LOCUS       CP021465                2576 bp    DNA     circular BCT 06-JUN-2018
DEFINITION  Salmonella enterica subsp. enterica serovar Typhimurium strain UGA14
            plasmid pUGA14_3, complete sequence.
ACCESSION   CP021465
VERSION     CP021465.1
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 2576)
  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  JOURNAL   Unpublished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 2576)
  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..2576
                     /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_3"
                     /geo_loc_name="Kenya"
                     /lat_lon="0.26 N 33.58 E"
                     /collection_date="2003"
                     /collected_by="DJ Perkins"
     gene            complement(204..317)
                     /locus_tag="CCE20_27770"
     CDS             complement(204..317)
                     /locus_tag="CCE20_27770"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_007772075.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="replication initiation protein"
                     /protein_id="AWR41194.1"
                     /translation="MHEPPVQSDRCALSGNYHLESNPERHAKAPLAAATGN"
                     /name="replication initiation protein"
     gene            complement(342..602)
                     /locus_tag="CCE20_27775"
     CDS             complement(342..602)
                     /locus_tag="CCE20_27775"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001326445.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="AWR41196.1"
                     /translation="MALKSGKAGKRMRRCRFSIGSAPLTSITKSDAQISGGETRQDYKD
                     TRRFPLMAPSCALLFLPFGLPVSFRCYGRVYLIPRLTLSSG"
                     /name="hypothetical protein"
     gene            523..747
                     /locus_tag="CCE20_27780"
                     /pseudo=""
     CDS             523..747
                     /locus_tag="CCE20_27780"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001332449.1"
                     /note="internal stop; Derived by automated computational
                     analysis using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /name="hypothetical protein"
     gene            complement(1877..2464)
                     /locus_tag="CCE20_27785"
     CDS             complement(1877..2464)
                     /locus_tag="CCE20_27785"
                     /inference="COORDINATES: ab initio prediction:GeneMarkS+"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GeneMarkS+."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="AWR41195.1"
                     /translation="MIRKIFFASAIVVAISGCTAMDKLAGMGVVSQQTSTFDNSTVIDV
                     SPNSLYDPNSTWGTQLQLGAIWSSSQPDQVGLILSYNSNVSNGSSAYLGFIGIDINIDG
                     KISSYKAQQLTNLSNSGYNTVSKTIYTSSKNTVVIPYEVLEKMVSAKNCRLRIHTTEGN
                     QDIDFSAASIPGGKATAIVSIKEFMTKVAKVK"
                     /name="hypothetical protein"
     Typing          692..907
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="88.636"
                     /coverage="100.0"
                     /evalue="7.33e-68"
     Typing          complement(205..742)
                     /name="ColRNAI_rep_cluster_1987"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="89.259"
                     /coverage="99.0"
                     /evalue="0.0"
ORIGIN
        1 gatcttcttg agatccttaa gcgagcgtcg taatctcttg accacgaaac gaaaaaaccg
       61 ccttgcaggg cggtttttcg aaggttctca gagctaccaa ctctttgaac cgaggtaact
      121 ggcttggagg agcgcagtca ccaaaacttg tcctttcagt ttagccttaa ccggcgcata
      181 acttcaagac taactcctct aaatcagtta ccagtggctg ctgccagtgg cgcttttgca
      241 tgtctttccg ggttggactc aagatgatag ttaccggaca aggcgcagcg gtcggactga
      301 acggggggtt cgtgcataca gtccagcttg gagcgaactg cctacccgga actgagtgtc
      361 aggcgtggaa tgagataaac gcggccataa cagcggaatg acaccggtaa accgaaaggc
      421 aggaacagga gagcgcacga gggagccatc agggggaaac gcctggtatc tttatagtcc
      481 tgtcgggttt cgccaccact gatttgagcg tcagatttcg tgatgcttgt caggggggcg
      541 gagcctatgg aaaagcggca gcgccgcatc ctttttccgg cctttcctga cttgagtgcc
      601 atctctttat cttgtcattc gtgagcaggt cttgtcattc gtgagcaggt aacgcccgcc
      661 gcagcctcac ggcaggagcg tagcgaccga gtgagcgagg aggcgtcata tcaccgtaac
      721 tcccattttc tcccttacgc cctgtagctg cattttcccc tgtcacatga agcactttca
      781 ttaggtgcta ctccgccgta acatattcag ccactgtaca ctccgctagc gctacgtgac
      841 tggttcaggg ctgtgccccg aaacccgcta acaacctctc cgctactgga tatcacccca
      901 tgccatctga atatgatgaa caactggatt cgactgatac gcagcttccc ggcaaatatg
      961 atctttttga tttaatggcg caggttactg aagagaacct gcacgccccg gtggattttg
     1021 gaccgcctgt cggccgggaa gcgttatagc tttttcgctt acccgcgtac gtgtaatacg
     1081 ccggtattac atcttatttc tttattttca tgtgattaca ggtggttgta atacgttgcg
     1141 tattacataa ataaacggga acttcagttt ttacctttta attcatgcaa ttgcgatgaa
     1201 aatcgcggtt gcgtatggtg tatgaccatt ttgaggttga aaaataatca accatggagg
     1261 gtgatttacg caggttaagg ggagatcgtg acaaaaaaaa gcgttcctca ctgtatcgtt
     1321 catgcctgca tgaacgggtt attcttcctg actacagaat tacatcgctc cttcagttca
     1381 tacatcactt ttacaacact tttacaacac tccttcagtc tgcacatcac ttttacaaca
     1441 cttttgcatc acttttacat catttataca tcacttttac atcattcctt cagctcatac
     1501 gtcactttca tcctctgtgc catttgtaca tcaccccctt cctgaacgtg ctgacagcgg
     1561 gttttccggc tgcgccggca acgcttcacg gccacgcaat aaattgcgtc cccgttcacc
     1621 gttttcggat gggaagaacg ccggaaacag gacttcccct ggctgaatgg tgtgaatttc
     1681 cgcgctatgc acttgcgcgc atactcatgc atgccgtaaa aacagagcct gcgcgtttct
     1741 ggcgggtttt cgggtggttt gttgcctgtt ttaccggttt cccgtcagaa acgccctgag
     1801 agcctctgag gcggtgcacg caacggatgt tatggtaaat agtgtgaagt gccgcctgta
     1861 atggcggctt agttacctat ttaacttttg ccactttagt catgaattct ttaatggaaa
     1921 caatcgcagt agctttcccc ccagggatac ttgcagctga gaaatcgatg tcttgattac
     1981 cttcagttgt atgtatgcga aggcggcagt ttttagccga caccatcttt tctagcactt
     2041 catatgggat aacaacggta tttttgctgg atgtgtagat cgttttggat acagtattgt
     2101 atccactgtt acttagatta gttagttgct gtgctttata gctagatatc ttgccatcaa
     2161 tatttatatc tattcctatg aaacctaagt atgcggaact tccattagat acatttgaat
     2221 tgtaggaaag gatcagccct acttgatctg gttgggagct ggaccatatt gctcctaact
     2281 gaagttgtgt tccccaagtg ctgttcgggt cgtatagcga atttggagag acatctatga
     2341 cagttgagtt gtcaaaagtg gatgtttgtt gagaaaccac acccattccc gccagtttat
     2401 ccattgctgt acagccagag atggctacta cgatcgcaga agcaaaaaaa atcttcctta
     2461 tcatttcgtt atcctatttt tttcttgtta ccagagagtg aaaaaaagca tcgtattacc
     2521 gaaactattt tgcacgcgat tttcttttta agaaggattt tgaaaggata cgggca
//
