LOCUS       NZ_CP117304             1316 bp    DNA     circular CON 25-JUN-2023
DEFINITION  Salmonella enterica subsp. enterica serovar Derby strain RM006
            plasmid pRM006_3, complete sequence.
ACCESSION   NZ_CP117304
VERSION     NZ_CP117304.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN32950811
            Assembly: GCF_028892955.1
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 1316)
  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 1316)
  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                   :: Unicycler v. v0.4.9
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 248X
            Sequencing Technology :: illumina MiSeq + Nanopore Gridion
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 06/25/2023 10:08:28
            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)                     :: 4,705
            CDSs (total)                      :: 4,587
            Genes (coding)                    :: 4,449
            CDSs (with protein)               :: 4,449
            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)              :: 138
            CDSs (without protein)            :: 138
            Pseudo Genes (ambiguous residues) :: 0 of 138
            Pseudo Genes (frameshifted)       :: 63 of 138
            Pseudo Genes (incomplete)         :: 78 of 138
            Pseudo Genes (internal stop)      :: 30 of 138
            Pseudo Genes (multiple problems)  :: 30 of 138
            Pseudo Genes (short protein)      :: 1 of 138
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP117304.1.
            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..1316
                     /organism="Salmonella enterica subsp. enterica serovar
                     Derby"
                     /mol_type="genomic DNA"
                     /strain="RM006"
                     /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="pRM006_3"
                     /geo_loc_name="USA: midwestern"
                     /collection_date="2000-10-30"
                     /collected_by="University of Nebraska-Lincoln"
     gene            1..531
                     /locus_tag="PQP83_RS23525"
                     /old_locus_tag="PQP83_23525"
     CDS             1..531
                     /locus_tag="PQP83_RS23525"
                     /old_locus_tag="PQP83_23525"
                     /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 atgatttcgg ggttagacaa aagatctcaa agacggatga gagagatcga tttagagcgc
       61 gctaaagagg cccaggaacg gcgtgaagac caaaagaaca gtaagttcac ccaagtatcc
      121 ccaaagggct gggaacgcat tagagagctt tctaaggaca aacagggtgt agctgcaatc
      181 gcgctgtact cgtttttagc tgagcacatc gatccaacgt gtggggctgt cgttgctgaa
      241 caacagtttt tggctgacaa actgaacgtt agcaggagca cgatcaagcg ttggttaaac
      301 taccttgagg ccaaaaatgc ggtagtaaga atcccagttg ccggcaacgt ctgcgcctat
      361 gcgctagacc cccatgaggt ttggaagggt tacaactcca gcaaaggcta tgcagcattc
      421 gtaagcaaaa cgttggttaa cgttgacggt gatgtacagc gccgaatcgt tgccatgttc
      481 aaagggcagg aaggcgacgc taaagaccaa tgcgacctgc ctttagagtg aaagccggtc
      541 aagggcgcgt tagcggcgcc agcgaaccct tgacgggctg taacgacccc cacacttggc
      601 aaaggtggtt gtgatcacgc agtgagcgca accacctgtt aagccgcctt tgacgttgac
      661 cttcccgaac atcaaaacat cctgatagct ccctcgctgc gctcaggcgt aacagcgttc
      721 gggtgtcggg gccatgccct gaccaagatg ttttggagtg tccgcggcgt gtcggcggta
      781 ctccaaaaac acatcttgtc ccgtgcgttt tgtcaccgtc acaaagtggc ggtaatacaa
      841 aacatatcct gtcccttcct tggtatctct gaagttaagc cagtatacac tccgctagcg
      901 ctacgtgact ggttcagggc tgcgccccga aacccgcaaa ggtcaaaacc aaaagcgcct
      961 ggcaggtggt tgcgctcact gcgtgatcac aaccacctac gggtagcatg ttgggcattt
     1021 ttgagcgtca aggtcgagcc gcttcgcggt cgctaaagcg aaccttgacc cccaaaaatg
     1081 cccgccgaaa ggcgggaggt aactttagcc ttgggtgttg aatttaggtt tttaaagatt
     1141 agataagtgg aaaactataa gtatctgatt tatatacatt tcaataaatg agctagacca
     1201 cacatgcgtg agctagctct agaccatgca tgcgtgagct agcttgagct aagatagttt
     1261 acttttgagc taaggtagct tatttttgag ctaccaatgg ctcatgagga atagcg
//
