LOCUS       NZ_CP039515             2450 bp    DNA     circular CON 14-OCT-2023
DEFINITION  Salmonella enterica subsp. enterica serovar Worthington strain
            7102.58 plasmid p7102_58-4, complete sequence.
ACCESSION   NZ_CP039515
VERSION     NZ_CP039515.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN11445820
            Assembly: GCF_004923415.2
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 2450)
  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  JOURNAL   Unpublished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 2450)
  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 Date                   :: 10/14/2023 03:11:15
            Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline
            (PGAP)
            Annotation Method :: Best-placed reference protein set; GeneMarkS-2+
            Annotation Software revision      :: 6.6
            Features Annotated                :: Gene; CDS; rRNA; tRNA; ncRNA
            Genes (total)                     :: 4,876
            CDSs (total)                      :: 4,757
            Genes (coding)                    :: 4,602
            CDSs (with protein)               :: 4,602
            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)              :: 155
            CDSs (without protein)            :: 155
            Pseudo Genes (ambiguous residues) :: 0 of 155
            Pseudo Genes (frameshifted)       :: 63 of 155
            Pseudo Genes (incomplete)         :: 97 of 155
            Pseudo Genes (internal stop)      :: 36 of 155
            Pseudo Genes (multiple problems)  :: 37 of 155
            Pseudo Genes (short protein)      :: 1 of 155
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP039515.1.
            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..2450
                     /organism="Salmonella enterica subsp. enterica serovar
                     Worthington"
                     /mol_type="genomic DNA"
                     /strain="7102.58"
                     /serovar="Worthington"
                     /isolation_source="Stools"
                     /host="Homo sapiens"
                     /sub_species="enterica"
                     /db_xref="taxon:1160769"
                     /plasmid="p7102_58-4"
                     /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="FAF09_RS24660"
                     /old_locus_tag="FAF09_24825"
     CDS             1..237
                     /locus_tag="FAF09_RS24660"
                     /old_locus_tag="FAF09_24825"
                     /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..1264)
                     /locus_tag="FAF09_RS24665"
                     /old_locus_tag="FAF09_24830"
                     /pseudo=""
     CDS             complement(619..1264)
                     /locus_tag="FAF09_RS24665"
                     /old_locus_tag="FAF09_24830"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_017900990.1"
                     /note="frameshifted; Derived by automated computational
                     analysis using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="quinolone resistance pentapeptide repeat protein
                     QnrB19"
                     /name="quinolone resistance pentapeptide repeat protein
                     QnrB19"
     gene            complement(1358..>1483)
                     /locus_tag="FAF09_RS24670"
                     /old_locus_tag="FAF09_24835"
                     /pseudo=""
     CDS             complement(1358..>1483)
                     /locus_tag="FAF09_RS24670"
                     /old_locus_tag="FAF09_24835"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:NP_460649.1"
                     /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            complement(<1686..1751)
                     /locus_tag="FAF09_RS25220"
                     /pseudo=""
     CDS             complement(<1686..1751)
                     /locus_tag="FAF09_RS25220"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_005761324.1"
                     /note="incomplete; partial in the middle of a contig;
                     missing C-terminus; Derived by automated computational
                     analysis using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="replication initiation protein"
                     /name="replication initiation protein"
     ARG             complement(681..1300)
                     /name="QnrB10"
                     /gene="QnrB10"
                     /gene_name="quinolone resistance protein (qnr)"
                     /tool="rgi"
                     /drug_class="fluoroquinolone antibiotic"
                     /identity="99.01"
                     /coverage="91.15"
     Typing          2113..2286
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="2.5600000000000002e-86"
     Typing          complement(1687..2140)
                     /name="rep_cluster_2335"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="91.685"
                     /coverage="86.0"
                     /evalue="4.59e-178"
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 taaaatcaac accccgaata tctaagtcac
      721 ctaactccga attggtcaga tcgcaatgtg tgaagtttgc tgctcgccag tcgaaagtcg
      781 aaaactcgcc gccggagaga tctgaaccac tgaacgtcgc acccagtacc tgagtcccca
      841 tccagcggtt ttcccacagc tcacactttt ccaacacgac tttcgaaaaa ttggcgtagc
      901 ttagattagt attagtgata tatgcgctgc aaaaccaggt gcgcgtggtg atcatattca
      961 taaagcttgc accgcggaaa tctgcgcctt gtgcgcggca gtggcgaatt tcaatgccca
     1021 aggcactgac gttgcggaaa tctgccattg ataaatcaca gcttttgaaa atggcatctt
     1081 tcagcattgc gcgactaaaa ttgcaccctt tctgactttc gcgatcatag aactggcagc
     1141 cgataaattc agtgccgctc aggtcggcac ctgaaaaatc gcagttaaaa aatgtactat
     1201 tttcaacttt ctcaccggtg aagcgatttc tgtcaatttt ttcgccaact aatgccagag
     1261 tcatatctat gcctgtgttt ttatacagta atgacgccat ggtaaacctt atgacgttat
     1321 gcgtcaaacc cgccagtatg acacctgcaa atgcgtatta gatctggtgt ttcttcagca
     1381 aggcacgtag ctgatgataa gtcagaccca gtaattcagc ggcttttttc tggttaaatt
     1441 tagcctgctg taagctggtt tgtagaaagt ctttctcttg ctgctgcttt cacggatggt
     1501 gaaggatctt cttgagatcc tttctgtggc gtcgtaatct cttgctctgt aaacgaaaaa
     1561 accgccctgc aaggcggttt ttcgaaggtt ctcagagcag caactctttg aaccgtggta
     1621 actggcttac gaggagcgca gtaaccaaat ctgttctttc agtttagcct taacaggcag
     1681 ctgaagttgg actcaagatg atagttaccg gataaggcgc agcagtcgga ctgaacgggg
     1741 ggttcgtgca tacagtccat ccaggagcga actgccttcg cggaactgag tgtcaggcgt
     1801 ggaatgagat aaacgcggcc ataacagcgg aatgacaccg gtaaaccgaa aggcaggaat
     1861 gcgggggagc acgagggagc caccaggggg aaacgcctgg tatctttaag ccgcatcggg
     1921 tttcgccacc actgatttga gcgtcagatt tcatgatgtt tgtcaggggg gcggagccta
     1981 tggaaaaacg gcttcgccgc ggccttatct cttccctgtt aagctccttc ctggtatctc
     2041 ccaggaaatt tccgccccgc ctgtaagccg gcaccgctcg ccgcagccga acgaccgagc
     2101 gcagcgagtc agtgagcgag gaagcggaat atatcctgta ctacatatcc tgctgacgcg
     2161 ctggtgccgc cttttttctc ctgctacatg aagcacttca ctgatttcca catccgtgcc
     2221 aacatagtca gccagtatac actccgctag cgctacgtga ctggttcagg gctgcgcccc
     2281 gaaaccggct aaaagctaat gacgcgcctg cggcttgtcc aacgcctcac ggcaccggat
     2341 taaaatccgc tcccgttcac cgtttctgac tgcctttcac cgtcgctggc gcttcatcgt
     2401 ttctactgtg tctggcagac tgtgctgatt tattctgact ggagaacgtt
//
