LOCUS       NZ_CP117325             1035 bp    DNA     circular CON 25-JUN-2023
DEFINITION  Salmonella enterica subsp. enterica serovar Derby strain RM001
            plasmid pRM001_3, complete sequence.
ACCESSION   NZ_CP117325
VERSION     NZ_CP117325.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN32950806
            Assembly: GCF_028893035.1
KEYWORDS    RefSeq.
SOURCE      Salmonella enterica subsp. enterica serovar Derby
  ORGANISM  Salmonella enterica subsp. enterica serovar Derby
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Salmonella.
REFERENCE   1  (bases 1 to 1035)
  AUTHORS   Lewis,G.L., Fenton,R.J., Moriyama,E.N., Loy,J.D. and Moxley,R.A.
  TITLE     Association of ISVsa3 with Multidrug Resistance in Salmonella
            enterica Isolates from Cattle (Bos taurus)
  JOURNAL   Microorganisms 11 (3), 631 (2023)
   PUBMED   36985205
  REMARK    Publication Status: Online-Only
REFERENCE   2  (bases 1 to 1035)
  AUTHORS   Moxley,R.A.
  TITLE     Direct Submission
  JOURNAL   Submitted (01-FEB-2023) School of Biological Sciences, University of
            Nebraska-Lincoln, 403 Manter Hall, Lincoln, NE 68588-0118, USA
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Date                     :: 04-OCT-2021
            Assembly Method                   :: Raven v. 1.5.1
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 343X
            Sequencing Technology :: illumina MiSeq + Nanopore Gridion
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 06/25/2023 10:17:09
            Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline
            (PGAP)
            Annotation Method :: Best-placed reference protein set; GeneMarkS-2+
            Annotation Software revision      :: 6.5
            Features Annotated                :: Gene; CDS; rRNA; tRNA; ncRNA
            Genes (total)                     :: 4,745
            CDSs (total)                      :: 4,627
            Genes (coding)                    :: 4,490
            CDSs (with protein)               :: 4,490
            Genes (RNA)                       :: 118
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 84
            ncRNAs                            :: 12
            Pseudo Genes (total)              :: 137
            CDSs (without protein)            :: 137
            Pseudo Genes (ambiguous residues) :: 0 of 137
            Pseudo Genes (frameshifted)       :: 65 of 137
            Pseudo Genes (incomplete)         :: 87 of 137
            Pseudo Genes (internal stop)      :: 19 of 137
            Pseudo Genes (multiple problems)  :: 31 of 137
            Pseudo Genes (short protein)      :: 1 of 137
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP117325.1.
            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..1035
                     /organism="Salmonella enterica subsp. enterica serovar
                     Derby"
                     /mol_type="genomic DNA"
                     /strain="RM001"
                     /serovar="Derby"
                     /isolation_source="Manila ropes placed above water tanks
                     and feed bunks used as sampling devices"
                     /host="Bos taurus"
                     /sub_species="enterica"
                     /db_xref="taxon:28144"
                     /plasmid="pRM001_3"
                     /geo_loc_name="USA: midwestern"
                     /collection_date="2000-09-19"
                     /collected_by="University of Nebraska-Lincoln"
     gene            471..1001
                     /locus_tag="PQP82_RS23725"
                     /old_locus_tag="PQP82_23725"
     CDS             471..1001
                     /locus_tag="PQP82_RS23725"
                     /old_locus_tag="PQP82_23725"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000634347.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="helix-turn-helix domain-containing protein"
                     /protein_id="WP_023565501.1"
                     /translation="MISGLDKRSQRRMREIDLERAKEAQERREDQKNSKFTQVSPKGWE
                     RIRELSKDKQGVAAIALYSFLAEHIDPTCGAVVAEQQFLADKLNVSRSTIKRWLNYLEA
                     KNAVVRIPVAGNVCAYALDPHEVWKGYNSSKGYAAFVSKTLVNVDGDVQRRIVAMFKGQ
                     EGDAKDQCDLPLE"
                     /name="helix-turn-helix domain-containing protein"
ORIGIN
        1 acccttgacg ggctgtaacg acccccacac ttggcaaagg tggttgtgat cacgcagtga
       61 gcgcaaccac ctgttaagcc gcctttgacg ttgaccttcc cgaacatcaa aacatcctga
      121 tagctccctc gctgcgctca ggcgtaacag cgttcgggtg tcggggccat atttttgagc
      181 gtcaaggtcg agccgcttcg cggtcgctaa agcgaacctt gacccccaaa aatgcccgcc
      241 gaaaggcggg aggtaacttt agccttgggt gttgaattta ggtttttaaa gattagataa
      301 gtggaaaact ataagtatct gatttatata catttcaata aatgagctag accacacatg
      361 cgtgagctag ctctagacca tgcatgcgtg agctagcttg agctaagata gtttactttt
      421 gagctaaggt agcttatttt tgagctacca atggctcatg aggaatagcg atgatttcgg
      481 ggttagacaa aagatctcaa agacggatga gagagatcga tttagagcgc gctaaagagg
      541 cccaggaacg gcgtgaagac caaaagaaca gtaagttcac ccaagtatcc ccaaagggct
      601 gggaacgcat tagagagctt tctaaggaca aacagggtgt agctgcaatc gcgctgtact
      661 cgtttttagc tgagcacatc gatccaacgt gtggggctgt cgttgctgaa caacagtttt
      721 tggctgacaa actgaacgtt agcaggagca cgatcaagcg ttggttaaac taccttgagg
      781 ccaaaaatgc ggtagtaaga atcccagttg ccggcaacgt ctgcgcctat gcgctagacc
      841 cccatgaggt ttggaagggt tacaactcca gcaaaggcta tgcagcattc gtaagcaaaa
      901 cgttggttaa cgttgacggt gatgtacagc gccgaatcgt tgccatgttc aaagggcagg
      961 aaggcgacgc taaagaccaa tgcgacctgc ctttagagtg aaagccggtc aagggcgcgt
     1021 tagcggcgcc agcga
//
