNRYDYLEERREALQAWADYL 180
FimB COG0582
Integrase/recombinase, includes phage integrase [Replication, recombination and repair, ...
 1-273 3.09e-48

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


Pssm-ID: 440347 [Multi-domain]  Cd Length: 391  Bit Score: 165.21  E-value: 3.09e-48
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1873298962   1 VIPR--ETKAKDVTPLQIKTILSGIIQRDAVVHANRIRSYLMAAFNYGLKadndpintsvgiTFGLEVNPVSAIPKQSSA 78
Cdd:COG0582   130 IFPVlgDRPIAEITPPDLLAVLRPIEARGAPETARRVRQRLRQVFRYAVA------------RGLIERNPAADLKGALPK 197

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1873298962  79 EKVG-DTWLTLEELRVVMEQFAGAtNVGPLMQHLIRFCVYaGGQRPFEMIASQWSAIDWQQKTLLVIADVSKNKREHLIP 157
Cdd:COG0582   198 PKVKhHPALTPEELPELLRALDAY-RGSPVTRLALRLLLL-TGVRPGELRGARWSEIDLEAALWTIPAERMKTRRPHIVP 275

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1873298962 158 LTESALQELASVKELTkeSNSPYIFPLSTNGDRPVRTDSLARsimYFRAfnPEFKVFTARDLRRTCKTLMGEAGISKEIR 237
Cdd:COG0582   276 LSRQALEILKELKPLT--GDSEYVFPSRRGPKKPMSENTLNK---ALRR--MGYGRFTPHGFRHTASTLLNEAGFPPDVI 348

                         250       260       270
                  ....*....|....*....|....*....|....*.
gi 1873298962 238 DRIQNHALNDVSSKHYDRYDYLPEKRRALEIWEDRV 273
Cdd:COG0582   349 ERQLAHKDGNKVRAAYNRADYLEERREMMQWWADYL 384
PRK09692 PRK09692
integrase; Provisional
 122-274 9.70e-13

integrase; Provisional


Pssm-ID: 170049 [Multi-domain]  Cd Length: 413  Bit Score: 67.74  E-value: 9.70e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1873298962 122 RPFEMIASQWSAIDWQQKTLLVIADVSKNKREHLIPLTESALQELASVKELTkeSNSPYIFPLSTNGDRPVRTDSLarsi 201
Cdd:PRK09692  248 RPAEAAEARWEEIDIEAQEWKIPAARMKMNRDHTVPLSDEALAILEMMKPLS--GNREFIFPSRIKPNQPMNSQTV---- 321

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1873298962 202 myfrafNPEFK------VFTARDLRRTCKTLMGEAGISKEIRDRIQNHALNDVSSKHYDRYDYLPEKRRALEIWEDRVN 274
Cdd:PRK09692  322 ------NAALKraglggVLVSHGLRSIASTALNEQGFPPDVIEAALAHVDKNEVRRAYNRSDYLEQRRPMMQWWADFVM 394
Phage_integrase pfam00589
Phage integrase family; Members of this family cleave DNA substrates by a series of staggered ...
 85-233 1.15e-08

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: 53.48  E-value: 1.15e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1873298962  85 WLTLEELrvvmEQFAGATNVGPLMQH---LIRFCvYAGGQRPFEMIASQWSAIDWQQKTLLViaDVSKNKREHLIPLTE- 160
Cdd:pfam00589   1 RLTEDEV----ERLLDAAETGPLSIRdkaLLELL-YATGLRISELCSLRWSDIDFENGVIRV--HRGKGNKERTVPLSDa 73

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1873298962 161 --SALQELASVKELTKESNSpYIFPlstngdrpvrtdSLARSIMYFRAFNPEFK----------VFTARDLRRTCKTLMG 228
Cdd:pfam00589  74 alELLKEWLSKRLLEAPKSD-YLFA------------SKRGKPLSRQTVRKIFKragkeaglelPLHPHMLRHSFATHLL 140


                  ....*
gi 1873298962 229 EAGIS 233
Cdd:pfam00589 141 EAGVD 145
 
Name Accession Description Interval E-value
INT_P4_C cd00801
Bacteriophage P4 integrase, C-terminal catalytic domain; P4-like integrases are found in ...
 87-273 4.67e-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: 4.67e-54
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1873298962  87 TLEELRVVMEQFaGATNVGPLMQHLIRFCVyAGGQRPFEMIASQWSAIDWQQKTLLVIADVSKNKREHLIPLTESALQEL 166
Cdd:cd00801     1 SPDELPELWRAL-DTANLSPPTKLALRLLL-LTGQRIGELARARWSEIDLEEKTWTIPAERTKNKRPHRVPLSDQALEIL 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1873298962 167 ASVKELTKesNSPYIFPLSTNGDRPVRTDSLARSImyfRAFNPEFKVFTARDLRRTCKTLMGEAGISKEIRDRIQNHALN 246
Cdd:cd00801    79 EELKEFTG--DSGYLFPSRRKKKKPISENTINKAL---KRLGYKGKEFTPHDLRRTFSTLLNELGIDPEVIERLLNHVLG 153

                         170       180
                  ....*....|....*....|....*..
gi 1873298962 247 DVSSKHYDRYDYLPEKRRALEIWEDRV 273
Cdd:cd00801   154 GVVRAAYNRYDYLEERREALQAWADYL 180
FimB COG0582
Integrase/recombinase, includes phage integrase [Replication, recombination and repair, ...
 1-273 3.09e-48

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


Pssm-ID: 440347 [Multi-domain]  Cd Length: 391  Bit Score: 165.21  E-value: 3.09e-48
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1873298962   1 VIPR--ETKAKDVTPLQIKTILSGIIQRDAVVHANRIRSYLMAAFNYGLKadndpintsvgiTFGLEVNPVSAIPKQSSA 78
Cdd:COG0582   130 IFPVlgDRPIAEITPPDLLAVLRPIEARGAPETARRVRQRLRQVFRYAVA------------RGLIERNPAADLKGALPK 197

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1873298962  79 EKVG-DTWLTLEELRVVMEQFAGAtNVGPLMQHLIRFCVYaGGQRPFEMIASQWSAIDWQQKTLLVIADVSKNKREHLIP 157
Cdd:COG0582   198 PKVKhHPALTPEELPELLRALDAY-RGSPVTRLALRLLLL-TGVRPGELRGARWSEIDLEAALWTIPAERMKTRRPHIVP 275

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1873298962 158 LTESALQELASVKELTkeSNSPYIFPLSTNGDRPVRTDSLARsimYFRAfnPEFKVFTARDLRRTCKTLMGEAGISKEIR 237
Cdd:COG0582   276 LSRQALEILKELKPLT--GDSEYVFPSRRGPKKPMSENTLNK---ALRR--MGYGRFTPHGFRHTASTLLNEAGFPPDVI 348

                         250       260       270
                  ....*....|....*....|....*....|....*.
gi 1873298962 238 DRIQNHALNDVSSKHYDRYDYLPEKRRALEIWEDRV 273
Cdd:COG0582   349 ERQLAHKDGNKVRAAYNRADYLEERREMMQWWADYL 384
XerD COG4974
Site-specific recombinase XerD [Replication, recombination and repair];
9-265 3.01e-21

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


Pssm-ID: 443999 [Multi-domain]  Cd Length: 291  Bit Score: 90.82  E-value: 3.01e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1873298962   9 KDVTPLQIKTILSGIIQRD-AVVHANRIRSYLMAAFNYGLKADndpintsvgitfGLEVNPVSAIPKQSSAEKVgDTWLT 87
Cdd:COG4974    48 AEITPEDIRAYLNYLRERGlSPSTINRYLAALRSFFRYAVREG------------LLEDNPAAKVKLPKKPRKL-PRVLT 114

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1873298962  88 LEELRVVMEQFAGATNVGPLMQHLIRFCvYAGGQRPFEMIASQWSAIDWQQKTLLVIAdvSKNKREHLIPLTESALQELA 167
Cdd:COG4974   115 EEEIEALLEALDTETPEGLRDRALLLLL-YATGLRVSELLGLKWSDIDLDRGTIRVRR--GKGGKERTVPLSPEALEALR 191

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1873298962 168 SVKELTKESNSPYIFPlSTNGdRPVRTDSLARSI-MYFRAFNPEFKVfTARDLRRTCKTLMGEAGISKEIRDRIQNHAln 246
Cdd:COG4974   192 EYLEERRPRDSDYLFP-TRRG-RPLSRRAIRKILkRLAKRAGIPKRV-TPHSLRHTFATHLLEAGVDLRTVQELLGHS-- 266

                         250       260
                  ....*....|....*....|
gi 1873298962 247 DVSS-KHYDRYDylPEKRRA 265
Cdd:COG4974   267 SISTtQIYTHVS--DEELRE 284
XerC COG4973
Site-specific recombinase XerC [Replication, recombination and repair];
10-258 3.37e-13

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


Pssm-ID: 443998 [Multi-domain]  Cd Length: 287  Bit Score: 68.45  E-value: 3.37e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1873298962  10 DVTPLQIKTILSGIIQRD-AVVHANRIRSYLMAAFNYGLKADndpintsvgitfGLEVNPVSAI--PKQssaEKVGDTWL 86
Cdd:COG4973    48 ELTPADVRRFLARLHRRGlSPRTLNRRLSALRSFFNWAVREG------------LLEANPAAGVkaPKA---PRKLPRAL 112

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1873298962  87 TLEELRVVMEQFAGATnVGPLMQHLIRFCvYAGGQRPFEMIASQWSAIDWQQKTLLVIAdvsKNKREHLIPLTESALQEL 166
Cdd:COG4973   113 TVDELAQLLDALADDP-LAVRDRAIVELL-YSTGLRLGELVGLDWEDVDLDAGEVRVRG---KTGKSRTVPLGPKALAAL 187

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1873298962 167 A---SVKELTKESNSPYIFPlSTNGdRPVRTDSLaRSIMYFRAFNPEF-KVFTARDLRRTCKTLMGEAGISKEIRDRIQN 242
Cdd:COG4973   188 RewlAVRPELAAPDEGALFP-SRRG-TRLSPRNV-QKRLRRLAKKAGLpKHVHPHDLRHSFATHLLESGGDLRAVQELLG 264

                         250
                  ....*....|....*..
gi 1873298962 243 HAlnDVSS-KHYDRYDY 258
Cdd:COG4973   265 HA--SISTtQIYTHLDF 279
PRK09692 PRK09692
integrase; Provisional
 122-274 9.70e-13

integrase; Provisional


Pssm-ID: 170049 [Multi-domain]  Cd Length: 413  Bit Score: 67.74  E-value: 9.70e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1873298962 122 RPFEMIASQWSAIDWQQKTLLVIADVSKNKREHLIPLTESALQELASVKELTkeSNSPYIFPLSTNGDRPVRTDSLarsi 201
Cdd:PRK09692  248 RPAEAAEARWEEIDIEAQEWKIPAARMKMNRDHTVPLSDEALAILEMMKPLS--GNREFIFPSRIKPNQPMNSQTV---- 321

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1873298962 202 myfrafNPEFK------VFTARDLRRTCKTLMGEAGISKEIRDRIQNHALNDVSSKHYDRYDYLPEKRRALEIWEDRVN 274
Cdd:PRK09692  322 ------NAALKraglggVLVSHGLRSIASTALNEQGFPPDVIEAALAHVDKNEVRRAYNRSDYLEQRRPMMQWWADFVM 394
INT_Rci_Hp1_C cd00796
Shufflon-specific DNA recombinase Rci and Bacteriophage Hp1_like integrase, C-terminal ...
 83-256 3.12e-09

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: 55.03  E-value: 3.12e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1873298962  83 DTWLTLEELRVVMEQFAGATNvgPLMQHLIRFCVYAGgQRPFEMIASQWSAIDWQQKTllVIADVSKNKREHLIPLTESA 162
Cdd:cd00796     2 DRFLTEDEEARLLAALEESTN--PHLRLIVLLALYTG-ARRGEILSLRWDDIDLEVGL--IVLPETKNGKPRTVPLSDEA 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1873298962 163 LQELasvKELTKESNSPYIFPlsTNGDRPVRTDSLARSIMyfRAF-NPEFKVFTARDLRRTCKTLMGEAGIS-KEIRdRI 240
Cdd:cd00796    77 IAIL---KELKRKRGKDGFFV--DGRFFGIPIASLRRAFK--KARkRAGLEDLRFHDLRHTFASRLVQAGVPiKTVA-KI 148

                         170
                  ....*....|....*.
gi 1873298962 241 QNHAlndvSSKHYDRY 256
Cdd:cd00796   149 LGHS----SIKMTMRY 160
Phage_integrase pfam00589
Phage integrase family; Members of this family cleave DNA substrates by a series of staggered ...
 85-233 1.15e-08

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: 53.48  E-value: 1.15e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1873298962  85 WLTLEELrvvmEQFAGATNVGPLMQH---LIRFCvYAGGQRPFEMIASQWSAIDWQQKTLLViaDVSKNKREHLIPLTE- 160
Cdd:pfam00589   1 RLTEDEV----ERLLDAAETGPLSIRdkaLLELL-YATGLRISELCSLRWSDIDFENGVIRV--HRGKGNKERTVPLSDa 73

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1873298962 161 --SALQELASVKELTKESNSpYIFPlstngdrpvrtdSLARSIMYFRAFNPEFK----------VFTARDLRRTCKTLMG 228
Cdd:pfam00589  74 alELLKEWLSKRLLEAPKSD-YLFA------------SKRGKPLSRQTVRKIFKragkeaglelPLHPHMLRHSFATHLL 140


                  ....*
gi 1873298962 229 EAGIS 233
Cdd:pfam00589 141 EAGVD 145
DNA_BRE_C cd00397
DNA breaking-rejoining enzymes, C-terminal catalytic domain; The DNA breaking-rejoining enzyme ...
 90-257 1.52e-07

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: 50.17  E-value: 1.52e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1873298962  90 ELRVVMEQFAGATNVGPLMQHLIRFCvYAGGQRPFEMIASQWSAIDWQQKTLLVIADVSKNKREHLIPLTESALQELAS- 168
Cdd:cd00397     1 ELEKLLDAIDEDKKIDLRDRAILLLL-LETGLRISELLALKVKDIDLDNGTIRVRGKKTKGGKERTVPLPKELAEELKEy 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1873298962 169 VKELTKESNSPYIFPLSTNGDRPVRTDSLARSIM--YF-RAFNPEFKVFTARDLRRTCKTLMGEAGIS-KEIRDRiqnha 244
Cdd:cd00397    80 LKERRDKRGPLLKSLYLNKLFGTKLGERLSRRTLrrIFkKAGIEAGRKITPHSLRHTFATNLLENGVDiKVVQKL----- 154

                         170
                  ....*....|...
gi 1873298962 245 LNDVSSKHYDRYD 257
Cdd:cd00397   155 LGHSSISTTQRYL 167
INT_RitA_C_like cd01188
C-terminal catalytic domain of recombinase RitA, a component of the recombinase trio; ...
 87-238 2.64e-06

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: 46.85  E-value: 2.64e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1873298962  87 TLEELRVVMEQFAGATNVGpLMQHLIRFCVYAGGQRPFEMIASQWSAIDWQQKTLLVIAdvSKNKREHLIPLTESALQEL 166
Cdd:cd01188     1 SPDEVRRLLAAIDRLTPVG-LRDYAILLLLARLGLRAGDVAGLRLDDIDWRSGTITVRQ--KKTGRPVELPLTEPVGEAL 77

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1873298962 167 AS-VKELTKESNSPYIFPLSTNGDRPVRTDSLARSIM--YFRAFNPEFKVFTARDLRRTCKTLMGEAGIS-KEIRD 238
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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