LOCUS       CP082480                3605 bp    DNA     circular BCT 13-JAN-2022
DEFINITION  Salmonella enterica subsp. enterica serovar Newport strain
            FSIS1607290 plasmid pF18S009-2, complete sequence.
ACCESSION   CP082480
VERSION     CP082480.1
DBLINK      BioProject: PRJNA292666
            BioSample: SAMN05514416
KEYWORDS    .
SOURCE      Salmonella enterica subsp. enterica serovar Newport
  ORGANISM  Salmonella enterica subsp. enterica serovar Newport
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Salmonella.
REFERENCE   1  (bases 1 to 3605)
  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 3605)
  CONSRTM   NARMS: The National Antimicrobial Resistance Monitoring System
  TITLE     Direct Submission
  JOURNAL   Submitted (22-JUL-2018) Center for Veterinary Medicine, US Food and
            Drug Administration, 8401 Muirkirk Rd, Laurel, MD, USA
REFERENCE   3  (bases 1 to 3605)
  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
            Assembly Name                     :: F18S009
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 360x
            Sequencing Technology             :: PacBio Sequel
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI
            Annotation Date                   :: 09/02/2021 13:34:50
            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)                     :: 4,911
            CDSs (total)                      :: 4,788
            Genes (coding)                    :: 4,693
            CDSs (with protein)               :: 4,693
            Genes (RNA)                       :: 123
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 88
            ncRNAs                            :: 13
            Pseudo Genes (total)              :: 95
            CDSs (without protein)            :: 95
            Pseudo Genes (ambiguous residues) :: 0 of 95
            Pseudo Genes (frameshifted)       :: 40 of 95
            Pseudo Genes (incomplete)         :: 62 of 95
            Pseudo Genes (internal stop)      :: 17 of 95
            Pseudo Genes (multiple problems)  :: 24 of 95
            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..3605
                     /organism="Salmonella enterica subsp. enterica serovar
                     Newport"
                     /mol_type="genomic DNA"
                     /strain="FSIS1607290"
                     /serovar="Newport"
                     /isolation_source="animal-cattle-heifer"
                     /sub_species="enterica"
                     /db_xref="taxon:108619"
                     /plasmid="pF18S009-2"
                     /geo_loc_name="USA:KS"
                     /collection_date="2016"
                     /collected_by="USDA-FSIS"
     gene            complement(join(2097..3605,1..24))
                     /locus_tag="BFE24_024535"
     CDS             complement(join(2097..3605,1..24))
                     /locus_tag="BFE24_024535"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_017899153.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="NERD domain-containing protein"
                     /protein_id="UAE26927.1"
                     /translation="MKKSVVRQVLEMSGPCISSDLAERIQWQYPSMSPEAIRKMISRST
                     DIGKLPFLKFSHNRRFIYLKDDFGSFKFWRALEKCMYEANSTYSHAILSVINNGGYLKV
                     KDFGIVSGSPIKQAKHLSYETVLRNLLSAKILRAVYIDGVGDCVLINNNIANDVNIRTM
                     ANCESFFDKPIFELVKAWLRNLGLVAFNQIKTKYDGEGNPVVGSFEWDMTAPSYVSPLA
                     EYVGGKLMPGFVACDFSLGFNRDEITTAAAETFIRKVQMTKSSRASQRIMFVIFARRFG
                     KIAFNKLRSEGVLAVTIANAFGNKVDESLTRLSRVVQGSLSIEKHPDELLQMVKDLESV
                     SGENGNLRGYVFELFVSSQISNFYGLGNIYINREYKINGKHAEADVVLESSDDIYIIEC
                     KNVKVLPSTELTRWMKERVPIINSYYKINNLEKKNIHHYLWVTGNVYNKDLKRLDSFKN
                     NNKNIDVDYLFGEHLDDFFYKKKRVFNLYRKVISPDYKKGVMPDFELEDDFF"
                     /name="NERD domain-containing protein"
     gene            complement(1042..1191)
                     /locus_tag="BFE24_024540"
     CDS             complement(1042..1191)
                     /locus_tag="BFE24_024540"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_017880354.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="UAE26928.1"
                     /translation="MPSEYDEQRDATDTQLPGEYDLFDLMAKVTEENLHAPVDFGPPVG
                     REAL"
                     /name="hypothetical protein"
     Typing          complement(1185..1400)
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="85.845"
                     /coverage="100.0"
                     /evalue="7.43e-58"
     Typing          1569..2049
                     /name="rep_cluster_2358"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="98.344"
                     /coverage="91.0"
                     /evalue="0.0"
ORIGIN
        1 ctgtctaaca acactttttt tcatatcctc accttatttc tgtcacacta cgctatttat
       61 aatattacac tacgtgtaat agggcgcagt cttttaaaaa aaagtgacta taaaaaataa
      121 ttaaaaatca gatggttaat tacttacttt aaattgagca caaagaaata tcgtctttat
      181 aattatttaa tccttttaaa tcataaagat agtattgtga cattttttta tcgaactatc
      241 agctactcca tttaccataa catccgttgc gtgcaccgcc tgagaggctc tcagggcgtt
      301 tctgacggga aaccggtaaa acaaggcaac aaaccacccg aaaaccagcc agaaacgcgc
      361 aggctctgtt tttacggcat gcatgagtat gcgcgcaagt gcatagcgca gaatttcacg
      421 ccgtgcagcc agtggaagtc ctgttttcga cgttcttctc atccgaaaac ggtgaacggg
      481 gacgcaattt attgcgtgac cgtaaagcgt tggcaagagc atcaagcatg aagagaaggg
      541 ggtcggatgt acgaatggtt cagagaactg ttatgacgta attcagtagt aattcagtag
      601 taaatcagta gtagataagt agtcatcctc ctccgatttg tagtaaatca gtagtaaatc
      661 agtagtgttt ctgtagtccc ccccctccgg tttgtagtaa atcagtagta aatcagtagt
      721 gacgctgtag tttattagta gtcaggagga ataagctgtt catacaagta tgaacgagct
      781 agttatggac gctttttttc acagatctcc tcagaatagg caaagctcag cccggtaagg
      841 agatgattct ttatccctta aatggccata caccatacgc aaccgcgatt ttcatcgcaa
      901 ttgcatgaat taaaaggtaa aaactgaagt tcccgtttat ttatgtaata cgcaacgtat
      961 tacaaccacc tgtaatcaca tgaaaataaa gaaataagat gtaataccgg cgtattacac
     1021 gtacgcgggt aagcgaaaaa gctataacgc ttcccggccg acaggcggcc caaaatccac
     1081 cggggcgtgc aggttctctt cagtaacctt cgccattaaa tcaaaaaggt catattcgcc
     1141 gggaagctgc gtatcagtcg catcccgttg ttcatcatat tcagatggca tggggtgata
     1201 tccagtagct aaggggttgt tagcgggttt cggagcgcag ccctgaacca gtcacgtagc
     1261 gctagcggag tctaaactag ctgaatatgt tacggcgggg tcggggttca ggaaagtgct
     1321 tcatgtgaca ggggaaaatg cagctacagg gcgtacggga gaaaatgggg gttactgtga
     1381 tatgacgcct cctcgctcac tcggtcgcta ccgctcctgc cgttcggctg cggcgggcgt
     1441 tagctgcaca cggataagag caaaagcatg tggcatgaca aacagggcag gaaaaggacg
     1501 cggcgctgcc gtttttccat aggctccgcc cccctgacaa gcatcacgaa atctgacact
     1561 caaatcagtg gtggcgaaac ccgacaggac tataaagatc ccaggcgttt ccccctggta
     1621 gctccctcgt gcgctctcct gttcctgcct ttcggtttac cggtgtcact ccgctgttat
     1681 ggccgcgttt atctcattcc acgcctgaca ctcagttccg ggaaggcagt tcgctccaag
     1741 ctggactgta tgcacgaacc ccccgttcag tccgactgct gcgcctgttc cggtaactat
     1801 cgacttgagt ccaacccgga aagacacgac aaaacgccac tggcagcagc cattggtatc
     1861 tggtttacgg agcggagagg cgtgtacaag catacacaga gttcttgaag tgttgacctg
     1921 actacggcta cactggaagg acagatttgg tcactgcgct ccgtttaagc cagttaccac
     1981 ggttcagaaa cttgccggtt tcctgaacct tcgaaaaacc accttgccgg gtggtttttt
     2041 cgtttcagag atggaagata cgcctttcaa agcgccatcg tcaagaaacg cagtagctag
     2101 aaaaaatcgt cctctaactc aaaatcaggc attacgcctt ttttataatc aggtgaaatg
     2161 acttttctat ataagttgaa cacccgcttt ttcttgtaaa agaaatcatc caaatgctca
     2221 ccaaacaaat aatcaacatc gatattctta ttattattct taaaagagtc taaccttttt
     2281 aaatctttgt tgtacacatt ccctgtaacc cacaaataat ggtggatatt ctttttttct
     2341 aaattattta ttttatagta agagtttata attggaaccc tttctttcat ccaacgcgta
     2401 agttcagttg aaggtaagac cttaacattt ttgcactcta ttatataaat atcgtcacta
     2461 ctctccaata caacatcagc ttctgcatgc ttaccattta tcttatactc tctattaatg
     2521 taaatattac caaggccata aaaattagaa atttgcgagg atacaaaaag ctcaaaaaca
     2581 taccctctca aattgccatt ctctccagaa acagactcca gatctttaac catctgaagc
     2641 aactcatctg gatgcttttc aatggacaaa gaaccctgaa ccaccctcga caacctggtt
     2701 aagctttcat caactttatt accaaacgca tttgctatag ttacagccag aaccccctca
     2761 cttctcaact tattgaaggc tattttgccg aaacgccttg cgaaaataac aaacattatc
     2821 ctctgactcg ctcgagaaga cttggtcatc tggacttttc ttatgaatgt ttctgctgca
     2881 gcggtagtaa tttcatcacg attaaagccg agagaaaaat cacaggcaac gaaaccaggc
     2941 atcagttttc cgccgacata ttcagcgaga ggggaaacgt aacttggagc ggtcatatcc
     3001 cattcaaaag agcctacaac tggatttccc tccccatcat attttgtttt tatctgatta
     3061 aaagcgacta ggcctaaatt cctcaaccaa gctttaacaa gctcaaatat tggtttgtca
     3121 aaaaaggatt cgcaatttgc cattgttcta atattaacat cgttggctat gttgttattt
     3181 atcagtacgc aatcaccaac tccatcaata tacacggctc taagtatttt tgccgaaagt
     3241 agatttctta gaactgtttc ataacttaaa tgtttagctt gttttatagg agatccagac
     3301 acaatcccaa aatctttcac cttcaaataa ccgccattat ttattacgga aagtatcgcg
     3361 tgtgagtaag ttgagtttgc ttcgtacatg cacttttcga gagctcgcca aaatttgaaa
     3421 ctgccaaaat catcttttag ataaatgaat ctcctgttat ggctgaattt caaaaatggc
     3481 agcttaccta tgtccgtgct tcgcgagatc attttacgta tcgcttcagg ggacattgag
     3541 ggatattgcc actgaattct ctctgcaaga tccgaagaga tgcatggccc gctcatttca
     3601 agcac
//
