LOCUS       NZ_CP039514             2498 bp    DNA     circular CON 14-OCT-2023
DEFINITION  Salmonella enterica subsp. enterica serovar Worthington strain
            7102.58 plasmid p7102_58-5, complete sequence.
ACCESSION   NZ_CP039514
VERSION     NZ_CP039514.1
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 2498)
  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  JOURNAL   Unpublished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 2498)
  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
            CP039514.1.
            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..2498
                     /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_58-5"
                     /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..228
                     /locus_tag="FAF09_RS24630"
                     /old_locus_tag="FAF09_24795"
     CDS             1..228
                     /locus_tag="FAF09_RS24630"
                     /old_locus_tag="FAF09_24795"
                     /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..782
                     /locus_tag="FAF09_RS24635"
                     /old_locus_tag="FAF09_24800"
     CDS             594..782
                     /locus_tag="FAF09_RS24635"
                     /old_locus_tag="FAF09_24800"
                     /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_136655349.1"
                     /translation="MTRQESAALNMAKFIRAQTLLLLERLEQMDLDEAAGCCEHLHDQA
                     EDALYAMLNAQIGEENA"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            complement(1073..1264)
                     /locus_tag="FAF09_RS24645"
                     /old_locus_tag="FAF09_24810"
     CDS             complement(1073..1264)
                     /locus_tag="FAF09_RS24645"
                     /old_locus_tag="FAF09_24810"
                     /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(830..917)
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="6.86e-39"
     Typing          1556..2084
                     /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 agacgcgctt tacgccatgc tgaacgcaca gataggcgag gaaaatgcgt
      781 gaaaatcggt gaacgggtgc gcaattcagt gcgcggccgt gaggcgatgg cggggtgtcg
      841 gggcgcagcc ctgaccaggg tatttgtgat gccggcgcgt gcgcggtatt acaaatgcac
      901 atcctgtccc ggaacggaca ccgggaaaca gcaaaaaaaa ccgggcggca cgcccggaac
      961 tcaatcaagt tagattagat tactctcact cgtccataac agcatcatgg aacgacgacc
     1021 accgtccgtg acggccgcct cgtttaagta tggacagaaa tacagaaaat gctcaggacg
     1081 aaatgtaatg aatgcgaacg gattcaagaa attcgagcat gacagtcctt acggccggtt
     1141 cggtttcaga caaaatctgc cggtatgcat ccagcatcat ggctccggca tcccctccgg
     1201 cacgccgtag ccagaccgaa acaacggaca caagcaggtg tcgctcatca tcactaagag
     1261 tcatcagggc tccggaagaa aaaccaaaca tggcttacct actgttaacg gcaacgcaga
     1321 agaaaggttt acagggtagc gggcagggat gaaaaaaaaa aaattgcagt caggccggaa
     1381 cggctgctga accggtacag gcgggttccg ggcgcagcgc cggaccagtc acggagcact
     1441 agcggagtgt atactggctt aagatgtagc atggcagtaa cacatagcat taatgccaca
     1501 taagacaggc gcagaaagtg aaagaaaacg cgtcaggaga aaatgtgata cagaatatat
     1561 tccgcttcct cgctcactga ctcgctccgc tcggtcgttc ggctgcggcg agcgggacgg
     1621 gcttacggat ggatcagaaa tttcctgggg gatgccagga agatacttaa cgaagaaagc
     1681 ataaggccgc gccaaagccg tttttccata ggctccgccc ccctgacaag catcacagaa
     1741 tctgacgctc aaatcagtgg tggcgaaacc cgatgcggct taaagatacc aggcgtttcc
     1801 ccctggtggc tccctcgtgc tcccccgcat tcctgccttt cggtttaccg gtgtcactcc
     1861 gctgttatgg ccgcggtttc tcattccacg cctgacactc agttccggga aggcagttcg
     1921 ctccaggatg gactgtatgc acgaaccccc cgttcagtcc gaccgctgcg ccttatccgg
     1981 taactatcaa cttgagtcca acccggaaag acacgactaa tcgccattgg caacggccat
     2041 tggcaaacag gatgtgcgag agatgtctca agagttcttg aagtggcggc cttagtgagg
     2101 ctacactgaa aggacaaatt tggtgacatg tctcgcacaa gactgttacc acggttaggg
     2161 gatctgccag gattacctaa ccttcgaaaa accacctgcc agggtggttt tttcgtttac
     2221 agggcaagag attacgcgcg gaaaaaaagg atctcaagaa gatcctttat aaattagaca
     2281 tccaacctca caaagaggaa tacttaaatc atcttggtat atgtatcggc cggattacat
     2341 ctcatataag cctcctcccc gcctgacacc acactttgac catagcacct cgcgcctaac
     2401 tcgatataca gcccaccatc aagcctcttt tcacataaaa aatgacctat agttagatgg
     2461 ttagtgacca aaactgatat ggataaaagg agctggct
//
