LOCUS       NZ_CP039571             4418 bp    DNA     circular CON 29-JUL-2023
DEFINITION  Salmonella enterica subsp. enterica serovar 1,4,[5],12:i:- strain
            PNCS014852 plasmid p09-0642.2, complete sequence.
ACCESSION   NZ_CP039571
VERSION     NZ_CP039571.1
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 4418)
  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  JOURNAL   Unpublished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 4418)
  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
            CP039571.1.
            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..4418
                     /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="p09-0642.2"
                     /geo_loc_name="Canada: QC"
                     /collection_date="2009-01-22"
                     /collected_by="Laboratoire de sante publique du Quebec"
     gene            205..756
                     /locus_tag="E5N93_RS24425"
                     /old_locus_tag="E5N93_24425"
     CDS             205..756
                     /locus_tag="E5N93_RS24425"
                     /old_locus_tag="E5N93_24425"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000654246.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_000654246.1"
                     /translation="MKDMKAVVVFTGKDLNIMRTEGGSGYWHARTDRLNDADYLIAVRN
                     RRETWAVKDLEHGTAFLIAKITGCFKSPDYDDRNVITFDEYAEIHTPKAWKMLTDGQRY
                     PVAYLSAQEAFLRIGVTPEQLEWKKFHPSSPSVPNTVIPGLAEEKTEKLSLNEAIERAK
                     KDISNATGIDSSAITISIKI"
                     /name="hypothetical protein"
     gene            complement(955..1170)
                     /locus_tag="E5N93_RS24430"
                     /old_locus_tag="E5N93_24430"
     CDS             complement(955..1170)
                     /locus_tag="E5N93_RS24430"
                     /old_locus_tag="E5N93_24430"
                     /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_000137421.1"
                     /translation="MTELEKQLLSALEQLQQDYSKRLDEWENAFAEWRTMSGLMQRENA
                     ALSERVTGLSRQVQSLSEQLRRLSQG"
                     /name="MbeD family mobilization/exclusion protein"
     gene            complement(1174..1659)
                     /locus_tag="E5N93_RS24435"
                     /old_locus_tag="E5N93_24435"
     CDS             complement(1174..1659)
                     /locus_tag="E5N93_RS24435"
                     /old_locus_tag="E5N93_24435"
                     /inference="COORDINATES: protein motif:HMM:NF016710.2"
                     /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            complement(<1694..2128)
                     /locus_tag="E5N93_RS24860"
                     /pseudo=""
     CDS             complement(<1694..2128)
                     /locus_tag="E5N93_RS24860"
                     /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(2337..2660)
                     /locus_tag="E5N93_RS24445"
                     /old_locus_tag="E5N93_24445"
     CDS             complement(2337..2660)
                     /locus_tag="E5N93_RS24445"
                     /old_locus_tag="E5N93_24445"
                     /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            complement(3950..4225)
                     /locus_tag="E5N93_RS24455"
                     /old_locus_tag="E5N93_24455"
     CDS             complement(3950..4225)
                     /locus_tag="E5N93_RS24455"
                     /old_locus_tag="E5N93_24455"
                     /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_031611837.1"
                     /translation="MVIVSVVGGISLLLLVFLWSIKRGQKTVRAFVFLSAVADGNSVES
                     ANELAKRIDLFAASELQKKAMIMVEMVFGGSQLKLISHARREGFDQ"
                     /name="hypothetical protein"
     Typing          complement(2762..2947)
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="88.421"
                     /coverage="87.0"
                     /evalue="9.61e-57"
     Typing          2923..3410
                     /name="ColRNAI_rep_cluster_1987"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="88.081"
                     /coverage="94.0"
                     /evalue="7.71e-161"
     Typing          complement(852..2347)
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="92.585"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 atggctcatg cttttaatgt atatcctcgt ccaagcccct gttttaaccg gtttatcaaa
       61 aaaaccaaac aggaagtctt accactaaca ataaaagagg taggggagac tgtattttat
      121 cgcataaaaa aacatttaca acaccaattc tatcgtatag atttcataaa aaatgaaatt
      181 tactcaccta ttaagggttt ctatatgaaa gatatgaaag ctgttgtggt ttttaccggg
      241 aaggatttga acataatgag aactgagggg ggatcaggct actggcatgc cagaacagac
      301 aggctcaacg atgccgatta cctcatagca gtaagaaaca gaagggaaac gtgggcagta
      361 aaagacctgg aacacggcac agcattcctg atcgccaaaa ttaccgggtg ttttaaaagc
      421 cctgattacg acgacaggaa cgtcataacc tttgatgaat acgcagaaat tcacacgcca
      481 aaagcatgga aaatgctaac cgatggtcag cgctatccgg ttgcttacct gagcgcacag
      541 gaagcttttt tacgtattgg ggtaacaccg gaacaactgg aatggaagaa attccatcct
      601 tcatccccat cggttcctaa tacagtgatt cctggtctgg ctgaagagaa aacagaaaaa
      661 ctctccctta acgaggcaat tgaaagagcc aaaaaggata ttagcaacgc aacagggatt
      721 gatagctcag ccataacaat aagcatcaag atctgatgaa gcgtgaacaa taagatagca
      781 gcctcatgtt ctagaactga acctgtgcgc cagaaacagc aagcccatgc ttttccggcg
      841 cacagattca aagtgacgga ccgttgtacg ttcgctgtcg ctgagatcgt tccagctcca
      901 gcgctttctg atgctgcgcc gcccgttcct gctcacgatg tgcctctatc acgttcagcc
      961 ttgtgacaac cggcgcagct gctcgctcaa actctgcacc tgcctgctca agcccgtgac
     1021 gcgctcgctc agcgccgcgt tctcccgttg cataagacca gacatcgtcc gccattccgc
     1081 gaaggcgttc tcccactcgt ccagcctttt cgagtagtcc tgctgtagct gctctaatgc
     1141 gctcagcaac tgtttttcca gctccgtcat gtgctatttc cccgccagta tcatccagct
     1201 cgaatcctct ccgaaccgtc ccgcttccgg gttcaccctc acgcagcggc gtctctgctc
     1261 tccgcaggtc gagagctgca cgccgctgtt cctctcggac agcatggcct gcgtgctctt
     1321 ctgctcccgg atgatcgtgt aattgtcgag tatctgctgc ccctgccacc acagaatgct
     1381 tgcgcccgat gctgtcagca gtgtagacac caggacgatg gtcagccacg tctggctgac
     1441 catacgcacc atgcctttcg tgcgctggct catggctgag gacagcttcc ggtcgtggtc
     1501 gaggatggcg gcgctgattc tcttctcgct ttcgctcagt tccgctctga cagacttctc
     1561 gtgctcgctg aatgcggctt tcagcatctc gccggtactc tgctgctgcg ctttcgattt
     1621 ctgctctaag tcctttgcca gcgttaaaag actgttcata gatggctccc ttcagtcgga
     1681 tgtttcgccc cccgtccggg tcggcaatgc tgatgctgct ttttgtggtg cgtaccacct
     1741 caaaacctgc gctttccagc gcctcagtga cgtcctggcg ggttttcagc tccccggacg
     1801 aggctaaggc cagtaaaccc cgtgtaattg cctgagcggc ttcctgcttc gttttcggca
     1861 gcgcggacgg cgtgaccagc gcccgccggt tttcaggcgc gttcgggtca tgcagcccca
     1921 gcctgccgtt cacgatggtc tgccaggcat caatgcgcgg acggtcggcg cggtcgtaat
     1981 acggctggag acgcttgccg gtcagcagct ccgtgttcgg gatcaggaag ttcagctcca
     2041 gccgcccctt atcctggtgc tcaacccaca gcacgctgta ctggtcttta tcgagtccgg
     2101 gcatcagaac ccgttcaaag ctcgccatca gcttttcgcg ctgcccgggc ggtaaatcct
     2161 tttcggcaaa ggacaggacg ccggatgtgt acttttttgc gtagggcgag gcgtcgataa
     2221 gctccctgac ttcttccggc ttcccctgca gaacggtggc gccgtcgcgc tgtcggtctt
     2281 tccccagcag ataatccacc ggaccggcgc caccgccgcg ccctcgcggg tgaaacttaa
     2341 cgatcatcgt ctgcaccctt ttccagcacg gcatgccgca gccgctcgag tccggcatct
     2401 atggccatca gcgcggcgac gacctgcacg cggtcgtgcc cgctgccacc accggcgtta
     2461 acctgccggg caatctggtt gaggttgttc cccatgccgg caagctgacg aagcagcgcc
     2521 ggcgagagcg agggaagctt gccggcgcgg gcgggtttct cgtccaggca cgtctggcgc
     2581 atccaggctg caagctgttt accgtcgcag cgctccagca gacggcggtg ctcatcttcg
     2641 gtcacccaca tcgtgagcat tttgctgcgt ttgtctgcca atccggcctc ctgataacgc
     2701 cgggacgggc gggaaatctt ttcccggtcg gcgcggtgtt ggacaagccg caggcgcgtc
     2761 agtggtttta gcgggtttcg gggcgcagcc ctgaaccagt cacgtagcgc tagcggagtg
     2821 tatactggct gaatatgtta gatcggagtg gtaattcagg gaagttattc atgttgcaag
     2881 ggaaaatgcg gctatagggc gtaagtgcaa aatgcaggta acggtgacat gacgcctcct
     2941 cgctcactcg gtcgctacgc tcctgccgtg aggctgcggc gggcgttacc tgctcacgaa
     3001 tgacaagata aagagatggc actcaagtca ggaaaggccg gaaaaaggat acggcgctgc
     3061 cgtttttcca taggctccgc ccccctgacg agcatcacaa aatcagacgc tcaaatcagt
     3121 ggtggcgaaa cccgatgcgg cttagagata ccaggcgttt ccccctgatg gctccctcgt
     3181 gctcccccgc attcctgccc ttcggtttac cggtgtcatt ccgctgttat ggccgcgttt
     3241 gtctcattcc acgcctgaca ctcagttccg ggtaggcagt tcgctccagg atggactgta
     3301 tgcacgaacc ccccgttcag tccgactgct gcgccttgtc cggtaactat cgtcttgagt
     3361 ccaacccgga aagacatgca aaagcgccac tggcagcagc cactggtaac aggtttagag
     3421 gaggagagtc ttgaaatttc gggtgcgata aggctacact gaaaggacag ttttggtgac
     3481 tgtgctcctc caagccagtt accgcggttc aaaagagcgt caactcttgc gaaccttcga
     3541 aaaaccaccc ggcaaggtgg ttttttcgtt ttcaaggcaa gagattacgc gcagaaaaaa
     3601 aggatctcaa gaagatcctt ttagattagt gttcagagtt ggtttcttcg gttgtcatcc
     3661 gcctcccttt atctagccga tgccatatca taagggaaaa gtcttatgta taaatctatc
     3721 tccccctatc aattaggggc tactatagaa ctaataaggg cggactatag aaggatagaa
     3781 tccttatccg ccatagaata gaaaaaggag gttaaatgct aaatgagttt atctatcttc
     3841 tacagatact gtctaaaaac ccgccgaaaa agaatatata tttcgcagta gcgacctggt
     3901 cacttagtct ctttatcata gttgtccaac acgttggaca atctacattt cactgatcga
     3961 aaccttcccg tctggcatgt gagatcagtt taagctgact tcccccaaat accatttcaa
     4021 ccattatcat agcctttttc tgcagttcac tcgcagcaaa aagatctatc cgctttgcca
     4081 actcgttagc tgattcaaca ctatttccat cagcaacggc actcagaaaa acaaatgctc
     4141 tcactgtttt ctgacctcgt tttatcgacc ataaaaacac aagaagcaaa agtgatattc
     4201 cacccacgac actaacaatc accatatttc gatcacctta tcttagataa cttcagaagt
     4261 tgcttcattt accataacat cccttgcccg caccgctccg gacgggttca acgtgaaagc
     4321 ggcgttagcc cggtaaaacc ggcagtaaac tccccgctaa actgcgcatt ctgcgcctga
     4381 taaatttcac gcggctgcat agccatgcag ccacgtga
//
