LOCUS       CP042613                2506 bp    DNA     circular BCT 15-AUG-2019
DEFINITION  Escherichia coli strain NCYU-29-19 plasmid pNCYU-29-19-7, complete
            sequence.
ACCESSION   CP042613
VERSION     CP042613.1
DBLINK      BioProject: PRJNA558860
            BioSample: SAMN12500849
KEYWORDS    .
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 2506)
  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  JOURNAL   Unpublished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 2506)
  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..2506
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="NCYU-29-19"
                     /host="Sus scrofa domesticus"
                     /db_xref="taxon:562"
                     /plasmid="pNCYU-29-19-7"
                     /geo_loc_name="Taiwan"
                     /collection_date="2017"
                     /collected_by="National Chiayi University"
     gene            complement(374..487)
                     /locus_tag="FTV94_23960"
     CDS             complement(374..487)
                     /locus_tag="FTV94_23960"
                     /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="QED69349.1"
                     /translation="MHEPPVQSDCCALSGNYHLESNPERHDKAPLAAATGN"
                     /name="replication initiation protein"
     gene            complement(512..747)
                     /locus_tag="FTV94_23965"
                     /pseudo=""
     CDS             complement(512..747)
                     /locus_tag="FTV94_23965"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_012579059.1"
                     /note="frameshifted; incomplete; partial on complete
                     genome; missing N-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"
     gene            907..1098
                     /locus_tag="FTV94_23970"
     CDS             907..1098
                     /locus_tag="FTV94_23970"
                     /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="QED69350.1"
                     /translation="MNKQQKTAVNMAKFIRDQSLLLLDRLNELDLDHEADFCEKLHEDA
                     ERLYRSLSARLNEQQDGA"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            complement(2010..2435)
                     /locus_tag="FTV94_23975"
     CDS             complement(2010..2435)
                     /locus_tag="FTV94_23975"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001676030.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="PH domain-containing protein"
                     /protein_id="QED69351.1"
                     /translation="MGSYVDQSLTRNESVISRAQTSRIPTIIPVIIGILLLPFYGLGLL
                     IIIPVLLRVWSTELALTNQRVIAKVGFIRRNTVELRIDKVESLGIHQGILGRIFNYGSI
                     VIKGTGGTNTPIPNIKAPMQFRSIVNNHIEEMNSKQQ"
                     /name="PH domain-containing protein"
     Typing          complement(371..725)
                     /name="rep_cluster_2373"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="95.225"
                     /coverage="82.0"
                     /evalue="1.37e-157"
ORIGIN
        1 ctccgtggtg ggtatacaaa atttacggag agcgtagcga ccgtcgcaca gttcggttct
       61 ttcctttcgt gacgcaactg gcttgattct gtggtggtgg tggctgctgc tatgtctcac
      121 atactcttgg cgttgcaatc ctttatccca tatctgtcga atatcacaga tgatcttctt
      181 gagatcctgt ccgttgcgtc gtaatctctt tctctggaaa cgaaaaaacc gccttgcagg
      241 gcggtttttc gaaggttctc agagctacca actctttgaa ccgcggtaac tggcttggag
      301 gagcgcagta accaaatctg tcctttcagt ttagccttaa ccggcgcata acttcaagac
      361 taactcctct aaatcagtta ccagtggctg ctgccagtgg cgctttgtcg tgtctttccg
      421 ggttggactc aagatgatag ttaccggaca aggcgcagca gtcggactga acggggggtt
      481 cgtgcataca gtccagcttg gagcgaactg cctacccgga actgagtgtc aggcgtggaa
      541 tgagataaac gcggccataa cagcggaatg acaccggtaa accgaaaggc aggaacagga
      601 gagcgcacga gggagctacc gaggggaaac gcacgggatc tttatagtcc tgtcgggttt
      661 cgccaccact gatttgagcg tcagattttc gtgatgcttg tcaggggggc ggagcctatg
      721 gaaaaacgcc ccggcggggc gtggcctttt cgcccttgtc cttagctttc gttatgctta
      781 ccgttacgtt atctgcttat cctccctccg ctcgccgcag actcatgacc gaacggagtg
      841 agcgaatgag cgaggaagcg gaaaaccatc cgaacgtaca gtaagcactt tcgcgccggg
      901 gctttcatga acaaacaaca aaagactgcc gttaacatgg ctaaattcat ccgggatcag
      961 tccctgcttc ttctggacag gcttaatgag ctggatctgg atcatgaggc tgatttctgc
     1021 gagaaactcc atgaggatgc ggaacgcctt taccgaagcc tgtcagcgcg cctgaatgag
     1081 cagcaggacg gtgcgtaatg gctccgttct gggtattacc ggagtaatac cggcatcgcc
     1141 ttaattttca ttgtgttagc gcttaacatt attaccccgg taatacccag aatccctgtg
     1201 ttttttcttt tttatttatt tttcatgaag ttgcgatgaa aatcgcagct gcgttaggtg
     1261 tatgtcattt tttagtatat aaaacgacca ctcccgagtg ctggcgccgc aggttaagga
     1321 tgattctggc taaaaagcgt ccttttccgg gaaagggtca tgctcgtatg accctatggg
     1381 ttcagcgact acacataaac tacaaaattg catctgcttt taccccagaa cgcgggtgta
     1441 caacagaatt acatcaaaag tacatcaaaa ttacatcact tttacgtcag atcgcgggtg
     1501 tacaacagat cgcatttatc gtgaaacgct ttcgcgtttt tcgtgcgccg cttcaccgat
     1561 tacatcaaaa gtacatcact ttttacatca tttttacgtc agatctgacc tctgagctat
     1621 tcgtacatcc gccccctctt cccgggcctc ctgcacgtgc tgaaaatggt ttttccggct
     1681 gtgccggcaa cgcctcacgg ccacgcaata aattgcgcat ccgttcaccg ttatcggggt
     1741 ggttcgtggt ggctttcagg gcgttcatcg gattttagcc gctaaaatcc cggcggtatg
     1801 tccgtgcata gccatgcagt cgcgccagaa tcatcagggg cgttttttct cgatatgggc
     1861 acagaaaggt gtgtgtttca ggccggaggc ctcagaaacg ccctgagggc ctctgaggcg
     1921 gtgcgggcaa cggatgttat ggtaaatcca gctgattggc aggtacaaaa aaagccctac
     1981 ggggcttttt ttgtaatgct acgaggaagc tactgctgct tagaattcat ttcctcgata
     2041 tgattgttca caatcgatct gaattgcatt ggcgccttga tgtttggaat tggagtgttg
     2101 gttccgccag tgcctttaat cacgatagac ccatagttaa agattcgtcc cagtatccct
     2161 tgatgtatgc caaggctttc aactttatca atacggagtt ccaccgtatt gcgtcggata
     2221 aaacccactt ttgcgatgac tctttggtta gttaatgcaa gctccgttga ccaaactcta
     2281 aggagcacag ggattattat aagtaaccct aagccgtaaa aaggcagcaa caagattccg
     2341 ataattactg ggatgattgt tggaatccgg gaggtttgag cgcgagatat tacggattca
     2401 tttctcgtta atgattggtc tacgtagctt cccataaggt tatatccatt tagaaaaaat
     2461 aggatttttc cctttttaag gcgaatcagc aatagaaact ttatgt
//
