LOCUS       NZ_AP024121             1867 bp    DNA     circular CON 20-SEP-2023
DEFINITION  Escherichia coli strain JML285 plasmid JML285_P7, complete sequence.
ACCESSION   NZ_AP024121
VERSION     NZ_AP024121.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMD00077348
            Sequence Read Archive: DRR102940, DRR252635
            Assembly: GCF_005389605.2
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1
  AUTHORS   Frederic,A., Alexandre,P., Arimizu,Y., Camille,V.C., Nadege,G.,
            Clemence,M., Hubert,B., Jean-Philippe,N., Hayashi,T., Priscilla,B.,
            Ogura,Y. and Eric,O.
  TITLE     Insights into the acquisition of the pks island and production of
            colibactin in the Escherichia coli population
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 1867)
  AUTHORS   Hayashi,T., Ogura,Y. and Katsura,K.
  TITLE     Direct Submission
  JOURNAL   Submitted (23-OCT-2020) Contact:Yoshitoshi Ogura Kurume University
            School of Medicine, Department of Bacteriology; 67 asahi-machi,
            Kurume, Fukuoka 830-0011, Japan
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: unicycler v. 0.4.8
            Genome Coverage                   :: 40x
            Sequencing Technology             :: Illumina Miseq, MinION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 09/20/2023 05:13:43
            Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline
            (PGAP)
            Annotation Method :: Best-placed reference protein set; GeneMarkS-2+
            Annotation Software revision      :: 6.6
            Features Annotated                :: Gene; CDS; rRNA; tRNA; ncRNA
            Genes (total)                     :: 5,202
            CDSs (total)                      :: 5,084
            Genes (coding)                    :: 4,867
            CDSs (with protein)               :: 4,867
            Genes (RNA)                       :: 118
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 86
            ncRNAs                            :: 10
            Pseudo Genes (total)              :: 217
            CDSs (without protein)            :: 217
            Pseudo Genes (ambiguous residues) :: 0 of 217
            Pseudo Genes (frameshifted)       :: 91 of 217
            Pseudo Genes (incomplete)         :: 131 of 217
            Pseudo Genes (internal stop)      :: 49 of 217
            Pseudo Genes (multiple problems)  :: 48 of 217
            Pseudo Genes (short protein)      :: 3 of 217
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            AP024121.1.
            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/
            COMPLETENESS: full length.
FEATURES             Location/Qualifiers
     source          1..1867
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="JML285"
                     /isolation_source="feces"
                     /host="Homo sapiens"
                     /db_xref="taxon:562"
                     /plasmid="JML285_P7"
                     /geo_loc_name="Japan"
                     /collection_date="2015"
     gene            join(1867,1..1322)
                     /gene="uhpC"
                     /locus_tag="FFF71_RS25785"
                     /old_locus_tag="HmCmsJML285_5078"
     CDS             join(1867,1..1322)
                     /gene="uhpC"
                     /locus_tag="FFF71_RS25785"
                     /old_locus_tag="HmCmsJML285_5078"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000021853.1"
                     /GO_function="GO:0022857 - transmembrane 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="MFS transporter family glucose-6-phosphate
                     receptor UhpC"
                     /protein_id="WP_001491303.1"
                     /translation="MSIFSESPDKEITMSKTDIDKTYRYWRLHLMIVSYIGYAVFYFTR
                     KSFNFVMPEMLSDLGITKSDIGMVGTAFYLTYGASKFISGVIGDRSNPRWFMGIGLIMT
                     GCVNILFGLTSSIPLFIFLWMVNAFFQGWGWPPCSKILNTWYSRNERGFWWSIWNTSHN
                     IGGAIIPILSGSVALWLGWRYGMIIPGAIAVIIGILLCFLLRDRPRSMGLPTVGEWRND
                     IAEINHEEQGIGLSQWNILKDYIFKNNIIWVLAISYAVIYVIRTGINDWGNLYLIETHK
                     YDLLTANATVMMFEVGGFFGAIVAGWGSDILFKGNRSQMNVIYTIGIIIASACLWLVSI
                     DSKYVFSLLFFITGFFIFGPQFLIAMAAAENSHKYASGASTGFVSLFAYLGASAAGYPL
                     SKIIEIYHWNGFYALLLTLSLILVVLLLIAMKLQTLRAKCN"
                     /name="uhpC"
ORIGIN
        1 tgtccatatt ttcagagtct cctgacaaag aaataacaat gagtaaaact gatattgata
       61 aaacatatag atattggcga cttcatttaa tgattgtgag ctatatagga tatgctgtat
      121 tttatttcac acgaaagagc tttaacttcg taatgcctga gatgctatct gatttaggta
      181 ttacaaaatc agatattggt atggtcggaa cggcatttta tctaacttat ggggcatcaa
      241 aatttatttc tggagttata ggtgatcgtt ctaatccaag atggtttatg gggattggat
      301 tgataatgac tggatgtgtc aatatattgt ttggtttaac atcatctata cctttgttta
      361 tatttttatg gatggttaat gctttttttc agggatgggg atggcctccg tgttcaaaaa
      421 ttttaaatac ttggtattcc cgaaatgaac gtggattctg gtggtccata tggaatacat
      481 ctcataatat cggtggagca attatcccta ttttatcagg tagtgttgcc ttatggctag
      541 gttggcgtta tggcatgatt attccggggg ccattgctgt tattattggc attttattat
      601 gtttcttatt gcgtgatcga ccaagatcga tgggattacc aacagttgga gagtggcgta
      661 atgatatagc tgagattaat catgaagaac aaggtatagg gttgtcacaa tggaatatct
      721 taaaagatta tatatttaaa aataatataa tttgggtatt ggcaatatca tatgcagtta
      781 tttatgttat tcgtacagga atcaatgact ggggaaattt gtatttgatt gagactcata
      841 aatatgactt gctaacagca aatgcaacag taatgatgtt tgaggttgga ggcttttttg
      901 gtgctatcgt agctggatgg ggatcagata ttctgtttaa gggcaatcgc tctcaaatga
      961 atgttattta tacaattggt ataatcattg cttctgcatg tctatggttg gtttctatcg
     1021 atagtaaata tgttttttcg ttgttatttt tcatcactgg cttctttatc tttgggccac
     1081 aatttctgat cgcaatggca gctgctgaaa actcacataa atatgcatct ggtgcttcta
     1141 ctggttttgt tagtttattc gcatatcttg gtgcatccgc ggctggctat ccattgtcta
     1201 aaataataga aatataccac tggaatggtt tctatgctct tctcttaacg ttatcactta
     1261 ttcttgttgt ccttttactc attgcgatga aactacaaac acttagagct aaatgtaact
     1321 aaaatatatt gattcttacg aagcccatag aaatggcata tttctgtggg ttttattttt
     1381 accagaggtc gtgtgactga caaaattaat gagatgcata attttgatgt tcctaagctc
     1441 aaagattatt acagccttcc attaggaaga atgaaaatgc tataagtatt acaaattaga
     1501 tataaaaata agataactaa aaatactggg accacagaat ccttttgact tctgaaagac
     1561 ctgcttttag cgatacggaa caatttatta aatacaagaa agtagaaact gtagcatatt
     1621 actgttcctg aacacattga attattatat tacagcataa cacaaatatc ctcgcacaga
     1681 taactccctg ccgagttatt ggtaagcgcc ccatctgcga cgtcttgtga aaattgtcct
     1741 gtctggcaac aatcgtgccc aactatattg atggacacaa acgatgaatt cccagacaac
     1801 agtaagcgca tcatttaaac cgtctttcgc ctccctttcc tgtttccgat actaatgtcc
     1861 attttcg
//
