LOCUS       CP043749                3071 bp    DNA     circular BCT 09-JAN-2020
DEFINITION  Escherichia coli strain CVM N16EC0140 plasmid pN16EC0140-2, complete
            sequence.
ACCESSION   CP043749
VERSION     CP043749.1
DBLINK      BioProject: PRJNA292663
            BioSample: SAMN12698091
KEYWORDS    .
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 3071)
  AUTHORS   Tyson,G.H., Li,C., Hsu,C.H., Bodeis-Jones,S. and McDermott,P.F.
  TITLE     Diverse Fluoroquinolone Resistance Plasmids From Retail Meat E. coli
            in the United States
  JOURNAL   Front Microbiol 10, 2826 (2019)
   PUBMED   31866986
  REMARK    Publication Status: Online-Only
REFERENCE   2  (bases 1 to 3071)
  AUTHORS   Li,C.
  TITLE     Direct Submission
  JOURNAL   Submitted (06-SEP-2019) CVM/OR, FDA-CVM, 8401 Muirkirk Rd, MOD2,
            Laurel, MD 20708, USA
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Date                     :: MAR-2019
            Assembly Method                   :: Overlpa-Layout-Consensus v. 4
            Assembly Name                     :: HGAP
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 480x
            Sequencing Technology             :: PacBio
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI
            Annotation Date                   :: 09/10/2019 00:18:45
            Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline
            (PGAP)
            Annotation Method :: Best-placed reference protein set; GeneMarkS-2+
            Annotation Software revision      :: 4.9
            Features Annotated :: Gene; CDS; rRNA; tRNA; ncRNA; repeat_region
            Genes (total)                     :: 5,327
            CDSs (total)                      :: 5,203
            Genes (coding)                    :: 4,953
            CDSs (with protein)               :: 4,953
            Genes (RNA)                       :: 124
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 93
            ncRNAs                            :: 9
            Pseudo Genes (total)              :: 250
            CDSs (without protein)            :: 250
            Pseudo Genes (ambiguous residues) :: 0 of 250
            Pseudo Genes (frameshifted)       :: 124 of 250
            Pseudo Genes (incomplete)         :: 120 of 250
            Pseudo Genes (internal stop)      :: 53 of 250
            Pseudo Genes (multiple problems)  :: 43 of 250
            CRISPR Arrays                     :: 1
            ##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/
FEATURES             Location/Qualifiers
     source          1..3071
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="CVM N16EC0140"
                     /isolation_source="Pork chops"
                     /db_xref="taxon:562"
                     /plasmid="pN16EC0140-2"
                     /geo_loc_name="USA:OR"
                     /collection_date="2016"
                     /collected_by="FDA"
     gene            join(3067..3071,1..151)
                     /gene="pspF"
                     /locus_tag="F1L20_26605"
                     /pseudo=""
     CDS             join(3067..3071,1..151)
                     /gene="pspF"
                     /locus_tag="F1L20_26605"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:NP_309907.2"
                     /note="transcriptional activator for pspABCE which are
                     induced in response to phage proteins, membrane altering
                     stresses, and impaired proton expor; 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="phage shock protein operon transcriptional
                     activator"
                     /name="pspF"
     gene            245..889
                     /locus_tag="F1L20_26610"
     CDS             245..889
                     /locus_tag="F1L20_26610"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_017900990.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="quinolone resistance pentapeptide repeat protein
                     QnrB19"
                     /protein_id="QEP73067.1"
                     /translation="MTLALVGEKIDRNRFTGEKVENSTFFNCDFSGADLSGTEFIGCQF
                     YDRESQKGCNFSRAMLKDAIFKSCDLSMADFRNVSALGIEIRHCRAQGADFRGASFMNM
                     ITTRTWFCSAYITNTNLSYANFSKVVLEKCELWENRWMGTQVLGATFSGSDLSGGEFST
                     FDWRAANFTHCDLTNSELGDLDIRGVDLQGVKLDSYQASLLMERLGIAVIG"
                     /name="quinolone resistance pentapeptide repeat protein
                     QnrB19"
     gene            complement(898..1113)
                     /locus_tag="F1L20_26615"
                     /pseudo=""
     CDS             complement(898..1113)
                     /locus_tag="F1L20_26615"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_016153231.1"
                     /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="hypothetical protein"
                     /name="hypothetical protein"
     gene            2225..2341
                     /locus_tag="F1L20_26620"
                     /pseudo=""
     CDS             2225..2341
                     /locus_tag="F1L20_26620"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001557753.1"
                     /note="internal stop; 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            complement(2294..2513)
                     /locus_tag="F1L20_26625"
                     /pseudo=""
     CDS             complement(2294..2513)
                     /locus_tag="F1L20_26625"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_015675076.1"
                     /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            2699..2812
                     /locus_tag="F1L20_26630"
     CDS             2699..2812
                     /locus_tag="F1L20_26630"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_006122515.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="replication initiation protein"
                     /protein_id="QEP73066.1"
                     /translation="MHEPPVQSDCCALSGNYHLESNPERHDLSPLAAATGN"
                     /name="replication initiation protein"
     gene            2837..3053
                     /locus_tag="F1L20_26635"
                     /pseudo=""
     CDS             2837..3053
                     /locus_tag="F1L20_26635"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000255616.1"
                     /note="frameshifted; 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"
     ARG             246..886
                     /name="qnrB19"
                     /gene="qnrB19"
                     /gene_name="quinolone resistance pentapeptide repeat
                     protein QnrB19"
                     /tool="amrfinderplus"
                     /drug_class="QUINOLONE"
                     /identity="100.0"
                     /coverage="100.0"
     Typing          complement(2165..2338)
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="2.5600000000000002e-86"
     Typing          2317..2808
                     /name="rep_cluster_2335"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="92.51"
                     /coverage="81.0"
                     /evalue="0.0"
ORIGIN
        1 gctggatctg cgtgaattcc agcagcagca agagaaagac tttctacaaa ccagcttaca
       61 gcaggctaaa tttaaccaga aaaaagccgc tgaattactg ggtctgactt atcatcagct
      121 acgtgccttg ctgaagaaac accagatcta atacgcattt gcaggtgtca tactggcggg
      181 tttgacgcat aacgtcataa ggtttaccat ggcgtcatta ctgtataaaa acacaggcat
      241 agatatgact ctggcattag ttggcgaaaa aattgacaga aatcgcttca ccggtgagaa
      301 agttgaaaat agtacatttt ttaactgcga tttttcaggt gccgacctga gcggcactga
      361 atttatcggc tgccagttct atgatcgcga aagtcagaaa gggtgcaatt ttagtcgcgc
      421 aatgctgaaa gatgccattt tcaaaagctg tgatttatca atggcagatt tccgcaacgt
      481 cagtgccttg ggcattgaaa ttcgccactg ccgcgcacaa ggcgcagatt tccgcggtgc
      541 aagctttatg aatatgatca ccacgcgcac ctggttttgc agcgcatata tcactaatac
      601 taatctaagc tacgccaatt tttcgaaagt cgtgttggaa aagtgtgagc tgtgggaaaa
      661 ccgctggatg gggactcagg tactgggtgc gacgttcagt ggttcagatc tctccggcgg
      721 cgagttttcg actttcgact ggcgagcagc aaacttcaca cattgcgatc tgaccaattc
      781 ggagttaggt gacttagata ttcggggtgt tgatttacaa ggcgttaagt tagacagcta
      841 ccaggcatcg ttgctcatgg agcggcttgg catcgctgtg attggttagt tcagcgttta
      901 caccgggaga tgcgtttgac gatttacttt taaccagtac gactcctggc aagcattgtg
      961 aaacgttttc tccagtggac gaatatcctg acctaccgca tcaacgacat gccatctaat
     1021 gctgcattct ggacaggaat ttgatgaata tctaaccaat tcattttcgc gagaacaacg
     1081 aataaccact cccgaatcat gaagccatgt cttaacgaaa atatggctaa ctcatagcaa
     1141 aaaaaaagcc ccctaagggc ttttttttgt acctgacggt cagaccgatt aaacataaca
     1201 tcccttgcgt gcaccgcctg agaggctctg agggcgtttc tgacgggaaa ccggtaaaac
     1261 aggcaacaaa ccacccgaaa acccgccaga aacgcgcagg ctctgttttt acggcatgca
     1321 tgagtatgcg cgcaagtgca tagcgcggaa attcacacca ttcagccagg ggaagtcctg
     1381 tttccggcgt tcttcccatc cgaaaacggt gaacggggac gcaatttatt gcgtggccgt
     1441 gaagcgttgc cggcgcagcc ggaaaacccg ctgtcagcac gttcaggaag ggggtgatgt
     1501 acaaatggca cagaggatga aagtgacgta tgagctgaag gaatgatgta aaagtgatgt
     1561 ataaatgatg taaaagtgat gcaaaagtgt tgtaaaagtg atgtacaggc cgaaggagtg
     1621 ttgtaaaagt gttgtaaaag tgatgtatga actgaaggag cgatgtaatt ctgtagtcag
     1681 gaagaataac ccgttcatgc ctgcatgaac gatacagtga ggaacgcttt tttttgtcac
     1741 gatctcccct taacctgcgt aaatcacccg ccatggttga ttatttttca acctcaaaat
     1801 ggtcatacac ctaacgcagc cgcgattttc atcgcaactg catgaattaa aagaaaaaaa
     1861 agtaatgttt cgttttcacg agtaataccc aggtattaaa aacccactgt aattacatga
     1921 aaataaagaa ataaaaggta ataccggcgt attaccacgt acgcgggcaa gcgaaaaagc
     1981 tataacgctt cccggccgac aggcggccca gaatccacag gggcatgcag gatctcttca
     2041 gtaaccttcg ccattaaatc aaaaaggtca tattcgccgg gaagctgcgt atcagtcgaa
     2101 ccccgttgtt catcatattc agatggcatg gggtgatatc cagtagcaga gaggttgtta
     2161 gcgggtttcg gggcgcagcc ctgaaccagt cacgtagcgc tagcggagtg tatactggct
     2221 gactatgttg gcacggatgt ggaaatcagt gaagtgcttc atgtagcagg agaaaaaagg
     2281 cggcaccagc gcgtcagcag gatatgtagt acaggatata ttccgcttcc tcgctcactg
     2341 actcgctgcg ctcggtcgtt cggctgcggc gagcggtgcc ggcttacagg cggggcggaa
     2401 atttcctggg agataccagg aaggagctta acagggaaga gataaggccg cggcgaagcc
     2461 gtttttccat aggctccgcc cccctgacaa acatcatgaa atctgacgct caaatcagtg
     2521 gtggcgaaac ccgatgcggc ttaaagatac caggcgtttc cccctggtgg ctccctcgtg
     2581 ctcccccgca ttcctgcctt tcggtttacc ggtgtcattc cgctgttatg gccgcgttta
     2641 tctcattcca cgcctgacac tcagttccgc gaaggcagtt cgctcctgga tggactgtat
     2701 gcacgaaccc cccgttcagt ccgactgctg cgccttatcc ggtaactatc atcttgagtc
     2761 caacccggaa agacacgact tatcgccact ggcagcagcc actggtaact gatttagagg
     2821 agttagtctt gaagttatgc gcctgttaag gctaaactga aagaacagat ttggttactg
     2881 cgctcctcgt aagccagtta ccacggttca aagagttgct gctctgagaa ccttcgaaaa
     2941 accgccttgc agggcggttt tttcgtttac agagcaagag attacgacgc cacagaaagg
     3001 atctcaagaa gatccttcac cgtaatggaa atctatccaa tccgagcaca taggatacac
     3061 atcgttataa c
//
