LOCUS       NZ_CP051419             3372 bp    DNA     circular CON 18-MAY-2024
DEFINITION  Salmonella enterica subsp. enterica serovar Uganda strain CVM 20723
            plasmid p20723-5, complete sequence.
ACCESSION   NZ_CP051419
VERSION     NZ_CP051419.1
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 3372)
  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 3372)
  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
            CP051419.1.
            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..3372
                     /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="p20723-5"
                     /geo_loc_name="USA:TN"
                     /collection_date="2002"
                     /collected_by="TN State Veterinary Diagnostic Lab"
     gene            join(3214..3372,1..165)
                     /locus_tag="HFQ25_RS00005"
                     /old_locus_tag="HFQ25_00005"
     CDS             join(3214..3372,1..165)
                     /locus_tag="HFQ25_RS00005"
                     /old_locus_tag="HFQ25_00005"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000956000.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MobC family plasmid mobilization relaxosome
                     protein"
                     /protein_id="WP_024132211.1"
                     /translation="MLTIRVTDEEHARLLERCEGKRLAEWMRRVCLGEPVARTGKLPTL
                     SPPLLRHLAAIGNNLNQTARKVNSGQWSSIDRVHVVAALMAIEGELRQLRQAVREQGVR
                     DDS"
                     /name="MobC family plasmid mobilization relaxosome protein"
     gene            374..>811
                     /locus_tag="HFQ25_RS24735"
                     /old_locus_tag="HFQ25_00010"
                     /pseudo=""
     CDS             374..>811
                     /locus_tag="HFQ25_RS24735"
                     /old_locus_tag="HFQ25_00010"
                     /inference="COORDINATES: protein motif:HMM:NF015397.4"
                     /note="incomplete; partial in the middle of a contig;
                     missing C-terminus; Derived by automated computational
                     analysis using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="relaxase/mobilization nuclease domain-containing
                     protein"
                     /name="relaxase/mobilization nuclease domain-containing
                     protein"
     gene            843..1403
                     /locus_tag="HFQ25_RS00015"
                     /old_locus_tag="HFQ25_00015"
     CDS             843..1403
                     /locus_tag="HFQ25_RS00015"
                     /old_locus_tag="HFQ25_00015"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000067488.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MbeB family mobilization protein"
                     /protein_id="WP_032329292.1"
                     /translation="MSNLLQMGTDFEKKLKERAASTENMLNSEFRKLEESVDKALSLNR
                     QKIRDAISGHTTSVKQQLDTLSATVSTQFSTTEAELSRQQKKLLWQVIKGRILFPALTA
                     LSVTGGIFLGCWGLMEWQESKIAKNILTIREQENTLAKLEAKTWGVTFVNGENGKFLVL
                     PDGVKGENTWTVGDKNAVRLVRE"
                     /name="MbeB family mobilization protein"
     gene            1410..1643
                     /locus_tag="HFQ25_RS00020"
                     /old_locus_tag="HFQ25_00020"
     CDS             1410..1643
                     /locus_tag="HFQ25_RS00020"
                     /old_locus_tag="HFQ25_00020"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000137389.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MbeD family mobilization/exclusion protein"
                     /protein_id="WP_000137389.1"
                     /translation="MTELEGHLLNALEHLQQDYMRRLNEWESAFAELQKMHEVTQRNNA
                     ILNERVVILSQQVQRLAGQVDRLSRLFIANNS"
                     /name="MbeD family mobilization/exclusion protein"
     gene            complement(2959..3150)
                     /locus_tag="HFQ25_RS00025"
                     /old_locus_tag="HFQ25_00025"
     CDS             complement(2959..3150)
                     /locus_tag="HFQ25_RS00025"
                     /old_locus_tag="HFQ25_00025"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000165979.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="Rop family plasmid primer RNA-binding protein"
                     /protein_id="WP_000165979.1"
                     /translation="MTKQEKTALNMARFIRSQTLTLLEKLNDLDADEQADICESLHDHA
                     DELYRSCLARFGDDGESN"
                     /name="Rop family plasmid primer RNA-binding protein"
     Typing          2795..2878
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="87.059"
                     /coverage="95.0"
                     /evalue="8.83e-18"
     Typing          156..1726
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="93.006"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 gctgccatcg ggaacaacct gaaccagaca gcccggaagg tgaacagcgg ccagtggtct
       61 tcgattgacc gggttcatgt ggtggccgca ctgatggcca tcgagggtga attgcgccag
      121 ttgcggcagg ctgtcaggga acagggggta cgggatgata gttaaatttc atgccagggg
      181 gaaaggcggt ggaagtggcc cggtcgatta cctgctgggg cgggagcgta accgcgaagg
      241 cgcaacggtg ctccggggta acccggaaga agtgcgggaa ctcattgatt ccacgccatt
      301 ttcgaagaaa tacacgtcag gcgttctgtc tttcgcggag aaggagttac cgccgggtga
      361 acgcgaaaga gtgatgacga gctttgagcg tgttcttatg cccggtctcg aaaaagacca
      421 gtacagcatt ctctgggtgg aacaccagga taaggggcgg ctcgaactga attttgtcat
      481 cccgaacatg gagctacaga gcggtaagcg cctccagccg tactacgacc gtgcggacag
      541 gccgaggata aatgcctggc agacgctggt taatcatcat tacgggctgc gtgacccgaa
      601 cgcaccggag aacagacgga cgcttgtcac gccaaataat ctgccaaaag cgaaacagga
      661 ggccgcagaa gcgattacac ggggtcttga ggcgctttac catgccggag caataaaaac
      721 gcgtcaggat gtcactgagg cgctcacagc ggcaggtttt gaggtggtga ggacaaccag
      781 aagcagtatc agtattgccg acccggaggg tgggcggaat ctcaggctaa agggggcgct
      841 gtatgagcaa tcttttacaa atgggaacag acttcgagaa gaaactgaaa gagcgagccg
      901 cttctaccga gaacatgctg aacagcgagt tcaggaagct cgaagagtct gtagacaagg
      961 cactgagctt aaacaggcag aaaatcagag acgctatcag cggacataca acatccgtga
     1021 aacagcaact ggatacactg agcgccaccg tgagcacgca gttcagcacc acagaggccg
     1081 aactgtcccg gcagcagaaa aaactgctct ggcaggtgat caaagggcgg atactgtttc
     1141 cggcgctgac cgcgctcagc gtcacgggcg gcattttcct ggggtgctgg gggctgatgg
     1201 agtggcaaga aagcaagatt gcgaaaaata tcctgactat cagagagcag gaaaacacgc
     1261 tggcgaaact cgaggcaaaa acctgggggg tgacgttcgt caatggcgag aacgggaaat
     1321 ttctggtgct gccggacggg gtgaaagggg aaaacacctg gacggtgggc gacaagaacg
     1381 ccgtgaggct ggtcagggag taaacgagta tgacggaact ggaagggcat ttgctgaacg
     1441 ccttagagca tttgcaacag gactatatgc ggcggctgaa cgagtgggag agcgccttcg
     1501 cggaattgca gaagatgcac gaggttacgc aacggaacaa cgcgatactg aacgagcgcg
     1561 tcgtgatatt gagtcagcag gtgcagagat tagccgggca agtggatcgc ttgagtcggt
     1621 tatttatcgc gaacaacagc taagggatga acaggagcgt gcccggtaca gacatgaggt
     1681 acaggaacgc gcggcacggg ttcggagtgg gccatcaatg gagatgtgac cggggaagtg
     1741 acgaaatctt gccattttga ccagttcgac ggctggggcg agcgaaacaa atcgtgtgcc
     1801 gtatttgtgc atagctatgc aacatcctga aaacgcattt cacgcgtttt tggggattca
     1861 gccaggggaa aacatggttt ttttactttt tgagcgtaaa gacgtgaaaa atctcgttat
     1921 tgcacttgcg atctttcgtc ggcgggcgta gaacgaaaac agctcgccag gaaggcgagc
     1981 tgtttcgggt tcattgaggt ctctgacctc ctcaatgttc ctgtggaaac tgttgagatc
     2041 cacaacagaa accagttcat tcagtttgca tgagccttct gtattcttca agaatttttc
     2101 aacagcacag tctcccagga accccgaaaa aaacctgttt ttgcagatac ttgcgtattt
     2161 gcgagaatcg tttgcggttg ggggagctgt gacgacggcg accgcacgcg tgagagttcc
     2221 gctaccggcg cagagagttt catcgacagc ggacacctga tgagttgcca caaaaaccgt
     2281 atgtagcgcg gctagattgg ttgagttaga ccttggcggc agttcccggt atgtggtggc
     2341 gtgacgggtg agatggtgcg gcgaagacgc atacgtcacg caggcgcggg ttcttccact
     2401 gacgcgcccc gtgatcgatg gccttggctc cgtccggcat atcgagagcg gcaaactacc
     2461 cgtcccttca ctgggagggg tgagttgttg ccgttccctc caacctttca ccatccggca
     2521 tatcgcacga tcccatgtgc accgcaactc ctgataactc cagtgcaaaa aaaaaaacgg
     2581 atctgcatca caacgagagt gatcccaccg ctcgccgcag ccccagcgac cgaacgtagt
     2641 gagcgagtgg gcgaggaagc ggaagagtca cagatgcaag cattgtgcac ttacgcgcct
     2701 gtgccagtgt ccgcgtgtgt gctgtttatc gggtgcgctg tttttacatc tgtgcggctt
     2761 tttactcctg acatggtgca cttcccatcc atgtctgcac cgatgcaaaa tgagataagc
     2821 cagtatacac atcgctatcg ctctgtgaac tgggtcaggg ctgcgccccg acacccgcac
     2881 tgacgcgccc tggcgggctt gtctgctccc ggcatccgct cacaggcaag ctgtgaacgt
     2941 ctccgggagc tgcatgtttc agttgctttc accgtcatcg ccgaagcgtg cgaggcaact
     3001 gcggtagagt tcgtcggcgt ggtcgtgaag tgattcgcag atgtctgcct gttcgtccgc
     3061 gtccagatcg ttgagttttt ccagcagggt tagcgtctgg cttctgataa agcgagccat
     3121 gttaagggct gttttttcct gtttggtcat ggtcttaagg ctccttgtat gggggatttg
     3181 ttagggggaa tgataccgat gaaacgcgag aagatgctca cgatacgggt taccgatgag
     3241 gagcacgccc ggttactgga acgctgcgag ggtaaacgac tggcggaatg gatgcggcgg
     3301 gtctgtctgg gggagccggt tgcacgcaca ggaaaactgc cgacactatc gccgccattg
     3361 ctgcggcatc tg
//
