LOCUS       CP042610                4870 bp    DNA     circular BCT 15-AUG-2019
DEFINITION  Escherichia coli strain NCYU-29-19 plasmid pNCYU-29-19-4, complete
            sequence.
ACCESSION   CP042610
VERSION     CP042610.1
DBLINK      BioProject: PRJNA558860
            BioSample: SAMN12500849
KEYWORDS    .
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 4870)
  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  JOURNAL   Unpublished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 4870)
  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..4870
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="NCYU-29-19"
                     /host="Sus scrofa domesticus"
                     /db_xref="taxon:562"
                     /plasmid="pNCYU-29-19-4"
                     /geo_loc_name="Taiwan"
                     /collection_date="2017"
                     /collected_by="National Chiayi University"
     gene            complement(293..406)
                     /locus_tag="FTV94_23900"
     CDS             complement(293..406)
                     /locus_tag="FTV94_23900"
                     /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="QED69341.1"
                     /translation="MHEPPVQSDRCALSGNYHLESNPERHDKAPLAAATGN"
                     /name="replication initiation protein"
     gene            complement(471..658)
                     /locus_tag="FTV94_23905"
                     /pseudo=""
     CDS             complement(471..658)
                     /locus_tag="FTV94_23905"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_012579059.1"
                     /note="frameshifted; incomplete; partial on complete
                     genome; missing N-terminus and C-terminus; Derived by
                     automated computational analysis using gene prediction
                     method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="plasmid replication initiation protein"
                     /name="plasmid replication initiation protein"
     gene            826..1017
                     /locus_tag="FTV94_23910"
     CDS             826..1017
                     /locus_tag="FTV94_23910"
                     /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="QED69342.1"
                     /translation="MNKQQKTAVNMAKFIRDQSLLLLDRLNDLDLDHEADFCEKLHEDA
                     ERLYRSLSARLNEQQDGA"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            complement(1838..2240)
                     /locus_tag="FTV94_23915"
                     /pseudo=""
     CDS             complement(1838..2240)
                     /locus_tag="FTV94_23915"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001676030.1"
                     /note="frameshifted; Derived by automated computational
                     analysis using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="PH domain-containing protein"
                     /name="PH domain-containing protein"
     gene            complement(2280..2570)
                     /locus_tag="FTV94_23920"
                     /pseudo=""
     CDS             complement(2280..2570)
                     /locus_tag="FTV94_23920"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_004661993.1"
                     /note="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="restriction endonuclease"
                     /name="restriction endonuclease"
     gene            complement(2655..4226)
                     /locus_tag="FTV94_23925"
     CDS             complement(2655..4226)
                     /locus_tag="FTV94_23925"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:YP_857517.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="ABC-F family ATP-binding cassette
                     domain-containing protein"
                     /protein_id="QED69343.1"
                     /translation="MTHIACHINTLQLPFVACTVPLTFTLPAAGCTLIGRNGIGKSLLL
                     ELLAGQRRADSGKIEWLTPISWLSQFAPAQDHDCAASVADLIGWGEPLRALERIEQGSC
                     ARDDFELLADRWNLRSDLADLLAEAGLRLDPHVPVSTLSGGQLTRLRLLALFARPAHFL
                     LLDEPDNHLDASGIDWLSQQLARHRGGYLLVSHDRRLLNQTSHILELSEQGLQSARLSF
                     DEFLAQQAEVQAARSTSLAQAVRSEKAAARSLQKVREQAARRASQGRRERGSQAKILLD
                     FKAEQAGKSLGRVLDRHERGHSAQVEARTEAAAALAAVQPLIMQWPEEIERKGAAQPLV
                     ITAASHVRWHGQRVDLVLQRGERCLLGGRNGCGKSSLLQMLRGVLEPETGSFRINGKMA
                     CLDQGLSLIARDLSPLANLLTVAPTLAESDARTRLAGIALRGDRALTPCHGLSGGERLK
                     LGLLMVLAQLPDLLLLDEPDNHLDHPSRQLLTQVLADYPGTLLLVSHDPDFVAGVGVGK
                     ELNLSE"
                     /name="ABC-F family ATP-binding cassette domain-containing
                     protein"
     Typing          complement(290..659)
                     /name="rep_cluster_2373"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="94.355"
                     /coverage="86.0"
                     /evalue="8.2e-160"
ORIGIN
        1 cttgattctg tggtggtggt ggcggctgct atgtctcata tactcctggc gttgcaatcc
       61 tttatcccat atctgtcgaa tatcacagat gaacttcttg agatcctgtc cgttgcgtcg
      121 taatctcttg ctctgaaaac gaaaaaccgc cttgcagggc ggtttttcga aggttctcag
      181 agctagcaac tctttgaacc gaggtaactg gcttggagga gcgcagtcac caaaacttgt
      241 cctttcagtt tagccttaac cggcgcataa cttcaagact aactcctcta aatcagttac
      301 cagtggctgc tgccagtggc gctttgtcgt gtctttccgg gttggactca agatgatagt
      361 taccggacaa ggcgcagcgg tcggactgaa cggggggttc gtgcatacag tccagcttgg
      421 agcgaactgc cttcccggaa ctggagtgtc aggcgtggaa tgagataaac gcggccataa
      481 cagcggaatg acaccggtaa accgaaaggc aggaacagga gagcgcacga gggagctacc
      541 gaggggaaac gcctgggatc tttatagtcc tgtcgggttt cgccgccact gatttgagcg
      601 tcagattttg tgatgcttgt caggggggcg gagcctatgg aaaaacgccc cgccggggcg
      661 tggccttttc gcccttgttc ttagctttcg ttatgcttac cgttacgtta tctgcttatc
      721 ctccctccgc tcgccgcaga ctcatgaccg aacggagtga gcgaatgagc gaggaagcgg
      781 aaaaccatcc gaacgtacag taagcacttt cgcgccgggg ctttcatgaa caaacaacaa
      841 aagactgccg ttaacatggc taaattcatc cgagatcagt ccctgcttct tctggacagg
      901 cttaatgacc tggatctgga tcatgaggct gatttctgcg agaaactcca tgaggatgcg
      961 gaacgccttt accgaagcct gtcagcgcgc ctgaatgagc agcaggacgg tgcgtaatgg
     1021 ctccgttctg ggtattaccg gagtaatacc ggcatcgcct taattttcat tgtgttagcg
     1081 cttaacatta ttaccccggt aatacccaga atccctgtat tttttctttt ttatttattt
     1141 ttcatgaagt tgcgatgaaa atcgcagctg cgttaggtgt atgtcatttt ttagtatata
     1201 aaacgaccac ccccgagtgc tggcgccgca ggttaaggat gattctggct aaaaagcgtc
     1261 cttttccggg aaagggtcat gctcgtatga ccctatgggt tcagcgacta cacataaact
     1321 acaaaattgc atctgctttt accccagaac gcgggtgtac aacagaatta catcaaaagt
     1381 acatcaaaat tacatcactt ttacgtcact tttacatcat ttttgcgtca gatctgacct
     1441 ctgaactatt cgtacatccg ccccctcttc ccgggcctcc tgcacgtgct gaaaatggtt
     1501 tttccggctg tgccggcaac gcctcacggc cacgcaataa attgcgcatc cgttcaccgt
     1561 tatcggggtg gttcgtggtg gctttcaggg cgttcatcgg attttagccg ctaaaatccc
     1621 ggcggtatgt ccgtgcatag ccatgcagtc gcgccagaat catcaggggc gttttttctc
     1681 gatatgggca cagaaaggtg tgtgtttcag gccggaggcc tcagaaacgc cctgagggcc
     1741 tctgaggcgg tgcgggcaac ggatgttatg gtaaatccag ctgattggca ggtacaaaaa
     1801 agccccgcag ggcttttttt gtaatgctac gaggaagcta ctgctgctta gaattcattt
     1861 cctcgatatg attgttcaca atcgatctga attgcattgg cgccttgatg tttggaattg
     1921 gcgtgttggt tccgccagtg cctttaatca cgatagagcc atagttaaag attcgtccca
     1981 gtatcccttg atgtatgcca aggctttcaa ctttatcaat acggagttcc accgtattgc
     2041 gtcggatcaa acccactttt gcgatgactc tttggttagt taatgcaagc tccgttgacc
     2101 aaactctaag gagcactggg attattataa gtaaccctaa gccgtaaaaa ggcagcaaca
     2161 agattccgat aattactggg atgattgttg gaatccggtg aggtttgagc gcgagatatt
     2221 acggattggg gtcggctcag aaaacggaaa aaatcgtacg ctaagccgaa gttcagcact
     2281 cacgcattct gtcgagcacg taccagttcc gtgaaactga caacatccat caaccatgcc
     2341 tgctgggctg gcgtataggt ctggtgcaga ctgcgcggca gaacgagttg cagccgcttt
     2401 gctgccattt cgtcggtctg atgcgtggag attgctgttt ccagcgtcag cagatgcttg
     2461 tcatcaatgc ggtctgcttc ggcgagaacc tgccgccagc ggtccttgca ggtcgatttc
     2521 acaccaagca tggtcagctt cagcgagtcg aacgccgggt tatggtattc ggggttgtaa
     2581 gccggaaccg ccgaaatttc cgtcaactcc tctaaccccc tgccacaagg gcatctaggt
     2641 caatcatctt gcggtcactc tgaaagattt aattctttac caaccccaac ccctgcaacg
     2701 aagtcgggat cgtgagaaac caatagcaga gtgcccgggt agtccgccag gacctgagtg
     2761 agcaactgac gcgaggggtg atccagatgg ttgtccggtt catcgagcag cagcaggtcg
     2821 ggcagttgcg ccagtaccat cagcagaccc agttttaacc tctccccccc actcagacca
     2881 tgacaaggcg tcagagcacg atcgccgcgc agggctatgc ccgccagccg tgttctcgca
     2941 tcactctcgg ccagtgtcgg agccactgtc aacaggttgg caagcgggct gagatcccgc
     3001 gcaatcaggc tgagcccctg atcgaggcaa gccatcttgc cattgatgcg aaagctgccc
     3061 gtctcgggct ccagcacccc acgcaacatc tgcagcagac tcgatttgcc gcagccattg
     3121 cgaccgccga gcaaacagcg ctcaccccgt tgcagcacca gatcaacccg ctggccatgc
     3181 cagcgcacgt gagacgcagc cgtaatcacc agcggctggg cagccccctt gcgctcgatc
     3241 tcctccggcc actgcatgat gagcggctgc accgccgcca gcgcggctgc tgcctcggtg
     3301 cgggcctcca cttgcgcact gtggccccgc tcgtggcggt ccagcactct gccaagggat
     3361 ttgcctgcct gttccgcctt gaaatcaagc aggattttgg cttgggagcc gcgctcacgc
     3421 cgcccctgac tggctcgtct ggccgcctgt tcacgcactt tttgcaagct gcgcgccgcc
     3481 gccttttcgc ttcgcaccgc ttgcgccaaa ctggtgctgc gggcagcctg tacctcggcc
     3541 tgctgtgcca gaaactcgtc aaacgagagg cgggcactct gcaacccctg ctcgctcagc
     3601 tccagaatat gactggtttg attgagcagg cgccggtcgt ggctcaccag caggtaacct
     3661 ccgcgatgtc tggccagttg ctggcttagc cagtcgatgc cagaggcatc gaggtggttg
     3721 tctggctcat caagcaacag aaagtgagca ggcctcgcaa acagcgccag caggcgcaaa
     3781 cgggtgagct ggccaccgct cagggtgctg accgggacat ggggatcgag tctgaggcct
     3841 gcttctgcca gcaggtcggc aagatcgctg cgcaggttcc agcgatcagc cagcaactcg
     3901 aaatcgtccc gggcgcagct cccctgctcg atgcgctcaa gggcccgtag cggctcgccc
     3961 cagccgataa ggtcggccac actggctgcg cagtcatgat cttgagccgg tgcaaactgg
     4021 gacaaccagc tgatgggggt caaccactcg atcttgccag aatccgcgcg gcgctggccc
     4081 gccagcagtt ccagcagcag gctcttgccg atgccgttac ggccgatcag ggtgcagccc
     4141 gcagcgggca aagtgaaggt aaggggcaca gtacaggcga cgaagggcag ctgcaaagtg
     4201 ttgatatgac atgcgatatg ggtcatctga actcctgtag gccaatgcgg aagccgcagg
     4261 ccaagagcta aaccaaatga cagggacacg tgtccactag tgggaaaaca gcagaggaat
     4321 cagcatcaac ctgtcacggt gagacgcacc cgctctcccg gcgggagaag aatcaaaagt
     4381 ggggtgcgga caggttaaat gcgcatcggc gaaatactct ttactgatga aagtaaaatc
     4441 atacttcaga tagtaaaaaa tgccaaatgt tccggtatca ctcacttgca tgttgtatca
     4501 ataagtcaag tgtcagtctg ggctatacct caactgggcg tcagtcggct cactggcatc
     4561 gcgtcagact agggccgctt tctgcattat ctgacgccta aacgtcaaac tctatggcct
     4621 caacctgaca ggccgcatgc ttagcgtacg attttgtccg ttttctctac cgtccccgat
     4681 tcatttctcg tcaatgattg gtctacgtag cttcccataa ggttatatcc atttagaaaa
     4741 aataggattt ttcccttttt aaggcgaatc agcaatagaa actttatgtc tccgtggtag
     4801 gtatacaaaa tttacggaga gcgtagcgac cgtcgcacag ttcggttctt tcctttcgtg
     4861 ccgcaactgg
//
