LOCUS       CP123667                5282 bp    DNA     circular BCT 14-JUN-2023
DEFINITION  Salmonella enterica subsp. enterica serovar Johannesburg strain
            FSIS1709981 plasmid pFSIS1709981-2, complete sequence.
ACCESSION   CP123667
VERSION     CP123667.1
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 5282)
  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  JOURNAL   Unpublished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 5282)
  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 5282)
  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..5282
                     /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="pFSIS1709981-2"
                     /geo_loc_name="USA:MO"
                     /collection_date="2016"
                     /collected_by="USDA-FSIS"
                     /note="subgroup: enterica"
     gene            join(5226..5282,1..258)
                     /locus_tag="B0D47_23750"
                     /pseudo=""
     CDS             join(5226..5282,1..258)
                     /locus_tag="B0D47_23750"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_021138877.1"
                     /note="incomplete; partial on complete genome; missing
                     N-terminus and C-terminus; Derived by automated
                     computational analysis using gene prediction method:
                     Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="Tn3 family transposase"
                     /name="Tn3 family transposase"
     gene            complement(268..1083)
                     /locus_tag="B0D47_23755"
     CDS             complement(268..1083)
                     /locus_tag="B0D47_23755"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_032492145.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="aminoglycoside O-phosphotransferase APH(3')-Ia"
                     /protein_id="WGN22810.1"
                     /translation="MSHIQRETSCSRQRLNSNLDADLYGYKWARDNVGQSGATIYRLYG
                     KPDAPELFLKHGKGSVANDVTDEMVRLNWLTEFMPLPTIKHFIRTPDDAWLLTTAIPGK
                     TAFQVLEEYPDSGENIVDALAAFLRRLHSIPVCNCPFNSDRVFRLAQAQSRMNNGLVDA
                     SDFDDERNGWPVEQVWKEMHKLLPFSPDSVVTHGDFSLDNLIFDEGKLIGCIDVGRVGI
                     ADRYQDLAILWNCLGEFSPSLQKRLFQKYGIDNPDMNKLQFHLMLDEFF"
                     /name="aminoglycoside O-phosphotransferase APH(3')-Ia"
     gene            complement(1229..1327)
                     /locus_tag="B0D47_23760"
                     /pseudo=""
     CDS             complement(1229..1327)
                     /locus_tag="B0D47_23760"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_013356662.1"
                     /note="incomplete; partial on complete genome; missing
                     N-terminus and C-terminus; Derived by automated
                     computational analysis using gene prediction method:
                     Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="amino acid ABC transporter substrate-binding
                     protein"
                     /name="amino acid ABC transporter substrate-binding
                     protein"
     gene            complement(2200..2433)
                     /locus_tag="B0D47_23765"
     CDS             complement(2200..2433)
                     /locus_tag="B0D47_23765"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000137438.1"
                     /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="WGN22811.1"
                     /translation="MTELEGHLLNALEHLQQDYMRRLNEWESAFAELQKMHAVTQQNNA
                     ILNERVVNLSQQVQLLAGQVDRLSRLFITNNR"
                     /name="MbeD family mobilization/exclusion protein"
     gene            complement(2440..3000)
                     /locus_tag="B0D47_23770"
     CDS             complement(2440..3000)
                     /locus_tag="B0D47_23770"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000067488.1"
                     /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="WGN22812.1"
                     /translation="MSNLLQMGTDFEKKLKERAASTENMLNSEFRKLEESVDKALSLNR
                     QKIRDAISEHTTSVKQQLDTLSTTVSTQLSTTEAELSRQQKNLLWQVIKGRVLFPALTA
                     LSVTGGIFLGCWGLIQWQESRIAKNILTIREQENTLAKLEAKTWGVTFVNGENGKFLVL
                     PDGVKGENTWTVGDKNAVRLVRE"
                     /name="MbeB family mobilization protein"
     gene            complement(3029..3469)
                     /locus_tag="B0D47_23775"
                     /pseudo=""
     CDS             complement(3029..3469)
                     /locus_tag="B0D47_23775"
                     /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(3678..4001)
                     /locus_tag="B0D47_23780"
     CDS             complement(3678..4001)
                     /locus_tag="B0D47_23780"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000956000.1"
                     /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="WGN22813.1"
                     /translation="MLTIRVSDEEHARLLERCEGKRLAEWMRRVCLGEPVARTGKLPTL
                     SPPLLRHLAAIGNNLNQTARKVNSGHWSSIDRVHVVAALMAIEGELRQLRQAVREQGGR
                     DDS"
                     /name="MobC family plasmid mobilization relaxosome protein"
     gene            4064..4255
                     /locus_tag="B0D47_23785"
     CDS             4064..4255
                     /locus_tag="B0D47_23785"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000165979.1"
                     /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="WGN22809.1"
                     /translation="MTKQEKTALNMARFIRSQTLTLLEKLNELDADEQADICESLHDHA
                     DELYRSCLARFGDDGESN"
                     /name="Rop family plasmid primer RNA-binding protein"
     ARG             complement(272..1083)
                     /name="aph(3')-Ia"
                     /gene="aph(3')-Ia"
                     /gene_name="aminoglycoside O-phosphotransferase APH(3')-Ia"
                     /tool="amrfinderplus"
                     /drug_class="AMINOGLYCOSIDE"
                     /identity="100.0"
                     /coverage="100.0"
     Typing          complement(4344..4428)
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="3.03e-37"
     Typing          4439..4994
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="93.728"
                     /coverage="99.0"
                     /evalue="0.0"
     Typing          complement(2103..3688)
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="99.622"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 gttatgccct gggacacctt cgccgccagc gtcaccgaag cgcaaacatt ggcgcggcct
       61 gccgactttg atttcctgca ccacatcggt gaaagctatg ccacgctacg ccgctacgcg
      121 ccgcagttcc tgggcgtgct caaattgcgg gctgcgcccg ccgccaaggg tgtgctcgat
      181 gccatcgaca tgctgcgcgg catgaacagc gacagcgcgc gcaaggtgcc cgccgatgcg
      241 ccaaccgcat tcattaaaga ctaactatca gaaaaactca tcgagcatca aatgaaactg
      301 caatttattc atatcaggat tatcaatacc atatttttga aaaagccgtt tctgtaatga
      361 aggagaaaat tcaccgaggc agttccatag aatggcaaga tcctggtatc ggtctgcgat
      421 tccgactcgt ccaacatcaa tacaacctat taatttcccc tcgtcaaaaa taagattatc
      481 aagtgagaaa tcaccatgag tgacgactga atccggtgag aatggcaaaa gcttatgcat
      541 ttctttccag acttgttcaa caggccagcc attacgctca tcatcaaaat cactcgcatc
      601 aaccaaaccg ttattcattc gtgattgcgc ctgagcgaga cgaaatacgc gatcgctgtt
      661 aaaaggacaa ttacaaacag gaatcgaatg caaccggcgc aggaacgctg ccagcgcatc
      721 aacaatattt tcacctgaat caggatattc ttctaatacc tggaatgctg ttttcccggg
      781 gatcgcagtg gtgagtaacc atgcatcatc aggagtacgg ataaaatgct tgatggtcgg
      841 aagaggcata aattccgtca gccagtttag tctgaccatc tcatctgtaa catcattggc
      901 aacgctacct ttgccatgtt tcagaaacaa ctctggcgca tcgggcttcc catacaatcg
      961 atagattgtc gcacctgatt gcccgacatt atcgcgagcc catttatacc catataaatc
     1021 agcatccagg ttggaattta atcgctgcct cgagcaagac gtttcccgtt gaatatggct
     1081 cataacaccc cttgtattac tgtttatgta agcagacagt tttattgttc atgatgatat
     1141 atttttatct tgtgcaatgt aacatcagag attttgagac acaacgtggt tcccgccata
     1201 tgaaaatccg gccagaccaa catcattctg gcgctccgaa agaagggata ttcgccgccg
     1261 tgaccagcct ggagcgggtc gcataatctt tggccgcttc gtagtcgagg aacatggcat
     1321 caagactagt aaactcaatc aaagatcctt ctagatttaa gttcacgaca gagtcattag
     1381 aaatggagtt actagaatac ttagagttaa gaaatgaatt attcaatgac atagaagaag
     1441 taatgggtag ctatgctcag agggcaccat agttcatgat agccctcgat agtacttact
     1501 tatattttta gagaggttta agtgtaagta gagggagtaa cacctggttt ttcagcatcc
     1561 actccaatga atgctgacac cgatacgcga taattctctt tatcgtagca aaatcatcct
     1621 ccagattgcg gttgagaata ggttcatggt gcgcaatacg attgcgcagt tttctcacgg
     1681 gacttgttag cagtaatgct tccccccggg gacaaacgac agagatatac aacaaaggcc
     1741 cgctgtatag agtacagcgg gcctttgttg ttttaattcc cgcaattaaa atactccgta
     1801 tttaccataa cgtcgcattg cgcgtaccgc ttaaacgcgt tcagcgcgat cacggcagca
     1861 gacaggtaaa aacagcaaca aaccacccga aaaactgccg cgatcgcgcc tggtaaattt
     1921 taacctcatg catagttatg cgcgaaactg aatgacgatc agtttcgcac gttccagccg
     1981 tcgaacgggg caaaatgggg aggtttggat attgttaatg ctaatgtacg tacattaaca
     2041 ttggcgccat ccgggtaggg cgtgccacaa actggctcga tttcaggggg caccccggtc
     2101 acatccccat tgacgggcca cgccagatcc gcgcttcggg ttcctgctct tcatgccagc
     2161 gccgggcaag ctcctgcgcc tgacgctcct gttcatccct tatctgttgt tcgtgataaa
     2221 taaccgactc aagcggtcga cttgtccggc taatagctgc acctgctgac tcaagttcac
     2281 gacacgctcg ttcagtatcg cgttgttctg ttgcgtaacc gcgtgcatct tctgcaattc
     2341 tgcgaaggcg ctctcccact cgttcagccg ccgcatatag tcctgttgca aatgctctaa
     2401 ggcgttcagc aaatgccctt ccagttccgt catactcgtt tactccctga ccagcctcac
     2461 ggcgttcttg tcgcccaccg tccaggtgtt ttcccctttc accccgtccg gcagcaccag
     2521 aaatttcccg ttctcgccat tgacgaacgt caccccccag gtttttgcct cgagtttcgc
     2581 cagcgtgttt tcctgctctc tgatggtcaa gatatttttc gcaatcctgc tttcctgcca
     2641 ctgaatcagc ccccagcacc ccaggaaaat gccgcccgtg acgctgagcg cggtcagcgc
     2701 cggaaacagt acccgccctt tgatcacctg ccagagcagg tttttctgct gccgggacag
     2761 ttcggcctct gtggtgctga gctgcgtgct cacggtggtg ctcagcgtat ccagttgctg
     2821 tttcacggat gttgtatgtt cgctgatagc gtctctgatt ttctgcctgt ttaagctcag
     2881 tgccttgtct acagactctt ctagcttcct gaactcgctg ttcagcatgt tctcggtaga
     2941 agcggctcgc tctttcagtt tcttctcgaa gtctgttccc atttgtaaaa gattgctcat
     3001 acagcgcccc ctttagcctg agattccgcc ccccctccgg gtcggcaata ctgatactgc
     3061 ttctggttgt cctcaccacc tcaaaacctg ccgctgagag cgcctcagtg acatcctgac
     3121 gcgtttttat tgctccggca cggtaaagcg cctcaagacc ccgtgtaatc gcttctgcgg
     3181 cctcctgttt cgcttttggc agattattcg gtgtgacaag cgtccgtctg ttctccggtg
     3241 cgttcgggtc acgcagcccg taatgatgat taaccagcgt ctgccaggca tttatcctcg
     3301 gcctgtccgc acggtcgtag tacggctgga ggcgcttacc gctctgtagt tccatgttcg
     3361 gaatgacaaa attcagttcg agccgcccct tatcctggtg ttccacccag agaatgctgt
     3421 actggtcttt ttcgagaccg ggcataagaa cacgctcaaa gctcgtcatc actctttcgc
     3481 gttcacccgg cggtaactcc ttctccgcga acgacagaac gcctgacgtg tatttcttcg
     3541 aaaatggcgt ggcatcaatg agttcccgga tttcttccgg gttaccccgg agcaccgttg
     3601 cgccttcgcg gttacgctcc cgccccagca ggtaatcgac cgggccactt ccaccgcctt
     3661 tccccctggc atgaaattta actatcatcc cgtcccccct gttccctgac agcctgccgc
     3721 aactggcgca attcaccctc gatggccatc agtgcggcca ccacatgaac ccggtcaatc
     3781 gaagaccagt ggccgctgtt caccttccgg gctgtctggt tcagattgtt cccgatggca
     3841 gccagatgcc gcagcaatgg cggcgatagt gtcggcagtt ttcctgtgcg cgcaaccggc
     3901 tcccccagac agacccgccg catccattct gccagtcgtt taccctcgca gcgttccagt
     3961 aaccgggcgt gctcctcatc gctaacccgt atcgtgagca tcttctcgcg tttcatcggt
     4021 atcattcccc ctaaaaaatc ccctattaag gagccttaag accatgacca aacaggaaaa
     4081 aacagccctt aacatggccc gctttatcag aagccagacg ctgaccctgc tggaaaaact
     4141 caacgagctg gacgcggacg aacaggcaga catctgcgaa tcacttcacg accacgccga
     4201 cgaactctac cgtagttgcc tcgcacgctt cggcgatgac ggtgaaagca actgaaacat
     4261 gcagctcccg gagacgttca cagcttgcct gtgagcggat gccgggagca gacaagcccg
     4321 tcagggcgcg tcagcgggtt ttagcgggtg tcggggcgca gccctgaccc agtcacgtag
     4381 cgatagcgga gtgtatactg gcttaactat gtggcatcag tgcggattat aagaaaagtg
     4441 caccatatgc ggtgtgaaat accgcacaga tgcgtaagga gaaaatgccg catcaggcgc
     4501 tcttccgctt cctcgctcac tgactcgcta cgctcggtcg ttcggctgcg gcgagcggta
     4561 tcagctcact caaagacggt gatgcggtta tccacagaat caggggataa cgccaaaaga
     4621 aacatgtgag caaaaggcca agaacaggaa gaaagccgcg ccgctggcgt ttttccatag
     4681 gctccgcccc cctgacgagc atcacaaaaa cagacgctca agtcagaggt ggcgaaaccc
     4741 gacaggacta taaagatacc aggcgtttcc ccctggaagc tccctcgtgc gctctcctgt
     4801 tccgaccctg ccgcttaccg gatacctgtc cgcctttctc ccttcgggaa gcgtggcgct
     4861 ttctcatagc tcacgctgtt ggtatctcgg cccggtgtag gtcgttcgct ccaagctggg
     4921 ctgtgtgcac gaaccccccg ttcagcccga ccgctgcgcc ttatccggta actatcgtct
     4981 tgagtccaac ccggaaagac acgtaaaaac gccactggca gcagccattg gtaaccgttt
     5041 agaggagtta gtcttgaagt tatgcgccgg ttaaggctaa actgaaagga cagatttggt
     5101 ggctgtgctc ctccaagcca gttaccttgg ttcaaagagt tgctgctctg agaaccttcg
     5161 aaaagccgcc ttgctgggcg gttttttcgt ttacggacaa gactaccttc aggatcgtta
     5221 gatctcaagc gttgattgag gccaagcaaa gcggcagcga tccgttcgcc gccatcgagg
     5281 cc
//
