LOCUS       CP082443                3223 bp    DNA     circular BCT 11-JAN-2022
DEFINITION  Salmonella enterica subsp. enterica serovar Johannesburg strain
            FSIS1608038 plasmid pF18S023-3223, complete sequence.
ACCESSION   CP082443
VERSION     CP082443.1
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 3223)
  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 3223)
  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 3223)
  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..3223
                     /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="pF18S023-3223"
                     /geo_loc_name="USA:IA"
                     /collection_date="2016"
                     /collected_by="USDA-FSIS"
     gene            complement(42..257)
                     /locus_tag="BL362_000030"
     CDS             complement(42..257)
                     /locus_tag="BL362_000030"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000137421.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MbeD family mobilization/exclusion protein"
                     /protein_id="UAE73512.1"
                     /translation="MTELEKQLLSALEQLQQDYSKRLDEWENAFAEWRTMSGLIQRENA
                     ALNERVTVLSRQVQSLSEQLRRLSKG"
                     /name="MbeD family mobilization/exclusion protein"
     gene            complement(261..746)
                     /locus_tag="BL362_000035"
     CDS             complement(261..746)
                     /locus_tag="BL362_000035"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_012565228.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MbeB family mobilization protein"
                     /protein_id="UAE73513.1"
                     /translation="MNSLLTLAKDLEQKSKAQQQTTGEMLKAAFSEHEKSVRAELSESE
                     KRISAAILDHDRKLSSAMSQRTKGMLRMVSQTWLTIVLVSALLIASSAGILWWQGQQIL
                     ENYTTIREQKSTQAMLSERNSGVQLSTCGEQRRRCVRVNPEAGQFGEDSSWMILAGK"
                     /name="MbeB family mobilization protein"
     gene            complement(721..1485)
                     /locus_tag="BL362_000040"
                     /pseudo=""
     CDS             complement(721..1485)
                     /locus_tag="BL362_000040"
                     /inference="COORDINATES: protein motif:HMM:NF015397.2"
                     /note="incomplete; partial on complete genome; missing
                     C-terminus; Derived by automated computational analysis
                     using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="relaxase/mobilization nuclease domain-containing
                     protein"
                     /name="relaxase/mobilization nuclease domain-containing
                     protein"
     gene            complement(1424..1747)
                     /locus_tag="BL362_000045"
     CDS             complement(1424..1747)
                     /locus_tag="BL362_000045"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000957083.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MobC family plasmid mobilization relaxosome
                     protein"
                     /protein_id="UAE73514.1"
                     /translation="MLTMWVTEDEHRRLLERCEGKQLAAWMRQTCLDEKPARAGKLPSI
                     SPALLRQLAGMGNNLNQIARQVNAGGGSGHDRVQIVAALMAIDAGLERLRHAVLEKGAD
                     DDR"
                     /name="MobC family plasmid mobilization relaxosome protein"
     gene            2386..2556
                     /locus_tag="BL362_000050"
     CDS             2386..2556
                     /locus_tag="BL362_000050"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_005761324.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="replication initiation protein"
                     /protein_id="UAE73510.1"
                     /translation="MHEPPVQSDYHARSGNYQLESNPERHDKSPVAVAIGNWVHGAEIV
                     ENAYRVLEVKA"
                     /name="replication initiation protein"
     gene            complement(2765..3097)
                     /locus_tag="BL362_000055"
     CDS             complement(2765..3097)
                     /locus_tag="BL362_000055"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001070439.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="EmrE family multidrug efflux SMR transporter"
                     /protein_id="UAE73511.1"
                     /translation="MNTYIFLGGAIVAEVIGTTFMKYSEGFTRLWPSVGTAISYCAAFY
                     LLSQTLENIPTGIAYAIWSGAGIVLISLAGWLVSGQKLDWPAIAGMFLICVGVLVINIF
                     SKSSAH"
                     /name="EmrE family multidrug efflux SMR transporter"
     ARG             complement(2766..3097)
                     /name="qacG"
                     /gene="qacG"
                     /gene_name="small multidrug resistance (SMR) antibiotic
                     efflux pump"
                     /tool="rgi"
                     /drug_class="disinfecting agents and antiseptics"
                     /identity="41.35"
                     /coverage="102.8"
     Typing          complement(1844..2035)
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="92.308"
                     /coverage="89.0"
                     /evalue="3.38e-71"
     Typing          2015..2498
                     /name="ColRNAI_rep_cluster_1987"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="84.756"
                     /coverage="93.0"
                     /evalue="1.73e-132"
     Typing          complement(2..1434)
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="92.469"
                     /coverage="96.0"
                     /evalue="0.0"
ORIGIN
        1 ctgcaccgcc cgctcctgct gccggtgagt ttctatcgcg ttcagccttt cgacaaccgg
       61 cgcagctgct cgctcaaact ctgcacctgc ctgctcaaga ccgtgacgcg ctcgttcagc
      121 gccgcgttct cccgttgaat aagaccagac atcgtccgcc attccgcgaa ggcgttctcc
      181 cactcgtcca gccttttcga gtagtcctgc tgtagctgct ctaatgcgct cagcaactgt
      241 ttttccagct ccgtcatgtg ctatttcccc gccagtatca tccagctcga gtcctctccg
      301 aactgtcccg cttccgggtt caccctcacg cagcggcgtc tctgctcgcc gcaggtcgag
      361 agctgtacgc cgctgttcct ctctgacagc atggcctgcg tgctcttctg ctcccggatg
      421 gtcgtatagt tctcgagtat ctgctgcccc tgccaccaca gaatgcccgc gctcgacgct
      481 atcagcagcg cggagaccag aacgatggtc agccacgtct ggctgaccat gcgcagcatc
      541 cctttcgtgc gctggctcat ggctgaggac agcttccggt cgtggtcgag gatggcggcg
      601 ctgattctct tctcgctttc gctcagttcc gctctgacag acttctcgtg ctcgctgaat
      661 gcggctttca gcatctcgcc ggtagtctgc tgctgcgctt tcgatttctg ctctaagtcc
      721 ttcgccagcg ttaaaagact gttcatagat ggctcccttc agtcggatgt ttcgcccccc
      781 gtccgggtcg gcaatgctga tgctgctttt tgtggtgcgc accacctcaa aacctgcgct
      841 ttccagcgcc tcagtgacgt cctgacgcgt tttcagctcc ccggatgagg caagggcaag
      901 caggccgctc gtaatcgcct gggcggcttc ctgcttcgct tccggcagcg cggaaggcga
      961 gaccagcacc cgccggttct ccggcgcgtt cgggtcatgc agccccagcc tgccgttcac
     1021 tatggtctgc caggcatcga tgcgcggacg gtcggcgcgg tcgtaatacg gctgtagccg
     1081 cttgccggtc agaagctccg tgttcgggat caggaagttc agctccagcc gccccttgtc
     1141 ccggtgctca acccacagca cgctgtactg gtctttatcg agtccgggca tcagaacccg
     1201 ctcgaaactc gccatcagct tttcgcgctg gccgggcggt aaatcctgtt cggcaaaaga
     1261 cagaacgccg gaagtgtact ttttggcgta gggcgaggcg tcgataagct cccggacttc
     1321 atccggcttc ccctgcagaa cgctggcgcc gtcgcgctgg cgatctttac ccagcagata
     1381 atcgaccggc ccgccgccgc cgccgcgccc ccgaggatga aacttaacga tcatcatcag
     1441 cacccttttc cagtacggca tgccgcaacc gctcgagtcc ggcatcgatg gccatcagcg
     1501 cggcgacaat ctgcacgcgg tcgtgtccgc ttccaccacc ggcgttaacc tggcgggcaa
     1561 tctggttaag gttgttcccc atgccggcaa gctgacgaag cagcgccggc gagatcgacg
     1621 gaagtttgcc ggcgcgtgcg ggcttctcgt ccaggcacgt ctgccgcatc caggccgcga
     1681 gttgcttacc ctcgcagcgc tccagcagac gccggtgctc gtcctcagtc acccacatgg
     1741 tgagcatttt gctgcgtttg tctgccaatc cggcctcctg ataacgccgg gacggacggg
     1801 aaatcttttc ccggtcggca cggtgttgga caagccgcag gcgcggcagt ggttttagcg
     1861 ggtttcgggg cgcagccctg aaccagtcac gtagcgctag cggagtgtat actggctaaa
     1921 catgttatga cggagtggca atttatgaaa gtgcttcatg tgacagggga aaaatgcggc
     1981 tgccgggcgt aagtgcaaaa tgcaggtggt gatgaaatga cgcctcctcg ctcactcggt
     2041 cgctacgctc ctgccgtgag actgcggcgg gcgttaccag ctcacagatt acgggataag
     2101 caaatgccgc tcgaagcagg aaaggccaag aaaaggatgc ggagttgccg tttttccata
     2161 ggctccgccc ccctgacgag tatcacgaaa atgacgctca aatcagcggt ggcgaaaccc
     2221 gatgcggctt aaagatacca ggcgtttccc cctggtggct ccctcgtgct cccccgcatt
     2281 cctgcctttc ggtttaccgg tgtcattccg ctgttatggc cgcggtttct cattccacgc
     2341 ctgaaactcg gttccgggta ggcagttcgc tccaggatgg actgtatgca cgaacccccc
     2401 gttcagtccg actaccacgc ccgttccggt aactatcaac ttgagtccaa cccggaaaga
     2461 cacgacaaat cgccagtggc ggtagccatt ggtaactggg ttcacggagc agagattgta
     2521 gagaatgcct acagagttct tgaagtgaaa gcctgagtgc ggctacactg aaaggacagt
     2581 ttaggtatct gcgctccgtg aaagccagtt accatcggaa caaagagttg gtagctctga
     2641 attccggcaa acgaaccacc gttggtagcg gtggtttttt tgtttacagg gaaaaagatt
     2701 acgcgcagaa agaaaggatc tcaaggaaat ccttttgctt tggccaatat gcttcggtaa
     2761 aaagttaatg cgcagaagat tttgaaaaaa tattaataac caaaactcca acgcaaataa
     2821 ggaacattcc tgcaattgcg ggccaatcaa gtttttgacc gctaaccaac caaccagcta
     2881 ggcttattag tacaattccc gcaccagacc aaattgcgta agcaataccg gtaggtatat
     2941 tttccaatgt ttgggaaagc agataaaagg cagcgcaata acttattgca gttcctacag
     3001 acggccacag gcgtgtaaat ccttctgaat atttcataaa ggtggtgcct atgacttcag
     3061 ccacaatagc ccctcccagg aaaatatatg tattcataaa aatacctcat gttgaaaaat
     3121 ttaaatatct ttacataaca actaattaat agaacccggc ttatcatagc gaaggaccat
     3181 gatgctgcca ctgcgatcgt tccagctcca gcgctttctg gtg
//
