LOCUS       NZ_CP039511             2733 bp    DNA     circular CON 14-OCT-2023
DEFINITION  Salmonella enterica subsp. enterica serovar Worthington strain
            7102.58 plasmid p7102_58-2, complete sequence.
ACCESSION   NZ_CP039511
VERSION     NZ_CP039511.1
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 2733)
  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  JOURNAL   Unpublished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 2733)
  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
            CP039511.1.
            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..2733
                     /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_58-2"
                     /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..432
                     /locus_tag="FAF09_RS24000"
                     /old_locus_tag="FAF09_24075"
     CDS             1..432
                     /locus_tag="FAF09_RS24000"
                     /old_locus_tag="FAF09_24075"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001233485.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="helix-turn-helix domain-containing protein"
                     /protein_id="WP_054623595.1"
                     /translation="MRRITQVDQTTGEELGGFVAVIRPKQKSSFQRHFTMNQAALITIA
                     NELNHDQMRVLMALLAELDYENYIQVAQMDIAEALTMQKTNVSRAVKNLIDFGIILEGP
                     KIGRSKTYRLNPQFGWKGTVSNHKKALKNGLSVIQGGRT"
                     /name="helix-turn-helix domain-containing protein"
     gene            complement(496..1512)
                     /gene="mobV"
                     /locus_tag="FAF09_RS24005"
                     /old_locus_tag="FAF09_24080"
     CDS             complement(496..1512)
                     /gene="mobV"
                     /locus_tag="FAF09_RS24005"
                     /old_locus_tag="FAF09_24080"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000024818.1"
                     /GO_function="GO:0003677 - DNA binding [Evidence IEA]"
                     /GO_process="GO:0006310 - DNA recombination [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MobV family relaxase"
                     /protein_id="WP_136655212.1"
                     /translation="MRSPDWLDGRQNEGVSMANYAIMRCKKLTGMGSVASALQHCYRER
                     ETPNADAERTPENYCSVSQSADEAMGKLRELLPEKRRKDAVLAVEYVMTASPEWWKEAT
                     PRQQAEFFARSEQWLEKKYGKDRVVAAVVHRDEATPHLSAFVVPLTQDGRLSAKEFIGG
                     RSKMRDDQSTYAESVKKLGLERGIEGSRATHQTVQHYYESINRGTRSQVSISPEALEPR
                     VLRKGIFTKDVEDQAAIAKRLSHAVNDGFAGTIAMASQSAQNAKRARELQKTMDSQQKR
                     LQSVTEPFKGLSREQMTEILMMAQRFKQQNQEKEKQQRVEREKQRQMRSRGMGGMER"
                     /name="mobV"
     gene            1714..2319
                     /locus_tag="FAF09_RS24010"
                     /old_locus_tag="FAF09_24085"
     CDS             1714..2319
                     /locus_tag="FAF09_RS24010"
                     /old_locus_tag="FAF09_24085"
                     /inference="COORDINATES: ab initio prediction:GeneMarkS-2+"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GeneMarkS-2+."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_054623596.1"
                     /translation="MSFIKSLNKKNQTDQIEVTINVRLTQEEDHLLTLATQQSGYKRNE
                     LFYLLAKEYIFDDESLKEMAEESGAEFSEGLYQNCYVVNTNRVHHEEDDKFMISEGVAA
                     TFEDGYKEKMEQVKKGDLVFLYRSGEGIVAHGIASGDVLKKDHNGVPDKTYYQKLSGFV
                     RYEKPLTASEIQRILGRNVVFMHTLFSIRDGYKLLKKD"
                     /name="hypothetical protein"
     Typing          complement(500..1512)
                     /name="MOBV"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="97.337"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 atgcggagaa tcacgcaggt agaccaaact acaggggagg aattaggtgg ttttgtagca
       61 gtgattcgtc ctaaacaaaa gtcatcattc cagaggcact ttactatgaa ccaagccgcg
      121 ctaattacca ttgccaatga gctaaaccat gaccagatgc gtgtgctgat ggccttgctc
      181 gcagaactgg attacgagaa ctacatccaa gttgcgcaga tggatattgc ggaagcgctg
      241 actatgcaaa aaacaaatgt cagtcgtgcg gtaaaaaacc tgattgattt cgggatcata
      301 ctggaagggc cgaagattgg gcggagcaaa acgtaccgcc taaatcccca gttcggctgg
      361 aaaggtactg tcagcaacca caaaaaagca ctgaaaaacg gcctcagcgt tatacagggc
      421 ggcagaacct gatctctgga atgccgcaaa tggcgtcatt ttgcggcgtt agccctatcc
      481 tgcatcgcat caaaactaac gctccatacc gcccatgcca cgcgatcgca tctgtcgctg
      541 tttctcacgt tcaacacgct gctgtttctc cttctcctgg ttttgctgct taaaccgctg
      601 agccatcatc aggatttctg tcatctgctc tctggaaagc cccttaaaag gctctgtaac
      661 gctctgtagg cgtttctgct gcgaatccat agtcttctgt agctcgcgcg ctctttttgc
      721 attctgggcg ctctgagagg ccatagcgat ggttcctgca aagccatcgt tcactgcgtg
      781 gcttagacgt ttggctatgg ctgcctgatc ttccacgtct ttggtgaaaa tgcccttccg
      841 caatacacgc ggctccagcg cctccggcga gatcgatacc tggctacggg tgccacggtt
      901 tatcgattcg tagtagtgct gaactgtctg atgcgtggcg cggcttccct cgatgccgcg
      961 ctcaagaccc agttttttta ctgattcagc gtaggtgctc tgatcgtcac gcatctttga
     1021 ccgcccgcca ataaactctt tcgcggacag ccgtccatcc tgcgtcaatg gcaccacgaa
     1081 cgctgacaag tgcggggtgg cctcgtcccg gtgaaccacc gccgccacaa cacgatcctt
     1141 cccgtatttc ttctccagcc attgctcaga gcgggcgaaa aactccgcct gctgccgcgg
     1201 tgtcgcttct ttccaccact cagggcttgc cgtcataacg tattcaacag ccagtaccgc
     1261 atctttacgg cgtttttccg gcaacagctc ccgcagcttt cccatcgcct catctgccga
     1321 ctgagacaca gagcagtagt tttctggtgt ccgttcagcg tcagcattcg gcgtctcacg
     1381 ctccctgtag cagtgctgca aagcgctggc cacactgccc attcccgtca gctttttgca
     1441 gcgcattatc gcgtaattcg ccatgcttac cccctcgttc tggcgtccat ccagccagtc
     1501 gggggatcgc attgcgatgc ctccggcggg ccactatcag gatgatagtg tactcactag
     1561 actttgctac gcaaaatcgt tcgttaaatt caacttaata aaaatatatg acataaagtc
     1621 attgcttaaa tcaaagatgt gatcaatgct tctgtttcaa tgtagtgatt cactatcatt
     1681 gattagtaca ttaactctgg tgaggaaagt aagatgtcat tcataaaatc gctaaacaaa
     1741 aaaaatcaaa cagaccaaat agaagtgacg attaacgtta ggttaaccca agaagaggac
     1801 catttactga cattagcaac ccagcaatct ggttataaaa ggaacgagct attctacctc
     1861 ctagcaaagg aatacatctt tgatgatgaa agcttaaagg aaatggctga ggagtctggc
     1921 gctgagtttt cagaaggctt ataccaaaat tgttatgtgg ttaacactaa cagagttcat
     1981 catgaagaag atgataagtt catgatttca gagggcgtag cggcaacatt tgaagatggt
     2041 tataaggaaa aaatggagca ggttaaaaaa ggagatttag tctttcttta tcgctccggc
     2101 gaaggaattg ttgcacatgg tatcgccagt ggtgatgttt taaagaaaga tcataatggc
     2161 gtgccagaca agacctacta ccagaagcta tcaggctttg ttaggtacga aaaaccacta
     2221 accgcgtctg agatccagag aatactgggg agaaacgttg tgtttatgca cacgctattt
     2281 agcattagag atggctataa actgcttaaa aaagattaaa cccagtctac aggtggttgg
     2341 catcactttg tgacaccaac caccttccgg aagtgttttt tacagtgcat cgtcaagggt
     2401 aaatgaactc gctacgctcg cccttgacga aataaagctc cgaatatcgt tttaaaaaat
     2461 caagaaccgc tcgccgcaga ctcatgaccg aacgtagtga gcgaatgagc gaggaagcgg
     2521 aatttccact tcccgtacat agaaattcgt tcgcaccgaa cgggcagaaa aacgcctgat
     2581 tttgccgatg tgtgattgtg gagagtaata agatacagaa ggggatggct gggaagccgc
     2641 gccacaagcg gaaagttttt gacaatagtt atctctagag ataacttagt tatcttgaga
     2701 gataactatt ttttcctgaa tggagatttt tag
//
