LOCUS       NZ_CP041210             3605 bp    DNA     circular CON 30-SEP-2023
DEFINITION  Salmonella enterica subsp. enterica serovar Newport strain
            SAP18-8729 plasmid pCFSAN074384_2, complete sequence.
ACCESSION   NZ_CP041210
VERSION     NZ_CP041210.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN09943626
            Assembly: GCF_004224885.1
KEYWORDS    RefSeq.
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   Hoffmann,M., Sanchez,M., Trees,E. and Timme,R.
  TITLE     GEN-FS coordinated proficiency test data for genomic foodborne
            pathogen surveillance, 2017 and 2018
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 3605)
  AUTHORS   Hoffmann,M., Sanchez,M., Trees,E. and Timme,R.
  TITLE     Direct Submission
  JOURNAL   Submitted (21-MAY-2019) CFSAN-ORS-DM-MMSB, FDA Center for Food
            Safety and Applied Nutrition, 5100 Paint Branch Parkway, College
            Park, MD 20740, USA
REFERENCE   3  (bases 1 to 3605)
  CONSRTM   GenomeTrakr: Next Generation Sequencing Network for Food Pathogen
            Tracability
  TITLE     Direct Submission
  JOURNAL   Submitted (05-SEP-2018) Center for Food Safety and Applied
            Nutrition, US Food and Drug Administraion, 5100 Paint Branch Pkwy,
            College Park, MD, USA
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: HGAP v. 3
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 120x
            Sequencing Technology             :: PacBio
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 09/30/2023 02:51:20
            Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline
            (PGAP)
            Annotation Method :: Best-placed reference protein set; GeneMarkS-2+
            Annotation Software revision      :: 6.6
            Features Annotated                :: Gene; CDS; rRNA; tRNA; ncRNA
            Genes (total)                     :: 4,859
            CDSs (total)                      :: 4,738
            Genes (coding)                    :: 4,614
            CDSs (with protein)               :: 4,614
            Genes (RNA)                       :: 121
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 86
            ncRNAs                            :: 13
            Pseudo Genes (total)              :: 124
            CDSs (without protein)            :: 124
            Pseudo Genes (ambiguous residues) :: 0 of 124
            Pseudo Genes (frameshifted)       :: 47 of 124
            Pseudo Genes (incomplete)         :: 93 of 124
            Pseudo Genes (internal stop)      :: 19 of 124
            Pseudo Genes (multiple problems)  :: 32 of 124
            Pseudo Genes (short protein)      :: 1 of 124
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP041210.1.
            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/
            COMPLETENESS: full length.
FEATURES             Location/Qualifiers
     source          1..3605
                     /organism="Salmonella enterica subsp. enterica serovar
                     Newport"
                     /mol_type="genomic DNA"
                     /strain="SAP18-8729"
                     /serovar="Newport"
                     /sub_species="enterica"
                     /db_xref="taxon:108619"
                     /plasmid="pCFSAN074384_2"
                     /geo_loc_name="USA:GA"
                     /collection_date="2018"
                     /collected_by="CDC"
     gene            334..483
                     /locus_tag="D2X89_RS24620"
     CDS             334..483
                     /locus_tag="D2X89_RS24620"
                     /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="WP_001138881.1"
                     /translation="MPSEYDEQRDATDTQLPGEYDLFDLMAKVTEENLHAPVDFGPPVG
                     REAL"
                     /name="hypothetical protein"
     gene            1501..3033
                     /locus_tag="D2X89_RS24520"
                     /old_locus_tag="D2X89_24520"
     CDS             1501..3033
                     /locus_tag="D2X89_RS24520"
                     /old_locus_tag="D2X89_24520"
                     /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="WP_000750321.1"
                     /translation="MKKSVVRQVLEMSGPCISSDLAERIQWQYPSMSPEAIRKMISRST
                     DIGKLPFLKFSHNRRFIYLKDDFGSFKFWRALEKCMYEANSTYSHAILSVINNGGYLKV
                     KDFGIVSGSPIKQAKHLSYETVLRNLLSAKILRAVYIDGVGDCVLINNNIANDVNIRTM
                     ANCESFFDKPIFELVKAWLRNLGLVAFNQIKTKYDGEGNPVVGSFEWDMTAPSYVSPLA
                     EYVGGKLMPGFVACDFSLGFNRDEITTAAAETFIRKVQMTKSSRASQRIMFVIFARRFG
                     KIAFNKLRSEGVLAVTIANAFGNKVDESLTRLSRVVQGSLSIEKHPDELLQMVKDLESV
                     SGENGNLRGYVFELFVSSQISNFYGLGNIYINREYKINGKHAEADVVLESSDDIYIIEC
                     KNVKVLPSTELTRWMKERVPIINSYYKINNLEKKNIHHYLWVTGNVYNKDLKRLDSFKN
                     NNKNIDVDYLFGEHLDDFFYKKKRVFNLYRKVISPDYKKGVMPDFELEDDFF"
                     /name="NERD domain-containing protein"
     gene            complement(3222..3380)
                     /locus_tag="D2X89_RS25005"
                     /old_locus_tag="D2X89_24530"
     CDS             complement(3222..3380)
                     /locus_tag="D2X89_RS25005"
                     /old_locus_tag="D2X89_24530"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001326446.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_001403044.1"
                     /translation="MHEPPVQSDCCACSGNYRLESNPERHDKTPLAAAIGIWFTERRGV
                     YKHTQSS"
                     /name="hypothetical protein"
     Typing          126..341
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="85.845"
                     /coverage="100.0"
                     /evalue="7.43e-58"
     Typing          complement(2..176)
                     /name="ColRNAI_rep_cluster_1987"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="88.068"
                     /coverage="99.0"
                     /evalue="9.01e-51"
     Typing          complement(3082..3562)
                     /name="rep_cluster_2358"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="98.344"
                     /coverage="91.0"
                     /evalue="0.0"
ORIGIN
        1 gcctatggaa aaacggcagc gccgcgtcct tttcctgccc tgtttgtcat gccacatgct
       61 tttgctctta tccgtgtgca gctaacgccc gccgcagccg aacggcagga gcggtagcga
      121 ccgagtgagc gaggaggcgt catatcacag taacccccat tttctcccgt acgccctgta
      181 gctgcatttt cccctgtcac atgaagcact ttcctgaacc ccgaccccgc cgtaacatat
      241 tcagctagtt tagactccgc tagcgctacg tgactggttc agggctgcgc tccgaaaccc
      301 gctaacaacc ccttagctac tggatatcac cccatgccat ctgaatatga tgaacaacgg
      361 gatgcgactg atacgcagct tcccggcgaa tatgaccttt ttgatttaat ggcgaaggtt
      421 actgaagaga acctgcacgc cccggtggat tttgggccgc ctgtcggccg ggaagcgtta
      481 tagctttttc gcttacccgc gtacgtgtaa tacgccggta ttacatctta tttctttatt
      541 ttcatgtgat tacaggtggt tgtaatacgt tgcgtattac ataaataaac gggaacttca
      601 gtttttacct tttaattcat gcaattgcga tgaaaatcgc ggttgcgtat ggtgtatggc
      661 catttaaggg ataaagaatc atctccttac cgggctgagc tttgcctatt ctgaggagat
      721 ctgtgaaaaa aagcgtccat aactagctcg ttcatacttg tatgaacagc ttattcctcc
      781 tgactactaa taaactacag cgtcactact gatttactac tgatttacta caaaccggag
      841 gggggggact acagaaacac tactgattta ctactgattt actacaaatc ggaggaggat
      901 gactacttat ctactactga tttactactg aattactact gaattacgtc ataacagttc
      961 tctgaaccat tcgtacatcc gacccccttc tcttcatgct tgatgctctt gccaacgctt
     1021 tacggtcacg caataaattg cgtccccgtt caccgttttc ggatgagaag aacgtcgaaa
     1081 acaggacttc cactggctgc acggcgtgaa attctgcgct atgcacttgc gcgcatactc
     1141 atgcatgccg taaaaacaga gcctgcgcgt ttctggctgg ttttcgggtg gtttgttgcc
     1201 ttgttttacc ggtttcccgt cagaaacgcc ctgagagcct ctcaggcggt gcacgcaacg
     1261 gatgttatgg taaatggagt agctgatagt tcgataaaaa aatgtcacaa tactatcttt
     1321 atgatttaaa aggattaaat aattataaag acgatatttc tttgtgctca atttaaagta
     1381 agtaattaac catctgattt ttaattattt tttatagtca ctttttttta aaagactgcg
     1441 ccctattaca cgtagtgtaa tattataaat agcgtagtgt gacagaaata aggtgaggat
     1501 atgaaaaaaa gtgttgttag acaggtgctt gaaatgagcg ggccatgcat ctcttcggat
     1561 cttgcagaga gaattcagtg gcaatatccc tcaatgtccc ctgaagcgat acgtaaaatg
     1621 atctcgcgaa gcacggacat aggtaagctg ccatttttga aattcagcca taacaggaga
     1681 ttcatttatc taaaagatga ttttggcagt ttcaaatttt ggcgagctct cgaaaagtgc
     1741 atgtacgaag caaactcaac ttactcacac gcgatacttt ccgtaataaa taatggcggt
     1801 tatttgaagg tgaaagattt tgggattgtg tctggatctc ctataaaaca agctaaacat
     1861 ttaagttatg aaacagttct aagaaatcta ctttcggcaa aaatacttag agccgtgtat
     1921 attgatggag ttggtgattg cgtactgata aataacaaca tagccaacga tgttaatatt
     1981 agaacaatgg caaattgcga atcctttttt gacaaaccaa tatttgagct tgttaaagct
     2041 tggttgagga atttaggcct agtcgctttt aatcagataa aaacaaaata tgatggggag
     2101 ggaaatccag ttgtaggctc ttttgaatgg gatatgaccg ctccaagtta cgtttcccct
     2161 ctcgctgaat atgtcggcgg aaaactgatg cctggtttcg ttgcctgtga tttttctctc
     2221 ggctttaatc gtgatgaaat tactaccgct gcagcagaaa cattcataag aaaagtccag
     2281 atgaccaagt cttctcgagc gagtcagagg ataatgtttg ttattttcgc aaggcgtttc
     2341 ggcaaaatag ccttcaataa gttgagaagt gagggggttc tggctgtaac tatagcaaat
     2401 gcgtttggta ataaagttga tgaaagctta accaggttgt cgagggtggt tcagggttct
     2461 ttgtccattg aaaagcatcc agatgagttg cttcagatgg ttaaagatct ggagtctgtt
     2521 tctggagaga atggcaattt gagagggtat gtttttgagc tttttgtatc ctcgcaaatt
     2581 tctaattttt atggccttgg taatatttac attaatagag agtataagat aaatggtaag
     2641 catgcagaag ctgatgttgt attggagagt agtgacgata tttatataat agagtgcaaa
     2701 aatgttaagg tcttaccttc aactgaactt acgcgttgga tgaaagaaag ggttccaatt
     2761 ataaactctt actataaaat aaataattta gaaaaaaaga atatccacca ttatttgtgg
     2821 gttacaggga atgtgtacaa caaagattta aaaaggttag actcttttaa gaataataat
     2881 aagaatatcg atgttgatta tttgtttggt gagcatttgg atgatttctt ttacaagaaa
     2941 aagcgggtgt tcaacttata tagaaaagtc atttcacctg attataaaaa aggcgtaatg
     3001 cctgattttg agttagagga cgattttttc tagctactgc gtttcttgac gatggcgctt
     3061 tgaaaggcgt atcttccatc tctgaaacga aaaaaccacc cggcaaggtg gtttttcgaa
     3121 ggttcaggaa accggcaagt ttctgaaccg tggtaactgg cttaaacgga gcgcagtgac
     3181 caaatctgtc cttccagtgt agccgtagtc aggtcaacac ttcaagaact ctgtgtatgc
     3241 ttgtacacgc ctctccgctc cgtaaaccag ataccaatgg ctgctgccag tggcgttttg
     3301 tcgtgtcttt ccgggttgga ctcaagtcga tagttaccgg aacaggcgca gcagtcggac
     3361 tgaacggggg gttcgtgcat acagtccagc ttggagcgaa ctgccttccc ggaactgagt
     3421 gtcaggcgtg gaatgagata aacgcggcca taacagcgga gtgacaccgg taaaccgaaa
     3481 ggcaggaaca ggagagcgca cgagggagct accaggggga aacgcctggg atctttatag
     3541 tcctgtcggg tttcgccacc actgatttga gtgtcagatt tcgtgatgct tgtcaggggg
     3601 gcgga
//
