LOCUS       CP082746                2096 bp    DNA     circular BCT 09-SEP-2021
DEFINITION  Salmonella enterica subsp. enterica serovar Typhimurium var. 5-
            strain CVM N16S070 plasmid pN16S070-6, complete sequence.
ACCESSION   CP082746
VERSION     CP082746.1
DBLINK      BioProject: PRJNA292661
            BioSample: SAMN08113949
KEYWORDS    .
SOURCE      Salmonella enterica subsp. enterica serovar Typhimurium var. 5-
  ORGANISM  Salmonella enterica subsp. enterica serovar Typhimurium var. 5-
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Salmonella.
REFERENCE   1  (bases 1 to 2096)
  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  JOURNAL   Unpublished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 2096)
  CONSRTM   NARMS: The National Antimicrobial Resistance Monitoring System
  TITLE     Direct Submission
  JOURNAL   Submitted (27-JUL-2018) Center for Veterinary Medicine, US Food and
            Drug Administration, 8401 Muirkirk Rd, Laurel, MD, USA
REFERENCE   3  (bases 1 to 2096)
  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                   :: 671x
            Sequencing Technology             :: PacBio Sequel
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI
            Annotation Date                   :: 08/31/2021 18:30:13
            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)                     :: 4,994
            CDSs (total)                      :: 4,872
            Genes (coding)                    :: 4,744
            CDSs (with protein)               :: 4,744
            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)              :: 128
            CDSs (without protein)            :: 128
            Pseudo Genes (ambiguous residues) :: 0 of 128
            Pseudo Genes (frameshifted)       :: 42 of 128
            Pseudo Genes (incomplete)         :: 85 of 128
            Pseudo Genes (internal stop)      :: 24 of 128
            Pseudo Genes (multiple problems)  :: 20 of 128
            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..2096
                     /organism="Salmonella enterica subsp. enterica serovar
                     Typhimurium var. 5-"
                     /mol_type="genomic DNA"
                     /strain="CVM N16S070"
                     /serovar="Typhimurium var. 5-"
                     /isolation_source="chicken breast"
                     /sub_species="enterica"
                     /db_xref="taxon:1620419"
                     /plasmid="pN16S070-6"
                     /geo_loc_name="USA:NM"
                     /collection_date="2016"
                     /collected_by="FDA"
     gene            complement(75..1064)
                     /locus_tag="CWX32_024970"
     CDS             complement(75..1064)
                     /locus_tag="CWX32_024970"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001362017.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="protein rep"
                     /protein_id="UAG07362.1"
                     /translation="MKNPDLQNLTDYSPSDAPWDAHRSVSDDVGGIYLLAAEYERYGAR
                     MALCGGLLRFGWSTLKETGETRLRLREAHFCRVRHCPVCQWRRSLMWQARFYQSLPRIV
                     ADYPDARWMFLTLTVRNCAIGELGEMLNRMNAAFQRMKVRKEFRPVQGWIRTTEVTRGS
                     DGSAHPHFHTLMMVPPGMLNGKSYVRHERWVELWRECLRVDYDPNVDVRAVKPRKPKGG
                     ESLACATAELVRGAVAETLKYSTKPADMVADPEWFLELTRQTHKRRFVATGGALKDVLK
                     LDQETDADMVIGDDISEGDDDGSRIAFEWKTEVRKYRRSPTKDKTESG"
                     /name="protein rep"
     Typing          158..349
                     /name="ColpVC"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="98.964"
                     /coverage="100.0"
                     /evalue="6.14e-93"
ORIGIN
        1 tgtgtaattg taataccgtc acacgcgacg ctatcacaat tgccatctgg tcaggggtgc
       61 accccgacac cccgctagcc tgattcagtt ttatctttcg tcggtgagcg acggtacttt
      121 ctgacctcgg ttttccactc gaacgcgatt cgtgaaccgt catcgtcgcc ctcggaaata
      181 tcatcaccga tcaccatgtc ggcgtcagtt tcctgatcga gtttcagcac gtctttgagt
      241 gcgccgccgg tcgccacaaa gcggcgcttg tgcgtctggc gggtcagttc gaggaaccat
      301 tcaggatcgg ccaccatgtc agccggcttc gtggaatatt tcagggtttc ggccaccgca
      361 ccgcgcacca gttcggcggt cgcgcaggcc agcgattcgc cgcccttcgg cttacgaggt
      421 ttcactgccc ggacatcaac attcgggtca taatcgaccc gcagacactc ccgccagagt
      481 tcaacccagc gttcatgcct gacgtaactt ttcccattta gcatgccagg cggcaccatc
      541 atcagggtgt ggaagtgcgg gtgtgcgctg ccgtcgctcc cgcgggtgac ttccgtggta
      601 cgtatccagc cctgcacagg ccggaactcc ttgcgaacct tcatgcgctg aaaagctgca
      661 ttcatccggt tcagcatctc gcccagctcc ccgatcgcac agttgcgcac ggtcagagtc
      721 aggaacatcc agcgggcatc gggataatcc gccacgatac gcggcaggga ctggtagaaa
      781 cgggcttgcc acatcaggga gcgcctccac tggcagacag gacaatgccg gacacggcag
      841 aaatgcgcct cacgcagcct cagacgcgtt tctccggttt ccttgagggt agaccacccg
      901 aaacgcagta aaccaccaca gagggccata cgcgccccgt agcgctcata ttcggctgca
      961 agcaggtaaa tccctcccac gtcatcagaa acgcttctgt gagcgtccca gggcgcatct
     1021 gagggggaat agtccgtgag gttctggaga tcagggtttt tcatgcgcac cacccgatag
     1081 tgggcgatgg ctcatctgac gtgttatcat tgccatatca cctgttgtgt tagtcgtatc
     1141 accaattcga attcctacag gtggtcacac ccccgaacga ttgccctcgt tgcgggggtc
     1201 gcttttaatg cgaccactcc cgacagaata actccaaaac cattttccga caaatccccc
     1261 ttcaggcctt gcggcacaag ggctggaggc gaatttgaat cctagagtta tcccttaagt
     1321 ataaatacaa ggatcgcgcg cgagattcgc ttgaattttg agcgggattt tcagtaaccc
     1381 aaaacaccca accccaccca cttacaccca tctcatccac agactttcac cccgattttg
     1441 tgaacaacaa aaaaaaccgt cttgcaggtg gttggcctca ctgcgtgaca ccaaccacca
     1501 tccccagtgt ttttcccgtg ccgtcgtcaa tcacaaaatc ggaacccacg ccggaggcgc
     1561 gggcccccgc gattttctgt ttgacgaatc agggaacggt gaacggtacg cggaattttt
     1621 tcgcgttccg tgaggcgttg gcggggtgtc ggggcgcagt cctgaccagg ttcgtagaac
     1681 cgcacagggt tgcaaagggg tgtccccttt ggcacaagcg acggagcgaa acgccccgtt
     1741 ttgtgtacgc cgcttatcgt gcctgtgttt taggagaaca aaaaaatgcc gtgcatacag
     1801 cccacacaat gacccacata atcacccaca actcaaaaca cacagcccac acaatcaccc
     1861 acactttaac ccacaaaaaa gaccacaacc ccattgacac cccacaaaac aacccacaca
     1921 aacggcgagt aaatcatttt gccgttttcg tgccgcagcc gttccgcgca atcgacaaac
     1981 tggcagtcag ggaatctcac gaagtgcgca cttatacaaa ctcaccttag gttcgtttgt
     2041 cgtgcggtct gcgacgctca aaaaaccgag aaacggcggg aattttcggg acagga
//
