LOCUS       CP021466                1995 bp    DNA     circular BCT 06-JUN-2018
DEFINITION  Salmonella enterica subsp. enterica serovar Typhimurium strain UGA14
            plasmid pUGA14_4, complete sequence.
ACCESSION   CP021466
VERSION     CP021466.1
DBLINK      BioProject: PRJNA387603
            BioSample: SAMN07159261
KEYWORDS    .
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 1995)
  AUTHORS   Xie,G., Daligault,H., Davenport,K., Dighe,P., Kempaiah,P.,
            Kubicek-Sutherland,J., Mukundan,H., Perkins,D., Doggett,N. and
            McMahon,B.
  TITLE     Comparative genomic and phenotypic analysis of invasive nontyphoidal
            Salmonella isolates from Siaya Kenya
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 1995)
  AUTHORS   Xie,G., Daligault,H., Davenport,K., Dighe,P., Kempaiah,P.,
            Kubicek-Sutherland,J., Mukundan,H., Perkins,D., Doggett,N. and
            McMahon,B.
  TITLE     Direct Submission
  JOURNAL   Submitted (23-MAY-2017) Biosciences Division, Los Alamos National
            Laboratory, MS M888, Los Alamos, NM 87545, United States of America
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method :: Velvet v. 1.2.08; IDBA v. 1.1.0; Phrap v.
            SPS-4.24; HGAP v. 2.3.0
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 389.0x
            Sequencing Technology             :: Illumina HiSeq; PacBio
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI
            Annotation Date                   :: 05/25/2017 13:20:13
            Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline
            Annotation Method :: Best-placed reference protein set; GeneMarkS+
            Annotation Software revision      :: 4.2
            Features Annotated :: Gene; CDS; rRNA; tRNA; ncRNA; repeat_region
            Genes (total)                     :: 5,559
            CDS (total)                       :: 5,435
            Genes (coding)                    :: 5,228
            CDS (coding)                      :: 5,228
            Genes (RNA)                       :: 124
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 87
            ncRNAs                            :: 15
            Pseudo Genes (total)              :: 207
            Pseudo Genes (ambiguous residues) :: 0 of 207
            Pseudo Genes (frameshifted)       :: 110 of 207
            Pseudo Genes (incomplete)         :: 84 of 207
            Pseudo Genes (internal stop)      :: 69 of 207
            Pseudo Genes (multiple problems)  :: 52 of 207
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            Bacteria and source DNA available from DJ Perkins,Center for Global
            Health, UNM.
            Annotation was added by the NCBI Prokaryotic Genome Annotation
            Pipeline (released 2013). Information about the Pipeline can be
            found here: https://www.ncbi.nlm.nih.gov/genome/annotation_prok/
FEATURES             Location/Qualifiers
     source          1..1995
                     /organism="Salmonella enterica subsp. enterica serovar
                     Typhimurium"
                     /mol_type="genomic DNA"
                     /strain="UGA14"
                     /serovar="Typhimurium"
                     /isolation_source="blood"
                     /host="Homo sapiens"
                     /sub_species="enterica"
                     /db_xref="taxon:90371"
                     /plasmid="pUGA14_4"
                     /geo_loc_name="Kenya"
                     /lat_lon="0.26 N 33.58 E"
                     /collection_date="2003"
                     /collected_by="DJ Perkins"
     gene            310..741
                     /locus_tag="CCE20_27790"
     CDS             310..741
                     /locus_tag="CCE20_27790"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001233485.1"
                     /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="AWR41197.1"
                     /translation="MRKVTQVDLETGEDLGGFVAVIRPKQKSSFERHFTMNQAALKIIA
                     TELNHEQTKVLMMLLADLDYENYIQVAQIDIAESLGMKKPNVSKAVKNLIEFGIILEGP
                     KIGRSKTYRLNPQFGWKGTVSNHKKALKNGLSVIQGGKV"
                     /name="helix-turn-helix domain-containing protein"
     gene            complement(754..1158)
                     /locus_tag="CCE20_27795"
     CDS             complement(754..1158)
                     /locus_tag="CCE20_27795"
                     /inference="COORDINATES: ab initio prediction:GeneMarkS+"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GeneMarkS+."
                     /codon_start=1
                     /transl_table=11
                     /product="transcriptional regulator"
                     /protein_id="AWR41198.1"
                     /translation="MNNREFKEVRLSLGLTQAEFATQLGLTRETVCRIERCAFPLSRRV
                     SLSAANLSKPVMTQVHESESDLRSHDNEALDIASRLDAMSLLIRLDTMIFNFRLSRPVY
                     GRNKVSGKHVAEFLSALRSEIRPYLPESLK"
                     /name="transcriptional regulator"
ORIGIN
        1 acgcgagtct gtcacgtcga ggaagcggaa tatcacctga acgggcatag aaaaccgtac
       61 gcacagtacc cacagaaaaa cacgatgcag gatagggcaa acgccgcaaa atgctagcat
      121 tttactcgtt tgcccggtga cctacagcag tttccagaag tgatgttttc gtggctggca
      181 tcgcgcacag agttacaaga tacagaaggg aacctcccgc aagccgcgcc acaagcggaa
      241 tcatttgaca gatagttatg ttcaggcata acttagttat gttcaggcat aactatttaa
      301 ggaattttca tgcgaaaagt cacacaggtt gacctcgaaa ccggagagga tttgggcggg
      361 tttgtcgccg tgatccgtcc caagcaaaaa tcatcgttcg agaggcattt cactatgaat
      421 caggcagcac tcaaaatcat cgctacagaa ctgaaccatg agcagacaaa agtactcatg
      481 atgcttctcg cagacctgga ctacgaaaat tacattcagg tggcacaaat cgacattgca
      541 gaatcattgg gaatgaaaaa accaaatgtt agcaaagctg ttaaaaacct gattgagttc
      601 ggaataatcc ttgaggggcc aaagataggc cgaagcaaaa cctaccgcct gaatcctcaa
      661 ttcggctgga aaggcacggt aagcaaccac aagaaagcgc tcaaaaacgg cctcagcgtc
      721 attcagggtg gcaaggtgtg atccaagatc acatcacttc aacgactccg gcaggtaagg
      781 cctaatctca gatcgaaggg ctgaaagaaa ctcagcgaca tgcttgccgg aaaccttatt
      841 ccgtccataa accgggcgtg aaagccggaa attaaaaatc atcgtatcaa gccggattaa
      901 caggctcata gcatcaagtc tggaagctat atccagcgcc tcattgtcat gtgatctcag
      961 atcactttca ctctcatgaa cctgcgtcat tactggcttt gaaagattcg cagcagagag
     1021 cgaaacacga cgagaaagcg gaaaggcgca gcgctcaatc cggcaaaccg tctcacgggt
     1081 taacccaagc tgcgttgcaa actctgcctg cgtaagcccc agtgagagcc ttacttcttt
     1141 aaattctctg ttattcatag agttagaatc actccgttaa tcaattaaac aatgtgatct
     1201 cagatcacat cgacaaagta acgagtctac ccgcacgcta ccagaagtta ggttttaact
     1261 ggaaaactcc gtgtttccgt tgactctacc cccgtgttac agggcggggg tatcggtgcg
     1321 gcggtgtaca caatgcacat cctgtcctgc ctttgatgtc gaaaccggac aagatgtgtt
     1381 tttggagtac cgccattcgc ggcaacatcc aaaaacggct catcagggcg atggcttcac
     1441 tgcgtgaacc atcacctgtt agcagtgtta tttctccggc gtgtcgtcaa tcactaaatc
     1501 ggaaccctga aagggaaccc ccgatttagc gtttgacgag ttcaggccgc agagatgcgg
     1561 atgaatatcc agaaaagaag cctccagatt cgcactcaga agctctatga cgcactcaga
     1621 agctctatga ggggatgaag gtcatcatca aggggatgga gtgaggcaaa cgccgtaaac
     1681 gcctctacgg cgttctggtg acgtgtaatc agggtaagca tggtagaatt cgtgtcagtc
     1741 atggagacct ccgtaacagg ttttcgtgat agcagggggc gggaactcgt aattccttcc
     1801 ccctgcgccc atcagatcat aattccgcta cacgggcaag ccgccacggg aagagtgcac
     1861 tcctcgtggg aactcggtgc gctcccttcc cgtgcccgcc tgccagctcg tgccattctg
     1921 acccgtccgg cacagatagc cagaaaccac gcgagagagt ccgcaccgct cgccgcaaga
     1981 cgtgattagc gagca
//
