LOCUS       NZ_AP023204             2459 bp    DNA     circular CON 14-JUN-2023
DEFINITION  Escherichia coli strain TUM18780 plasmid pMTY18780-7, complete
            sequence.
ACCESSION   NZ_AP023204
VERSION     NZ_AP023204.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMD00172787
            Assembly: GCF_013340805.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1
  AUTHORS   Ito,Y., Aoki,K., Nakayama,N., Ohtsuka,M., Ota,M., Kaneko,N.,
            Yoshida,M., Ishii,Y., Tateda,K. and Matsuse,H.
  TITLE     Whole-genome sequencing of blaNDM-5 positive Escherichia coli
            isolated from a Japanese patient with no history of travel abroad
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 2459)
  AUTHORS   Ito,Y., Aoki,K., Nakayama,N., Ohtsuka,M., Ota,M., Kaneko,N.,
            Yoshida,M., Ishii,Y., Tateda,K. and Matsuse,H.
  TITLE     Direct Submission
  JOURNAL   Submitted (03-JUN-2020) Contact:Yukitaka Ito Toho University,
            Clinical Microbiology Laboratory; 2-22-36 ohashi, Meguro-ku
            153-8515, Japan
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: Unicycler Assembly v. 0.4.4
            Genome Coverage                   :: 173x
            Sequencing Technology             :: MiSeq; MinION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 06/14/2023 02:30:10
            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)                     :: 5,360
            CDSs (total)                      :: 5,240
            Genes (coding)                    :: 5,050
            CDSs (with protein)               :: 5,050
            Genes (RNA)                       :: 120
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 90
            ncRNAs                            :: 8
            Pseudo Genes (total)              :: 190
            CDSs (without protein)            :: 190
            Pseudo Genes (ambiguous residues) :: 0 of 190
            Pseudo Genes (frameshifted)       :: 63 of 190
            Pseudo Genes (incomplete)         :: 131 of 190
            Pseudo Genes (internal stop)      :: 32 of 190
            Pseudo Genes (multiple problems)  :: 31 of 190
            Pseudo Genes (short protein)      :: 2 of 190
            CRISPR Arrays                     :: 1
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            AP023204.1.
            Annotated at DFAST https://dfast.nig.ac.jp/
            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..2459
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="TUM18780"
                     /isolation_source="human stool"
                     /host="Homo sapiens"
                     /db_xref="taxon:562"
                     /plasmid="pMTY18780-7"
                     /geo_loc_name="Japan:Tokyo, Meguro-ku"
                     /collection_date="2018-05-01"
     gene            join(2433..2459,1..87)
                     /locus_tag="HUV22_RS26550"
     CDS             join(2433..2459,1..87)
                     /locus_tag="HUV22_RS26550"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_005761324.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="replication initiation protein"
                     /protein_id="WP_077253755.1"
                     /translation="MHEPPVQSDCCVLSGNYRLESNPVRHAKAPLAAATGN"
                     /name="replication initiation protein"
     gene            386..1012
                     /locus_tag="HUV22_RS26510"
                     /old_locus_tag="TUM18780_51420"
     CDS             386..1012
                     /locus_tag="HUV22_RS26510"
                     /old_locus_tag="TUM18780_51420"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_010307272.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_117102740.1"
                     /translation="MKPGFTAILITLALSGCSIQSPKPSWITSSQKDQFTDKTSCTIQL
                     AKYYTRTSAYTQTGEYYPFISMVDNQLRVGVRSGGRALIPVGDVQLRIDSNPAWNITTA
                     ETPIDSSAATNYQLPSYTNLTSEQQALITETQKSAMASITKTMSPYTATTGDKAQKIIQ
                     QLISGNKLIYRTVGLNQTGSTTGEYDLASMKESLIAGLNQCGIKY"
                     /name="hypothetical protein"
     gene            complement(1823..2014)
                     /locus_tag="HUV22_RS26515"
                     /old_locus_tag="TUM18780_51430"
     CDS             complement(1823..2014)
                     /locus_tag="HUV22_RS26515"
                     /old_locus_tag="TUM18780_51430"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001041614.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="Rop family plasmid primer RNA-binding protein"
                     /protein_id="WP_128335088.1"
                     /translation="MNKQQKTAVNMAKFIQDQSLLLLDRLNELDLDHEADFCEKLYEDA
                     ERLYRSLSARLNEQQDGA"
                     /name="Rop family plasmid primer RNA-binding protein"
     Typing          3..87
                     /name="ColRNAI_rep_cluster_1987"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="98.837"
                     /coverage="99.0"
                     /evalue="4.99e-35"
     Typing          1890..2459
                     /name="rep_cluster_2327"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="84.014"
                     /coverage="99.0"
                     /evalue="7.349999999999999e-147"
ORIGIN
        1 tgctgcgtct tatccggtaa ctatcgtctt gagtccaacc cggtaagaca tgcaaaagcg
       61 ccactggcag cagccactgg taactgattt agaggagata gtcttgaagt catgcgccag
      121 ttaaggctaa actaaacgaa cagttttggt gactgcgctc ctccaagcca gttacctcgg
      181 ttcaaagagt tggtagctct gagaaccttc gaaaaaccgc cctgcaaggc ggttttttcg
      241 tttgcgacaa ctaatctacg cggtaacccc ttatcaggtc aagataacta tccatcagtg
      301 catctttcca atacaatcca ttaagcaacc aagttaacca ccttagaaaa taagaagata
      361 tcctacttcc ttcggggcta tgactatgaa accaggattc acagcaatat taataacact
      421 tgcgctcagt ggttgttcaa ttcagtcgcc gaaacctagc tggataacca gcagccaaaa
      481 agaccagttt acagacaaaa caagttgcac gatccagctc gccaagtact acacaagaac
      541 atctgcttac acgcaaactg gtgaatacta tccatttatt tcaatggtag ataatcaact
      601 aagagtcgga gtaagaagtg gtgggcgcgc tttaatccct gttggtgatg ttcaattaag
      661 aattgatagt aaccccgcat ggaatataac aactgcggaa acacctatag acagtagtgc
      721 tgcaactaac tatcaactcc catcttacac aaatctgaca agcgaacagc aagctctgat
      781 tactgaaaca caaaaatcag caatggcttc tattaccaag accatgtcac cctataccgc
      841 tacgactggt gataaggcgc agaaaattat tcagcagcta atatcgggaa ataaattaat
      901 ttaccgtact gttggcttga accaaactgg ttctacaact ggagagtacg acttagcatc
      961 aatgaaagag tcgctaattg caggtttaaa ccagtgtgga attaagtact aaactctgca
     1021 tttaacataa gagttcttgc gtgcaccgac tcatacgctc tcagcgcgtt tctgacggga
     1081 aaccggtaaa acaggcaaca aaccacccga aaacccgcca ggaacgcgca ggctatgttt
     1141 ttacggcatg catgagtatg cgcgcaagtg catagcgcgg aaattcacgc cattcagccg
     1201 gggtaagtcc tgtttccggc attcttccca ccagaaaacg gtgaacggga acgcaattta
     1261 ttgtgtggcc gtgaggcgtt gccggcgcag ccggaaaacc cgctgtcagc acgttcagga
     1321 agggggtgat gtacaaatgg cacagaggat ggaactgacg taaaagtgac gtatgagctg
     1381 aaggaatgat gtaaaagtgt tgtaagagtg ttgtaaaagt gatgtacagg ccgaaggaat
     1441 gatgcaaaag tgatgtaaaa gtgttgtaga agtgatgtaa aagtgttgta gaagtgatgt
     1501 attaactgaa ggagcgatgt aattctgtag tcaggaagaa taacccgttc atgcctgcat
     1561 gaacgataca gtgaggaacg ctttttttgt cacgatctcc ccttaacctg cgtaaattac
     1621 ccgccatggt tgattatttt tcaatctcaa aatggtcata cacctaacgc agccgcgatt
     1681 ttcatcgcaa cttcatgaaa aataaataaa aaagaaaaaa tacagggatt ctgggtatta
     1741 ccggggtaat aattttaagc gccaagacaa tgaaaattaa ggcgatgccg gtattactcc
     1801 ggtaataccc aggacggagc cattacgcac cgtcctgctg ctcattcagg cgcgctgaca
     1861 ggcttcggta aaggcgttcc gcatcctcat agagtttctc gcagaaatca gcctcatgat
     1921 ccagatccag ctcattaagc ctgtccagaa gaagcaggga ctgatcctgg atgaatttag
     1981 ccatgttaac ggctgtcttt tgttgtttgt tcatgaaggc cccggcgcga aagtgcttac
     2041 tgtacgttct gatggttttc cgcttcctcg ctcattcgct cactccgttc ggtcatgagt
     2101 ctgcggcgag cggagggaag ataagcagat aacataacgg taagcataac gaaagctaag
     2161 gacaagggcg aaaaggccac gccccggcgg ggcgtttttc cataggctcc gcccccctga
     2221 caagcatcac gaaatctgac gctcaaatca gtggtggcga aacccgacag gactataaag
     2281 ataccaggcg tttccccctg gtggctccct cgtgcgctct cctgttcctg cctttcggtt
     2341 taccggtgtc attccgctgt tatggccgcg tttatctcat tccacgcctg acactcagtt
     2401 ccgggtaggc agttcgctcc aagctggact gtatgcacga accccccgtt cagtccgac
//
