LOCUS       NZ_AP024122             1306 bp    DNA     circular CON 20-SEP-2023
DEFINITION  Escherichia coli strain JML285 plasmid JML285_P8, complete sequence.
ACCESSION   NZ_AP024122
VERSION     NZ_AP024122.1
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  JOURNAL   Unpublished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 1306)
  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
            AP024122.1.
            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..1306
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="JML285"
                     /isolation_source="feces"
                     /host="Homo sapiens"
                     /db_xref="taxon:562"
                     /plasmid="JML285_P8"
                     /geo_loc_name="Japan"
                     /collection_date="2015"
     gene            complement(725..1261)
                     /locus_tag="FFF71_RS25790"
                     /old_locus_tag="HmCmsJML285_5080"
     CDS             complement(725..1261)
                     /locus_tag="FFF71_RS25790"
                     /old_locus_tag="HmCmsJML285_5080"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:YP_005221105.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="helix-turn-helix domain-containing protein"
                     /protein_id="WP_001194694.1"
                     /translation="MQTQNVITEKEREIRSRDLTENAKKLAHERREAEKNSNFTQVSPL
                     GWKRLMELAKGNQGAFGLYSFFAQHIDGSCGAVVADQSFLAAQFNVSTRTIIRWINYLE
                     ENRAVVRIPVAGKVCAYALNPNEVWKGYGNTKEYAAFITKTLVNKDGDIQRRIMAMFHG
                     NDARQGMEGDTPEAE"
                     /name="helix-turn-helix domain-containing protein"
ORIGIN
        1 acgacatttt atgtcgtagt atatgtcatt tatgtcacat attacgaaat gatgtgacat
       61 cctagggtgt cataacgttg tgacatccta gggtgtcata tcagaaatgt taaatgtctt
      121 ttaaatcaat gaattattaa tttttgctat tcttatctaa agagatctca cagcgcgctg
      181 cgagatctcc tggtagcacc ctcctttcag tcgggcaaac ggcgaaaatt taaccattgg
      241 caaccgaaaa atcgtggggg ccccttcagg ggttccgatt tttttgttgc caacgcaccg
      301 gtcgaaaaaa ataggggaag gtggttgtgt tcacgcagtg agcgcaacca cctgccagac
      361 gggttttcgc gccgcaggcc gcacatgttt ctgagccaac ggcgaagaaa catataagtg
      421 cgcatctctc taattttgcg aatttgagag atgaaaccag tctgggggat cggagtattc
      481 cgcctctagc cgtcctggtg gcccagtccg gcaagaccca cgaaatcacc cgtaaaacgc
      541 cctaaaacgc gctctgacgc gttttttgac gttttacggg ctcacgtggg ctttgggcgg
      601 aaaaatggct tacgtgcgtt ctgagagcgt tttagggctt tgcagggcgg agggggtgaa
      661 gcagctccct gtggaacctg taccgccctt gcgggcgggc ttcggcgatt tggcgaacgg
      721 gaatctattc ggcttctggc gtgtcgcctt ccatgccctg acgggcatca tttccgtgga
      781 acatggccat gattcggcgc tgaatgtcgc cgtctttgtt gactagggtt tttgttataa
      841 acgccgcata ttccttggta ttcccatacc ccttccaaac ttcatttgga ttcaatgcgt
      901 atgcacaaac cttaccggcg acaggaatcc tcacaacagc cctgttttcc tctaaatagt
      961 tgatccatct aattattgtt cttgtcgata cattgaactg cgccgccaaa aatgactgat
     1021 ccgccactac tgcgccacaa gatccatcga tatgctgagc aaaaaaagaa tacaagccaa
     1081 aagctccctg atttcctttg gctaattcca ttaaacgctt ccagcctaat ggggacactt
     1141 gtgtgaaatt tgagttcttt tctgcctctc gcctctcatg agccagtttt ttggcatttt
     1201 cggttagatc cctagatcga atttctcgct ctttttcggt gattacattt tgagtttgca
     1261 tctcaatctc catgtcattt caatgtgaca agataagtca tactat
//
