LOCUS       CP042609                5518 bp    DNA     circular BCT 15-AUG-2019
DEFINITION  Escherichia coli strain NCYU-29-19 plasmid pNCYU-29-19-3, complete
            sequence.
ACCESSION   CP042609
VERSION     CP042609.1
DBLINK      BioProject: PRJNA558860
            BioSample: SAMN12500849
KEYWORDS    .
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 5518)
  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  JOURNAL   Unpublished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 5518)
  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..5518
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="NCYU-29-19"
                     /host="Sus scrofa domesticus"
                     /db_xref="taxon:562"
                     /plasmid="pNCYU-29-19-3"
                     /geo_loc_name="Taiwan"
                     /collection_date="2017"
                     /collected_by="National Chiayi University"
     gene            join(4930..5518,1..32)
                     /locus_tag="FTV94_23860"
     CDS             join(4930..5518,1..32)
                     /locus_tag="FTV94_23860"
                     /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="QED69339.1"
                     /translation="MLFLFIPITIYFSGIDNVWSVLDKAMSSCSGADGKFQCVLDYSNS
                     RLTFSVLRSVICGALILTCSYTYIWYRWVLKNLDSGAVSRKLKVVSCKKESGEYLSFLS
                     TYIMPLVFTDLSKPSNIVNFLFVLIIVGFLHIKTKRIHCNPTLSLFNVSAYKITYSVVA
                     NGREKTQDGELIVLSKDLIKENDFIRVINHDDYLTFAKKIIEE"
                     /name="hypothetical protein"
     gene            29..1177
                     /locus_tag="FTV94_23865"
     CDS             29..1177
                     /locus_tag="FTV94_23865"
                     /inference="COORDINATES: protein motif:HMM:PF16162.3"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="DUF4868 domain-containing protein"
                     /protein_id="QED69340.1"
                     /translation="MMMSDDALDLDALEHNEEKAQELLELYKHFDCDINDVTLHTYFNF
                     KNKGKAGAKDSFSYKIAILKNDSELKQSIIDNVIKKTISDLENRVVIVSDVNTLSDRTN
                     TISFLNDAEQYDNEQMKFLTGIVFDAGFGGDGNENIPIVDFDSVDLISKVDSIIFVLSK
                     NNDDNCITIYKKQYPVQNLSRKKNNFYGFSKKELSRVDQDMISIDGKASLVFAGDTVFI
                     YDQNVFERFFGYKAWIKNAATDFVNNMSTRFKGFVDLSKFIERVNKDSHDADAFSRKLA
                     KAYARSETKQTLQTITNEHLKSVLDENGYLAGVLKYKKGDATICIASHNQQDTFIAMVS
                     EGVLRSLITGIDYLSLGSKRKISSAASNTTTSTTSDSSSAAV"
                     /name="DUF4868 domain-containing protein"
     gene            1404..1730
                     /locus_tag="FTV94_23870"
     CDS             1404..1730
                     /locus_tag="FTV94_23870"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001715145.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MobC family plasmid mobilization relaxosome
                     protein"
                     /protein_id="QED69334.1"
                     /translation="MEKRTKEIKIRLTEAEHQRLLERCDRKHLAEWLRAVGLGESRTAR
                     RRPLPTVDPTLLRQVSGIGNNLNQIARYLNQHGLPPQERVSLLAVLNSIDQHLAELLEQ
                     HRDR"
                     /name="MobC family plasmid mobilization relaxosome protein"
     gene            1720..2895
                     /locus_tag="FTV94_23875"
     CDS             1720..2895
                     /locus_tag="FTV94_23875"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000635821.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="QED69335.1"
                     /translation="MIVKIHGRGAGGGSGPVDYLLGPDRQREQATVLRGNPEHVKELID
                     GCEFARTYTSGVLSFQESDLPEGEKQRLMDEWEQTLMTGLDKDQYACLWVQHQDKGRLE
                     LNFVIPNIELQSGKRLQPYFDRADRPRVNAWQTLTNDRLGLRDPNDPANRRALTPSNDL
                     PRNKQQAAEAITKGLISLIEQGEITDRKGVISHLTDAGLSVVRETKSSISIADPAGGPN
                     IRLKGVLYERDFKFSAGVREQIEAASQDYRNERRERIREARETYHRGLEIKLREHTDRY
                     PRRERQPAKTDTPLSRNDMAVQPLALSGILFAILIGVAWYLGTIVVERQNEISEQSQIL
                     QDLKSQTGAGVSIIHDSKNKSVYYLILPQGAKKIDEYKNAQHRQVIKYSAK"
                     /name="hypothetical protein"
     gene            2956..3189
                     /gene="mbeD"
                     /locus_tag="FTV94_23880"
     CDS             2956..3189
                     /gene="mbeD"
                     /locus_tag="FTV94_23880"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_016946053.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MbeD family mobilization/exclusion protein"
                     /protein_id="QED69336.1"
                     /translation="MTEMEQQLLSALESLQRHYEQQQQAWQDSYANLQRMFEVTSQELA
                     KNDRVCQALSMQVTGLAQQVESLNRTVRRLSN"
                     /name="mbeD"
     gene            complement(3234..3518)
                     /locus_tag="FTV94_23885"
     CDS             complement(3234..3518)
                     /locus_tag="FTV94_23885"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000323025.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="type II toxin-antitoxin system RelE/ParE family
                     toxin"
                     /protein_id="QED69337.1"
                     /translation="MSYNLEFDPRALKEWRKLGDDVRLQFKKKLEQVLQHPRIDKNRLR
                     ELHDCYKIKLRASGYRLVYQVRDQTITVFVVAVGKRERSAAYDAADKRL"
                     /name="type II toxin-antitoxin system RelE/ParE family
                     toxin"
     gene            complement(3508..3750)
                     /locus_tag="FTV94_23890"
     CDS             complement(3508..3750)
                     /locus_tag="FTV94_23890"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000534858.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="type II toxin-antitoxin system RelB/DinJ family
                     antitoxin"
                     /protein_id="QED69338.1"
                     /translation="MATINIRIDDELKSRSYAALEKLGVTPSEVLRQTLEYVAQSGRLP
                     FQQVLLTEDDADLMAIVRDRLENPQAGVKVSLDEL"
                     /name="type II toxin-antitoxin system RelB/DinJ family
                     antitoxin"
     gene            4015..4913
                     /locus_tag="FTV94_23895"
                     /pseudo=""
     CDS             4015..4913
                     /locus_tag="FTV94_23895"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_006674370.1"
                     /note="frameshifted; Derived by automated computational
                     analysis using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="replicase"
                     /name="replicase"
     Typing          3878..4913
                     /name="rep_cluster_2486"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="99.807"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          1721..2679
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="95.625"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 taacgttcgc gaaaaaaatc atagaggaat gatgatgagt gacgatgcct tagatcttga
       61 tgctttggag cataatgaag aaaaagcaca agagctttta gaactgtata agcattttga
      121 ttgtgatatt aacgatgtta cattgcacac ttactttaac tttaaaaata aaggtaaagc
      181 gggtgctaag gactctttta gctataaaat tgccatcctt aaaaatgaca gtgagctaaa
      241 acagtccatt attgataatg tgataaagaa aactatatct gatttagaaa atcgggttgt
      301 gatagtatca gatgttaata cactaagtga ccgcaccaac accatttcat ttttaaatga
      361 tgctgagcag tatgataatg agcaaatgaa gtttctgact ggcattgtgt ttgatgctgg
      421 gtttggtggt gatggcaatg aaaatatccc aattgttgat tttgacagtg tggatctaat
      481 atcaaaagtt gactcaatca ttttcgtttt gagtaagaat aatgacgaca attgtataac
      541 catatacaag aagcaatatc cagttcaaaa cttatcaaga aagaaaaata atttttatgg
      601 gtttagcaaa aaagaactat ctcgagtaga tcaagatatg atttctattg atggtaaggc
      661 atctcttgtt tttgctggcg atacggtatt tatctacgac caaaatgttt tcgagcgttt
      721 ttttggctat aaagcatgga taaaaaatgc tgccactgat tttgttaaca atatgtccac
      781 tcgttttaag ggatttgttg acttaagcaa atttattgag cgagtaaata aagatagtca
      841 tgatgcggat gctttttctc ggaagctagc taaggcgtat gctcgaagcg aaacaaagca
      901 aacgctacaa acaataacaa atgaacatct taagagtgtt ctagatgaaa atggatattt
      961 agcaggtgtt ttaaagtata aaaaaggtga tgctacgatt tgcatcgcaa gccataacca
     1021 gcaagatacg tttatcgcta tggtatccga aggcgtattg agatcgttga ttacaggcat
     1081 tgattattta agccttgggt caaagcggaa aatatcgtca gcagcatcca atactactac
     1141 cagtaccact tcggattcct cttccgctgc tgtgtgagac aaaacaacct atatcagata
     1201 acagccctgc ttttgcgggg ctttttgttt gtgcgtgatg cgacctcgat gtacgataga
     1261 tgctgtatta agccagtaca cacagcgtcc cctcttcgag gtgccgtctg tgactgtttc
     1321 agggggctcg ccgccccccg aaaccccttg catccactgc gaaaattcgc actttgggtg
     1381 cgaaactttc tcagcggatt ctcatggaaa agcgcaccaa agagattaaa atcagactca
     1441 ccgaagcgga gcatcagcgg ctacttgaac gctgtgaccg taagcatttg gccgagtggt
     1501 tacgagccgt tggcttaggc gaatcgcgta cagctcggcg tcgtccgcta cctaccgtag
     1561 acccgacctt gttacgtcag gtcagcggga tcggtaataa cctcaatcaa atagcccgtt
     1621 acttgaatca gcatggctta ccgccgcaag aacgggtgtc gttgttagcg gtgctcaata
     1681 gcattgacca acatcttgcc gaactgctgg agcaacatcg tgatcgttaa gattcatggt
     1741 cgtggtgccg gtggcgggag tggtcctgtc gattaccttc tgggccctga tcgtcagcgc
     1801 gaacaagcga cggtgttacg gggtaaccct gagcacgtca aagagctgat tgatggctgc
     1861 gaatttgccc gaacttatac ctctggcgtg ctctcttttc aggagagtga tttacccgaa
     1921 ggcgaaaagc agcgattgat ggatgaatgg gagcagacat tgatgaccgg tctagataaa
     1981 gaccagtatg cctgcctctg ggttcaacat caggacaaag ggcgtcttga attgaatttt
     2041 gttatcccga acatcgaatt gcagagcgga aaacggctac aaccttactt tgatcgggct
     2101 gaccggcctc gtgttaacgc atggcaaacc ctcaccaatg accggcttgg gttacgcgac
     2161 ccgaatgacc ctgctaatcg ccgagcatta accccctcta atgaccttcc tcgcaacaaa
     2221 cagcaggcag cggaagccat taccaaaggg ctaatcagct tgattgagca gggagaaatt
     2281 acggatcgta aaggggtgat ttcccacctt accgatgccg gattgtcggt cgtacgggaa
     2341 accaaatcca gtatcagtat tgctgatccg gcaggtggcc cgaatattcg cttaaaagga
     2401 gtgctgtatg agcgagattt taaatttagc gcgggagttc gagagcaaat cgaagcagca
     2461 agccaagact accgcaacga gcgtcgcgaa cgcattcgag aagcacgaga aacgtatcac
     2521 cgaggccttg aaattaagct cagggaacat acagaccgct atccaagaag agaacgacag
     2581 ccagctaaaa cagatacacc gcttagtcgg aatgacatgg ctgtacagcc cctggcatta
     2641 agtgggatcc tgtttgcgat attgattgga gtagcttggt atctcgggac tatcgtggtc
     2701 gaacgccaga acgaaatcag cgagcagagc cagatcctgc aggacttaaa gagccagacc
     2761 ggagccggcg tatcgataat tcacgattcc aagaacaaga gcgtgtatta cctgatcctt
     2821 ccgcaggggg cgaagaagat cgacgagtac aagaacgctc aacatcgtca ggtcatcaag
     2881 tacagcgcca aataacctca tcagacgcca cagaatcgat tctgggcggt tttatctatc
     2941 agggtgaaga gattcatgac cgaaatggag cagcagcttc tgagcgcatt agagagctta
     3001 cagaggcact acgaacaaca gcagcaagcg tggcaggaca gctacgccaa cttacagcgc
     3061 atgttcgagg ttacctcgca ggagttggcg aaaaacgaca gggtttgtca ggccttgagc
     3121 atgcaagtca ccggcttggc gcagcaagtc gagagcttaa acagaacagt gcgccgcttg
     3181 agcaattagc caagcggcac gaacagcggt attctcgcgg tcacggcatg agtttataag
     3241 cgtttatcgg ccgcatcgta agcggcagaa cgctcgcgct taccgaccgc caccacgaat
     3301 accgtaatgg tttgatcgcg aacctgatag accaagcgat aaccggatgc acggagcttg
     3361 attttgtagc agtcatgcag ctctcgcagg cgatttttat cgatccgcgg gtgttgtaga
     3421 acctgctcga gttttttctt gaactgcaga cggacatcat ccccgagctt gcgccattcc
     3481 ttcagggctc ggggatcaaa ttcaaggtta tagctcatcc agtgacacct ttacgcccgc
     3541 ctgtgggttt tccagacgat cccgaacgat agccatcaaa tcggcatcat cctcggtcag
     3601 caaaacctgc tggaacggca aacgtccgct ttgggccaca tattccagtg tttggcgcag
     3661 aacctcggac ggcgttacgc ccagcttttc cagtgcggca taagagcggc ttttcagctc
     3721 gtcatcgatc cgaatattaa tcgtggccat catctcacct cttgatgtag tgacaagtgt
     3781 atctacaaga agtagtatga gcgtaaagcc gtgcgagaac aagcaggaat aacggattgt
     3841 cggggatgac aaaaaccgtt gttgaggtgt aacttagtgg cagaaaaaac aaagccccga
     3901 aatcatgctc tactttggcg agcggacatg acattcaggg ctaggtcgaa acctagaaag
     3961 gatattagca catgcagcgt gcaaaacaac agccccgcca taaggctggg agccttggat
     4021 aatcaggctt taacgctttt taacgaccgg ttaccccaca agccgtactt ctccgatgat
     4081 ttacagtttg gtgttcgcat tgccggtaaa gagcgtgctc tcctcgcaaa atacatccag
     4141 tttaatcagc ctcacgccat gtactggctt tgctttgacg tggacagagc cggagccgcg
     4201 attgattggg ccgatctggg ggcacctgcg cccacactca ccatcaaaaa ccccgagaac
     4261 ggacatgctc acctgttgta tgccttgcat acggcggtac gtaccgcgcc ggatggtcga
     4321 gctgcccccc ccttaaatac gccgccgcca tcgagaatgc gctgcgtaaa aaattgggcg
     4381 cagatgcggg gtattcaggg ctaatttgca agaatccgaa ccacctgcac tggcagatca
     4441 ccgtctggca gccagagctc tatacccttg actggttagc cgattacctc gaccttggcg
     4501 cagccaatga ccgcgaaatc ctgccggact acggtttagg ccgtaactgc accctcttcg
     4561 ataaaacccg caagtgggct taccgcgcta tccgccaagg ctggccgcag tatgaccaat
     4621 ggctacaagc ctgcattgaa cgcgctaaag cctacaacct gcagttctcc gcacctttag
     4681 acgagaacga agtcatggga attgctaaaa gtgtggctaa gtggacaagt aagaacctta
     4741 cagagcttgg ctttgaagag tatgttaaac aaacacatac ttctgaaatt cagcgtcaac
     4801 gtggaaaaaa aagctctggt ggtggaaggc cgaaagttag agatggagaa tggatttctt
     4861 taggaataag tagatcaacg tggtacagga aattttacaa aaatgaaaat tagaatgtat
     4921 ctcttatcaa tgttgttttt atttataccg ataacaatat atttttctgg tattgataac
     4981 gtatggtctg ttttagataa ggccatgtct tcgtgttctg gcgcggatgg aaaatttcaa
     5041 tgcgtactcg actattcaaa tagcagatta acattttctg tattgaggtc agtgatctgc
     5101 ggggctttga ttttaacttg ttcttataca tacatttggt atcgatgggt tttgaaaaac
     5161 ttagactccg gtgcggtgtc aagaaagtta aaggtcgttt catgtaaaaa agaatccggt
     5221 gagtatcttt cttttttatc aacgtacata atgccgttgg tctttactga tttaagcaaa
     5281 ccatcaaata tagttaattt tttgtttgtt ttgattatcg tcggtttttt gcacatcaaa
     5341 acaaaaagaa ttcactgcaa cccaacattg tcattattta atgtttctgc ctataagatt
     5401 acttacagtg tggtagctaa tggaagggaa aaaacgcaag acggtgagtt gatagtttta
     5461 tctaaagatt taataaaaga aaatgatttt atcagagtta taaatcatga tgattatt
//
