LOCUS       CP042612                2997 bp    DNA     circular BCT 15-AUG-2019
DEFINITION  Escherichia coli strain NCYU-29-19 plasmid pNCYU-29-19-6, complete
            sequence.
ACCESSION   CP042612
VERSION     CP042612.1
DBLINK      BioProject: PRJNA558860
            BioSample: SAMN12500849
KEYWORDS    .
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 2997)
  AUTHORS   Hsu,C.-Y., Huang,W.-C. and Lauderdale,T.-L.
  TITLE     Plasmid- and chromosome-located mcr-3 in mcr-1-positive Escherichia
            coli from diseased swine, Taiwan
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 2997)
  AUTHORS   Chen,F.-J., Wu,H.-C., Liao,Y.-C. and Kuo,S.-C.
  TITLE     Direct Submission
  JOURNAL   Submitted (06-AUG-2019) National Institute of Infectious Diseases
            and Vaccinology, National Health Research Institutes, 35 Keyan Road,
            Zhunan, Miaoli 35053, Taiwan
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Date                     :: 2019
            Assembly Method                   :: CCBGpipe v. 1
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 80x
            Sequencing Technology             :: Oxford Nanopore MiniION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI
            Annotation Date                   :: 08/07/2019 15:46:13
            Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline
            (PGAP)
            Annotation Method :: Best-placed reference protein set; GeneMarkS-2+
            Annotation Software revision      :: 4.8
            Features Annotated :: Gene; CDS; rRNA; tRNA; ncRNA; repeat_region
            Genes (total)                     :: 4,799
            CDSs (total)                      :: 4,678
            Genes (coding)                    :: 2,848
            CDSs (with protein)               :: 2,848
            Genes (RNA)                       :: 121
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 86
            ncRNAs                            :: 13
            Pseudo Genes (total)              :: 1,830
            CDSs (without protein)            :: 1,830
            Pseudo Genes (ambiguous residues) :: 0 of 1,830
            Pseudo Genes (frameshifted)       :: 1,694 of 1,830
            Pseudo Genes (incomplete)         :: 169 of 1,830
            Pseudo Genes (internal stop)      :: 47 of 1,830
            Pseudo Genes (multiple problems)  :: 77 of 1,830
            CRISPR Arrays                     :: 3
            ##Genome-Annotation-Data-END##
            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/
            NCBI analysis of this genome has determined that >30% of the
            predicted CDS features contain frameshifts, which is well above the
            usually observed value of <10%.
FEATURES             Location/Qualifiers
     source          1..2997
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="NCYU-29-19"
                     /host="Sus scrofa domesticus"
                     /db_xref="taxon:562"
                     /plasmid="pNCYU-29-19-6"
                     /geo_loc_name="Taiwan"
                     /collection_date="2017"
                     /collected_by="National Chiayi University"
     gene            complement(join(2944..2997,1..297))
                     /locus_tag="FTV94_23950"
     CDS             complement(join(2944..2997,1..297))
                     /locus_tag="FTV94_23950"
                     /inference="COORDINATES: protein motif:HMM:PF07751.9"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="QED69348.1"
                     /translation="MRLKQVHLLRNRISHFEPVWKFGELKNEAGNKTMRKAPTNIVECL
                     SRTKTEYKYIVDIISWMSSDMHNFYEKTLNHKEILELLELNAINSFKEKSQTIQIDIKS
                     GRSFPTNRNRHV"
                     /name="hypothetical protein"
     gene            complement(1096..1209)
                     /locus_tag="FTV94_23955"
     CDS             complement(1096..1209)
                     /locus_tag="FTV94_23955"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_007772075.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="replication initiation protein"
                     /protein_id="QED69347.1"
                     /translation="MHEPPVQSDCCACPGNYRLESNPERHDKAPLAAAIGN"
                     /name="replication initiation protein"
     Typing          complement(1083..1481)
                     /name="rep_cluster_2373"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="95.761"
                     /coverage="93.0"
                     /evalue="0.0"
ORIGIN
        1 ttgtattgtt tgtgattttt ctttaaacga atttattgca ttcagttcaa gtagttctaa
       61 aatttcttta tgatttaagg ttttttcata gaaattatgc atgtccgaag acatccaaga
      121 tatgatgtct acaatgtatt tatattctgt tttagttctg ctaagacatt cgactatgtt
      181 cgttggggct tttctcatag ttttgttgcc tgcttcattc tttaattccc caaatttcca
      241 aactggttca aaatgggaaa ttctgttccg tagcagatga acctgtttca gtctcatgaa
      301 aacaggttct ttcgcactag gttttttaaa gtcagatcga tactctggga aaacctcatg
      361 aagcagccta tcccacggta tgtctttacc gtttagagtt tttgttactt tgaaggcatt
      421 cctccatttt ccgtggctta gctttgatat aatttgatgg gggtatggtg gcggggatag
      481 tggatttcct ttctcgtcgg taagttcgct ttttatataa gagctgaatt ttgaattttc
      541 tgatatatga ttataccagt cgcaagattc aaatgttccg ttcagcgcac cgctgcaata
      601 atttttatta ttaaaaaaga atccacttaa agttttatgg atcttgtttc ttaaaagaac
      661 ctcgtaaatc cctattgcta agcttattct tgaagaaagc tctccattcc agcaatatat
      721 cccataggcc tcttcatcat ttgtggtttt aaaaaagatt tatagcttcc aattcttaat
      781 gaagatattt cattgatatg gttgctgatg ttttcagggc ttatgcgata catgtaaagt
      841 ttttccctta tttaggatta cctttggaga cgataaggat atgttgacac tttttcgatg
      901 ctaggcatac tggaggcata aaaaaaccgc cggggaggcg gctttttaag gttcaacagg
      961 ttggggaact tgttgaaccc cggtgactgg ctttcacgga gcgcagtaac ctaattcgtc
     1021 cttccagtgt agccgcagtc tggctcctac ttcaagaact cttgttaagt tagcttaaca
     1081 actctgctcc gtgaatcagt taccaatggc tgctgccagt ggcgctttgt cgtgcctttc
     1141 cgggttggac tcaagacgat agttaccggg gcaggcgcag cagtcggact gaacgggggg
     1201 ttcgtgcata cagtccagct tggagcgaac tgcctacccg gaactgagtg tcaggcgtgg
     1261 aatgagaaac cgcggccata acagcggaat gacaccggta aaccgaaagg caggaacagg
     1321 agagcgcacg agggagctac ctgggggaaa cgcacgggat ctttatagtc ctgtcgggtt
     1381 tcgccaccac tgatttgagc gtcagattct gtgatgcttg tcaggggggc ggagcctatg
     1441 gaaaaccggc aacgccgcgg cctttcttgt tgcttctcca ttctctctca ttgcctatgg
     1501 cttaatgtct ctgttccctc cgctcgccgc agccgaacga ccgagcggag cgagtcagtg
     1561 agcgaggaag cggaatatct gcgggcttct ctttggcacc gtacgcgcca tagctgcatt
     1621 ttttaatacg atgcaggata gggcgaacgc cgcaaagtga cgtcacctga cgttcctgga
     1681 ttacaaaggt taaagcagcg gacaggaaat gttttgtggc tacacgacag cgggacaaga
     1741 tgtatttttg gagtaccgcc ggcacgccaa tgactcctgg tcaggttccg cccgacaccg
     1801 tatgtttgct acttttttgc tatttttttg ctatcttttt gctatttcag gggcctttga
     1861 gcctttcggt tgctctcctt ttgctatctt tttgctactt ttttgctatc ggactgctac
     1921 cactctcttt ttgcgctcca taaacaaggc acgttagcga tgtatacatc gccgcgccgc
     1981 aagggtgccc cttccgaatc ccgttcatca ctgtgtgctg attaatccgg gttaaatccg
     2041 acccccttag caataaatcc tgccatgcct gacggcacgg ccaacgcctc acggtcgcac
     2101 agtaaactgc gcaccctttc accgttatcg gtggggttcg tggtggcttt cagggcgctc
     2161 gccggatttt agccgctaaa atgacgtcca tgcgttcgta tgcatagcca tgcagacgcg
     2221 aagaaatcat caggcgcgtt ttttcacgat atggacaggg aaagatgccg gaaataggca
     2281 ggagggcgca gaaatgctct gagggcgtct gagatggtgc gggcaacgga tgttatggta
     2341 aatagattaa agcacagatt aaaaattgct tataattcaa tgaaatcgac tttctatttt
     2401 tttatcaata attctttgaa tctattgact ttattcatta attatgataa gctctgccgc
     2461 tccactggcg ctcgctacca aatgcattaa tgatttgcgt gcgagcgcca gtggagcggc
     2521 gatatttaga caagttattg attttaaaag attttttaca gcgcaaaaca tttttttcat
     2581 ttccatttta cttctcctgc attatttttt atcagatgga acagtaattg actttataaa
     2641 acaattactt ggatggataa ttgtaccatt tttgagcgct tttataaagc caaaagacta
     2701 atctgagagc ttattgttga cgatgtcgtc aatattatgc tattgttccg ctgtagtcgt
     2761 ttcatgtgtg ctgatcttca gcaacatcca taccgaaggc gcgtatagat ggccatgtaa
     2821 cgcataggac accatgaaaa agccacccct aaagggtggc tttttcacat ttaattttag
     2881 cgcaaaatcg ctatacattt tccggctttt gttagttcca ctttgttgtt tctttgcttt
     2941 gctttagaca tggcgatttc tatttgttgg gaaagatctt ccagatttaa tatcaat
//
