LOCUS       NZ_CP051399             4198 bp    DNA     circular CON 18-MAY-2024
DEFINITION  Salmonella enterica subsp. enterica serovar Uganda strain CVM 22436
            plasmid p22436-2, complete sequence.
ACCESSION   NZ_CP051399
VERSION     NZ_CP051399.1
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 4198)
  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 4198)
  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
            CP051399.1.
            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..4198
                     /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="p22436-2"
                     /geo_loc_name="USA:AZ"
                     /collection_date="2003"
                     /collected_by="AZ State Veterinary Diagnostic Lab"
     gene            complement(join(3532..4198,1..473))
                     /gene="dcm"
                     /locus_tag="HFQ88_RS23545"
                     /old_locus_tag="HFQ88_23545"
     CDS             complement(join(3532..4198,1..473))
                     /gene="dcm"
                     /locus_tag="HFQ88_RS23545"
                     /old_locus_tag="HFQ88_23545"
                     /EC_number="2.1.1.37"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000131511.1"
                     /GO_function="GO:0003886 - DNA
                     (cytosine-5-)-methyltransferase activity [Evidence IEA]"
                     /GO_process="GO:0006304 - DNA modification [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="DNA (cytosine-5-)-methyltransferase"
                     /protein_id="WP_000131512.1"
                     /translation="MTDNIAATIKGKRERLHMTQKEFADALGLSKYGDRTIRRWERGET
                     KPTGAELKAVMDFPDTPPYPNNENGRYRMIDLFAGIGGTRLGFHQTNAVNVVFSSEWDK
                     FAQKTYHANYGDFPDGDITKIDEKDIPDHEILVGGFPCVAFSQAGLKKGFNDTRGTLFF
                     DIARIIKEKKPHAFLLENVKNLLGHDKGRTFSIIKNTLEELNYTVYYNIFAAKDFGVPQ
                     NRERIYIVGFNKEKVRNHEHFTFPTPLKTKTRVGDILEKSVDNKYTLSDALWNGHQRRK
                     LVNAAAGKGFGYGLFNENSPYTNTISARYYKDGSEILIEQKGSNPRKITPREASRLQGF
                     PSDFIIPVSDTQAYKQFGNSVAVPVINAIAEKIISTLDS"
                     /name="dcm"
     gene            544..1500
                     /locus_tag="HFQ88_RS23550"
                     /old_locus_tag="HFQ88_23550"
     CDS             544..1500
                     /locus_tag="HFQ88_RS23550"
                     /old_locus_tag="HFQ88_23550"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_014640333.1"
                     /GO_function="GO:0003677 - DNA binding [Evidence IEA];
                     GO:0009036 - type II site-specific deoxyribonuclease
                     activity [Evidence IEA]"
                     /GO_process="GO:0009307 - DNA restriction-modification
                     system [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="type II restriction endonuclease"
                     /protein_id="WP_223152166.1"
                     /translation="MKKLSSRYKRLFFMQRLSPGEFKTLISKERKSHFITPFALVHKTF
                     CDLGYDQKNSDYFLNNPSEYIIAMRKNCWKEFEPFEKEFTTRMLSYLIDEERIKDMSPY
                     DAIRDFTMEYPTHIYDLALSNTQSRRSRAGKEFESILELLMMGAGIPVDVQGAIGKSFF
                     QKNQIGKLVDLVMPGVVQYTSNKRNTMLISAKTTLRERWQEVPEEVNRTGIREMYLATL
                     DDSFSEETINILYEANVVVVTTIENKNFKYKNNNRVLTFEDMLQSAMELSRKWNNVSYT
                     DSEKEEIQQSILKQIEKYSDFPYVVNYYRNRLSALVD"
                     /name="type II restriction endonuclease"
     gene            complement(1692..1853)
                     /locus_tag="HFQ88_RS25090"
     CDS             complement(1692..1853)
                     /locus_tag="HFQ88_RS25090"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001354639.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="replication initiation protein"
                     /protein_id="WP_071596883.1"
                     /translation="MHEPPVQPDRCALSGNYRLESNPVRHALTPLAAATGNRISRARFI
                     QMLTEFLK"
                     /name="replication initiation protein"
     gene            complement(2518..2712)
                     /locus_tag="HFQ88_RS23555"
                     /old_locus_tag="HFQ88_23560"
     CDS             complement(2518..2712)
                     /locus_tag="HFQ88_RS23555"
                     /old_locus_tag="HFQ88_23560"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001041627.1"
                     /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_001041631.1"
                     /translation="MNKQQQTALNMARFIKSQSLTLLEKLDALDADEQAAMCERLHELA
                     EELQNSIQIRFEAESETGT"
                     /name="Rop family plasmid primer RNA-binding protein"
     Typing          2351..2435
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="3.03e-37"
     Typing          2749..2847
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="98.0"
                     /coverage="100.0"
                     /evalue="1.35e-41"
     Typing          2972..3227
                     /name="MOBF"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="96.899"
                     /coverage="89.0"
                     /evalue="2.61e-118"
     Typing          complement(1782..2327)
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="93.989"
                     /coverage="99.0"
                     /evalue="0.0"
ORIGIN
        1 cttgtatcat taaatccttt tttgagccct gcttgagaga atgctacgca aggaaaccca
       61 ccgacaagaa tttcatgatc aggaatatct ttttcatcga tttttgttat gtccccatca
      121 gggaaatcac cataatttgc atgatatgtc ttttgagcaa acttatccca ttcgctggaa
      181 aaaacaacat ttacagcgtt agtttgatga aatccaagtc tggttccacc gattccagca
      241 aataaatcga tcatgcgata tctgccattc tcgttgtttg ggtaaggtgg tgtgtctgga
      301 aagtccataa ctgcttttag ttccgcccca gtaggttttg tttccccgcg ctcccatctt
      361 cttatggttc tgtctccata ttttgaaaga ccaagggcgt ctgcaaactc tttttgagtc
      421 atatgaagtc tttctctttt tcctttgatt gttgctgcga tattatcagt catgcatgtc
      481 taccagaatt aagtgttggt tttaggacaa tttgtcctgt tttgattcca attatgaacg
      541 tgcatgaaaa aactttcaag tagatataaa aggttatttt ttatgcaaag attgagtcct
      601 ggtgaattta aaactctaat ttctaaagag agaaagtcgc attttattac gccatttgct
      661 ttggttcata aaacattttg tgatttaggg tatgatcaaa aaaatagtga ttattttttg
      721 aataatccaa gtgaatatat aattgcaatg aggaaaaact gttggaaaga atttgaacca
      781 tttgaaaaag aattcacaac aagaatgtta tcatatctta ttgatgaaga aagaataaaa
      841 gatatgagtc cttatgatgc cattcgtgat tttacgatgg aataccctac acacatatat
      901 gatttggcac tgtctaacac tcaatccaga cgtagcaggg caggaaaaga gtttgagtct
      961 attcttgagc tattgatgat gggggcagga attcctgttg atgtgcaggg ggctattggg
     1021 aagtcatttt ttcaaaaaaa ccaaataggt aaacttgtag atcttgttat gccaggtgta
     1081 gtccagtaca catctaacaa aagaaataca atgttgattt ccgctaaaac aacgctgagg
     1141 gagcgatggc aagaagtacc tgaagaggtt aatagaacag gaattagaga aatgtatcta
     1201 gctacactag atgattcttt tagcgaggag acaataaata tattatacga ggctaatgtg
     1261 gtcgttgtaa cgacgataga aaataaaaat ttcaaatata aaaataataa tagggtgcta
     1321 acctttgaag atatgctaca gtcagcaatg gaattatcaa gaaagtggaa taatgtaagt
     1381 tacacagact ctgaaaaaga ggaaattcaa cagtcaatat taaaacaaat agaaaaatat
     1441 agtgatttcc cttatgttgt taattattat agaaataggc ttagtgctct tgttgactaa
     1501 aaaactaaaa ggatctcttg agatcctttt tttctgcgcg taatcttgga cctgtaaacg
     1561 aaaaaaccac cctggcaggt ggttttttcg aaggttagct aatcctggca gattatctaa
     1621 ccgaggtaat ctggcttcag cagagcacag ataccaaata ctgtccttcc agtgtagccg
     1681 tagttaggcc atcacttcaa gaactctgta agcatctgga taaatctcgc tctgctaatc
     1741 cggttaccag tggctgctgc cagtggcgtt aaggcgtgtc ttactgggtt ggactcaaga
     1801 cgatagttac cggataaggc gcagcggtcg ggctgaacgg ggggttcgtg cacacagccc
     1861 agcttggagc gaacgaccta caccgggccg agataccaac agcgtgagct atgagaaagc
     1921 gccacgcttc ccgaagggag aaaggcggac aggtatccgg taagcggcag ggtcggaaca
     1981 ggagagcgca cgagggagct tccaggggga aacgcctggt atctttatag tcctgtcggg
     2041 tttcgccacc cctgacttga gcgtcgattt ttgtgatgct cgtcaggggg gcggagccta
     2101 tggaaaaacg ccagcggcgc ggccttttgt tgccctttgc ctttttacgc acatgttctt
     2161 tccggcctta tcccctgatt ctgtggataa ccgtatttcc gcctttgagt gagccggcac
     2221 cgcttgccgc agccgaacga ccgagcgcag cgagtcagtg agcgaggaag cggaagagcg
     2281 cctgatgcgg tatgttctcc ttacgcatct gtgcggcatt tcacacccgg catggcgtgc
     2341 ttttcataca atccgcactg atgccgcata gttaagccag tatacactcc gctatcgcta
     2401 cgtgactggg tcatggctgc gccccgacac ccgctaaaac cccctgacgc gccctgacgg
     2461 gcttgtctgc tgacgaaaac gcccacggga aagccgtgac cgcctccgtc agcttcgtta
     2521 tgttcctgtt tcactttcgg cctcaaagcg aatctggatg ctgttctgga gttcttctgc
     2581 gagttcgtgc agtcgttcgc acatggccgc ctgttcgtcg gcatccagag catccagttt
     2641 ttcaagcagt gtcaggctct ggcttttgat aaatcgcgcc atattcagcg cagtttgttg
     2701 ttgtttgttc accttccgtt gttctccgtc agttccgggt gtcgggggga ccctgagcag
     2761 gtggtaattg taagacgttg cgggcgacgg tattacaatt gcacatcctg tcctgtttct
     2821 ttaggacgta tcatggcaca gcatatcaac tgataaataa tccctgtgca gtgcagccgc
     2881 tgttgcataa aatttcgctc tgcgtcgagt gtttcttaat caataattcc gctgatactc
     2941 cggaaaaacg cgagtctgtt ctcatgcctg aaatgcccac accccacgca aaaacaagtt
     3001 tttgctgatt tttctttata aatagagagt tatgacaaat tagttcttct tgctctcttt
     3061 gtgatattta aaaaagcggt gtcggcgcgg tgttgtagct gcgccaacac cgctttttag
     3121 gggtggtact gactattttc ataaaaaaca tcatcttata ttaggggtgc tgctagcggc
     3181 gcggtgtgtt tttttacagg acacccctgg gggcgctgct aggggtgtct gttcagatat
     3241 gtagcaatga gtcagggatt cacgaactga aaatgtccga aaatgtgtct catgggcact
     3301 gtatgcgccc aaaccgatcg tcattcactt tcatgcatag ctatgcagtg agctgaaagc
     3361 gatcctgacg catttttccg gtttaccccg gggagaacat ctctttttgc ggtgttcgcg
     3421 gcagaatcgc tttcagcgcg ttttagcggt gcgcgcaatg cgacgttatg gtaaatccat
     3481 atgggggggg ggaattggat tctgggccgc attgtgtcct tatgacttag tttatgaatc
     3541 taaggtcgat atgatttttt ctgctattgc attgataaca gggactgcga ctgaattccc
     3601 aaattgctta taagcctgtg tatccgatac agggataata aaatcactag gaaacccttg
     3661 aagtcttgac gcttcccgcg gagttatttt tcttgggtta cttccttttt gctctattaa
     3721 tatttcgcta ccatctttat agtacctcgc acttatggta ttagtatatg ggctattttc
     3781 attaaataaa ccatacccaa agcctttacc ggctgctgca tttacaagtt tcctgcgttg
     3841 gtgtccattc cagagcgcat ctgatagcgt atatttattg tctacgctct tttcaagaat
     3901 atctccaact cttgtttttg tttttaatgg ggttggaaaa gtaaaatgtt catgatttct
     3961 tactttttct ttattaaagc ctacaatgta tatgcgttct ctattttgtg gaacaccaaa
     4021 gtcttttgca gcgaagatat tgtaatacac agtgtaattc aattcttcaa gtgtgttttt
     4081 tattattgaa aaagttctac ctttatcatg tcctagcaag ttttttacat tttcaagtaa
     4141 aaaagcatga ggtttttttt cctttattat ccttgctata tcaaaaaaca aagttcct
//
