LOCUS       NZ_CP039570             4593 bp    DNA     circular CON 29-JUL-2023
DEFINITION  Salmonella enterica subsp. enterica serovar 1,4,[5],12:i:- strain
            PNCS014852 plasmid p09-0642.1, complete sequence.
ACCESSION   NZ_CP039570
VERSION     NZ_CP039570.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN11333146
            Assembly: GCF_004919305.1
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 4593)
  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  JOURNAL   Unpublished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 4593)
  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 MiSeq; Oxford Nanopore MiniION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 07/29/2023 04:02:21
            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)                     :: 4,831
            CDSs (total)                      :: 4,710
            Genes (coding)                    :: 4,591
            CDSs (with protein)               :: 4,591
            Genes (RNA)                       :: 121
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 86
            ncRNAs                            :: 13
            Pseudo Genes (total)              :: 119
            CDSs (without protein)            :: 119
            Pseudo Genes (ambiguous residues) :: 0 of 119
            Pseudo Genes (frameshifted)       :: 44 of 119
            Pseudo Genes (incomplete)         :: 82 of 119
            Pseudo Genes (internal stop)      :: 19 of 119
            Pseudo Genes (multiple problems)  :: 25 of 119
            Pseudo Genes (short protein)      :: 1 of 119
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP039570.1.
            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..4593
                     /organism="Salmonella enterica subsp. enterica serovar
                     1,4,[5],12:i:-"
                     /mol_type="genomic DNA"
                     /strain="PNCS014852"
                     /serovar="1,4,[5],12:i:-"
                     /host="Homo sapiens"
                     /sub_species="enterica"
                     /db_xref="taxon:2583588"
                     /plasmid="p09-0642.1"
                     /geo_loc_name="Canada: QC"
                     /collection_date="2009-01-22"
                     /collected_by="Laboratoire de sante publique du Quebec"
     gene            join(4281..4593,1..11)
                     /locus_tag="E5N93_RS24380"
                     /old_locus_tag="E5N93_24380"
     CDS             join(4281..4593,1..11)
                     /locus_tag="E5N93_RS24380"
                     /old_locus_tag="E5N93_24380"
                     /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_001677263.1"
                     /translation="MLTIRVSDEEHARLLERCEGKRLAEWMRRVCLGEPVARTGKLPTL
                     SPPLLRHLAAIGNNLNQTARKVNSGHWSSIDRVHVVAALMAIEGELRQLRQAVREQGGR
                     DDS"
                     /name="MobC family plasmid mobilization relaxosome protein"
     gene            220..>654
                     /locus_tag="E5N93_RS24855"
                     /pseudo=""
     CDS             220..>654
                     /locus_tag="E5N93_RS24855"
                     /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            689..1249
                     /locus_tag="E5N93_RS24390"
                     /old_locus_tag="E5N93_24390"
     CDS             689..1249
                     /locus_tag="E5N93_RS24390"
                     /old_locus_tag="E5N93_24390"
                     /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_000067488.1"
                     /translation="MSNLLQMGTDFEKKLKERAASTENMLNSEFRKLEESVDKALSLNR
                     QKIRDAISEHTTSVKQQLDTLSTTVSTQLSTTEAELSRQQKNLLWQVIKGRVLFPALTA
                     LSVTGGIFLGCWGLIQWQESRIAKNILTIREQENTLAKLEAKTWGVTFVNGENGKFLVL
                     PDGVKGENTWTVGDKNAVRLVRE"
                     /name="MbeB family mobilization protein"
     gene            1256..1489
                     /locus_tag="E5N93_RS24395"
                     /old_locus_tag="E5N93_24395"
     CDS             1256..1489
                     /locus_tag="E5N93_RS24395"
                     /old_locus_tag="E5N93_24395"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000137438.1"
                     /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_000137388.1"
                     /translation="MTELEGHLLNALEHLQQDYMRRLNEWESAFAELQKMHAVTQQNNA
                     ILNERVVNLSQQVQLLAGQVDRLSRLFITNNR"
                     /name="MbeD family mobilization/exclusion protein"
     gene            complement(2177..3016)
                     /locus_tag="E5N93_RS24405"
                     /old_locus_tag="E5N93_24405"
     CDS             complement(2177..3016)
                     /locus_tag="E5N93_RS24405"
                     /old_locus_tag="E5N93_24405"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001354646.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_001354646.1"
                     /translation="MLTLFIFFVLLIAACFFCFAPPRRGYDRNEIIPYKIKLSINKYRL
                     YIYSSGKVRQYLLFLVILSLYYSIAEPFKSELIKNISYSLMAAFIFDTGLNFSKENITK
                     GVISTRWHNDLYSSFERMKAINKIYYPSNKEINTEGLSKAITSSLFNDDANSFAKRDFR
                     LMWDLSSEKYLSYKEIIIRKGDKLDAVCLRFINDDYKFLVNFNRDEEVFKYFPSIMQPS
                     LKTYRALSRLVNSIKDPSRFKFTTESLEMELLEYLELRNELFNDIEEVMGSYAQRAP"
                     /name="hypothetical protein"
     gene            complement(4027..4218)
                     /locus_tag="E5N93_RS24420"
                     /old_locus_tag="E5N93_24420"
     CDS             complement(4027..4218)
                     /locus_tag="E5N93_RS24420"
                     /old_locus_tag="E5N93_24420"
                     /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_000165986.1"
                     /translation="MTKQEKTALNMARFIRSQTLTLLEKLNELDADEQADICESLHDHA
                     DELYRSCLARFGDDGESN"
                     /name="Rop family plasmid primer RNA-binding protein"
     Typing          3855..3939
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="3.03e-37"
     Typing          3016..3467
                     /name="ColRNAI_rep_cluster_1857"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="83.0"
                     /evalue="0.0"
     Typing          2..1587
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          4249..4592
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="82.609"
                     /coverage="97.0"
                     /evalue="2.51e-55"
ORIGIN
        1 atgatagtta aatttcatgc cagggggaaa ggcggtggaa gtggcccggt cgattacctg
       61 ctggggcggg agcgtaaccg cgaaggcgca acggtgctcc ggggtaaccc ggaagaaatc
      121 cgggaactca ttgatgccac gccattttcg aagaaataca cgtcaggcgt tctgtcgttc
      181 gcggagaagg agttaccgcc gggtgaacgc gaaagagtga tgacgagctt tgagcgtgtt
      241 cttatgcccg gtctcgaaaa agaccagtac agcattctct gggtggaaca ccaggataag
      301 gggcggctcg aactgaattt tgtcattccg aacatggaac tacagagcgg taagcgcctc
      361 cagccgtact acgaccgtgc ggacaggccg aggataaatg cctggcagac gctggttaat
      421 catcattacg ggctgcgtga cccgaacgca ccggagaaca gacggacgct tgtcacaccg
      481 aataatctgc caaaagcgaa acaggaggcc gcagaagcga ttacacgggg tcttgaggcg
      541 ctttaccgtg ccggagcaat aaaaacgcgt caggatgtca ctgaggcgct cacagcggca
      601 ggttttgagg tggtgaggac aaccagaagc agtatcagta ttgccgaccc ggaggggggg
      661 cggaatctca ggctaaaggg ggcgctgtat gagcaatctt ttacaaatgg gaacggactt
      721 cgagaagaaa ctgaaagagc gagccgcttc taccgagaac atgctgaaca gcgagttcag
      781 gaagctagaa gagtctgtag acaaggcact gagcttaaac aggcagaaaa tcagagacgc
      841 tatcagcgaa catacaacat ccgtgaaaca gcaactggat acgctgagca ccaccgtgag
      901 cacgcagctc agcaccacag aggccgaact gtcccggcag cagaaaaacc tgctctggca
      961 ggtgatcaaa gggcgggtac tgtttccggc gctgaccgcg ctcagcgtca cgggcggcat
     1021 tttcctgggg tgctgggggc tgattcagtg gcaggaaagc aggattgcga aaaatatctt
     1081 gaccatcaga gagcaggaaa acacgctggc gaaactcgag gcaaaaacct ggggggtgac
     1141 gttcgtcaat ggcgagaacg ggaaatttct ggtgctgccg gacggggtga aaggggaaaa
     1201 cacctggacg gtgggcgaca agaacgccgt gaggctggtc agggagtaaa cgagtatgac
     1261 ggaactggaa gggcatttgc tgaacgcctt agagcatttg caacaggact atatgcggcg
     1321 gctgaacgag tgggagagcg ccttcgcaga attgcagaag atgcacgcgg ttacgcaaca
     1381 gaacaacgcg atactgaacg agcgtgtcgt gaacttgagt cagcaggtgc agctattagc
     1441 cggacaagtc gaccgcttga gtcggttatt tatcacgaac aacagataag ggatgaacag
     1501 gagcgtcagg cgcaggagct tgcccggcgc tggcatgaag agcaggaacc cgaagcgcgg
     1561 atctggcgtg gcccgtcaat ggggatgtga ccggggtacc ccctgaaatc gagccagttt
     1621 gtggcacgcc ctacccggat ggcgccaatg ttaatgtacg tacattagca ttaacaatat
     1681 ccaaacctcc ccattttgcc ccgttcgacg gctggaacgt gcgaaactga tcgtcattca
     1741 gtttcgcgca taactatgca tgaggttaaa atttaccagg cgcgatcgcg gcagtttttc
     1801 gggtggtttg ttgctgtttt tacctgtctg ctgccgtgat cgcgctgaac gcgtttaagc
     1861 ggtacgcgca atgcgacgtt atggtaaata cggagtattt taattgcggg cctttgttgt
     1921 atatctctgt cgtttgtccc cggggggaag cattactgct aacaagtccc gtgagaaaac
     1981 tgcgcaatcg tattgcgcac catgaaccta ttctcaaccg caatctggag gatgattttg
     2041 ctacgataaa gagaattatc gcgtatcggt gtcagcattc attggagtgg atgctgaaaa
     2101 accaggtgtt actccctcta cttacactta aacctctcta aaaatataag taagtactat
     2161 cgagggctat catgaactat ggtgccctct gagcatagct acccattact tcttctatgt
     2221 cattgaataa ttcatttctt aactctaagt attctagtaa ctccatttct aatgactctg
     2281 tcgtgaactt aaatctagaa ggatctttga ttgagtttac tagtcttgat aacgctctat
     2341 atgttttgag tgaaggttgc attatagatg gaaagtattt gaaaacctct tcatctctgt
     2401 tgaaattaac taaaaacttg tagtcatcat ttataaatct caagcataca gcgtcaagct
     2461 tatcgccttt tcttattatt atttctttat aggaaagata tttttcagaa gataagtccc
     2521 acatcaagcg aaaatctctc tttgcgaacg agttcgcgtc atcattgaaa agagatgatg
     2581 tgatggcttt ggatagacct tctgtgttta tctctttgtt ggatgggtag taaattttat
     2641 taattgcttt cattctctca aatgatgaat ataggtcatt atgccacctt gttgaaatca
     2701 ctcctttagt tatattctcc ttgctaaaat taagccctgt atcaaaaata aatgcagcca
     2761 tcagtgaata tgatatgttt tttattaact cagacttaaa tggttccgct atggagtagt
     2821 acagtgataa aataactaaa aataaaaggt attgtcttac ctttcccgat gagtatatgt
     2881 aaaggcgata tttatttatt gatagtttta ttttgtatgg aatgatctca tttctgtcat
     2941 atcctcttcg tggtggagca aaacaaaaga aacatgcagc tattaataaa acaaaaaaga
     3001 tgaacagtgt aagcaagttc ggctcctgtg tatgctcact atgcatgatt gtcttgagat
     3061 ctaacgatcc tgaaggtagt cttgtccgta aacgaaaaaa ccgcccagca aggcggcttt
     3121 tcgaaggttc tcagagcagc aactctttga accaaggtaa ctggcttgga ggagcacagc
     3181 caccaaatct gtcctttcag tttagcctta accggcgcat aacttcaaga ctaactcctc
     3241 taaacggtta ccaatggctg ctgccagtgg cgtttttacg tgtctttccg ggttggactc
     3301 aagacgatag ttaccggata aggcgcagcg gtcgggctga acggggggtt cgtgcacaca
     3361 gcccagcttg gagcgaacga cctacaccgg gccgagatac caacagcgtg agctatgaga
     3421 aagcgccacg cttcccgaag ggagaaaggc ggacaggtat ccggtaagcg gcagggtcgg
     3481 aacaggagag cgcacgaggg agcttccagg gggaaacgcc tggtatcttt atagtcctgt
     3541 cgggtttcgc cacctctgac ttgagcatct gtttttgtga tgctcgtcag gggggcggag
     3601 cctatggaaa aacgccagcg gcgcagcctt cttcctgttc ctggcctttt gctcacatgt
     3661 ttcttttggc gttatcccct gattctgtgg ataaccgcat caccgtcttt gagtgagctg
     3721 ataccgctcg ccgcagccga acgaccgagc gtagcgagtc agtgagcgag gaagcggaag
     3781 agcgcctgat gcggcatttt ctccttacgc atctgtgcgg tatttcacac cgcatatggt
     3841 gcacttttct tataatccgc actgatgcca catagttaag ccagtataca ctccgctatc
     3901 gctacgtgac tgggtcaggg ctgcgccccg acacccgcta aaacccgctg acgcgccctg
     3961 acgggcttgt ctgctcccgg catccgctca caggcaagct gtgaacgtct ccgggagctg
     4021 catgtttcag ttgctttcac cgtcatcgcc gaagcgtgcg aggcaactac ggtagagttc
     4081 gtcggcgtgg tcgtgaagtg attcgcagat gtctgcctgt tcgtccgcgt ccagctcgtt
     4141 gagtttttcc agcagggtca gcgtctggct tctgataaag cgggccatgt taagggctgt
     4201 tttttcctgt ttggtcatgg tcttaaggct ccttaatagg ggatttttta gggggaatga
     4261 taccgatgaa acgcgagaag atgctcacga tacgggttag cgatgaggag cacgcccggt
     4321 tactggaacg ctgcgagggt aaacgactgg cagaatggat gcggcgggtc tgtctggggg
     4381 agccggttgc gcgcacagga aaactgccga cactatcgcc gccattgctg cggcatctgg
     4441 ctgccatcgg gaacaatctg aaccagacag cccggaaggt gaacagcggc cactggtctt
     4501 cgattgaccg ggttcatgtg gtggccgctc tgatggccat cgagggtgaa ttgcgccagt
     4561 tgcggcaggc tgtcagggaa caggggggac ggg
//
