LOCUS       CP119509                4593 bp    DNA     circular BCT 14-MAY-2024
DEFINITION  Salmonella enterica subsp. enterica serovar Newport strain
            FSIS11816184 plasmid pFSIS11816184-2, complete sequence.
ACCESSION   CP119509
VERSION     CP119509.1
DBLINK      BioProject: PRJNA242847
            BioSample: SAMN10579127
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   Ge,B., Mukherjee,S., Li,C., Harrison,L.B., Hsu,C.H., Tran,T.T.,
            Whichard,J.M., Dessai,U., Singh,R., Gilbert,J.M., Strain,E.A.,
            McDermott,P.F. and Zhao,S.
  TITLE     Genomic analysis of azithromycin-resistant Salmonella from food
            animals at slaughter and processing, and retail meats, 2011-2021,
            United States
  JOURNAL   Microbiol Spectr 12 (1), e0348523 (2024)
   PUBMED   37991374
REFERENCE   2  (bases 1 to 4593)
  CONSRTM   GenomeTrakr network: Whole genome sequencing for foodborne pathogen
            traceback
  TITLE     Direct Submission
  JOURNAL   Submitted (14-DEC-2018) Center for Food Safety and Applied
            Nutrition, US Food and Drug Administration, 5100 Paint Branch Pkwy,
            College Park, MD, USA
REFERENCE   3  (bases 1 to 4593)
  AUTHORS   Li,C.
  TITLE     Direct Submission
  JOURNAL   Submitted (02-MAR-2023) CVM/OAS, FDA-CVM, 8401 Muirkirk Rd, MOD2,
            Laurel, MD 20708, USA
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Date                     :: 24-SEP-2021
            Assembly Method                   :: HGAP v. 4
            Assembly Name                     :: Microbial assembly
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 304x
            Sequencing Technology             :: PacBio Sequel
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI
            Annotation Date                   :: 03/08/2023 12:34:33
            Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline
            (PGAP)
            Annotation Method :: Best-placed reference protein set; GeneMarkS-2+
            Annotation Software revision      :: 6.4
            Features Annotated                :: Gene; CDS; rRNA; tRNA; ncRNA
            Genes (total)                     :: 4,766
            CDSs (total)                      :: 4,647
            Genes (coding)                    :: 4,518
            CDSs (with protein)               :: 4,518
            Genes (RNA)                       :: 119
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 85
            ncRNAs                            :: 12
            Pseudo Genes (total)              :: 129
            CDSs (without protein)            :: 129
            Pseudo Genes (ambiguous residues) :: 0 of 129
            Pseudo Genes (frameshifted)       :: 54 of 129
            Pseudo Genes (incomplete)         :: 92 of 129
            Pseudo Genes (internal stop)      :: 21 of 129
            Pseudo Genes (multiple problems)  :: 34 of 129
            Pseudo Genes (short protein)      :: 1 of 129
            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="FSIS11816184"
                     /serovar="Newport"
                     /isolation_source="comminuted beef"
                     /sub_species="enterica"
                     /db_xref="taxon:108619"
                     /plasmid="pFSIS11816184-2"
                     /geo_loc_name="USA:TX"
                     /collection_date="2018"
                     /collected_by="USDA-FSIS"
     gene            complement(66..299)
                     /locus_tag="EJW32_23805"
     CDS             complement(66..299)
                     /locus_tag="EJW32_23805"
                     /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="WEN75197.1"
                     /translation="MTELEGHLLNALEHLQQDYMRRLNEWESAFAELQKMHAVTQQNNA
                     ILNERVVNLSQQVQLLAGQVDRLSRLFITNNR"
                     /name="MbeD family mobilization/exclusion protein"
     gene            complement(306..866)
                     /locus_tag="EJW32_23810"
     CDS             complement(306..866)
                     /locus_tag="EJW32_23810"
                     /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="WEN75198.1"
                     /translation="MSNLLQMGTDFEKKLKERAASTENMLNSEFRKLEESVDKALSLNR
                     QKIRDAISEHTTSVKQQLDTLSTTVSTQLSTTEAELSRQQKNLLWQVIKGRVLFPALTA
                     LSVTGGIFLGCWGLIQWQESRIAKNILTIREQENTLAKLEAKTWGVTFVNGENGKFLVL
                     PDGVKGENTWTVGDKNAVRLVRE"
                     /name="MbeB family mobilization protein"
     gene            complement(901..1335)
                     /locus_tag="EJW32_23815"
                     /pseudo=""
     CDS             complement(901..1335)
                     /locus_tag="EJW32_23815"
                     /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(1544..1867)
                     /locus_tag="EJW32_23820"
     CDS             complement(1544..1867)
                     /locus_tag="EJW32_23820"
                     /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="WEN75199.1"
                     /translation="MLTIRVSDEEHARLLERCEGKRLAEWMRRVCLGEPVARTGKLPTL
                     SPPLLRHLAAIGNNLNQTARKVNSGHWSSIDRVHVVAALMAIEGELRQLRQAVREQGGR
                     DDS"
                     /name="MobC family plasmid mobilization relaxosome protein"
     gene            1930..2121
                     /locus_tag="EJW32_23825"
     CDS             1930..2121
                     /locus_tag="EJW32_23825"
                     /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="WEN75200.1"
                     /translation="MTKQEKTALNMARFIRSQTLTLLEKLNELDADEQADICESLHDHA
                     DELYRSCLARFGDDGESN"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            3132..3971
                     /locus_tag="EJW32_23830"
     CDS             3132..3971
                     /locus_tag="EJW32_23830"
                     /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="WEN75196.1"
                     /translation="MLTLFIFFVLLIAACFFCFAPPRRGYDRNEIIPYKIKLSINKYRL
                     YIYSSGKVRQYLLFLVILSLYYSIAEPFKSELIKNISYSLMAAFIFDTGLNFSKENITK
                     GVISTRWHNDLYSSFERMKAINKIYYPSNKEINTEGLSKAITSSLFNDDANSFAKRDFR
                     LMWDLSSEKYLSYKEIIIRKGDKLDAVCLRFINDDYKFLVNFNRDEEVFKYFPSIMQPS
                     LKTYRALSRLVNSIKDPSRFKFTTESLEMELLEYLELRNELFNDIEEVMGSYAQRAP"
                     /name="hypothetical protein"
     Typing          complement(2210..2294)
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="3.03e-37"
     Typing          2305..2860
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="93.907"
                     /coverage="99.0"
                     /evalue="0.0"
     Typing          complement(2..1554)
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="98.0"
                     /evalue="0.0"
ORIGIN
        1 ttcgggttcc tgctcttcat gccagcgccg ggcaagctcc tgcgcctgac gctcctgttc
       61 atcccttatc tgttgttcgt gataaataac cgactcaagc ggtcgacttg tccggctaat
      121 agctgcacct gctgactcaa gttcacgaca cgctcgttca gtatcgcgtt gttctgttgc
      181 gtaaccgcgt gcatcttctg caattctgcg aaggcgctct cccactcgtt cagccgccgc
      241 atatagtcct gttgcaaatg ctctaaggcg ttcagcaaat gcccttccag ttccgtcata
      301 ctcgtttact ccctgaccag cctcacggcg ttcttgtcgc ccaccgtcca ggtgttttcc
      361 cctttcaccc cgtccggcag caccagaaat ttcccgttct cgccattgac gaacgtcacc
      421 ccccaggttt ttgcctcgag tttcgccagc gtgttttcct gctctctgat ggtcaagata
      481 tttttcgcaa tcctgctttc ctgccactga atcagccccc agcaccccag gaaaatgccg
      541 cccgtgacgc tgagcgcggt cagcgccgga aacagtaccc gccctttgat cacctgccag
      601 agcaggtttt tctgctgccg ggacagttcg gcctctgtgg tgctgagctg cgtgctcacg
      661 gtggtgctca gcgtatccag ttgctgtttc acggatgttg tatgttcgct gatagcgtct
      721 ctgattttct gcctgtttaa gctcagtgcc ttgtctacag actcttctag cttcctgaac
      781 tcgctgttca gcatgttctc ggtagaagcg gctcgctctt tcagtttctt ctcgaagtcc
      841 gttcccattt gtaaaagatt gctcatacag cgcccccttt agcctgagat tccgcccccc
      901 ctccgggtcg gcaatactga tactgcttct ggttgtcctc accacctcaa aacctgccgc
      961 tgtgagcgcc tcagtgacat cctgacgcgt ttttattgct ccggcacggt aaagcgcctc
     1021 aagaccccgt gtaatcgctt ctgcggcctc ctgtttcgct tttggcagat tattcggtgt
     1081 gacaagcgtc cgtctgttct ccggtgcgtt cgggtcacgc agcccgtaat gatgattaac
     1141 cagcgtctgc caggcattta tcctcggcct gtccgcacgg tcgtagtacg gctggaggcg
     1201 cttaccgctc tgtagttcca tgttcggaat gacaaaattc agttcgagcc gccccttatc
     1261 ctggtgttcc acccagagaa tgctgtactg gtctttttcg agaccgggca taagaacacg
     1321 ctcaaagctc gtcatcactc tttcgcgttc acccggcggt aactccttct ccgcgaacga
     1381 cagaacgcct gacgtgtatt tcttcgaaaa tggcgtggca tcaatgagtt cccggatttc
     1441 ttccgggtta ccccggagca ccgttgcgcc ttcgcggtta cgctcccgcc ccagcaggta
     1501 atcgaccggg ccacttccac cgcctttccc cctggcatga aatttaacta tcatcccgtc
     1561 ccccctgttc cctgacagcc tgccgcaact ggcgcaattc accctcgatg gccatcagag
     1621 cggccaccac atgaacccgg tcaatcgaag accagtggcc gctgttcacc ttccgggctg
     1681 tctggttcag attgttcccg atggcagcca gatgccgcag caatggcggc gatagtgtcg
     1741 gcagttttcc tgtgcgcgca accggctccc ccagacagac ccgccgcatc cattctgcca
     1801 gtcgtttacc ctcgcagcgt tccagtaacc gggcgtgctc ctcatcgcta acccgtatcg
     1861 tgagcatctt ctcgcgtttc atcggtatca ttccccctaa aaaatcccct attaaggagc
     1921 cttaagacca tgaccaaaca ggaaaaaaca gcccttaaca tggcccgctt tatcagaagc
     1981 cagacgctga ccctgctgga aaaactcaac gagctggacg cggacgaaca ggcagacatc
     2041 tgcgaatcac ttcacgacca cgccgacgaa ctctaccgta gttgcctcgc acgcttcggc
     2101 gatgacggtg aaagcaactg aaacatgcag ctcccggaga cgttcacagc ttgcctgtga
     2161 gcggatgccg ggagcagaca agcccgtcag ggcgcgtcag cgggttttag cgggtgtcgg
     2221 ggcgcagccc tgacccagtc acgtagcgat agcggagtgt atactggctt aactatgtgg
     2281 catcagtgcg gattataaga aaagtgcacc atatgcggtg tgaaataccg cacagatgcg
     2341 taaggagaaa atgccgcatc aggcgctctt ccgcttcctc gctcactgac tcgctacgct
     2401 cggtcgttcg gctgcggcga gcggtatcag ctcactcaaa gacggtgatg cggttatcca
     2461 cagaatcagg ggataacgcc aaaagaaaca tgtgagcaaa aggccaggaa caggaagaag
     2521 gccgcgccgc tggcgttttt ccataggctc cgcccccctg acgagcatca caaaaacaga
     2581 tgctcaagtc agaggtggcg aaacccgaca ggactataaa gataccaggc gtttccccct
     2641 ggaagctccc tcgtgcgctc tcctgttccg accctgccgc ttaccggata cctgtccgcc
     2701 tttctccctt cgggaagcgt ggcgctttct catagctcac gctgttggta tctcggcccg
     2761 gtgtaggtcg ttcgctccaa gctgggctgt gtgcacgaac cccccgttca gcccgaccgc
     2821 tgcgccttat ccggtaacta tcgtcttgag tccaacccgg aaagacacgt aaaaacgcca
     2881 ctggcagcag ccattggtaa ccgtttagag gagttagtct tgaagttatg cgccggttaa
     2941 ggctaaactg aaaggacaga tttggtggct gtgctcctcc aagccagtta ccttggttca
     3001 aagagttgct gctctgagaa ccttcgaaaa gccgccttgc tgggcggttt tttcgtttac
     3061 ggacaagact accttcagga tcgttagatc tcaagacaat catgcatagt gagcatacac
     3121 aggagccgaa cttgcttaca ctgttcatct tttttgtttt attaatagct gcatgcttct
     3181 tttgttttgc tccaccacga agaggatatg acagaaatga gatcattcca tacaaaataa
     3241 aactatcaat aaataaatat cgcctttaca tatactcatc gggaaaggta agacaatacc
     3301 ttttattttt agttatttta tcactgtact actccatagc ggaaccattt aagtctgagt
     3361 taataaaaaa catatcatat tcactgatgg ctgcatttat ttttgataca gggcttaatt
     3421 ttagcaagga gaatataact aaaggagtga tttcaacaag gtggcataat gacctatatt
     3481 catcatttga gagaatgaaa gcaattaata aaatttacta cccatccaac aaagagataa
     3541 acacagaagg tctatccaaa gccatcacat catctctttt caatgatgac gcgaactcgt
     3601 tcgcaaagag agattttcgc ttgatgtggg acttatcttc tgaaaaatat ctttcctata
     3661 aagaaataat aataagaaaa ggcgataagc ttgacgctgt atgcttgaga tttataaatg
     3721 atgactacaa gtttttagtt aatttcaaca gagatgaaga ggttttcaaa tactttccat
     3781 ctataatgca accttcactc aaaacatata gagcgttatc aagactagta aactcaatca
     3841 aagatccttc tagatttaag ttcacgacag agtcattaga aatggagtta ctagaatact
     3901 tagagttaag aaatgaatta ttcaatgaca tagaagaagt aatgggtagc tatgctcaga
     3961 gggcaccata gttcatgata gccctcgata gtacttactt atatttttag agaggtttaa
     4021 gtgtaagtag agggagtaac acctggtttt tcagcatcca ctccaatgaa tgctgacacc
     4081 gatacgcgat aattctcttt atcgtagcaa aatcatcctc cagattgcgg ttgagaatag
     4141 gttcatggtg cgcaatacga ttgcgcagtt ttctcacggg acttgttagc agtaatgctt
     4201 ccccccgggg acaaacgaca gagatataca acaaaggccc gcaattaaaa tactccgtat
     4261 ttaccataac gtcgcattac gcgcaccgct aaaacgcgtt cagcgcgatc acggcagcag
     4321 acaggtaaaa atggcaacaa accacccgaa aaactgccgc gatcgcgcct ggtaaatttt
     4381 aacctcatgc atagttatgc gcgaaactga atgacgatca gtttcgcacg ttccagccgt
     4441 cgaacggggc aaaatgggga ggtttggata ttgttaatgc taatgtacgt acattaacat
     4501 tggcgccatc cgggtagggc gtgccacaaa ctggctcgat ttcagggggt accccggtca
     4561 catccccatt gacgggccac gccagatccg cgc
//
