LOCUS       NZ_CP051376             3829 bp    DNA     circular CON 15-MAY-2024
DEFINITION  Salmonella enterica subsp. enterica serovar Typhimurium strain CVM
            24362 plasmid p24362-3, complete sequence.
ACCESSION   NZ_CP051376
VERSION     NZ_CP051376.1
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 3829)
  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 3829)
  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
            CP051376.1.
            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..3829
                     /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="p24362-3"
                     /geo_loc_name="USA:MO"
                     /collection_date="2002"
                     /collected_by="MO State Veterinary Diagnostic Lab"
     gene            complement(join(2061..3829,1..136))
                     /locus_tag="HFS07_RS00005"
                     /old_locus_tag="HFS07_00025"
     CDS             complement(join(2061..3829,1..136))
                     /locus_tag="HFS07_RS00005"
                     /old_locus_tag="HFS07_00025"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_003839290.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="methyl-accepting chemotaxis protein"
                     /protein_id="WP_052895204.1"
                     /translation="MSWAYRISMQMKLFIALFPLLLALVWFAGSGIVSRINTEQQMNTI
                     GQLTTLARSAGDVVHQLQSERGMSAGFIGARGQKFRDDLAAQRQLTDKVLATFKRLLTD
                     TNKDLLQGNIAAPLKTFNESIQFLDSTRTAISELTIDSPKASQFYTQTISDVLKFVGGM
                     GHLSTSGSMVNELAAYYSLLNLKEQAGVERALLSNIFSMDRFDDGQFSMFSDVVGQQDA
                     WLTAARSFSTPVQAAELDKSLQSAEATRALELRETAFNKAAEGGFGVNPTDWFNLQTQR
                     IETLQKVENRAVDALQEHAALLAHNARVDWQSFLVISLVALLIAIAFAVMVARSIQQQL
                     NGTLKTIAEMDGDLTRRLDVPGSDELSALNRAYNQAIENIQHIVQEIKSGAVVLRSASS
                     DIAAGNQDLAQRTDEQAASIVETAASMEQISTAITQTADNASEAERLIHSMERDVLEAN
                     RVSNEASQSMAEIRSSSEQISQIVASIDEISFQTNLLALNAAVEAARAGELGKGFAVVA
                     TEVRNLSQRCAREASQIRELINQNMDKIGEGVARVTASGTALKAAAENTGRMKQYVSDI
                     ARAANEQSLGVSQVHQALNQLEQVTQQNAALVSQAASASQMLDGQSEAMSTLVDRFIV"
                     /name="methyl-accepting chemotaxis protein"
     gene            complement(442..591)
                     /locus_tag="HFS07_RS25845"
                     /old_locus_tag="HFS07_00005"
     CDS             complement(442..591)
                     /locus_tag="HFS07_RS25845"
                     /old_locus_tag="HFS07_00005"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001333247.1"
                     /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_077464408.1"
                     /translation="MHEPPVQSDCCAFSGNYRLESNPERHEKSPLAAATGKQDVREMYR
                     EFLK"
                     /name="replication initiation protein"
     gene            1269..1535
                     /locus_tag="HFS07_RS00010"
                     /old_locus_tag="HFS07_00015"
     CDS             1269..1535
                     /locus_tag="HFS07_RS00010"
                     /old_locus_tag="HFS07_00015"
                     /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_213069224.1"
                     /translation="MKRSQLTLIDGCFMFGFSPGELMNLCPDERLLFVRMISAMLRRSG
                     GDAGAVMFEAYRHIVSDTNQARRSCMLDLLESVRHDYVHGGYT"
                     /name="hypothetical protein"
     gene            complement(1583..1771)
                     /locus_tag="HFS07_RS00015"
                     /old_locus_tag="HFS07_00020"
     CDS             complement(1583..1771)
                     /locus_tag="HFS07_RS00015"
                     /old_locus_tag="HFS07_00020"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000165998.1"
                     /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_000165998.1"
                     /translation="MTKQESAALNMAKFIRAQSLLLLEKLDVLDLDDEAADCERMHEQA
                     EALYQKLSARFGIQDGE"
                     /name="Rop family plasmid primer RNA-binding protein"
     Typing          953..1125
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="91.379"
                     /coverage="100.0"
                     /evalue="9.47e-61"
     Typing          complement(433..1028)
                     /name="rep_cluster_2335"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="91.045"
                     /coverage="99.0"
                     /evalue="0.0"
ORIGIN
        1 caatggtgtt catctgctgt tcggtattga tacggctgac aatacccgaa ccggcgaacc
       61 agaccaaggc aagcagtagc gggaataatg caataaacaa cttcatttgc attgaaatac
      121 gataagccca tgacatatcg atactttcct tactttcttg agggatcgca ggagtatcgg
      181 tagatacatg cataaacttt atagtttatt gttgggggaa cgggcaccac attcggcagt
      241 ggcgctggta gcaatccata aaggatcttc ttgagatcct ttgacgatcg tcgtaatctc
      301 ttgctctgta aacgaaaaaa ccacccttgc aggtggtttt tcgaaggtta gataatcctg
      361 gcagattctc taaccgtggt aacagtcttg tgcgagacat gtcaccaaat ttgtccttct
      421 agtgtagcct cagtcaggcc actacttcaa gaactctcga tacatctctc gcacatcctg
      481 tttaccagtg gccgctgcca gtggcgattt ttcgtgtctt tccgggttgg actcaagacg
      541 atagttaccg gaaaaggcgc agcagtcgga ctgaacgggg ggttcgtgca tacagtccag
      601 cttggagcga actgccttcc cggaactgag tgtcaggcgt ggaatgagat aaacgcggcc
      661 ataacagcgg aatgacaccg gtaaaccgaa aggcaggaac aggagagcgc acgagggagc
      721 taccaggggg aaacgcctgg gatctttata gtcctgtcgg gtttcgccgc cactgatttg
      781 agcgtcagat ttcgtgatgc ttgtcagggg gcggagccta tggaaaaacg gcttcgccgc
      841 ggccttaccg tttccctgtt aagtttcttc ctggcatctc ccaggaaatt tccgccccat
      901 tcgtaatccc gcaccgctcg ccgcagccga acgaccgagc gcagcgagtc agtgagcgag
      961 gaagcggaat atctcctgtc tcatatattc cgcttacgct ctgctgctgc attttcctcc
     1021 tgccacatga agcacttcac tgattcccgc acccgtgcct acataataag ccagtataca
     1081 ctccgctagc gctacgtgac tggttcaggg ctgcgccccg acacccgcta aaagcactga
     1141 cgcgcctgcg gcttgcccaa ccccgcgccg tccgggaaag aatttcccga tcgacccgac
     1201 gtttctgttt acctgtgatg ttaacgtttg gatctttttc ccgggtttac ctattttaat
     1261 gaagcgtaat gaagcgttca cagctgacgt taatagatgg gtgcttcatg tttggttttt
     1321 caccaggaga acttatgaac ctttgccccg atgaacgtct gctctttgtg cggatgattt
     1381 ccgctatgct tcgccgttcg ggcggtgatg cgggtgctgt tatgtttgag gcgtatcgcc
     1441 atattgtgtc cgataccaat caagctcgtc gttcctgcat gctcgacctg ctcgaaagcg
     1501 tcaggcatga ctatgtacac ggtggatata catagttgcc ctggatacgc ttttcgtcta
     1561 agtgagcgtt cttttcgtct ctttattcgc cgtcctgtat accgaagcgt gcgctcagct
     1621 tctgataaag cgcttctgcc tgttcgtgca ttcgctcaca gtcggctgcc tcgtcatcaa
     1681 gatcgagcac gtcgagtttt tcgagcagca gcagcgactg cgcccggata aattttgcca
     1741 tgttcagtgc ggctgattcc tgttttgtca tacggctttt tcccggtttt atggtgatcg
     1801 cagactgaaa tcttacttca ttcacttgag tgcatagcca tgcaggtacg cagaaatcat
     1861 caggggcgtt ttttctcgat atgggcacag aaaggtgtat gtttcaggtc ggagtcctca
     1921 gaaacgctct cagagcctct caggcggtgc acgcaacaga tgttatggta aatcctagtt
     1981 atttgcaggc ataaaaaagc cgccttttag gcggtttttt ctgattgtaa gttatcaaga
     2041 ccggatgctg aacggcagta tcagacaata aagcgatcga ccagcgtgga catcgcttca
     2101 gactggccgt ccagcatctg gctggcgctc gccgcctgag agaccagcgc tgcgttttgc
     2161 tgagtgacct gctccagctg attcagtgcc tgatgcacct gcgacacgcc aagcgactgc
     2221 tcattcgccg cacgggcaat atcgctcacg tactgtttca tccgcccggt attttccgcc
     2281 gctgctttca gcgcggtgcc ggacgcggtg actcgtgcta ccccttcgcc aatcttatcc
     2341 atattctggt taatcagctc acggatctga ctggcctctc gtgcacagcg ctgggaaagg
     2401 ttacgcacct ccgtcgccac taccgcaaag cctttgccaa gctcaccggc acgtgccgct
     2461 tcaacggcgg cgttaagcgc cagcaagttg gtctggaaag aaatctcatc aattgacgca
     2521 acaatctggg aaatctgctc gctggaagaa cgaatttccg ccatgctctg actggcctcg
     2581 ttagagacgc gattagcttc cagtacgtcc cgctccatcg aatgtatcag acgctccgcc
     2641 tcgctggcgt tatcggcggt ctgggtgatc gcagtagaaa tctgctccat gctggcggcc
     2701 gtttccacaa tcgatgccgc ctgttcatcc gtacgctggg ccagatcctg attaccggca
     2761 gcgatatcac tactggcgct acgcaacacc accgcaccgg acttaatttc ttgcacgata
     2821 tgctgaatat tctcaatcgc ttggttatag gcacggttca gggctgagag ctcgtcgctg
     2881 ccggggacgt caagacgacg tgtcaggtcg ccgtccatct ctgcgatggt tttcagcgta
     2941 ccgttcagtt gctgctggat actgcgtgcc accatcaccg caaaggcgat agcaatcagt
     3001 agggcaacca ggctgattac caggaaggac tgccagtcga cacgggcatt gtgggcaagc
     3061 agcgcagcat gttcctgcaa ggcatccacc gcgcgatttt ccaccttttg cagcgtttca
     3121 atacgctggg tctgaaggtt aaaccagtca gtcgggttga ctccaaatcc gccttcggcg
     3181 gctttattaa aagccgtctc ccgcagttca agagcacgag ttgcttcagc ggactgaaga
     3241 gatttgtcca gctcagccgc ctgcacaggt gtgctaaagc tgcgagctgc cgtcagccag
     3301 gcatcctgct ggcctaccac atcgctaaac atgctgaact ggccgtcgtc aaagcgatcc
     3361 atcgagaaga tattggacag cagcgcacgt tctacaccag cctgctcctt caaattcaag
     3421 agactataat aagccgccag ttcgttcacc atcgagcctg aggtgcttaa atgccccatc
     3481 ccgccgacaa acttcagcac gtcagagatg gtttgggtat agaactgact cgcttttggt
     3541 gaatcgatag ttaattcgct gatggcggta cgggttgagt cgagaaactg aatactttca
     3601 ttaaacgttt tcaggggggc ggcaatattt ccctggagta aatccttatt cgtatcggtc
     3661 agcaaccgct taaatgttgc cagcaccttg tcggttaact gccgctgggc agctaagtca
     3721 tcgcgaaact tttggccgcg cgcgccgata aatccagcgc tcattccacg ttcgctctgg
     3781 agttgatgca ccacatcacc cgcgctgcgg gcgagcgtgg tgagctgtc
//
