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Protein

Diguanylate cyclase DosC

Gene

dosC

Organism
Escherichia coli (strain K12)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Globin-coupled heme-based oxygen sensor protein displaying diguanylate cyclase (DGC) activity in response to oxygen availability. Thus, catalyzes the synthesis of cyclic diguanylate (c-di-GMP) via the condensation of 2 GTP molecules. Is involved in the modulation of intracellular c-di-GMP levels, in association with DosP which catalyzes the degradation of c-di-GMP (PDE activity). Cyclic-di-GMP is a second messenger which controls cell surface-associated traits in bacteria. DosC regulates biofilm formation through the oxygen-dependent activation of the csgBAC operon, which encodes curli structural subunits, while not affecting the expression of the regulatory operon csgDEFG. DosC, but not the other DGCs in E.coli, also promotes the production of the exopolysaccharide poly-N-acetylglucosamine (PNAG) through up-regulation of the expression of the PNAG biosynthetic pgaABCD operon, independently of CsrA.
Overexpression leads to an increased level of c-di-GMP, which leads to changes in the cell surface, to abnormal cell division, increased biofilm formation and decreased swimming (the latter 2 in strain W3110). In a strain able to produce cellulose (strain TOB1, a fecal isolate) overexpression leads to an increase in cellulose production.

Catalytic activityi

2 GTP = 2 diphosphate + cyclic di-3',5'-guanylate.2 Publications

Cofactori

Protein has several cofactor binding sites:
  • hemeNote: Binds 1 heme group per subunit. The Fe2+ state binds O(2) and CO while the Fe3+ state can bind CN- and imidazole.
  • Mg2+By similarityNote: Binds 1 Mg2+ ion per subunit.By similarity

Enzyme regulationi

Activity depends on O(2)-binding and heme redox state: the Fe(III), Fe(II)-O2, and Fe(II)-CO complexes of DosC are active forms, whereas Fe(II) and Fe(II)-NO complexes are inactive forms.1 Publication

Redox potential

E0 is -17 mV.

Kineticsi

The Fe(III), Fe(II)-O2, and Fe(II)-CO complexes of DosC display DGC activity with turnover numbers of 0.066, 0.022, and 0.022 min(-1), respectively. The DGC reaction catalyzed by DosC is the rate-determining step for c-di-GMP homeostasis. Binds O2, CO, cyanide and imidazole with a dissociation constant of 14 µM, 0.095 µM, 4.7 µM and 0.055 µM, respectively.1 Publication

      Pathwayi: 3',5'-cyclic di-GMP biosynthesis

      This protein is involved in the pathway 3',5'-cyclic di-GMP biosynthesis, which is part of Purine metabolism.
      View all proteins of this organism that are known to be involved in the pathway 3',5'-cyclic di-GMP biosynthesis and in Purine metabolism.

      Sites

      Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
      Sitei43 – 431Involved in oxygen binding and important for the stability of the Fe(II)-O(2) complex
      Sitei60 – 601Important for oxygen binding and stability of the Fe(II)-O(2) complex
      Sitei65 – 651Critical for restricting water access to the heme distal side to avoid rapid autoxidation
      Metal bindingi98 – 981Iron (heme proximal ligand)
      Metal bindingi333 – 3331MagnesiumBy similarity
      Sitei338 – 3381Transition state stabilizerSequence analysis
      Binding sitei341 – 3411SubstrateBy similarity
      Binding sitei350 – 3501SubstrateBy similarity
      Active sitei376 – 3761Proton acceptorSequence analysis
      Metal bindingi376 – 3761MagnesiumBy similarity

      GO - Molecular functioni

      • diguanylate cyclase activity Source: EcoCyc
      • GTP binding Source: UniProtKB-KW
      • heme binding Source: EcoCyc
      • metal ion binding Source: UniProtKB-KW
      • oxygen binding Source: EcoCyc

      GO - Biological processi

      Complete GO annotation...

      Keywords - Molecular functioni

      Transferase

      Keywords - Biological processi

      Transcription, Transcription regulation

      Keywords - Ligandi

      GTP-binding, Heme, Iron, Magnesium, Metal-binding, Nucleotide-binding

      Enzyme and pathway databases

      BioCyciEcoCyc:G6784-MONOMER.
      ECOL316407:JW5241-MONOMER.
      MetaCyc:G6784-MONOMER.
      BRENDAi2.7.7.65. 2026.
      UniPathwayiUPA00599.

      Names & Taxonomyi

      Protein namesi
      Recommended name:
      Diguanylate cyclase DosC (EC:2.7.7.65)
      Short name:
      DGC
      Alternative name(s):
      Direct oxygen-sensing cyclase
      Gene namesi
      Name:dosC
      Synonyms:yddV
      Ordered Locus Names:b1490, JW5241
      OrganismiEscherichia coli (strain K12)
      Taxonomic identifieri83333 [NCBI]
      Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
      Proteomesi
      • UP000000318 Componenti: Chromosome
      • UP000000625 Componenti: Chromosome

      Organism-specific databases

      EcoGeneiEG13793. dosC.

      Pathology & Biotechi

      Disruption phenotypei

      Disruption results in a 2.5-fold reduction in surface adhesion, a 3.5-fold reduction in biofilm formation, a large reduction in curli production, a drastic decrease in csgB expression (400-fold reduction in aerobic growth) and in an approximately 3.5-fold reduction in pgaA transcript levels in comparison with wild-type. Disruption partially suppresses the reduced motility of a yhjH disruption; concomitant disruption of dosC, yegE, yedQ and yfiN completely restores motility, suggesting these 4 genes, together with the c-di-GMP phosphodiesterase YhjH, form a network that regulates cell motility by altering levels of c-di-GMP.3 Publications

      Mutagenesis

      Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
      Mutagenesisi43 – 431Y → A or L: Same biofilm formation activity as wild-type. Large decrease in O(2) affinity. 1 Publication
      Mutagenesisi43 – 431Y → F or W: Same biofilm formation activity as wild-type. Markedly enhanced O(2) dissociation but not association rate constants. Highly enhanced autoxidation rate constant. 1 Publication
      Mutagenesisi60 – 601Q → A or E: Same biofilm formation activity as wild-type. Enhanced O(2) dissociation but not association rate constants. Enhanced autoxidation rate constant. 1 Publication
      Mutagenesisi60 – 601Q → L: Same biofilm formation activity as wild-type. 5-fold reduction in O(2) dissociation rate constant. Significant decrease in the autoxidation rate constant. 1 Publication
      Mutagenesisi65 – 651L → G or T: Enhanced autoxidation rate constant. Markedly enhanced O(2) association rate constant. 1 Publication
      Mutagenesisi65 – 651L → M or Q: Enhanced autoxidation rate constant. Decrease in O(2) association rate constant. 1 Publication
      Mutagenesisi98 – 981H → A: Same biofilm formation activity as wild-type. Loss of heme-binding ability. 1 Publication
      Mutagenesisi223 – 2231H → A: Same biofilm formation activity as wild-type. 1 Publication
      Mutagenesisi365 – 3651R → A: Same biofilm formation activity as wild-type. 1 Publication
      Mutagenesisi368 – 3681D → A: Lacks biofilm formation activity, and thus is probably devoid of diguanylate cyclase activity. 1 Publication
      Mutagenesisi376 – 3772DE → AA: Loss of DGC activity. Stimulation of PNAG production and activation of pgaABCD expression are abolished. 1 Publication
      Mutagenesisi376 – 3761D → A: Lacks biofilm formation activity, and thus is probably devoid of diguanylate cyclase activity. 1 Publication
      Mutagenesisi377 – 3771E → A: Lacks biofilm formation activity, and thus is probably devoid of diguanylate cyclase activity. 1 Publication

      PTM / Processingi

      Molecule processing

      Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
      Chaini1 – 460460Diguanylate cyclase DosCPRO_0000201321Add
      BLAST

      Proteomic databases

      EPDiP0AA89.
      PaxDbiP0AA89.
      PRIDEiP0AA89.

      Expressioni

      Inductioni

      By RpoS in the late exponential growth phase and upon entry into stationary phase. Expression is higher at 28 than 37 degrees Celsius. In rich medium DosC and YdaM are the major RpoS-dependent GGDEF-domain containing proteins in the cell, whereas in minimal medium it is the major RpoS-dependent GGDEF-domain containing protein. Highly expressed on solid medium. A member of the dosCP operon.2 Publications

      Interactioni

      Subunit structurei

      Forms a complex with DosP.

      Protein-protein interaction databases

      BioGridi4262162. 6 interactions.
      STRINGi511145.b1490.

      Structurei

      Secondary structure

      1
      460
      Legend: HelixTurnBeta strand
      Show more details
      Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
      Helixi8 – 1811Combined sources
      Helixi21 – 4828Combined sources
      Helixi50 – 534Combined sources
      Helixi59 – 7719Combined sources
      Helixi81 – 833Combined sources
      Helixi84 – 10118Combined sources
      Helixi105 – 12420Combined sources
      Beta strandi126 – 1283Combined sources
      Helixi130 – 15223Combined sources
      Helixi178 – 20326Combined sources
      Helixi212 – 2143Combined sources
      Helixi216 – 2238Combined sources
      Helixi225 – 2284Combined sources
      Turni229 – 2313Combined sources
      Helixi233 – 25422Combined sources
      Helixi256 – 2605Combined sources
      Helixi262 – 29130Combined sources
      Helixi299 – 3024Combined sources
      Beta strandi303 – 3053Combined sources
      Helixi306 – 3083Combined sources
      Helixi309 – 32315Combined sources
      Beta strandi327 – 3348Combined sources
      Helixi337 – 3448Combined sources
      Helixi346 – 36318Combined sources
      Beta strandi368 – 3747Combined sources
      Beta strandi377 – 3848Combined sources
      Helixi387 – 40216Combined sources
      Beta strandi409 – 4113Combined sources
      Beta strandi418 – 4247Combined sources
      Helixi431 – 44717Combined sources
      Beta strandi453 – 4553Combined sources

      3D structure databases

      Select the link destinations:
      PDBei
      RCSB PDBi
      PDBji
      Links Updated
      EntryMethodResolution (Å)ChainPositionsPDBsum
      4ZVAX-ray2.00A/B8-170[»]
      4ZVBX-ray2.40A/B/C/D1-155[»]
      4ZVCX-ray1.50A/B173-298[»]
      4ZVDX-ray1.90A/B173-298[»]
      4ZVEX-ray1.20A297-460[»]
      4ZVFX-ray1.15A297-460[»]
      4ZVGX-ray2.20A/B297-460[»]
      4ZVHX-ray3.30A/B297-460[»]
      ProteinModelPortaliP0AA89.
      SMRiP0AA89. Positions 271-455.
      ModBaseiSearch...
      MobiDBiSearch...

      Family & Domainsi

      Domains and Repeats

      Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
      Domaini325 – 458134GGDEFPROSITE-ProRule annotationAdd
      BLAST

      Domaini

      Is composed of an N-terminal sensory globin-fold domain that binds heme and oxygen, and a C-terminal GGDEF diguanylate cyclase domain.1 Publication

      Sequence similaritiesi

      Contains 1 GGDEF domain.PROSITE-ProRule annotation

      Phylogenomic databases

      eggNOGiENOG4105BZU. Bacteria.
      ENOG410XNMH. LUCA.
      HOGENOMiHOG000006777.
      InParanoidiP0AA89.
      KOiK13069.
      OMAiDGHPDYE.
      OrthoDBiEOG6G4VQG.

      Family and domain databases

      Gene3Di1.10.490.10. 1 hit.
      InterProiIPR000160. GGDEF_dom.
      IPR009050. Globin-like.
      IPR012292. Globin/Proto.
      IPR029787. Nucleotide_cyclase.
      [Graphical view]
      PfamiPF00990. GGDEF. 1 hit.
      [Graphical view]
      SMARTiSM00267. GGDEF. 1 hit.
      [Graphical view]
      SUPFAMiSSF46458. SSF46458. 1 hit.
      SSF55073. SSF55073. 1 hit.
      TIGRFAMsiTIGR00254. GGDEF. 1 hit.
      PROSITEiPS50887. GGDEF. 1 hit.
      [Graphical view]

      Sequencei

      Sequence statusi: Complete.

      P0AA89-1 [UniParc]FASTAAdd to basket

      « Hide

              10         20         30         40         50
      MEMYFKRMKD EWTGLVEQAD PPIRAKAAEI AVAHAHYLSI EFYRIVRIDP
      60 70 80 90 100
      HAEEFLSNEQ VERQLKSAME RWIINVLSAQ VDDVERLIQI QHTVAEVHAR
      110 120 130 140 150
      IGIPVEIVEM GFRVLKKILY PVIFSSDYSA AEKLQVYHFS INSIDIAMEV
      160 170 180 190 200
      MTRAFTFSDS SASKEDENYR IFSLLENAEE EKERQIASIL SWEIDIIYKI
      210 220 230 240 250
      LLDSDLGSSL PLSQADFGLW FNHKGRHYFS GIAEVGHISR LIQDFDGIFN
      260 270 280 290 300
      QTMRNTRNLN NRSLRVKFLL QIRNTVSQII TLLRELFEEV SRHEVGMDVL
      310 320 330 340 350
      TKLLNRRFLP TIFKREIAHA NRTGTPLSVL IIDVDKFKEI NDTWGHNTGD
      360 370 380 390 400
      EILRKVSQAF YDNVRSSDYV FRYGGDEFII VLTEASENET LRTAERIRSR
      410 420 430 440 450
      VEKTKLKAAN GEDIALSLSI GAAMFNGHPD YERLIQIADE ALYIAKRRGR
      460
      NRVELWKASL
      Length:460
      Mass (Da):53,178
      Last modified:September 13, 2005 - v1
      Checksum:i79168311553E61C3
      GO

      Sequence cautioni

      The sequence BAA15155.2 differs from that shown. Reason: Erroneous initiation. Translation N-terminally extended.Curated

      Sequence databases

      Select the link destinations:
      EMBLi
      GenBanki
      DDBJi
      Links Updated
      U00096 Genomic DNA. Translation: AAC74563.3.
      AP009048 Genomic DNA. Translation: BAA15155.2. Different initiation.
      PIRiE64902.
      RefSeqiNP_416007.3. NC_000913.3.
      WP_000426292.1. NZ_LN832404.1.

      Genome annotation databases

      EnsemblBacteriaiAAC74563; AAC74563; b1490.
      BAA15155; BAA15155; BAA15155.
      GeneIDi945835.
      KEGGiecj:JW5241.
      eco:b1490.
      PATRICi32118274. VBIEscCol129921_1557.

      Cross-referencesi

      Sequence databases

      Select the link destinations:
      EMBLi
      GenBanki
      DDBJi
      Links Updated
      U00096 Genomic DNA. Translation: AAC74563.3.
      AP009048 Genomic DNA. Translation: BAA15155.2. Different initiation.
      PIRiE64902.
      RefSeqiNP_416007.3. NC_000913.3.
      WP_000426292.1. NZ_LN832404.1.

      3D structure databases

      Select the link destinations:
      PDBei
      RCSB PDBi
      PDBji
      Links Updated
      EntryMethodResolution (Å)ChainPositionsPDBsum
      4ZVAX-ray2.00A/B8-170[»]
      4ZVBX-ray2.40A/B/C/D1-155[»]
      4ZVCX-ray1.50A/B173-298[»]
      4ZVDX-ray1.90A/B173-298[»]
      4ZVEX-ray1.20A297-460[»]
      4ZVFX-ray1.15A297-460[»]
      4ZVGX-ray2.20A/B297-460[»]
      4ZVHX-ray3.30A/B297-460[»]
      ProteinModelPortaliP0AA89.
      SMRiP0AA89. Positions 271-455.
      ModBaseiSearch...
      MobiDBiSearch...

      Protein-protein interaction databases

      BioGridi4262162. 6 interactions.
      STRINGi511145.b1490.

      Proteomic databases

      EPDiP0AA89.
      PaxDbiP0AA89.
      PRIDEiP0AA89.

      Protocols and materials databases

      DNASUi945835.
      Structural Biology KnowledgebaseSearch...

      Genome annotation databases

      EnsemblBacteriaiAAC74563; AAC74563; b1490.
      BAA15155; BAA15155; BAA15155.
      GeneIDi945835.
      KEGGiecj:JW5241.
      eco:b1490.
      PATRICi32118274. VBIEscCol129921_1557.

      Organism-specific databases

      EchoBASEiEB3554.
      EcoGeneiEG13793. dosC.

      Phylogenomic databases

      eggNOGiENOG4105BZU. Bacteria.
      ENOG410XNMH. LUCA.
      HOGENOMiHOG000006777.
      InParanoidiP0AA89.
      KOiK13069.
      OMAiDGHPDYE.
      OrthoDBiEOG6G4VQG.

      Enzyme and pathway databases

      UniPathwayiUPA00599.
      BioCyciEcoCyc:G6784-MONOMER.
      ECOL316407:JW5241-MONOMER.
      MetaCyc:G6784-MONOMER.
      BRENDAi2.7.7.65. 2026.

      Miscellaneous databases

      PROiP0AA89.

      Family and domain databases

      Gene3Di1.10.490.10. 1 hit.
      InterProiIPR000160. GGDEF_dom.
      IPR009050. Globin-like.
      IPR012292. Globin/Proto.
      IPR029787. Nucleotide_cyclase.
      [Graphical view]
      PfamiPF00990. GGDEF. 1 hit.
      [Graphical view]
      SMARTiSM00267. GGDEF. 1 hit.
      [Graphical view]
      SUPFAMiSSF46458. SSF46458. 1 hit.
      SSF55073. SSF55073. 1 hit.
      TIGRFAMsiTIGR00254. GGDEF. 1 hit.
      PROSITEiPS50887. GGDEF. 1 hit.
      [Graphical view]
      ProtoNetiSearch...

      Publicationsi

      « Hide 'large scale' publications
      1. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
        Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
      2. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
        Strain: K12 / MG1655 / ATCC 47076.
      3. "Highly accurate genome sequences of Escherichia coli K-12 strains MG1655 and W3110."
        Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S., Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.
        Mol. Syst. Biol. 2:E1-E5(2006) [PubMed] [Europe PMC] [Abstract]
        Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
        Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
      4. "Genome-wide transcriptional profile of Escherichia coli in response to high levels of the second messenger 3',5'-cyclic diguanylic acid."
        Mendez-Ortiz M.M., Hyodo M., Hayakawa Y., Membrillo-Hernandez J.
        J. Biol. Chem. 281:8090-8099(2006) [PubMed] [Europe PMC] [Abstract]
        Cited for: FUNCTION AS A DIGUANYLATE CYCLASE, OPERON STRUCTURE.
        Strain: K12 / MG1655 / ATCC 47076, K12 / W3110 / ATCC 27325 / DSM 5911 and TOB1.
      5. "Cyclic-di-GMP-mediated signalling within the sigma network of Escherichia coli."
        Weber H., Pesavento C., Possling A., Tischendorf G., Hengge R.
        Mol. Microbiol. 62:1014-1034(2006) [PubMed] [Europe PMC] [Abstract]
        Cited for: RPOS-DEPENDENCE.
        Strain: K12 / MC4100.
      6. "An oxygen-sensing diguanylate cyclase and phosphodiesterase couple for c-di-GMP control."
        Tuckerman J.R., Gonzalez G., Sousa E.H., Wan X., Saito J.A., Alam M., Gilles-Gonzalez M.A.
        Biochemistry 48:9764-9774(2009) [PubMed] [Europe PMC] [Abstract]
        Cited for: CATALYTIC ACTIVITY, HEME COFACTOR, O(2)-BINDING, INTERACTION WITH DOSP, OPERON STRUCTURE.
      7. "Gene expression patterns and differential input into curli fimbriae regulation of all GGDEF/EAL domain proteins in Escherichia coli."
        Sommerfeldt N., Possling A., Becker G., Pesavento C., Tschowri N., Hengge R.
        Microbiology 155:1318-1331(2009) [PubMed] [Europe PMC] [Abstract]
        Cited for: INDUCTION, RPOS-DEPENDENCE.
        Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
      8. "Important roles of Tyr43 at the putative heme distal side in the oxygen recognition and stability of the Fe(II)-O2 complex of YddV, a globin-coupled heme-based oxygen sensor diguanylate cyclase."
        Kitanishi K., Kobayashi K., Kawamura Y., Ishigami I., Ogura T., Nakajima K., Igarashi J., Tanaka A., Shimizu T.
        Biochemistry 49:10381-10393(2010) [PubMed] [Europe PMC] [Abstract]
        Cited for: FUNCTION, CATALYTIC ACTIVITY, ENZYME REGULATION, DOMAIN, O(2)-BINDING, CO-BINDING, CYANIDE-BINDING, IMIDAZOLE-BINDING, KINETIC PARAMETERS, REDOX POTENTIAL, MUTAGENESIS OF TYR-43; GLN-60; HIS-98; HIS-223; ARG-365; ASP-368; ASP-376 AND GLU-377, ABSORPTION SPECTROSCOPY, RESONANCE RAMAN SPECTROSCOPY.
        Strain: K12.
      9. "Second messenger-mediated adjustment of bacterial swimming velocity."
        Boehm A., Kaiser M., Li H., Spangler C., Kasper C.A., Ackermann M., Kaever V., Sourjik V., Roth V., Jenal U.
        Cell 141:107-116(2010) [PubMed] [Europe PMC] [Abstract]
        Cited for: ROLE IN MOTILITY, DISRUPTION PHENOTYPE.
        Strain: K12 / MG1655 / ATCC 47076.
      10. "The yddV-dos operon controls biofilm formation through the regulation of genes encoding curli fibers' subunits in aerobically growing Escherichia coli."
        Tagliabue L., Maciag A., Antoniani D., Landini P.
        FEMS Immunol. Med. Microbiol. 59:477-484(2010) [PubMed] [Europe PMC] [Abstract]
        Cited for: FUNCTION IN REGULATION OF CSGBAC EXPRESSION, DISRUPTION PHENOTYPE, INDUCTION.
        Strain: K12 / MG1655 / ATCC 47076.
      11. "The diguanylate cyclase YddV controls production of the exopolysaccharide poly-N-acetylglucosamine (PNAG) through regulation of the PNAG biosynthetic pgaABCD operon."
        Tagliabue L., Antoniani D., Maciag A., Bocci P., Raffaelli N., Landini P.
        Microbiology 156:2901-2911(2010) [PubMed] [Europe PMC] [Abstract]
        Cited for: FUNCTION IN REGULATION OF PGAABCD EXPRESSION, DISRUPTION PHENOTYPE, MUTAGENESIS OF 376-ASP-GLU-377.
        Strain: K12 / MG1655 / ATCC 47076.
      12. "Leu65 in the heme distal side is critical for the stability of the Fe(II)-O(2) complex of YddV, a globin-coupled oxygen sensor diguanylate cyclase."
        Nakajima K., Kitanishi K., Kobayashi K., Kobayashi N., Igarashi J., Shimizu T.
        J. Inorg. Biochem. 108:163-170(2012) [PubMed] [Europe PMC] [Abstract]
        Cited for: MUTAGENESIS OF LEU-65, ABSORPTION SPECTROSCOPY.
        Strain: K12.

      Entry informationi

      Entry nameiDOSC_ECOLI
      AccessioniPrimary (citable) accession number: P0AA89
      Secondary accession number(s): P77793
      Entry historyi
      Integrated into UniProtKB/Swiss-Prot: September 13, 2005
      Last sequence update: September 13, 2005
      Last modified: March 16, 2016
      This is version 93 of the entry and version 1 of the sequence. [Complete history]
      Entry statusiReviewed (UniProtKB/Swiss-Prot)
      Annotation programProkaryotic Protein Annotation Program

      Miscellaneousi

      Keywords - Technical termi

      3D-structure, Complete proteome, Reference proteome

      Documents

      1. Escherichia coli
        Escherichia coli (strain K12): entries and cross-references to EcoGene
      2. PATHWAY comments
        Index of metabolic and biosynthesis pathways
      3. PDB cross-references
        Index of Protein Data Bank (PDB) cross-references
      4. SIMILARITY comments
        Index of protein domains and families

      Similar proteinsi

      Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
      100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
      90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
      50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.