LOCUS       NZ_CP039581             3208 bp    DNA     circular CON 29-JUL-2023
DEFINITION  Salmonella enterica subsp. enterica serovar 1,4,[5],12:i:- strain
            PNCS014857 plasmid p10-3881.2, complete sequence.
ACCESSION   NZ_CP039581
VERSION     NZ_CP039581.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN11333152
            Assembly: GCF_004919325.1
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 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  JOURNAL   Unpublished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 RefSeq
            Annotation Date                   :: 07/29/2023 04:17:59
            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)                     :: 4,964
            CDSs (total)                      :: 4,852
            Genes (coding)                    :: 4,716
            CDSs (with protein)               :: 4,716
            Genes (RNA)                       :: 112
            rRNAs                             :: 8, 7, 6 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 6 (5S, 16S, 23S)
            tRNAs                             :: 79
            ncRNAs                            :: 12
            Pseudo Genes (total)              :: 136
            CDSs (without protein)            :: 136
            Pseudo Genes (ambiguous residues) :: 0 of 136
            Pseudo Genes (frameshifted)       :: 48 of 136
            Pseudo Genes (incomplete)         :: 95 of 136
            Pseudo Genes (internal stop)      :: 25 of 136
            Pseudo Genes (multiple problems)  :: 30 of 136
            Pseudo Genes (short protein)      :: 1 of 136
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP039581.1.
            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..3208
                     /organism="Salmonella enterica subsp. enterica serovar
                     1,4,[5],12:i:-"
                     /mol_type="genomic DNA"
                     /strain="PNCS014857"
                     /serovar="1,4,[5],12:i:-"
                     /host="Homo sapiens"
                     /sub_species="enterica"
                     /db_xref="taxon:2583588"
                     /plasmid="p10-3881.2"
                     /geo_loc_name="Canada: QC"
                     /collection_date="2010-06-09"
                     /collected_by="Laboratoire de sante publique du Quebec"
     gene            1..195
                     /locus_tag="E5N99_RS25135"
                     /old_locus_tag="E5N99_25135"
     CDS             1..195
                     /locus_tag="E5N99_RS25135"
                     /old_locus_tag="E5N99_25135"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001041624.1"
                     /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_001041640.1"
                     /translation="MNKQQQTVLNMAGFIKSQSLTLLEKLDALDADEQAAMCEKLHELA
                     EELQNSIQTRFEAENRTGI"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            complement(1301..2116)
                     /locus_tag="E5N99_RS25145"
                     /old_locus_tag="E5N99_25145"
     CDS             complement(1301..2116)
                     /locus_tag="E5N99_RS25145"
                     /old_locus_tag="E5N99_25145"
                     /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="WP_000018330.1"
                     /translation="MSHIQRETSCSRQRLNSNLDADLYGYKWARDNVGQSGATIYRLYG
                     KPDAPELFLKHGKGSVANDVTDEMVRLNWLTEFMPLPTIKHFIRTPDDAWLLTTAIPGK
                     TAFQVLEEYPDSGENIVDALAAFLRRLHSIPVCNCPFNSDRVFRLAQAQSRMNNGLVDA
                     SDFDDERNGWPVEQVWKEMHKLLPFSPDSVVTHGDFSLDNLIFDEGKLIGCIDVGRVGI
                     ADRYQDLAILWNCLGEFSPSLQKRLFQKYGIDNPDMNKLQFHLMLDEFF"
                     /name="aminoglycoside O-phosphotransferase APH(3')-Ia"
     gene            complement(<2262..>2357)
                     /locus_tag="E5N99_RS25625"
                     /old_locus_tag="E5N99_25150"
                     /pseudo=""
     CDS             complement(<2262..>2357)
                     /locus_tag="E5N99_RS25625"
                     /old_locus_tag="E5N99_25150"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_013356662.1"
                     /note="incomplete; partial in the middle of a contig;
                     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            complement(2602..2925)
                     /gene="mobA"
                     /locus_tag="E5N99_RS25160"
                     /old_locus_tag="E5N99_25160"
     CDS             complement(2602..2925)
                     /gene="mobA"
                     /locus_tag="E5N99_RS25160"
                     /old_locus_tag="E5N99_25160"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:NP_052604.1"
                     /GO_process="GO:0006355 - regulation of DNA-templated
                     transcription [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="plasmid mobilization protein MobA"
                     /protein_id="WP_000166966.1"
                     /translation="MTKRSGSNTRRRAISRPVRLTAEEDQEIRKRAAECGKTVSGFLRA
                     AALGKKVNSLTDDRVLKEVMRLGALQKKLFIDGKRVGDREYAEVLIAITEYHRALLSRL
                     MAD"
                     /name="mobA"
     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
//
