NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|1413331943|emb|SRM22666|]
View 

putative Integrase [Shigella flexneri]

Protein Classification

site-specific integrase( domain architecture ID 332)

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:  10577069|10047575|9278480
SCOP:  4002347

Graphical summary

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

List of domain hits

 Name Accession Description Interval E-value
FimB super family cl43194
Integrase/recombinase, includes phage integrase [Replication, recombination and repair, ...
 9-209 6.16e-17

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


The actual alignment was detected with superfamily member COG0582:

Pssm-ID: 440347 [Multi-domain]  Cd Length: 391  Bit Score: 78.16  E-value: 6.16e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1413331943   9 TFGEREVfSDVTYNRLVEVLDEWIATRSNNNALELFAELRRFWKFCAPTLCNGRNVAASLPDDYVSSRVQKPtptRLFTD 88
Cdd:COG0582   133 VLGDRPI-AEITPPDLLAVLRPIEARGAPETARRVRQRLRQVFRYAVARGLIERNPAADLKGALPKPKVKHH---PALTP 208

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1413331943  89 IEsIARLWLNVAACTSVHQ-KNAVRFMIITGVRPINVHNLRWDYVYEEAGEIVYPEGVigmrgaMKTQKAFRLPITPEIR 167
Cdd:COG0582   209 EE-LPELLRALDAYRGSPVtRLALRLLLLTGVRPGELRGARWSEIDLEAALWTIPAER------MKTRRPHIVPLSRQAL 281

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|..
gi 1413331943 168 RIIDEQKAWRdsvpeCNRDYVFLQPRDPMQPFSKRSLDKLVK 209
Cdd:COG0582   282 EILKELKPLT-----GDSEYVFPSRRGPKKPMSENTLNKALR 318
 
Name Accession Description Interval E-value
FimB COG0582
Integrase/recombinase, includes phage integrase [Replication, recombination and repair, ...
 9-209 6.16e-17

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


Pssm-ID: 440347 [Multi-domain]  Cd Length: 391  Bit Score: 78.16  E-value: 6.16e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1413331943   9 TFGEREVfSDVTYNRLVEVLDEWIATRSNNNALELFAELRRFWKFCAPTLCNGRNVAASLPDDYVSSRVQKPtptRLFTD 88
Cdd:COG0582   133 VLGDRPI-AEITPPDLLAVLRPIEARGAPETARRVRQRLRQVFRYAVARGLIERNPAADLKGALPKPKVKHH---PALTP 208

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1413331943  89 IEsIARLWLNVAACTSVHQ-KNAVRFMIITGVRPINVHNLRWDYVYEEAGEIVYPEGVigmrgaMKTQKAFRLPITPEIR 167
Cdd:COG0582   209 EE-LPELLRALDAYRGSPVtRLALRLLLLTGVRPGELRGARWSEIDLEAALWTIPAER------MKTRRPHIVPLSRQAL 281

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|..
gi 1413331943 168 RIIDEQKAWRdsvpeCNRDYVFLQPRDPMQPFSKRSLDKLVK 209
Cdd:COG0582   282 EILKELKPLT-----GDSEYVFPSRRGPKKPMSENTLNKALR 318
INT_P4_C cd00801
Bacteriophage P4 integrase, C-terminal catalytic domain; P4-like integrases are found in ...
 88-215 3.52e-16

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: 73.07  E-value: 3.52e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1413331943  88 DIESIARLWLNVAACT-SVHQKNAVRFMIITGVRPINVHNLRWDYVYEEAGEIVYPEGVigmrgaMKTQKAFRLPITPEI 166
Cdd:cd00801     1 SPDELPELWRALDTANlSPPTKLALRLLLLTGQRIGELARARWSEIDLEEKTWTIPAER------TKNKRPHRVPLSDQA 74

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*....
gi 1413331943 167 RRIIDEQKAWRDsvpecNRDYVFLQPRDPMQPFSKRSLDKLVKTYSPDG 215
Cdd:cd00801    75 LEILEELKEFTG-----DSGYLFPSRRKKKKPISENTINKALKRLGYKG 118
 
Name Accession Description Interval E-value
FimB COG0582
Integrase/recombinase, includes phage integrase [Replication, recombination and repair, ...
 9-209 6.16e-17

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


Pssm-ID: 440347 [Multi-domain]  Cd Length: 391  Bit Score: 78.16  E-value: 6.16e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1413331943   9 TFGEREVfSDVTYNRLVEVLDEWIATRSNNNALELFAELRRFWKFCAPTLCNGRNVAASLPDDYVSSRVQKPtptRLFTD 88
Cdd:COG0582   133 VLGDRPI-AEITPPDLLAVLRPIEARGAPETARRVRQRLRQVFRYAVARGLIERNPAADLKGALPKPKVKHH---PALTP 208

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1413331943  89 IEsIARLWLNVAACTSVHQ-KNAVRFMIITGVRPINVHNLRWDYVYEEAGEIVYPEGVigmrgaMKTQKAFRLPITPEIR 167
Cdd:COG0582   209 EE-LPELLRALDAYRGSPVtRLALRLLLLTGVRPGELRGARWSEIDLEAALWTIPAER------MKTRRPHIVPLSRQAL 281

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|..
gi 1413331943 168 RIIDEQKAWRdsvpeCNRDYVFLQPRDPMQPFSKRSLDKLVK 209
Cdd:COG0582   282 EILKELKPLT-----GDSEYVFPSRRGPKKPMSENTLNKALR 318
INT_P4_C cd00801
Bacteriophage P4 integrase, C-terminal catalytic domain; P4-like integrases are found in ...
 88-215 3.52e-16

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: 73.07  E-value: 3.52e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1413331943  88 DIESIARLWLNVAACT-SVHQKNAVRFMIITGVRPINVHNLRWDYVYEEAGEIVYPEGVigmrgaMKTQKAFRLPITPEI 166
Cdd:cd00801     1 SPDELPELWRALDTANlSPPTKLALRLLLLTGQRIGELARARWSEIDLEEKTWTIPAER------TKNKRPHRVPLSDQA 74

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*....
gi 1413331943 167 RRIIDEQKAWRDsvpecNRDYVFLQPRDPMQPFSKRSLDKLVKTYSPDG 215
Cdd:cd00801    75 LEILEELKEFTG-----DSGYLFPSRRKKKKPISENTINKALKRLGYKG 118
XerC COG4973
Site-specific recombinase XerC [Replication, recombination and repair];
2-209 2.27e-11

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


Pssm-ID: 443998 [Multi-domain]  Cd Length: 287  Bit Score: 61.52  E-value: 2.27e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1413331943   2 RIDRIKVTFGEREV-FSDVTYNRLVEVLDEW----IATRSNNNALELfaeLRRFWKFCAPtlcngRNVAASLPDDYVSS- 75
Cdd:COG4973    31 DLRRLIPLLGDADLpLEELTPADVRRFLARLhrrgLSPRTLNRRLSA---LRSFFNWAVR-----EGLLEANPAAGVKAp 102

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1413331943  76 RVQKPTPTRLftDIESIARLW-LNVAACTSVHQKNAVRFMIITGVRPINVHNLRWDYVYEEAGEIVypegVIGmrgamKT 154
Cdd:COG4973   103 KAPRKLPRAL--TVDELAQLLdALADDPLAVRDRAIVELLYSTGLRLGELVGLDWEDVDLDAGEVR----VRG-----KT 171

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1413331943 155 QKAFRLPITPEIRRIIDEQKAWRDSVPECNRDYVFLQPRDpmQPFSKRSLDKLVK 209
Cdd:COG4973   172 GKSRTVPLGPKALAALREWLAVRPELAAPDEGALFPSRRG--TRLSPRNVQKRLR 224
XerD COG4974
Site-specific recombinase XerD [Replication, recombination and repair];
16-211 1.62e-10

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


Pssm-ID: 443999 [Multi-domain]  Cd Length: 291  Bit Score: 59.24  E-value: 1.62e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1413331943  16 FSDVTYNRLVEVLDEW----IATRSNNNALelfAELRRFWKFCAPtlcngRNVAASLPDDYVSS-RVQKPTPTRLftDIE 90
Cdd:COG4974    47 LAEITPEDIRAYLNYLrergLSPSTINRYL---AALRSFFRYAVR-----EGLLEDNPAAKVKLpKKPRKLPRVL--TEE 116

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1413331943  91 SIARLWLNVAACTSVHQKNA--VRFMIITGVRPINVHNLRWDYVYEEAGEIVYPEGvigmrgamKTQKAFRLPITPEIRR 168
Cdd:COG4974   117 EIEALLEALDTETPEGLRDRalLLLLYATGLRVSELLGLKWSDIDLDRGTIRVRRG--------KGGKERTVPLSPEALE 188

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|...
gi 1413331943 169 IIdeqKAWRDSVPECNRDYVFLQPRDpmQPFSKRSLDKLVKTY 211
Cdd:COG4974   189 AL---REYLEERRPRDSDYLFPTRRG--RPLSRRAIRKILKRL 226
INT_RitA_C_like cd01188
C-terminal catalytic domain of recombinase RitA, a component of the recombinase trio; ...
 90-203 1.77e-05

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: 43.77  E-value: 1.77e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1413331943  90 ESIARLWLNVAACTSVHQKNA--VRFMIITGVRPINVHNLRWDyvyeeagEIVYPEGVIGMRGAmKTQKAFRLPITPEIR 167
Cdd:cd01188     3 DEVRRLLAAIDRLTPVGLRDYaiLLLLARLGLRAGDVAGLRLD-------DIDWRSGTITVRQK-KTGRPVELPLTEPVG 74

                          90       100       110
                  ....*....|....*....|....*....|....*..
gi 1413331943 168 R-IIDEQKAWRdsvPECNRDYVFLQPRDPMQPFSKRS 203
Cdd:cd01188    75 EaLADYLRDGR---PRTDSREVFLRARAPYRPLSSTS 108
INTN1_C_like cd01185
Integrase IntN1 of Bacteroides mobilizable transposon NBU1 and similar proteins, C-terminal ...
 113-192 1.39e-04

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: 40.71  E-value: 1.39e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1413331943 113 FMIITGVRPINVHNLRWD--YVYEEAGEIVYPegvigmrgAMKTQKAFRLPITPEIRRIIDEQKAWRDSvpecnrDYVFL 190
Cdd:cd01185    26 FSCYTGLRFSDLKNLTWKniVEASGRTWIRYR--------RKKTGKPVTVPLLPVAREILEKYKDDRSE------GKLFP 91


                  ..
gi 1413331943 191 QP 192
Cdd:cd01185    92 VL 93
INT_Rci_Hp1_C cd00796
Shufflon-specific DNA recombinase Rci and Bacteriophage Hp1_like integrase, C-terminal ...
 82-209 3.59e-03

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: 36.92  E-value: 3.59e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1413331943  82 PTRLFTDIEsIARLWLNVAACTSVHQKNAVRFMIITGVRPINVHNLRWDYVYEEAGEIVYPEgvigmrgaMKTQKAFRLP 161
Cdd:cd00796     1 RDRFLTEDE-EARLLAALEESTNPHLRLIVLLALYTGARRGEILSLRWDDIDLEVGLIVLPE--------TKNGKPRTVP 71

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*...
gi 1413331943 162 ITPEIRRIIDEQKAWRDSvpecNRDYVFLQPRDPMQPFSKRSLDKLVK 209
Cdd:cd00796    72 LSDEAIAILKELKRKRGK----DGFFVDGRFFGIPIASLRRAFKKARK 115
 
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.
Help | Disclaimer | Write to the Help Desk
NCBI | NLM | NIH