LOCUS       NZ_CP039507             2495 bp    DNA     circular CON 17-JUN-2024
DEFINITION  Salmonella enterica subsp. enterica serovar Worthington strain
            7101.67 plasmid p7101_67-4, complete sequence.
ACCESSION   NZ_CP039507
VERSION     NZ_CP039507.1
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 2495)
  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  JOURNAL   Unpublished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 2495)
  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
            CP039507.1.
            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..2495
                     /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_67-4"
                     /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..228
                     /locus_tag="FAF08_RS24040"
                     /old_locus_tag="FAF08_24100"
     CDS             1..228
                     /locus_tag="FAF08_RS24040"
                     /old_locus_tag="FAF08_24100"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_010615788.1"
                     /GO_component="GO:0005886 - plasma membrane [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="YgdI/YgdR family lipoprotein"
                     /protein_id="WP_021243043.1"
                     /translation="MKKIFVSVFAAAVALSALTGCTRTSYAIHTNDGRTIVSDGKPKES
                     DSGLLGYTDANGVKQQINKTDVKEVSEIPH"
                     /name="YgdI/YgdR family lipoprotein"
     gene            594..779
                     /locus_tag="FAF08_RS24045"
                     /old_locus_tag="FAF08_24105"
     CDS             594..779
                     /locus_tag="FAF08_RS24045"
                     /old_locus_tag="FAF08_24105"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000165998.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="Rop family plasmid primer RNA-binding protein"
                     /protein_id="WP_013772937.1"
                     /translation="MTRQESAALNMAKFIRAQTLLLLERLEQMDLDEAAGCCEHLHDQA
                     EALYAMLNAQIGEENA"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            complement(1070..1261)
                     /locus_tag="FAF08_RS24055"
                     /old_locus_tag="FAF08_24115"
     CDS             complement(1070..1261)
                     /locus_tag="FAF08_RS24055"
                     /old_locus_tag="FAF08_24115"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001046776.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_021243041.1"
                     /translation="MTLSDDERHLLVSVVSVWLRRAGGDAGAMMLDAYRQILSETEPAV
                     RTVMLEFLESVRIHYISS"
                     /name="hypothetical protein"
     Typing          complement(827..914)
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="6.86e-39"
     Typing          1553..2081
                     /name="rep_cluster_2335"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="88.598"
                     /coverage="88.0"
                     /evalue="0.0"
ORIGIN
        1 ttgaaaaaga tttttgtttc agtgttcgca gcggcagttg cgctttcagc cctcaccggc
       61 tgcacgcgca caagctatgc catacacacc aatgacggtc gcactattgt cagcgacggc
      121 aaacctaaag aatcagactc aggcctgctt ggctatacag acgcgaatgg tgtcaaacag
      181 cagatcaata aaaccgacgt taaagaagtc tccgaaattc cgcactgagc atcttctccg
      241 aaaaaggccg ctaatgtggc ctttttcttt acctgtggtt ctccgccaaa atcccagcaa
      301 attgcatcac caaagctaaa agctttcagg gttgtctaaa aagcacaaga cataagagga
      361 agtgcggtat tttataatca agcccccaag aatttaccat aacatccgtt gcccgcaccg
      421 cctgagacgc gttcagcgcg ttcctgacga aaccatgaca aaaaccacaa caaaccaccc
      481 cggaacccgt cagaaacgcg cctgttaaat tttaacggca tgcatgacta tgcaccagaa
      541 tgacgccatg ctcttttcac gcaaaaatca tcaccagacg gggaaaatca ccagtgacca
      601 gacaggaatc cgccgccctc aatatggcca aatttatccg cgcacagaca cttctcctcc
      661 ttgagcggct cgagcagatg gatctggatg aggctgccgg ctgctgtgag cacctgcacg
      721 atcaggccga agcgctttac gccatgctga acgcacagat aggcgaggaa aatgcgtgaa
      781 aatcggtgaa cgggtgcgca attcagtgcg cggccgtgag gcgatggcgg ggtgtcgggg
      841 cgcagccctg accagggtat ttgtgatgcc ggcgcgtgcg cggtattaca aatgcacatc
      901 ctgtcccgga acggacaccg ggaaacagca aaaaaaaccg ggcggcacgc ccggaactca
      961 atcaagttag attagattac tctcactcgt ccataacagc atcatggaac gacgaccacc
     1021 gtccgtgacg gccgcctcgt ttaagtatgg acagaaatac agaaaatgct caggacgaaa
     1081 tgtaatgaat gcgaacggat tcaagaaatt cgagcatgac agtccttacg gccggttcgg
     1141 tttcagacaa aatctgccgg tatgcatcca gcatcatggc tccggcatcc cctccggcac
     1201 gccgtagcca gaccgaaaca acggacacaa gcaggtgtcg ctcatcatca ctaagagtca
     1261 tcagggctcc ggaagaaaaa ccaaacatgg cttacctact gttaacggca acgcagaaga
     1321 aaggtttaca gggtagcggg cagggatgaa aaaaaaaaaa ttgcagtcag gccggaacgg
     1381 ctgctgaacc ggtacaggcg ggttccgggc gcagcgccgg accagtcacg gagcactagc
     1441 ggagtgtata ctggcttaag atgtagcatg gcagtaacac atagcattaa tgccacataa
     1501 gacaggcgca gaaagtgaaa gaaaacgcgt caggagaaaa tgtgatacag aatatattcc
     1561 gcttcctcgc tcactgactc gctccgctcg gtcgttcggc tgcggcgagc gggacgggct
     1621 tacggatgga tcagaaattt cctgggggat gccaggaaga tacttaacga agaaagcata
     1681 aggccgcgcc aaagccgttt ttccataggc tccgcccccc tgacaagcat cacagaatct
     1741 gacgctcaaa tcagtggtgg cgaaacccga tgcggcttaa agataccagg cgtttccccc
     1801 tggtggctcc ctcgtgctcc cccgcattcc tgcctttcgg tttaccggtg tcactccgct
     1861 gttatggccg cggtttctca ttccacgcct gacactcagt tccgggaagg cagttcgctc
     1921 caggatggac tgtatgcacg aaccccccgt tcagtccgac cgctgcgcct tatccggtaa
     1981 ctatcaactt gagtccaacc cggaaagaca cgactaatcg ccattggcaa cggccattgg
     2041 caaacaggat gtgcgagaga tgtctcaaga gttcttgaag tggcggcctt agtgaggcta
     2101 cactgaaagg acaaatttgg tgacatgtct cgcacaagac tgttaccacg gttaggggat
     2161 ctgccaggat tacctaacct tcgaaaaacc acctgccagg gtggtttttt cgtttacagg
     2221 gcaagagatt acgcgcggaa aaaaaggatc tcaagaagat cctttataaa ttagacatcc
     2281 aacctcacaa agaggaatac ttaaatcatc ttggtatatg tatcggccgg attacatctc
     2341 atataagcct cctccccgcc tgacaccaca ctttgaccat agcacctcgc gcctaactcg
     2401 atatacagcc caccatcaag cctcttttca cataaaaaat gacctatagt tagatggtta
     2461 gtgaccaaaa ctgatatgga taaaaggagc tggct
//
