LOCUS       NZ_CP060171             1975 bp    DNA     circular CON 13-DEC-2023
DEFINITION  Salmonella enterica subsp. enterica serovar Typhimurium strain
            BKQZM9 plasmid pBT3, complete sequence.
ACCESSION   NZ_CP060171
VERSION     NZ_CP060171.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN15796617
            Assembly: GCF_014250355.1
KEYWORDS    RefSeq.
SOURCE      Salmonella enterica subsp. enterica serovar Typhimurium (Salmonella
            typhimurium)
  ORGANISM  Salmonella enterica subsp. enterica serovar Typhimurium
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Salmonella.
REFERENCE   1  (bases 1 to 1975)
  AUTHORS   Pulford,C.V., Perez-Sepulveda,B., Kumwenda,B., Predeus,A.V. and
            Hinton,J.C.
  TITLE     The stepwise evolution of Salmonella Typhimurium responsible for
            bloodstream infection in Africa
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 1975)
  AUTHORS   Pulford,C.V., Perez-Sepulveda,B., Kumwenda,B., Predeus,A.V. and
            Hinton,J.C.
  TITLE     Direct Submission
  JOURNAL   Submitted (12-AUG-2020) Institute of Infection, Veterinary &
            Ecological Sciences, University of Liverpool, Crown St, Liverpool L7
            3EA, United Kingdom
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Date                     :: 07-JUL-2019
            Assembly Method                   :: Unicycler v. v0.4.4
            Assembly Name                     :: BKQZM9_v1
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 200.0x
            Sequencing Technology :: Illumina HiSeq 4000; Oxford Nanopore 9.4.1
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 12/13/2023 03:11:33
            Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline
            (PGAP)
            Annotation Method :: Best-placed reference protein set; GeneMarkS-2+
            Annotation Software revision      :: 6.6
            Features Annotated                :: Gene; CDS; rRNA; tRNA; ncRNA
            Genes (total)                     :: 4,893
            CDSs (total)                      :: 4,768
            Genes (coding)                    :: 4,605
            CDSs (with protein)               :: 4,605
            Genes (RNA)                       :: 125
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 89
            ncRNAs                            :: 14
            Pseudo Genes (total)              :: 163
            CDSs (without protein)            :: 163
            Pseudo Genes (ambiguous residues) :: 0 of 163
            Pseudo Genes (frameshifted)       :: 92 of 163
            Pseudo Genes (incomplete)         :: 82 of 163
            Pseudo Genes (internal stop)      :: 31 of 163
            Pseudo Genes (multiple problems)  :: 37 of 163
            Pseudo Genes (short protein)      :: 1 of 163
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP060171.1.
            Bacteria and source DNA available from University of Liverpool, Jay
            Hinton laboratory.
            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..1975
                     /organism="Salmonella enterica subsp. enterica serovar
                     Typhimurium"
                     /mol_type="genomic DNA"
                     /strain="BKQZM9"
                     /serovar="Typhimurium"
                     /isolation_source="blood"
                     /host="Homo sapiens"
                     /sub_species="enterica"
                     /db_xref="taxon:90371"
                     /plasmid="pBT3"
                     /geo_loc_name="Malawi"
                     /lat_lon="15.783678 S 35.016929 E"
                     /collection_date="2018"
                     /collected_by="College of Medicine, University of Malawi"
     gene            complement(join(1740..1975,1..169))
                     /locus_tag="H7H28_RS24265"
     CDS             complement(join(1740..1975,1..169))
                     /locus_tag="H7H28_RS24265"
                     /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="helix-turn-helix domain-containing protein"
                     /protein_id="WP_057484157.1"
                     /translation="MNNREFKEVRLSLGLTQAEFATQLGLTRETVCRIERCAFPLSRRV
                     SLSAANLSKPVMTQVHESESDLRSHDNEALDIASRLDAMSLLIRLDTMIFNFRLSRPVY
                     GRNKVSGKHVAEFLSALRSEIRPYLPESLK"
                     /name="helix-turn-helix domain-containing protein"
     gene            complement(479..733)
                     /locus_tag="H7H28_RS24270"
     CDS             complement(479..733)
                     /locus_tag="H7H28_RS24270"
                     /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_057484158.1"
                     /translation="MTDTNSTMLTLITRHQNAVEAFTAFASLHPLDDDLHPLIELLSAN
                     LEASFLDIHPHLCGLNSSNAKSGVPFQGSDLVIDDTPEK"
                     /name="hypothetical protein"
     gene            1296..1727
                     /locus_tag="H7H28_RS24275"
     CDS             1296..1727
                     /locus_tag="H7H28_RS24275"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001233485.1"
                     /GO_function="GO:0003677 - DNA binding [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="helix-turn-helix domain-containing protein"
                     /protein_id="WP_057484156.1"
                     /translation="MRKVTQVDLETGEDLGGFVAVIRPKQKSSFERHFTMNQAALKIIA
                     TELNHEQTKVLMMLLADLDYENYIQVAQIDIAESLGMKKPNVSKAVKNLIEFGIILEGP
                     KIGRSKTYRLNPQFGWKGTVSNHKKALKNGLSVIQGGKV"
                     /name="helix-turn-helix domain-containing protein"
ORIGIN
        1 ttactggctt tgaaagattc gcagcagaga gcgaaacacg acgagaaagc ggaaaggcgc
       61 agcgctcaat ccggcaaacc gtctcacggg ttaacccaag ctgcgttgca aactctgcct
      121 gcgtaagccc cagtgagagc cttacttctt taaattctct gttattcata gagttagaat
      181 cactccgtta atcaattaaa caatgtgatc tcagatcaca tcgacaaagt aacgagtcta
      241 cccgcacgct accagaagtt aggttttaac tggaaaactc cgtgtttccg ttgactctac
      301 ccccgtgtta cagggcgggg gtatcggtgc ggcggtgtac acaatgcaca tcctgtcctg
      361 cctttgatgt cgaaaccgga caagatgtgt ttttggagta ccgccattcg cggcaacatc
      421 caaaaacggc tcatcagggc gatggcttca ctgcgtgaac catcacctgt tagcagtgtt
      481 atttctccgg cgtgtcgtca atcactaaat cggaaccctg aaagggaacc cccgatttag
      541 cgtttgacga gttcaggccg cagagatgcg gatgaatatc cagaaaagaa gcctccagat
      601 tcgcactcag aagctctatg aggggatgaa ggtcatcatc aaggggatgg agtgaggcaa
      661 acgccgtaaa cgcctctacg gcgttctggt gacgtgtaat cagggtaagc atggtagaat
      721 tcgtgtcagt catggagacc tccgtaacag gttttcgtga tagcaggggg cgggaactcg
      781 taattccttc cccctgcgcc catcagatca taattccgct acacgggcaa gccgccacgg
      841 gaagagtgca ctcctcgtgg gaactcggtg cgctcccttc ccgtgcccgc ctgccagctc
      901 gtgccattct gacccgtccg gcacagatag ccagaaacca cgcgagagag tccgcaccgc
      961 tcgccgcaag acgtgattag cgagcaacgc gagtctgtca cgtcgaggaa gcggaatatc
     1021 acctgaacgg gcatagaaaa ccgtacgcac agtacccaca gaaaaacacg atgcaggata
     1081 gggcaaacgc cgcaaaatgc tagcatttta ctcgtttgcc cggtgaccta cagcagtttc
     1141 cagaagtgat gttttcgtgg ctggcatcgc gcacagagtt acaagataca gaagggaacc
     1201 tcccgcaagc cgcgccacaa gcggaatcat ttgacagata gttatgttca ggcataactt
     1261 agttatgttc aggcataact atttaaggaa ttttcatgcg aaaagtcaca caggttgacc
     1321 tcgaaaccgg agaggatttg ggcgggtttg tcgccgtgat ccgtcccaag caaaaatcat
     1381 cgttcgagag gcatttcact atgaatcagg cagcactcaa aatcatcgct acagaactga
     1441 accatgagca gacaaaagta ctcatgatgc ttctcgcaga cctggactac gaaaattaca
     1501 ttcaggtggc acaaatcgac attgcagaat cattgggaat gaaaaaacca aatgttagca
     1561 aagctgttaa aaacctgatt gagttcggaa taatccttga ggggccaaag ataggccgaa
     1621 gcaaaaccta ccgcctgaat cctcaattcg gctggaaagg cacggtaagc aaccacaaga
     1681 aagcgctcaa aaacggcctc agcgtcattc agggtggcaa ggtgtgatcc aagatcacat
     1741 cacttcaacg actccggcag gtaaggccta atctcagatc gaagggctga aagaaactca
     1801 gcgacatgct tgccggaaac cttattccgt ccataaaccg ggcgtgaaag ccggaaatta
     1861 aaaatcatcg tatcaagccg gattaacagg ctcatagcat caagtctgga agctatatcc
     1921 agcgcctcat tgtcatgtga tctcagatca ctttcactct catgaacctg cgtca
//
