LOCUS       CP082441                4593 bp    DNA     circular BCT 11-JAN-2022
DEFINITION  Salmonella enterica subsp. enterica serovar Newport strain
            FSIS1608364 plasmid pF18S024-2, complete sequence.
ACCESSION   CP082441
VERSION     CP082441.1
DBLINK      BioProject: PRJNA292666
            BioSample: SAMN06015765
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 4593)
  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 4593)
  CONSRTM   NARMS: The National Antimicrobial Resistance Monitoring System
  TITLE     Direct Submission
  JOURNAL   Submitted (23-JUL-2018) Center for Veterinary Medicine, US Food and
            Drug Administration, 8401 Muirkirk Rd, Laurel, MD, USA
REFERENCE   3  (bases 1 to 4593)
  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                     :: F18S024
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 732x
            Sequencing Technology             :: PacBio Sequel
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI
            Annotation Date                   :: 09/02/2021 13:04:45
            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)                     :: 4,973
            CDSs (total)                      :: 4,849
            Genes (coding)                    :: 4,752
            CDSs (with protein)               :: 4,752
            Genes (RNA)                       :: 124
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 89
            ncRNAs                            :: 13
            Pseudo Genes (total)              :: 97
            CDSs (without protein)            :: 97
            Pseudo Genes (ambiguous residues) :: 0 of 97
            Pseudo Genes (frameshifted)       :: 41 of 97
            Pseudo Genes (incomplete)         :: 61 of 97
            Pseudo Genes (internal stop)      :: 16 of 97
            Pseudo Genes (multiple problems)  :: 21 of 97
            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..4593
                     /organism="Salmonella enterica subsp. enterica serovar
                     Newport"
                     /mol_type="genomic DNA"
                     /strain="FSIS1608364"
                     /serovar="Newport"
                     /isolation_source="animal-cattle-beef cow"
                     /sub_species="enterica"
                     /db_xref="taxon:108619"
                     /plasmid="pF18S024-2"
                     /geo_loc_name="USA:WA"
                     /collection_date="2016"
                     /collected_by="USDA-FSIS"
     gene            787..1626
                     /locus_tag="BOS35_024840"
     CDS             787..1626
                     /locus_tag="BOS35_024840"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001354646.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="UAE82886.1"
                     /translation="MLTLFIFFVLLIAACFFCFAPPRRGYDRNEIIPYKIKLSINKYRL
                     YIYSSGKVRQYLLFLVILSLYYSIAEPFKSELIKNISYSLMAAFIFDTGLNFSKENITK
                     GVISTRWHNDLYSSFERMKAINKIYYPSNKEINTEGLSKAITSSLFNDDANSFAKRDFR
                     LMWDLSSEKYLSYKEIIIRKGDKLDAVCLRFINDDYKFLVNFNRDEEVFKYFPSIMQPS
                     LKTYRALSRLVNSIKDPSRFKFTTESLEMELLEYLELRNELFNDIEEVMGSYAQRAP"
                     /name="hypothetical protein"
     gene            complement(2314..2547)
                     /locus_tag="BOS35_024845"
     CDS             complement(2314..2547)
                     /locus_tag="BOS35_024845"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000137438.1"
                     /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="UAE82882.1"
                     /translation="MTELEGHLLNALEHLQQDYMRRLNEWESAFAELQKMHAVTQQNNA
                     ILNERVVNLSQQVQLLAGQVDRLSRLFITNNR"
                     /name="MbeD family mobilization/exclusion protein"
     gene            complement(2554..3114)
                     /locus_tag="BOS35_024850"
     CDS             complement(2554..3114)
                     /locus_tag="BOS35_024850"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000067488.1"
                     /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="UAE82883.1"
                     /translation="MSNLLQMGTDFEKKLKERAASTENMLNSEFRKLEESVDKALSLNR
                     QKIRDAISEHTTSVKQQLDTLSTTVSTQLSTTEAELSRQQKNLLWQVIKGRVLFPALTA
                     LSVTGGIFLGCWGLIQWQESRIAKNILTIREQENTLAKLEAKTWGVTFVNGENGKFLVL
                     PDGVKGENTWTVGDKNAVRLVRE"
                     /name="MbeB family mobilization protein"
     gene            complement(3089..3802)
                     /locus_tag="BOS35_024855"
                     /pseudo=""
     CDS             complement(3089..3802)
                     /locus_tag="BOS35_024855"
                     /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(3792..4115)
                     /locus_tag="BOS35_024860"
     CDS             complement(3792..4115)
                     /locus_tag="BOS35_024860"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000956000.1"
                     /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="UAE82884.1"
                     /translation="MLTIRVSDEEHARLLERCEGKRLAEWMRRVCLGEPVARTGKLPTL
                     SPPLLRHLAAIGNNLNQTARKVNSGHWSSIDRVHVVAALMAIEGELRQLRQAVREQGGR
                     DDS"
                     /name="MobC family plasmid mobilization relaxosome protein"
     gene            4178..4369
                     /locus_tag="BOS35_024865"
     CDS             4178..4369
                     /locus_tag="BOS35_024865"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000165979.1"
                     /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="UAE82885.1"
                     /translation="MTKQEKTALNMARFIRSQTLTLLEKLNELDADEQADICESLHDHA
                     DELYRSCLARFGDDGESN"
                     /name="Rop family plasmid primer RNA-binding protein"
     Typing          complement(4458..4542)
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="3.03e-37"
     Typing          complement(337..788)
                     /name="ColRNAI_rep_cluster_1857"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="83.0"
                     /evalue="0.0"
     Typing          complement(2217..3802)
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 agaaaatgcc gcatcaggcg ctcttccgct tcctcgctca ctgactcgct acgctcggtc
       61 gttcggctgc ggcgagcggt atcagctcac tcaaagacgg tgatgcggtt atccacagaa
      121 tcaggggata acgccaaaag aaacatgtga gcaaaaggcc aggaacagga agaaggccgc
      181 gccgctggcg tttttccata ggctccgccc ccctgacgag catcacaaaa acagatgctc
      241 aagtcagagg tggcgaaacc cgacaggact ataaagatac caggcgtttc cccctggaag
      301 ctccctcgtg cgctctcctg ttccgaccct gccgcttacc ggatacctgt ccgcctttct
      361 cccttcggga agcgtggcgc tttctcatag ctcacgctgt tggtatctcg gcccggtgta
      421 ggtcgttcgc tccaagctgg gctgtgtgca cgaacccccc gttcagcccg accgctgcgc
      481 cttatccggt aactatcgtc ttgagtccaa cccggaaaga cacgtaaaaa cgccactggc
      541 agcagccatt ggtaaccgtt tagaggagtt agtcttgaag ttatgcgccg gttaaggcta
      601 aactgaaagg acagatttgg tggctgtgct cctccaagcc agttaccttg gttcaaagag
      661 ttgctgctct gagaaccttc gaaaagccgc cttgctgggc ggttttttcg tttacggaca
      721 agactacctt caggatcgtt agatctcaag acaatcatgc atagtgagca tacacaggag
      781 ccgaacttgc ttacactgtt catctttttt gttttattaa tagctgcatg tttcttttgt
      841 tttgctccac cacgaagagg atatgacaga aatgagatca ttccatacaa aataaaacta
      901 tcaataaata aatatcgcct ttacatatac tcatcgggaa aggtaagaca atacctttta
      961 tttttagtta ttttatcact gtactactcc atagcggaac catttaagtc tgagttaata
     1021 aaaaacatat catattcact gatggctgca tttatttttg atacagggct taattttagc
     1081 aaggagaata taactaaagg agtgatttca acaaggtggc ataatgacct atattcatca
     1141 tttgagagaa tgaaagcaat taataaaatt tactacccat ccaacaaaga gataaacaca
     1201 gaaggtctat ccaaagccat cacatcatct cttttcaatg atgacgcgaa ctcgttcgca
     1261 aagagagatt ttcgcttgat gtgggactta tcttctgaaa aatatctttc ctataaagaa
     1321 ataataataa gaaaaggcga taagcttgac gctgtatgct tgagatttat aaatgatgac
     1381 tacaagtttt tagttaattt caacagagat gaagaggttt tcaaatactt tccatctata
     1441 atgcaacctt cactcaaaac atatagagcg ttatcaagac tagtaaactc aatcaaagat
     1501 ccttctagat ttaagttcac gacagagtca ttagaaatgg agttactaga atacttagag
     1561 ttaagaaatg aattattcaa tgacatagaa gaagtaatgg gtagctatgc tcagagggca
     1621 ccatagttca tgatagccct cgatagtact tacttatatt tttagagagg tttaagtgta
     1681 agtagaggga gtaacacctg gtttttcagc atccactcca atgaatgctg acaccgatac
     1741 gcgataattc tctttatcgt agcaaaatca tcctccagat tgcggttgag aataggttca
     1801 tggtgcgcaa tacgattgcg cagttttctc acgggacttg ttagcagtaa tgcttccccc
     1861 cggggacaaa cgacagagat atacaacaaa ggcccgcaat taaaatactc cgtatttacc
     1921 ataacgtcgc attgcgcgta ccgcttaaac gcgttcagcg cgatcacggc agcagacagg
     1981 taaaaacagc aacaaaccac ccgaaaaact gccgcgatcg cgcctggtaa attttaacct
     2041 catgcatagt tatgcgcgaa actgaatgac gatcagtttc gcacgttcca gccgtcgaac
     2101 ggggcaaaat ggggaggttt ggatattgtt aatgctaatg tacgtacatt aacattggcg
     2161 ccatccgggt agggcgtgcc acaaactggc tcgatttcag ggggtacccc ggtcacatcc
     2221 ccattgacgg gccacgccag atccgcgctt cgggttcctg ctcttcatgc cagcgccggg
     2281 caagctcctg cgcctgacgc tcctgttcat cccttatctg ttgttcgtga taaataaccg
     2341 actcaagcgg tcgacttgtc cggctaatag ctgcacctgc tgactcaagt tcacgacacg
     2401 ctcgttcagt atcgcgttgt tctgttgcgt aaccgcgtgc atcttctgca attctgcgaa
     2461 ggcgctctcc cactcgttca gccgccgcat atagtcctgt tgcaaatgct ctaaggcgtt
     2521 cagcaaatgc ccttccagtt ccgtcatact cgtttactcc ctgaccagcc tcacggcgtt
     2581 cttgtcgccc accgtccagg tgttttcccc tttcaccccg tccggcagca ccagaaattt
     2641 cccgttctcg ccattgacga acgtcacccc ccaggttttt gcctcgagtt tcgccagcgt
     2701 gttttcctgc tctctgatgg tcaagatatt tttcgcaatc ctgctttcct gccactgaat
     2761 cagcccccag caccccagga aaatgccgcc cgtgacgctg agcgcggtca gcgccggaaa
     2821 cagtacccgc cctttgatca cctgccagag caggtttttc tgctgccggg acagttcggc
     2881 ctctgtggtg ctgagctgcg tgctcacggt ggtgctcagc gtatccagtt gctgtttcac
     2941 ggatgttgta tgttcgctga tagcgtctct gattttctgc ctgtttaagc tcagtgcctt
     3001 gtctacagac tcttctagct tcctgaactc gctgttcagc atgttctcgg tagaagcggc
     3061 tcgctctttc agtttcttct cgaagtccgt tcccatttgt aaaagattgc tcatacagcg
     3121 ccccctttag cctgagattc cgccccccct ccgggtcggc aatactgata ctgcttctgg
     3181 ttgtcctcac cacctcaaaa cctgccgctg tgagcgcctc agtgacatcc tgacgcgttt
     3241 ttattgctcc ggcacggtaa agcgcctcaa gaccccgtgt aatcgcttct gcggcctcct
     3301 gtttcgcttt tggcagatta ttcggtgtga caagcgtccg tctgttctcc ggtgcgttcg
     3361 ggtcacgcag cccgtaatga tgattaacca gcgtctgcca ggcatttatc ctcggcctgt
     3421 ccgcacggtc gtagtacggc tggaggcgct taccgctctg tagttccatg ttcggaatga
     3481 caaaattcag ttcgagccgc cccttatcct ggtgttccac ccagagaatg ctgtactggt
     3541 ctttttcgag accgggcata agaacacgct caaagctcgt catcactctt tcgcgttcac
     3601 ccggcggtaa ctccttctcc gcgaacgaca gaacgcctga tgtgtatttc ttcgaaaatg
     3661 gcgtggcatc aatgagttcc cggatttctt ccgggttacc ccggagcacc gttgcgcctt
     3721 cgcggttacg ctcccgcccc agcaggtaat cgaccgggcc acttccaccg cctttccccc
     3781 tggcatgaaa tttaactatc atcccgtccc ccctgttccc tgacagcctg ccgcaactgg
     3841 cgcaattcac cctcgatggc catcagagcg gccaccacat gaacccggtc aatcgaagac
     3901 cagtggccgc tgttcacctt ccgggctgtc tggttcagat tgttcccgat ggcagccaga
     3961 tgccgcagca atggcggcga tagtgtcggc agttttcctg tgcgcgcaac cggctccccc
     4021 agacagaccc gccgcatcca ttctgccagt cgtttaccct cgcagcgttc cagtaaccgg
     4081 gcgtgctcct catcgctaac ccgtatcgtg agcatcttct cgcgtttcat cggtatcatt
     4141 ccccctaaaa aatcccctat taaggagcct taagaccatg accaaacagg aaaaaacagc
     4201 ccttaacatg gcccgcttta tcagaagcca gacgctgacc ctgctggaaa aactcaacga
     4261 gctggacgcg gacgaacagg cagacatctg cgaatcactt cacgaccacg ccgacgaact
     4321 ctaccgtagt tgcctcgcac gcttcggcga tgacggtgaa agcaactgaa acatgcagct
     4381 cccggagacg ttcacagctt gcctgtgagc ggatgccggg agcagacaag cccgtcaggg
     4441 cgcgtcagcg ggttttagcg ggtgtcgggg cgcagccctg acccagtcac gtagcgatag
     4501 cggagtgtat actggcttaa ctatgtggca tcagtgcgga ttataagaaa agtgcaccat
     4561 atgcggtgtg aaataccgca cagatgcgta agg
//
