LOCUS       NZ_AP023234             2101 bp    DNA     circular CON 18-JUN-2023
DEFINITION  Escherichia coli strain YJ4 plasmid pYJ4-c, complete sequence.
ACCESSION   NZ_AP023234
VERSION     NZ_AP023234.2
DBLINK      BioProject: PRJNA224116
            BioSample: SAMD00157545
            Sequence Read Archive: DRR165512, DRR232349
            Assembly: GCF_013374295.2
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1
  AUTHORS   Sugawara,Y., Hagiya,H., Akeda,Y., Takeuchi,D., Sakamoto,N.,
            Matsumoto,Y., Motooka,D., Nishi,I., Tomono,K. and Hamada,S.
  TITLE     Community spread and acquisition of clinically relevant
            carbapenemase-producing Escherichia coli in healthy Japanese
            residents of Yangon, Myanmar, 2018
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 2101)
  AUTHORS   Sugawara,Y., Akeda,Y. and Hamada,S.
  TITLE     Direct Submission
  JOURNAL   Submitted (17-JUN-2020) Contact:Yo Sugawara Osaka University,
            Research Institute for Microbial Diseases; 3-1 Yamadaoka, Suita,
            Osaka 565-0871, Japan
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: Flye v. 2.5
            Genome Coverage                   :: 158x
            Sequencing Technology             :: MinION; Illumina MiSeq
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 06/18/2023 03:25:30
            Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline
            (PGAP)
            Annotation Method :: Best-placed reference protein set; GeneMarkS-2+
            Annotation Software revision      :: 6.5
            Features Annotated                :: Gene; CDS; rRNA; tRNA; ncRNA
            Genes (total)                     :: 5,031
            CDSs (total)                      :: 4,907
            Genes (coding)                    :: 4,633
            CDSs (with protein)               :: 4,633
            Genes (RNA)                       :: 124
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 91
            ncRNAs                            :: 11
            Pseudo Genes (total)              :: 274
            CDSs (without protein)            :: 274
            Pseudo Genes (ambiguous residues) :: 0 of 274
            Pseudo Genes (frameshifted)       :: 118 of 274
            Pseudo Genes (incomplete)         :: 165 of 274
            Pseudo Genes (internal stop)      :: 51 of 274
            Pseudo Genes (multiple problems)  :: 58 of 274
            Pseudo Genes (short protein)      :: 4 of 274
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            AP023234.2.
            On Apr 28, 2021 this sequence version replaced NZ_AP023234.1.
            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..2101
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="YJ4"
                     /isolation_source="human stool"
                     /host="Homo sapiens"
                     /db_xref="taxon:562"
                     /plasmid="pYJ4-c"
                     /geo_loc_name="Myanmar:Yangon"
                     /lat_lon="16.866069 N 96.195132 E"
                     /collection_date="2018-03"
     gene            join(1984..2101,1..848)
                     /locus_tag="HXS62_RS24750"
     CDS             join(1984..2101,1..848)
                     /locus_tag="HXS62_RS24750"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_012421200.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="protein rep"
                     /protein_id="WP_001287824.1"
                     /translation="MSEDKFLSDYSPRDAVWDTQRTLTDSVGGIYQTAAEFERYALRMA
                     SCSGLLRFGWSTIMETGETRLRLRSAQFCRVRHCPVCQWRRTLMWQARFYQALPKIVVD
                     YPSSRWLFLTLTVRNCEIGELGTVLTAMNAAFKRMEKRKELSPVQGWIRATEVTRGKDG
                     SAHPHFHCLLMVQPSWFKGKNYVKHERWVELWRDCLRVNYEPNIDIRAVKTKTGEVVAN
                     VAEQLQSAVAETLKYSVKPEDMANDPEWFLELTRQLHKRRFISTGGALKNVLQLDRETN
                     EDLVIADDVGDGTDDGKRTAFVWDSGKRRYKRAPEKDKSD"
                     /name="protein rep"
     gene            852..1118
                     /locus_tag="HXS62_RS24755"
     CDS             852..1118
                     /locus_tag="HXS62_RS24755"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001024536.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_001024536.1"
                     /translation="MNINIEYLNGNKTIGLFFLRSEAVIPDRFKNLILLIDGLSFGTFG
                     FHPHEGFEDELILYIQKTNERVKTLFVKIDLNGIKFGFLRTHS"
                     /name="hypothetical protein"
     Typing          277..508
                     /name="Col(BS512)"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="2.05e-118"
ORIGIN
        1 atgcactccg tatggcctcc tgtagcggtt tgttacgttt tggttggtct accatcatgg
       61 aaaccggaga aacgcgccta cggcttcgta gtgcgcaatt ttgccgtgtc cgtcattgcc
      121 ctgtctgcca gtggagaaga accctcatgt ggcaagcccg tttttatcag gctctaccga
      181 aaatcgttgt ggattacccg tcttcccgat ggttgtttct gacgttaact gtcaggaact
      241 gcgagatagg tgaacttgga acagtcctta cagcaatgaa tgcggcgttt aagcgaatgg
      301 aaaagcgaaa ggagctatca cctgttcagg ggtggatcag ggctacggag gtgacgcgag
      361 gtaaggatgg cagcgcacat ccgcattttc actgtctgct gatggtgcaa ccttcttggt
      421 ttaaagggaa gaactacgtt aagcacgaac gttgggtaga actctggcgc gattgcttgc
      481 gggtgaacta tgagccgaat atcgatattc gggcagtaaa aactaagaca ggtgaggttg
      541 tggccaacgt tgccgagcaa ctgcaaagcg cggttgctga aacgctgaaa tactccgtta
      601 aaccggaaga tatggcaaac gatcctgagt ggtttcttga gctgacgcgg cagcttcaca
      661 agcgccgttt tatctcgacc ggtggggcgc taaaaaacgt cctccagttg gatcgagaaa
      721 ccaatgagga tcttgtcatt gccgacgatg taggggatgg cactgatgac gggaagcgga
      781 cggcgtttgt ctgggattca ggtaaacggc gttacaaacg cgcccctgag aaggataaat
      841 cggattaacg tatgaatatt aatattgaat acctgaatgg aaataagact attggtttat
      901 tttttttaag aagtgaagcg gtgattcctg acaggtttaa aaaccttatt ttgcttattg
      961 atggattaag ttttggcaca tttggttttc atccgcacga aggttttgag gatgaattaa
     1021 ttttatatat tcagaaaaca aacgagaggg taaaaactct ttttgtgaaa atagatttaa
     1081 acggtatcaa gtttggattt ttaagaacgc attcttagtt ctggaaaaga gccagcggca
     1141 ggctgaggtg ataggtacga gattgcatgc aatctctagt gctctgtcta tcctgcatta
     1201 tcctcagcat tatcctcagc attatcctca gccttgccaa ctcgacacca atgcaggata
     1261 gacaatccga tgtcaaatgt taacactctg cgagtggtac attttccccg gattatcgtc
     1321 ctgagcctgc cgctggctct ctttctaccg cctcgctttg ctcgttgctc aacgcctcac
     1381 agacacggat taaaatccgc atccgttcac cgttttttaa agtccgttaa aagcatgatg
     1441 ccatctccga gagttaatct cgtcaaatgc taaatcgtgg gggtcccctt tggggttccg
     1501 atttagtgat tgacgacacc accgattaaa aaacttatgc ggggtggatg gtttcacgaa
     1561 gtgaggccat ccacctgtaa gacagggttt tgtttttatt ccctgttttg gtgatcgggt
     1621 gtgtggaaaa ggttggggta agccgttcgg gggtgcttgt tttggggggt taaaattgtg
     1681 gttatttttt gcgcaattct cgcgcgtgat ccttgtattt atacttaagg gataaatggc
     1741 ggatatgaaa tagtggttta gcccagtaat gacgaggctt tgagtgggtt ttgacaggtc
     1801 aaagaaaatg gagcagaatt gaggcgtttt taatcggcgt tggggagtgc gtcaacactc
     1861 cccaacattt cgaatgtgtc acctcagcgg caaactctgg tgacatgtac tggctcgcaa
     1921 tgcacaggta cgtgatgaat ataccacatc aaatcacagc ctgcccagat cggagcaggc
     1981 ttaatgtcag aagataaatt cctttcggac tacagccccc gtgatgcagt ttgggatacc
     2041 cagcgcacgc ttaccgattc tgtcgggggt atctaccaga ctgctgctga attcgagcgc
     2101 t
//
