LOCUS       CP042611                3089 bp    DNA     circular BCT 15-AUG-2019
DEFINITION  Escherichia coli strain NCYU-29-19 plasmid pNCYU-29-19-5, complete
            sequence.
ACCESSION   CP042611
VERSION     CP042611.1
DBLINK      BioProject: PRJNA558860
            BioSample: SAMN12500849
KEYWORDS    .
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 3089)
  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  JOURNAL   Unpublished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 3089)
  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..3089
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="NCYU-29-19"
                     /host="Sus scrofa domesticus"
                     /db_xref="taxon:562"
                     /plasmid="pNCYU-29-19-5"
                     /geo_loc_name="Taiwan"
                     /collection_date="2017"
                     /collected_by="National Chiayi University"
     gene            complement(41..274)
                     /locus_tag="FTV94_23930"
     CDS             complement(41..274)
                     /locus_tag="FTV94_23930"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_017096688.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="QED69344.1"
                     /translation="MQFDLPEDRLDELDSLMKKCGISTKKELFNYALTMLEWAVDESES
                     GHEIAAIDRDSKQFYALRMPILKRVNRTSTAN"
                     /name="hypothetical protein"
     gene            complement(1641..1802)
                     /locus_tag="FTV94_23935"
     CDS             complement(1641..1802)
                     /locus_tag="FTV94_23935"
                     /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="QED69345.1"
                     /translation="MAKFIHDQSLLLLDRLNELDLDHEADFCEKLHEDAERLYRSLSAR
                     LNEQQDGA"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            1914..2210
                     /locus_tag="FTV94_23940"
                     /pseudo=""
     CDS             1914..2210
                     /locus_tag="FTV94_23940"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001692121.1"
                     /note="internal stop; Derived by automated computational
                     analysis using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /name="hypothetical protein"
     gene            complement(2626..2997)
                     /locus_tag="FTV94_23945"
     CDS             complement(2626..2997)
                     /locus_tag="FTV94_23945"
                     /inference="COORDINATES: ab initio prediction:GeneMarkS-2+"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GeneMarkS-2+."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="QED69346.1"
                     /translation="MSDSLDGFTEGDTSKEKQAVKQPKKFFSDVDDSADRRHLRWTKSG
                     VTLAMTILVAVMNWMVISMLYHVVDEELSLIRSGFMQADARTVTTSVYLALIAGTVAEV
                     SALFLIIVKSVFKNNNNDI"
                     /name="hypothetical protein"
     Typing          2133..2557
                     /name="rep_cluster_2374"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="99.065"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 agtttaagct ggccttctcc ttaacacatc aagtgataag ttaatttgca gtagatgtac
       61 ggttcactcg cttaagaata ggcattcgta gagcataaaa ttgcttactg tctctatcga
      121 tagctgcgat ttcgtgacca ctttcggact cgtccacagc ccactcaagc attgttaacg
      181 cgtagttgaa caactctttt ttagtactta tgccgcactt cttcattaaa gaatcgagtt
      241 catccaacct atcttcaggt agatcgaatt gcatacgtac attttcataa ctaatctccg
      301 aggggccagc atgtcatcct tgtactctat gctgcacatt cttcaccatt aggaccgttg
      361 gtatttatat atctctacct ataaataaat taagtttcat atacttatga tactcctaat
      421 ttggataagg cttagcctta tctcttctcc acaagcaggt tatccccacc atggaggagg
      481 ttgtgaaaac tcctccatgg tggttattac tcatcgacct cagtaaagac tgagaaccaa
      541 tccttcaaag aaagctcttt aggaggcagt tcttcgaagt cggtgcagtc ctcactgttc
      601 acggaggtcg aggagcagtt ttgagttaac tcgctcacag gtgaaatctc cagtttaccc
      661 accacacctc gtaatgggct ccagattgta tcttacactc aaacatctcc attgtcgagt
      721 gtaattggag catattacga gtataaaacg atataggtta aaaagacaac agtagttgta
      781 acgagatagg aacaatcatc caaatcttag gtgcatttaa cataactcaa gtattgtacg
      841 caccgctaaa acggcctcag ggcgtttctg acggaaaacc ggtaaaacag gcaacaaacc
      901 acccgaaaac ccgccagaaa cgcgcaggct ctgtttttac ggcatgcatg agtatgcgcg
      961 caagtgcata gcgcggaaat tcacgccatt cagccggggt aagtcctgtt tccgatgttc
     1021 ttcttatccg aaaacggtga acggggacgc aatttattgc gtggccgtga ggcgttgccg
     1081 gcacagccgg aaaaaccgtt ttcagcacgt tcaggaaggg ggtcggatgt acaaatggca
     1141 cagaggatgg aactgacgta aaagtgacgt atgagctgaa ggaatgatgt aaaagtgatg
     1201 tacaaatgat gtaaaagtga tgcaaaagtg ttgtaaaagt gatgtacaga ctgaaggagt
     1261 gttgtaaaag tgttgtaaaa gtgatgtaca gactgaagga gtgttgtaaa agtgatgtat
     1321 gaactgaagg agcgatataa ttctgtagtc aggaagaata acccgttcat gcaggcatga
     1381 acgatacagt gaggaacgct ttttttgtca cgatctcccc ttaacctgcg taaatcaccc
     1441 gccatggttg attatttttc aacctcaaaa tggtcataca cctaacgcag ccgcgacttt
     1501 catcgcaact gcatgaaaaa taaataaaaa agaaaaaata cagggattct gggtattacc
     1561 ggggtaataa tgttaagcgc taagacaatg aaaattaagg cgatgccggt attactccgg
     1621 taatacccag aacggaacca ttacgcaccg tcctgctgct cattcaggcg cgctgacagg
     1681 cttcggtaaa ggcgttccgc atcctcatgg agtttctcgc agaaatcagc ctcatgatcc
     1741 agatccagct cattaagcct gtccagaaga agcagggact gatcatggat gaatttagcc
     1801 atgttaacgg cagtcttttt gttgtttgtt catgaaagcc ccggcgcgaa agtgcttact
     1861 gtacgttctg atggttttcc gcttcctcgc tcattcgctc actccgttcg gtcatgagtc
     1921 tgcggcgagc ggagggaaga taagcagata acgtaacggt aagcataacg aaagctaagg
     1981 acaagggcta aaaggcaacg ccccggcggg gcgtttttcc ataggctccg ccccccctga
     2041 caagcatcac agaatcggac gctcaaatca gtggtggcga aacccgacag gactataaag
     2101 ataccaggcg tttccccacg gtggctccct cgtgcgctct cctgttcctg cctttcggtt
     2161 taccggtgtc attccgctgt tatggccgcg ttttctcact ccacgcctga cactccagat
     2221 ccgggaaggc agttcgctcc aagctggact gtatgcacga accccccgtt cagtccgact
     2281 gctgcgtttt tccagtaact atcaccttga gtccaacccg gaaaaaacgc gttaaaacgc
     2341 caatggcagc agccacaggt aacagattcg cagaacaaag aagcgttgag gtgttgaagt
     2401 gtaaggcaga ctacggctac actgttaaaa cgaattcggt ttctgtgctc tgcgaaagcc
     2461 agttaccacg gttcagaaac ttgccggtta atgaaccttc gaaaaaacca ccttgccggg
     2521 tggtttttcg tttcagtccc aagagattac attttgatta gagtgatctc aagacagaca
     2581 gaacaaaacc atgtgtgaca ctacatctaa cgactggaat caacttcata tatcattgtt
     2641 attgttctta aaaactgact ttacaattat caaaaataaa gcagatacct cagcaactgt
     2701 tccagcaatc aaagccaaat aaacactagt agttacagtc cttgcgtctg cttgcataaa
     2761 gccacttcgt atcagagaaa gctcttcatc aactacgtga tatagcatgc ttatgaccat
     2821 ccagttcatt acagcaacca aaattgtcat agccagagta acgccacttt ttgtccatct
     2881 cagatgccgt ctatctgctg aatcgtcgac gtcactaaag aacttcttgg gttgttttac
     2941 cgcttgtttt tcttttgagg tatcgccttc agtaaatcca tctaggctat cggacacaat
     3001 caaaccctct tgaataaaaa aagtcgcatt tatcgtgaaa cgctttcgcg tttttcgtgc
     3061 gccgcttcaa caaaccctct tgaaaggcc
//
