LOCUS       CP042614                2454 bp    DNA     circular BCT 15-AUG-2019
DEFINITION  Escherichia coli strain NCYU-29-19 plasmid pNCYU-29-19-8, complete
            sequence.
ACCESSION   CP042614
VERSION     CP042614.1
DBLINK      BioProject: PRJNA558860
            BioSample: SAMN12500849
KEYWORDS    .
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 2454)
  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  JOURNAL   Unpublished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 2454)
  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..2454
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="NCYU-29-19"
                     /host="Sus scrofa domesticus"
                     /db_xref="taxon:562"
                     /plasmid="pNCYU-29-19-8"
                     /geo_loc_name="Taiwan"
                     /collection_date="2017"
                     /collected_by="National Chiayi University"
     gene            join(1949..2454,1..37)
                     /locus_tag="FTV94_23980"
     CDS             join(1949..2454,1..37)
                     /locus_tag="FTV94_23980"
                     /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="QED69352.1"
                     /translation="MANKEKERKLKALSLEIEKIQIETSEEMELFKSKIHSSNTNTLNV
                     INKKIKENNKTEKHEWMPEELYRISCNSLTLALIARHAIRLAMEGDENKYLTDKIDNDI
                     TSLFDEIMDMRDISIDKYKSHDKTSNKQKSIESELSNAINKINELESENEKLLINLNAL
                     KEKGNLTSYIHASNHSP"
                     /name="hypothetical protein"
     gene            27..209
                     /locus_tag="FTV94_23985"
     CDS             27..209
                     /locus_tag="FTV94_23985"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001328717.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="QED69353.1"
                     /translation="MHPKQTHRSFYHNASLRAPLRRPERVSDGKPVKQATNHPKTRQKR
                     AGSVFTACMSMRTSA"
                     /name="hypothetical protein"
     gene            1229..1486
                     /locus_tag="FTV94_23990"
                     /pseudo=""
     CDS             1229..1486
                     /locus_tag="FTV94_23990"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001326445.1"
                     /note="frameshifted; 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            1613..1829
                     /locus_tag="FTV94_23995"
                     /pseudo=""
     CDS             1613..1829
                     /locus_tag="FTV94_23995"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000255616.1"
                     /note="frameshifted; internal stop; incomplete; partial on
                     complete genome; missing C-terminus; Derived by automated
                     computational analysis using gene prediction method:
                     Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /name="hypothetical protein"
     Typing          complement(946..1161)
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="89.545"
                     /coverage="100.0"
                     /evalue="3.38e-71"
     Typing          1111..1621
                     /name="ColRNAI_rep_cluster_1987"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="91.051"
                     /coverage="99.0"
                     /evalue="0.0"
ORIGIN
        1 gacatcttat attcacgctt caaatcattc accctaagca aacccacaga tcattttacc
       61 ataacgcgtc attacgcgca ccgctcagac ggcctgagcg cgtttctgac gggaaaccgg
      121 taaaacaggc aacaaaccac ccgaaaaccc gccagaaacg cgcaggctct gtttttacgg
      181 catgcatgag tatgcgcaca agtgcatagc gcggaaattc acgccattca gccggggtaa
      241 gtcctgtttc cgatgttctt cttacccgaa aacggtgaac ggggacgcaa tttattgcgt
      301 ggccgtgagg cgttgccggc acagccggaa aaaccatttt cagcacgtgc aggaggcccg
      361 ggaagagggg gcggatgtac gaatagctca gaggtcagat ctgacgtaaa aatgatgtaa
      421 aagtgatgta cttttgatgt aattctgttg tacacccgcg ttctggggta aaagcagatg
      481 caattttgta gtttatgtgt agtcgctgaa cccatagggt catacgagca tgaccctttc
      541 ccggaaaagg acgcttttta gccagaatca tccttaacct gcggcgccag cactcgggag
      601 tggtcgtttt atatactaaa aaatgacata cacctaacgc agccgcgatt ttcatcgcaa
      661 ctgcatgaat tacataaaaa aaatgggatg caccgtttat tacggtaata cgcaagtatt
      721 aaaatcatct gtaatcacat gaaaataaag aaataagatg taataccggc gtattaccac
      781 gtacgcgggc aagcgaaaaa agctataacg cttcccggcc gacaggcggc ccagaatcca
      841 caggggcatg caggttctct tcagtaacct tcgccattaa atcaaaaagg tcatattcgc
      901 cgggaagctg cgtatcagtc gaatcccgtt gttcatcata ttcagatggc atggggtgat
      961 atccagtagc tgagaggttg ttagcgggtt tcggggcgca gccctgaacc agtcacgtag
     1021 cgctagcgga gtgtatactg gctaaatatg ttacggcgga gtaacactta ataaaagtgc
     1081 ttcatgtgac aggggaaaat gcagctacag ggcgtaaggg agaaaatggg agttacggtg
     1141 atatgacgcc tcctcgctca ctcggtcgct gccgctcctg ccgttcggct gcggcgggcg
     1201 ttacctgcac acggataaga gcaaaggcat acggcatgac aggcagggca aaaaaaggat
     1261 acggcgctgc cgtttttcca taggctccgc cccccctgac aagcatcacg aaatctgacg
     1321 ctcaaatcag tggtggcgaa acccgacagg acttaaagat accaggcgtt tccccctggt
     1381 ggctccctcg tgcgctctcc tgttcctgcc tttcggttta ccggtgtcat tccgctgtta
     1441 tggccgcgtt tatctcattc cacgcctgac actcagttcc gggtaggcag ttcgctccaa
     1501 gctggactgt atgcacgaac ccccgttcag tccgactacc gcgccatgca aggtaactat
     1561 catcttgagt ccaaccctta cagacacaac aattcgccag tggcggtagc cattggtaac
     1621 ttggtatacg agaggtcttg aagtatgggc cttagagagg ctacactgga agaacagttt
     1681 tggtttctgt ggtctcgtat acccagttac cttcggaaga aagagttggt agctctgaat
     1741 tccggcaaac gaaccaccgt tggtagcggt ggtttttttg tttgcaaggc aagagactac
     1801 gacgagaccg gtataataac aagaagatat ttacaaaaat cacgccagca aataacattc
     1861 gaacaaccca gttacatgag aaaaagcaaa gatgcaatca tcaattataa tcagcataat
     1921 ccttctaata ttattgttat tttttatcat ggcaaataaa gaaaaagaac ggaaattaaa
     1981 agccttatct ttggaaatag aaaaaataca aattgaaacg tcagaagaaa tggaactctt
     2041 caaatcaaag attcattcat ccaatacaaa cactttaaat gtcataaaca aaaaaataaa
     2101 agaaaataat aaaacagaaa aacacgaatg gatgccagaa gagctttatc gtatatcatg
     2161 caactcacta acactcgctt taatagcccg ccacgcaata cgtctcgcaa tggaaggtga
     2221 tgaaaataaa tacctgacag acaaaatcga taatgatata acgagtttat ttgatgaaat
     2281 aatggatatg cgagacattt ctattgataa atacaaatca cacgacaaaa catcaaataa
     2341 acaaaaatcc attgaatcag aattatctaa cgcaataaac aaaataaacg aattagaatc
     2401 cgaaaatgaa aagctactaa tcaaccttaa cgccctaaaa gagaaaggaa actt
//
