LOCUS       CP123668                3223 bp    DNA     circular BCT 14-JUN-2023
DEFINITION  Salmonella enterica subsp. enterica serovar Johannesburg strain
            FSIS1709981 plasmid pFSIS1709981-3, complete sequence.
ACCESSION   CP123668
VERSION     CP123668.1
DBLINK      BioProject: PRJNA292666
            BioSample: SAMN06289184
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   Ge,B.
  TITLE     Genomic Analysis of Azithromycin-Resistant Salmonella from Food
            Animals and Retail Meats, 2015-2021, United States
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 3223)
  CONSRTM   NARMS: The National Antimicrobial Resistance Monitoring System
  TITLE     Direct Submission
  JOURNAL   Submitted (24-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 (02-MAR-2023) CVM/OAS, FDA-CVM, 8401 Muirkirk Rd, MOD2,
            Laurel, MD 20708, USA
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Date                     :: 24-SEP-2021
            Assembly Method                   :: HGAP v. 4
            Assembly Name                     :: Microbial assembly
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 265x
            Sequencing Technology             :: PacBio Sequel
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI
            Annotation Date                   :: 04/20/2023 10:47:28
            Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline
            (PGAP)
            Annotation Method :: Best-placed reference protein set; GeneMarkS-2+
            Annotation Software revision      :: 6.5
            Features Annotated                :: Gene; CDS; rRNA; tRNA; ncRNA
            Genes (total)                     :: 4,763
            CDSs (total)                      :: 4,645
            Genes (coding)                    :: 4,514
            CDSs (with protein)               :: 4,514
            Genes (RNA)                       :: 118
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 83
            ncRNAs                            :: 13
            Pseudo Genes (total)              :: 131
            CDSs (without protein)            :: 131
            Pseudo Genes (ambiguous residues) :: 0 of 131
            Pseudo Genes (frameshifted)       :: 54 of 131
            Pseudo Genes (incomplete)         :: 90 of 131
            Pseudo Genes (internal stop)      :: 22 of 131
            Pseudo Genes (multiple problems)  :: 33 of 131
            Pseudo Genes (short protein)      :: 1 of 131
            CRISPR Arrays                     :: 1
            ##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="FSIS1709981"
                     /serovar="Johannesburg"
                     /isolation_source="animal-swine-market swine"
                     /sub_species="enterica"
                     /db_xref="taxon:913076"
                     /plasmid="pFSIS1709981-3"
                     /geo_loc_name="USA:MO"
                     /collection_date="2016"
                     /collected_by="USDA-FSIS"
                     /note="subgroup: enterica"
     gene            complement(61..384)
                     /locus_tag="B0D47_23790"
     CDS             complement(61..384)
                     /locus_tag="B0D47_23790"
                     /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="WGN22818.1"
                     /translation="MLTMWVTEDEHRRLLERCEGKQLAAWMRQTCLDEKPARAGKLPSI
                     SPALLRQLAGMGNNLNQIARQVNAGGGSGHDRVQIVAALMAIDAGLERLRHAVLEKGAD
                     DDR"
                     /name="MobC family plasmid mobilization relaxosome protein"
     gene            1023..1193
                     /locus_tag="B0D47_23795"
     CDS             1023..1193
                     /locus_tag="B0D47_23795"
                     /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="WGN22816.1"
                     /translation="MHEPPVQSDYHARSGNYQLESNPERHDKSPVAVAIGNWVHGAEIV
                     ENAYRVLEVKA"
                     /name="replication initiation protein"
     gene            complement(1402..1734)
                     /locus_tag="B0D47_23800"
     CDS             complement(1402..1734)
                     /locus_tag="B0D47_23800"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_008784643.1"
                     /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="WGN22817.1"
                     /translation="MNTYIFLGGAIVAEVIGTTFMKYSEGFTRLWPSVGTAISYCAAFY
                     LLSQTLENIPTGIAYAIWSGAGIVLISLAGWLVSGQKLDWPAIAGMFLICVGVLVINIF
                     SKSSAH"
                     /name="EmrE family multidrug efflux SMR transporter"
     gene            complement(1902..2117)
                     /locus_tag="B0D47_23805"
     CDS             complement(1902..2117)
                     /locus_tag="B0D47_23805"
                     /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="WGN22814.1"
                     /translation="MTELEKQLLSALEQLQQDYSKRLDEWENAFAEWRTMSGLIQRENA
                     ALNERVTVLSRQVQSLSEQLRRLSKG"
                     /name="MbeD family mobilization/exclusion protein"
     gene            complement(2121..2606)
                     /locus_tag="B0D47_23810"
     CDS             complement(2121..2606)
                     /locus_tag="B0D47_23810"
                     /inference="COORDINATES: protein motif:HMM:NF016710.2"
                     /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="WGN22815.1"
                     /translation="MNSLLTLAKDLEQKSKAQQQTTGEMLKAAFSEHEKSVRAELSESE
                     KRISAAILDHDRKLSSAMSQRTKGMLRMVSQTWLTIVLVSALLIASSAGILWWQGQQIL
                     ENYTTIREQKSTQAMLSERNSGVQLSTCGEQRRRCVRVNPEAGQFGEDSSWMILAGK"
                     /name="MbeB family mobilization protein"
     gene            complement(2641..3075)
                     /locus_tag="B0D47_23815"
                     /pseudo=""
     CDS             complement(2641..3075)
                     /locus_tag="B0D47_23815"
                     /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"
     ARG             complement(1403..1734)
                     /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(481..672)
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="92.308"
                     /coverage="89.0"
                     /evalue="3.38e-71"
     Typing          652..1135
                     /name="ColRNAI_rep_cluster_1987"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="84.756"
                     /coverage="93.0"
                     /evalue="1.73e-132"
     Typing          complement(65..384)
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="97.196"
                     /coverage="100.0"
                     /evalue="8.510000000000001e-64"
     Typing          complement(1805..3222)
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="91.579"
                     /coverage="95.0"
                     /evalue="0.0"
ORIGIN
        1 tctttaccca gcagataatc gaccggcccg ccgccgccgc cgcgcccccg aggatgaaac
       61 ttaacgatca tcatcagcac ccttttccag tacggcatgc cgcaaccgct cgagtccggc
      121 atcgatggcc atcagcgcgg cgacaatctg cacgcggtcg tgtccgcttc caccaccggc
      181 gttaacctgg cgggcaatct ggttaaggtt gttccccatg ccggcaagct gacgaagcag
      241 cgccggcgag atcgacggaa gtttgccggc gcgtgcgggc ttctcgtcca ggcacgtctg
      301 ccgcatccag gccgcgagtt gcttaccctc gcagcgctcc agcagacgcc ggtgctcgtc
      361 ctcagtcacc cacatggtga gcattttgct gcgtttgtct gccaatccgg cctcctgata
      421 acgccgggac ggacgggaaa tcttttcccg gtcggcacgg tgttggacaa gccgcaggcg
      481 cggcagtggt tttagcgggt ttcggggcgc agccctgaac cagtcacgta gcgctagcgg
      541 agtgtatact ggctaaacat gttatgacgg agtggcaatt tatgaaagtg cttcatgtga
      601 caggggaaaa atgcggctgc cgggcgtaag tgcaaaatgc aggtggtgat gaaatgacgc
      661 ctcctcgctc actcggtcgc tacgctcctg ccgtgagact gcggcgggcg ttaccagctc
      721 acagattacg ggataagcaa atgccgctcg aagcaggaaa ggccaagaaa aggatgcgga
      781 gttgccgttt ttccataggc tccgcccccc tgacgagtat cacgaaaatg acgctcaaat
      841 cagcggtggc gaaacccgat gcggcttaaa gataccaggc gtttccccct ggtggctccc
      901 tcgtgctccc ccgcattcct gcctttcggt ttaccggtgt cattccgctg ttatggccgc
      961 ggtttctcat tccacgcctg aaactcggtt ccgggtaggc agttcgctcc aggatggact
     1021 gtatgcacga accccccgtt cagtccgact accacgcccg ttccggtaac tatcaacttg
     1081 agtccaaccc ggaaagacac gacaaatcgc cagtggcggt agccattggt aactgggttc
     1141 acggagcaga gattgtagag aatgcctaca gagttcttga agtgaaagcc tgagtgcggc
     1201 tacactgaaa ggacagttta ggtatctgcg ctccgtgaaa gccagttacc atcggaacaa
     1261 agagttggta gctctgaatt ccggcaaacg aaccaccgtt ggtagcggtg gtttttttgt
     1321 ttacagggaa aaagattacg cgcagaaaga aaggatctca aggaaatcct tttgctttgg
     1381 ccaatatgct tcggtaaaaa gttaatgcgc agaagatttt gaaaaaatat taataaccaa
     1441 aactccaacg caaataagga acattcctgc aattgcgggc caatcaagtt tttgaccgct
     1501 aaccaaccaa ccagctaggc ttattagtac aattcccgca ccagaccaaa ttgcgtaagc
     1561 aataccggta ggtatatttt ccaatgtttg ggaaagcaga taaaaggcag cgcaataact
     1621 tattgcagtt cctacagacg gccacaggcg tgtaaatcct tctgaatatt tcataaaggt
     1681 ggtgcctatg acttcagcca caatagcccc tcccaggaaa atatatgtat tcataaaaat
     1741 acctcatgtt gaaaaattta aatatcttta cataacaact aattaataga acccggctta
     1801 tcatagcgaa ggaccatgat gctgccactg cgatcgttcc agctccagcg ctttctggtg
     1861 ctgcaccgcc cgctcctgct gccggtgagt ttctatcgcg ttcagccttt cgacaaccgg
     1921 cgcagctgct cgctcaaact ctgcacctgc ctgctcaaga ccgtgacgcg ctcgttcagc
     1981 gccgcgttct cccgttgaat aagaccagac atcgtccgcc attccgcgaa ggcgttctcc
     2041 cactcgtcca gccttttcga gtagtcctgc tgtagctgct ctaatgcgct cagcaactgt
     2101 ttttccagct ccgtcatgtg ctatttcccc gccagtatca tccagctcga gtcctctccg
     2161 aactgtcccg cttccgggtt caccctcacg cagcggcgtc tctgctcgcc gcaggtcgag
     2221 agctgtacgc cgctgttcct ctctgacagc atggcctgcg tgctcttctg ctcccggatg
     2281 gtcgtatagt tctcgagtat ctgctgcccc tgccaccaca gaatgcccgc gctcgacgct
     2341 atcagcagcg cggagaccag aacgatggtc agccacgtct ggctgaccat gcgcagcatc
     2401 cctttcgtgc gctggctcat ggctgaggac agcttccggt cgtggtcgag gatggcggcg
     2461 ctgattctct tctcgctttc gctcagttcc gctctgacag acttctcgtg ctcgctgaat
     2521 gcggctttca gcatctcgcc ggtagtctgc tgctgcgctt tcgatttctg ctctaagtcc
     2581 ttcgccagcg ttaaaagact gttcatagat ggctcccttc agtcggatgt ttcgcccccc
     2641 gtccgggtcg gcaatgctga tgctgctttt tgtggtgcgc accacctcaa aacctgcgct
     2701 ttccagcgcc tcagtgacgt cctgacgcgt tttcagctcc ccggatgagg caagggcaag
     2761 caggccgctc gtaatcgcct gggcggcttc ctgcttcgct tccggcagcg cggaaggcga
     2821 gaccagcacc cgccggttct ccggcgcgtt cgggtcatgc agccccagcc tgccgttcac
     2881 tatggtctgc caggcatcga tgcgcggacg gtcggcgcgg tcgtaatacg gctgtagccg
     2941 cttgccggtc agaagctccg tgttcgggat caggaagttc agctccagcc gccccttgtc
     3001 ccggtgctca acccacagca cgctgtactg gtctttatcg agtccgggca tcagaacccg
     3061 ctcgaaactc gccatcagct tttcgcgctg gccgggcggt aaatcctgtt cggcaaaaga
     3121 cagaacgccg gaagtgtact ttttggcgta gggcgaggcg tcgataagct cccggacttc
     3181 atccggcttc ccctgcagaa cgctggcgcc gtcgcgctgg cga
//
