LOCUS       CP082676                3257 bp    DNA     circular BCT 09-SEP-2021
DEFINITION  Salmonella enterica subsp. enterica serovar Typhimurium strain CVM
            N18S0645 plasmid pN18S0645-4, complete sequence.
ACCESSION   CP082676
VERSION     CP082676.1
DBLINK      BioProject: PRJNA292661
            BioSample: SAMN11968052
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 3257)
  AUTHORS   Li,C., Tyson,G., Hsu,C.-H., Harrison,L., Strain,E., Tran,T.-T.,
            Tillman,G., Dessai,U., McDermott,P. and Zhao,S.
  TITLE     Long-read sequencing reveals evolution and acquisition of
            antimicrobial resistance and virulence genes in Salmonella enterica
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 3257)
  CONSRTM   NARMS: The National Antimicrobial Resistance Monitoring System
  TITLE     Direct Submission
  JOURNAL   Submitted (06-JUN-2019) Center for Veterinary Medicine, US Food and
            Drug Administration, 8401 Muirkirk Rd, Laurel, MD, USA
REFERENCE   3  (bases 1 to 3257)
  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
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 345x
            Sequencing Technology             :: PacBio Sequel
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI
            Annotation Date                   :: 09/01/2021 10:44:50
            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)                     :: 4,885
            CDSs (total)                      :: 4,763
            Genes (coding)                    :: 4,641
            CDSs (with protein)               :: 4,641
            Genes (RNA)                       :: 122
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 85
            ncRNAs                            :: 15
            Pseudo Genes (total)              :: 122
            CDSs (without protein)            :: 122
            Pseudo Genes (ambiguous residues) :: 0 of 122
            Pseudo Genes (frameshifted)       :: 43 of 122
            Pseudo Genes (incomplete)         :: 79 of 122
            Pseudo Genes (internal stop)      :: 23 of 122
            Pseudo Genes (multiple problems)  :: 20 of 122
            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..3257
                     /organism="Salmonella enterica subsp. enterica serovar
                     Typhimurium"
                     /mol_type="genomic DNA"
                     /strain="CVM N18S0645"
                     /serovar="Typhimurium"
                     /isolation_source="Chicken Legs"
                     /sub_species="enterica"
                     /db_xref="taxon:90371"
                     /plasmid="pN18S0645-4"
                     /geo_loc_name="USA:PA"
                     /collection_date="2018"
                     /collected_by="FDA"
     gene            complement(42..338)
                     /locus_tag="FH358_023330"
     CDS             complement(42..338)
                     /locus_tag="FH358_023330"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000609270.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="HigA family addiction module antidote protein"
                     /protein_id="UAH78657.1"
                     /translation="MINLVDPVHPGVFIREMFMEPFEISAADLSEKLHVSPSTLSRVLN
                     GKADLSVEMALRLSRVLGRSAESWINMQTQYSLNASRKSPNVIKELDELVPIF"
                     /name="HigA family addiction module antidote protein"
     gene            683..964
                     /locus_tag="FH358_023335"
     CDS             683..964
                     /locus_tag="FH358_023335"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000586174.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="type II toxin-antitoxin system RelE/ParE family
                     toxin"
                     /protein_id="UAH78658.1"
                     /translation="MIINIKHKGLRKFAETGNNAGIPQQFTQRLKLILTALSTATNLQD
                     MMDLKALRCHPLKGDRQGEYSLEVNGNWRVVFKLEEPNVFDVDLEDYH"
                     /name="type II toxin-antitoxin system RelE/ParE family
                     toxin"
     gene            2108..2302
                     /locus_tag="FH358_023340"
     CDS             2108..2302
                     /locus_tag="FH358_023340"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001041627.1"
                     /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="UAH78656.1"
                     /translation="MNKQQQTALNMARFIKSQSLTLLEKLDALDADEQAAMCERLHELA
                     EELQNSIQVRFETESKTGT"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            2956..3068
                     /locus_tag="FH358_023345"
                     /pseudo=""
     CDS             2956..3068
                     /locus_tag="FH358_023345"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_007772075.1"
                     /note="frameshifted; Derived by automated computational
                     analysis using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="replication initiation protein"
                     /name="replication initiation protein"
     Typing          complement(1594..1842)
                     /name="MOBF"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="97.2"
                     /coverage="86.0"
                     /evalue="4.37e-116"
     Typing          complement(1974..2072)
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="98.0"
                     /coverage="100.0"
                     /evalue="1.35e-41"
     Typing          complement(2376..2458)
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="3.79e-36"
     Typing          2471..3025
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="94.434"
                     /coverage="99.0"
                     /evalue="0.0"
ORIGIN
        1 tcaagacaga aaaaggccgc atatagcggc cttttctttt ctcaaaatat aggaaccaat
       61 tcatctaatt ccttaatgac attaggtgac ttcctgctcg cgttaagact gtattgagtc
      121 tgcatgttta tccacgactc ggcactgcga ccaagaactc gagaaagcct taatgccatc
      181 tcaacactta aatcagcttt tccattcagc actctactta gagtggaagg tgatacatgc
      241 agtttttcag acaggtccgc ggctgatatt tcaaacggtt ccataaacat ctcacggata
      301 aaaacccctg gatgtactgg atcgacaaga ttaatcatac cttcctctga agcctatatt
      361 agttttaaaa agataggcct attgcgtttt cagattgcgc attgcgcata acgcaactca
      421 ttgttgacta aaaaaaagaa tgacattatg atgcacattg gtgcgtctaa tcattcctta
      481 tgatgtgggt acttgatgtg aaattcaagg ccccggcatt gtacagcgca tcaaaccaat
      541 gtcaacagat taaaatgcga cttggttaag taaaacctac gtcatttatt caaatagagc
      601 aaggggtttg caatggaaat acggatgaac cggaaaaata aactgcgatg tttctatcta
      661 aacaaatatg ggatggtgat taatgatcat aaatatcaag cataaaggtt tgcgtaagtt
      721 tgccgaaaca ggtaacaacg caggaattcc gcaacagttt actcaacgtc tgaagctgat
      781 cctaacagcc ttaagcacag cgacgaactt gcaggatatg atggatttaa aggcattgcg
      841 ctgccatcca ttgaagggag accgtcaagg agagtattcg ttagaggtca atggaaactg
      901 gcgcgtagtg tttaagctcg aagaacctaa cgtctttgac gtggatctcg aggattatca
      961 ctaagaaggt ccttaaagca tcaaagtgac agtatcgatg ctttagggtc tcataaaaaa
     1021 gcaaaacctc ggggtaagtt atatgaagta ttttctgtac cagatagtcc ctatagcagc
     1081 catcattagc gcagcaattc tagcgctaaa aggtatcaat ggctgggggt ggttcttaac
     1141 tgttgggttc ctgcttgcag gggcagatac agtaaaggct cagttatcta agtagtaata
     1201 aacactatca atagtggttg gataattgcc aaaaaagcct ctatctgttc tgaaacagac
     1261 aacaaggaaa aatcggtgta agccacctcc ataggaggtg gtattgatat caacatagat
     1321 aaaaccatcc cgtaaatcac agcatttacc ataacgtcgc attacgcgca ccgctaaaac
     1381 gcgctgaacg cgattctgcc gcgaacaccg caaaaagaga tgttttacca agcgaaaacc
     1441 ggaaaaatgc gtcaggatcg ctttcagctc actgcatagc tatgcatgaa agtgaatggc
     1501 gatcggtttg ggcgcatacg gtgcccatga gacacatttt cggacatttt cagttcgtga
     1561 atccctgact cattgctaca tatctgaaca gacaccccta gcagcgcccc caggggcgtc
     1621 ctgtaaaaaa acacaccgcg ccgctagcag cacccctaat ataaaatgat gttttttatg
     1681 aaaatagtca gtaccacccc taaaaagcgg tgttggcgca gctacaacac cgcgccgaca
     1741 ccgctttttt aaatatcaca aagagagcaa gaagaactaa tttgtcataa ctctctattt
     1801 ataaagaaaa atcagcaaaa aattgttttt gcgtggggtg tgagcatttc aggcatgaga
     1861 acagactcgc gtttttccgg agtatcagcg gaattattga ttaagaaaca ctcgacgcag
     1921 agcgaaattt tatgcaacag cggctgcact gcacagggat tatttatcag ttgatatgct
     1981 gtgccatgat acgtcctaaa gaaacaggac aggatgtgca attgtaatac cgtcgcccgc
     2041 aacgtcttac aattaccacc tgctcagggt ccccccgaca cccggaactg acggagaaca
     2101 acggaaggtg aacaaacaac aacaaactgc gctgaatatg gcgcgattta tcaaaagcca
     2161 gagcctgaca ctgcttgaaa aactggatgc tctggatgcc gacgaacagg cggccatgtg
     2221 cgaacgactg cacgaactcg cggaagaact ccagaacagc atccaggttc gctttgagac
     2281 cgaaagtaaa acaggaacat aacgaagctg acggaggcgc tcacggcttg tccgcgagcg
     2341 ttttcggcag cagacaagcc cgccagggcg cgtcagcggg tgtcggggcg aagccctgac
     2401 ccagtcacgt agcgatagcg gagtgtatac tggcttaact atgcggcatc agtgcagatt
     2461 gtatgaaaag tgccccatgc cgggtgtgaa attccgcaca gatgcgtaag gagaaaatgc
     2521 gcgtccaggc gcttttccgc ttcctcgctc actgactcgc tacgctcggt cgttcggctg
     2581 cggcgagcgg tactgactta cacaaaaacg gcagcacggt tatctacaga atcaggggat
     2641 aaggccggaa agaacatgtg agcaaaagac caagaacagg aagaaggccg cgccgcaggc
     2701 gtttttccat aggctccgcc cccctgacga gcatcacaga aatcgacgct caagtcagag
     2761 gtggcgaaac ccgacaggac ttaaagatac cagacgtttc cccctggtgg ctccctcgtg
     2821 cgctctcctg ttccgaccct gccgcttacc ggatacctgt ccgcctttct cccttcggga
     2881 agcgtggcgc tttctcatag ctcacgctgt aggtatctcg gttcagtgta ggtcgttcgc
     2941 tccaagctgg gctgtgtgca cgaacccccc gttcagcccg accgctgcgc cttatccggt
     3001 aactatcatc ttgagtccaa cccggaaaga catgcaaaac accattggca gcagccactg
     3061 gtaactgatt tagaggagtt agtcttgaag ttatgcgcca gttaaggcta aactgaaaga
     3121 acaagttttg gtgactgcgc tcctccaagc cagttaccct ggttcagaaa cttgccggtt
     3181 actgaacctt cgaaaaaacc accttgccgg gtggtttttt cgtttacgag aaacgatacg
     3241 atccagttgc ctgagag
//
