LOCUS       NZ_CP039598             1968 bp    DNA     circular CON 29-JUL-2023
DEFINITION  Salmonella enterica subsp. enterica serovar 1,4,[5],12:i:- strain
            PNCS014865 plasmid p12-4331.3, complete sequence.
ACCESSION   NZ_CP039598
VERSION     NZ_CP039598.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN11333162
            Assembly: GCF_004919405.1
KEYWORDS    RefSeq.
SOURCE      Salmonella enterica subsp. enterica serovar 1,4,[5],12:i:-
  ORGANISM  Salmonella enterica subsp. enterica serovar 1,4,[5],12:i:-
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Salmonella.
REFERENCE   1  (bases 1 to 1968)
  AUTHORS   Schonfeld,J., Clark,C., Johnson,R., Labbe,G., Liu,K. and Nash,J.H.E.
  TITLE     Complete genome sequences of Canadian Typhimurium and I
            1,4,[5],12:i:-
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 1968)
  AUTHORS   Schonfeld,J., Clark,C., Johnson,R., Labbe,G., Liu,K. and Nash,J.H.E.
  TITLE     Direct Submission
  JOURNAL   Submitted (18-APR-2019) Public Health Agency of Canada, National
            Microbiology Laboratory at Guelph, 110 Stone Road West, Guelph,
            Ontario N1G3W4, Canada
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: unicycler v. 0.4.7; canu v. 1.8
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 100.0x
            Sequencing Technology :: Illumina MiSeq; Oxford Nanopore MiniION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 07/29/2023 04:14:33
            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)                     :: 4,844
            CDSs (total)                      :: 4,729
            Genes (coding)                    :: 4,611
            CDSs (with protein)               :: 4,611
            Genes (RNA)                       :: 115
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 78
            ncRNAs                            :: 15
            Pseudo Genes (total)              :: 118
            CDSs (without protein)            :: 118
            Pseudo Genes (ambiguous residues) :: 0 of 118
            Pseudo Genes (frameshifted)       :: 51 of 118
            Pseudo Genes (incomplete)         :: 74 of 118
            Pseudo Genes (internal stop)      :: 24 of 118
            Pseudo Genes (multiple problems)  :: 29 of 118
            Pseudo Genes (short protein)      :: 1 of 118
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP039598.1.
            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..1968
                     /organism="Salmonella enterica subsp. enterica serovar
                     1,4,[5],12:i:-"
                     /mol_type="genomic DNA"
                     /strain="PNCS014865"
                     /serovar="1,4,[5],12:i:-"
                     /host="Homo sapiens"
                     /sub_species="enterica"
                     /db_xref="taxon:2583588"
                     /plasmid="p12-4331.3"
                     /geo_loc_name="Canada: NL"
                     /collection_date="2012-03-08"
                     /collected_by="Eastern Health Microbiology Services"
     gene            1..192
                     /locus_tag="E5O09_RS24705"
                     /old_locus_tag="E5O09_24510"
     CDS             1..192
                     /locus_tag="E5O09_RS24705"
                     /old_locus_tag="E5O09_24510"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_020324555.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_136612534.1"
                     /translation="MIVRLDNRLFEILDEMGARVDREMFMAAYAQRKAEKENDPRHVRQ
                     RKMTQLTHDLMSESDPEL"
                     /name="hypothetical protein"
     gene            521..1504
                     /locus_tag="E5O09_RS24515"
                     /old_locus_tag="E5O09_24515"
     CDS             521..1504
                     /locus_tag="E5O09_RS24515"
                     /old_locus_tag="E5O09_24515"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001362017.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="protein rep"
                     /protein_id="WP_136612535.1"
                     /translation="MKHDKLQNLTDYSPSDSPWDAHRSVSDDVGGIYLHASEFERYAAR
                     MASCGGLLRFGWSTLKETGETRLRLRSAEFCRVRHCPICQWRRSLMWQARFYQSLPRIV
                     ADFPQSRWIFLTLTVRNCAIEELGETLTAMNAAFKRMEKRKEFRPVQGWIRTTEVTRGR
                     DGSAHPHFHTLMMVPPGMLNGKSYVTHAEWVALWRDVLRVNYDPNVDVRAVKPRKPKNG
                     ESLASVTAELVRGAVAETLKYSTKPSDMVADPEWFLELTRQTHKRRFVATGGALKDVLK
                     LEQETDQDMVIADDISEGDDDGTRIAFEWNRLVKKYRRAPEKDKSD"
                     /name="protein rep"
ORIGIN
        1 atgatcgtca gactggataa ccggctgttt gagattctcg atgagatggg tgcgcgtgtg
       61 gatcgggaaa tgttcatggc ggcttatgcg cagcggaagg ctgagaagga aaatgatccc
      121 cgacatgtac gtcagaggaa aatgactcag ttgacccacg acctgatgtc agaatccgac
      181 cctgaattgt gagtctcgcg tgcgcgcgag gcgagagggt gggaaattgg tcaaaaaatc
      241 gccgagcctc atgcgcgcga tccttatatt tatacctaag ggataaatgg cggattgaaa
      301 agtgtctcta agccttgtgg cagtagggct gagaggggat ttgctggaaa atgactttgc
      361 gcgtagtatt tgttcaacgg tgatatgtga aacccctgca agtgggcaaa cacttcaggg
      421 gcgcgatcac ctgacaaatt cggtttttgc gacagacatt caggtgatac ggaaatgata
      481 ccacagcatt ccagagcctg cccactacgg agcgggcagc atgaaacacg ataaacttca
      541 gaatctcacc gattactccc cctcagattc gccgtgggac gctcacagga gcgtttccga
      601 cgacgtggga gggatttacc tgcatgcatc agaattcgag cgctacgcgg cacgtatggc
      661 ctcctgcggc ggtttattac ggttcggctg gtctaccctc aaagaaaccg gagaaacgcg
      721 cctgcggctt cgtagcgcgg aattctgccg tgtccgtcat tgtcccatct gtcagtggag
      781 gcgatccctg atgtggcaag cccgtttcta tcagtccctt ccgcgtattg tcgcggattt
      841 tccccaatcc cgatggatct tcctgacgtt gaccgtgcgt aactgcgcga ttgaggagtt
      901 gggcgaaacc ctcacggcaa tgaatgccgc ctttaagcgc atggaaaaac gtaaggaatt
      961 tcgccccgtt caaggctgga tacgcaccac agaagtgacg cggggtaggg atggcagcgc
     1021 ccatccgcat tttcacactc tgatgatggt tcctcctggc atgctgaacg ggaaaagtta
     1081 cgttactcat gctgagtggg tggcgctatg gcgggatgtt ctgcgggtaa attacgatcc
     1141 caatgttgat gtccgggctg tgaaaccacg caaaccaaaa aatggtgagt cgctggcttc
     1201 cgttactgcc gaactggtgc gcggcgcggt ggctgaaacc ctgaaatact ccactaaacc
     1261 atctgacatg gtggctgatc ctgaatggtt cctcgaactg actcgccaga cgcacaagcg
     1321 tcgttttgtg gcgacgggtg gagcactgaa agacgtgctg aagctggagc aggaaaccga
     1381 tcaggatatg gtgatcgcgg atgatatttc cgaaggtgat gacgacggaa cgcgtatcgc
     1441 gtttgagtgg aatcgtctgg tgaaaaaata tcggagagca ccggaaaaag ataaatcaga
     1501 ctgacccgct acggcgggtt ttttattggg tgtcggggct ttgccctgac caagaatgtt
     1561 ttttgaagcc gactgtgtgc aggcggttca acaaaacaca tcttgtcctt tttttcgtgc
     1621 agagtttgat tttagaaatc tgcaagggga ctgttaatcc ccgtgtcgat aatctcaaac
     1681 aaatcgggga caagatgtgt tttgtagcac cgccacacgc ggcagtacct ccaaaccact
     1741 tggtcagggc aaagccccga cacccgccaa cgcctcacga gccgcgaaaa atttcgcagc
     1801 ccgctcaccg tttctgaatt cgtcaaacgc taaatcgtgg ggtcccgctg gcttgccagt
     1861 gggttccgat ttagtgattg acgactgtac tcgtggaata cttgcaggag gtggttgtga
     1921 tcacgcagtg agcgcaacca cctgataagc gtttttgagg aggtagac
//
