LOCUS       CP082481                3070 bp    DNA     circular BCT 13-JAN-2022
DEFINITION  Salmonella enterica subsp. enterica serovar Newport strain
            FSIS1607290 plasmid pF18S009-3, complete sequence.
ACCESSION   CP082481
VERSION     CP082481.1
DBLINK      BioProject: PRJNA292666
            BioSample: SAMN05514416
KEYWORDS    .
SOURCE      Salmonella enterica subsp. enterica serovar Newport
  ORGANISM  Salmonella enterica subsp. enterica serovar Newport
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Salmonella.
REFERENCE   1  (bases 1 to 3070)
  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 3070)
  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 3070)
  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                     :: F18S009
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 360x
            Sequencing Technology             :: PacBio Sequel
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI
            Annotation Date                   :: 09/02/2021 13:34:50
            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)                     :: 4,911
            CDSs (total)                      :: 4,788
            Genes (coding)                    :: 4,693
            CDSs (with protein)               :: 4,693
            Genes (RNA)                       :: 123
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 88
            ncRNAs                            :: 13
            Pseudo Genes (total)              :: 95
            CDSs (without protein)            :: 95
            Pseudo Genes (ambiguous residues) :: 0 of 95
            Pseudo Genes (frameshifted)       :: 40 of 95
            Pseudo Genes (incomplete)         :: 62 of 95
            Pseudo Genes (internal stop)      :: 17 of 95
            Pseudo Genes (multiple problems)  :: 24 of 95
            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..3070
                     /organism="Salmonella enterica subsp. enterica serovar
                     Newport"
                     /mol_type="genomic DNA"
                     /strain="FSIS1607290"
                     /serovar="Newport"
                     /isolation_source="animal-cattle-heifer"
                     /sub_species="enterica"
                     /db_xref="taxon:108619"
                     /plasmid="pF18S009-3"
                     /geo_loc_name="USA:KS"
                     /collection_date="2016"
                     /collected_by="USDA-FSIS"
     gene            join(2987..3070,1..71)
                     /gene="pspF"
                     /locus_tag="BFE24_024545"
                     /pseudo=""
     CDS             join(2987..3070,1..71)
                     /gene="pspF"
                     /locus_tag="BFE24_024545"
                     /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; 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="phage shock protein operon transcriptional
                     activator"
                     /name="pspF"
     gene            165..809
                     /locus_tag="BFE24_024550"
     CDS             165..809
                     /locus_tag="BFE24_024550"
                     /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="UAE26930.1"
                     /translation="MTLALVGEKIDRNRFTGEKVENSTFFNCDFSGADLSGTEFIGCQF
                     YDRESQKGCNFSRAMLKDAIFKSCDLSMADFRNVSALGIEIRHCRAQGADFRGASFMNM
                     ITTRTWFCSAYITNTNLSYANFSKVVLEKCELWENRWMGTQVLGATFSGSDLSGGEFST
                     FDWRAANFTHCDLTNSELGDLDIRGVDLQGVKLDSYQASLLMERLGIAVIG"
                     /name="quinolone resistance pentapeptide repeat protein
                     QnrB19"
     gene            complement(1900..2049)
                     /locus_tag="BFE24_024555"
     CDS             complement(1900..2049)
                     /locus_tag="BFE24_024555"
                     /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="UAE26929.1"
                     /translation="MPSEYDEQRGSTDTQLPGEYDLFDLMAKVTEEILHAPVDSGPPVG
                     REAL"
                     /name="hypothetical protein"
     ARG             166..806
                     /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(2085..2258)
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="2.5600000000000002e-86"
     Typing          2237..2728
                     /name="rep_cluster_2335"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="92.51"
                     /coverage="81.0"
                     /evalue="0.0"
ORIGIN
        1 aaaaagccgc tgaattactg ggtctgactt atcatcagct acgtgccttg ctgaagaaac
       61 accagatcta atacgcattt gcaggtgtca tactggcggg tttgacgcat aacgtcataa
      121 ggtttaccat ggcgtcatta ctgtataaaa acacaggcat agatatgact ctggcattag
      181 ttggcgaaaa aattgacaga aatcgcttca ccggtgagaa agttgaaaat agtacatttt
      241 ttaactgcga tttttcaggt gccgacctga gcggcactga atttatcggc tgccagttct
      301 atgatcgcga aagtcagaaa gggtgcaatt ttagtcgcgc aatgctgaaa gatgccattt
      361 tcaaaagctg tgatttatca atggcagatt tccgcaacgt cagtgccttg ggcattgaaa
      421 ttcgccactg ccgcgcacaa ggcgcagatt tccgcggtgc aagctttatg aatatgatca
      481 ccacgcgcac ctggttttgc agcgcatata tcactaatac taatctaagc tacgccaatt
      541 tttcgaaagt cgtgttggaa aagtgtgagc tgtgggaaaa ccgctggatg gggactcagg
      601 tactgggtgc gacgttcagt ggttcagatc tctccggcgg cgagttttcg actttcgact
      661 ggcgagcagc aaacttcaca cattgcgatc tgaccaattc ggagttaggt gacttagata
      721 ttcggggtgt tgatttacaa ggcgttaagt tagacagcta ccaggcatcg ttgctcatgg
      781 agcggcttgg catcgctgtg attggttagt tcagcgttta caccgggaga tgcgtttgac
      841 gatttacttt taaccagtac gactcctggc aagcattgtg aaacgttttc tccagtggac
      901 gaatatcctg acctaccgca tcaacgacat gccatctaat gctgcattct ggacaggaat
      961 ttgatgaata tctaaccaat tcattttcgc gagaacaacg aataaccact cccgaatcat
     1021 gaagccatgt cttaacgaaa atatggctaa ctcatagcaa aaaaaaagcc ccctaagggc
     1081 ttttttttgt acctgacggt cagaccgatt aaacataaca tcccttgcgt gcaccgcctg
     1141 agaggctctg agggcgtttc tgacgggaaa ccggtaaaac aggcaacaaa ccacccgaaa
     1201 acccgccaga aacgcgcagg ctctgttttt acggcatgca tgagtatgcg cgcaagtgca
     1261 tagcgcggaa attcacacca ttcagccagg ggaagtcctg tttccggcgt tcttcccatc
     1321 cgaaaacggt gaacggggac gcaatttatt gcgtggccgt gaagcgttgc cggcgcagcc
     1381 ggaaaacccg ctgtcagcac gttcaggaag ggggtgatgt acaaatggca cagaggatga
     1441 aagtgacgta tgagctgaag gaatgatgta aaagtgatgt ataaatgatg taaaagtgat
     1501 gcaaaagtgt tgtaaaagtg atgtacaggc cgaaggagtg ttgtaaaagt gttgtaaaag
     1561 tgatgtatga actgaaggag cgatgtaatt ctgtagtcag gaagaataac ccgttcatgc
     1621 ctgcatgaac gatacagtga ggaacgcttt tttttgtcac gatctcccct taacctgcgt
     1681 aaatcacccg ccatggttga ttatttttca acctcaaaat ggtcatacac ctaacgcagc
     1741 cgcgattttc atcgcaactg catgaattaa aagaaaaaaa agtaatgttt cgttttcacg
     1801 agtaataccc aggtattaaa aacccactgt aattacatga aaataaagaa ataaaaggta
     1861 ataccggcgt attaccacgt acgcgggcaa gcgaaaaagc tataacgctt cccggccgac
     1921 aggcggccca gaatccacag gggcatgcag gatctcttca gtaaccttcg ccattaaatc
     1981 aaaaaggtca tattcgccgg gaagctgcgt atcagtcgaa ccccgttgtt catcatattc
     2041 agatggcatg gggtgatatc cagtagcaga gaggttgtta gcgggtttcg gggcgcagcc
     2101 ctgaaccagt cacgtagcgc tagcggagtg tatactggct gactatgttg gcacggatgt
     2161 ggaaatcagt gaagtgcttc atgtagcagg agaaaaaagg cggcaccagc gcgtcagcag
     2221 gatatgtagt acaggatata ttccgcttcc tcgctcactg actcgctgcg ctcggtcgtt
     2281 cggctgcggc gagcggtgcc ggcttacagg cggggcggaa atttcctggg agataccagg
     2341 aaggagctta acagggaaga gataaggccg cggcgaagcc gtttttccat aggctccgcc
     2401 cccctgacaa acatcatgaa atctgacgct caaatcagtg gtggcgaaac ccgatgcggc
     2461 ttaaagatac caggcgtttc cccctggtgg ctccctcgtg ctcccccgca ttcctgcctt
     2521 tcggtttacc ggtgtcattc cgctgttatg gccgcgttta tctcattcca cgcctgacac
     2581 tcagttccgc gaaggcagtt cgctcctgga tggactgtat gcacgaaccc cccgttcagt
     2641 ccgactgctg cgccttatcc ggtaactatc atcttgagtc caacccggaa agacacgact
     2701 tatcgccact ggcagcagcc actggtaact gatttagagg agttagtctt gaagttatgc
     2761 gcctgttaag gctaaactga aagaacagat ttggttactg cgctcctcgt aagccagtta
     2821 ccacggttca aagagttgct gctctgagaa ccttcgaaaa accgccttgc agggcggttt
     2881 tttcgtttac agagcaagag attacgacgc cacagaaagg atctcaagaa gatccttcac
     2941 cgtaatggaa atctatccaa tccgagcaca taggatacac atcgttataa cgctggatct
     3001 gcgtgaattc cagcagcagc aagagaaaga ctttctacaa accagcttac agcaggctaa
     3061 atttaaccag
//
