LOCUS       CP082561                3660 bp    DNA     circular BCT 13-JAN-2022
DEFINITION  Salmonella enterica subsp. enterica serovar Typhimurium strain CVM
            N18S1595 plasmid pN18S1595-3, complete sequence.
ACCESSION   CP082561
VERSION     CP082561.1
DBLINK      BioProject: PRJNA292661
            BioSample: SAMN12360196
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 3660)
  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 3660)
  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 3660)
  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                   :: 414x
            Sequencing Technology             :: PacBio Sequel
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI
            Annotation Date                   :: 08/30/2021 17:19:57
            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)                     :: 4,990
            CDSs (total)                      :: 4,868
            Genes (coding)                    :: 4,741
            CDSs (with protein)               :: 4,741
            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)              :: 127
            CDSs (without protein)            :: 127
            Pseudo Genes (ambiguous residues) :: 0 of 127
            Pseudo Genes (frameshifted)       :: 41 of 127
            Pseudo Genes (incomplete)         :: 82 of 127
            Pseudo Genes (internal stop)      :: 25 of 127
            Pseudo Genes (multiple problems)  :: 18 of 127
            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..3660
                     /organism="Salmonella enterica subsp. enterica serovar
                     Typhimurium"
                     /mol_type="genomic DNA"
                     /strain="CVM N18S1595"
                     /serovar="Typhimurium"
                     /isolation_source="Chicken Wings"
                     /sub_species="enterica"
                     /db_xref="taxon:90371"
                     /plasmid="pN18S1595-3"
                     /geo_loc_name="USA:TN"
                     /collection_date="2018"
                     /collected_by="FDA"
     gene            complement(join(3535..3660,1..420))
                     /locus_tag="FQD68_024925"
     CDS             complement(join(3535..3660,1..420))
                     /locus_tag="FQD68_024925"
                     /inference="COORDINATES: protein motif:HMM:NF021378.2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="SHOCT domain-containing protein"
                     /protein_id="UAI34101.1"
                     /translation="MRERYLNKISNFDMARIVLFIAIQIISCIFMFWGAIPALIVFFSY
                     LAMRKECNLKPIENSKIYISVYMLLTAALVLFLFVYKAGMFRGGSDYFPLVFVFILLYV
                     YHLAFHKLWLRTIDENSTIIIENGIFNFNRKNAPVGFSRKDVNNIDTLLKLNEARKEGI
                     ISEDEFNKLKNRLNILDD"
                     /name="SHOCT domain-containing protein"
     gene            complement(521..814)
                     /locus_tag="FQD68_024930"
     CDS             complement(521..814)
                     /locus_tag="FQD68_024930"
                     /inference="COORDINATES: ab initio prediction:GeneMarkS-2+"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GeneMarkS-2+."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="UAI34102.1"
                     /translation="MSRIGRCSTRKRWSWNDLSGSGRMTVRRCNKPDKTGLWAAIFAES
                     RCHSPDCIAMQPGEIYQAQAARFAGEFTAGFTGLTPHSRRTRSGRCGQGVLW"
                     /name="hypothetical protein"
     gene            complement(833..1048)
                     /locus_tag="FQD68_024935"
     CDS             complement(833..1048)
                     /locus_tag="FQD68_024935"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000137421.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MbeD family mobilization/exclusion protein"
                     /protein_id="UAI34103.1"
                     /translation="MTELEKQLLNALEQLQQDYSKRLDEWENAFAEWRTMSGLMQRENA
                     ALSERVTGLSRQVQSLSEQLRRLSQG"
                     /name="MbeD family mobilization/exclusion protein"
     gene            complement(1052..1537)
                     /locus_tag="FQD68_024940"
     CDS             complement(1052..1537)
                     /locus_tag="FQD68_024940"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_012565228.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MbeB family mobilization protein"
                     /protein_id="UAI34104.1"
                     /translation="MNSLLTLAKDLEQKSKAQQQSTGEMLKVAFSEHEKSVRAELSESE
                     KRISAAILDHDRKLSSAMSQRTKGMVRMVSQTWLTIVLVSALLTASGAGILWWQGQQIL
                     DNYTTIREQKRTQAMLSERNSGVQLSTCGEQRRRCVRVNPEAGRFGEDSSWMILAGK"
                     /name="MbeB family mobilization protein"
     gene            complement(1512..2276)
                     /locus_tag="FQD68_024945"
                     /pseudo=""
     CDS             complement(1512..2276)
                     /locus_tag="FQD68_024945"
                     /inference="COORDINATES: protein motif:HMM:NF015397.2"
                     /note="incomplete; partial on complete genome; missing
                     C-terminus; Derived by automated computational analysis
                     using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="relaxase/mobilization nuclease domain-containing
                     protein"
                     /name="relaxase/mobilization nuclease domain-containing
                     protein"
     gene            complement(2215..2538)
                     /locus_tag="FQD68_024950"
     CDS             complement(2215..2538)
                     /locus_tag="FQD68_024950"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000957083.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MobC family plasmid mobilization relaxosome
                     protein"
                     /protein_id="UAI34105.1"
                     /translation="MLTMWVTEDEHRRLLERCDGKQLAAWMRQTCLDEKPARAGKLPSL
                     SPALLRQLAGMGNNLNQIARQVNAGGGSGHDRVQVVAALMAIDAGLERLRHAVLEKGAD
                     DDR"
                     /name="MobC family plasmid mobilization relaxosome protein"
     Typing          complement(2647..2825)
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="87.432"
                     /coverage="83.0"
                     /evalue="3.48e-51"
     Typing          2805..3277
                     /name="ColRNAI_rep_cluster_1987"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="80.285"
                     /coverage="93.0"
                     /evalue="5.09e-93"
     Typing          complement(730..2225)
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="91.583"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 tcctacaggt gcatttttac gattaaaatt aaaaatcccg ttttcaatta ttattgttga
       61 gttttcatct atcgttcgca accataattt atgaaaagcg agatggtaaa cataaagcaa
      121 aataaaaaca aaaacgagag ggaaataatc actgccccct ctaaacatgc cagctttata
      181 cacgaaaaga aacagtacca aagcggctgt aagaagcatg taaacggata tgtaaatctt
      241 agagttttct atcggcttta aattacattc cttcctcatg gctaaatatg agaaaaaaac
      301 aatcaaggca ggaatagccc cccagaacat aaaaatacaa gagataattt gaatggctat
      361 aaataacact attcttgcca tatcaaaatt agatatttta tttaaatacc gttcgcgcat
      421 aaattaccgc cattcaatca tagttaatta atttaaaatc aatcgactga tattaatgtc
      481 atttcaaaaa atagaaaagc agtaactgaa tatggggtgt ttaccataac accccttggc
      541 cgcaccgccc cgaacgggtt cggcgcgaat gcggcgtcag tccggtaaaa ccggcagtaa
      601 actccccggc aaaccgcgcc gcctgcgcct gataaatttc acccggctgc atggctatgc
      661 agtcgggtga atggcaccgg ctttcagcga aaatagccgc ccaaagcccc gttttatccg
      721 gtttgttaca gcgacggacc gtcatacgtc cgctgccgct gagatcgttc cagctccagc
      781 gttttctggt gctgcaccgc ccgatcctgc tcacgctgtg cctctatcca gttcagcctt
      841 gcgacaaccg gcgcagctgc tcgctcaaac tctgcacctg cctgctcaag cccgtgacgc
      901 gctcgctcag cgccgcgttc tcccgttgca taagaccaga catcgtccgc cattccgcga
      961 aggcgttctc ccactcgtcc agccttttcg agtagtcctg ctgtagctgc tctaatgcgt
     1021 tcagcaactg tttttccagc tccgtcatgt gctatttccc cgccagtatc atccagctcg
     1081 aatcctctcc gaaccgtccc gcttccgggt tcaccctcac gcagcggcgt ctctgctctc
     1141 cgcaggtcga gagctgcacg ccgctgttcc tctcggacag catggcctgc gtgcgcttct
     1201 gctcccggat ggtcgtgtaa ttgtcgagta tctgctgccc ctgccaccac agaatgcctg
     1261 cgcccgatgc tgtcagcagt gcagacacca ggacgatggt cagccacgtc tggctgacca
     1321 tacgcaccat gcctttcgtg cgctggctca tggctgagga cagcttccgg tcgtggtcga
     1381 ggatggcggc gctgattctc ttctcgcttt cgctcagttc cgctctgaca gacttctcgt
     1441 gctcgctgaa tgcgactttc agcatctcgc cggtactctg ctgctgcgct ttcgatttct
     1501 gctctaagtc ctttgccagc gttaaaagac tgttcataga tggctccctt cagtcggatg
     1561 tttcgccccc cgtccgggtc ggcaatgctg atgctgcttt ttgtggtgcg taccacatca
     1621 aaacctgcgc tttccagcgc ctcagtgacg tcctggcggg ttttcagctc cccggacgag
     1681 gccaaggcca gtaaaccccg tgtaattgcc tgagcggctt cctgcttcgt ttccggcagc
     1741 gcggacggcg tgaccagcgc ccgccggttt tcaggcgcgt tcgggtcatg cagccccagc
     1801 ctgccgttca cgatggtctg ccaggcatca atgcgcggac ggtcggcgcg gtcgtaatac
     1861 ggctggagac gcctgccggt cagcagctcc gtgttcggga tcaggaagtt cagctccagc
     1921 cgccccttat cctggtgctc aacccacagc acgctgtact ggtctttatc gagtccgggc
     1981 atcagaaccc gttcaaagct cgccatcagc ttttcgcgct gcccgggcgg taaatccttt
     2041 tcggcaaagg acaggacgcc ggatgtgtac ttttttgcat acggcgaggc gtcgataagc
     2101 tccctgactt cttccggctt cccctgcaga acggtggcgc cgtcgcgctg tcggtctttc
     2161 cccagcagat aatccaccgg accggcgcca ccgccgcgcc ctcgcgggtg aaacttaacg
     2221 atcatcgtct gcaccctttt ccagcacggc atgccgcagc cgctcgagtc cggcatctat
     2281 ggccatcagc gcggcgacga cctgcacgcg gtcgtgcccg ctgccaccac cggcgttaac
     2341 ctgccgggca atctggttga ggttgttccc catgccggca agctgacgaa gcagcgccgg
     2401 cgagagcgag ggaagcttgc cggcgcgggc gggtttctcg tccaggcacg tctggcgcat
     2461 ccaggctgca agctgtttac cgtcgcagcg ctccagcaga cggcggtgct catcttcggt
     2521 cacccacatc gtgagcattt tgctgcgttt gtctgccaat ccggcctcct gataacgccg
     2581 ggacgggcgg gaatgttttc ccggtcggcg cggtgttgga caagccgcag gcgcgtcagt
     2641 ggcttttagc gggtttcggg gcgcagccct gaaccagtca cgtagcgcta gcggagtgta
     2701 tactggctta gtatgttagg ccagagtggt aatttaggga agtgcttcat gtagcaaggg
     2761 aaaatgcgac tgcggtgtgt aagtgcgaaa tgcaggtgac agtgaaatga cgcctcctcg
     2821 ctcactcggt cgctacgctc ctgccgtgag actgcggcgg gcgttatcag cttacagatg
     2881 acgggatagg caagtagcgc tcgaatcagt aagggccaga aaaaggatgc ggcgttgccg
     2941 tttttccata ggctccgccc ccctgacgag catcataaaa tctgacgctc aaatcagtgg
     3001 tggcgaaacc cgacaggact ataaagatac caggcgtttc cccctgatgg ctccctcgtg
     3061 cgctctcctg ttcctgtcct gcggtgaccg tgttgtggtg gaagctttac ctacatcacc
     3121 acgtcccgtt tccgtttaga cagttcgctc caagctggac tgtatgcacg aaccccccgt
     3181 tcagtccgac taccacgcca tgtaaggtaa ctatcaactt gagtccaacc cttacagaca
     3241 cgacaattcg ccagtggcgg tagccatcgg caactgattt agaggaggag tgtcttgaat
     3301 ctatacgccg atatcggcta aactgattgg accgtatttg gtgactgcgc tcctcttaag
     3361 ccagttaccg cggttcaaag agttgctgct ctgagaacct tcaaaaaaac cgccttgctg
     3421 ggcggttttt ttgtttgcag ggaagaagat tacgacgata aaaaatcaat gacaagaaga
     3481 tattcaatct tatcaaagat tcataagctt actttacctt tagttagcaa aaaatcagtc
     3541 gtcaagaata tttagtctat tttttaattt attaaactca tcttcactta taataccttc
     3601 ttttctagcc tcgtttaatt taagaagagt atcaatgtta tttacatctt tccgactaaa
//
