LOCUS       CP082445                3811 bp    DNA     circular BCT 11-JAN-2022
DEFINITION  Salmonella enterica subsp. enterica serovar Johannesburg strain
            FSIS1608038 plasmid pF18S023-3811, complete sequence.
ACCESSION   CP082445
VERSION     CP082445.1
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 3811)
  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 3811)
  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 3811)
  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..3811
                     /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="pF18S023-3811"
                     /geo_loc_name="USA:IA"
                     /collection_date="2016"
                     /collected_by="USDA-FSIS"
     gene            87..428
                     /locus_tag="BL362_001570"
     CDS             87..428
                     /locus_tag="BL362_001570"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_012963543.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="helix-turn-helix domain-containing protein"
                     /protein_id="UAE73785.1"
                     /translation="MAKPPSATPPDTPSSCDVSALPGIIQNFGLINFNVSCNNGELTVT
                     GTDQNGKHIRVNSYQGNGFTEGTMSTFQPGGKEARRLEAVRLRESGLTQQEIANRLGVS
                     QKTISNDLK"
                     /name="helix-turn-helix domain-containing protein"
     gene            1583..1906
                     /locus_tag="BL362_001575"
     CDS             1583..1906
                     /locus_tag="BL362_001575"
                     /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="UAE73786.1"
                     /translation="MLTMWVTEDEHRRLLERCDGRQLAAWMRQICLDEKPARTGKLPSI
                     SPALLRQLAGMGNNLNQIARRVNAGGGTGHDRVQIVAALMAIDAGLERLRHAVLEKGTD
                     DDR"
                     /name="MobC family plasmid mobilization relaxosome protein"
     gene            1845..2609
                     /locus_tag="BL362_001580"
                     /pseudo=""
     CDS             1845..2609
                     /locus_tag="BL362_001580"
                     /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            2584..3075
                     /locus_tag="BL362_001585"
     CDS             2584..3075
                     /locus_tag="BL362_001585"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_015060400.1"
                     /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="UAE73783.1"
                     /translation="MSNLFTASRDFEEKLKAQQQSTGEMLKAAFSEHEQSVRAELSASA
                     RRISDAILAHEQSMSEAMEKNRRSVLRTAGRTWLTILMVSALLIGTSGSILWWQGQQIT
                     DNYTHLRQQEDTLAKMTARTWGVRYQESSDGRRFLILPPGMQTEAIPYDGTTWIRLKQE
                     "
                     /name="MbeB family mobilization protein"
     gene            3082..3297
                     /locus_tag="BL362_001590"
     CDS             3082..3297
                     /locus_tag="BL362_001590"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000137422.1"
                     /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="UAE73784.1"
                     /translation="MTELEKQLLSALEQLQQDYSQRLDEWESAFAEWQSMCGLMQRENA
                     MLNERVSDLSTQVLSLSEQLRRLSGS"
                     /name="MbeD family mobilization/exclusion protein"
     Typing          1297..1470
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="93.714"
                     /coverage="100.0"
                     /evalue="5.6599999999999995e-68"
     Typing          complement(822..1330)
                     /name="rep_cluster_2335"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="94.118"
                     /coverage="96.0"
                     /evalue="0.0"
     Typing          1897..3389
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="93.6"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 tggcctaaag ggatatggat tattgatatt actagttttc tagtatttac tagtatggat
       61 gcatcgtaaa aatcaaggaa cgcacaatgg caaaacctcc atcagctaca ccaccggata
      121 caccatcttc atgtgatgtt agtgctctcc caggcattat ccaaaatttt ggcttaatta
      181 actttaacgt atcctgcaat aacggtgagc taacggtaac gggtacggat caaaatggga
      241 aacacataag agttaacagc taccaaggga acggctttac cgaaggtaca atgtcaacgt
      301 ttcagcccgg aggtaaagag gccagaagac ttgaggctgt tcgtttaaga gaaagtgggc
      361 ttacgcagca agaaatagca aaccggttag gcgtttctca aaaaactata agcaatgatt
      421 taaaatgagt cacttgcttt aagcccgtct taacgggctt ttcatcgcta ctgaaatgcc
      481 atgataaatc cggcgtagtt gctcgtcccg cagtggtgaa acacctaaag atacatttca
      541 gatgtttatt ttaagccatg gtgcagatcc ccatatatgt cgaacatcaa taatgatctt
      601 cttgagatcc tttccattgc atcgtaatct ctttctctga aaacgaaaaa accgcctggg
      661 gaggcggttt ttcgaaggtt aagtcagttg gggaactgct taacctggta actggcttca
      721 gcagagcgca gataccaaat actgtccttc cagtgtagcc gtagttaggc caccacttca
      781 agaactctgt agcaccgcct acatatctcg ctctgctaat cctgttacca gtggctgctg
      841 ccagtggcgt tttttcgtgt ctttccgggt tggactcaag acgatagtta ccggataagg
      901 cgcagcagtc ggactgaacg gggggttcgt gcatacagtc cagcttggag cgaactgcct
      961 acccggaacc gagtgtcagg cgtggaatga gataaacgcg gccataacag cggagtgaca
     1021 ccggtaaacc gaaaggcagg aacaggagag cgcacgaggg agccatcagg gggaaacgcc
     1081 tggtatcttt atagtcctgt cgggtttcgc caccactgat ttgagcgtca gatttcgtga
     1141 tgcttgtcag gggggcggag cctatggaaa aacggctttg ccgcggcctt atcgtttccc
     1201 tgttaagttc cttcctggca tctaccagga aatttccgcc ccattcgtaa gccggtaccg
     1261 ctcgccgcag ccgaacgacc gagcgcagcg agtcagtgag cgaggaagcg gaatatctcc
     1321 tgtattgcat cttctgttga cgcgccggtg ccaccttttt tctcctgcca catgaagcac
     1381 ttcactgatt tccgcatcca tgccaacata gtaagccagt atacactccg ctagcgctgc
     1441 gtgactggtt cagggctgcg ccccgaaacc cgccaaaagc ctgacgcgcc tgcggcttgt
     1501 ccaaccccgc gccgaccggg aaaggctttc ccgcccgtcc cggcgttatc aggaggccgg
     1561 tttgtcagag aaacggagca agatgctcac catgtgggtg acggaggacg agcaccggcg
     1621 gctgctcgag cgctgtgacg gcaggcagct ggcggcgtgg atgcggcaga tctgcctgga
     1681 cgaaaagcct gcgcgtaccg gaaagcttcc ctcaatctcg ccggcgctgc tgcgccagct
     1741 tgccggcatg ggcaataacc tgaaccagat agcccgccgt gttaacgccg gcggcggtac
     1801 cggccatgac agggtgcaga ttgtggcggc gctgatggcc atcgatgccg gacttgagcg
     1861 gctgcggcac gccgttcttg agaaaggaac ggacgatgat cgttaaattt catccacggg
     1921 gtcgcggcgg tggcgccggg ccggtggact atctgctggg taaagaccgg cagcgtgaag
     1981 gcgccaccgt cctgcagggg aagccggaag aagtccggga gctgattgac gcgtcgcctt
     2041 acgtgaagaa atacacctcc ggcgtcctgt cgtttgcgga ggccgatctc cctcccggcc
     2101 agcgggaaaa actgatggcc agcttcgagc gggttctgat gcccggactc gataaagatc
     2161 agtacagcat tctgtgggtg gagcacgcgg acaaggggcg tctggagctg aactttctga
     2221 tccccaatac cgagctgctg accggcaggc ggctccagcc ttactacgac cacgccgacc
     2281 ggccgcgcat cgatgcctgg cagactatcg tgaacgggag actggggctg cacgacccga
     2341 acgcgccgga aaaccgccgg gcgctggtca cgccgtccgg gctgccgaaa acgacgcagg
     2401 aggccgcaga agccattacc cggggactac tgagcttagc ctcgtccggg gagctgaaaa
     2461 gccgtcagga cgtcactgag gctcttgaag gtgcaggttt tgaggtggtg cgcaccacga
     2521 aaagcagtat cagcattgcc gacccggacg gggggcgaaa catccgactg aagggagcta
     2581 tctatgagca atctttttac ggcctcgagg gacttcgagg agaaattgaa agcgcagcag
     2641 cagagtaccg gcgagatgct gaaagccgca ttcagcgagc acgagcagtc tgtcagagcg
     2701 gaactgagcg caagcgcgag gagaatcagc gacgccatcc tcgcccacga gcagagtatg
     2761 agcgaggcga tggagaaaaa ccggcggagc gtactgcgga ctgccgggcg gacatggctc
     2821 accatcctga tggtgtcagc gctgctgatc ggcacgagcg ggagcattct gtggtggcag
     2881 gggcagcaga taaccgacaa ttacacgcat cttcgtcagc aggaagatac cctggcgaaa
     2941 atgaccgccc ggacgtgggg agtgcgctat caggagagca gcgacggccg gaggtttctt
     3001 atcctgccgc cggggatgca aaccgaagcc atcccttacg acgggacgac atggatccgc
     3061 ctgaaacagg agtagcggaa aatgacagag ctggaaaagc agttgctgag cgcattagag
     3121 cagctacagc aggactactc gcaaaggctg gacgaatggg agagcgcctt cgcggaatgg
     3181 cagagcatgt gtggtcttat gcaacgggag aacgcgatgc tgaacgagcg cgtgtcggac
     3241 ttgagcacgc aggtgctgag tttaagcgag cagctgcgcc gcttgtccgg gagctgaatg
     3301 ccatcgagct ccggcacagg gagcatgagt atcagaaaac actggagctg gagcaccagc
     3361 cgcagaaaac ctaccgtggc ccaacgctgg gctgacggcc cgtgacaaac cccaagaaga
     3421 agggctcata aatttcccgc taaatacggt cgtgatggaa acatcacagc gtatacaacg
     3481 gagggattat gagactgttt aacgtgattg agacggtgct gaactgcctg tacatggcgc
     3541 tggagatctg ggactggctg gagaagcact ttcctgtttt taaggcgttc gcgctgattt
     3601 tagtgtgact ttacgcggca tgcatctggc tgcatgacta tgcatcagtg taatatccag
     3661 cggctgcgtt tctggtgttt tttcgttatg tctgtcgcca ctttctcgcg tctggcaccg
     3721 gaaacgcagc caaccccgtt tcagcggtgc gggcaacgga tgttatggta aatgtagggg
     3781 gagaagtgac tataagcagg ggcttcggtg a
//
