LOCUS       NZ_CP040653             3372 bp    DNA     circular CON 25-JUL-2023
DEFINITION  Salmonella enterica subsp. enterica serovar 1,4,[5],12:i:- strain
            SA20070548 plasmid pSA20070548.2, complete sequence.
ACCESSION   NZ_CP040653
VERSION     NZ_CP040653.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN10833327
            Assembly: GCF_005890175.1
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 3372)
  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  JOURNAL   Unpublished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 3372)
  AUTHORS   Schonfeld,J., Clark,C., Johnson,R., Labbe,G., Liu,K., Robertson,J.
            and Nash,J.H.E.
  TITLE     Direct Submission
  JOURNAL   Submitted (23-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 NextSeq; Oxford Nanopore MiniION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 07/25/2023 04:26:01
            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)                     :: 4,930
            CDSs (total)                      :: 4,807
            Genes (coding)                    :: 4,680
            CDSs (with protein)               :: 4,680
            Genes (RNA)                       :: 123
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 88
            ncRNAs                            :: 13
            Pseudo Genes (total)              :: 127
            CDSs (without protein)            :: 127
            Pseudo Genes (ambiguous residues) :: 0 of 127
            Pseudo Genes (frameshifted)       :: 44 of 127
            Pseudo Genes (incomplete)         :: 92 of 127
            Pseudo Genes (internal stop)      :: 21 of 127
            Pseudo Genes (multiple problems)  :: 29 of 127
            Pseudo Genes (short protein)      :: 1 of 127
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP040653.1.
            Bacteria and source DNA available from SA20070548.
            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..3372
                     /organism="Salmonella enterica subsp. enterica serovar
                     1,4,[5],12:i:-"
                     /mol_type="genomic DNA"
                     /strain="SA20070548"
                     /serovar="1,4,[5],12:i:-"
                     /isolation_source="porcine"
                     /sub_species="enterica"
                     /db_xref="taxon:2583588"
                     /plasmid="pSA20070548.2"
                     /geo_loc_name="Canada: Quebec"
                     /collection_date="2007-01-16"
                     /collected_by="FNC/CIPARS"
     gene            join(3060..3372,1..11)
                     /locus_tag="FGF59_RS24850"
                     /old_locus_tag="FGF59_24850"
     CDS             join(3060..3372,1..11)
                     /locus_tag="FGF59_RS24850"
                     /old_locus_tag="FGF59_24850"
                     /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_024132211.1"
                     /translation="MLTIRVTDEEHARLLERCEGKRLAEWMRRVCLGEPVARTGKLPTL
                     SPPLLRHLAAIGNNLNQTARKVNSGQWSSIDRVHVVAALMAIEGELRQLRQAVREQGVR
                     DDS"
                     /name="MobC family plasmid mobilization relaxosome protein"
     gene            220..>660
                     /locus_tag="FGF59_RS25260"
                     /pseudo=""
     CDS             220..>660
                     /locus_tag="FGF59_RS25260"
                     /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="FGF59_RS24860"
                     /old_locus_tag="FGF59_24860"
     CDS             689..1249
                     /locus_tag="FGF59_RS24860"
                     /old_locus_tag="FGF59_24860"
                     /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_000067487.1"
                     /translation="MSNLLQMGTDFEKKLKERAASTENMLNSEFRKLEESVDKALSLNR
                     QKIRDAISEHTTSVKKQLDTLSTTVSMQFSTTEAELSRQQKKLLWRVIKGRILFPALTA
                     LSVTGGIFLGCWGLMEWQESKIAKNILTIREQENTLAKLEAKTWGVTFVNGENGKFLVL
                     PDGVKGENTWTVGDKNAVRLVRE"
                     /name="MbeB family mobilization protein"
     gene            1256..1489
                     /locus_tag="FGF59_RS24865"
                     /old_locus_tag="FGF59_24865"
     CDS             1256..1489
                     /locus_tag="FGF59_RS24865"
                     /old_locus_tag="FGF59_24865"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000137389.1"
                     /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_000137389.1"
                     /translation="MTELEGHLLNALEHLQQDYMRRLNEWESAFAELQKMHEVTQRNNA
                     ILNERVVILSQQVQRLAGQVDRLSRLFIANNS"
                     /name="MbeD family mobilization/exclusion protein"
     gene            complement(2805..2996)
                     /locus_tag="FGF59_RS24875"
                     /old_locus_tag="FGF59_24875"
     CDS             complement(2805..2996)
                     /locus_tag="FGF59_RS24875"
                     /old_locus_tag="FGF59_24875"
                     /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_000165979.1"
                     /translation="MTKQEKTALNMARFIRSQTLTLLEKLNDLDADEQADICESLHDHA
                     DELYRSCLARFGDDGESN"
                     /name="Rop family plasmid primer RNA-binding protein"
     Typing          2641..2724
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="87.059"
                     /coverage="95.0"
                     /evalue="8.83e-18"
     Typing          2..1572
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="92.817"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          3028..3371
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="84.348"
                     /coverage="97.0"
                     /evalue="2.15e-56"
ORIGIN
        1 atgatagtta aatttcatgc cagggggaaa ggcggtggaa gtggcccggt cgattacctg
       61 ctggggcggg agcgtaaccg cgaaggcgca acggtgctcc ggggtaaccc ggaagaagtg
      121 cgggaactca ttgattccac gccattctcg aagaaataca cttcaggcgt tctgtcgttc
      181 gcggagaagg agttaccgcc gggtgaacgc gaaagagtga tgacgagctt tgagcgtgtt
      241 cttatgcccg gtctcgaaaa agaccagtac agcattctct gggtggaaca ccaggataag
      301 gggcggctcg aactgaattt tgtcatcccg aacatggagc tacagagcgg taagcgcctc
      361 cagccgtact acgaccgcgc ggacaggccg aggataaatg cctggcagac gctggttaat
      421 catcattacg ggctgcgtga cccgaacgca ccggagaaca gacggacgct tgtcacgcca
      481 aataatctgc caaaagcgaa acaggaggcc gcagaagcga ttacacgggg tcttgaggct
      541 ctttaccatg ccggagcaat aaaaacgcgt caggatgtca cagaggcgct tacagcggca
      601 ggttttgagg tggtgaggac aaccaaaagc agcatcagta ttgccgaccc ggaggggggg
      661 cggaatctca ggctaaaggg ggcgctgtat gagcaatctt ttacaaatgg gaacagactt
      721 cgagaagaaa ctgaaagagc gagccgcttc taccgagaac atgctgaaca gcgagttcag
      781 gaagctcgaa gagtctgtag acaaggcatt gagcttaaac aggcagaaaa tcagagacgc
      841 tatcagcgaa catacaacat ccgtgaaaaa gcaactggat acgctgagca ccaccgtgag
      901 catgcagttc agcaccacag aggccgaact gtcccggcag cagaaaaaac tgctctggcg
      961 ggtgatcaaa gggcggatac tgtttccggc gctgaccgcg ctcagcgtca cgggcggcat
     1021 tttcctgggg tgctgggggc tgatggagtg gcaggaaagc aagattgcga aaaatatcct
     1081 gactatcaga gagcaggaaa acacgctggc gaaactcgag gcaaaaacct ggggggtgac
     1141 gttcgtcaat ggcgagaacg ggaaatttct ggtgttgccg gacggggtga aaggggaaaa
     1201 cacctggacg gtgggcgaca agaacgccgt gaggctggtc agggagtaaa cgagtatgac
     1261 ggaactggaa gggcatttgc tgaacgcctt agagcatttg caacaggact atatgcggcg
     1321 gctgaacgag tgggagagcg ccttcgcgga attgcagaag atgcacgagg ttacgcaacg
     1381 gaacaacgcg atactgaacg agcgcgtcgt gatattgagt cagcaggtgc agagattagc
     1441 cgggcaagtg gatcgcttga gtcggttatt tatcgcgaac aacagctaag ggatgaacag
     1501 gagcgtgccc ggtacagaca tgaggtacag gaacgcgcgg cacgggttcg gagtgggcca
     1561 tcaatggaga tgtgaccggg gaagtgacga aatcttgcca ttttgaccag ttcgacggct
     1621 ggggcgagcg aaacaaatcg tgtgccgtat ttgtgcatag ctatgcaaca tcctgaaaac
     1681 gcatttcacg cgtttttggg gattcagcca ggggaaaaca tggttttttt actttttgag
     1741 cgtaaagacg tgaaaaatct cgttattgca cttgcgatct ttcgtcggcg ggcgtagaac
     1801 gaaaacagct cgccaggaag gcgagctgtt tcgggttcat tgaggtctct gacctcctca
     1861 atgttcctgt ggaaactgtt gagatccaca acagaaacca gttcattcag tttgcatgag
     1921 ccttctgtat tcttcaagaa tttttcaaca gcacagtctc ccaggaaccc cgaaaaaaac
     1981 ctgtttttgc agatacttgc gtatttgcga gaatcgtttg cggttggggg agctgtgacg
     2041 acggcgaccg cacgcgtgag agttccgcta ccggcgcaga gagtttcatc gacagcggac
     2101 acctgatgag ttgccacaaa aaccgtatgt agcgcggcta gattggttga gttagacctt
     2161 ggcggcagtt cccggtatgt ggtggcgtga cgggtgagat ggtgcggcga agacgcatac
     2221 gtcacgcagg cgcgggttct tccactgacg cgccccgtga tcgatggcct tggctccgtc
     2281 cggcatatcg agagcggcaa actacccgtc ccttcactgg gaggggtgag ttgttgccgt
     2341 tccctccaac ctttcaccat ccggcatatc gcacgatccc atgtgcaccg caactcctga
     2401 taactccagt gcaaaaaaaa aaaacggatc agcatcacaa cgagagtgat cccaccgctc
     2461 gccgcagccc cagcgaccga acgtagtgag cgagtgggcg aggaagcgga agagtcacag
     2521 atgcaagcat tgtgcactta cgcgcctgtg ccagtgtccg cgtgtgtgct gtttatcggg
     2581 tgcgctgttt ttacatctgt gcggcttttt actcctgaca tggtgcactt cccatccatt
     2641 ctgcaccgat gcaaaatgag ataagccagt atacacatcg ctatcgctct gtgaactggg
     2701 tcagggctgc gccccgacac ccgcactgac gcgccctggc gggcttgtct gctcccggca
     2761 tccgctcaca ggcaagctgt gaacgtctcc gggagctgca tgtttcagtt gctttcaccg
     2821 tcatcgccga agcgtgcgag gcaactgcgg tagagttcgt cggcgtggtc gtgaagtgat
     2881 tcgcagatgt ctgcctgttc gtccgcgtcc agatcgttga gtttttccag cagggttagc
     2941 gtctggcttc tgataaagcg agccatgtta agggctgttt tttcctgttt ggtcatggtc
     3001 ttaaggctcc ttgtatgggg gatttgttag ggggaatgat accgatgaaa cgcgagaaga
     3061 tgctcacgat acgggttacc gatgaggagc acgcccggtt actggaacgc tgcgagggta
     3121 aacgactggc ggaatggatg cggcgggtct gtctggggga gccggttgca cgcacaggaa
     3181 aactgccgac actatcgccg ccattgctgc ggcatctggc tgccatcggg aacaacctga
     3241 accagacagc ccggaaggtg aacagcggcc agtggtcttc gattgaccgg gttcatgtgg
     3301 tggccgcact gatggccatc gagggtgaat tgcgccagtt gcggcaggct gtcagggaac
     3361 agggggtacg gg
//
