LOCUS       NZ_CP040323             5491 bp    DNA     circular CON 22-MAR-2024
DEFINITION  Salmonella enterica subsp. enterica serovar Typhimurium strain
            PNCS014879 plasmid p16-6397.2, complete sequence.
ACCESSION   NZ_CP040323
VERSION     NZ_CP040323.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN11333169
            Assembly: GCF_005537375.1
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 5491)
  AUTHORS   Schonfeld,J., Clark,C., Johnson,R., Labbe,G., Liu,K., Robertson,J.
            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  JOURNAL   Unpublished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 5491)
  AUTHORS   Schonfeld,J., Clark,C., Johnson,R., Labbe,G., Liu,K., Robertson,J.
            and Nash,J.H.E.
  TITLE     Direct Submission
  JOURNAL   Submitted (10-MAY-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 Date                     :: MAY-2019
            Assembly Method                   :: Unicycler v. 0.4.7
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 100.0x
            Sequencing Technology             :: Illumina MiSeq
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_005537375.1-RS_2024_03_22
            Annotation Date                   :: 03/22/2024 01:09:59
            Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline
            (PGAP)
            Annotation Method :: Best-placed reference protein set; GeneMarkS-2+
            Annotation Software revision      :: 6.7
            Features Annotated                :: Gene; CDS; rRNA; tRNA; ncRNA
            Genes (total)                     :: 4,951
            CDSs (total)                      :: 4,830
            Genes (coding)                    :: 4,693
            CDSs (with protein)               :: 4,693
            Genes (RNA)                       :: 121
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 85
            ncRNAs                            :: 14
            Pseudo Genes (total)              :: 137
            CDSs (without protein)            :: 137
            Pseudo Genes (ambiguous residues) :: 0 of 137
            Pseudo Genes (frameshifted)       :: 58 of 137
            Pseudo Genes (incomplete)         :: 90 of 137
            Pseudo Genes (internal stop)      :: 25 of 137
            Pseudo Genes (multiple problems)  :: 33 of 137
            Pseudo Genes (short protein)      :: 1 of 137
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP040323.1.
            Bacteria and source DNA available from 16-6397.
            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..5491
                     /organism="Salmonella enterica subsp. enterica serovar
                     Typhimurium"
                     /mol_type="genomic DNA"
                     /strain="PNCS014879"
                     /serovar="Typhimurium"
                     /host="Homo sapiens"
                     /sub_species="enterica"
                     /db_xref="taxon:90371"
                     /plasmid="p16-6397.2"
                     /geo_loc_name="Canada: BC"
                     /collection_date="2016-08-25"
                     /collected_by="BC Centre for Disease Control"
     gene            1..519
                     /locus_tag="E5O16_RS24940"
                     /old_locus_tag="E5O16_24975"
     CDS             1..519
                     /locus_tag="E5O16_RS24940"
                     /old_locus_tag="E5O16_24975"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_016246513.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_011017199.1"
                     /translation="MKCFWACSVSVVLVMSFTVASAENITHTKPLARSDLYLTCKGYQV
                     KGASVINVEKPSYLEGTGEQVEFAIISLGDASDGLKVFFDSWGFSPFGLIESHVMHEHW
                     SLVHVGGRVSVKGEKIDYSFVDNQPQEGGSYKPKTGVFLYGCINSDKRPSWVEKIYTRT
                     GVFRGGIED"
                     /name="hypothetical protein"
     gene            1335..1853
                     /locus_tag="E5O16_RS24945"
                     /old_locus_tag="E5O16_24980"
     CDS             1335..1853
                     /locus_tag="E5O16_RS24945"
                     /old_locus_tag="E5O16_24980"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001445155.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_045342112.1"
                     /translation="MSEKAKQVGRRSLSKRRENLIKELWGDELSELNIWNRKEHDGFTT
                     IPRTLNYINRIIDHLAGAGSPVSQTYLSLWCRVFDEGFVEIRDKDALAFESGFSGQRAV
                     TTWLGRMKKLRELGLISTKPGTSGEFHYVIMLNPLYVIKKSYESNGWARDERYNALFSR
                     MQEVGAEWE"
                     /name="hypothetical protein"
     gene            1850..2413
                     /locus_tag="E5O16_RS24950"
                     /old_locus_tag="E5O16_24985"
     CDS             1850..2413
                     /locus_tag="E5O16_RS24950"
                     /old_locus_tag="E5O16_24985"
                     /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_052686588.1"
                     /translation="MNDMKAVRHRYKQRYDFAASEVVGAFDELKSLDWSLEIASLSDVE
                     MSKRWIGAVDPNGVARLPPNGGWDWVKLYNGYLKNPSAFVCAIKSEGKLCALIGGGVSD
                     SKVVTKLHYLESAPYDTALSGYALDISVTYVVTVANAMGSEYTAIYEPNSKVRDIAIND
                     YGFSEDNLFGTSKDFALYLPMSRG"
                     /name="hypothetical protein"
     gene            complement(2423..2575)
                     /locus_tag="E5O16_RS25050"
     CDS             complement(2423..2575)
                     /locus_tag="E5O16_RS25050"
                     /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_161976623.1"
                     /translation="MLAHVVELKKATEPCSSGTARAFRQRVKARRAEQGRSNQQPEKLY
                     GVLVG"
                     /name="hypothetical protein"
     gene            3658..3981
                     /locus_tag="E5O16_RS24965"
                     /old_locus_tag="E5O16_25000"
     CDS             3658..3981
                     /locus_tag="E5O16_RS24965"
                     /old_locus_tag="E5O16_25000"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000957083.1"
                     /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_001347450.1"
                     /translation="MLTMWVTEDEHRRLLERCDGKQLAAWMRQTCLDEKPARAGKLPSL
                     SPALLRQLAGMGNNLNQIARQVNAGGGSGHDRVQVVAALMAIDAGLERLRHAVLEKGAD
                     DDR"
                     /name="MobC family plasmid mobilization relaxosome protein"
     gene            4190..>4624
                     /locus_tag="E5O16_RS25445"
                     /pseudo=""
     CDS             4190..>4624
                     /locus_tag="E5O16_RS25445"
                     /inference="COORDINATES: protein motif:HMM:NF015397.4"
                     /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            4659..5144
                     /locus_tag="E5O16_RS24975"
                     /old_locus_tag="E5O16_25010"
     CDS             4659..5144
                     /locus_tag="E5O16_RS24975"
                     /old_locus_tag="E5O16_25010"
                     /inference="COORDINATES: protein motif:HMM:NF016710.4"
                     /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_015059929.1"
                     /translation="MNSLLTLAKDLEQKSKAQQQSTGEMLKAAFSEHEKSVRAELSESE
                     KRISAAILDHDRKLSSAMSQRTKGMVRMVSQTWLTIVLVSTLLTASGASILWWQGQQIL
                     DNYTIIREQKSTQAMLSERNSGVQLSTCGEQRRRCVRVNPEAGRFGEDSSWMILAGK"
                     /name="MbeB family mobilization protein"
     gene            5148..5363
                     /locus_tag="E5O16_RS24980"
                     /old_locus_tag="E5O16_25015"
     CDS             5148..5363
                     /locus_tag="E5O16_RS24980"
                     /old_locus_tag="E5O16_25015"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000137421.1"
                     /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_058671277.1"
                     /translation="MTELEKQLLSALEQLQQDYSKRLDEWENAFAEWRTMSGLMQRENA
                     ALSERVTGLSRQVQSLSDQLRRLSKG"
                     /name="MbeD family mobilization/exclusion protein"
     Typing          3371..3554
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="85.561"
                     /coverage="86.0"
                     /evalue="2.7100000000000003e-47"
     Typing          complement(2909..3395)
                     /name="ColRNAI_rep_cluster_1987"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="86.263"
                     /coverage="93.0"
                     /evalue="2.83e-145"
     Typing          3972..5455
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="91.717"
                     /coverage="99.0"
                     /evalue="0.0"
ORIGIN
        1 atgaagtgtt tctgggcttg ctcagtctca gtagttttgg ttatgtcatt tacagtcgct
       61 tctgcggaga acattacaca cacaaaaccg ttagccagga gcgacttata tcttacctgt
      121 aaaggttatc aggtgaaggg ggcgtctgta attaacgtcg agaaaccttc ttaccttgaa
      181 ggtacaggtg agcaggttga gtttgcaatc atttctctcg gtgatgcatc tgatggactc
      241 aaggtttttt ttgattcatg gggtttttct ccttttggat tgattgaaag tcatgtaatg
      301 catgagcact ggtctttagt tcatgttggg gggcgtgttt cagtcaaggg tgaaaagatt
      361 gattattcat ttgtagataa ccagccacag gagggtggga gctataaacc caaaacaggt
      421 gtgttcctgt atggctgcat taactctgat aaaaggccat cttgggtcga aaaaatctac
      481 acaagaacag gcgtgtttcg agggggcata gaagactaaa atactgcgta cagcatgaaa
      541 attcattgaa cagagtgtta gttcattttc gtgcatggct atgcatacac gcaaaactta
      601 tcagcgcgat tccgggcggt tttcggtgag aagacgggct cttttgtggc ttaggacgga
      661 aaaacgccct gagcgcgtct gagcggtgcg cccaagggat gttatgttca attgtttctg
      721 aggtgtaggc taaaactcga gttttgacgc cattctgagt aggaaatttg cagacggaat
      781 aaatactggt gagcaataag ctcatcaaca aaaaaatgga gatcctaaga tggatagaga
      841 aaccctatac ctgctcaaaa cgttagaccg taacaatgcc ttacttgacg atattgtccg
      901 aagaaagatg ggcaggtact acaacacgaa gattttgcgt gattcctgtg atgctattga
      961 agccgaacta cgacatcgag gaatcattta acaagacgaa gcccgcttat gtgggctttt
     1021 tcatgcgcat tcagaatacc ccttcccccc cttaaacccc ctaagaaccc cattcagcac
     1081 agcgagcaca acgattacat tggagcacac cgaggacagc gagtacaaaa tgatgtataa
     1141 gtggttgaaa aataaaacca taactgtaaa taatattaca cttcaatatt tgtattgaca
     1201 aaaaacaaga ataatatcaa atgagatgtt ggttaatgat gtgcttggtt tttgtgttat
     1261 tacacataac tcattgaata taatggcttt tttgtcaata atggtttcat gttgaattga
     1321 cttttggggg agaaatgtca gagaaggcaa aacaagtagg taggcgctct ctatcaaaaa
     1381 gaagagaaaa tctaataaaa gagctttggg gggatgagct ttccgaactg aatatatgga
     1441 acaggaaaga acacgatgga tttacaacaa tcccaagaac attgaattat atcaatagga
     1501 taatcgatca ccttgctggc gctggatctc ctgtatcaca gacatacctc agtttatggt
     1561 gtcgggtttt tgacgaggga ttcgtcgaaa ttagggataa agatgctctg gcatttgagt
     1621 cagggtttag tgggcagcga gcggtgacta cttggctagg aagaatgaaa aagttacggg
     1681 agctgggact gatatcaacg aagcctggta cttctggtga gtttcattat gtaatcatgt
     1741 tgaatccact ttacgtaatt aaaaaatcat atgaatcaaa cggatgggca agagatgagc
     1801 gttacaacgc tctattttct aggatgcagg aagtgggggc tgagtgggaa tgaacgacat
     1861 gaaagctgtt cgtcaccgat ataagcagag atatgatttt gctgcgtcag aagtagtggg
     1921 ggcgtttgat gaacttaaaa gtttggattg gagtttagaa attgcatctt taagcgatgt
     1981 ggaaatgtca aagagatgga ttggggctgt tgatcctaac ggtgttgcaa gactaccacc
     2041 taatggtgga tgggactggg ttaagctcta taacggctat ttgaagaacc ctagcgcatt
     2101 cgtctgtgct attaaatcag aaggtaagct atgcgctctg attggtggtg gggtttctga
     2161 tagtaaagtg gtaaccaagc tgcattacct tgaatcagcc ccttatgaca cggcgctttc
     2221 aggatatgca ctcgatattt ctgttacgta tgttgttact gtcgcgaatg cgatgggtag
     2281 cgagtacaca gccatctatg agccaaatag caaggtcaga gatatagcta taaatgatta
     2341 tggatttagc gaggacaact tgtttgggac aagtaaagat ttcgctctgt atctaccaat
     2401 gagccggggt taaccggctc atttagccta ccagtacgcc gtagagtttt tcaggctgtt
     2461 ggtttgatcg gccttgctct gctcgtcttg ctttcacgcg ctggcgaaat gctctggctg
     2521 tgccagaaga gcatggttcc gtcgcttttt taagttcgac cacgtgagct aacatattat
     2581 ttccgttttt tcgtgagtta gtacaaagca tatgaggtga cggatacgtc aacttcatag
     2641 taactgtact gtattgtaga agagatgcgc aagtcgcaga attaatgcga cccttcattg
     2701 acgaggcgaa gagtaaacgc gtatcttctt tgaaaacgaa aaaaccaccc ggcaaggtgg
     2761 tttttcgaag gttcattaaa ccggcaagtt tatgaaccgt ggtaacaggg tgtacaagac
     2821 cactgccacc aaattcgtcc ttccagttta gccgtagttg ggctgatact tcaagaactc
     2881 tgcgttagta atctcttgta catcctctta ccgttggctg ctgccagtgg cgttaagtcg
     2941 tgcctatccg ggttggactc aagacgatag ttaccggaca aggcgcagca gtcggactga
     3001 acggggggtt cgtgcataca gtccatcctg gagcgaactg cctacccgga actgagtgtc
     3061 aggcgtggaa tgagacaaac gcggccataa cagcggaatg acaccggtaa accgaagggc
     3121 aggaatgcgg gggagcacga gggagccatc agggggaaac gcctggtatc tctaagccgc
     3181 atcgggtttc gccaccactg atttgagcgt ctgattttgt gatgctcgtc aggggggcgg
     3241 agcctatgga aaaacggcag cgccgtatcc tttttccggc ctttcctgac ttgagtgcca
     3301 tctctttatc ttgtcattcg tgagcaggta acgcccgccg cagcctcacg gcaggagcgt
     3361 agcgaccgag tgagcgagga ggcgtcatgt caccgacacc ggcatttcgc acctactccc
     3421 tgcagcagca ttttccccct atcacatgaa gcactttcct gaatcgccac ttcgatttac
     3481 catattcagc cagtatacac tccgctagcg ctacgtgact ggttcagggc tgcgccccga
     3541 aacccgctaa aaccactgac gcgcctgcgg cttgtccaac accgcgccga ccgggaaaag
     3601 atttcccgcc cgtcccggcg ttatcaggag gccggattgg cagacaaacg cagcaaaatg
     3661 ctcacgatgt gggtgaccga agatgagcac cgccgtctgc tggagcgctg cgacggtaaa
     3721 cagcttgcag cctggatgcg ccagacgtgc ctggacgaga aacccgcccg cgccggcaag
     3781 cttccctcgc tctcgccggc gctgcttcgt cagcttgccg gcatggggaa caacctcaac
     3841 cagattgccc ggcaggttaa cgccggtggt ggcagcgggc acgaccgcgt gcaggtcgtc
     3901 gccgcgctga tggccataga tgccggactc gagcggctgc ggcatgctgt gctggaaaag
     3961 ggtgcagacg atgatcgtta agtttcaccc gcgagggcgc ggcggtggcg ccggtccggt
     4021 ggattatctg ctggggaaag accgacagcg cgacggcgcc accgttctgc aggggaagcc
     4081 ggaagaagtc agggagctta tcgacgcctc gccctacgca aaaaagtaca catccggcgt
     4141 cctgtccttt gccgaaaagg atttaccgcc cgggcagcgc gaaaagctga tggcgagctt
     4201 tgaacgggtt ctgatgcccg gactcgataa agaccagtac agcgtgctgt gggttgagca
     4261 ccaggataag gggcggctgg agctgaactt cctgatcccg aacacggagc tgctgaccgg
     4321 caagcgtctc cagccgtatt acgaccgcgc cgaccgtccg cgcattgatg cctggcagac
     4381 catcgtgaac ggcaggctgg ggctgcatga cccgaacgcg cctgaaaacc ggcgggcgct
     4441 ggtcacgccg tccgcgctgc cgaaaacgaa gcaggaagcc gctcaggcaa ttacacgggg
     4501 tttactggcc ttagcctcgt ccggggagct gaaaacccgc caggacgtca ctgaggcgct
     4561 ggaaagcgca ggttttgagg tggtacgcac cacaaaaagc agcatcagca ttgccgaccc
     4621 ggacgggggg cgaaacatcc gactgaaggg agccatctat gaacagtctt ttaacgctgg
     4681 caaaggactt agagcagaaa tcgaaagcgc agcagcagag taccggcgag atgctgaaag
     4741 ccgcattcag cgagcacgag aagtctgtca gagcggaact gagcgaaagc gagaagagaa
     4801 tcagcgccgc catcctcgac cacgaccgga agctgtcctc agccatgagc cagcgcacga
     4861 aaggcatggt gcgtatggtc agccagacgt ggctgaccat cgtcctggtg tctacactgc
     4921 tgacagcatc gggcgcaagc attctgtggt ggcaggggca gcagatactc gacaattaca
     4981 cgatcatccg ggagcagaag agcacgcagg ccatgctgtc cgagaggaac agcggcgtgc
     5041 agctctcgac ctgcggagag cagagacgcc gctgcgtgag ggtgaacccg gaagcgggac
     5101 ggttcggaga ggattcgagc tggatgatac tggcggggaa atagcacatg acggagctgg
     5161 aaaaacagtt gctgagcgca ttagagcagc tacagcagga ctactcgaaa aggctggacg
     5221 agtgggagaa cgccttcgcg gaatggcgga cgatgtctgg tcttatgcaa cgggagaacg
     5281 cggcgctgag cgagcgcgtc acgggcttga gcaggcaggt gcagagtttg agcgatcagc
     5341 tgcgccggtt gtcgaaaggc tgaactcgat tgaagcacac aggcagcagg agcgggcggc
     5401 gcagcatcag aaaacgctgg agctggaacg atcgcagcgg cagaaaggtt ttgagcttgg
     5461 aatgtagtta atcaatgaaa agggatgcgt t
//
