LOCUS       NZ_CP051401             3372 bp    DNA     circular CON 18-MAY-2024
DEFINITION  Salmonella enterica subsp. enterica serovar Uganda strain CVM 22436
            plasmid p22436-3, complete sequence.
ACCESSION   NZ_CP051401
VERSION     NZ_CP051401.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN14504594
            Assembly: GCF_016454545.1
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, USA
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: HGAP v. 4
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 354x
            Sequencing Technology             :: PacBio Sequel
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_016454545.1-RS_2024_05_18
            Annotation Date                   :: 05/18/2024 02:40:11
            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)                     :: 4,962
            CDSs (total)                      :: 4,839
            Genes (coding)                    :: 4,700
            CDSs (with protein)               :: 4,700
            Genes (RNA)                       :: 123
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 87
            ncRNAs                            :: 14
            Pseudo Genes (total)              :: 139
            CDSs (without protein)            :: 139
            Pseudo Genes (ambiguous residues) :: 0 of 139
            Pseudo Genes (frameshifted)       :: 60 of 139
            Pseudo Genes (incomplete)         :: 101 of 139
            Pseudo Genes (internal stop)      :: 25 of 139
            Pseudo Genes (multiple problems)  :: 40 of 139
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP051401.1.
            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 22436"
                     /serovar="Uganda"
                     /isolation_source="bovine"
                     /sub_species="enterica"
                     /db_xref="taxon:487004"
                     /plasmid="p22436-3"
                     /geo_loc_name="USA:AZ"
                     /collection_date="2003"
                     /collected_by="AZ State Veterinary Diagnostic Lab"
     gene            complement(join(3246..3372,1..197))
                     /locus_tag="HFQ88_RS24620"
                     /old_locus_tag="HFQ88_24685"
     CDS             complement(join(3246..3372,1..197))
                     /locus_tag="HFQ88_RS24620"
                     /old_locus_tag="HFQ88_24685"
                     /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            261..452
                     /locus_tag="HFQ88_RS24625"
                     /old_locus_tag="HFQ88_24690"
     CDS             261..452
                     /locus_tag="HFQ88_RS24625"
                     /old_locus_tag="HFQ88_24690"
                     /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"
     gene            complement(1768..2001)
                     /locus_tag="HFQ88_RS24630"
                     /old_locus_tag="HFQ88_24695"
     CDS             complement(1768..2001)
                     /locus_tag="HFQ88_RS24630"
                     /old_locus_tag="HFQ88_24695"
                     /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(2008..2568)
                     /locus_tag="HFQ88_RS24635"
                     /old_locus_tag="HFQ88_24700"
     CDS             complement(2008..2568)
                     /locus_tag="HFQ88_RS24635"
                     /old_locus_tag="HFQ88_24700"
                     /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_000067487.1"
                     /translation="MSNLLQMGTDFEKKLKERAASTENMLNSEFRKLEESVDKALSLNR
                     QKIRDAISEHTTSVKKQLDTLSTTVSMQFSTTEAELSRQQKKLLWRVIKGRILFPALTA
                     LSVTGGIFLGCWGLMEWQESKIAKNILTIREQENTLAKLEAKTWGVTFVNGENGKFLVL
                     PDGVKGENTWTVGDKNAVRLVRE"
                     /name="MbeB family mobilization protein"
     gene            complement(<2600..3256)
                     /locus_tag="HFQ88_RS24970"
                     /old_locus_tag="HFQ88_24705"
                     /pseudo=""
     CDS             complement(<2600..3256)
                     /locus_tag="HFQ88_RS24970"
                     /old_locus_tag="HFQ88_24705"
                     /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"
     Typing          complement(534..616)
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="91.667"
                     /coverage="99.0"
                     /evalue="6.43e-24"
     Typing          complement(4..230)
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="85.526"
                     /coverage="99.0"
                     /evalue="2.25e-36"
     Typing          complement(1686..3256)
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="92.817"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 ttccgggctg tctggttcag gttgttcccg atggcagcca gatgccgcag caatggcggc
       61 gatagtgtcg gcagttttcc tgtgcgtgca accggctccc ccagacagac ccgccgcatc
      121 cattccgcca gtcgtttacc ctcgcagcgt tccagtaacc gggcgtgctc ctcatcggta
      181 acccgtatcg tgagcatctt ctcgcgtttc atcggtatca ttccccctaa caaatccccc
      241 atacaaggag ccttaagacc atgaccaaac aggaaaaaac agcccttaac atggctcgct
      301 ttatcagaag ccagacgcta accctgctgg aaaaactcaa cgatctggac gcggacgaac
      361 aggcagacat ctgcgaatca cttcacgacc acgccgacga actctaccgc agttgcctcg
      421 cacgcttcgg cgatgacggt gaaagcaact gaaacatgca gctcccggag acgttcacag
      481 cttgcctgtg agcggatgcc gggagcagac aagcccgcca gggcgcgtca gtgcgggtgt
      541 cggggcgaag ccctgaccca gtcacgtagc gctagcggag tgtatactgg cttatctcat
      601 tttgcatcgg tgcagacatg gatgggaagt gcaccatgtc aggagtaaaa agccgcacag
      661 atgtaaaaac agcgcacccg ataaacagca cacacgcgga cactggcaca ggcgcgtaag
      721 tgcacaatgc ttgcatctgt gactcttccg cttcctcgcc cactcgctca ctacgttcgg
      781 tcgctggggc tgcggcgagc ggtgggatca ctctcgttgt gatgcagatc cgtttttttt
      841 ttttgcactg gagttatcag gagttgcggt gcacatggga tcgtgcgata tgccggatgg
      901 tgaaaggttg gagggaacgg caacaactca cccctcccag tgaagggacg ggtagtttgc
      961 cgctctcgat atgccggacg gagccaaggc catcgatcac ggggcgcgtc agtggaagaa
     1021 cccgcgcctg cgtgacgtat gcgtcttcgc cgcaccatct cacccgtcac gccaccacat
     1081 accgggaact gccgccaagg tctaactcaa ccaatctagc cgcgctacat acggtttttg
     1141 tggcaactca tcaggtgtcc gctgtcgatg aaactctctg cgccggtagc ggaactctca
     1201 cgcgtgcggt cgccgtcgtc acagctcccc caaccgcaaa cgattctcgc aaatacgcaa
     1261 gtatctgcaa aaacaggttt ttttcggggt tcctgggaga ctgtgctgtt gaaaaattct
     1321 tgaagaatac agaaggctca tgcaaactga atgaactggt ttctgttgtg gatctcaaca
     1381 gtttccacag gaacattgag gaggtcagag acctcaatga acccgaaaca gctcgccttc
     1441 ctggcgagct gttttcgttc tacgcccgcc gacgaaagat cgcaagtgca ataacgagat
     1501 ttttcacgtc tttacgctca aaaagtaaaa aaaccatgtt ttcccctggc tgaatcccca
     1561 aaaacgcgtg aaatgcgttt tcaggatgtt gcatagctat gcacaaatac ggcacacgat
     1621 ttgtttcgct cgccccagcc gtcgaactgg tcaaaatggc aagatttcgt cacttccccg
     1681 gtcacatctc cattgatggc ccactccgaa cccgtgccgc gcgttcctgt acctcatgtc
     1741 tgtaccgggc acgctcctgt tcatccctta gctgttgttc gcgataaata accgactcaa
     1801 gcgatccact tgcccggcta atctctgcac ctgctgactc aatatcacga cgcgctcgtt
     1861 cagtatcgcg ttgttccgtt gcgtaacctc gtgcatcttc tgcaattccg cgaaggcgct
     1921 ctcccactcg ttcagccgcc gcatatagtc ctgttgcaaa tgctctaagg cgttcagcaa
     1981 atgcccttcc agttccgtca tactcgttta ctccctgacc agcctcacgg cgttcttgtc
     2041 gcccaccgtc caggtgtttt cccctttcac cccgtccggc aacaccagaa atttcccgtt
     2101 ctcgccattg acgaacgtca ccccccaggt ttttgcctcg agtttcgcca gcgtgttttc
     2161 ctgctctctg atagtcagga tatttttcgc aatcttgctt tcctgccact ccatcagccc
     2221 ccagcacccc aggaaaatgc cgcccgtgac gctgagcgcg gtcagcgccg gaaacagtat
     2281 ccgccctttg atcacccgcc agagcagttt tttctgctgc cgggacagtt cggcctctgt
     2341 ggtgctgaac tgcatgctca cggtggtgct cagcgtatcc agttgctttt tcacggatgt
     2401 tgtatgttcg ctgatagcgt ctctgatttt ctgcctgttt aagctcaatg ccttgtctac
     2461 agactcttcg agcttcctga actcgctgtt cagcatgttc tcggtagaag cggctcgctc
     2521 tttcagtttc ttctcgaagt ctgttcccat ttgtaaaaga ttgctcatac agcgccccct
     2581 ttagcctgag attccgcccc ccctccgggt cggcaatact gatgctgctt ttggttgtcc
     2641 tcaccacctc aaaacctgcc gctgtaagcg cctctgtgac atcctgacgc gtttttattg
     2701 ctccggcatg gtaaagagcc tcaagacccc gtgtaatcgc ttctgcggcc tcctgtttcg
     2761 cttttggcag attatttggc gtgacaagcg tccgtctgtt ctccggtgcg ttcgggtcac
     2821 gcagcccgta atgatgatta accagcgtct gccaggcatt tatcctcggc ctgtccgcgc
     2881 ggtcgtagta cggctggagg cgcttaccgc tctgtagctc catgttcggg atgacaaaat
     2941 tcagttcgag ccgcccctta tcctggtgtt ccacccagag aatgctgtac tggtcttttt
     3001 cgagaccggg cataagaaca cgctcaaagc tcgtcatcac tctttcgcgt tcacccggcg
     3061 gtaactcctt ctccgcgaac gacagaacgc ctgaagtgta tttcttcgag aatggcgtgg
     3121 aatcaatgag ttcccgcact tcttccgggt taccccggag caccgttgcg ccttcgcggt
     3181 tacgctcccg ccccagcagg taatcgaccg ggccacttcc accgcctttc cccctggcat
     3241 gaaatttaac tatcatcccg taccccctgt tccctgacag cctgccgcaa ctggcgcaat
     3301 tcaccctcga tggccatcag tgcggccacc acatgaaccc ggtcaatcga agaccactgg
     3361 ccgctgttca cc
//
