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P00582

- DPO1_ECOLI

UniProt

P00582 - DPO1_ECOLI

Protein

DNA polymerase I

Gene

polA

Organism
Escherichia coli (strain K12)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 163 (01 Oct 2014)
      Sequence version 1 (21 Jul 1986)
      Previous versions | rss
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    Functioni

    In addition to polymerase activity, this DNA polymerase exhibits 3' to 5' and 5' to 3' exonuclease activity. It is able to utilize nicked circular duplex DNA as a template and can unwind the parental DNA strand from its template.

    Catalytic activityi

    Deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1).

    GO - Molecular functioni

    1. 3'-5' exonuclease activity Source: EcoCyc
    2. 5'-3' exonuclease activity Source: EcoCyc
    3. DNA binding Source: EcoCyc
    4. DNA-directed DNA polymerase activity Source: EcoCyc

    GO - Biological processi

    1. base-excision repair Source: EcoCyc
    2. DNA-dependent DNA replication Source: EcoCyc
    3. DNA repair Source: EcoCyc
    4. DNA replication Source: EcoCyc
    5. nucleic acid phosphodiester bond hydrolysis Source: GOC

    Keywords - Molecular functioni

    DNA-directed DNA polymerase, Exonuclease, Hydrolase, Nuclease, Nucleotidyltransferase, Transferase

    Keywords - Biological processi

    DNA damage, DNA repair, DNA replication

    Keywords - Ligandi

    DNA-binding

    Enzyme and pathway databases

    BioCyciEcoCyc:EG10746-MONOMER.
    ECOL316407:JW3835-MONOMER.
    MetaCyc:EG10746-MONOMER.
    RETL1328306-WGS:GSTH-159-MONOMER.
    SABIO-RKP00582.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    DNA polymerase I (EC:2.7.7.7)
    Short name:
    POL I
    Gene namesi
    Name:polA
    Synonyms:resA
    Ordered Locus Names:b3863, JW3835
    OrganismiEscherichia coli (strain K12)
    Taxonomic identifieri83333 [NCBI]
    Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
    ProteomesiUP000000318: Chromosome, UP000000625: Chromosome

    Organism-specific databases

    EcoGeneiEG10746. polA.

    Subcellular locationi

    GO - Cellular componenti

    1. cytoplasm Source: EcoCyc

    Pathology & Biotechi

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 928928DNA polymerase IPRO_0000101239Add
    BLAST

    Proteomic databases

    PaxDbiP00582.
    PRIDEiP00582.

    2D gel databases

    SWISS-2DPAGEP00582.

    Expressioni

    Gene expression databases

    GenevestigatoriP00582.

    Interactioni

    Subunit structurei

    Single-chain monomer with multiple functions.

    Protein-protein interaction databases

    DIPiDIP-10524N.
    IntActiP00582. 28 interactions.
    MINTiMINT-1225247.
    STRINGi511145.b3863.

    Structurei

    Secondary structure

    1
    928
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Beta strandi327 – 3326
    Helixi336 – 34712
    Beta strandi349 – 35911
    Turni363 – 3653
    Beta strandi368 – 3769
    Beta strandi379 – 3846
    Helixi398 – 40912
    Beta strandi416 – 4205
    Helixi421 – 4299
    Turni430 – 4323
    Beta strandi438 – 4414
    Helixi442 – 4498
    Helixi451 – 4533
    Helixi458 – 4658
    Helixi473 – 4775
    Helixi480 – 4823
    Helixi486 – 4883
    Helixi491 – 51525
    Helixi520 – 5289
    Helixi530 – 54314
    Beta strandi545 – 5473
    Helixi549 – 57325
    Beta strandi574 – 5763
    Turni582 – 5854
    Helixi587 – 5904
    Turni591 – 5933
    Turni608 – 6103
    Helixi613 – 6175
    Turni618 – 6203
    Helixi623 – 63917
    Turni640 – 6434
    Helixi644 – 6474
    Turni650 – 6523
    Beta strandi653 – 6553
    Beta strandi658 – 6625
    Beta strandi665 – 6673
    Beta strandi670 – 6745
    Helixi676 – 6783
    Beta strandi681 – 6833
    Helixi684 – 6918
    Beta strandi699 – 7068
    Helixi709 – 7179
    Helixi721 – 7288
    Helixi733 – 7419
    Helixi746 – 7483
    Helixi751 – 76515
    Helixi772 – 7776
    Turni781 – 7833
    Helixi784 – 79411
    Helixi796 – 81217
    Beta strandi813 – 8164
    Beta strandi822 – 8243
    Turni826 – 8294
    Helixi833 – 87038
    Beta strandi873 – 8808
    Beta strandi883 – 8897
    Turni890 – 8923
    Helixi893 – 90614
    Beta strandi910 – 9123
    Beta strandi916 – 9238
    Helixi924 – 9274

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    1D8YX-ray2.08A324-928[»]
    1D9DX-ray2.18A324-928[»]
    1D9FX-ray3.00A324-928[»]
    1DPIX-ray2.80A324-928[»]
    1KFDX-ray3.90A324-928[»]
    1KFSX-ray2.10A324-928[»]
    1KLNX-ray3.20A324-928[»]
    1KRPX-ray2.20A324-928[»]
    1KSPX-ray2.30A324-928[»]
    1QSLX-ray2.20A324-928[»]
    2KFNX-ray2.03A324-928[»]
    2KFZX-ray2.03A324-928[»]
    2KZMX-ray2.60A324-928[»]
    2KZZX-ray2.25A324-928[»]
    ProteinModelPortaliP00582.
    SMRiP00582. Positions 5-284, 324-928.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP00582.

    Family & Domainsi

    Domains and Repeats

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Domaini1 – 3233235'-3' exonucleaseAdd
    BLAST
    Domaini324 – 5171943'-5' exonucleaseAdd
    BLAST

    Region

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Regioni324 – 928605Klenow fragmentAdd
    BLAST
    Regioni521 – 928408PolymeraseAdd
    BLAST

    Sequence similaritiesi

    Belongs to the DNA polymerase type-A family.Curated
    Contains 1 3'-5' exonuclease domain.Curated
    Contains 1 5'-3' exonuclease domain.Curated

    Phylogenomic databases

    eggNOGiCOG0258.
    HOGENOMiHOG000020998.
    KOiK02335.
    OMAiAPMQGSA.
    OrthoDBiEOG6SJJH7.
    PhylomeDBiP00582.

    Family and domain databases

    Gene3Di3.30.420.10. 1 hit.
    3.40.50.1010. 1 hit.
    InterProiIPR002562. 3'-5'_exonuclease_dom.
    IPR020046. 5-3_exonucl_a-hlix_arch_N.
    IPR020045. 5-3_exonuclease_C.
    IPR002421. 5-3_exonuclease_N.
    IPR019760. DNA-dir_DNA_pol_A_CS.
    IPR001098. DNA-dir_DNA_pol_A_palm_dom.
    IPR018320. DNA_polymerase_1.
    IPR002298. DNA_polymerase_A.
    IPR008918. HhH2.
    IPR003583. Hlx-hairpin-Hlx_DNA-bd_motif.
    IPR029060. PIN_domain-like.
    IPR012337. RNaseH-like_dom.
    [Graphical view]
    PfamiPF01367. 5_3_exonuc. 1 hit.
    PF02739. 5_3_exonuc_N. 1 hit.
    PF00476. DNA_pol_A. 1 hit.
    PF01612. DNA_pol_A_exo1. 1 hit.
    [Graphical view]
    PRINTSiPR00868. DNAPOLI.
    SMARTiSM00474. 35EXOc. 1 hit.
    SM00475. 53EXOc. 1 hit.
    SM00278. HhH1. 1 hit.
    SM00279. HhH2. 1 hit.
    SM00482. POLAc. 1 hit.
    [Graphical view]
    SUPFAMiSSF47807. SSF47807. 1 hit.
    SSF53098. SSF53098. 1 hit.
    SSF88723. SSF88723. 1 hit.
    TIGRFAMsiTIGR00593. pola. 1 hit.
    PROSITEiPS00447. DNA_POLYMERASE_A. 1 hit.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

    P00582-1 [UniParc]FASTAAdd to Basket

    « Hide

    MVQIPQNPLI LVDGSSYLYR AYHAFPPLTN SAGEPTGAMY GVLNMLRSLI    50
    MQYKPTHAAV VFDAKGKTFR DELFEHYKSH RPPMPDDLRA QIEPLHAMVK 100
    AMGLPLLAVS GVEADDVIGT LAREAEKAGR PVLISTGDKD MAQLVTPNIT 150
    LINTMTNTIL GPEEVVNKYG VPPELIIDFL ALMGDSSDNI PGVPGVGEKT 200
    AQALLQGLGG LDTLYAEPEK IAGLSFRGAK TMAAKLEQNK EVAYLSYQLA 250
    TIKTDVELEL TCEQLEVQQP AAEELLGLFK KYEFKRWTAD VEAGKWLQAK 300
    GAKPAAKPQE TSVADEAPEV TATVISYDNY VTILDEETLK AWIAKLEKAP 350
    VFAFDTETDS LDNISANLVG LSFAIEPGVA AYIPVAHDYL DAPDQISRER 400
    ALELLKPLLE DEKALKVGQN LKYDRGILAN YGIELRGIAF DTMLESYILN 450
    SVAGRHDMDS LAERWLKHKT ITFEEIAGKG KNQLTFNQIA LEEAGRYAAE 500
    DADVTLQLHL KMWPDLQKHK GPLNVFENIE MPLVPVLSRI ERNGVKIDPK 550
    VLHNHSEELT LRLAELEKKA HEIAGEEFNL SSTKQLQTIL FEKQGIKPLK 600
    KTPGGAPSTS EEVLEELALD YPLPKVILEY RGLAKLKSTY TDKLPLMINP 650
    KTGRVHTSYH QAVTATGRLS STDPNLQNIP VRNEEGRRIR QAFIAPEDYV 700
    IVSADYSQIE LRIMAHLSRD KGLLTAFAEG KDIHRATAAE VFGLPLETVT 750
    SEQRRSAKAI NFGLIYGMSA FGLARQLNIP RKEAQKYMDL YFERYPGVLE 800
    YMERTRAQAK EQGYVETLDG RRLYLPDIKS SNGARRAAAE RAAINAPMQG 850
    TAADIIKRAM IAVDAWLQAE QPRVRMIMQV HDELVFEVHK DDVDAVAKQI 900
    HQLMENCTRL DVPLLVEVGS GENWDQAH 928
    Length:928
    Mass (Da):103,118
    Last modified:July 21, 1986 - v1
    Checksum:iDAAE1C448A59030C
    GO

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    V00317 Genomic DNA. Translation: CAA23607.1.
    L19201 Genomic DNA. Translation: AAB02998.1.
    U00096 Genomic DNA. Translation: AAC76861.1.
    AP009048 Genomic DNA. Translation: BAE77445.1.
    J01663 Genomic DNA. Translation: AAA24402.1.
    J01664 Genomic DNA. Translation: AAA24404.1.
    PIRiA92360. DJECI.
    RefSeqiNP_418300.1. NC_000913.3.
    YP_491586.1. NC_007779.1.

    Genome annotation databases

    EnsemblBacteriaiAAC76861; AAC76861; b3863.
    BAE77445; BAE77445; BAE77445.
    GeneIDi12933188.
    948356.
    KEGGiecj:Y75_p3322.
    eco:b3863.
    PATRICi32123225. VBIEscCol129921_3973.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    V00317 Genomic DNA. Translation: CAA23607.1 .
    L19201 Genomic DNA. Translation: AAB02998.1 .
    U00096 Genomic DNA. Translation: AAC76861.1 .
    AP009048 Genomic DNA. Translation: BAE77445.1 .
    J01663 Genomic DNA. Translation: AAA24402.1 .
    J01664 Genomic DNA. Translation: AAA24404.1 .
    PIRi A92360. DJECI.
    RefSeqi NP_418300.1. NC_000913.3.
    YP_491586.1. NC_007779.1.

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    1D8Y X-ray 2.08 A 324-928 [» ]
    1D9D X-ray 2.18 A 324-928 [» ]
    1D9F X-ray 3.00 A 324-928 [» ]
    1DPI X-ray 2.80 A 324-928 [» ]
    1KFD X-ray 3.90 A 324-928 [» ]
    1KFS X-ray 2.10 A 324-928 [» ]
    1KLN X-ray 3.20 A 324-928 [» ]
    1KRP X-ray 2.20 A 324-928 [» ]
    1KSP X-ray 2.30 A 324-928 [» ]
    1QSL X-ray 2.20 A 324-928 [» ]
    2KFN X-ray 2.03 A 324-928 [» ]
    2KFZ X-ray 2.03 A 324-928 [» ]
    2KZM X-ray 2.60 A 324-928 [» ]
    2KZZ X-ray 2.25 A 324-928 [» ]
    ProteinModelPortali P00582.
    SMRi P00582. Positions 5-284, 324-928.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    DIPi DIP-10524N.
    IntActi P00582. 28 interactions.
    MINTi MINT-1225247.
    STRINGi 511145.b3863.

    Chemistry

    BindingDBi P00582.
    ChEMBLi CHEMBL4298.
    DrugBanki DB00548. Azelaic Acid.

    2D gel databases

    SWISS-2DPAGE P00582.

    Proteomic databases

    PaxDbi P00582.
    PRIDEi P00582.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblBacteriai AAC76861 ; AAC76861 ; b3863 .
    BAE77445 ; BAE77445 ; BAE77445 .
    GeneIDi 12933188.
    948356.
    KEGGi ecj:Y75_p3322.
    eco:b3863.
    PATRICi 32123225. VBIEscCol129921_3973.

    Organism-specific databases

    EchoBASEi EB0739.
    EcoGenei EG10746. polA.

    Phylogenomic databases

    eggNOGi COG0258.
    HOGENOMi HOG000020998.
    KOi K02335.
    OMAi APMQGSA.
    OrthoDBi EOG6SJJH7.
    PhylomeDBi P00582.

    Enzyme and pathway databases

    BioCyci EcoCyc:EG10746-MONOMER.
    ECOL316407:JW3835-MONOMER.
    MetaCyc:EG10746-MONOMER.
    RETL1328306-WGS:GSTH-159-MONOMER.
    SABIO-RK P00582.

    Miscellaneous databases

    EvolutionaryTracei P00582.
    PROi P00582.

    Gene expression databases

    Genevestigatori P00582.

    Family and domain databases

    Gene3Di 3.30.420.10. 1 hit.
    3.40.50.1010. 1 hit.
    InterProi IPR002562. 3'-5'_exonuclease_dom.
    IPR020046. 5-3_exonucl_a-hlix_arch_N.
    IPR020045. 5-3_exonuclease_C.
    IPR002421. 5-3_exonuclease_N.
    IPR019760. DNA-dir_DNA_pol_A_CS.
    IPR001098. DNA-dir_DNA_pol_A_palm_dom.
    IPR018320. DNA_polymerase_1.
    IPR002298. DNA_polymerase_A.
    IPR008918. HhH2.
    IPR003583. Hlx-hairpin-Hlx_DNA-bd_motif.
    IPR029060. PIN_domain-like.
    IPR012337. RNaseH-like_dom.
    [Graphical view ]
    Pfami PF01367. 5_3_exonuc. 1 hit.
    PF02739. 5_3_exonuc_N. 1 hit.
    PF00476. DNA_pol_A. 1 hit.
    PF01612. DNA_pol_A_exo1. 1 hit.
    [Graphical view ]
    PRINTSi PR00868. DNAPOLI.
    SMARTi SM00474. 35EXOc. 1 hit.
    SM00475. 53EXOc. 1 hit.
    SM00278. HhH1. 1 hit.
    SM00279. HhH2. 1 hit.
    SM00482. POLAc. 1 hit.
    [Graphical view ]
    SUPFAMi SSF47807. SSF47807. 1 hit.
    SSF53098. SSF53098. 1 hit.
    SSF88723. SSF88723. 1 hit.
    TIGRFAMsi TIGR00593. pola. 1 hit.
    PROSITEi PS00447. DNA_POLYMERASE_A. 1 hit.
    [Graphical view ]
    ProtoNeti Search...

    Publicationsi

    1. "Nucleotide sequence of the Escherichia coli polA gene and primary structure of DNA polymerase I."
      Joyce C.M., Kelley W.S., Grindley N.D.F.
      J. Biol. Chem. 257:1958-1964(1982) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
      Strain: K12.
    2. "Analysis of the Escherichia coli genome. III. DNA sequence of the region from 87.2 to 89.2 minutes."
      Plunkett G. III, Burland V., Daniels D.L., Blattner F.R.
      Nucleic Acids Res. 21:3391-3398(1993) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: K12 / MG1655 / ATCC 47076.
    3. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: K12 / MG1655 / ATCC 47076.
    4. "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.
    5. "Identification of two genes immediately downstream from the polA gene of Escherichia coli."
      Joyce C.M., Grindley N.D.
      J. Bacteriol. 152:1211-1219(1982) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 918-928.
      Strain: K12.
    6. "Genetic characterization of early amber mutations in the Escherichia coli polA gene and purification of the amber peptides."
      Kelley W.S., Joyce C.M.
      J. Mol. Biol. 164:529-560(1983) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 284-350.
    7. "Escherichia coli DNA polymerase I. Sequence characterization and secondary structure prediction."
      Brown W.E., Stump K.H., Kelley W.S.
      J. Biol. Chem. 257:1965-1972(1982) [PubMed] [Europe PMC] [Abstract]
      Cited for: AMINO-ACID COMPOSITION, PARTIAL PROTEIN SEQUENCE.
    8. "Escherichia coli proteome analysis using the gene-protein database."
      VanBogelen R.A., Abshire K.Z., Moldover B., Olson E.R., Neidhardt F.C.
      Electrophoresis 18:1243-1251(1997) [PubMed] [Europe PMC] [Abstract]
      Cited for: IDENTIFICATION BY 2D-GEL.
    9. "Structure of large fragment of Escherichia coli DNA polymerase I complexed with dTMP."
      Ollis D.L., Brick P., Hamlin R., Xuong N.G., Steitz T.A.
      Nature 313:762-766(1985) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (2.8 ANGSTROMS) OF KLENOW FRAGMENT.
    10. "Structural basis for the 3'-5' exonuclease activity of Escherichia coli DNA polymerase I: a two metal ion mechanism."
      Beese L.S., Steitz T.A.
      EMBO J. 10:25-33(1991) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (2.6 ANGSTROMS) OF KLENOW FRAGMENT.
    11. "Structure of DNA polymerase I Klenow fragment bound to duplex DNA."
      Beese L.S., Derbyshire V., Steitz T.A.
      Science 260:352-355(1993) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (3.2 ANGSTROMS) OF KLENOW FRAGMENT.
    12. "Crystal structures of the Klenow fragment of DNA polymerase I complexed with deoxynucleoside triphosphate and pyrophosphate."
      Beese L.S., Friedman J.M., Steitz T.A.
      Biochemistry 32:14095-14101(1993) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (3.9 ANGSTROMS) OF KLENOW FRAGMENT.
    13. "Structural principles for the inhibition of the 3'-5' exonuclease activity of Escherichia coli DNA polymerase I by phosphorothioates."
      Brautigam C.A., Steitz T.A.
      J. Mol. Biol. 277:363-377(1998) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (2.1 ANGSTROMS) OF KLENOW FRAGMENT.
    14. "Structures of normal single-stranded DNA and deoxyribo-3'-S-phosphorothiolates bound to the 3'-5' exonucleolytic active site of DNA polymerase I from Escherichia coli."
      Brautigam C.A., Sun S., Piccirilli J.A., Steitz T.A.
      Biochemistry 38:696-704(1999) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (2.6 ANGSTROMS) OF KLENOW FRAGMENT.
    15. Cited for: X-RAY CRYSTALLOGRAPHY (2.08 ANGSTROMS) OF KLENOW FRAGMENT.
    16. "Sequential proton NMR resonance assignments, circular dichroism, and structural properties of a 50-residue substrate-binding peptide from DNA polymerase I."
      Mullen G.P., Vaughn J.B. Jr., Mildvan A.S.
      Arch. Biochem. Biophys. 301:174-183(1993) [PubMed] [Europe PMC] [Abstract]
      Cited for: STRUCTURE BY NMR OF 728-777.

    Entry informationi

    Entry nameiDPO1_ECOLI
    AccessioniPrimary (citable) accession number: P00582
    Secondary accession number(s): Q2M8G1
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: July 21, 1986
    Last sequence update: July 21, 1986
    Last modified: October 1, 2014
    This is version 163 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, Direct protein sequencing, Reference proteome

    Documents

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

    External Data

    Dasty 3