LOCUS       NZ_CP051423             2444 bp    DNA     circular CON 18-MAY-2024
DEFINITION  Salmonella enterica subsp. enterica serovar Uganda strain CVM 20723
            plasmid p20723-6, complete sequence.
ACCESSION   NZ_CP051423
VERSION     NZ_CP051423.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN14504525
            Assembly: GCF_016454725.1
KEYWORDS    RefSeq.
SOURCE      Salmonella enterica subsp. enterica serovar Uganda
  ORGANISM  Salmonella enterica subsp. enterica serovar Uganda
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Salmonella.
REFERENCE   1  (bases 1 to 2444)
  AUTHORS   Zhao,S., Li,C., Hsu,C.H., Tyson,G.H., Strain,E., Tate,H., Tran,T.T.,
            Abbott,J. and McDermott,P.F.
  TITLE     Comparative Genomic Analysis of 450 Strains of Salmonellaenterica
            Isolated from Diseased Animals
  JOURNAL   Genes (Basel) 11 (9), 1025 (2020)
   PUBMED   32883017
  REMARK    Publication Status: Online-Only
REFERENCE   2  (bases 1 to 2444)
  AUTHORS   Li,C.
  TITLE     Direct Submission
  JOURNAL   Submitted (10-APR-2020) CVM/OR, FDA-CVM, 8401 Muirkirk Rd, MOD2,
            Laurel, MD 20708, United States of America
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Date                     :: FEB-2020
            Assembly Method                   :: HGAP v. 4
            Assembly Name                     :: Microbial Assembly
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 448x
            Sequencing Technology             :: PacBio Sequel
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_016454725.1-RS_2024_05_18
            Annotation Date                   :: 05/18/2024 02:49:22
            Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline
            (PGAP)
            Annotation Method :: Best-placed reference protein set; GeneMarkS-2+
            Annotation Software revision      :: 6.7
            Features Annotated                :: Gene; CDS; rRNA; tRNA; ncRNA
            Genes (total)                     :: 4,974
            CDSs (total)                      :: 4,853
            Genes (coding)                    :: 4,717
            CDSs (with protein)               :: 4,717
            Genes (RNA)                       :: 121
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 85
            ncRNAs                            :: 14
            Pseudo Genes (total)              :: 136
            CDSs (without protein)            :: 136
            Pseudo Genes (ambiguous residues) :: 0 of 136
            Pseudo Genes (frameshifted)       :: 61 of 136
            Pseudo Genes (incomplete)         :: 97 of 136
            Pseudo Genes (internal stop)      :: 26 of 136
            Pseudo Genes (multiple problems)  :: 41 of 136
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP051423.1.
            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..2444
                     /organism="Salmonella enterica subsp. enterica serovar
                     Uganda"
                     /mol_type="genomic DNA"
                     /strain="CVM 20723"
                     /serovar="Uganda"
                     /isolation_source="bovine"
                     /sub_species="enterica"
                     /db_xref="taxon:487004"
                     /plasmid="p20723-6"
                     /geo_loc_name="USA:TN"
                     /collection_date="2002"
                     /collected_by="TN State Veterinary Diagnostic Lab"
     gene            complement(join(2317..2444,1..112))
                     /locus_tag="HFQ25_RS00575"
                     /old_locus_tag="HFQ25_00575"
     CDS             complement(join(2317..2444,1..112))
                     /locus_tag="HFQ25_RS00575"
                     /old_locus_tag="HFQ25_00575"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001560795.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_001560795.1"
                     /translation="MIKKICITVIVVFLLLVGYGAWIGSEQNQRGVSLFEVAYTYNAMN
                     PISRIGYTFMLKRNHALVERAGEVKKSIDSMSGE"
                     /name="hypothetical protein"
     gene            complement(932..1081)
                     /locus_tag="HFQ25_RS00580"
                     /old_locus_tag="HFQ25_00580"
     CDS             complement(932..1081)
                     /locus_tag="HFQ25_RS00580"
                     /old_locus_tag="HFQ25_00580"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_017880354.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_001442891.1"
                     /translation="MPSEYDEQLDSTDTQLPGEYDLFDLMAQVTEENLHAPVDFGPPVG
                     REAL"
                     /name="hypothetical protein"
     gene            complement(1994..2293)
                     /locus_tag="HFQ25_RS00585"
                     /old_locus_tag="HFQ25_00595"
     CDS             complement(1994..2293)
                     /locus_tag="HFQ25_RS00585"
                     /old_locus_tag="HFQ25_00595"
                     /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_016247612.1"
                     /translation="MKKILFCSLLLLSASSFAQQFHYQCEGRDLKIMLSPNAAFLDGKS
                     FEYKNGETNGETTKMTFFGPSGEVLKFLVNPVNNLYRMGLTSGATFEEINCTEI"
                     /name="hypothetical protein"
     Typing          complement(1117..1290)
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="97.143"
                     /coverage="100.0"
                     /evalue="5.58e-78"
     Typing          1214..1761
                     /name="rep_cluster_2335"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="91.123"
                     /coverage="90.0"
                     /evalue="0.0"
ORIGIN
        1 caacctcaaa taaagatact cctcgctgat tttgctcaga tccaatccaa gcaccatagc
       61 caaccaacag caaaaaaacg acgataacag taatgcagat tttttttatc attccctatc
      121 cagataatat gaagaaaaca gaattgaaca taacatccgt tgcgtgcacc gcctgagagg
      181 ccctcagggc gtttctgacg ggaaaccggt aaaacaggca acaaaccacc cgaaaacccg
      241 ccagaaacgc gcaggctctg tttttacgca tgcatgagta tgcgcgcaag tgcatagcgc
      301 agaatttcac accattcagc caggggaagt cctgtttccg gcgttcttct tacccgaaaa
      361 cggtgaacgg ggacgcaatt tattgcgtga ccgtgaagcg ttgccggcgc agccggaaaa
      421 cccgctgtca gcacgttcag gaagggggtg atgtacaaat ggcacagagg atgaaagtga
      481 cgtatgagct gaaggaatga tgtaaaagtg atgtacaaat gatgtaaaag tgatgcaaaa
      541 gtgttgtaaa agtgatgtac agactgaagg agtgttgtaa aagtgttgta aaagtgatgt
      601 atgaactgaa ggagcgatgt aattctgtag tcaggaagaa taacccgttc atgcaggcat
      661 gaacgataca gtgaggaacg ctttttttgt cacgatctcc ccttaacctg cgtaaatcac
      721 cctccatggt tgattatttt tcaacctcaa aatggtcata caccatacgc aaccgcgatt
      781 ttcatcgcaa ttgcatgaat taaaaggtaa aaactgaagt tcccgtttat ttatgtaata
      841 cgcaacgtat tacaaccacc tgtaatcaca tgaaaataaa gaaataagat gtaataccgg
      901 cgtattacac gtacgcgggt aagcgaaaaa gctataacgc ttcccggccg acaggcggcc
      961 caaaatccac cggggcgtgc aggttctctt cagtaacctg cgccattaaa tcaaaaaggt
     1021 catattcgcc gggaagctgc gtatcagtcg aatccagttg ttcatcatat tcagatggca
     1081 tggagtgata tccagtagcg gagaggttgt tagcgggttt cggggcgcag ccctgaacca
     1141 gtcacgtagc gctagcagag tgtatactgg cttactatgt tggcactgat gagggtgtca
     1201 gtgaagtgct tcatgtggca ggagaaaaaa ggctgcaccg gtgcgtcagc agaatatgtg
     1261 atacaggata tattccgctt cctcgctcac tgactcgcta cgctcggtcg ttcggctgcg
     1321 gcgagcggta ccggcttaca aatggggcgg aaatttccgg gtagatgcca ggagcgaact
     1381 taacagggaa acgagaaggc cgcggcgctg ccgtttttcc ataggctccg cccccctgac
     1441 aagcatcacg aaatctgacg ctcaaatcag tggcggcgaa acccgacagg actataaaga
     1501 taccaggcgt ttccccctgg cggctccctc gtgcgctctc ctgttcctgc ctttcggttt
     1561 accggtgtca ttccgctgtt atggccgcgt ttgtctcatt ccacgcctga cactcagttc
     1621 cgggtaggca gttcgctcca agctggactg tatgcacgaa ccccccgttc agtccgaccg
     1681 ctgcgcctta tccggtaact atcgtcttga gtccaacccg gaaagacatg caaaagcacc
     1741 actggcagca gccactggta attgatttag aggagttagt cttgaagtca tgcgccggtt
     1801 aaggctaaac tgaaaggaca agttttggtg actgcgctcc tccaagccag ttacctcggt
     1861 tcaaagagtt ggtagctcag agaaccttcg aaaaaccgcc ctgcaaggcg gttttttcgt
     1921 tttcagagca agagattacg cgcagaccaa aacgatctca agaagatcat cttattaatc
     1981 agataaaata tttctagatt tcagtgcaat ttatctcttc aaatgtagca cctgaagtca
     2041 gccccatacg atataagtta ttgacaggat taaccaaaaa cttgagaacc tcaccagaag
     2101 gaccaaagaa tgtcatcttt gtcgtttccc cattcgtctc tccattctta tattcgaatg
     2161 atttaccatc aagaaaagct gcattaggtg aaagcattat ctttaaatct cgtccttcac
     2221 actgataatg gaattgttgt gcaaatgaac ttgcagaaag aagaagcagc gaacaaaaaa
     2281 gtatcttttt catatcagtc ctttaaattt aaaaaatcac tcaccactca tgctatcaat
     2341 agatttctta acctctccag ccctctcgac taaagcatga tttctcttca gcataaatgt
     2401 atagccgatc cgactaattg gattcattgc gttgtatgta tatg
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