LOCUS       NZ_AP027967             4286 bp    DNA     circular CON 25-JUN-2023
DEFINITION  Escherichia coli strain VE-T9 plasmid pVE-T9_4, complete sequence.
ACCESSION   NZ_AP027967
VERSION     NZ_AP027967.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMD00587239
            Assembly: GCF_030162155.2
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1
  AUTHORS   Suzuki,M., Vu,T.M.H. and Kasuga,I.
  TITLE     Whole genome sequencing of colistin-resistant Escherichia coli
            isolated from Vietnam
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 4286)
  AUTHORS   Suzuki,M., Vu,T.M.H. and Kasuga,I.
  TITLE     Direct Submission
  JOURNAL   Submitted (05-APR-2023) Contact:Masato Suzuki National Institute of
            Infectious Diseases, Antimicrobial Resistance Research Center; 4-2-1
            Aobacho, Higashimurayama, Tokyo 189-0002, Japan
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: Unicycler v. 0.5.0
            Genome Coverage                   :: 581x
            Sequencing Technology             :: Illumina MiSeq; ONT MinION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 06/23/2023 18:15:34
            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)                     :: 4,719
            CDSs (total)                      :: 4,604
            Genes (coding)                    :: 4,363
            CDSs (with protein)               :: 4,363
            Genes (RNA)                       :: 115
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 86
            ncRNAs                            :: 7
            Pseudo Genes (total)              :: 241
            CDSs (without protein)            :: 241
            Pseudo Genes (ambiguous residues) :: 0 of 241
            Pseudo Genes (frameshifted)       :: 87 of 241
            Pseudo Genes (incomplete)         :: 150 of 241
            Pseudo Genes (internal stop)      :: 44 of 241
            Pseudo Genes (multiple problems)  :: 38 of 241
            Pseudo Genes (short protein)      :: 4 of 241
            CRISPR Arrays                     :: 1
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            AP027967.1.
            Annotated by DFAST https://dfast.ddbj.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..4286
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="VE-T9"
                     /db_xref="taxon:562"
                     /plasmid="pVE-T9_4"
                     /geo_loc_name="Viet Nam:Hanoi"
                     /lat_lon="20.96321052 N 105.81806181 E"
                     /collection_date="2020-07-03"
     gene            576..770
                     /locus_tag="QQK52_RS23550"
                     /old_locus_tag="VET9_45320"
     CDS             576..770
                     /locus_tag="QQK52_RS23550"
                     /old_locus_tag="VET9_45320"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001041627.1"
                     /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_001041631.1"
                     /translation="MNKQQQTALNMARFIKSQSLTLLEKLDALDADEQAAMCERLHELA
                     EELQNSIQIRFEAESETGT"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            1793..2803
                     /locus_tag="QQK52_RS23555"
                     /old_locus_tag="VET9_45330"
     CDS             1793..2803
                     /locus_tag="QQK52_RS23555"
                     /old_locus_tag="VET9_45330"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000395670.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_001522447.1"
                     /translation="MEFQELENSACLYWPKELAERAASISAISPLIETQDEFLSILTIS
                     TNKPTSCFDAVRLCNKISPNLFVKHLMVLSDIGGERLHRFFKDLDKIYPDRIMEFNIGN
                     NSYSYQFNSNRAWTTKNLNVEKSRLLQPVSDFTREMLDVCMLILWGGNTINNTNLPTEI
                     ENNCILGNLIGNKEAIEQFVKERYIMVSRQTGGATANDLGHICEIFIKEKLYKLIDDNI
                     SLDGHHIDGVTHNDKDLTTFDIVAKNTITKKCVGIEISFQVTTNSTIERKAGLAKSRRD
                     LLNSIGHKIAYVIDGSGNFQRSNAIKTIINHSDMTVNFSDNGINSLATFICETLK"
                     /name="hypothetical protein"
     gene            2800..4047
                     /locus_tag="QQK52_RS23560"
                     /old_locus_tag="VET9_45340"
     CDS             2800..4047
                     /locus_tag="QQK52_RS23560"
                     /old_locus_tag="VET9_45340"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001522448.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="DNA cytosine methyltransferase"
                     /protein_id="WP_001522448.1"
                     /translation="MIKFVDLFSGTGGIRLGFEQAMKEIGLSTKCVKSSEIDKKACETY
                     KLNFDEESYCDIHDVDIDESFDVLLAGFPCQAFSYAGKQLGFADTRGTLFFEVERIIKK
                     NKPKLCLLENVRGLTSHDKGRTFSTILKSLHDLGYHVEYRLLNTSNFGVPQNRVRIYII
                     ASLKKEVTLTIPNDLGAKDTHNYKPSKGGHDFYTESKVSDILEDSPDKSYDCSDWFKQR
                     LEDIFKGDLNKVHGIRLIDTRNGNSLHSWDLGLKGECSNDEIAFMNSLIANRRKHIFGT
                     HQDGKALSKAQIETFFKHSETTNIIKNLIKKGYLKEKNGLYNPVCGNMSFEVFKFLDPN
                     KVSITLTASDANRLGVYHNNRLRRLTPRECARLQGYPDSYILHPKDSMAYKQLGNAVSV
                     PVIKNIFLDIMKNNFI"
                     /name="DNA cytosine methyltransferase"
     Typing          complement(62..317)
                     /name="MOBF"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="96.899"
                     /coverage="89.0"
                     /evalue="2.61e-118"
     Typing          complement(442..540)
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="98.0"
                     /coverage="100.0"
                     /evalue="1.35e-41"
     Typing          complement(851..936)
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="8.58e-38"
     Typing          958..1503
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="94.565"
                     /coverage="99.0"
                     /evalue="0.0"
ORIGIN
        1 cacattttcg gacattttca gttcgtgaat ccctgactca ttgctacata tctgaacaga
       61 cacccctagc agcgccccca ggggtgtcct gtaaaaaaac acaccgcgcc gctagcagca
      121 cccctaatat aagatgatgt tttttatgaa aatagtcagt accaccccta aaaagcggtg
      181 ttggcgcagc tacaacaccg cgccgacacc gcttttttaa atatcacaaa gagagcaaga
      241 agaactaatt tgtcataact ctctatttat aaagaaaaat cagcaaaaac ttgtttttgc
      301 gtggggtgtg ggcatttcag gcatgagaac agactcgcgt ttttccggag tatcagcgga
      361 attattgatt aagaaacact cgacgcagag cgaaatttta tgcaacagcg gctgcactgc
      421 acagggatta tttatcagtt gatatgctgt gccatgatac gtcctaaaga aacaggacag
      481 gatgtgcaat tgtaataccg tcgcccgcaa cgtcttacaa ttaccacctg ctcagggtcc
      541 ccccgacacc cggaactgac ggagaacaac ggaaggtgaa caaacaacaa caaactgcgc
      601 tgaatatggc gcgatttatc aaaagccaga gcctgacact gcttgaaaaa ctggatgctc
      661 tggatgccga cgaacaggcg gccatgtgcg aacgactgca cgaactcgca gaagaactcc
      721 agaacagcat ccagattcgc tttgaggccg aaagtgaaac aggaacataa cgaagctgac
      781 ggaggcggtc acggctttcc cgtgggcgtt ttcgtcagca gacaagcccg tcagggcgcg
      841 tcagggggtt ttagcgggtg tcggggcgca gccatgaccc agtcacgtag cgatagcgga
      901 gtgtatactg gcttaaccat gcggcatcag tgcagattgt aagaaaagag cgccatatgc
      961 ggtgtgaaat gccgcacaga tgcgtaagga gaaaatgcac gttccggcgc tcttccgctt
     1021 cctcgctcac tgactcgcta cgctcggtcg ttcggctgcg gcgagcggtg tcggctcact
     1081 caaaagcgga gatgcggtta tccacagaat caggggataa cgccaaaaga aacatgtgag
     1141 caaaaaacga gaacccggaa aaggccacgc cgctggcgtt tttccatagg ctccgccccc
     1201 ctgacgagca tcacaaaaac cgacgctcaa gtcagaggtg gcgaaacccg acaggactat
     1261 aaagatacca ggcgtttccc cctggaagct ccctcgtgcg ctctcctgtt ccgaccctgc
     1321 cgcttaccgg atacctgtcc gcctttctcc cttcgggaag cgtggcgctt tctcatagct
     1381 cacgctgttg gtatctcagt tcggtgtagg tcgttcgctc caagctgggc tgtgtgcacg
     1441 aaccccccgt tcagcccgac cgctgcgcct tatccggtaa ctgtcgtctt gagtccaacc
     1501 cggaaagaca tgcaaaagca ccactggcag cagccattgg tagagggtgt acaagaaatt
     1561 gctgatacgg agttcttgaa gtgaaggccc gactgcggct acactgaaag gacagatttg
     1621 gtggcagcgg tcttgtacgc cctgttacct tgggttagaa agcctgagaa acttctaacc
     1681 ttcgaaaaac ccacgcctga gaacgtgggt tttttcgttt acgcccgtag agattaccca
     1741 tcataggggt gtaactcaag gtctatttgg atagttttac caaggaataa tcatggagtt
     1801 ccaagaatta gaaaatagcg catgcttata ctggcccaaa gaacttgcag aaagagcagc
     1861 atctattagc gccataagcc ctcttataga gacccaagat gaatttttat caatactaac
     1921 aatatcaaca aataagccta catcttgttt tgatgctgta cggttatgca ataagatatc
     1981 acccaaccta tttgtcaagc acctaatggt tttgtcagat attggaggcg aaagacttca
     2041 tcgctttttt aaagatttag ataaaatcta tcctgacaga ataatggagt tcaatatagg
     2101 gaataactct tactcttacc aattcaatag caatagagca tggacaacca agaatttaaa
     2161 cgtggaaaaa tcacgacttt tgcaacctgt aagtgatttt acacgagaaa tgcttgatgt
     2221 ttgcatgctg atcctgtggg gaggtaacac tataaacaat acaaaccttc caactgaaat
     2281 agaaaataac tgtattttgg gaaatttaat tgggaacaaa gaagcaatag aacaatttgt
     2341 aaaagaaaga tatataatgg ttagcagaca aacaggaggt gcaacggcaa atgatcttgg
     2401 acacatatgc gagatcttta taaaagaaaa actttataaa cttattgatg ataatatatc
     2461 tctagatgga caccatatcg atggtgtaac tcataacgat aaagacctta cgacttttga
     2521 tattgtagca aaaaacacga taacaaaaaa atgtgttggt attgaaataa gttttcaagt
     2581 tacaacaaac tcaacaatag aaagaaaagc aggattagcc aaaagcagaa gagatttact
     2641 caattcaata gggcataaaa tagcatatgt gattgatggg tctggtaatt ttcagcgctc
     2701 aaatgccata aaaacaataa ttaaccatag tgacatgact gttaactttt cagataatgg
     2761 tataaattca ctagcaacat tcatctgcga gacattgaaa tgattaaatt tgttgacctt
     2821 ttttctggca caggtggtat tagacttggt tttgagcaag ccatgaaaga aattggattg
     2881 tcaacaaaat gtgtaaaaag ctcagaaatt gacaaaaaag catgcgaaac atacaaactt
     2941 aacttcgacg aagaatcata ttgtgatata catgatgttg atatagatga aagcttcgat
     3001 gttttattgg caggatttcc ttgccaagca ttctcttatg ctggaaaaca acttggtttt
     3061 gcagacaccc gaggtacatt attttttgaa gtagaaagaa ttataaagaa aaacaagcct
     3121 aaattgtgtc ttttggagaa tgtacgtgga ttaacttcac atgataaagg aaggacattt
     3181 tcaacaatat taaaatccct tcacgattta gggtatcatg ttgaatacag actattaaat
     3241 acaagtaatt ttggcgtccc tcaaaatagg gttagaatat atataatagc ctcattaaaa
     3301 aaagaggtaa cgcttactat tcctaatgat cttggagcca aagatacgca caattacaaa
     3361 ccatccaaag gtggtcatga tttttataca gaatcaaaag tttctgacat actagaggat
     3421 agtccagaca agtcatatga ttgcagcgat tggttcaagc aacgccttga agatattttt
     3481 aaaggtgacc tgaataaagt tcatggaatc aggctaattg acacaaggaa cggcaactcc
     3541 ttgcactctt gggatcttgg gctaaaaggc gagtgctcaa atgatgaaat agctttcatg
     3601 aattcattaa ttgcaaatcg tagaaagcat atttttggca cacaccaaga cggcaaggct
     3661 ttgtcaaaag cacaaattga aacatttttc aaacatagcg aaaccaccaa cataataaaa
     3721 aatctaatta aaaagggtta ccttaaagaa aaaaacggac tatacaaccc agtttgcgga
     3781 aatatgtctt ttgaagtatt caaattcctt gacccaaata aagtgtcaat tacacttact
     3841 gcatctgatg ccaatagact tggagtctat cacaacaata gactgcgacg ccttacacca
     3901 agagaatgtg caaggctaca aggttaccca gactcatata tcttacaccc aaaagatagc
     3961 atggcatata aacaattggg gaatgctgta agcgttccag tcattaaaaa tatttttctt
     4021 gatataatga agaataactt catataaact atattactag caaaactgct ctatggttat
     4081 ttaattaaat ttaacagatt taccataatg tcgcattgcg cgcaccgcta aaacgcgctg
     4141 aaagcgattc tgccgcgaac accgcaaaaa gagatgttct ccccggggta aaccggaaaa
     4201 atgcgtcagg atcgctttca gctcactgca tagctatgca tgaaagtgaa tgacgatcgg
     4261 tttgggcgca tacagtgccc atgaga
//
