LOCUS       NZ_CP117335             2699 bp    DNA     circular CON 25-JUN-2023
DEFINITION  Salmonella enterica subsp. enterica serovar Muenster strain RM055
            plasmid pRM055_3, complete sequence.
ACCESSION   NZ_CP117335
VERSION     NZ_CP117335.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN32950802
            Assembly: GCF_028893115.1
KEYWORDS    RefSeq.
SOURCE      Salmonella enterica subsp. enterica serovar Muenster
  ORGANISM  Salmonella enterica subsp. enterica serovar Muenster
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Salmonella.
REFERENCE   1  (bases 1 to 2699)
  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 2699)
  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                   :: 321X
            Sequencing Technology :: illumina MiSeq + Nanopore Gridion
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 06/25/2023 10:22:51
            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)                     :: 4,713
            CDSs (total)                      :: 4,592
            Genes (coding)                    :: 4,418
            CDSs (with protein)               :: 4,418
            Genes (RNA)                       :: 121
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 84
            ncRNAs                            :: 15
            Pseudo Genes (total)              :: 174
            CDSs (without protein)            :: 174
            Pseudo Genes (ambiguous residues) :: 0 of 174
            Pseudo Genes (frameshifted)       :: 76 of 174
            Pseudo Genes (incomplete)         :: 95 of 174
            Pseudo Genes (internal stop)      :: 41 of 174
            Pseudo Genes (multiple problems)  :: 34 of 174
            Pseudo Genes (short protein)      :: 1 of 174
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP117335.1.
            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..2699
                     /organism="Salmonella enterica subsp. enterica serovar
                     Muenster"
                     /mol_type="genomic DNA"
                     /strain="RM055"
                     /serovar="Muenster"
                     /isolation_source="feces"
                     /host="Bos taurus"
                     /sub_species="enterica"
                     /db_xref="taxon:82689"
                     /plasmid="pRM055_3"
                     /geo_loc_name="USA: Nebraska"
                     /collection_date="2017-05-11"
                     /collected_by="Nebraska Veterinary Diagnostic Center"
     gene            complement(189..425)
                     /locus_tag="PQP79_RS23555"
                     /old_locus_tag="PQP79_23555"
     CDS             complement(189..425)
                     /locus_tag="PQP79_RS23555"
                     /old_locus_tag="PQP79_23555"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001676031.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_012772745.1"
                     /translation="MARLTNLTPAEKKFLDDAVAAAERASGKKLNQPNRHIVLNRARAQ
                     IELQRYADRQRALREDERQQSDFAWSRPRAPRR"
                     /name="hypothetical protein"
     gene            <1493..1648
                     /locus_tag="PQP79_RS23560"
                     /old_locus_tag="PQP79_23560"
                     /pseudo=""
     CDS             <1493..1648
                     /locus_tag="PQP79_RS23560"
                     /old_locus_tag="PQP79_23560"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:NP_707212.3"
                     /GO_function="GO:0043565 - sequence-specific DNA binding
                     [Evidence IEA]"
                     /note="incomplete; partial in the middle of a contig;
                     missing N-terminus; Derived by automated computational
                     analysis using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="helix-turn-helix domain-containing protein"
                     /name="helix-turn-helix domain-containing protein"
     gene            1742..2386
                     /locus_tag="PQP79_RS23565"
                     /old_locus_tag="PQP79_23565"
     CDS             1742..2386
                     /locus_tag="PQP79_RS23565"
                     /old_locus_tag="PQP79_23565"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_017900990.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="quinolone resistance pentapeptide repeat protein
                     QnrB19"
                     /protein_id="WP_012954666.1"
                     /translation="MTLALVGEKIDRNRFTGEKVENSTFFNCDFSGADLSGTEFIGCQF
                     YDRESQKGCNFSRAMLKDAIFKSCDLSMADFRNVSALGIEIRHCRAQGADFRGASFMNM
                     ITTRTWFCSAYITNTNLSYANFSKVVLEKCELWENRWMGTQVLGATFSGSDLSGGEFST
                     FDWRAANFTHCDLTNSELGDLDIRGVDLQGVKLDSYQASLLMERLGIAVIG"
                     /name="quinolone resistance pentapeptide repeat protein
                     QnrB19"
     ARG             1743..2383
                     /name="qnrB19"
                     /gene="qnrB19"
                     /gene_name="quinolone resistance pentapeptide repeat
                     protein QnrB19"
                     /tool="amrfinderplus"
                     /drug_class="QUINOLONE"
                     /identity="100.0"
                     /coverage="100.0"
     Typing          complement(591..764)
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="2.5600000000000002e-86"
     Typing          743..1234
                     /name="rep_cluster_2335"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="92.51"
                     /coverage="81.0"
                     /evalue="0.0"
ORIGIN
        1 ccttgcccgc acccccgcag gcgccctcag cgcaatcctg ctgcatcagg gccgtttcca
       61 gcacctttcc tcaccagtat cccggaaaaa cgcccctgat gatttctgcg cgactgcatg
      121 gctatgcacg caggtgaatg gcaggtgatt tcgcagcgtc agcaccacta aaccgccaaa
      181 agccaaaatc agcggcgcgg cgcgcgcgga cgtgaccagg caaaatcgga ctgctgccgc
      241 tcatcctcac gtaatgcacg ctggcggtcg gcgtaacgct gcaactcaat ttgcgcacgc
      301 gctctgttca ggacgatgtg ccggttaggc tgatttagct ttttacctga cgctctttca
      361 gctgcggcaa cagcatcatc aagaaatttt ttctctgcag gcgtcaagtt tgtcagtctg
      421 gccataacgt tctccagtca gaataaatca gcacagtctg ccagacacag tagaaacgat
      481 gaagcgccag cgacggtgaa aggcagtcag aaacggtgaa cgggagcgga ttttaatccg
      541 gtgccgtgag gcgttggaca agccgcaggc gcgtcattag cttttagccg gtttcggggc
      601 gcagccctga accagtcacg tagcgctagc ggagtgtata ctggctgact atgttggcac
      661 ggatgtggaa atcagtgaag tgcttcatgt agcaggagaa aaaaggcggc accagcgcgt
      721 cagcaggata tgtagtacag gatatattcc gcttcctcgc tcactgactc gctgcgctcg
      781 gtcgttcggc tgcggcgagc ggtgccggct tacaggcggg gcggaaattt cctgggagat
      841 accaggaagg agcttaacag ggaagagata aggccgcggc gaagccgttt ttccataggc
      901 tccgcccccc tgacaaacat catgaaatct gacgctcaaa tcagtggtgg cgaaacccga
      961 tgcggcttaa agataccagg cgtttccccc tggtggctcc ctcgtgctcc cccgcattcc
     1021 tgcctttcgg tttaccggtg tcattccgct gttatggccg cgtttatctc attccacgcc
     1081 tgacactcag ttccgcgaag gcagttcgct cctggatgga ctgtatgcac gaaccccccg
     1141 ttcagtccga ctgctgcgcc ttatccggta actatcatct tgagtccaac ccggaaagac
     1201 acgacttatc gccactggca gcagccactg gtaactgatt tagaggagtt agtcttgaag
     1261 ttatgcgcct gttaaggcta aactgaaaga acagatttgg ttactgcgct cctcgtaagc
     1321 cagttaccac ggttcaaaga gttgctgctc tgagaacctt cgaaaaaccg ccttgcaggg
     1381 cggttttttc gtttacagag caagagatta cgacgccaca gaaaggatct caagaagatc
     1441 cttcaccgta atggaaatct atccaatccg agcacatagg atacacatcg ttataacgct
     1501 ggatctgcgt gaattccagc agcagcaaga gaaagacttt ctacaaacca gcttacagca
     1561 ggctaaattt aaccagaaaa aagccgctga attactgggt ctgacttatc atcagctacg
     1621 tgccttgctg aagaaacacc agatctaata cgcatttgca ggtgtcatac tggcgggttt
     1681 gacgcataac gtcataaggt ttaccatggc gtcattactg tataaaaaca caggcataga
     1741 tatgactctg gcattagttg gcgaaaaaat tgacagaaat cgcttcaccg gtgagaaagt
     1801 tgaaaatagt acatttttta actgcgattt ttcaggtgcc gacctgagcg gcactgaatt
     1861 tatcggctgc cagttctatg atcgcgaaag tcagaaaggg tgcaatttta gtcgcgcaat
     1921 gctgaaagat gccattttca aaagctgtga tttatcaatg gcagatttcc gcaacgtcag
     1981 tgccttgggc attgaaattc gccactgccg cgcacaaggc gcagatttcc gcggtgcaag
     2041 ctttatgaat atgatcacca cgcgcacctg gttttgcagc gcatatatca ctaatactaa
     2101 tctaagctac gccaattttt cgaaagtcgt gttggaaaag tgtgagctgt gggaaaaccg
     2161 ctggatgggg actcaggtac tgggtgcgac gttcagtggt tcagatctct ccggcggcga
     2221 gttttcgact ttcgactggc gagcagcaaa cttcacacat tgcgatctga ccaattcgga
     2281 gttaggtgac ttagatattc ggggtgttga tttacaaggc gttaagttag acagctacca
     2341 ggcatcgttg ctcatggagc ggcttggcat cgctgtgatt ggttagttca gcgtttacac
     2401 cgggagatgc gtttgacgat ttacttttaa ccagtacgac tcctggcaag cattgtgaaa
     2461 cgttttctcc agtggacgaa tatcctgacc taccgcatca acgacatgcc atctaatgct
     2521 gcattctgga caggaatttg atgaatatct aaccaattca ttttcgcgag aacaacgaat
     2581 aaccactccc gaatcatgaa gccatgtctt aacgaaaata tggctaactc atagcaaaaa
     2641 aaaagccccc taagggcttt tttttgtacc tgacggtcag accgattaaa cataacatc
//
