LOCUS       NZ_CP039602             3374 bp    DNA     circular CON 29-JUL-2023
DEFINITION  Salmonella enterica subsp. enterica serovar 1,4,[5],12:i:- strain
            PNCS014867 plasmid p12-6334.3, complete sequence.
ACCESSION   NZ_CP039602
VERSION     NZ_CP039602.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN11333164
            Assembly: GCF_004919425.1
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 3374)
  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  JOURNAL   Unpublished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 3374)
  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 04:10:43
            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)                     :: 4,854
            CDSs (total)                      :: 4,731
            Genes (coding)                    :: 4,624
            CDSs (with protein)               :: 4,624
            Genes (RNA)                       :: 123
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 86
            ncRNAs                            :: 15
            Pseudo Genes (total)              :: 107
            CDSs (without protein)            :: 107
            Pseudo Genes (ambiguous residues) :: 0 of 107
            Pseudo Genes (frameshifted)       :: 32 of 107
            Pseudo Genes (incomplete)         :: 86 of 107
            Pseudo Genes (internal stop)      :: 17 of 107
            Pseudo Genes (multiple problems)  :: 27 of 107
            Pseudo Genes (short protein)      :: 1 of 107
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP039602.1.
            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..3374
                     /organism="Salmonella enterica subsp. enterica serovar
                     1,4,[5],12:i:-"
                     /mol_type="genomic DNA"
                     /strain="PNCS014867"
                     /serovar="1,4,[5],12:i:-"
                     /host="Homo sapiens"
                     /sub_species="enterica"
                     /db_xref="taxon:2583588"
                     /plasmid="p12-6334.3"
                     /geo_loc_name="Canada: ON"
                     /collection_date="2012-09-07"
                     /collected_by="Public Health Ontario Laboratories"
     gene            complement(737..970)
                     /locus_tag="E5O11_RS24515"
                     /old_locus_tag="E5O11_24515"
     CDS             complement(737..970)
                     /locus_tag="E5O11_RS24515"
                     /old_locus_tag="E5O11_24515"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000137389.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MbeD family mobilization/exclusion protein"
                     /protein_id="WP_000137389.1"
                     /translation="MTELEGHLLNALEHLQQDYMRRLNEWESAFAELQKMHEVTQRNNA
                     ILNERVVILSQQVQRLAGQVDRLSRLFIANNS"
                     /name="MbeD family mobilization/exclusion protein"
     gene            complement(977..1537)
                     /locus_tag="E5O11_RS24520"
                     /old_locus_tag="E5O11_24520"
     CDS             complement(977..1537)
                     /locus_tag="E5O11_RS24520"
                     /old_locus_tag="E5O11_24520"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000067488.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MbeB family mobilization protein"
                     /protein_id="WP_000067486.1"
                     /translation="MSNLLQMGTDFEKKLKERAASTENMLNSEFRKLEESVDKALSLNR
                     QKIRDAISEHTTSVKKQLDTLSTTVSMQFSTTEAELSRQQKKLLWRVIKGRILFPALTA
                     LSVTGGIFLGCWGLMEWQESKIAKNILTIREQENTLAKLEAKTWGVTFVNGENGKFLVL
                     PDGMKGENTWTVGDKNAVRLVRE"
                     /name="MbeB family mobilization protein"
     gene            complement(<1566..2006)
                     /locus_tag="E5O11_RS24885"
                     /pseudo=""
     CDS             complement(<1566..2006)
                     /locus_tag="E5O11_RS24885"
                     /inference="COORDINATES: protein motif:HMM:NF015397.2"
                     /note="incomplete; partial in the middle of a contig;
                     missing C-terminus; Derived by automated computational
                     analysis using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="relaxase/mobilization nuclease domain-containing
                     protein"
                     /name="relaxase/mobilization nuclease domain-containing
                     protein"
     gene            complement(2215..2538)
                     /locus_tag="E5O11_RS24530"
                     /old_locus_tag="E5O11_24530"
     CDS             complement(2215..2538)
                     /locus_tag="E5O11_RS24530"
                     /old_locus_tag="E5O11_24530"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000956000.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MobC family plasmid mobilization relaxosome
                     protein"
                     /protein_id="WP_001696562.1"
                     /translation="MLTIRVTDEEHARLLERCEGKRLAEWMRRVCLGEPVARTGKLPTL
                     APPLLRHLAAIGNNLNQTARKVNSGQWSSIDRVHVVAALMAIEGELRQLRQAVREQGVR
                     DDS"
                     /name="MobC family plasmid mobilization relaxosome protein"
     gene            2602..2793
                     /locus_tag="E5O11_RS24535"
                     /old_locus_tag="E5O11_24535"
     CDS             2602..2793
                     /locus_tag="E5O11_RS24535"
                     /old_locus_tag="E5O11_24535"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000165979.1"
                     /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_000165979.1"
                     /translation="MTKQEKTALNMARFIRSQTLTLLEKLNDLDADEQADICESLHDHA
                     DELYRSCLARFGDDGESN"
                     /name="Rop family plasmid primer RNA-binding protein"
     Typing          complement(2875..2955)
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="87.805"
                     /coverage="93.0"
                     /evalue="8.68e-18"
     Typing          complement(655..2225)
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="92.439"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 gtgacgtatg cgtcttcgcc gcaccatctc acccgtcacg ccaccacata ccgggaactg
       61 ccgccaaggt ctaactcaac caatctagcc gcgctacata cggtttttgt ggcaactcat
      121 caggtgtccg ctgtcgatga aactctctgc gccggtagcg gaactctcac gcgtgcggtc
      181 gccgtcgtca cagctccccc aaccgcaaac gattctcgca aatacgcaag tatctgcaaa
      241 aacaggtttt tttcggggtt cctgggagac tgtgctgttg aaaaattctt gaagaataca
      301 gaaggctcat gcaaactgaa tgaactggtt tctgttgtgg atctcaacag tttccacagg
      361 aacattgagg aggtcagaga cctcaatgaa cccgaaacag ctcgccttcc tggcgagctg
      421 ttttcgttct acgcccgccg acgaaagatc gcaagtgcaa taacgagatt tttcacgtct
      481 ttacgctcaa aaagtaaaaa aaccatgttt tcccctggct gaatccccaa aaacgcgtga
      541 aatgcgtttt caggatgttg catagctatg cacaaatacg gcacacgatt tgtttcgctc
      601 gccccagccg tcgaacgggt caaaatggca agatttcgtc acttccccgg tcacatctcc
      661 attgatggcc cactccgaac ccgtgccgcg cgttcctgta cctcatgtct gtaccgggca
      721 cgctcctgtt catcccttag ctgttgttcg cgataaataa ccgactcaag cgatccactt
      781 gcccggctaa tctctgcacc tgctgactca atatcacgac gcgctcgttc agtatcgcgt
      841 tgttccgttg cgtaacctcg tgcatcttct gcaattccgc gaaggcgctc tcccactcgt
      901 tcagccgccg catatagtcc tgttgcaaat gctctaaggc gttcagcaaa tgcccttcca
      961 gttccgtcat actcgtttac tccctgacca gcctcacggc gttcttgtcg cccaccgtcc
     1021 aggtgttttc ccctttcatc ccgtccggca acaccagaaa tttcccgttc tcgccattga
     1081 cgaacgtcac cccccaggtt tttgcctcga gtttcgccag cgtgttttcc tgctctctga
     1141 tagtcaggat atttttcgca atcttgcttt cctgccactc catcagcccc cagcacccca
     1201 ggaaaatccc gcccgtgacg ctgagcgcgg tcagcgccgg aaacagtatc cgccctttga
     1261 tcacccgcca gagcagtttt ttctgctgcc gggacagttc ggcctctgtg gtgctgaact
     1321 gcatgctcac ggtggtgctc agcgtatcca gttgcttttt cacggatgtt gtatgttcgc
     1381 tgatagcgtc tctgattttc tgcctgttta agctcaatgc cttgtctaca gactcttcga
     1441 gcttcctgaa ctcgctgttc agcatgttct cggtagaagc ggctcgctct ttcagtttct
     1501 tctcgaagtc tgttcccatt tgtaaaagat tgctcataca gcgccccctt tagcctgaga
     1561 ttccgccccc cctccgggtc ggcaatactg atgctgcttt tggttgtcct caccacctca
     1621 aaacctgccg ctgtaagcgc ctctgtgaca tcctgacgcg tttttattgc tccggcatgg
     1681 taaagagcct caagaccccg tgtaatcgct tctgcggcct cctgtttcgc ttttggcaga
     1741 ttatttggcg tgacaagcgt ccgtctgttc tccggtgcgt tcgggtcacg cagcccgtaa
     1801 tgatgattaa ccagcgtctg ccaggcattt atcctcggcc tgtccgcacg gtcgtagtac
     1861 ggctggaggc gcttaccgct ctgtagctcc atgttcggga tgacaaaatt cagttcgagc
     1921 cgccccttat cctggtgttc cacccagaga atgctgtact ggtctttttc gagaccgggc
     1981 ataagaacac gctcaaagct cgtcatcact ctttcgcgtt cacccggtgg tagctccttc
     2041 tccgcgaacg acagaacgcc tgacgtgtat ttcttcgaaa atggcgtgga atcaatgagt
     2101 tcccgcactt cttccgggtt accccggagc accgttgcgc cttcgcggtt acgctcccgc
     2161 cccagcaggt aatcgaccgg gccacttcca ccgcctttcc ccctggcatg aaatttaact
     2221 atcatcccgt accccctgtt ccctgacagc ctgccgcaac tggcgcaatt caccctcgat
     2281 ggccatcagt gcggccacca catgaacccg gtcaatcgaa gaccactggc cgctgttcac
     2341 cttccgggct gtctggttca ggttgttccc gatggcagcc agatgccgca gcaatggcgg
     2401 tgccagtgtc ggcagttttc ctgtgcgtgc aaccggctcc cccagacaga cccgccgcat
     2461 ccattccgcc agtcgtttac cctcgcagcg ttccagtaac cgggcgtgct cctcatcggt
     2521 aacccgtatc gtgagcatct tctcgcgttt catcggtatc attcccccta acaaatcccc
     2581 catacaagga gccttaagac catgaccaaa caggaaaaaa cagcccttaa catggctcgc
     2641 tttatcagaa gccagacgct aaccctgctg gaaaaactca acgatctgga cgcggacgaa
     2701 caggcagaca tctgcgaatc acttcacgac cacgccgacg aactctaccg cagttgcctc
     2761 gcacgcttcg gcgatgacgg tgaaagcaac tgaaacatgc agctcccgga gacgttcaca
     2821 gcttgcctgt gagcggatgc cgggagcaga caagcccgcc agggcgcgtc agtgcgggtg
     2881 tcggggcgca gccctgaccc agttcacaga gcgatagcga tgtgtatact ggcttacctc
     2941 attttgcatc ggtgcagagt ggatgggaag tgcaccatgt caggagtaaa aagccgcaca
     3001 gatgcgtaaa aacagcgcgc ccgataaaca acacacacgc ggacactggc acaggcgcgt
     3061 aagtgcacaa tgcttgcctc tgtgactctt ccgcttcctc gcccactcgc tcactacgtt
     3121 cggtcgctgg ggctgcggcg agcggtggga tcactctcgt tgtgatgcag atccgttttt
     3181 tttttttgca ctggagttat caggagtagc ggtgcacatg ggatcgtgcg atatgctgga
     3241 tggtggaagg tcggagggaa cggcaacaac tcacccctcc cagtgaaggg acgggtagtt
     3301 tgccgctctc gatatgccgg acggagccaa ggccatcgat cacggggcgc gtcagtggaa
     3361 gaacccgcgc ctgc
//
