LOCUS       CP082548                1749 bp    DNA     circular BCT 13-JAN-2022
DEFINITION  Salmonella enterica subsp. enterica serovar Typhimurium strain CVM
            N18S1634 plasmid pN18S1634-5, complete sequence.
ACCESSION   CP082548
VERSION     CP082548.1
DBLINK      BioProject: PRJNA292661
            BioSample: SAMN12360211
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 1749)
  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 1749)
  CONSRTM   NARMS: The National Antimicrobial Resistance Monitoring System
  TITLE     Direct Submission
  JOURNAL   Submitted (29-JUL-2019) Center for Veterinary Medicine, US Food and
            Drug Administration, 8401 Muirkirk Rd, Laurel, MD, USA
REFERENCE   3  (bases 1 to 1749)
  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                   :: 507x
            Sequencing Technology             :: PacBio Sequel
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI
            Annotation Date                   :: 08/30/2021 17:28:48
            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)                     :: 4,935
            CDSs (total)                      :: 4,813
            Genes (coding)                    :: 4,698
            CDSs (with protein)               :: 4,698
            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)              :: 115
            CDSs (without protein)            :: 115
            Pseudo Genes (ambiguous residues) :: 0 of 115
            Pseudo Genes (frameshifted)       :: 37 of 115
            Pseudo Genes (incomplete)         :: 78 of 115
            Pseudo Genes (internal stop)      :: 20 of 115
            Pseudo Genes (multiple problems)  :: 18 of 115
            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..1749
                     /organism="Salmonella enterica subsp. enterica serovar
                     Typhimurium"
                     /mol_type="genomic DNA"
                     /strain="CVM N18S1634"
                     /serovar="Typhimurium"
                     /isolation_source="Chicken Mixed Parts"
                     /sub_species="enterica"
                     /db_xref="taxon:90371"
                     /plasmid="pN18S1634-5"
                     /geo_loc_name="USA:SC"
                     /collection_date="2018"
                     /collected_by="FDA"
     gene            complement(42..1031)
                     /locus_tag="FQD83_000005"
     CDS             complement(42..1031)
                     /locus_tag="FQD83_000005"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_020240588.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="protein rep"
                     /protein_id="UAI38520.1"
                     /translation="MKNPELQNLTDYSPSDAPWDAHRSVSDDVGGIYLLAAEYERYGAR
                     MASCGGLLRFGWSTLKETGETRLRLREAHFCRVRHCPVCQWRRSLMWQARFYQSLPRIV
                     ADYPDSRWMFLTLTVRNCAIGELGDTLSRMNTAFQRLKDRKEFRPVQGWIRTTEVTRGS
                     DGSAHPHFHTLMMVPPGMLNGKSYVKHARWVELWRECLRVSYDPNVDVRAVKPRKPKDG
                     ESLACATAELVRGAVAETLKYSTKPADMVADPEWFLELTRQTHKRRFVATGGALKDVLK
                     LDQETDADMVIGDDISEGDDDGSRIAFEWKIEVKKYRRSPTKDKTESE"
                     /name="protein rep"
     Typing          125..314
                     /name="ColpVC"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="96.859"
                     /coverage="99.0"
                     /evalue="3.7200000000000003e-85"
ORIGIN
        1 gtcattttgc ggcgtttgcc ctatcctgca tcgcagtgtt tttactctga ttcggtttta
       61 tctttcgtcg gcgaacgccg gtattttttg acctcgattt tccactcgaa cgcgatgcgg
      121 gaaccgtcat catcgccctc ggaaatatca tccccgatca ccatgtcggc atcggtttcc
      181 tgatcgagtt tcaatacgtc tttgagtgcg ccgccggtcg ccacaaagcg gcgcttgtgc
      241 gtctggcggg tcagttcgag gaaccattca ggatcggcga ccatgtcggc cggcttcgtg
      301 gaatatttca gggtctcggc caccgcgccg cgcaccagtt cggcggtcgc gcaggccagc
      361 gattcgccgt ccttcggctt ccggggtttc actgcccgga catcgacatt cggatcgtag
      421 ctgacccgaa ggcactcccg ccacagctca acccagcgcg catgtttgac gtaactcttc
      481 ccgttaagca tgccaggcgg aaccatcatc agtgtgtgga agtgcgggtg tgcgctgccg
      541 tcactgccgc gggtgacttc cgtggtgcgg atccatccct gaactggtct gaactctttg
      601 cgatccttca gccgctggaa agccgtgttc atccggctca gcgtatcgcc cagctccccg
      661 atcgcacagt tgcgcacggt cagggtcagg aacatccagc gggaatcggg gtaatccgcc
      721 acgatacgcg gcagggactg gtagaaacgg gcttgccaca tcagggagcg cctccactgg
      781 cagacaggac agtgccggac acggcagaaa tgcgcctcac gcagcctcag gcgcgtttct
      841 ccggtttctt tgagggtaga ccacccgaaa cgcagtaaac cgccgcagga ggccatacgc
      901 gccccgtagc gctcatattc ggccgcaagc aggtaaatcc ctcccacgtc gtcagaaacg
      961 cttctgtgag cgtcccaggg cgcatctgag ggggaatagt ccgtgaggtt ctggagttca
     1021 ggatttttca tgcgcaccgc cccatactgg gcgatggctc acttgacgtg ttatcattgc
     1081 cgtatcacct gtgttgtctg tcgcaaaata gaattcctac aggtggtcac gcccccgaac
     1141 gatggccgtc gttgcggggg tcgcttttaa cgcgaccact cccgacagaa taacttcaaa
     1201 gtcattttca ggcaaatcac gctgaaaccc ttgcggcaca agggctgagg cttattttta
     1261 acgccagagt tatcccttaa gtataaatac aaggaacgcg cgcgattttt ttgcccccaa
     1321 aatccacgtt aaatcggacc ccacaaaccc caaaaacgct tatcaggtgg ttgcgctcac
     1381 tgcgtgatca caaccacctg tcggcagtgt tttacgggtg cgctcgtcaa tcactaaatc
     1441 ggaacccact ggcaagccag cgggacccca cgatttagcg tttgacgatt tcaggaacgg
     1501 cgaacgctgg cagattttaa tctggcggcg tgaggtgttg gcagggtgtc ggggcgcagc
     1561 cctgaccaag atattttgga ctgtccgtcg cgtgtcggcg gtactccaaa aacacatctt
     1621 gtcccgtgcg ttttgtatta ccgccatcac gatggccgca atccaaaacc ccaggtcagg
     1681 gcgcagcccc gacaccccag agccgactgc aggtcactgg gcgaacgcgg cggaatgatg
     1741 tcggatgac
//
