LOCUS       NZ_CP051378             3188 bp    DNA     circular CON 15-MAY-2024
DEFINITION  Salmonella enterica subsp. enterica serovar Typhimurium strain CVM
            24362 plasmid p24362-4, complete sequence.
ACCESSION   NZ_CP051378
VERSION     NZ_CP051378.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN14504713
            Assembly: GCF_016454365.1
KEYWORDS    RefSeq.
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 3188)
  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 3188)
  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                   :: 929x
            Sequencing Technology             :: PacBio Sequel
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_016454365.1-RS_2024_05_15
            Annotation Date                   :: 05/15/2024 03:11:57
            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)                     :: 5,134
            CDSs (total)                      :: 5,013
            Genes (coding)                    :: 4,874
            CDSs (with protein)               :: 4,874
            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)              :: 139
            CDSs (without protein)            :: 139
            Pseudo Genes (ambiguous residues) :: 0 of 139
            Pseudo Genes (frameshifted)       :: 55 of 139
            Pseudo Genes (incomplete)         :: 91 of 139
            Pseudo Genes (internal stop)      :: 28 of 139
            Pseudo Genes (multiple problems)  :: 31 of 139
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP051378.1.
            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..3188
                     /organism="Salmonella enterica subsp. enterica serovar
                     Typhimurium"
                     /mol_type="genomic DNA"
                     /strain="CVM 24362"
                     /serovar="Typhimurium"
                     /isolation_source="swine"
                     /sub_species="enterica"
                     /db_xref="taxon:90371"
                     /plasmid="p24362-4"
                     /geo_loc_name="USA:MO"
                     /collection_date="2002"
                     /collected_by="MO State Veterinary Diagnostic Lab"
     gene            complement(join(2802..3188,1..201))
                     /locus_tag="HFS07_RS00585"
                     /old_locus_tag="HFS07_00600"
     CDS             complement(join(2802..3188,1..201))
                     /locus_tag="HFS07_RS00585"
                     /old_locus_tag="HFS07_00600"
                     /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_019842775.1"
                     /translation="MIRKIFFASAIVVAISGCTAMDKLAGMGVVSQQTSTFDNSTVIEV
                     SPNSLYDPNSTWGTPLQLGAIWSSAYPEEAGLILSYNSNVSSGNAAYLGLTGIDINVDG
                     KISSYKAQQQTNLSSSSYNSVSKTIYTSSKNTIVIPYKLLESMVSAKNCRIRIHTSQGN
                     QDIDFSAQSIPGGKATAIVSIKEFLAKVERFK"
                     /name="hypothetical protein"
     gene            complement(1282..1476)
                     /locus_tag="HFS07_RS00590"
                     /old_locus_tag="HFS07_00610"
     CDS             complement(1282..1476)
                     /locus_tag="HFS07_RS00590"
                     /old_locus_tag="HFS07_00610"
                     /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_001041633.1"
                     /translation="MNKQQQTALNMARFIKSQSLTLLEKLDALDADEQAAMCERLHELA
                     EELQNSIQVRFETESETGT"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            complement(2295..2792)
                     /locus_tag="HFS07_RS00595"
                     /old_locus_tag="HFS07_00615"
     CDS             complement(2295..2792)
                     /locus_tag="HFS07_RS00595"
                     /old_locus_tag="HFS07_00615"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_004793705.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_019842774.1"
                     /translation="MKKQILALALLSLPLIGMAKDSGYGNTEWGMTPNQVVAAQKGKAH
                     LIPPQKYKDQWGKVSIEDVNIGSGIYTVTFIFDASDKLVQTNVASKEKKNEGIANNQFN
                     TLNQLLTQKYGKPQFVSDEKATWKTDTTTIELNKMIISGIMAQTLVRYIPNKTVISDTS
                     NL"
                     /name="hypothetical protein"
     Typing          1127..1209
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="3.79e-36"
     Typing          1513..1611
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="6.22e-45"
     Typing          1736..1992
                     /name="MOBF"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="96.139"
                     /coverage="89.0"
                     /evalue="1.57e-115"
     Typing          complement(557..1114)
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="94.286"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 ccatatcgcg cccaactgaa gtggtgttcc ccaagtgctg ttaggatcgt atagcgaatt
       61 tggagatacc tctatgacag tcgagttatc aaaggttgat gtttgctgag aaacaacacc
      121 cattcccgcc aatttatcca ttgctgtaca gccagagatc gctactacga tcgcagaagc
      181 aaaaaaaatc ttccttatca tatcgttatc ctattttttt ctttttaaca gagactgaaa
      241 aaacatcgta ttcccgaaac cattttgcac acgatattct tttttaaaag gattttgaaa
      301 ggatgcgggc agatcttctt gagatcctta agcgagagtc gtaatctctt aaccacgaaa
      361 cgaaaaaacc gccttggagg gcggtttttc gaaggttctc agagctacca actctttgaa
      421 ccgaggtaac tggcttggag gagcgcagtc accaaaactt gtcctttcag tttagcctga
      481 accggcgcat aacttcaaga ctaactcctc taaatcagtt accagtggct gctgccagtg
      541 gcgctttgtc gtgtctttcc gggttggact caagatgata gttaccggat aaggcgcagc
      601 ggtcgggctg aacggggggt tcgtgcacac agcccagctt ggagcgaacg acctacactg
      661 aaccgagata cctacagcgt gagctatgag aaagcgccac gcttcccgaa gggagaaagg
      721 cggacaggta tccggtaagc ggcagggtcg gaacaggaga gcgcacgagg gagccaccag
      781 ggggaaacgt ctggtatctt taagtcctgt cgggtttcgc cacctctgac ttgagcgtcg
      841 atttctgtga tgctcgtcag gggggcggag cctatggaaa aacgcctgcg gcgcggcctt
      901 cttcctgttc ttggtctttt gctcacatgt tctttccggc cttatcccct gattctgtgg
      961 ataaccgtgc tgccgttttt gtgtaagtca gtaccgctcg ccgcagccga acgaccgagc
     1021 gtagcgagtc agtgagcgag gaagcggaaa agcgcctgga cgcgcatttt ctccttacgc
     1081 atctgtgcgg aatttcacac ccgccatggg gcacttttca tacaatctgc actgatgccg
     1141 catagttaag ccagtataca ctccgctatc gctacgtgac tgggtcaggg cttcgccccg
     1201 acacccgctg acgcgccctg gcgggcttgt ctgctgccga aaacgctcgc ggacaagccg
     1261 tgagcgcctc cgtcagcttc gttatgttcc tgtttcactt tcggtctcaa agcgaacctg
     1321 gatgctgttc tggagttctt ccgcgagttc gtgcagtcgt tcgcacatgg ccgcctgttc
     1381 gtcggcatcc agagcatcca gtttttcaag cagtgtcagg ctctggcttt tgataaatcg
     1441 cgccatattc agcgcagttt gttgctgttt gttcaccttc cgttgttctc cgtcagtacc
     1501 gggtgtcggg tggaccctga ccaggtggta attgtaagac gttgcgggcg acggtattac
     1561 aattgcacat cctgtcctgt ttttttagga cgtatcatgg cacagcatat caactgataa
     1621 ataatccctg tgcagtgcag ccgctgttgc ataaaatttc gctctgcgtc gagtgtttct
     1681 taatcaataa ttccgctgat actccggaaa aacgcgagtc tgttctcatg cctgaaatgc
     1741 ccacacccca cgcaaaaaca attttttgct gatttttctt tataaataga gagttatgac
     1801 aaattagttc ttcttgctct ctttgtgata tttaaaaaag cggtgtcggc gcggtgttgt
     1861 agctgcgcca acaccgcttt ttaggggtgg tactgactat tttcataaaa aacatcattt
     1921 tatattaggg gtgctgctag cggcgcggtg tgtttttttt acaggacgcc cctgggggcg
     1981 ctgctagggg tgtctgttca gatatgtagc aatgagtcag ggattcacga actgaaaatg
     2041 tccgaaaatg tgtctcatgg gcaccgtatg cgcccaaacc gatcgccatt cactttcatg
     2101 catagctatg cagtgagctg aaagcgatcc tgacgcattt ttccggtttt cgcttggtaa
     2161 aacatctctt tttgcggtgt tcgcggcaga atcgcgttca gcgcgtttta gcggtgcgcg
     2221 taatgcgacg ttatgttcaa tctcccacct caggtataga aacaggagag agacactcag
     2281 tgaggcgaca attattacag gttagacgtg tcagaaatca cggtcttatt aggaatgtag
     2341 cgaactagtg tttgagccat aattccggag atgatcatct tatttagctc aattgttgta
     2401 gtatcagttt tccatgttgc tttttcatca cttacaaact gtggtttgcc atacttttgt
     2461 gtaagtaatt gatttaatgt gttaaattgg ttgtttgcta ttccctcgtt tttcttttct
     2521 ttgctggcaa cgttggtttg gactaattta tctgatgcgt caaaaataaa cgtaactgta
     2581 tatattccac tacctatatt cacgtcttca atgctcactt ttccccattg gtctttatac
     2641 ttttgagggg ggattaaatg agcttttcct ttctgggctg caacgacctg atttggggtc
     2701 ataccccatt cggtattgcc ataaccagag tcctttgcca tgccaatcag tggcaatgat
     2761 agcaaagcga gtgcaagaat ctgcttcttc atgacgcctc cttatttaaa acgttcgact
     2821 ttggccaaga actctttaat ggaaacgatc gctgtcgctt tacctccggg gatactttgt
     2881 gctgagaagt cgatgtcttg atttccttgg cttgtgtgta tgcgaatgcg gcagttttta
     2941 gctgatacca tgctctccag caatttatac gggataacga tagtattctt gctagaggta
     3001 tagatcgtct tggatacgga gttatatgag ctgctgctta gattagtttg ttgctgtgct
     3061 ttatagctgg atattttacc atcaacattt atatcaatcc ccgtcaaacc taagtatgcg
     3121 gcatttccgc tagatacatt cgagttgtag gaaaggatta gtccagcctc ttctggatag
     3181 gcactaga
//
