LOCUS       NZ_CP016386             3904 bp    DNA     circular CON 09-DEC-2023
DEFINITION  Salmonella enterica subsp. enterica serovar Typhimurium strain
            ST931R plasmid p931-3904, complete sequence.
ACCESSION   NZ_CP016386
VERSION     NZ_CP016386.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN05356919
            Assembly: GCF_001729225.1
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 3904)
  AUTHORS   McCollister,B., Washburn,T., Kotter,C.V., Frank,D.N. and
            Jobling,M.G.
  TITLE     Whole genome sequencing identifies in vivo acquisition of a
            blaCTX-M-27-encoding IncFII transmissible plasmid as the cause of
            ceftriaxone treatment failure for an invasive Salmonella enterica
            serovar Typhimurium infection
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 3904)
  AUTHORS   McCollister,B., Washburn,T., Kotter,C.V., Frank,D.N. and
            Jobling,M.G.
  TITLE     Direct Submission
  JOURNAL   Submitted (07-JUL-2016) Immunology and Microbiology, University of
            Colorado Anschutz Medical Campus, 12800 E 19th Ave, Aurora, CO
            80045, USA
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: Geneious de novo v. 6.7.1
            Assembly Name :: Complete genome and plasmids of Salmonella 13-93
            Long Assembly Name :: Salmonella enterica subsp. enterica serovar
            Typhimurium 13-931 genome and five plasmids
            Genome Coverage                   :: 293x
            Sequencing Technology             :: Illumina MiSeq
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 12/09/2023 01:34:31
            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)                     :: 5,112
            CDSs (total)                      :: 4,989
            Genes (coding)                    :: 4,852
            CDSs (with protein)               :: 4,852
            Genes (RNA)                       :: 123
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 86
            ncRNAs                            :: 15
            Pseudo Genes (total)              :: 137
            CDSs (without protein)            :: 137
            Pseudo Genes (ambiguous residues) :: 0 of 137
            Pseudo Genes (frameshifted)       :: 55 of 137
            Pseudo Genes (incomplete)         :: 93 of 137
            Pseudo Genes (internal stop)      :: 28 of 137
            Pseudo Genes (multiple problems)  :: 36 of 137
            Pseudo Genes (short protein)      :: 1 of 137
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP016386.1.
            Source DNA and bacteria are available from Bruce McCollister,
            Division of Infectious Disease, University of Colorado Anschutz
            Medical Campus, Aurora, Colorado, USA 80045.
            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..3904
                     /organism="Salmonella enterica subsp. enterica serovar
                     Typhimurium"
                     /mol_type="genomic DNA"
                     /strain="ST931R"
                     /serovar="Typhimurium"
                     /isolation_source="blood culture"
                     /host="Homo sapiens"
                     /sub_species="enterica"
                     /db_xref="taxon:90371"
                     /plasmid="p931-3904"
                     /geo_loc_name="USA:Colorado"
                     /collection_date="2013"
                     /collected_by="Bruce McCollister"
     gene            24..470
                     /locus_tag="BBC45_RS23495"
                     /old_locus_tag="BBC45_01250"
     CDS             24..470
                     /locus_tag="BBC45_RS23495"
                     /old_locus_tag="BBC45_01250"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000184721.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="conjugal transfer protein TraD"
                     /protein_id="WP_000184723.1"
                     /translation="MTNREEWLSAKIAYINGLKSPSEQQRLLVLLAEKKNRTTTDEKTL
                     SALIRAEKTAEKAAAAKARVTAIIAAERKAAARAERKARDHELYKAAGLMIVAGLVDSK
                     TGKPKFSAAELVGALAGIAELPRNHPKWQEWERRGKELLTKDSA"
                     /name="conjugal transfer protein TraD"
     gene            complement(731..1750)
                     /locus_tag="BBC45_RS23500"
                     /old_locus_tag="BBC45_01255"
     CDS             complement(731..1750)
                     /locus_tag="BBC45_RS23500"
                     /old_locus_tag="BBC45_01255"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001271373.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="replication initiation protein"
                     /protein_id="WP_011017196.1"
                     /translation="MSAALQYFEENLPRRPYHTDDLAFGLRISGKGRALLARYIQQNQP
                     HAQFWLVFDVDREGAAIDWSDRNAPAPNITVKNPVNGHAHLLYALNIAVRTAPDASVKA
                     LKYAAAVERSLCEKLCADVNYSGLICKNPFHLEWQVMEWREEAYTLDELADYLDLSASA
                     RRSIDKHYGMGRNCHLFEMTRKWAYRAIRQGWPAFSQWLDAVIQRVEMYNASLPVPLSP
                     PECRAIGKSIAKYTHRNFTPETFAQYVADTHTPEIQAARGRKGGKANSSENQSDKGKKS
                     AAVRWTANDDKRRRALDMYILGASTEDIAVAVGVSSRTIRRWMDNSGEWLTKKQIIKF"
                     /name="replication initiation protein"
     gene            complement(2206..3756)
                     /locus_tag="BBC45_RS23505"
                     /old_locus_tag="BBC45_01260"
     CDS             complement(2206..3756)
                     /locus_tag="BBC45_RS23505"
                     /old_locus_tag="BBC45_01260"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001624483.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MobA/MobL family protein"
                     /protein_id="WP_032495511.1"
                     /translation="MASYHCTVKAGAKGSALKHADYISRSGEYKSYKSREDLEFSSSGN
                     MPSWAKKNPAELWKAADEFERKNGTAYREIEIALPRELTREQRIELVEDFVQKELGDRH
                     AYQYAIHNPPGAIDGKEQPHAHIMFCERINDGIERDPQQFFKRANSKSPERGGAKKASI
                     PQTAGERKAALVALRSRWADVQNEHLARYGHESRVDHRSLKEQGINRTPEVHLGPVQAA
                     SLNGERIVAIQERRNAERELKTARDAANAIQQEQEQKQKIKAVEPVRSARSPELLLQYR
                     KVMKTVIQGEARLARLGDANPNALKEHKLLQNAKAKKDSLSEWSRRIYEGARYLDKLGR
                     NVVSAQRELRELQEQRNALNGIRGLFRGADKREIDARILEQKSVLETAEHERNEFRNKL
                     QQAESEWDKENAAFKRTEGYKYVGDLDRYREREILAAASLENTRQKVAEEVSVARSQML
                     SLEPELSISGDEKAQMRHELLAEMAQERQQQEEKALRIQRSWAREASRSNERDQDMER"
                     /name="MobA/MobL family protein"
     Typing          complement(976..1750)
                     /name="Col156"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="99.613"
                     /coverage="83.0"
                     /evalue="0.0"
     Typing          complement(2210..3756)
                     /name="MOBQ"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="93.436"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 acggcaaaaa tgcagaggta agaatgacaa atcgtgaaga gtggttaagt gcaaaaattg
       61 cctacatcaa cggactgaaa tcaccgtcag agcagcagag attacttgtg ttactggcag
      121 agaaaaaaaa ccgaacaacg acggatgaaa aaacgttgtc cgcactgata cgggcagaaa
      181 aaaccgcaga gaaagcagcc gcagcaaaag ccagggtaac ggcaatcata gcggcagaac
      241 ggaaggcagc cgcaagggcg gaacgaaagg cgcgggatca tgaactctac aaggccgcag
      301 gcctcatgat tgtggcagga ctggtggaca gcaaaaccgg aaaaccaaag tttagtgctg
      361 ccgaactggt aggcgcactc gcaggaatcg cagagctacc gcgcaaccac ccaaaatggc
      421 aggaatggga aagacgcggg aaggagctac taaccaaaga cagtgcgtaa gagcctccgt
      481 tcacgttccg tttccctggt gcttcctcgc tcattcgctc gctacgctcg gtcatgagac
      541 tgcggcgagc acaaccacct caatcatgcg gtaagccgca ccattgctgg gctgacagga
      601 gaaaaccgcc ggaaagcccg ctgctcaaaa agacgccgaa aggcgctgtt atctgatata
      661 ggcttgttca tgtccgcgaa tttaaccacc cattaacaaa aacagggggt aattgtcatt
      721 tttctgttaa ttaaaattta attatttgtt tcttggttaa ccattctcca gaattatcca
      781 tccagcgtcg aatagtccgg ctgctaacac caaccgccac tgcaatatct tccgttgacg
      841 ctcccaagat atacatatca agcgccctac gacgtttgtc gtcgttagca gtccaccgaa
      901 cagcggcgct ttttttccct ttgtccgact gattttctga cgaattggcc ttcccgccct
      961 tgcgaccgcg tgctgcctga atttctggcg tgtgcgtatc agccacatac tgtgcgaaag
     1021 tttccggcgt gaagttcctg tgcgtgtatt tcgcaatgct cttgccaata gcccgacatt
     1081 caggcggaga aagcggaacg ggaagcgatg cgttgtacat ttcgacacgc tgaatcacgg
     1141 catcaagcca ctgtgagaat gctggccagc cctgacgaat cgccctgtaa gcccatttgc
     1201 gcgtcatttc gaacaggtgg cagtttcgcc ccatcccgta atgtttatcg atgctacgac
     1261 gcgctgaggc gctcaaatcg agataatcag ccagttcatc gagggtatag gcttcctcgc
     1321 gccactccat cacctgccat tccaggtgga acggattttt gcaaatcagt ccgctgtagt
     1381 tcacatcagc acaaagtttc tcacacagcg aacgttcaac cgctgcggca tatttcagcg
     1441 ccttaaccga cgcatcaggc gcggttctca cggcgatatt gagtgcatag agcaggtgag
     1501 cgtgtccgtt cacaggattt ttaacggtga tgttcggcgc gggggcgttc cggtcgctcc
     1561 agtcaatcgc tgccccctcg cggtcaacgt caaaaaccag ccagaactgc gcatgaggct
     1621 ggttctgctg gatgtaccgc gcaagcagcg cacgcccttt gccggagatg cgaagaccaa
     1681 aagcgagatc atccgtgtga tagggacggc ggggtaaatt ttcttcgaag tattgaagcg
     1741 cggcgctcat gtgttacgat tccttccagg ttatcgaccg acatcgcccc tgtattttcg
     1801 tgacagtctt ggcggataga cacgaatttc aggggcgttt gtttttcagt cgcttacact
     1861 acccccaacg acaaaacctg tcgagtcttc ccgcaaaccc gatccattta ccataactcc
     1921 tgttgtacgt accccgtaaa acgccctcag tcgcttcctg acgcaaaaaa cgcaaaaaga
     1981 caggaaaaca ccaggccaaa ccagaaaaac gcgtcagaat cgttttcaga gcgttgcata
     2041 actatgcacg aaagcgatgc gcgatctgtt tcgagcgttc agaagggcga acgggtcaaa
     2101 acagcaaact ttctcatcag aaaacggtga acgggacgcg gaattttttc gcgttccgtg
     2161 aaacgttggc ggggttcggg gcgcagtccc gatattgcta cattttcaac gctccatatc
     2221 ttgatcacgt tcgttactac gtgatgcctc cctggcccag gatcgctgta tacgcagtgc
     2281 cttttcctcc tgttgctgcc gttcctgcgc catttctgcc agtaactcat gtcgcatttg
     2341 agctttttca tctccagata tactgagttc aggctccaga gataacatct ggctacgggc
     2401 aacggatact tcttcagcaa ccttttgcct ggtattctct aaagatgccg cggccagaat
     2461 ctcacgttct ctgtacctgt ccagatcccc aacgtactta tatccctcgg tacgcttaaa
     2521 agcagcgttt tctttgtccc actcggattc ggcttgctgt agcttgttcc tgaattcatt
     2581 cctttcatgt tcagcggttt ccagcacact tttttgctcc agaatacgcg catcaatctc
     2641 ccttttgtca gccccccgaa acaggccacg aatcccattc aaagcattgc gttgttcctg
     2701 tagctcccgc agctcccttt gtgcggaaac gacattacgc cccagtttgt ctaaataccg
     2761 tgccccttca tatattcgcc tgctccattc ggaaagagag tctttttttg ctttcgcatt
     2821 ctgaagcagc ttatgttctt tgagcgcatt gggattggca tcccctaaac gagcaagcct
     2881 tgcttctccc tgaatgaccg ttttcataac cttgcggtac tgaagcaata actccggtga
     2941 acgggctgaa cgaacaggct caactgcctt gattttttgc ttttgctcct gttcctgctg
     3001 aatggcattt gcggcatctc tggcggtctt gagttcccgc tcggcattcc tccgttcctg
     3061 gattgcaaca atccgctcac cattgagact ggcggcctga acggggccaa gatgaacttc
     3121 cggcgtgcga ttgataccct gttctttcag agaacgatga tctacgcgcg actcgtgacc
     3181 gtatcgcgca aggtgctcat tctgcacatc tgcccagcgg gaacgcagcg caacaagggc
     3241 ggcttttcgc tctccggctg tctggggaat actcgctttt tttgcgcctc cccgttctgg
     3301 tgatttgctg ttggcacgtt taaaaaattg ctgcggatcg cgttcaatac catcattaat
     3361 ccgctcgcaa aacatgatat gcgcgtgtgg ctgttccttt ccgtcgattg cacctggcgg
     3421 attgtggatc gcgtactggt aggcatggcg atcgccaagt tccttttgca cgaaatcttc
     3481 aacaagttct atccgttgtt cgcgtgtcag ttcacgcggt aacgcgatct caatttcacg
     3541 gtatgcagtc ccgttttttc gttcaaattc atctgcggct ttccatagct ctgcgggatt
     3601 tttcttcgcc catgatggca tgttacctga tgacgaaaat tccagatcct cccgcgattt
     3661 gtagctctta tattcgccgg atctggaaat gtaatcagca tgttttaagg cactgccttt
     3721 tgctccagct ttgacggtgc aatggtagct tgccatctgc cttttagccc tccgcaggag
     3781 cgcacagttt ctcgacgaag gagagaaact actaagtgcg catccctgaa ttaatcaggg
     3841 atgattttac ggtctcacac gcaggcagac aaggtgatat tatgcacaat aacaactcac
     3901 atta
//
