LOCUS       CP082420                3830 bp    DNA     circular BCT 11-JAN-2022
DEFINITION  Salmonella enterica subsp. enterica serovar 4,[5],12:i:- strain
            FSIS11704067 plasmid pF18S032-3, complete sequence.
ACCESSION   CP082420
VERSION     CP082420.1
DBLINK      BioProject: PRJNA292666
            BioSample: SAMN07608142
KEYWORDS    .
SOURCE      Salmonella enterica subsp. enterica serovar 4,[5],12:i:-
  ORGANISM  Salmonella enterica subsp. enterica serovar 4,[5],12:i:-
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Salmonella.
REFERENCE   1  (bases 1 to 3830)
  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 3830)
  CONSRTM   NARMS: The National Antimicrobial Resistance Monitoring System
  TITLE     Direct Submission
  JOURNAL   Submitted (02-JUL-2019) Center for Veterinary Medicine, US Food and
            Drug Administration, 8401 Muirkirk Rd, Laurel, MD, USA
REFERENCE   3  (bases 1 to 3830)
  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                     :: F18S032
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 956x
            Sequencing Technology             :: PacBio Sequel
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI
            Annotation Date                   :: 09/02/2021 13:06:25
            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)                     :: 5,213
            CDSs (total)                      :: 5,092
            Genes (coding)                    :: 4,974
            CDSs (with protein)               :: 4,974
            Genes (RNA)                       :: 121
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 86
            ncRNAs                            :: 13
            Pseudo Genes (total)              :: 118
            CDSs (without protein)            :: 118
            Pseudo Genes (ambiguous residues) :: 0 of 118
            Pseudo Genes (frameshifted)       :: 39 of 118
            Pseudo Genes (incomplete)         :: 83 of 118
            Pseudo Genes (internal stop)      :: 17 of 118
            Pseudo Genes (multiple problems)  :: 19 of 118
            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..3830
                     /organism="Salmonella enterica subsp. enterica serovar
                     4,[5],12:i:-"
                     /mol_type="genomic DNA"
                     /strain="FSIS11704067"
                     /serovar="4,[5],12:i:-"
                     /isolation_source="animal-swine-market swine"
                     /sub_species="enterica"
                     /db_xref="taxon:440524"
                     /plasmid="pF18S032-3"
                     /geo_loc_name="USA:MN"
                     /collection_date="2017"
                     /collected_by="USDA-FSIS"
     gene            25..213
                     /locus_tag="CLN51_026055"
     CDS             25..213
                     /locus_tag="CLN51_026055"
                     /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="UAF06118.1"
                     /translation="MTKQESAALNMAKFIRAQSLLLLEKLDVLDLDDEAADCERMHEQA
                     EALYQKLSARFGIQDGE"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            complement(261..461)
                     /locus_tag="CLN51_026060"
     CDS             complement(261..461)
                     /locus_tag="CLN51_026060"
                     /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="UAF06120.1"
                     /translation="MNLCPDERLLFVRMISAMLRRSGGDAGAVMFEAYRHIVSDTNQAR
                     RSCMLDLLESVRHDYVHGGYT"
                     /name="hypothetical protein"
     gene            1661..3565
                     /locus_tag="CLN51_026065"
     CDS             1661..3565
                     /locus_tag="CLN51_026065"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_003839290.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="nitrate- and nitrite sensing domain-containing
                     protein"
                     /protein_id="UAF06119.1"
                     /translation="MSWAYRISMQMKLFIALFPLLLALVWFAGSGIVSRINTEQQMNTI
                     GQLTTLARSAGDVVHQLQSERGMSAGFIGARGQKFRDDLAAQRQLTDKVLATFKRLLTD
                     TNKDLLQGNIAAPLKTFNESIQFLDSTRTAISELTIDSPKASQFYTQTISDVLKFVGGM
                     GHLSTSGSMVNELAAYYSLLNLKEQAGVERALLSNIFSMDRFDDGQFSMFSDVVGQQDA
                     WLTAARSFSTPVQAAELDKSLQSAEATRALELRETAFNKAAEGGFGVNPTDWFNLQTQR
                     IETLQKVENRAVDALQEHAALLAHNARVDWQSFLVISLVALLIAIAFAVMVARSIQQQL
                     NGTLKTIAEMDGDLTRRLDVPGSDELSALNRAYNQAIENIQHIVQEIKSGAVVLRSASS
                     DIAAGNQDLAQRTDEQAASIVETAASMEQISTAITQTADNASEAERLIHSMERDVLEAN
                     RVSNEASQSMAEIRSSSEQISQIVASIDEISFQTNLLALNAAVEAARAGELGKGFAVVA
                     TEVRNLSQRCAREASQIRELINQNMDKIGEGVARVTASGTALKAAAENTGRMKQYVSDI
                     ARAANEQSLGVSQVHQALNQLEQVTQQNAALVSQAASASQMLDGQSEAMSTLVDRFIV"
                     /name="nitrate- and nitrite sensing domain-containing
                     protein"
     Typing          complement(672..844)
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="90.805"
                     /coverage="100.0"
                     /evalue="4.41e-59"
     Typing          769..1353
                     /name="rep_cluster_2335"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="91.709"
                     /coverage="97.0"
                     /evalue="0.0"
ORIGIN
        1 accataaaac cgggaaaaag ccgtatgaca aaacaggaat cagccgcact gaacatggca
       61 aaatttatcc gggcgcagtc gctgctgctg ctcgaaaaac tcgacgtgct cgatcttgat
      121 gacgaggcag ccgactgtga gcgaatgcac gaacaggcag aagcgcttta tcagaagctg
      181 agcgcacgct tcggtataca ggacggcgaa taaagagacg aaaagaacgc tcacttagac
      241 gaaaagcgta tccagggcaa ctatgtatat ccaccgtgta catagtcatg cctgacgctt
      301 tcgagcaggt cgagcatgca ggaacgacga gcttgattgg tatcggacac aatatggcga
      361 tacgcctcaa acataacagc acccgcatca ccgcccgaac ggcgaagcat agcggaaatc
      421 atccgcacaa agagcagacg ttcatcgggg caaaggttca taagttctcc tggtgaaaaa
      481 ccaaacatga agcacccatc tattaacgtc agctgtgaac gcttcattac gcttcattaa
      541 aataggtaaa cccgggaaaa agatccaaac gttaacatca caggtaaaca gaaacgtcgg
      601 gtcgatcggg aaattctttc ccggacggcg cggggttggg caagccgcag gcgcgtcagt
      661 gcttttagcg ggtgtcgggg cgcagccctg aaccagtcac gtaacgctag cggagtgtat
      721 actggcttat tatgtaggca cgggtgcggg aatcagtgaa gtgcttcatg tggcaggagg
      781 aaaatgcagc agcagagcgt aagcggaata tatgagacag gagatattcc gcttcctcgc
      841 tcactgactc gctgcgctcg gtcgttcggc tgcggcgagc ggtgcgggat tacgaatggg
      901 gcggaaattt cctgggagat gccaggaaga aacttaacag ggaaacggta aggccgcggc
      961 gaagccgttt ttccataggc tccgcccccc tgacaagcat cacgaaatct gacgctcaaa
     1021 tcagtggcgg cgaaacccga caggactata aagatcccag gcgtttcccc ctggtagctc
     1081 cctcgtgcgc tctcctgttc ctgcctttcg gtttaccggt gtcattccgc tgttatggcc
     1141 gcgtttatct cattccacgc ctgacactca gttccgggaa ggcagttcgc tccaagctgg
     1201 actgtatgca cgaacccccc gttcagtccg actgctgcgc cttttccggt aactatcgtc
     1261 ttgagtccaa cccggaaaga cacgaaaaat cgccactggc agcggccact ggtaaacagg
     1321 atgtgcgaga gatgtatcga gagttcttga agtagtggcc tgactgaggc tacactagaa
     1381 ggacaaattt ggtgacatgt ctcgcacaag actgttacca cggttagaga atctgccagg
     1441 attatctaac cttcgaaaaa ccacctgcaa gggtggtttt ttcgtttaca gagcaagaga
     1501 ttacgacgat cgtcaaagga tctcaagaag atcctttatg gattgctacc agcgccactg
     1561 ccgaatgtgg tgcccgttcc cccaacaata aactataaag tttatgcatg tatctaccga
     1621 tactcctgcg atccctcaag aaagtaagga aagtatcgat atgtcatggg cttatcgtat
     1681 ttcaatgcaa atgaagttgt ttattgcatt attcccgcta ctgcttgcct tggtctggtt
     1741 cgccggttcg ggtattgtca gccgtatcaa taccgaacag cagatgaaca ccattggaca
     1801 gctcaccacg ctcgcccgca gcgcgggtga tgtggtgcat caactccaga gcgaacgtgg
     1861 aatgagcgct ggatttatcg gcgcgcgcgg ccaaaagttt cgcgatgact tagctgccca
     1921 gcggcagtta accgacaagg tgctggcaac atttaagcgg ttgctgaccg atacgaataa
     1981 ggatttactc cagggaaata ttgccgcccc cctgaaaacg tttaatgaaa gtattcagtt
     2041 tctcgactca acccgtaccg ccatcagcga attaactatc gattcaccaa aagcgagtca
     2101 gttctatacc caaaccatct ctgacgtgct gaagtttgtc ggcgggatgg ggcatttaag
     2161 cacctcaggc tcgatggtga acgaactggc ggcttattat agtctcttga atttgaagga
     2221 gcaggctggt gtagaacgtg cgctgctgtc caatatcttc tcgatggatc gctttgacga
     2281 cggccagttc agcatgttta gcgatgtggt aggccagcag gatgcctggc tgacggcagc
     2341 tcgcagcttt agcacacctg tgcaggcggc tgagctggac aaatctcttc agtccgctga
     2401 agcaactcgt gctcttgaac tgcgggagac ggcttttaat aaagccgccg aaggcggatt
     2461 tggagtcaac ccgactgact ggtttaacct tcagacccag cgtattgaaa cgctgcaaaa
     2521 ggtggaaaat cgcgcggtgg atgccttgca ggaacatgct gcgctgcttg cccacaatgc
     2581 ccgtgtcgac tggcagtcct tcctggtaat cagcctggtt gccctactga ttgctatcgc
     2641 ctttgcggtg atggtggcac gcagtatcca gcagcaactg aacggtacgc tgaaaaccat
     2701 cgcagagatg gacggcgacc tgacacgtcg tcttgacgtc cccggcagcg acgagctctc
     2761 agccctgaac cgtgcctata accaagcgat tgagaatatt cagcatatcg tgcaagaaat
     2821 taagtccggt gcggtggtgt tgcgtagcgc cagtagtgat atcgctgccg gtaatcagga
     2881 tctggcccag cgtacggatg aacaggcggc atcgattgtg gaaacggccg ccagcatgga
     2941 gcagatttct actgcgatca cccagaccgc cgataacgcc agcgaggcgg agcgtctgat
     3001 acattcgatg gagcgggacg tactggaagc taatcgcgtc tctaacgagg ccagtcagag
     3061 catggcggaa attcgttctt ccagcgagca gatttcccag attgttgcgt caattgatga
     3121 gatttctttc cagaccaact tgctggcgct taacgccgcc gttgaagcgg cacgtgccgg
     3181 tgagcttggc aaaggctttg cggtagtggc gacggaggtg cgtaaccttt cccagcgctg
     3241 tgcacgagag gccagtcaga tccgtgagct gattaaccag aatatggata agattggcga
     3301 aggggtagca cgagtcaccg cgtccggcac cgcgctgaaa gcagcggcgg aaaataccgg
     3361 gcggatgaaa cagtacgtga gcgatattgc ccgtgcggcg aatgagcagt cgcttggcgt
     3421 gtcgcaggtg catcaggcac tgaatcagct ggagcaggtc actcagcaaa acgcagcgct
     3481 ggtctctcag gcggcgagcg ccagccagat gctggacggc cagtctgaag cgatgtccac
     3541 gctggtcgat cgctttattg tctgatactg ccgttcagca tccggtcttg ataacttaca
     3601 atcagaaaaa accgcctaaa aggcggcttt tttatgcctg caaataacta ggatttacca
     3661 taactcccgt tgcgtgcacc gcctgagagg ctctgagagc gtttctgagg actccgacct
     3721 gaaacataca cctttctgtg cccatatcga gaaaaaacgc ccctgatgat ttctgcgtac
     3781 ctgcatggct atgcactcaa gtgaatgaag taagatttca gtctgcgatc
//
