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)
//