LOCUS       CP082472                3133 bp    DNA     circular BCT 12-JAN-2022
DEFINITION  Salmonella enterica subsp. enterica serovar Typhimurium strain
            FSIS1607455 plasmid pF18S013-4, complete sequence.
ACCESSION   CP082472
VERSION     CP082472.1
DBLINK      BioProject: PRJNA292666
            BioSample: SAMN05661217
KEYWORDS    .
SOURCE      Salmonella enterica subsp. enterica serovar Typhimurium (Salmonella
            typhimurium)
  ORGANISM  Salmonella enterica subsp. enterica serovar Typhimurium
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Salmonella.
REFERENCE   1  (bases 1 to 3133)
  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 3133)
  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 3133)
  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                     :: F18S013
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 379x
            Sequencing Technology             :: PacBio Sequel
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI
            Annotation Date                   :: 09/02/2021 13:43:58
            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)                     :: 5,291
            CDSs (total)                      :: 5,168
            Genes (coding)                    :: 5,039
            CDSs (with protein)               :: 5,039
            Genes (RNA)                       :: 123
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 86
            ncRNAs                            :: 15
            Pseudo Genes (total)              :: 129
            CDSs (without protein)            :: 129
            Pseudo Genes (ambiguous residues) :: 0 of 129
            Pseudo Genes (frameshifted)       :: 51 of 129
            Pseudo Genes (incomplete)         :: 78 of 129
            Pseudo Genes (internal stop)      :: 23 of 129
            Pseudo Genes (multiple problems)  :: 20 of 129
            CRISPR Arrays                     :: 3
            ##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..3133
                     /organism="Salmonella enterica subsp. enterica serovar
                     Typhimurium"
                     /mol_type="genomic DNA"
                     /strain="FSIS1607455"
                     /serovar="Typhimurium"
                     /isolation_source="Animal-Turkey-Young Turkey"
                     /sub_species="enterica"
                     /db_xref="taxon:90371"
                     /plasmid="pF18S013-4"
                     /geo_loc_name="USA:VA"
                     /collection_date="2016"
                     /collected_by="USDA-FSIS"
     gene            complement(join(3054..3133,1..64))
                     /locus_tag="BGP52_026440"
     CDS             complement(join(3054..3133,1..64))
                     /locus_tag="BGP52_026440"
                     /inference="COORDINATES: ab initio prediction:GeneMarkS-2+"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GeneMarkS-2+."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="UAE45990.1"
                     /translation="MNTKVLFVKKALKSITCAILSLLPALSRAVTELRSLSAARLKAGK
                     SF"
                     /name="hypothetical protein"
     gene            complement(1016..1210)
                     /locus_tag="BGP52_026445"
     CDS             complement(1016..1210)
                     /locus_tag="BGP52_026445"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001041623.1"
                     /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="UAE45991.1"
                     /translation="MNKQQQTALNMAKFIKSQSLTLLEKLDSLDADAQAAMCEKLHELA
                     EELQNSIQTRFESESGTGE"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            1495..1818
                     /locus_tag="BGP52_026450"
     CDS             1495..1818
                     /locus_tag="BGP52_026450"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:NP_052604.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="nikA protein"
                     /protein_id="UAE45992.1"
                     /translation="MTKRSGSNTRRRAISRPVRLTAEEDQEIRKRAAECGKTVSGFLRA
                     AALGKKVNSLTDDRVLKEVMRLGALQKKLFIDGKRVGDREYAEVLIAITEYHRALLSRL
                     MAD"
                     /name="nikA protein"
     gene            2277..3029
                     /locus_tag="BGP52_026455"
     CDS             2277..3029
                     /locus_tag="BGP52_026455"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001127762.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="UAE45989.1"
                     /translation="MDTTSLISSISVPRLSFYETFLGCATDQEKVGAYVAYQDLSGDFF
                     CLVQMIEVALRNAINNTIKANHGPAWYDSIPQTKKSQDLVLNAKQKALDECGVRYTDDD
                     VICRLTFGFWVYMLDAPYRDTQRPCYIWTPENKAKTFPHAKNPLGGGDMKVKALFDEFH
                     KVLLFRNRLFHHEPIWKKHHCKSHSQAINNMLKEFNFLMNALSIVSNEKKELIEFIGHD
                     RRFYERCTIEYVMGIIGRIKCRELKVVG"
                     /name="hypothetical protein"
     Typing          1249..1486
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="99.167"
                     /coverage="99.0"
                     /evalue="2.15e-118"
     Typing          complement(269..718)
                     /name="rep_cluster_2358"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="88.494"
                     /coverage="90.0"
                     /evalue="1.02e-154"
     Typing          1496..1815
                     /name="MOBF"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="99.065"
                     /coverage="100.0"
                     /evalue="2.32e-62"
ORIGIN
        1 gcgaaagaat tgcgcaagta attgatttca aggctttttt cacaaaaaga actttagtat
       61 tcattttcat aatcctctat ttcttatgcc gttctaatgg cagcgttgac tttttattcc
      121 atctatttga atggttaatt ataccatatc tgacatcaaa tcttaaggat aaatagctga
      181 ttcacatcag tttttccatt aatccacaaa cttttataat ttaattgcgg atttccttga
      241 gttcatatcg cgcccatcgt aatcttaaaa acgaaaaaac cacccggcaa ggtggttttt
      301 cgaaggttca gcaaccggca agtttctgaa cctcggtaac tggcttaaga ggagcgcagt
      361 caccaaaact tgttcttcca gtttagcctt aactggcacg taacttcaag actaactcct
      421 ctaaatcagt taccagtggc tgctgccaat ggcgataagt cgtgcctttc cgggttggac
      481 tcaagacgat agttaccgga taaggcgcag tagtcggact gaacgggggg ttcgtgcata
      541 cagtccagct tggagcgaac tgcctacccg gaactgagtg tcaggcgtgg aatgagataa
      601 cgcggccata acagcggaat gacaccggta aaccgaaagg caggaacagg agagcgcacg
      661 agggagccat cagggggaaa cgcctggtat ctttatagtc ctgtcgggtt tcgccacctc
      721 tgacttgagc gtcgattttt gtgatgctcg tcaggggggc ggagcctatg gaaaaacgcc
      781 accggcgcgg cctttttcgg gttcttgttt tttgctcaca tgtttctttt ggcgttatcc
      841 cctgattctg tggataacct cattaccgtc tttgagtgag ctgataccgc tcgccgcagc
      901 cgaacgaccg agcgtagcga gttagtgagc gaggaagcgg aagagcgcct tatgtggtat
      961 tttctcctta cgcaccggta tatcgttctg catcctgtct ggtgtaggaa cactgttatt
     1021 ccccggtgcc actttccgat tcaaagcgtg tctgtatgct gttctggagt tcttctgcga
     1081 gttcgtgcag tttctcacac atggcggcct gtgcatcagc atcgagtgag tccagttttt
     1141 cgagcagcgt caggctctgg ctttttatga attttgccat gttaagtgcg gtttgctgct
     1201 gcttgttcat ctttctgttt tctccgttct gtctgtcatc tgcgtcgtgt gattatatcg
     1261 cgtaccactt ttcgacagtt ttgccgccgg tattctgccg tctgactctt tgacgggcat
     1321 ttctgcctga caatactgtc actgccaaaa aactgccgtg cctttgtcgg taattcgaac
     1381 ttgctgacag gacaggatgt gtaattgtta taccgcgcat acatgcgcgc tattacaatt
     1441 accctggtca gggcttcgcc ccgacacccc atgtcagata cggagccatg ttttatgaca
     1501 aaacgaagtg gaagtaatac gcgcaggcgg gctatcagtc gccctgttcg tctgacggca
     1561 gaagaagacc aggaaatcag aaaaagggct gctgaatgcg gcaagaccgt ttccggtttt
     1621 ttacgggcgg cagctctcgg taagaaagtt aactcactga ctgatgatcg ggtactgaaa
     1681 gaagttatga gactgggggc gttacagaaa aaactcttta tcgacggcaa gcgtgtcggg
     1741 gacagagagt atgcggaggt gctgatcgct attacggagt atcaccgggc cctgttatcc
     1801 aggcttatgg cagattagct tcccggagag aaactgtcga aaacagacgg tatgaacgcc
     1861 gtaaggcccc aaaccgatcg ccattcactt tcatgcatag ctatgcagtg agctgaaaac
     1921 ggtcctgacg catttttccg gttttcactg ggtaaaacat ctctttttgc ggtgtttgcg
     1981 gcagaatcgc gttcagcgcg ttttagcggt gcgcgtaagg ggagttatgg taaattggca
     2041 gcaaagtatt ttctgatgtt gtggattgtg aagagtattc aattcttatt atgaaacaat
     2101 aactataact ggttgtttca tatagataaa tataacaaaa aagcccactc tgtagtgggc
     2161 ttttttgtta tattttacgc tctagaggta cacagaaaaa cggtagttcg cctgctcctc
     2221 gaatgttgta atggtagtct gaaaaatatt catagtaaag agataagtga gttttcatgg
     2281 atacaacaag tttaattagc tcaatttctg taccaagatt atctttctat gaaacatttc
     2341 ttgggtgcgc tactgatcaa gaaaaggttg gggcatacgt tgcctaccaa gatctgtctg
     2401 gcgatttttt ttgtcttgtc cagatgattg aggttgctct gcgtaatgcg ataaacaata
     2461 caatcaaagc taatcatggg cctgcttggt acgactctat acctcaaaca aagaaatctc
     2521 aggatcttgt tttaaatgcg aaacaaaaag cgctagatga gtgtggcgta aggtatacgg
     2581 atgatgatgt tatttgccgt ctaacctttg gcttttgggt ttatatgtta gatgccccat
     2641 atagggatac gcaaaggccg tgctacatct ggactccaga gaacaaggca aaaacatttc
     2701 ctcatgcgaa gaatcctttg ggtggggggg atatgaaggt taaagcgttg tttgacgagt
     2761 ttcataaagt tcttttgttt aggaatcgac tttttcacca tgagcctatt tggaaaaaac
     2821 accactgcaa gtcgcatagt caagccataa ataatatgtt gaaagagttc aattttttaa
     2881 tgaatgcctt gagtatcgtc tctaacgaga aaaaggaact tattgagttt attgggcacg
     2941 ataggcgctt ttatgaacgc tgcacgatag agtatgttat ggggattata gggaggatta
     3001 agtgcaggga gcttaaggta gtcggttgac ttttaaggaa aaatgtgata caatcaaaag
     3061 ctcttaccgg ctttaagtcg cgcagccgaa aggctacgta actctgttac tgcgcgactt
     3121 aaagccggta aga
//
