LOCUS       CP082448                3071 bp    DNA     circular BCT 11-JAN-2022
DEFINITION  Salmonella enterica subsp. enterica serovar Johannesburg strain
            FSIS1608038 plasmid pF18S023-3071, complete sequence.
ACCESSION   CP082448
VERSION     CP082448.1
DBLINK      BioProject: PRJNA292666
            BioSample: SAMN05964744
KEYWORDS    .
SOURCE      Salmonella enterica subsp. enterica serovar Johannesburg
  ORGANISM  Salmonella enterica subsp. enterica serovar Johannesburg
            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 (23-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                     :: F18S023
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 531x
            Sequencing Technology             :: PacBio Sequel
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI
            Annotation Date                   :: 09/02/2021 13:30:53
            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)                     :: 4,873
            CDSs (total)                      :: 4,753
            Genes (coding)                    :: 4,630
            CDSs (with protein)               :: 4,630
            Genes (RNA)                       :: 120
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 85
            ncRNAs                            :: 13
            Pseudo Genes (total)              :: 123
            CDSs (without protein)            :: 123
            Pseudo Genes (ambiguous residues) :: 0 of 123
            Pseudo Genes (frameshifted)       :: 62 of 123
            Pseudo Genes (incomplete)         :: 67 of 123
            Pseudo Genes (internal stop)      :: 23 of 123
            Pseudo Genes (multiple problems)  :: 26 of 123
            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
                     Johannesburg"
                     /mol_type="genomic DNA"
                     /strain="FSIS1608038"
                     /serovar="Johannesburg"
                     /isolation_source="animal-swine-market swine"
                     /sub_species="enterica"
                     /db_xref="taxon:913076"
                     /plasmid="pF18S023-3071"
                     /geo_loc_name="USA:IA"
                     /collection_date="2016"
                     /collected_by="USDA-FSIS"
     gene            join(3064..3071,1..142)
                     /gene="pspF"
                     /locus_tag="BL362_024355"
                     /pseudo=""
     CDS             join(3064..3071,1..142)
                     /gene="pspF"
                     /locus_tag="BL362_024355"
                     /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            236..880
                     /locus_tag="BL362_024360"
     CDS             236..880
                     /locus_tag="BL362_024360"
                     /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="UAE78134.1"
                     /translation="MTLALVGEKIDRNRFTGEKVENSTFFNCDFSGADLSGTEFIGCQF
                     YDRESQKGCNFSRAMLKDAIFKSCDLSMADFRNVSALGIEIRHCRAQGADFRGASFMNM
                     ITTRTWFCSAYITNTNLSYANFSKVVLEKCELWENRWMGTQVLGATFSGSDLSGGEFST
                     FDWRAANFTHCDLTNSELGDLDIRGVDLQGVKLDSYQASLLMERLGIAVIG"
                     /name="quinolone resistance pentapeptide repeat protein
                     QnrB19"
     gene            complement(1971..2120)
                     /locus_tag="BL362_024365"
     CDS             complement(1971..2120)
                     /locus_tag="BL362_024365"
                     /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="UAE78133.1"
                     /translation="MPSEYDEQRGSTDTQLPGEYDLFDLMAKVTEEILHAPVDSGPPVG
                     REAL"
                     /name="hypothetical protein"
     ARG             237..877
                     /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(2156..2329)
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="2.5600000000000002e-86"
     Typing          2308..2799
                     /name="rep_cluster_2335"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="92.51"
                     /coverage="81.0"
                     /evalue="0.0"
ORIGIN
        1 gcgtgaattc cagcagcagc aagagaaaga ctttctacaa accagcttac agcaggctaa
       61 atttaaccag aaaaaagccg ctgaattact gggtctgact tatcatcagc tacgtgcctt
      121 gctgaagaaa caccagatct aatacgcatt tgcaggtgtc atactggcgg gtttgacgca
      181 taacgtcata aggtttacca tggcgtcatt actgtataaa aacacaggca tagatatgac
      241 tctggcatta gttggcgaaa aaattgacag aaatcgcttc accggtgaga aagttgaaaa
      301 tagtacattt tttaactgcg atttttcagg tgccgacctg agcggcactg aatttatcgg
      361 ctgccagttc tatgatcgcg aaagtcagaa agggtgcaat tttagtcgcg caatgctgaa
      421 agatgccatt ttcaaaagct gtgatttatc aatggcagat ttccgcaacg tcagtgcctt
      481 gggcattgaa attcgccact gccgcgcaca aggcgcagat ttccgcggtg caagctttat
      541 gaatatgatc accacgcgca cctggttttg cagcgcatat atcactaata ctaatctaag
      601 ctacgccaat ttttcgaaag tcgtgttgga aaagtgtgag ctgtgggaaa accgctggat
      661 ggggactcag gtactgggtg cgacgttcag tggttcagat ctctccggcg gcgagttttc
      721 gactttcgac tggcgagcag caaacttcac acattgcgat ctgaccaatt cggagttagg
      781 tgacttagat attcggggtg ttgatttaca aggcgttaag ttagacagct accaggcatc
      841 gttgctcatg gagcggcttg gcatcgctgt gattggttag ttcagcgttt acaccgggag
      901 atgcgtttga cgatttactt ttaaccagta cgactcctgg caagcattgt gaaacgtttt
      961 ctccagtgga cgaatatcct gacctaccgc atcaacgaca tgccatctaa tgctgcattc
     1021 tggacaggaa tttgatgaat atctaaccaa ttcattttcg cgagaacaac gaataaccac
     1081 tcccgaatca tgaagccatg tcttaacgaa aatatggcta actcatagca aaaaaaaagc
     1141 cccctaaggg cttttttttg tacctgacgg tcagaccgat taaacataac atcccttgcg
     1201 tgcaccgcct gagaggctct gagggcgttt ctgacgggaa accggtaaaa caggcaacaa
     1261 accacccgaa aacccgccag aaacgcgcag gctctgtttt tacggcatgc atgagtatgc
     1321 gcgcaagtgc atagcgcgga aattcacacc attcagccag gggaagtcct gtttccggcg
     1381 ttcttcccat ccgaaaacgg tgaacgggga cgcaatttat tgcgtggccg tgaagcgttg
     1441 ccggcgcagc cggaaaaccc gctgtcagca cgttcaggaa gggggtgatg tacaaatggc
     1501 acagaggatg aaagtgacgt atgagctgaa ggaatgatgt aaaagtgatg tataaatgat
     1561 gtaaaagtga tgcaaaagtg ttgtaaaagt gatgtacagg ccgaaggagt gttgtaaaag
     1621 tgttgtaaaa gtgatgtatg aactgaagga gcgatgtaat tctgtagtca ggaagaataa
     1681 cccgttcatg cctgcatgaa cgatacagtg aggaacgctt ttttttgtca cgatctcccc
     1741 ttaacctgcg taaatcaccc gccatggttg attatttttc aacctcaaaa tggtcataca
     1801 cctaacgcag ccgcgatttt catcgcaact gcatgaatta aaagaaaaaa aagtaatgtt
     1861 tcgttttcac gagtaatacc caggtattaa aaacccactg taattacatg aaaataaaga
     1921 aataaaaggt aataccggcg tattaccacg tacgcgggca agcgaaaaag ctataacgct
     1981 tcccggccga caggcggccc agaatccaca ggggcatgca ggatctcttc agtaaccttc
     2041 gccattaaat caaaaaggtc atattcgccg ggaagctgcg tatcagtcga accccgttgt
     2101 tcatcatatt cagatggcat ggggtgatat ccagtagcag agaggttgtt agcgggtttc
     2161 ggggcgcagc cctgaaccag tcacgtagcg ctagcggagt gtatactggc tgactatgtt
     2221 ggcacggatg tggaaatcag tgaagtgctt catgtagcag gagaaaaaag gcggcaccag
     2281 cgcgtcagca ggatatgtag tacaggatat attccgcttc ctcgctcact gactcgctgc
     2341 gctcggtcgt tcggctgcgg cgagcggtgc cggcttacag gcggggcgga aatttcctgg
     2401 gagataccag gaaggagctt aacagggaag agataaggcc gcggcgaagc cgtttttcca
     2461 taggctccgc ccccctgaca aacatcatga aatctgacgc tcaaatcagt ggtggcgaaa
     2521 cccgatgcgg cttaaagata ccaggcgttt ccccctggtg gctccctcgt gctcccccgc
     2581 attcctgcct ttcggtttac cggtgtcatt ccgctgttat ggccgcgttt atctcattcc
     2641 acgcctgaca ctcagttccg cgaaggcagt tcgctcctgg atggactgta tgcacgaacc
     2701 ccccgttcag tccgactgct gcgccttatc cggtaactat catcttgagt ccaacccgga
     2761 aagacacgac ttatcgccac tggcagcagc cactggtaac tgatttagag gagttagtct
     2821 tgaagttatg cgcctgttaa ggctaaactg aaagaacaga tttggttact gcgctcctcg
     2881 taagccagtt accacggttc aaagagttgc tgctctgaga accttcgaaa aaccgccttg
     2941 cagggcggtt ttttcgttta cagagcaaga gattacgacg ccacagaaag gatctcaaga
     3001 agatccttca ccgtaatgga aatctatcca atccgagcac ataggataca catcgttata
     3061 acgctggatc t
//
