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Conserved domains on  [gi|2054843050|ref|WP_216123134|]
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site-specific integrase, partial [Acinetobacter nosocomialis]

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 ...
 1-185 1.17e-59

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: 184.01  E-value: 1.17e-59
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2054843050   1 DFMHNLKKLDAHPIIKKALMFKLYTGVRGAELLLSEPHHFDLNKKIWKIPALNIKQFRrkvilgheipDFLVPLSDQALE 80
Cdd:cd00801     7 ELWRALDTANLSPPTKLALRLLLLTGQRIGELARARWSEIDLEEKTWTIPAERTKNKR----------PHRVPLSDQALE 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2054843050  81 ILKDAMQWSLGEKFIFASPRKQNHPIHFNTLNMAIRKMGYSKHQLSSHGLRSTFSTVLNDSGlFQDNWIEAQLSHIDKNR 160
Cdd:cd00801    77 ILEELKEFTGDSGYLFPSRRKKKKPISENTINKALKRLGYKGKEFTPHDLRRTFSTLLNELG-IDPEVIERLLNHVLGGV 155

                         170       180
                  ....*....|....*....|....*
gi 2054843050 161 TRASYNHADYLIQRTEMMQWWGDYL 185
Cdd:cd00801   156 VRAAYNRYDYLEERREALQAWADYL 180
 
Name Accession Description Interval E-value
INT_P4_C cd00801
Bacteriophage P4 integrase, C-terminal catalytic domain; P4-like integrases are found in ...
 1-185 1.17e-59

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: 184.01  E-value: 1.17e-59
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2054843050   1 DFMHNLKKLDAHPIIKKALMFKLYTGVRGAELLLSEPHHFDLNKKIWKIPALNIKQFRrkvilgheipDFLVPLSDQALE 80
Cdd:cd00801     7 ELWRALDTANLSPPTKLALRLLLLTGQRIGELARARWSEIDLEEKTWTIPAERTKNKR----------PHRVPLSDQALE 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2054843050  81 ILKDAMQWSLGEKFIFASPRKQNHPIHFNTLNMAIRKMGYSKHQLSSHGLRSTFSTVLNDSGlFQDNWIEAQLSHIDKNR 160
Cdd:cd00801    77 ILEELKEFTGDSGYLFPSRRKKKKPISENTINKALKRLGYKGKEFTPHDLRRTFSTLLNELG-IDPEVIERLLNHVLGGV 155

                         170       180
                  ....*....|....*....|....*
gi 2054843050 161 TRASYNHADYLIQRTEMMQWWGDYL 185
Cdd:cd00801   156 VRAAYNRYDYLEERREALQAWADYL 180
FimB COG0582
Integrase/recombinase, includes phage integrase [Replication, recombination and repair, ...
 1-189 3.06e-59

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


Pssm-ID: 440347 [Multi-domain]  Cd Length: 391  Bit Score: 189.86  E-value: 3.06e-59
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2054843050   1 DFMHNLKKLDAHPIIKKALMFKLYTGVRGAELLLSEPHHFDLNKKIWKIPALNIKQFRrkvilgheipDFLVPLSDQALE 80
Cdd:COG0582   213 ELLRALDAYRGSPVTRLALRLLLLTGVRPGELRGARWSEIDLEAALWTIPAERMKTRR----------PHIVPLSRQALE 282

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2054843050  81 ILKDAMQWSLGEKFIFASPRKQNHPIHFNTLNMAIRKMGYSKHqlSSHGLRSTFSTVLNDSGlFQDNWIEAQLSHIDKNR 160
Cdd:COG0582   283 ILKELKPLTGDSEYVFPSRRGPKKPMSENTLNKALRRMGYGRF--TPHGFRHTASTLLNEAG-FPPDVIERQLAHKDGNK 359

                         170       180
                  ....*....|....*....|....*....
gi 2054843050 161 TRASYNHADYLIQRTEMMQWWGDYLSTVR 189
Cdd:COG0582   360 VRAAYNRADYLEERREMMQWWADYLDALR 388
PRK09692 PRK09692
integrase; Provisional
 19-185 2.22e-39

integrase; Provisional


Pssm-ID: 170049 [Multi-domain]  Cd Length: 413  Bit Score: 138.62  E-value: 2.22e-39
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2054843050  19 LMFKLYTGVRGAELLLSEPHHFDLNKKIWKIPALNIKQFRrkvilgheipDFLVPLSDQALEILKDAMQWSLGEKFIFAS 98
Cdd:PRK09692  239 FMWQLLTITRPAEAAEARWEEIDIEAQEWKIPAARMKMNR----------DHTVPLSDEALAILEMMKPLSGNREFIFPS 308

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2054843050  99 PRKQNHPIHFNTLNMAIRKMGYSKhQLSSHGLRSTFSTVLNDSGlFQDNWIEAQLSHIDKNRTRASYNHADYLIQRTEMM 178
Cdd:PRK09692  309 RIKPNQPMNSQTVNAALKRAGLGG-VLVSHGLRSIASTALNEQG-FPPDVIEAALAHVDKNEVRRAYNRSDYLEQRRPMM 386


                  ....*..
gi 2054843050 179 QWWGDYL 185
Cdd:PRK09692  387 QWWADFV 393
Phage_integrase pfam00589
Phage integrase family; Members of this family cleave DNA substrates by a series of staggered ...
 2-170 4.92e-11

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: 58.48  E-value: 4.92e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2054843050   2 FMHNLKKLDAHPIIKKALMFKLYTGVRGAELLLSEPHHFDLNKKIWKIPalNIKqfrrkviLGHEIpdfLVPLSDQALEI 81
Cdd:pfam00589  10 LLDAAETGPLSIRDKALLELLYATGLRISELCSLRWSDIDFENGVIRVH--RGK-------GNKER---TVPLSDAALEL 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2054843050  82 LKDAMQWSLGEK----FIFASprKQNHPIHFNTLNMAIRKMGY---SKHQLSSHGLRSTFSTVLNDSGLFQDNwIEAQLS 154
Cdd:pfam00589  78 LKEWLSKRLLEApksdYLFAS--KRGKPLSRQTVRKIFKRAGKeagLELPLHPHMLRHSFATHLLEAGVDLRV-VQKLLG 154

                         170
                  ....*....|....*.
gi 2054843050 155 HIDKNRTRAsYNHADY 170
Cdd:pfam00589 155 HSSISTTQI-YTHVAD 169
 
Name Accession Description Interval E-value
INT_P4_C cd00801
Bacteriophage P4 integrase, C-terminal catalytic domain; P4-like integrases are found in ...
 1-185 1.17e-59

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: 184.01  E-value: 1.17e-59
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2054843050   1 DFMHNLKKLDAHPIIKKALMFKLYTGVRGAELLLSEPHHFDLNKKIWKIPALNIKQFRrkvilgheipDFLVPLSDQALE 80
Cdd:cd00801     7 ELWRALDTANLSPPTKLALRLLLLTGQRIGELARARWSEIDLEEKTWTIPAERTKNKR----------PHRVPLSDQALE 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2054843050  81 ILKDAMQWSLGEKFIFASPRKQNHPIHFNTLNMAIRKMGYSKHQLSSHGLRSTFSTVLNDSGlFQDNWIEAQLSHIDKNR 160
Cdd:cd00801    77 ILEELKEFTGDSGYLFPSRRKKKKPISENTINKALKRLGYKGKEFTPHDLRRTFSTLLNELG-IDPEVIERLLNHVLGGV 155

                         170       180
                  ....*....|....*....|....*
gi 2054843050 161 TRASYNHADYLIQRTEMMQWWGDYL 185
Cdd:cd00801   156 VRAAYNRYDYLEERREALQAWADYL 180
FimB COG0582
Integrase/recombinase, includes phage integrase [Replication, recombination and repair, ...
 1-189 3.06e-59

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


Pssm-ID: 440347 [Multi-domain]  Cd Length: 391  Bit Score: 189.86  E-value: 3.06e-59
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2054843050   1 DFMHNLKKLDAHPIIKKALMFKLYTGVRGAELLLSEPHHFDLNKKIWKIPALNIKQFRrkvilgheipDFLVPLSDQALE 80
Cdd:COG0582   213 ELLRALDAYRGSPVTRLALRLLLLTGVRPGELRGARWSEIDLEAALWTIPAERMKTRR----------PHIVPLSRQALE 282

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2054843050  81 ILKDAMQWSLGEKFIFASPRKQNHPIHFNTLNMAIRKMGYSKHqlSSHGLRSTFSTVLNDSGlFQDNWIEAQLSHIDKNR 160
Cdd:COG0582   283 ILKELKPLTGDSEYVFPSRRGPKKPMSENTLNKALRRMGYGRF--TPHGFRHTASTLLNEAG-FPPDVIERQLAHKDGNK 359

                         170       180
                  ....*....|....*....|....*....
gi 2054843050 161 TRASYNHADYLIQRTEMMQWWGDYLSTVR 189
Cdd:COG0582   360 VRAAYNRADYLEERREMMQWWADYLDALR 388
PRK09692 PRK09692
integrase; Provisional
 19-185 2.22e-39

integrase; Provisional


Pssm-ID: 170049 [Multi-domain]  Cd Length: 413  Bit Score: 138.62  E-value: 2.22e-39
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2054843050  19 LMFKLYTGVRGAELLLSEPHHFDLNKKIWKIPALNIKQFRrkvilgheipDFLVPLSDQALEILKDAMQWSLGEKFIFAS 98
Cdd:PRK09692  239 FMWQLLTITRPAEAAEARWEEIDIEAQEWKIPAARMKMNR----------DHTVPLSDEALAILEMMKPLSGNREFIFPS 308

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2054843050  99 PRKQNHPIHFNTLNMAIRKMGYSKhQLSSHGLRSTFSTVLNDSGlFQDNWIEAQLSHIDKNRTRASYNHADYLIQRTEMM 178
Cdd:PRK09692  309 RIKPNQPMNSQTVNAALKRAGLGG-VLVSHGLRSIASTALNEQG-FPPDVIEAALAHVDKNEVRRAYNRSDYLEQRRPMM 386


                  ....*..
gi 2054843050 179 QWWGDYL 185
Cdd:PRK09692  387 QWWADFV 393
Phage_integrase pfam00589
Phage integrase family; Members of this family cleave DNA substrates by a series of staggered ...
 2-170 4.92e-11

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: 58.48  E-value: 4.92e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2054843050   2 FMHNLKKLDAHPIIKKALMFKLYTGVRGAELLLSEPHHFDLNKKIWKIPalNIKqfrrkviLGHEIpdfLVPLSDQALEI 81
Cdd:pfam00589  10 LLDAAETGPLSIRDKALLELLYATGLRISELCSLRWSDIDFENGVIRVH--RGK-------GNKER---TVPLSDAALEL 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2054843050  82 LKDAMQWSLGEK----FIFASprKQNHPIHFNTLNMAIRKMGY---SKHQLSSHGLRSTFSTVLNDSGLFQDNwIEAQLS 154
Cdd:pfam00589  78 LKEWLSKRLLEApksdYLFAS--KRGKPLSRQTVRKIFKRAGKeagLELPLHPHMLRHSFATHLLEAGVDLRV-VQKLLG 154

                         170
                  ....*....|....*.
gi 2054843050 155 HIDKNRTRAsYNHADY 170
Cdd:pfam00589 155 HSSISTTQI-YTHVAD 169
XerD COG4974
Site-specific recombinase XerD [Replication, recombination and repair];
18-142 2.46e-06

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


Pssm-ID: 443999 [Multi-domain]  Cd Length: 291  Bit Score: 46.53  E-value: 2.46e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2054843050  18 ALMFKL--YTGVRGAELLLSEPHHFDLNKKIWKIPalnikqfRRKvilGHEipDFLVPLSDQALEILKD--AMQWSLGEK 93
Cdd:COG4974   136 RALLLLlyATGLRVSELLGLKWSDIDLDRGTIRVR-------RGK---GGK--ERTVPLSPEALEALREylEERRPRDSD 203

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|...
gi 2054843050  94 FIFASPRkqNHPIHFNTLNMAIRKM----GYSKHqLSSHGLRSTFSTVLNDSG 142
Cdd:COG4974   204 YLFPTRR--GRPLSRRAIRKILKRLakraGIPKR-VTPHSLRHTFATHLLEAG 253
INT_Rci_Hp1_C cd00796
Shufflon-specific DNA recombinase Rci and Bacteriophage Hp1_like integrase, C-terminal ...
 8-167 2.55e-04

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: 39.62  E-value: 2.55e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2054843050   8 KLDAHPIIKKALMFKLYTGVRGAELLLSEPHHFDLNKKIwkIPALNIKQFRRKVilgheipdflVPLSDQALEILKDAMQ 87
Cdd:cd00796    18 EESTNPHLRLIVLLALYTGARRGEILSLRWDDIDLEVGL--IVLPETKNGKPRT----------VPLSDEAIAILKELKR 85

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2054843050  88 WSLGEKFIFASPRKQNHPIHFNTLNMAIRKM-GYSKhqLSSHGLRSTFSTVLNDSGLfqDNWIEAQLS-HIDKNRTRAsY 165
Cdd:cd00796    86 KRGKDGFFVDGRFFGIPIASLRRAFKKARKRaGLED--LRFHDLRHTFASRLVQAGV--PIKTVAKILgHSSIKMTMR-Y 160


                  ..
gi 2054843050 166 NH 167
Cdd:cd00796   161 AH 162
 
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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