LOCUS       CP039578                3208 bp    DNA     circular BCT 06-JUL-2021
DEFINITION  Salmonella enterica subsp. enterica serovar Typhimurium strain
            PNCS014856 plasmid p10-3857.2, complete sequence.
ACCESSION   CP039578
VERSION     CP039578.1
DBLINK      BioProject: PRJNA316728
            BioSample: SAMN11333151
KEYWORDS    .
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 3208)
  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  JOURNAL   Unpublished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 3208)
  AUTHORS   Schonfeld,J., Clark,C., Johnson,R., Labbe,G., Liu,K., Robertson,J.
            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 NextSeq; Oxford Nanopore MiniION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI
            Annotation Date                   :: 04/19/2019 10:54:38
            Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline
            (PGAP)
            Annotation Method :: Best-placed reference protein set; GeneMarkS-2+
            Annotation Software revision      :: 4.8
            Features Annotated :: Gene; CDS; rRNA; tRNA; ncRNA; repeat_region
            Genes (total)                     :: 5,084
            CDSs (total)                      :: 4,968
            Genes (coding)                    :: 4,825
            CDSs (with protein)               :: 4,825
            Genes (RNA)                       :: 116
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 80
            ncRNAs                            :: 14
            Pseudo Genes (total)              :: 143
            CDSs (without protein)            :: 143
            Pseudo Genes (ambiguous residues) :: 0 of 143
            Pseudo Genes (frameshifted)       :: 54 of 143
            Pseudo Genes (incomplete)         :: 83 of 143
            Pseudo Genes (internal stop)      :: 37 of 143
            Pseudo Genes (multiple problems)  :: 28 of 143
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            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/
FEATURES             Location/Qualifiers
     source          1..3208
                     /organism="Salmonella enterica subsp. enterica serovar
                     Typhimurium"
                     /mol_type="genomic DNA"
                     /strain="PNCS014856"
                     /serovar="Typhimurium"
                     /host="Homo sapiens"
                     /sub_species="enterica"
                     /db_xref="taxon:90371"
                     /plasmid="p10-3857.2"
                     /geo_loc_name="Canada: BC"
                     /collection_date="2010-06-18"
                     /collected_by="BC Centre for Disease Control"
     gene            1..195
                     /locus_tag="E5N98_25395"
     CDS             1..195
                     /locus_tag="E5N98_25395"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001041640.1"
                     /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="QCG03840.1"
                     /translation="MNKQQQTVLNMAGFIKSQSLTLLEKLDALDADEQAAMCEKLHELA
                     EELQNSIQTRFEAENRTGI"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            complement(1001..1201)
                     /locus_tag="E5N98_25400"
                     /pseudo=""
     CDS             complement(1001..1201)
                     /locus_tag="E5N98_25400"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001427890.1"
                     /note="incomplete; partial on complete genome; missing
                     N-terminus; Derived by automated computational analysis
                     using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="NYN domain-containing protein"
                     /name="NYN domain-containing protein"
     gene            complement(1301..2116)
                     /locus_tag="E5N98_25405"
     CDS             complement(1301..2116)
                     /locus_tag="E5N98_25405"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_032492145.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="aminoglycoside O-phosphotransferase APH(3')-Ia"
                     /protein_id="QCG03841.1"
                     /translation="MSHIQRETSCSRQRLNSNLDADLYGYKWARDNVGQSGATIYRLYG
                     KPDAPELFLKHGKGSVANDVTDEMVRLNWLTEFMPLPTIKHFIRTPDDAWLLTTAIPGK
                     TAFQVLEEYPDSGENIVDALAAFLRRLHSIPVCNCPFNSDRVFRLAQAQSRMNNGLVDA
                     SDFDDERNGWPVEQVWKEMHKLLPFSPDSVVTHGDFSLDNLIFDEGKLIGCIDVGRVGI
                     ADRYQDLAILWNCLGEFSPSLQKRLFQKYGIDNPDMNKLQFHLMLDEFF"
                     /name="aminoglycoside O-phosphotransferase APH(3')-Ia"
     gene            complement(2262..2357)
                     /locus_tag="E5N98_25410"
                     /pseudo=""
     CDS             complement(2262..2357)
                     /locus_tag="E5N98_25410"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_014605854.1"
                     /note="incomplete; partial on complete genome; missing
                     N-terminus and C-terminus; Derived by automated
                     computational analysis using gene prediction method:
                     Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="amino acid ABC transporter substrate-binding
                     protein"
                     /name="amino acid ABC transporter substrate-binding
                     protein"
     gene            2384..2605
                     /locus_tag="E5N98_25415"
     CDS             2384..2605
                     /locus_tag="E5N98_25415"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001334687.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="QCG03843.1"
                     /translation="MYHNVSLRAPLKRAERDSAANTAKRDVFPGVNRKNASGLLSAHCI
                     AMHESEWRSVWGLTAFIPSVFDSFPPGS"
                     /name="hypothetical protein"
     gene            complement(2602..2925)
                     /locus_tag="E5N98_25420"
     CDS             complement(2602..2925)
                     /locus_tag="E5N98_25420"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:NP_052604.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="nikA protein"
                     /protein_id="QCG03842.1"
                     /translation="MTKRSGSNTRRRAISRPVRLTAEEDQEIRKRAAECGKTVSGFLRA
                     AALGKKVNSLTDDRVLKEVMRLGALQKKLFIDGKRVGDREYAEVLIAITEYHRALLSRL
                     MAD"
                     /name="nikA protein"
     ARG             complement(1305..2116)
                     /name="aph(3')-Ia"
                     /gene="aph(3')-Ia"
                     /gene_name="aminoglycoside O-phosphotransferase APH(3')-Ia"
                     /tool="amrfinderplus"
                     /drug_class="AMINOGLYCOSIDE"
                     /identity="100.0"
                     /coverage="100.0"
     Typing          complement(2935..3174)
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="7.6e-123"
     Typing          231..752
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="95.437"
                     /coverage="95.0"
                     /evalue="0.0"
     Typing          complement(2606..2925)
                     /name="MOBF"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="99.065"
                     /coverage="100.0"
                     /evalue="2.32e-62"
ORIGIN
        1 atgaacaagc agcagcaaac cgtactcaac atggcgggat tcataaaaag ccagagcctg
       61 acgctgctcg aaaaactgga cgcacttgat gctgacgaac aggccgccat gtgtgagaag
      121 ctgcacgaac tcgcggaaga acttcagaac agcatacaga cacgctttga agcggaaaat
      181 cgcaccggga tataacgcac ccggacagga tgcagaacgg catagcggag cgtaaggaga
      241 aaatgccacg tcagacgctc ttccgcttcc tcgctcactg actcgctacg ctcggtcgtt
      301 cgactgcggc gagcggtgtc agctcactca aaggcggtaa tacggttatc cacagaatca
      361 ggggataacg ccggaaagaa catgtgagca aaaagcaaag caccggaaca agccagcgcc
      421 gatgccgttt ttccataggc tccgcccccc tgacgagcat cacaaaaatc gacgctcaag
      481 tcagaggtgg cgaaacccga caggactata aagataccag gcgtttcccc ctggaagctc
      541 cctcgtgcgc tctcctgttc cgaccctgcc gcttaccgga tacctgtccg cctttctccc
      601 ttcgggaagc gtggcgcttt ctcatagctc acgctgttgg tatctcagtt cggtgtaggt
      661 cgttcgctcc aagctgggct gtgtgcacga accccccgtt cagcccgacc gctgcgcctt
      721 atccggtaac tatcgtcttg agtccaaccc ggaaagacac gacttaacgc cactggcagc
      781 agccattggt aactgattta gaggagttga gtcttgaagt tatgcacctg ataaggctaa
      841 actgaaagaa caagttttgg cgactgtgct cctcaaagcc agttacctcg gttcaaagag
      901 cgccaactct atgaaccttc gaaaaaccgc ccgccaaggc ggttttttcg ttttcaacct
      961 agttagatta atctccttgc gctagctgcg tcaacaaagc ctaacgactt ctagcccttc
     1021 tttgcctggt attggcaaca gctcgccatt cctgaggcct tctggctaca agtactccat
     1081 ctttgtagaa ctcatcacgc atacagcagg ctctcaaagc atcattcttg atctccatac
     1141 ttctcgatga cagagagcag agatctgtcg ctcgcctgat tctccccgga ggagctacaa
     1201 gggtgtgctc gatgccatcg acatgctgcg cggcatgaac agcgacagcg cgcgcaaggt
     1261 gcccgccgat gcgccaaccg cattcattaa agactaacta tcagaaaaac tcatcgagca
     1321 tcaaatgaaa ctgcaattta ttcatatcag gattatcaat accatatttt tgaaaaagcc
     1381 gtttctgtaa tgaaggagaa aattcaccga ggcagttcca tagaatggca agatcctggt
     1441 atcggtctgc gattccgact cgtccaacat caatacaacc tattaatttc ccctcgtcaa
     1501 aaataagatt atcaagtgag aaatcaccat gagtgacgac tgaatccggt gagaatggca
     1561 aaagcttatg catttctttc cagacttgtt caacaggcca gccattacgc tcatcatcaa
     1621 aatcactcgc atcaaccaaa ccgttattca ttcgtgattg cgcctgagcg agacgaaata
     1681 cgcgatcgct gttaaaagga caattacaaa caggaatcga atgcaaccgg cgcaggaacg
     1741 ctgccagcgc atcaacaata ttttcacctg aatcaggata ttcttctaat acctggaatg
     1801 ctgttttccc ggggatcgca gtggtgagta accatgcatc atcaggagta cggataaaat
     1861 gcttgatggt cggaagaggc ataaattccg tcagccagtt tagtctgacc atctcatctg
     1921 taacatcatt ggcaacgcta cctttgccat gtttcagaaa caactctggc gcatcgggct
     1981 tcccatacaa tcgatagatt gtcgcacctg attgcccgac attatcgcga gcccatttat
     2041 acccatataa atcagcatcc aggttggaat ttaatcgctg cctcgagcaa gacgtttccc
     2101 gttgaatatg gctcataaca ccccttgtat tactgtttat gtaagcagac agttttattg
     2161 ttcatgatga tatattttta tcttgtgcaa tgtaacatca gagattttga gacacaacgt
     2221 ggttcccgcc atatgaaaat ccggccagac caacatcatt ctggcgctcc gaaagaaggg
     2281 atattcgccg ccgtgaccag cctggagcgg gtcgcataat ctttggccgc ttcgtagtcg
     2341 aggaacatgg catcaagtaa atgggactgt ttctaacgct cccatttacc ataacgtctc
     2401 attacgcgca ccgctaaaac gcgctgaacg cgattctgcc gcaaacaccg caaaaagaga
     2461 tgttttcccc ggggtaaacc ggaaaaatgc gtcaggattg ctttcagctc actgcatagc
     2521 tatgcatgaa agtgaatggc gatcggtttg gggacttacg gcgttcatac cgtctgtttt
     2581 cgacagtttc cctccgggaa gctaatctgc cataagcctg gataacaggg cccggtgata
     2641 ctccgtaata gctatcagca cctccgcata ctctctgtcc ccgacacgct tgccgtcgat
     2701 aaagagtttt ttctgcaacg cccccagtcg catgacttct ttcagcactc ggtcatcagt
     2761 cagtgaatta actttcttac cgagagctgc cgcccgtaaa aaaccagaaa cggtcttgcc
     2821 gcattcagca gccctttttc tgatttcctg gtcttcttct gccgtcagac gaacagggcg
     2881 actgatagcc cgcctgcgcg tattacttcc acttcgtttt gtcataaaac atggctccgt
     2941 atctgacatg ggtgtcgggg caaagccctg accagggtaa ttgtaatagc gtgcatgtat
     3001 gcgcggtata acaattgcac atcctgtcct gtcagcaagc tcgaattacc gacaaaagca
     3061 cggcagtttt ttggcagtga cagtgttgtc tgacagaaat gcccgtcaaa gagtcagaca
     3121 gcagaatacc ggcggtaaaa cagtcgaaaa gtggtactcg atataatcac acaacgcaga
     3181 tgacagaaag aacggagaaa acagaaag
//
