LOCUS       NZ_CP129208             1939 bp    DNA     circular CON 08-AUG-2023
DEFINITION  Salmonella enterica subsp. enterica serovar Typhimurium strain
            HS_187Salm plasmid unnamed2, complete sequence.
ACCESSION   NZ_CP129208
VERSION     NZ_CP129208.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN30847004
            Sequence Read Archive: SRR21564522, SRR21564520
            Assembly: GCF_030644285.1
KEYWORDS    RefSeq.
SOURCE      Salmonella enterica subsp. enterica serovar Typhimurium (Salmonella
            typhimurium)
  ORGANISM  Salmonella enterica subsp. enterica serovar Typhimurium
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Salmonella.
REFERENCE   1  (bases 1 to 1939)
  AUTHORS   Shutinoski,B., Flint,A., Weedmark,K., Tamber,S., Gill,A. and
            Banerjee,S.
  TITLE     Direct Submission
  JOURNAL   Submitted (30-JUN-2023) Bureau of Microbial Hazards, Health Canada,
            251 Frederick Banting Driveway, Ottawa, ON K1Y 0M1, Canada
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Date                     :: SEP-2022
            Assembly Method                   :: Unicycler v. 0.5.0
            Assembly Name                     :: HS_187Salm
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 568x
            Sequencing Technology :: Illumina MiSeq; Oxford Nanopore MinION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 08/05/2023 08:01:51
            Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline
            (PGAP)
            Annotation Method :: Best-placed reference protein set; GeneMarkS-2+
            Annotation Software revision      :: 6.5
            Features Annotated                :: Gene; CDS; rRNA; tRNA; ncRNA
            Genes (total)                     :: 4,880
            CDSs (total)                      :: 4,758
            Genes (coding)                    :: 4,601
            CDSs (with protein)               :: 4,601
            Genes (RNA)                       :: 122
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 85
            ncRNAs                            :: 15
            Pseudo Genes (total)              :: 157
            CDSs (without protein)            :: 157
            Pseudo Genes (ambiguous residues) :: 0 of 157
            Pseudo Genes (frameshifted)       :: 79 of 157
            Pseudo Genes (incomplete)         :: 81 of 157
            Pseudo Genes (internal stop)      :: 26 of 157
            Pseudo Genes (multiple problems)  :: 27 of 157
            Pseudo Genes (short protein)      :: 1 of 157
            CRISPR Arrays                     :: 3
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP129208.1.
            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..1939
                     /organism="Salmonella enterica subsp. enterica serovar
                     Typhimurium"
                     /mol_type="genomic DNA"
                     /strain="HS_187Salm"
                     /serovar="Typhimurium"
                     /isolation_source="Oyster"
                     /sub_species="enterica"
                     /db_xref="taxon:90371"
                     /plasmid="unnamed2"
                     /geo_loc_name="Canada: New Brunswick"
                     /collection_date="2021-08-27"
                     /collected_by="Health Canada - Bureau of Microbial Hazards"
                     /genotype="invA positive (by PCR)"
     gene            complement(911..1900)
                     /locus_tag="N5C86_RS24400"
                     /old_locus_tag="N5C86_004879"
     CDS             complement(911..1900)
                     /locus_tag="N5C86_RS24400"
                     /old_locus_tag="N5C86_004879"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001529700.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="protein rep"
                     /protein_id="WP_304988710.1"
                     /translation="MQNPKLQNLTDYSPADAPWDAHRSVSDDVGGIYLLAAEYERYGAR
                     MASCGGLLRFGWSTLKETGETRLRLREAHFCRVRHCPVCQWRRSLMWQARFYQSLPRIV
                     ADYPDARWMFLTLTVRNCAIGELGETLNRMNAGFQRLKDRKEFSPVQGWIRTTEVTRGS
                     DGSAHPHFHTLMMVPPSMLSGRDYIKHERWVDLWRGCLRVDYDPNVDVRAVKPRKPKDG
                     ESLACATAELVRGAVAETLKYSTKPADMVADPEWFLELTRQTHKRRFVATGGALKDVLK
                     LDQETDADMVIGDDISEGDDDGSRIAFEWKTDVRKYRRSPTKDKTESD"
                     /name="protein rep"
     Typing          994..1185
                     /name="ColpVC"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="98.446"
                     /coverage="100.0"
                     /evalue="2.86e-91"
ORIGIN
        1 ttatcattgc cgtatcacct gtgttgtctg tcgcaaaata gaattcctac aggtggtcac
       61 ccccccgaac gattgccctc gttgcggggg tcgcttttaa cgcgaccact ccaaacagag
      121 tacttccaaa cccatttcca cgcaaatcac ctctcaggcc ttgccgcaca agggctgagg
      181 ccgaattcca atcccagagt tatcccttaa gtataaatat aaggatcgcg cgcgagagaa
      241 tgtttaaaaa ttgagcgctt tttaagtgac tcagaaccac acaaacccac ccccttacac
      301 ccatctcatc cacagacttt cacactaatt ttgtgaacaa caaaaaccgt cttgcaggtg
      361 gttggcctca ctgcgtgaca ccaaccacca tccccagtgt tttttcggtg ccgtcgtcaa
      421 tcacaaaatc ggaacccacg ccagaggcgc gggcccccgc gattttctgt ttgacgaatc
      481 agggaacggt gaacggtgcg cggaattttt tcgcgtaccg tgaagcgttg gcggggtgtc
      541 ggggcgcagc cctgaccagg tggagtttgg agtaccgacc gtgtggcggg aatacaaaca
      601 tgtatcttgt cccgattttt tcgcctgaac actggcagag catcgacagt cctgcgtcgt
      661 taagccctcc gcaggagcgc acagtttccc gacgaaggag agaaactact aagtgcgcat
      721 ccgcacttaa cgcgcggatg aattctggca accggacagc aaatcatttt gccgttttcg
      781 tcgtgcggtc tgcgacgcac aaaaaacgag aaacggcggg agttttcggg acaggatgtg
      841 caattgtgat accgtcacac acgacgctat cacaattgcc atttggtcag ggctgcgccc
      901 cgacaccctg ctagtctgat tcagttttat ctttcgtagg tgagcggcgg tactttctga
      961 catcggtttt ccattcgaac gcgatgcggg aaccatcatc gtcgccctcg gaaatatcat
     1021 ccccgatcac catgtcggcg tcggtttcct gatcgagctt cagtacgtct ttgagtgcgc
     1081 cgccggtcgc cacaaagcgg cgcttgtgcg tctggcgggt cagttcgagg aaccattcag
     1141 gatcggccac catgtcagcc ggcttcgtgg aatatttcag ggtttccgcc accgcgccgc
     1201 gcaccagttc ggcggtcgcg caggccagcg attcgccgtc cttcggcttc cggggtttta
     1261 ctgcccggac atcgacattc ggatcgtaat ccacccgaag acacccacgc cacagatcaa
     1321 cccagcgctc atgcttgatg taatcacgcc cagacaacat cgatggcggc accatcatca
     1381 gggtgtgaaa gtgcgggtgt gcgctgccgt cgctcccgcg ggtgacttcc gttgtgcgga
     1441 tccagccctg cactggactg aactccttgc gatccttcag tcgctggaaa cctgcgttca
     1501 tccggttcag cgtctcgccc agctccccga tcgcacagtt acgcacggtc agggtcagga
     1561 acatccagcg ggcatcggga taatccgcca cgatacgcgg cagagactgg tagaaacggg
     1621 cttgccacat cagggagcgc ctccactggc agacaggaca gtgccggaca cggcaaaaat
     1681 gcgcctcacg cagcctcagg cgcgtttctc cggtttcttt gagggtagac cacccaaaac
     1741 gcagcaaacc gccacaggag gccatacgcg ccccgtagcg ctcatattca gccgcaagca
     1801 ggtaaatccc tcccacgtcg tcagaaacgc ttctgtgagc gtcccagggc gcatctgcgg
     1861 gggaataatc cgtgaggttc tggagtttag gattttgcat gcacaccgcc ccatactggg
     1921 cgatggctca tttgacgtg
//
