LOCUS       CP082678                2096 bp    DNA     circular BCT 09-SEP-2021
DEFINITION  Salmonella enterica subsp. enterica serovar Typhimurium strain CVM
            N18S0645 plasmid pN18S0645-6, complete sequence.
ACCESSION   CP082678
VERSION     CP082678.1
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 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  JOURNAL   Unpublished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 (06-JUN-2019) 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                   :: 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..2096
                     /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="pN18S0645-6"
                     /geo_loc_name="USA:PA"
                     /collection_date="2018"
                     /collected_by="FDA"
     gene            join(2022..2096,1..915)
                     /locus_tag="FH358_023370"
     CDS             join(2022..2096,1..915)
                     /locus_tag="FH358_023370"
                     /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="UAH78663.1"
                     /translation="MKNPDLQNLTDYSPSDAPWDAHRSVSDDVGGIYLLAAEYERYGAR
                     MALCGGLLRFGWSTLKETGETRLRLREAHFCRVRHCPVCQWRRSLMWQARFYQSLPRIV
                     ADYPDARWMFLTLTVRNCAIGELGEMLNRMNAAFQRMKVRKEFRPVQGWIRTTEVTRGS
                     DGSAHPHFHTLMMVPPGMLNGKSYVRHERWVELWRECLRVDYDPNVDVRAVKPRKPKGG
                     ESLACATAELVRGAVAETLKYSTKPADMVADPEWFLELTRQTHKRRFVATGGALKDVLK
                     LDQETDADMVIGDDISEGDDDGSRIAFEWKTEVRKYRRSPTKDKTESG"
                     /name="protein rep"
     Typing          918..999
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="93.976"
                     /coverage="90.0"
                     /evalue="3.4000000000000004e-27"
     Typing          complement(642..833)
                     /name="ColpVC"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="98.964"
                     /coverage="100.0"
                     /evalue="6.14e-93"
ORIGIN
        1 tctgatgacg tgggagggat ttacctgctt gcagccgaat atgagcgcta cggggcgcgt
       61 atggccctct gtggtggttt actgcgtttc gggtggtcta ccctcaagga aaccggagaa
      121 acgcgtctga ggctgcgtga ggcgcatttc tgccgtgtcc ggcattgtcc tgtctgccag
      181 tggaggcgct ccctgatgtg gcaagcccgt ttctaccagt ccctgccgcg tatcgtggcg
      241 gattatcccg atgcccgctg gatgttcctg actctgaccg tgcgcaactg tgcgatcggg
      301 gagctgggcg agatgctgaa ccggatgaat gcagcttttc agcgcatgaa ggttcgcaag
      361 gagttccggc ctgtgcaggg ctggatacgt accacggaag tcacccgcgg gagcgacggc
      421 agcgcacacc cgcacttcca caccctgatg atggtgccgc ctggcatgct aaatgggaaa
      481 agttacgtca ggcatgaacg ctgggttgaa ctctggcggg agtgtctgcg ggtcgattat
      541 gacccgaatg ttgatgtccg ggcagtgaaa cctcgtaagc cgaagggcgg cgaatcgctg
      601 gcctgcgcga ccgccgaact ggtgcgcggt gcggtggccg aaaccctgaa atattccacg
      661 aagccggctg acatggtggc cgatcctgaa tggttcctcg aactgacccg ccagacgcac
      721 aagcgccgct ttgtggcgac cggcggcgca ctcaaagacg tgctgaaact cgatcaggaa
      781 actgacgccg acatggtgat cggtgatgat atttccgagg gcgacgatga cggttcacga
      841 atcgcgttcg agtggaaaac cgaggtcaga aagtaccgtc gctcaccgac gaaagataaa
      901 actgaatcag gctagcgggg tgtcggggtg cacccctgac cagatggcaa ttgtgatagc
      961 gtcgcgtgtg acggtattac aattacacat cctgtcccga aaattcccgc cgtttctcgg
     1021 ttttttgagc gtcgcagacc gcacgacaaa cgaacctaag gtgagtttgt ataagtgcgc
     1081 acttcgtgag attccctgac tgccagtttg tcgattgcgc ggaacggctg cggcacgaaa
     1141 acggcaaaat gatttactcg ccgtttgtgt gggttgtttt gtggggtgtc aatggggttg
     1201 tggtcttttt tgtgggttaa agtgtgggtg attgtgtggg ctgtgtgttt tgagttgtgg
     1261 gtgattatgt gggtcattgt gtgggctgta tgcacggcat ttttttgttc tcctaaaaca
     1321 caggcacgat aagcggcgta cacaaaacgg ggcgtttcgc tccgtcgctt gtgccaaagg
     1381 ggacacccct ttgcaaccct gtgcggttct acgaacctgg tcaggactgc gccccgacac
     1441 cccgccaacg cctcacggaa cgcgaaaaaa ttccgcgtac cgttcaccgt tccctgattc
     1501 gtcaaacaga aaatcgcggg ggcccgcgcc tccggcgtgg gttccgattt tgtgattgac
     1561 gacggcacgg gaaaaacact ggggatggtg gttggtgtca cgcagtgagg ccaaccacct
     1621 gcaagacggt tttttttgtt gttcacaaaa tcggggtgaa agtctgtgga tgagatgggt
     1681 gtaagtgggt ggggttgggt gttttgggtt actgaaaatc ccgctcaaaa ttcaagcgaa
     1741 tctcgcgcgc gatccttgta tttatactta agggataact ctaggattca aattcgcctc
     1801 cagcccttgt gccgcaaggc ctgaaggggg atttgtcgga aaatggtttt ggagttattc
     1861 tgtcgggagt ggtcgcatta aaagcgaccc ccgcaacgag ggcaatcgtt cgggggtgtg
     1921 accacctgta ggaattcgaa ttggtgatac gactaacaca acaggtgata tggcaatgat
     1981 aacacgtcag atgagccatc gcccactatc gggtggtgcg catgaaaaac cctgatctcc
     2041 agaacctcac ggactattcc ccctcagatg cgccctggga cgctcacaga agcgtt
//
