LOCUS       CP082477                3071 bp    DNA     circular BCT 13-JAN-2022
DEFINITION  Salmonella enterica subsp. enterica serovar 4,[5],12:i:- strain
            FSIS1607294 plasmid pF18S010-qnr, complete sequence.
ACCESSION   CP082477
VERSION     CP082477.1
DBLINK      BioProject: PRJNA292666
            BioSample: SAMN05514420
KEYWORDS    .
SOURCE      Salmonella enterica subsp. enterica serovar 4,[5],12:i:-
  ORGANISM  Salmonella enterica subsp. enterica serovar 4,[5],12:i:-
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Salmonella.
REFERENCE   1  (bases 1 to 3071)
  AUTHORS   Li,C., Tyson,G.H., Hsu,C.H., Harrison,L., Strain,E., Tran,T.T.,
            Tillman,G.E., Dessai,U., McDermott,P.F. and Zhao,S.
  TITLE     Long-Read Sequencing Reveals Evolution and Acquisition of
            Antimicrobial Resistance and Virulence Genes in Salmonella enterica
  JOURNAL   Front Microbiol 12, 777817 (2021)
   PUBMED   34867920
  REMARK    Publication Status: Online-Only
REFERENCE   2  (bases 1 to 3071)
  CONSRTM   NARMS: The National Antimicrobial Resistance Monitoring System
  TITLE     Direct Submission
  JOURNAL   Submitted (22-JUL-2018) Center for Veterinary Medicine, US Food and
            Drug Administration, 8401 Muirkirk Rd, Laurel, MD, USA
REFERENCE   3  (bases 1 to 3071)
  AUTHORS   Li,C.
  TITLE     Direct Submission
  JOURNAL   Submitted (26-AUG-2021) CVM/OR, FDA-CVM, 8401 Muirkirk Rd, MOD2,
            Laurel, MD 20708, USA
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Date                     :: 01-JUN-2020
            Assembly Method :: SMRTLink Microbial Assembly v. SMRTLink9.0
            Assembly Name                     :: F18S010
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 556x
            Sequencing Technology             :: PacBio Sequel
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI
            Annotation Date                   :: 09/02/2021 13:29:45
            Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline
            (PGAP)
            Annotation Method :: Best-placed reference protein set; GeneMarkS-2+
            Annotation Software revision      :: 5.2
            Features Annotated :: Gene; CDS; rRNA; tRNA; ncRNA; repeat_region
            Genes (total)                     :: 5,094
            CDSs (total)                      :: 4,970
            Genes (coding)                    :: 4,861
            CDSs (with protein)               :: 4,861
            Genes (RNA)                       :: 124
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 87
            ncRNAs                            :: 15
            Pseudo Genes (total)              :: 109
            CDSs (without protein)            :: 109
            Pseudo Genes (ambiguous residues) :: 0 of 109
            Pseudo Genes (frameshifted)       :: 32 of 109
            Pseudo Genes (incomplete)         :: 79 of 109
            Pseudo Genes (internal stop)      :: 19 of 109
            Pseudo Genes (multiple problems)  :: 19 of 109
            CRISPR Arrays                     :: 2
            ##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="Salmonella enterica subsp. enterica serovar
                     4,[5],12:i:-"
                     /mol_type="genomic DNA"
                     /strain="FSIS1607294"
                     /serovar="4,[5],12:i:-"
                     /isolation_source="Animal-Turkey-Young Turkey"
                     /sub_species="enterica"
                     /db_xref="taxon:440524"
                     /plasmid="pF18S010-qnr"
                     /geo_loc_name="USA:SD"
                     /collection_date="2016"
                     /collected_by="USDA-FSIS"
     gene            608..763
                     /gene="pspF"
                     /locus_tag="BFE20_025460"
                     /pseudo=""
     CDS             608..763
                     /gene="pspF"
                     /locus_tag="BFE20_025460"
                     /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            857..1501
                     /locus_tag="BFE20_025465"
     CDS             857..1501
                     /locus_tag="BFE20_025465"
                     /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="UAE31791.1"
                     /translation="MTLALVGEKIDRNRFTGEKVENSTFFNCDFSGADLSGTEFIGCQF
                     YDRESQKGCNFSRAMLKDAIFKSCDLSMADFRNVSALGIEIRHCRAQGADFRGASFMNM
                     ITTRTWFCSAYITNTNLSYANFSKVVLEKCELWENRWMGTQVLGATFSGSDLSGGEFST
                     FDWRAANFTHCDLTNSELGDLDIRGVDLQGVKLDSYQASLLMERLGIAVIG"
                     /name="quinolone resistance pentapeptide repeat protein
                     QnrB19"
     gene            complement(2592..2741)
                     /locus_tag="BFE20_025470"
     CDS             complement(2592..2741)
                     /locus_tag="BFE20_025470"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_017880354.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="UAE31790.1"
                     /translation="MPSEYDEQRGSTDTQLPGEYDLFDLMAKVTEEILHAPVDSGPPVG
                     REAL"
                     /name="hypothetical protein"
     ARG             858..1498
                     /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(2777..2950)
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="2.5600000000000002e-86"
     Typing          2..349
                     /name="rep_cluster_2335"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="92.837"
                     /coverage="81.0"
                     /evalue="9.33e-141"
ORIGIN
        1 cgtttttcca taggctccgc ccccctgaca aacatcatga aatctgacgc tcaaatcagt
       61 ggtggcgaaa cccgatgcgg cttaaagata ccaggcgttt ccccctggtg gctccctcgt
      121 gctcccccgc attcctgcct ttcggtttac cggtgtcatt ccgctgttat ggccgcgttt
      181 atctcattcc acgcctgaca ctcagttccg cgaaggcagt tcgctcctgg atggactgta
      241 tgcacgaacc ccccgttcag tccgactgct gcgccttatc cggtaactat catcttgagt
      301 ccaacccgga aagacacgac ttatcgccac tggcagcagc cactggtaac tgatttagag
      361 gagttagtct tgaagttatg cgcctgttaa ggctaaactg aaagaacaga tttggttact
      421 gcgctcctcg taagccagtt accacggttc aaagagttgc tgctctgaga accttcgaaa
      481 aaccgccttg cagggcggtt ttttcgttta cagagcaaga gattacgacg ccacagaaag
      541 gatctcaaga agatccttca ccgtaatgga aatctatcca atccgagcac ataggataca
      601 catcgttata acgctggatc tgcgtgaatt ccagcagcag caagagaaag actttctaca
      661 aaccagctta cagcaggcta aatttaacca gaaaaaagcc gctgaattac tgggtctgac
      721 ttatcatcag ctacgtgcct tgctgaagaa acaccagatc taatacgcat ttgcaggtgt
      781 catactggcg ggtttgacgc ataacgtcat aaggtttacc atggcgtcat tactgtataa
      841 aaacacaggc atagatatga ctctggcatt agttggcgaa aaaattgaca gaaatcgctt
      901 caccggtgag aaagttgaaa atagtacatt ttttaactgc gatttttcag gtgccgacct
      961 gagcggcact gaatttatcg gctgccagtt ctatgatcgc gaaagtcaga aagggtgcaa
     1021 ttttagtcgc gcaatgctga aagatgccat tttcaaaagc tgtgatttat caatggcaga
     1081 tttccgcaac gtcagtgcct tgggcattga aattcgccac tgccgcgcac aaggcgcaga
     1141 tttccgcggt gcaagcttta tgaatatgat caccacgcgc acctggtttt gcagcgcata
     1201 tatcactaat actaatctaa gctacgccaa tttttcgaaa gtcgtgttgg aaaagtgtga
     1261 gctgtgggaa aaccgctgga tggggactca ggtactgggt gcgacgttca gtggttcaga
     1321 tctctccggc ggcgagtttt cgactttcga ctggcgagca gcaaacttca cacattgcga
     1381 tctgaccaat tcggagttag gtgacttaga tattcggggt gttgatttac aaggcgttaa
     1441 gttagacagc taccaggcat cgttgctcat ggagcggctt ggcatcgctg tgattggtta
     1501 gttcagcgtt tacaccggga gatgcgtttg acgatttact tttaaccagt acgactcctg
     1561 gcaagcattg tgaaacgttt tctccagtgg acgaatatcc tgacctaccg catcaacgac
     1621 atgccatcta atgctgcatt ctggacagga atttgatgaa tatctaacca attcattttc
     1681 gcgagaacaa cgaataacca ctcccgaatc atgaagccat gtcttaacga aaatatggct
     1741 aactcatagc aaaaaaaaag ccccctaagg gctttttttt gtacctgacg gtcagaccga
     1801 ttaaacataa catcccttgc gtgcaccgcc tgagaggctc tgagggcgtt tctgacggga
     1861 aaccggtaaa acaggcaaca aaccacccga aaacccgcca gaaacgcgca ggctctgttt
     1921 ttacggcatg catgagtatg cgcgcaagtg catagcgcgg aaattcacac cattcagcca
     1981 ggggaagtcc tgtttccggc gttcttccca tccgaaaacg gtgaacgggg acgcaattta
     2041 ttgcgtggcc gtgaagcgtt gccggcgcag ccggaaaacc cgctgtcagc acgttcagga
     2101 agggggtgat gtacaaatgg cacagaggat gaaagtgacg tatgagctga aggaatgatg
     2161 taaaagtgat gtataaatga tgtaaaagtg atgcaaaagt gttgtaaaag tgatgtacag
     2221 gccgaaggag tgttgtaaaa gtgttgtaaa agtgatgtat gaactgaagg agcgatgtaa
     2281 ttctgtagtc aggaagaata acccgttcat gcctgcatga acgatacagt gaggaacgct
     2341 tttttttgtc acgatctccc cttaacctgc gtaaatcacc cgccatggtt gattattttt
     2401 caacctcaaa atggtcatac acctaacgca gccgcgattt tcatcgcaac tgcatgaatt
     2461 aaaagaaaaa aaagtaatgt ttcgttttca cgagtaatac ccaggtatta aaaacccact
     2521 gtaattacat gaaaataaag aaataaaagg taataccggc gtattaccac gtacgcgggc
     2581 aagcgaaaaa gctataacgc ttcccggccg acaggcggcc cagaatccac aggggcatgc
     2641 aggatctctt cagtaacctt cgccattaaa tcaaaaaggt catattcgcc gggaagctgc
     2701 gtatcagtcg aaccccgttg ttcatcatat tcagatggca tggggtgata tccagtagca
     2761 gagaggttgt tagcgggttt cggggcgcag ccctgaacca gtcacgtagc gctagcggag
     2821 tgtatactgg ctgactatgt tggcacggat gtggaaatca gtgaagtgct tcatgtagca
     2881 ggagaaaaaa ggcggcacca gcgcgtcagc aggatatgta gtacaggata tattccgctt
     2941 cctcgctcac tgactcgctg cgctcggtcg ttcggctgcg gcgagcggtg ccggcttaca
     3001 ggcggggcgg aaatttcctg ggagatacca ggaaggagct taacagggaa gagataaggc
     3061 cgcggcgaag c
//
