LOCUS       CP082677                3003 bp    DNA     circular BCT 09-SEP-2021
DEFINITION  Salmonella enterica subsp. enterica serovar Typhimurium strain CVM
            N18S0645 plasmid pN18S0645-5, complete sequence.
ACCESSION   CP082677
VERSION     CP082677.1
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 3003)
  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  JOURNAL   Unpublished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 3003)
  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 3003)
  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..3003
                     /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="pN18S0645-5"
                     /geo_loc_name="USA:PA"
                     /collection_date="2018"
                     /collected_by="FDA"
     gene            193..501
                     /locus_tag="FH358_023350"
     CDS             193..501
                     /locus_tag="FH358_023350"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_003341209.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="helix-turn-helix domain-containing protein"
                     /protein_id="UAH78660.1"
                     /translation="MKNSFELISTDPVKFNTWSIKSKLIIIIRKLMIDNNWSQSEAAEK
                     LGISQPRVSNMLNGKLDKFSIDTLLEMVFKMGYKLDMDFNPLKTESPLTMVVKKAMV"
                     /name="helix-turn-helix domain-containing protein"
     gene            complement(518..850)
                     /locus_tag="FH358_023355"
     CDS             complement(518..850)
                     /locus_tag="FH358_023355"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_013857758.1"
                     /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="UAH78661.1"
                     /translation="MSNDDTEYTFKPVNAQALKALRSLPEWVQVAFVHALDSVFYGVDP
                     GMPIVHLTSIGPGVVELKINGRPAYRCVYRSKAPGQVDLLHAFVKTCQGPDKKNMATAT
                     SRYKLL"
                     /name="type II toxin-antitoxin system RelE/ParE family
                     toxin"
     gene            complement(1437..1760)
                     /locus_tag="FH358_023360"
     CDS             complement(1437..1760)
                     /locus_tag="FH358_023360"
                     /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="UAH78662.1"
                     /translation="MTKRSGSNTRRRAISRPVRLTAEEDQEIRKRAAECGKTVSGFLRA
                     AALGKKVNSLTDDRVLKEVMRLGALQKKLFIDGKRVGDREYAEVLIAITEYHRALLSRL
                     MAD"
                     /name="nikA protein"
     gene            2045..2239
                     /locus_tag="FH358_023365"
     CDS             2045..2239
                     /locus_tag="FH358_023365"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001041624.1"
                     /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="UAH78659.1"
                     /translation="MNKQQQAVLNMAGFIKSQSLTLLEKLDALDADEQAAMCEKLHELA
                     EELQNSIQTRFEAENRTGI"
                     /name="Rop family plasmid primer RNA-binding protein"
     Typing          complement(1770..2010)
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="98.76"
                     /coverage="100.0"
                     /evalue="2.14e-118"
     Typing          2275..2779
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="86.742"
                     /coverage="95.0"
                     /evalue="4.94e-158"
     Typing          complement(1441..1760)
                     /name="MOBF"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="99.065"
                     /coverage="100.0"
                     /evalue="1.41e-62"
ORIGIN
        1 agactactct ttgcttaaga gtcacgtcaa taccatcatt gttacttgca agatcaaatg
       61 caattcacat ctttttctct tgaaagagat atcattactt gtataatgcc ccgcccatat
      121 atatatatat aaggagttcc ttgtcggaac ttttatcatc gaggtacagg taatccaaca
      181 tggagctgtt ctatgaaaaa ttcatttgag ctgataagta ccgacccggt gaaattcaac
      241 acatggtcga taaaatcaaa actcataata ataatcagaa agttaatgat cgataacaat
      301 tggtctcaat ctgaagcagc tgaaaagtta ggtatcagtc agccccgagt aagtaacatg
      361 ctgaacggga agctagacaa attctccatc gacacattgt tagaaatggt gttcaagatg
      421 ggttacaagc tagatatgga tttcaaccca ttaaaaacag aatcaccact cacaatggtt
      481 gtaaaaaagg cgatggtgta agcatcgcct ttatggatta caacaacttg tagcgtgatg
      541 ttgcggttgc catattcttc ttatcgggtc cttgacacgt tttcacgaac gcatgcagca
      601 agtccacttg acctggagct ttgctgcgat aaacgcaacg ataagcaggg cgaccattga
      661 ttttcaactc aacaacaccg ggtccgatgg acgtcaagtg cacgatgggc atccccggat
      721 ccactccgta gaaaactgaa tccaatgcgt gcacgaatgc aacctgaacc cactcaggga
      781 gtgatctcaa tgcctttaaa gcctgggcat taacaggttt gaacgtatat tcagtgtcgt
      841 cgtttgacat agcaatcctc tcttaggtta ttgatgttta acaaattaac taccgtattg
      901 atatttcgca taaatactcc gattaattga tctgtgagca taaaaaaacc acaccgccct
      961 attttttagg tcagtgcgcg tatggtcatt agctcgtaga accaataatt attggcaatc
     1021 tcgccaacac tgacacagta tacaaatact tatatgcaat caagttttat caaaggtata
     1081 caaaactaac cgctcaaaaa aaaagcggtt taccttaagt catgacacta aagagggtta
     1141 tttaggcaaa cagaactgta gccagagaag cccgattgct agataaaaac caatgaagaa
     1201 acctcgccaa tgatagattt accataatcc cttaattgta cgcaccgcag aaacgcgctg
     1261 aacgggattc tgccgcagac accgcaaaaa gagatgtgtt accaagcgaa aaccggaaaa
     1321 atgcgtcagg atcgttttca gctcgctgca tagctatgca tgaaagcgaa tggtgatcac
     1381 tttgggagct tacggtgttc ataccgtctg ttttcgacag ttttctctcc gggaagctaa
     1441 tctgccataa gcctggataa cagggcacgg tgatactccg taatagcgat cagcacctcc
     1501 gcatactccc tgtccccgac acgcttgccg tcgataaaga gttttttctg taacgccccc
     1561 agtctcataa cttctttcag tacccgatca tcagtcagtg agttaacttt cttaccgaga
     1621 gctgccgccc gtaaaaaacc ggaaacggtc ttgccgcatt cagcagccct ttttctgatt
     1681 tcctggtctt cttctgccgt cagacgaaca gggcgactga tagcccgcct gcgcgtatta
     1741 cttccacttc gttttgtcat aaaacatggc tccgtatctg acatggggtg tcggggcgaa
     1801 gccctgacca gggtaattgt aatagcgtgc atgtatgcgc ggtataacaa ttgcacatcc
     1861 tgtcctgtca gcaagttcga attaccgaca aaggcacggc agttttttgg cagtgacagt
     1921 attgtcaggc agaaatgccc gtcaaagagt cagacggcag aataccggcg gtaaaacagt
     1981 cgaaaagtgg tacgcgatat aatcacacaa cgcagatgat agacagaaca gagaaaacga
     2041 aaagatgaac aagcagcagc aagccgtact caacatggcc ggattcataa aaagccagag
     2101 cctgacgctg ctcgaaaaac tggacgcact cgatgctgac gaacaggccg ccatgtgtga
     2161 gaagctgcac gaactcgcgg aagaacttca gaacagcata cagacacgct ttgaagcgga
     2221 aaatcgcacc gggatataac gcatccggac aggatgcaga acggcataga ggagcgtaag
     2281 gagaaaatgt cacataaggc gctcttccgc ttcctcgctc actgactcgc tacgctcggt
     2341 cgttcgactg cggcgagcgg tgtcagctca ctcaaaagcg gtaatacggt tatccacaga
     2401 atcaggggat aaagccggaa agaacatgtg agcaaacagc aaagcaccgg aagaagccag
     2461 cgccgcaggc gtttttccat aggctccgcc cccctgacga gcatcacaaa aaccgacgct
     2521 caagtcagag gtggcgaaac ccgacaggac tataaagata ccaggcgttt ccccctggaa
     2581 gctccctcgt gcgctctcct gttcctgcct ttcggtttac caatgtcatt ccgctgttat
     2641 ggccgcgttt gtctcattcc acgcctgaca ctcagttccg ggtaggcagt tcgctccaag
     2701 ctggactgta tgcacgaacc ccccgttcag tccgaccgct gcgccttgtc cggtaactat
     2761 caacttgagt ccaacccgga aagacacgac aaagcgccac tggcagcagc cattgggaag
     2821 agggtgtaca agatattact gacgcagagt tcttgaagtc agagccaaac tacagctaaa
     2881 ctaaaaagac agaatttggt ttcagcggtc ttgtacaccc tgttaccatg gttcagaagt
     2941 tccccaactc actgaaccct caaaaaaacc gcctccccag gcggtttttt tgtttcttga
     3001 aca
//
