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Escherichia coli strain MOD1-EC6173 MOD1-EC6173_59_length_12637_cov_18.4469, whole genome shotgun sequence

NCBI Reference Sequence: NZ_NNYN01000059.1

FASTA Graphics 

LOCUS       NZ_NNYN01000059        12637 bp    DNA     linear   CON 27-MAY-2024
DEFINITION  Escherichia coli strain MOD1-EC6173
            MOD1-EC6173_59_length_12637_cov_18.4469, whole genome shotgun
            sequence.
ACCESSION   NZ_NNYN01000059 NZ_NNYN01000000
VERSION     NZ_NNYN01000059.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN06240049
            Assembly: GCF_002546965.1
KEYWORDS    WGS; RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadati; Pseudomonadota; Gammaproteobacteria;
            Enterobacterales; Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 12637)
  AUTHORS   Gangiredla,J., Mammel,M.K., Barnaba,T.J., Tartera,C., Gebru,S.T.,
            Patel,I.R., Leonard,S.R., Kotewicz,M.L., Lampel,K.A., Elkins,C.A.
            and Lacher,D.W.
  TITLE     Species-Wide Collection of Escherichia coli Isolates for
            Examination of Genomic Diversity
  JOURNAL   Genome Announc 5 (50), e01321-17 (2017)
   PUBMED   29242221
  REMARK    Publication Status: Online-Only
REFERENCE   2  (bases 1 to 12637)
  AUTHORS   Gangiredla,J., Lacher,D.W., Mammel,M.K., Barnaba,T., Tartera,C.,
            Gebru,S., Patel,I.R., Leonard,S.R., Lampel,K.A. and Elkins,C.A.
  TITLE     Direct Submission
  JOURNAL   Submitted (10-JUL-2017) CFSAN-ORS-DM-MMSB, US Food and Drug
            Administration, 5100 Paint Branch Parkway, College Park, MD 20740,
            USA
COMMENT     REFSEQ INFORMATION: The reference sequence is identical to
            NNYN01000059.1.
            The annotation was added by the NCBI Prokaryotic Genome Annotation
            Pipeline (PGAP). Information about PGAP can be found here:
            https://www.ncbi.nlm.nih.gov/genome/annotation_prok/
            
            ##Genome-Assembly-Data-START##
            Assembly Method        :: SPAdes v. 3.8.2
            Genome Representation  :: Full
            Expected Final Version :: Yes
            Genome Coverage        :: 21.6x
            Sequencing Technology  :: Illumina NextSeq 500
            ##Genome-Assembly-Data-END##
            
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_002546965.1-RS_2024_05_27
            Annotation Date                   :: 05/27/2024 01:16:42
            Annotation Pipeline               :: NCBI Prokaryotic Genome
                                                 Annotation Pipeline (PGAP)
            Annotation Method                 :: Best-placed reference protein
                                                 set; GeneMarkS-2+
            Annotation Software revision      :: 6.7
            Features Annotated                :: Gene; CDS; rRNA; tRNA; ncRNA
            Genes (total)                     :: 4,816
            CDSs (total)                      :: 4,727
            Genes (coding)                    :: 4,514
            CDSs (with protein)               :: 4,514
            Genes (RNA)                       :: 89
            rRNAs                             :: 7, 2, 2 (5S, 16S, 23S)
            complete rRNAs                    :: 6, 1 (5S, 16S)
            partial rRNAs                     :: 1, 1, 2 (5S, 16S, 23S)
            tRNAs                             :: 68
            ncRNAs                            :: 10
            Pseudo Genes (total)              :: 213
            CDSs (without protein)            :: 213
            Pseudo Genes (ambiguous residues) :: 0 of 213
            Pseudo Genes (frameshifted)       :: 72 of 213
            Pseudo Genes (incomplete)         :: 142 of 213
            Pseudo Genes (internal stop)      :: 43 of 213
            Pseudo Genes (multiple problems)  :: 39 of 213
            Pseudo Genes (short protein)      :: 1 of 213
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
FEATURES             Location/Qualifiers
     source          1..12637
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /submitter_seqid="MOD1-EC6173_59_length_12637_cov_18.4469"
                     /strain="MOD1-EC6173"
                     /serotype="O85:H40"
                     /isolation_source="feces"
                     /host="Homo sapiens"
                     /db_xref="taxon:562"
                     /geo_loc_name="USA:MA"
                     /collection_date="2013-12-13"
                     /collected_by="Pennsylvania State University | Escherichia
                     coli Reference Center"
     gene            complement(<1..533)
                     /gene="vgrG"
                     /locus_tag="BW341_RS23965"
     CDS             complement(<1..533)
                     /gene="vgrG"
                     /locus_tag="BW341_RS23965"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:NP_308634.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="type VI secretion system tip protein VgrG"
                     /protein_id="WP_072146393.1"
                     /translation="MSTGLRFTLEVDGLPPDAFAVVSFHLTQSLSSLFSLDLSLVSQQ
                     FLSLEFAQVLDKMAYLTVWQGDDVQRRVKGVVTWFELGENDKNQMLYSMKVCPPLWRT
                     GLRQNFRIFQNEDIESILATILKENGVTEWSPLFSEPHPSREFCVQYGETDYDFLCRM
                     AAEEGIFFYEEHAQKST"
     gene            complement(1353..1565)
                     /gene="yncH"
                     /locus_tag="BW341_RS23970"
     CDS             complement(1353..1565)
                     /gene="yncH"
                     /locus_tag="BW341_RS23970"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:NP_310086.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="YncH family protein"
                     /protein_id="WP_000882235.1"
                     /translation="MLCFLIYITLPFIQLVYFISSEKKLTIHIVQMFHLLSQVFYNLK
                     KFLMMDMLGVGDAININTNKNIRQVC"
     gene            complement(1641..2258)
                     /gene="yncG"
                     /locus_tag="BW341_RS23975"
     CDS             complement(1641..2258)
                     /gene="yncG"
                     /locus_tag="BW341_RS23975"
                     /EC_number="2.5.1.-"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:NP_415971.1"
                     /GO_function="GO:0005515 - protein binding [Evidence IEA]"
                     /GO_process="GO:0006749 - glutathione metabolic process
                     [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="glutathione S-transferase family protein"
                     /protein_id="WP_000598855.1"
                     /translation="MIKVYGVPGWGSTISELMLTLADIPYQFVDVSGFDHEGASRELL
                     KTLNPLCQVPTLALENDEIMTETAAIAFMVLDRRPDLAPPVGRAERQQFQRLLVWLVA
                     NVYPTFTFADYPERWASDAPEQLKKNVIEYRKSLYIWLNSQLTAEPYAFGEQLTLVDC
                     YLCTMRTWGPGHEWFQDNAQNISAIADAVCQLPKLQEVLKRNEII"
     gene            2524..4023
                     /gene="ansP"
                     /locus_tag="BW341_RS23980"
     CDS             2524..4023
                     /gene="ansP"
                     /locus_tag="BW341_RS23980"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:NP_310084.2"
                     /GO_component="GO:0016020 - membrane [Evidence IEA]"
                     /GO_process="GO:0006865 - amino acid transport [Evidence
                     IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="L-asparagine permease"
                     /protein_id="WP_001295649.1"
                     /translation="MSKHDTDTSDQHAAKRRWLNAHEEGYHKAMGNRQVQMIAIGGAI
                     GTGLFLGAGARLQMAGPALALVYLICGLFSFFILRALGELVLHRPSSGSFVSYAREFL
                     GEKAAYVAGWMYFINWAMTGIVDITAVALYMHYWGAFGGVPQWVFALAALTIVGTMNM
                     IGVKWFAEMEFWFALIKVLAIVTFLVVGTVFLGSGQPLDGNTTGFHLITDNGGFFPHG
                     LLPALVLIQGVVFAFASIEMVGTAAGECKDPQTMVPKAINSVIWRIGLFYVGSVVLLV
                     MLLPWSAYQAGQSPFVTFFSKLGVPYIGSIMNIVVLTAALSSLNSGLYCTGRILRSMA
                     MGGSAPSFMAKMSRQHVPYAGILATLVVYVVGVFLNYLVPSRVFEIVLNFASLGIIAS
                     WAFIIVCQMRLRKAIKQGKAADVSFKLPGAPFTSWLTLLFLLSVLVLMAFDYPNGTYT
                     IAALPIIGILLVIGWFGVRKRVAEIHSTAPVVEEDEEKQEIVFKPETAS"
     gene            complement(4138..5199)
                     /gene="yncE"
                     /locus_tag="BW341_RS23985"
     CDS             complement(4138..5199)
                     /gene="yncE"
                     /locus_tag="BW341_RS23985"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:NP_310083.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="YncE family protein"
                     /protein_id="WP_000550675.1"
                     /translation="MHLRHLFSSRLRGSLLLGSLLVASSFSTQAAEEMLRKAVGKGAY
                     EMAYSQQENALWLATSQSRKLDKGGVVYRLDPVTLEVTQAIHNDLKPFGATINNTTQT
                     LWFGNTVNSAVTAIDAKTGEVKGRLVLDDRKRTEEVRPLQPRELVADDATNTVYISGI
                     GKESVIWVVDGENIKLKTAIQNTGKMSTGLALDSKGKRLYTTNADGELITIDTADNKI
                     LSRKKLLDDGKEHFFINISLDTARQRAFITDSKAAEVLVVDTRNGNILAKVAAPESLA
                     VLFNPARNEAYVTHRQAGKVSVIDAKSYKVVKTFDTPTHPNSLALSADGKTLYVSVKQ
                     KSTKQQEATQPDDVIRIAL"
     gene            5441..7543
                     /gene="pqqU"
                     /locus_tag="BW341_RS24000"
     CDS             5441..7543
                     /gene="pqqU"
                     /locus_tag="BW341_RS24000"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:NP_415968.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="TonB-dependent receptor PqqU"
                     /protein_id="WP_000689303.1"
                     /translation="MKIFSVRQTVLPALLALSPVVFAADEQTMIVSAAPQVVSELDTP
                     AAVSVVDGEEMRLATPRINLSESLTGVPGLQVQNRQNYAQDLQLSIRGFGSRSTYGIR
                     GIRLYMDGIPATMPDGQGQTSNIDLSSVQNVEVLRGPFSALYGNASGGVMNVTTQTGQ
                     QPPTIEASSYYGSFGSWRYGLKATGATGDGTQPGDVDYTVSTTRFTTHGYRDHSGAQK
                     NLANAKLGVRIDEASKLSLIFNSVDIKADDPGGLTKAEWKANPQQAPRAEQYDTRKTI
                     KQTQAGLHYERSLSAQDDMSVMMYAGERETTQYQSIPMAPQLNPSHAGGVITLQRHYQ
                     GVDSRWTHRGELGVPVTFTTGLNYENMSENRKGYNNFRLNSGVPEYGQKGELRRDERN
                     LMWNVDPYLQTQWQLSEKLSLDAGVRYSSVWFDSNDHYVTPGNGDDSGDASYHKWLPA
                     GSLKYAMTDAWNIYLAAGRGFETPTINELSYRADGQSGMNFGLKPSTNDTIEIGSKTR
                     IGDGLLSLALFQTDTDDEIVVDSSSGGRTTYKNAGKTRRQGAELAWDQRFAGDFRVKA
                     SWTWLDATYRSNVCNEQDCNGNRMPGIARNMGFASIGYVPEDGWYAGTEARYMGDIMA
                     DDENTAKAPSYTLVGLFTGYKYNYHNLTVDLFGRVDNLFDKEYVGSVIVNESNGRYYE
                     PSPGRNYGVGMNIAWRFE"
     gene            complement(7579..8244)
                     /gene="mcbR"
                     /locus_tag="BW341_RS24005"
     CDS             complement(7579..8244)
                     /gene="mcbR"
                     /locus_tag="BW341_RS24005"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:NP_415967.2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="colanic acid/biofilm transcriptional regulator
                     McbR"
                     /protein_id="WP_001299369.1"
                     /translation="MPGMGKMKHVSLTLQVENDLKHQLSIGALKPGARLITKNLAEQL
                     GMSITPVREALLRLVSVNALSVAPAQAFTVPEVGKRQLDEINRIRYELELMAVALAVE
                     NLTPQDLAELQELLEKLQQAQEKGDMEQIINVNRLFRLAIYHRSNMPILCEMIEQLWV
                     RMGPGLHYLYEAINPAELREHIENYHLLLAALKAKDKEGCRHCLAEIMQQNIAILYQQ
                     YNR"
     gene            complement(8442..9479)
                     /gene="curA"
                     /locus_tag="BW341_RS24010"
     CDS             complement(8442..9479)
                     /gene="curA"
                     /locus_tag="BW341_RS24010"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:NP_415966.6"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="NADPH-dependent curcumin/dihydrocurcumin
                     reductase"
                     /protein_id="WP_000531452.1"
                     /translation="MGQQKQRNRRWVLASRPHGAPVPENFRLEEDDVATPGEGQVLLR
                     TVYLSLDPYMRGRMSDEPSYSPPVDIGGVMVGGTVSRVVESNHPDYQPGDWVLGYSGW
                     QDYDISSGDDLVKLGDHPQNPSWSLGVLGMPGFTAYMGLLDIGQPKEGETLVVAAATG
                     PVGATVGQIGKLKGCRVVGVAGGAEKCRHAIEVLGFDVCLDHHADDFAEQLVKACPKG
                     IDIYYENVGGKVFDAVLPLLNTSARIPVCGLVSSYNATELPPGPDRLPLLMATVLKKR
                     IRLQGFIIAQDYGHRIHEFQKEMGQWVKEDKIHYHEDITDGLENAPQTFIGLLKGKNF
                     GKVVIRVAGDD"
     gene            9660..10178
                     /gene="mddA"
                     /locus_tag="BW341_RS24020"
     CDS             9660..10178
                     /gene="mddA"
                     /locus_tag="BW341_RS24020"
                     /EC_number="2.3.-.-"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:NP_310079.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="GNAT family N-acetyltransferase"
                     /protein_id="WP_001353827.1"
                     /translation="MSIRFARKADCAAIAEIYNHAVLYTAAIWNDQTVDADNRIAWFE
                     ARTIAGYPVLVSEEDGVVTGYASFGDWRSFDGFRHTVEHSVYVHPDHQGKGLGRKLLS
                     RLIDEARDSGKHVMVAGIESQNQASLHLHHSLGFVVTAQMPQVGTKFGRWLDLTFMQL
                     QLDERTEPDAIG"
     gene            10175..10624
                     /gene="ydcZ"
                     /locus_tag="BW341_RS24025"
     CDS             10175..10624
                     /gene="ydcZ"
                     /locus_tag="BW341_RS24025"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:NP_415964.1"
                     /GO_component="GO:0005886 - plasma membrane [Evidence
                     IEA]"
                     /GO_function="GO:0005215 - transporter activity [Evidence
                     IEA]"
                     /GO_process="GO:0055085 - transmembrane transport
                     [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="DMT family transporter"
                     /protein_id="WP_001076535.1"
                     /translation="MNQSLTLAFLIAAGIGLVVQNTLMVRITQTSSTILIAMLLNSLV
                     GIVLFVSILWFKQGMAGFGELVSSVRWWTLIPGLLGSFFVFASISGYQNVGAATTIAV
                     LVASQLIGGLMLDIFRSHGVPLRALFGPICGAILLVVGAWLVARRSF"
     gene            complement(10625..10858)
                     /gene="ydcY"
                     /locus_tag="BW341_RS24030"
     CDS             complement(10625..10858)
                     /gene="ydcY"
                     /locus_tag="BW341_RS24030"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:NP_310077.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="DUF2526 family protein YdcY"
                     /protein_id="WP_000018633.1"
                     /translation="MSHLDEVIARVDAAIEESVIAHMNELLIALSDDAELSREDRYTQ
                     QQRLRTAIAHHGRKHKEDMEARHEQLTKGGTIL"
     gene            complement(10944..11117)
                     /gene="ortT"
                     /locus_tag="BW341_RS24035"
     CDS             complement(10944..11117)
                     /gene="ortT"
                     /locus_tag="BW341_RS24035"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:NP_415962.2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="orphan toxin OrtT"
                     /protein_id="WP_000061178.1"
                     /translation="MSLYQHMLVFYAVMAAIAFLITWFLSHDKKRIRFLSAFLVGATW
                     PMSFPVALLFSLF"
     gene            11312..11407
                     /gene="yncL"
                     /locus_tag="BW341_RS24045"
     CDS             11312..11407
                     /gene="yncL"
                     /locus_tag="BW341_RS24045"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:YP_001165318.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="stress response membrane protein YncL"
                     /protein_id="WP_001303494.1"
                     /translation="MNVSSRTVVLINVFAAVGLFTLISMRFGWFI"
     gene            complement(11809..>12576)
                     /locus_tag="BW341_RS24050"
                     /pseudo
     CDS             complement(11809..>12576)
                     /locus_tag="BW341_RS24050"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:NP_707637.1"
                     /GO_function="GO:0016746 - acyltransferase activity
                     [Evidence IEA]"
                     /GO_process="GO:0046677 - response to antibiotic [Evidence
                     IEA]"
                     /note="incomplete; partial in the middle of a contig;
                     missing N-terminus; Derived by automated computational
                     analysis using gene prediction method: Protein Homology."
                     /pseudo
                     /codon_start=1
                     /transl_table=11
                     /product="CatB-related O-acetyltransferase"
CONTIG      join(NNYN01000059.1:1..12637)
//
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