LOCUS       CP082442                2319 bp    DNA     circular BCT 11-JAN-2022
DEFINITION  Salmonella enterica subsp. enterica serovar Johannesburg strain
            FSIS1608038 plasmid pF18S023-2319, complete sequence.
ACCESSION   CP082442
VERSION     CP082442.1
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 2319)
  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 2319)
  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 2319)
  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..2319
                     /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="pF18S023-2319"
                     /geo_loc_name="USA:IA"
                     /collection_date="2016"
                     /collected_by="USDA-FSIS"
     gene            complement(join(2176..2319,1..96))
                     /locus_tag="BL362_000005"
     CDS             complement(join(2176..2319,1..96))
                     /locus_tag="BL362_000005"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001560795.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="UAE73507.1"
                     /translation="MIKKICITVIVVFLLLVGYGAWIGSEQNQRGVSLFEVAYTYNAMN
                     PISRIGYTFMLKRNHALVERAGEVKKSIDSMSGE"
                     /name="hypothetical protein"
     gene            329..517
                     /locus_tag="BL362_000010"
     CDS             329..517
                     /locus_tag="BL362_000010"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000165985.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="Rop family plasmid primer RNA-binding protein"
                     /protein_id="UAE73508.1"
                     /translation="MTKQESAALNMAKFIRAQSLLLLEKLDVLDLDDEAADCERMHEQA
                     EALYQKLSARFGIQDGE"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            complement(565..765)
                     /locus_tag="BL362_000015"
     CDS             complement(565..765)
                     /locus_tag="BL362_000015"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001046776.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="UAE73509.1"
                     /translation="MNLCPDERLLFVRMISAMLRRSGGDAGAVMFEAYRHIVSDTNQAR
                     RSYMLDLLESVRHDYVHGGYT"
                     /name="hypothetical protein"
     gene            1511..1624
                     /locus_tag="BL362_000020"
     CDS             1511..1624
                     /locus_tag="BL362_000020"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_007772075.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="replication initiation protein"
                     /protein_id="UAE73505.1"
                     /translation="MHEPPVQSDRCALSGNYRLESNPERHAKAPLAAATGN"
                     /name="replication initiation protein"
     gene            complement(1853..2152)
                     /locus_tag="BL362_000025"
     CDS             complement(1853..2152)
                     /locus_tag="BL362_000025"
                     /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="UAE73506.1"
                     /translation="MKKILFCSLLLLSASSFAQQFHYQCEGRDLKIMLSPNAAFLDGKS
                     FEYKNGETNGETTKMTFFGPSGEVLKFLVNPVNNLYRMGLTSGATFEEINCTEI"
                     /name="hypothetical protein"
     Typing          complement(977..1149)
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="91.954"
                     /coverage="100.0"
                     /evalue="2.04e-62"
     Typing          1074..1620
                     /name="rep_cluster_2335"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="93.091"
                     /coverage="90.0"
                     /evalue="0.0"
ORIGIN
        1 tactcctcgc tgattttgct cagatccaat ccaagcacca tagccaacca acagcaaaaa
       61 aacgacgata acagtaatgc agattttttt tatcattccc tatccagata atatgaagaa
      121 aacagaattg aacataacat ccgttgcccg caccgcctca ggcgccctca gggcgtttct
      181 gaggactccg gtctgaaaca tacacctttc tgtgcccata tcgagaaaaa acgcccctga
      241 tgatttctgc gtacctgcat ggctatgcac tcaagtgaat gaagtaagat ttcagtctgc
      301 gatcaccata aaaccgggaa aaagccgtat gacaaaacag gaatcagccg cactgaacat
      361 ggcaaaattt atccgggcgc agtcgctgct gctgctcgaa aaactcgacg tgctcgatct
      421 tgatgacgag gcagccgact gtgagcgaat gcacgaacag gcagaagcgc tttatcagaa
      481 gctgagcgca cgcttcggta tacaggacgg cgaataaaga gacgaaaaga acgctcactt
      541 agacgaaaag cgtatccagg gcaactatgt atatccaccg tgtacatagt catgcctgac
      601 gctttcgagc aggtcgagca tgtaggaacg acgagcttga ttggtatcgg acacaatatg
      661 gcgatacgcc tcaaacataa cagcacccgc atcaccgccc gaacggcgaa gcatagcgga
      721 aatcatccgc acaaagagca gacgttcatc ggggcaaagg ttcataagtt ctcctggtga
      781 aaaaaccaaa catgaagcac ccatctatta acgtcagctg tgaacgcttc attacgcttc
      841 attaaaatag gtaaacccgg gaaaaagatc caaacgttaa catcacaggt aaacagaaac
      901 gtcgggtcga tcgggaaatt ctttcccgga cggcgcgggg ttgggcaagc cgcaggcgcg
      961 tcagtgcttt tagcgggtgt cggggcgcag ccctgaacca gtcacgtagc gctagcggag
     1021 tgtatactgg cttactatgt aggcacgggt gcgggaatca gtgaagtgct tcatgtggca
     1081 ggaggaaaat gcagcagcag agcgtaagcg gaatatatga gacaggagat attccgcttc
     1141 ctcgctcact gactcgctgc gctcggtcgt tcggctgcgg cgagcggtgc gggcttacga
     1201 atggggcgga aatttcctgg gagatgccag gaagaaactt aacagggaaa cgataaggcc
     1261 gcggcgaagc cgtttttcca taggctccgc ccccctgaca agcatcacga aatctgacgc
     1321 tcaaatcagt ggtggcgaaa cccgacagga ctataaagat accaggcgtt tccccctggc
     1381 ggctccctcg tgcgctctcc tgttcctgcc tttcggttta ccggtgtcat tccgctgtta
     1441 tggccgcgtt tgtctcattc cacgcctgac actcagttcc gggtaggcag ttcgctccaa
     1501 gctggactgt atgcacgaac cccccgttca gtccgaccgc tgcgccttat ccggtaacta
     1561 tcgtcttgag tccaacccgg aaagacatgc aaaagcacca ctggcagcag ccactggtaa
     1621 ctgatttaga ggagttagtc ttgaagtcat gcgccggtta aggctaaact gaaaggacaa
     1681 gttttggtga ctgcgctcct ccaagccagt tacctcggtt caaagagttg gtagctcaga
     1741 gaaccttcga aaaaccgcct tgcagggcgg ttttttcgtt ttcagagcaa gagattacgc
     1801 gcagaccaaa acgatctcaa gaagatcatc ttattaatca gataaaatat ttctagattt
     1861 cagtgcaatt tatctcttca aatgtagcac ctgaagtcag ccccatacga tataagttgt
     1921 tgacaggatt aaccaaaaac ttgagaacct caccagaagg accaaagaat gtcatctttg
     1981 tcgtttcccc attcgtctct ccattcttat attcgaatga tttaccatca agaaaagctg
     2041 cattaggtga aagcattatc tttaaatctc gtccttcaca ctgataatgg aattgttgtg
     2101 caaatgaact tgcagaaaga agaagcagcg aacaaaaaag tatctttttc atatcagtcc
     2161 tttaaattta aaaaatcact caccactcat gctatcaata gatttcttaa cctctccagc
     2221 cctctcgact aaagcatgat ttctcttcag cataaatgta tagccgatcc gactaattgg
     2281 attcattgcg ttgtatgtat atgcaacctc aaataaaga
//
