LOCUS       NZ_CP039508             2579 bp    DNA     circular CON 17-JUN-2024
DEFINITION  Salmonella enterica subsp. enterica serovar Worthington strain
            7101.67 plasmid p7101_67-5, complete sequence.
ACCESSION   NZ_CP039508
VERSION     NZ_CP039508.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN11445819
            Assembly: GCF_004923395.1
KEYWORDS    RefSeq.
SOURCE      Salmonella enterica subsp. enterica serovar Worthington
  ORGANISM  Salmonella enterica subsp. enterica serovar Worthington
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Salmonella.
REFERENCE   1  (bases 1 to 2579)
  AUTHORS   Clement,M., Keller,P.M., Bernasconi,O.J., Frey,P.M., Bloemberg,G.V.,
            Sendi,P. and Endimiani,A.
  TITLE     First Clinical Case of In Vivo Acquisition of DHA-1 plasmid-mediated
            AmpC in a Salmonella enterica subsp. enterica Isolate
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 2579)
  AUTHORS   Clement,M.
  TITLE     Direct Submission
  JOURNAL   Submitted (18-APR-2019) Institute for Infectious Diseases,
            University of Bern, Friedbuehlstrasse 51, Bern, Bern 3001,
            Switzerland
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: Canu v. 1.7.1; Pilon v. 1.22
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 40.0x
            Sequencing Technology :: Oxford Nanopore MiniION; Illumina NovaSeq
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_004923395.1-RS_2024_06_17
            Annotation Date                   :: 06/17/2024 01:19:27
            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)                     :: 4,764
            CDSs (total)                      :: 4,645
            Genes (coding)                    :: 4,508
            CDSs (with protein)               :: 4,508
            Genes (RNA)                       :: 119
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 86
            ncRNAs                            :: 11
            Pseudo Genes (total)              :: 137
            CDSs (without protein)            :: 137
            Pseudo Genes (ambiguous residues) :: 0 of 137
            Pseudo Genes (frameshifted)       :: 55 of 137
            Pseudo Genes (incomplete)         :: 84 of 137
            Pseudo Genes (internal stop)      :: 34 of 137
            Pseudo Genes (multiple problems)  :: 31 of 137
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP039508.1.
            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..2579
                     /organism="Salmonella enterica subsp. enterica serovar
                     Worthington"
                     /mol_type="genomic DNA"
                     /strain="7101.67"
                     /serovar="Worthington"
                     /isolation_source="Stools"
                     /host="Homo sapiens"
                     /sub_species="enterica"
                     /db_xref="taxon:1160769"
                     /plasmid="p7101_67-5"
                     /geo_loc_name="Switzerland: Bern"
                     /lat_lon="46.947578 N 7.423210 E"
                     /collection_date="2018-11"
                     /collected_by="Insel Spital, Bern, Switzerland"
     gene            1..237
                     /locus_tag="FAF08_RS24240"
                     /old_locus_tag="FAF08_24130"
     CDS             1..237
                     /locus_tag="FAF08_RS24240"
                     /old_locus_tag="FAF08_24130"
                     /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            complement(619..1263)
                     /locus_tag="FAF08_RS24075"
                     /old_locus_tag="FAF08_24135"
     CDS             complement(619..1263)
                     /locus_tag="FAF08_RS24075"
                     /old_locus_tag="FAF08_24135"
                     /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"
     gene            complement(1357..>1512)
                     /locus_tag="FAF08_RS24080"
                     /old_locus_tag="FAF08_24140"
                     /pseudo=""
     CDS             complement(1357..>1512)
                     /locus_tag="FAF08_RS24080"
                     /old_locus_tag="FAF08_24140"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:NP_309907.2"
                     /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"
     ARG             complement(623..1263)
                     /name="qnrB19"
                     /gene="qnrB19"
                     /gene_name="quinolone resistance pentapeptide repeat
                     protein QnrB19"
                     /tool="amrfinderplus"
                     /drug_class="QUINOLONE"
                     /identity="100.0"
                     /coverage="100.0"
     Typing          2242..2415
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="2.5600000000000002e-86"
     Typing          complement(1772..2263)
                     /name="rep_cluster_2335"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="92.51"
                     /coverage="81.0"
                     /evalue="0.0"
ORIGIN
        1 atggccagac tgacaaactt gacgcctgca gagaaaaaat ttcttgatga tgctgttgcc
       61 gcagctgaaa gagcgtcagg taaaaagcta aatcagccta accggcacat cgtcctgaac
      121 agagcgcgtg cgcaaattga gttgcagcgt tacgccgacc gccagcgtgc attacgtgag
      181 gatgagcggc agcagtccga ttttgcctgg tcacgtccgc gcgcgccgcg ccgctgattt
      241 tggcttttgg cggtttagtg gtgctgacgc tgcgaaatca cctgccattc acctgcgtgc
      301 atagccatgc agtcgcgcag aaatcatcag gggcgttttt ccgggatact ggtgaggaaa
      361 ggtgctggaa acggccctga tgcagcagga ttgcgctgag ggcgcctgcg ggggtgcggg
      421 caagggatgt tatgtttaat cggtctgacc gtcaggtaca aaaaaaagcc cttagggggc
      481 tttttttttg ctatgagtta gccatatttt cgtgcgaatt tttcatcgga atcgcataga
      541 taaataataa actcaataaa cgcgatgatc gcgggtaaaa gtaaatcgtc aaacgcatct
      601 cccggtgtaa acgctgaact aaccaatcac agcgatgcca agccgctcca tgagcaacga
      661 tgcctggtag ctgtctaact taacgccttg taaatcaaca ccccgaatat ctaagtcacc
      721 taactccgaa ttggtcagat cgcaatgtgt gaagtttgct gctcgccagt cgaaagtcga
      781 aaactcgccg ccggagagat ctgaaccact gaacgtcgca cccagtacct gagtccccat
      841 ccagcggttt tcccacagct cacacttttc caacacgact ttcgaaaaat tggcgtagct
      901 tagattagta ttagtgatat atgcgctgca aaaccaggtg cgcgtggtga tcatattcat
      961 aaagcttgca ccgcggaaat ctgcgccttg tgcgcggcag tggcgaattt caatgcccaa
     1021 ggcactgacg ttgcggaaat ctgccattga taaatcacag cttttgaaaa tggcatcttt
     1081 cagcattgcg cgactaaaat tgcacccttt ctgactttcg cgatcataga actggcagcc
     1141 gataaattca gtgccgctca ggtcggcacc tgaaaaatcg cagttaaaaa atgtactatt
     1201 ttcaactttc tcaccggtga agcgatttct gtcaattttt tcgccaacta atgccagagt
     1261 catatctatg cctgtgtttt tatacagtaa tgacgccatg gtaaacctta tgacgttatg
     1321 cgtcaaaccc gccagtatga cacctgcaaa tgcgtattag atctggtgtt tcttcagcaa
     1381 ggcacgtagc tgatgataag tcagacccag taattcagcg gcttttttct ggttaaattt
     1441 agcctgctgt aagctggttt gtagaaagtc tttctcttgc tgctgctgga attcacgcag
     1501 atccagcgtt ataacgatgt gtatcctatg tgctcggatt ggatagattt ccattacggt
     1561 gaaggatctt cttgagatcc tttctgtggc gtcgtaatct cttgctctgt aaacgaaaaa
     1621 accgccctgc aaggcggttt ttcgaaggtt ctcagagcag caactctttg aaccgtggta
     1681 actggcttac gaggagcgca gtaaccaaat ctgttctttc agtttagcct taacaggcgc
     1741 ataacttcaa gactaactcc tctaaatcag ttaccagtgg ctgctgccag tggcgataag
     1801 tcgtgtcttt ccgggttgga ctcaagatga tagttaccgg ataaggcgca gcagtcggac
     1861 tgaacggggg gttcgtgcat acagtccatc caggagcgaa ctgccttcgc ggaactgagt
     1921 gtcaggcgtg gaatgagata aacgcggcca taacagcgga atgacaccgg taaaccgaaa
     1981 ggcaggaatg cgggggagca cgagggagcc accaggggga aacgcctggt atctttaagc
     2041 cgcatcgggt ttcgccacca ctgatttgag cgtcagattt catgatgttt gtcagggggg
     2101 cggagcctat ggaaaaacgg cttcgccgcg gccttatctc ttccctgtta agctccttcc
     2161 tggtatctcc caggaaattt ccgccccgcc tgtaagccgg caccgctcgc cgcagccgaa
     2221 cgaccgagcg cagcgagtca gtgagcgagg aagcggaata tatcctgtac tacatatcct
     2281 gctgacgcgc tggtgccgcc ttttttctcc tgctacatga agcacttcac tgatttccac
     2341 atccgtgcca acatagtcag ccagtataca ctccgctagc gctacgtgac tggttcaggg
     2401 ctgcgccccg aaaccggcta aaagctaatg acgcgcctgc ggcttgtcca acgcctcacg
     2461 gcaccggatt aaaatccgct cccgttcacc gtttctgact gcctttcacc gtcgctggcg
     2521 cttcatcgtt tctactgtgt ctggcagact gtgctgattt attctgactg gagaacgtt
//
