LOCUS       NZ_CP025238             3605 bp    DNA     circular CON 19-MAY-2024
DEFINITION  Salmonella enterica subsp. enterica serovar Newport str.
            USDA-ARS-USMARC-1928 plasmid pSNE1-1928, complete sequence.
ACCESSION   NZ_CP025238
VERSION     NZ_CP025238.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN02716897
            Assembly: GCF_004136135.1
KEYWORDS    RefSeq.
SOURCE      Salmonella enterica subsp. enterica serovar Newport str.
            USDA-ARS-USMARC-1928
  ORGANISM  Salmonella enterica subsp. enterica serovar Newport str. USDA-AR...
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Salmonella.
REFERENCE   1  (bases 1 to 3605)
  AUTHORS   Nguyen,S.V., Harhay,D.M., Bono,J.L., Smith,T.P.L., Fields,P.I.,
            Dinsmore,B.A., Santovenia,M., Kelley,C.M., Wang,R., Bosilevac,J.M.
            and Harhay,G.P.
  TITLE     Comparative Genomics of Salmonella Newport
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 3605)
  AUTHORS   Nguyen,S.V., Harhay,D.M., Bono,J.L., Smith,T.P.L., Fields,P.I.,
            Dinsmore,B.A., Santovenia,M., Kelley,C.M., Wang,R., Bosilevac,J.M.
            and Harhay,G.P.
  TITLE     Direct Submission
  JOURNAL   Submitted (07-DEC-2017) Meat Safety and Quality Research Unit,
            USDA-ARS-USMARC, State Spur 18D, Clay Center, NE 68933, USA
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: HGAP v. 3
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 128.75x
            Sequencing Technology             :: PacBio
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_004136135.1-RS_2024_05_19
            Annotation Date                   :: 05/19/2024 04:12:23
            Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline
            (PGAP)
            Annotation Method :: Best-placed reference protein set; GeneMarkS-2+
            Annotation Software revision      :: 6.7
            Features Annotated                :: Gene; CDS; rRNA; tRNA; ncRNA
            Genes (total)                     :: 5,001
            CDSs (total)                      :: 4,880
            Genes (coding)                    :: 4,758
            CDSs (with protein)               :: 4,758
            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)              :: 122
            CDSs (without protein)            :: 122
            Pseudo Genes (ambiguous residues) :: 0 of 122
            Pseudo Genes (frameshifted)       :: 46 of 122
            Pseudo Genes (incomplete)         :: 91 of 122
            Pseudo Genes (internal stop)      :: 20 of 122
            Pseudo Genes (multiple problems)  :: 31 of 122
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP025238.1.
            Bacteria and source DNA available from USMARC.
            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 str. USDA-ARS-USMARC-1928"
                     /mol_type="genomic DNA"
                     /strain="USDA-ARS-USMARC-1928"
                     /serovar="Newport"
                     /isolation_source="bovine peripheral lymph node"
                     /host="Bovine"
                     /sub_species="enterica"
                     /db_xref="taxon:1454621"
                     /plasmid="pSNE1-1928"
                     /geo_loc_name="USA: BIFSCo Region 2"
                     /collection_date="2011-07"
                     /collected_by="USMARC"
     gene            435..593
                     /locus_tag="AW84_RS26445"
                     /old_locus_tag="AW84_24840"
     CDS             435..593
                     /locus_tag="AW84_RS26445"
                     /old_locus_tag="AW84_24840"
                     /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"
     gene            complement(782..2314)
                     /locus_tag="AW84_RS24295"
                     /old_locus_tag="AW84_24850"
     CDS             complement(782..2314)
                     /locus_tag="AW84_RS24295"
                     /old_locus_tag="AW84_24850"
                     /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(3332..3481)
                     /locus_tag="AW84_RS25925"
     CDS             complement(3332..3481)
                     /locus_tag="AW84_RS25925"
                     /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"
     Typing          254..734
                     /name="rep_cluster_2358"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="98.344"
                     /coverage="91.0"
                     /evalue="0.0"
ORIGIN
        1 gtgcttcatg tgacagggga aaatgcagct acagggcgta cgggagaaaa tgggggttac
       61 tgtgatatga cgcctcctcg ctcactcggt cgctaccgct cctgccgttc ggctgcggcg
      121 ggcgttagct gcacacggat aagagcaaaa gcatgtggca tgacaaacag ggcaggaaaa
      181 ggacgcggcg ctgccgtttt tccataggct ccgcccccct gacaagcatc acgaaatctg
      241 acactcaaat cagtggtggc gaaacccgac aggactataa agatcccagg cgtttccccc
      301 tggtagctcc ctcgtgcgct ctcctgttcc tgcctttcgg tttaccggtg tcactccgct
      361 gttatggccg cgtttatctc attccacgcc tgacactcag ttccgggaag gcagttcgct
      421 ccaagctgga ctgtatgcac gaaccccccg ttcagtccga ctgctgcgcc tgttccggta
      481 actatcgact tgagtccaac ccggaaagac acgacaaaac gccactggca gcagccattg
      541 gtatctggtt tacggagcgg agaggcgtgt acaagcatac acagagttct tgaagtgttg
      601 acctgactac ggctacactg gaaggacaga tttggtcact gcgctccgtt taagccagtt
      661 accacggttc agaaacttgc cggtttcctg aaccttcgaa aaaccacctt gccgggtggt
      721 tttttcgttt cagagatgga agatacgcct ttcaaagcgc catcgtcaag aaacgcagta
      781 gctagaaaaa atcgtcctct aactcaaaat caggcattac gcctttttta taatcaggtg
      841 aaatgacttt tctatataag ttgaacaccc gctttttctt gtaaaagaaa tcatccaaat
      901 gctcaccaaa caaataatca acatcgatat tcttattatt attcttaaaa gagtctaacc
      961 tttttaaatc tttgttgtac acattccctg taacccacaa ataatggtgg atattctttt
     1021 tttctaaatt atttatttta tagtaagagt ttataattgg aaccctttct ttcatccaac
     1081 gcgtaagttc agttgaaggt aagaccttaa catttttgca ctctattata taaatatcgt
     1141 cactactctc caatacaaca tcagcttctg catgcttacc atttatctta tactctctat
     1201 taatgtaaat attaccaagg ccataaaaat tagaaatttg cgaggataca aaaagctcaa
     1261 aaacataccc tctcaaattg ccattctctc cagaaacaga ctccagatct ttaaccatct
     1321 gaagcaactc atctggatgc ttttcaatgg acaaagaacc ctgaaccacc ctcgacaacc
     1381 tggttaagct ttcatcaact ttattaccaa acgcatttgc tatagttaca gccagaaccc
     1441 cctcacttct caacttattg aaggctattt tgccgaaacg ccttgcgaaa ataacaaaca
     1501 ttatcctctg actcgctcga gaagacttgg tcatctggac ttttcttatg aatgtttctg
     1561 ctgcagcggt agtaatttca tcacgattaa agccgagaga aaaatcacag gcaacgaaac
     1621 caggcatcag ttttccgccg acatattcag cgagagggga aacgtaactt ggagcggtca
     1681 tatcccattc aaaagagcct acaactggat ttccctcccc atcatatttt gtttttatct
     1741 gattaaaagc gactaggcct aaattcctca accaagcttt aacaagctca aatattggtt
     1801 tgtcaaaaaa ggattcgcaa tttgccattg ttctaatatt aacatcgttg gctatgttgt
     1861 tatttatcag tacgcaatca ccaactccat caatatacac ggctctaagt atttttgccg
     1921 aaagtagatt tcttagaact gtttcataac ttaaatgttt agcttgtttt ataggagatc
     1981 cagacacaat cccaaaatct ttcaccttca aataaccgcc attatttatt acggaaagta
     2041 tcgcgtgtga gtaagttgag tttgcttcgt acatgcactt ttcgagagct cgccaaaatt
     2101 tgaaactgcc aaaatcatct tttagataaa tgaatctcct gttatggctg aatttcaaaa
     2161 atggcagctt acctatgtcc gtgcttcgcg agatcatttt acgtatcgct tcaggggaca
     2221 ttgagggata ttgccactga attctctctg caagatccga agagatgcat ggcccgctca
     2281 tttcaagcac ctgtctaaca acactttttt tcatatcctc accttatttc tgtcacacta
     2341 cgctatttat aatattacac tacgtgtaat agggcgcagt cttttaaaaa aaagtgacta
     2401 taaaaaataa ttaaaaatca gatggttaat tacttacttt aaattgagca caaagaaata
     2461 tcgtctttat aattatttaa tccttttaaa tcataaagat agtattgtga cattttttta
     2521 tcgaactatc agctactcca tttaccataa catccgttgc gtgcaccgcc tgagaggctc
     2581 tcagggcgtt tctgacggga aaccggtaaa acaaggcaac aaaccacccg aaaaccagcc
     2641 agaaacgcgc aggctctgtt tttacggcat gcatgagtat gcgcgcaagt gcatagcgca
     2701 gaatttcacg ccgtgcagcc agtggaagtc ctgttttcga cgttcttctc atccgaaaac
     2761 ggtgaacggg gacgcaattt attgcgtgac cgtaaagcgt tggcaagagc atcaagcatg
     2821 aagagaaggg ggtcggatgt acgaatggtt cagagaactg ttatgacgta attcagtagt
     2881 aattcagtag taaatcagta gtagataagt agtcatcctc ctccgatttg tagtaaatca
     2941 gtagtaaatc agtagtgttt ctgtagtccc ccccctccgg tttgtagtaa atcagtagta
     3001 aatcagtagt gacgctgtag tttattagta gtcaggagga ataagctgtt catacaagta
     3061 tgaacgagct agttatggac gctttttttc acagatctcc tcagaatagg caaagctcag
     3121 cccggtaagg agatgattct ttatccctta aatggccata caccatacgc aaccgcgatt
     3181 ttcatcgcaa ttgcatgaat taaaaggtaa aaactgaagt tcccgtttat ttatgtaata
     3241 cgcaacgtat tacaaccacc tgtaatcaca tgaaaataaa gaaataagat gtaataccgg
     3301 cgtattacac gtacgcgggt aagcgaaaaa gctataacgc ttcccggccg acaggcggcc
     3361 caaaatccac cggggcgtgc aggttctctt cagtaacctt cgccattaaa tcaaaaaggt
     3421 catattcgcc gggaagctgc gtatcagtcg catcccgttg ttcatcatat tcagatggca
     3481 tggggtgata tccagtagct aaggggttgt tagcgggttt cggagcgcag ccctgaacca
     3541 gtcacgtagc gctagcggag tctaaactag ctgaatatgt tacggcgggg tcggggttca
     3601 ggaaa
//
