LOCUS       NZ_CP039575             3003 bp    DNA     circular CON 29-JUL-2023
DEFINITION  Salmonella enterica subsp. enterica serovar 1,4,[5],12:i:- strain
            PNCS014855 plasmid p10-2080.3, complete sequence.
ACCESSION   NZ_CP039575
VERSION     NZ_CP039575.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN11333149
            Assembly: GCF_004919225.1
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 3003)
  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  JOURNAL   Unpublished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 3003)
  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 04:02:09
            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)                     :: 4,897
            CDSs (total)                      :: 4,772
            Genes (coding)                    :: 4,660
            CDSs (with protein)               :: 4,660
            Genes (RNA)                       :: 125
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 88
            ncRNAs                            :: 15
            Pseudo Genes (total)              :: 112
            CDSs (without protein)            :: 112
            Pseudo Genes (ambiguous residues) :: 0 of 112
            Pseudo Genes (frameshifted)       :: 33 of 112
            Pseudo Genes (incomplete)         :: 87 of 112
            Pseudo Genes (internal stop)      :: 19 of 112
            Pseudo Genes (multiple problems)  :: 26 of 112
            Pseudo Genes (short protein)      :: 1 of 112
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP039575.1.
            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..3003
                     /organism="Salmonella enterica subsp. enterica serovar
                     1,4,[5],12:i:-"
                     /mol_type="genomic DNA"
                     /strain="PNCS014855"
                     /serovar="1,4,[5],12:i:-"
                     /host="Homo sapiens"
                     /sub_species="enterica"
                     /db_xref="taxon:2583588"
                     /plasmid="p10-2080.3"
                     /geo_loc_name="Canada: QC"
                     /collection_date="2010-03-11"
                     /collected_by="Laboratoire de sante publique du Quebec"
     gene            join(2330..3003,1..4)
                     /locus_tag="E5N96_RS24785"
                     /old_locus_tag="E5N96_24785"
     CDS             join(2330..3003,1..4)
                     /locus_tag="E5N96_RS24785"
                     /old_locus_tag="E5N96_24785"
                     /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_022631128.1"
                     /translation="MENKAVTISTQLAIFIDSTIARPDLLFNSLNSEIGEVIDAMPQTL
                     PLPADAPADIPRVIGTSSFGKFNLNISLNRIDFVENYTPTEEIEKSVTEFKLKCNTLIA
                     TIFQKYGVVRIGLVGNYYIPHKNPSQLIADLYLNENKRNLDEITIRINNRDTFKNIQIN
                     NVINLSQGQVTAQNYNGNAVIVQLDYNSTDNNTPLEEGLTLALFKEKSIAYNSKHVEDV
                     SGL"
                     /name="hypothetical protein"
     gene            1..384
                     /locus_tag="E5N96_RS25005"
                     /old_locus_tag="E5N96_24790"
     CDS             1..384
                     /locus_tag="E5N96_RS25005"
                     /old_locus_tag="E5N96_24790"
                     /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_022631129.1"
                     /translation="MKFFKPKTDAIEYIRVEPSFSKTSSNINNAKSGSDTNSQPGFILR
                     SQIEEMIKNHRPKTEKEIKAESEGLIRLCSMAFIFLIVLSIFMLIVYFGIKDRELPDFA
                     NNLMALMTTLVGAIGGFIYGTKK"
                     /name="hypothetical protein"
     gene            complement(692..1015)
                     /gene="mobA"
                     /locus_tag="E5N96_RS24800"
                     /old_locus_tag="E5N96_24800"
     CDS             complement(692..1015)
                     /gene="mobA"
                     /locus_tag="E5N96_RS24800"
                     /old_locus_tag="E5N96_24800"
                     /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"
     gene            1287..1481
                     /locus_tag="E5N96_RS24805"
                     /old_locus_tag="E5N96_24805"
     CDS             1287..1481
                     /locus_tag="E5N96_RS24805"
                     /old_locus_tag="E5N96_24805"
                     /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_022631127.1"
                     /translation="MNKQQQTALNMAKFIKSQSLTLLEKLDALDADEQATMCEKLHELA
                     EELQNSIQTRFEVENSTEI"
                     /name="Rop family plasmid primer RNA-binding protein"
     Typing          complement(1025..1250)
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="89.167"
                     /coverage="99.0"
                     /evalue="4.88e-75"
     Typing          1511..2040
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="94.413"
                     /coverage="97.0"
                     /evalue="0.0"
     Typing          complement(696..1015)
                     /name="MOBF"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="99.065"
                     /coverage="100.0"
                     /evalue="1.96e-62"
ORIGIN
        1 atgaaatttt tcaaaccaaa aacagatgcg attgaataca ttcgtgtaga accatcattc
       61 tcaaaaacaa gtagcaatat aaataatgcg aaatcaggaa gtgacacaaa ctcacagcct
      121 ggattcattt taagatctca aatagaggaa atgataaaaa accacagacc gaaaacagaa
      181 aaagaaataa aagctgaaag cgaaggtctt ataaggcttt gctccatggc ctttatattt
      241 ttaatagttt tatcaatttt tatgttaatc gtttatttcg gaataaaaga tagagaacta
      301 ccagattttg caaataacct gatggcacta atgacaacat tagttggagc gataggtggt
      361 tttatatatg gaacaaaaaa ataacacaga caaaaacaca aataaaaaaa acaaataaca
      421 cacaagcaca ccagccccat acttcggggc ttttacaacc gttacctgac accatttacc
      481 ataacgtctc attacgcgca ccgccaaaac gcgctgaacg cgattctgac gcagacaccg
      541 caaaaagaga tgttttcccc gggataaacc ggaaaaatgc gtcaggatcg ctttcagctc
      601 actgcatagc tatgcatgaa agtgaatggc gatcggtttg ggggcttacg gcgttcatac
      661 cgtctgtttt cgacagtttc tctccgggaa gctaatctgc cataagcctg gataacaggg
      721 cacggtgata ctccgtaata gcgatcagca cctccgcata ctccctgtcc ccgacacgct
      781 tgccgtcgat aaagagtttt ttctgcaacg cccccagtcg cataacttct ttcagcaccc
      841 ggtcatcagt cagtgagtta actttcttac cgagagctgc cgcccgtaaa aaaccagaaa
      901 cggtcttgcc gcattcagca gccctttttc tgatttcctg gtcttcttct gccgtcagac
      961 gaacagggcg actgatagcc cgcctgcgcg tattacttcc acttcgtttt gtcataaaac
     1021 atggctccgt atctgacatg gggtgtcggg gcgaagccct gaccaaggta attgtaatag
     1081 cgtgcatgta tgcgcggtat aacaattaca catcctgtcc tgtctgcaag ttcgaattac
     1141 caacaaagca ctgctgtttt ttggcagtga cagtgttgtc tgactgaaat gtccgtcggc
     1201 agaataccgg cggtaagacg gtcgaaaagt ggtgcgcgat ataatcacac gacgcagatg
     1261 acagacagaa cggagaaagc agaaagatga acaagcagca gcaaaccgca ctcaacatgg
     1321 caaaattcat aaaaagccag agcctgacgc tgctcgaaaa actggacgca ctcgatgctg
     1381 acgagcaggc caccatgtgt gagaagctgc acgaactcgc agaagaactc cagaacagca
     1441 tacagacacg ctttgaagta gaaaatagca cagagatata acgctcaggg caggatgccg
     1501 aacggcacaa cagagcgtaa ggagaaaatg tcacataagg cgctcttccg cttcctcgct
     1561 cactgactcg ctacgctcgg tcgttcgact gcggcgagcg gtgtcagctc actcaaaggc
     1621 ggtaatacgg ttatccacag aatcagggga taaagccgga aagaacatgt gagcaaaaag
     1681 caaagcaccg gaagaagcca gcaccgcagg cgtttttcca taggctccgc ccccctgacg
     1741 agcatcacaa aaatcgacgc tcaagtcaga ggtggcgaaa cccgacagga ctataaagat
     1801 accaggcgtt tccccctgga agctccctcg tgcgctctcc tgttccgacc ctgccgctta
     1861 ccggatacct gtccgccttt ctcccttcgg gaagcgtggc gctttctcat agctcacgct
     1921 gtaggtatct cggcccggtg taggtcgttc gctccaagct gggctgtgtg cacgaacccc
     1981 ccgttcagcc cgaccactgc gccttatccg gtaactatcg tcttgagtcc aacccggtaa
     2041 gacatgcaaa agcaccactg gcagcagcca ttggtaaccg agttagcaga gcgagatttg
     2101 tccagatgct tacagagttc ttgaagtgat ggcctgacta cggctacact agaaggacag
     2161 tatttggtat ctgcgctctg ctgaagccag ttacccggtt agacaatctg ccaggattag
     2221 ctaaccttcg aaaaaccacc tgccagggtg gttttttcgt ttaagatact cacaacacgt
     2281 taatttcgca atacttcaat taataccaat gcaaaatagg aaagaaaaaa tggaaaacaa
     2341 ggccgtcaca atatcaacac agctagcaat atttattgac agcaccatag ctagaccaga
     2401 tcttctcttt aatagcctaa actcagaaat tggcgaagtt atagacgcaa tgccacagac
     2461 gcttcccctg cctgcagatg cacccgcaga tatccctcgc gttattggca catcgtcctt
     2521 tggcaagttc aacttaaaca tatcactaaa cagaatagat tttgtagaaa actacacccc
     2581 tactgaggag atcgaaaaat cagtaacgga attcaaatta aagtgcaata cgctaatagc
     2641 aacaatattc caaaaatatg gagtcgtaag aatcggccta gttggtaact attacatccc
     2701 acataaaaat ccatctcaac taatagctga tctgtattta aacgaaaaca aaagaaattt
     2761 agatgaaata acaataagaa taaataaccg cgatacattc aaaaatatac aaataaacaa
     2821 tgtcatcaat ttaagccaag gacaagtaac cgcacagaac tacaatggaa atgcggtgat
     2881 agttcaactt gactacaact caaccgataa taacacacca cttgaagaag ggttaacctt
     2941 agccctattt aaagaaaaat ccattgctta taactccaag catgttgagg atgtgagtgg
     3001 att
//
