LOCUS       NZ_CP051362             3848 bp    DNA     circular CON 15-MAY-2024
DEFINITION  Salmonella enterica subsp. enterica serovar Typhimurium strain CVM
            28321-b plasmid p28321b-1, complete sequence.
ACCESSION   NZ_CP051362
VERSION     NZ_CP051362.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN14504768
            Assembly: GCF_016952595.1
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 3848)
  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 3848)
  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                   :: 508x
            Sequencing Technology             :: PacBio Sequel
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_016952595.1-RS_2024_05_15
            Annotation Date                   :: 05/15/2024 03:18:03
            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)                     :: 4,910
            CDSs (total)                      :: 4,789
            Genes (coding)                    :: 4,655
            CDSs (with protein)               :: 4,655
            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)              :: 134
            CDSs (without protein)            :: 134
            Pseudo Genes (ambiguous residues) :: 0 of 134
            Pseudo Genes (frameshifted)       :: 54 of 134
            Pseudo Genes (incomplete)         :: 88 of 134
            Pseudo Genes (internal stop)      :: 27 of 134
            Pseudo Genes (multiple problems)  :: 31 of 134
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP051362.1.
            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..3848
                     /organism="Salmonella enterica subsp. enterica serovar
                     Typhimurium"
                     /mol_type="genomic DNA"
                     /strain="CVM 28321-b"
                     /serovar="Typhimurium"
                     /isolation_source="swine"
                     /sub_species="enterica"
                     /db_xref="taxon:90371"
                     /plasmid="p28321b-1"
                     /geo_loc_name="USA:MO"
                     /collection_date="2002"
                     /collected_by="MO State Veterinary Diagnostic Lab"
     gene            join(3598..3848,1..1672)
                     /locus_tag="HFS62_RS00005"
                     /old_locus_tag="HFS62_00005"
     CDS             join(3598..3848,1..1672)
                     /locus_tag="HFS62_RS00005"
                     /old_locus_tag="HFS62_00005"
                     /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_205532515.1"
                     /translation="MSWAYRISMQMKLFIALFPLLLALVWFAGSGIVSRINTEQQMNTI
                     GQLTTLARSAGDVVHQLQSERGMSAGFIGARGQKFRDDLKFRDDLAAQRQLTDKVLATF
                     KRLLTDTNKDLLQGNIAAPLKTFNESIQFLDSTRTAISELTIDSPKASQFYTQTISDVL
                     KFVGGMGHLSTSGSMVNELAAYYSLLNLKEQAGVERALLSNIFSMDRFDDGQFSMFSDV
                     VGQQDAWLTAARSFSTPVQAAELDKSLQSAEATRALELRETAFNKAAEGGFGVNPTDWF
                     NLQTQRIETLQKVENRAVDALQEHAALLAHNARVDWQSFLVISLVALLIAIAFAVMVAR
                     SIQQQLNGTLKTIAEMDGDLTRRLDVPGSDELSALNRAYNQAIENIQHIVQEIKSGAVV
                     LRSASSDIAAGNQDLAQRTDEQAASIVETAASMEQISTAITQTADNASEAERLIHSMER
                     DVLEANRVSNEASQSMAEIRSSSEQISQIVASIDEISFQTNLLALNAAVEAARAGELGK
                     GFAVVATEVRNLSQRCAREASQIRELINQNMDKIGEGVARVTASGTALKAAAENTGRMK
                     QYVSDIARAANEQSLGVSQVHQALNQLEQVTQQNAALVSQAASASQMLDGQSEAMSTLV
                     DRFIV"
                     /name="methyl-accepting chemotaxis protein"
     gene            1962..2150
                     /locus_tag="HFS62_RS00010"
                     /old_locus_tag="HFS62_00010"
     CDS             1962..2150
                     /locus_tag="HFS62_RS00010"
                     /old_locus_tag="HFS62_00010"
                     /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"
     gene            complement(2198..2464)
                     /locus_tag="HFS62_RS00015"
                     /old_locus_tag="HFS62_00015"
     CDS             complement(2198..2464)
                     /locus_tag="HFS62_RS00015"
                     /old_locus_tag="HFS62_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            3143..3292
                     /locus_tag="HFS62_RS24705"
     CDS             3143..3292
                     /locus_tag="HFS62_RS24705"
                     /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"
     Typing          complement(2609..2781)
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="91.379"
                     /coverage="100.0"
                     /evalue="9.47e-61"
     Typing          2706..3290
                     /name="rep_cluster_2335"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="91.709"
                     /coverage="97.0"
                     /evalue="0.0"
ORIGIN
        1 aaagtttcgc gatgacttag ctgcccagcg gcagttaacc gacaaggtgc tggcaacatt
       61 taagcggttg ctgaccgata cgaataagga tttactccag ggaaatattg ccgcccccct
      121 gaaaacgttt aatgaaagta ttcagtttct cgactcaacc cgtaccgcca tcagcgaatt
      181 aactatcgat tcaccaaaag cgagtcagtt ctatacccaa accatctctg acgtgctgaa
      241 gtttgtcggc gggatggggc atttaagcac ctcaggctcg atggtgaacg aactggcggc
      301 ttattatagt ctcttgaatt tgaaggagca ggctggtgta gaacgtgcgc tgctgtccaa
      361 tatcttctcg atggatcgct ttgacgacgg ccagttcagc atgtttagcg atgtggtagg
      421 ccagcaggat gcctggctga cggcagctcg cagctttagc acacctgtgc aggcggctga
      481 gctggacaaa tctcttcagt ccgctgaagc aactcgtgct cttgaactgc gggagacggc
      541 ttttaataaa gccgccgaag gcggatttgg agtcaacccg actgactggt ttaaccttca
      601 gacccagcgt attgaaacgc tgcaaaaggt ggaaaatcgc gcggtggatg ccttgcagga
      661 acatgctgcg ctgcttgccc acaatgcccg tgtcgactgg cagtccttcc tggtaatcag
      721 cctggttgcc ctactgattg ctatcgcctt tgcggtgatg gtggcacgca gtatccagca
      781 gcaactgaac ggtacgctga aaaccatcgc agagatggac ggcgacctga cacgtcgtct
      841 tgacgtcccc ggcagcgacg agctctcagc cctgaaccgt gcctataacc aagcgattga
      901 gaatattcag catatcgtgc aagaaattaa gtccggtgcg gtggtgttgc gtagcgccag
      961 tagtgatatc gctgccggta atcaggatct ggcccagcgt acggatgaac aggcggcatc
     1021 gattgtggaa acggccgcca gcatggagca gatttctact gcgatcaccc agaccgccga
     1081 taacgccagc gaggcggagc gtctgataca ttcgatggag cgggacgtac tggaagctaa
     1141 tcgcgtctct aacgaggcca gtcagagcat ggcggaaatt cgttcttcca gcgagcagat
     1201 ttcccagatt gttgcgtcaa ttgatgagat ttctttccag accaacttgc tggcgcttaa
     1261 cgccgccgtt gaagcggcac gtgccggtga gcttggcaaa ggctttgcgg tagtggcgac
     1321 ggaggtgcgt aacctttccc agcgctgtgc acgagaggcc agtcagatcc gtgagctgat
     1381 taaccagaat atggataaga ttggcgaagg ggtagcacga gtcaccgcgt ccggcaccgc
     1441 gctgaaagca gcggcggaaa ataccgggcg gatgaaacag tacgtgagcg atattgcccg
     1501 tgcggcgaat gagcagtcgc ttggcgtgtc gcaggtgcat caggcactga atcagctgga
     1561 gcaggtcact cagcaaaacg cagcgctggt ctctcaggcg gcgagcgcca gccagatgct
     1621 ggacggccag tctgaagcga tgtccacgct ggtcgatcgc tttattgtct gatactgccg
     1681 ttcagcatcc ggtcttgata acttacaatc agaaaaaacc gcctaaaagg cggctttttt
     1741 atgcctgcaa ataactagga tttaccataa catctgttgc gtgcaccgcc tgagaggctc
     1801 tgagagcgtt tctgaggact ccgacctgaa acatacacct ttctgtgccc atatcgagaa
     1861 aaaacgcccc tgatgatttc tgcgtacctg catggctatg cactcaagtg aatgaagtaa
     1921 gatttcagtc tgcgatcacc ataaaaccgg gaaaaagccg tatgacaaaa caggaatcag
     1981 ccgcactgaa catggcaaaa tttatccggg cgcagtcgct gctgctgctc gaaaaactcg
     2041 acgtgctcga tcttgatgac gaggcagccg actgtgagcg aatgcacgaa caggcagaag
     2101 cgctttatca gaagctgagc gcacgcttcg gtatacagga cggcgaataa agagacgaaa
     2161 agaacgctca cttagacgaa aagcgtatcc agggcaacta tgtatatcca ccgtgtacat
     2221 agtcatgcct gacgctttcg agcaggtcga gcatgcagga acgacgagct tgattggtat
     2281 cggacacaat atggcgatac gcctcaaaca taacagcacc cgcatcaccg cccgaacggc
     2341 gaagcatagc ggaaatcatc cgcacaaaga gcagacgttc atcggggcaa aggttcataa
     2401 gttctcctgg tgaaaaacca aacatgaagc acccatctat taacgtcagc tgtgaacgct
     2461 tcattacgct tcattaaaat aggtaaaccc gggaaaaaga tccaaacgtt aacatcacag
     2521 gtaaacagaa acgtcgggtc gatcgggaaa ttctttcccg gacggcgcgg ggttgggcaa
     2581 gccgcaggcg cgtcagtgct tttagcgggt gtcggggcgc agccctgaac cagtcacgta
     2641 gcgctagcgg agtgtatact ggcttattat gtaggcacgg gtgcgggaat cagtgaagtg
     2701 cttcatgtgg caggaggaaa atgcagcagc agagcgtaag cggaatatat gagacaggag
     2761 atattccgct tcctcgctca ctgactcgct gcgctcggtc gttcggctgc ggcgagcggt
     2821 gcgggattac gaatggggcg gaaatttcct gggagatgcc aggaagaaac ttaacaggga
     2881 aacggtaagg ccgcggcgaa gccgtttttc cataggctcc gcccccctga caagcatcac
     2941 gaaatctgac gctcaaatca gtggcggcga aacccgacag gactataaag atcccaggcg
     3001 tttccccctg gtagctccct cgtgcgctct cctgttcctg cctttcggtt taccggtgtc
     3061 attccgctgt tatggccgcg tttatctcat tccacgcctg acactcagtt ccgggaaggc
     3121 agttcgctcc aagctggact gtatgcacga accccccgtt cagtccgact gctgcgcctt
     3181 ttccggtaac tatcgtcttg agtccaaccc ggaaagacac gaaaaatcgc cactggcagc
     3241 ggccactggt aaacaggatg tgcgagagat gtatcgagag ttcttgaagt agtggcctga
     3301 ctgaggctac actagaagga caaatttggt gacatgtctc gcacaagact gttaccacgg
     3361 ttagagaatc tgccaggatt atctaacctt cgaaaaacca cctgcaaggg tggttttttc
     3421 gtttacagag caagagatta cgacgatcgt caaaggatct caagaagatc ctttatggat
     3481 tgctaccagc gccactgccg aatgtggtgc ccgttccccc aacaataaac tataaagttt
     3541 atgcatgtat ctaccgatac tcctgcgatc cctcaagaaa gtaaggaaag tatcgatatg
     3601 tcatgggctt atcgtatttc aatgcaaatg aagttgttta ttgcattatt cccgctactg
     3661 cttgccttgg tctggttcgc cggttcgggt attgtcagcc gtatcaatac cgaacagcag
     3721 atgaacacca ttggacagct caccacgctc gcccgcagcg cgggtgatgt ggtgcatcaa
     3781 ctccagagcg aacgtggaat gagcgctgga tttatcggcg cgcgcggcca aaagtttcgc
     3841 gatgactt
//
