LOCUS       NZ_CP054465             3829 bp    DNA     circular CON 16-MAY-2024
DEFINITION  Salmonella enterica subsp. enterica serovar Typhimurium strain CVM
            28321-a plasmid p28321a-4, complete sequence.
ACCESSION   NZ_CP054465
VERSION     NZ_CP054465.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN14504767
            Assembly: GCF_016452165.1
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., Strain,E., Tate,H., Tran,T.-T.,
            Abbott,J. and McDermott,P.
  TITLE     Comparative Genomic Analysis of Four Hundred Fifty Salmonella
            Strains Isolated from Diseased Animals
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 3829)
  AUTHORS   Li,C.
  TITLE     Direct Submission
  JOURNAL   Submitted (26-MAY-2020) CVM/OR, FDA-CVM, 8401 Muirkirk Rd, MOD2,
            Laurel, MD 20708, USA
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Date                     :: MAY-2020
            Assembly Method                   :: HGAP v. 4.0
            Assembly Name                     :: Microbial Assembly
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 595.0x
            Sequencing Technology             :: PacBio
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_016452165.1-RS_2024_05_16
            Annotation Date                   :: 05/16/2024 03:40:21
            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)                     :: 5,170
            CDSs (total)                      :: 5,049
            Genes (coding)                    :: 4,899
            CDSs (with protein)               :: 4,899
            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)              :: 150
            CDSs (without protein)            :: 150
            Pseudo Genes (ambiguous residues) :: 0 of 150
            Pseudo Genes (frameshifted)       :: 63 of 150
            Pseudo Genes (incomplete)         :: 94 of 150
            Pseudo Genes (internal stop)      :: 28 of 150
            Pseudo Genes (multiple problems)  :: 31 of 150
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP054465.1.
            Bacteria and source DNA available from CVM.
            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 28321-a"
                     /serovar="Typhimurium"
                     /isolation_source="swine"
                     /sub_species="enterica"
                     /db_xref="taxon:90371"
                     /plasmid="p28321a-4"
                     /geo_loc_name="USA:MO"
                     /collection_date="2002"
                     /collected_by="MO State Veterinary Diagnostic Lab"
     gene            complement(join(3383..3829,1..1458))
                     /locus_tag="HFS61_RS25665"
                     /old_locus_tag="HFS61_25655"
     CDS             complement(join(3383..3829,1..1458))
                     /locus_tag="HFS61_RS25665"
                     /old_locus_tag="HFS61_25655"
                     /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(1763..1912)
                     /locus_tag="HFS61_RS26110"
     CDS             complement(1763..1912)
                     /locus_tag="HFS61_RS26110"
                     /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            2591..2857
                     /locus_tag="HFS61_RS25670"
                     /old_locus_tag="HFS61_25660"
     CDS             2591..2857
                     /locus_tag="HFS61_RS25670"
                     /old_locus_tag="HFS61_25660"
                     /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(2905..3093)
                     /locus_tag="HFS61_RS25675"
                     /old_locus_tag="HFS61_25665"
     CDS             complement(2905..3093)
                     /locus_tag="HFS61_RS25675"
                     /old_locus_tag="HFS61_25665"
                     /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          2275..2447
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="91.379"
                     /coverage="100.0"
                     /evalue="9.47e-61"
     Typing          complement(1754..2350)
                     /name="rep_cluster_2335"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="91.211"
                     /coverage="99.0"
                     /evalue="0.0"
ORIGIN
        1 atcaattgac gcaacaatct gggaaatctg ctcgctggaa gaacgaattt ccgccatgct
       61 ctgactggcc tcgttagaga cgcgattagc ttccagtacg tcccgctcca tcgaatgtat
      121 cagacgctcc gcctcgctgg cgttatcggc ggtctgggtg atcgcagtag aaatctgctc
      181 catgctggcg gccgtttcca caatcgatgc cgcctgttca tccgtacgct gggccagatc
      241 ctgattaccg gcagcgatat cactactggc gctacgcaac accaccgcac cggacttaat
      301 ttcttgcacg atatgctgaa tattctcaat cgcttggtta taggcacggt tcagggctga
      361 gagctcgtcg ctgccgggga cgtcaagacg acgtgtcagg tcgccgtcca tctctgcgat
      421 ggttttcagc gtaccgttca gttgctgctg gatactgcgt gccaccatca ccgcaaaggc
      481 gatagcaatc agtagggcaa ccaggctgat taccaggaag gactgccagt cgacacgggc
      541 attgtgggca agcagcgcag catgttcctg caaggcatcc accgcgcgat tttccacctt
      601 ttgcagcgtt tcaatacgct gggtctgaag gttaaaccag tcagtcgggt tgactccaaa
      661 tccgccttcg gcggctttat taaaagccgt ctcccgcagt tcaagagcac gagttgcttc
      721 agcggactga agagatttgt ccagctcagc cgcctgcaca ggtgtgctaa agctgcgagc
      781 tgccgtcagc caggcatcct gctggcctac cacatcgcta aacatgctga actggccgtc
      841 gtcaaagcga tccatcgaga agatattgga cagcagcgca cgttctacac cagcctgctc
      901 cttcaaattc aagagactat aataagccgc cagttcgttc accatcgagc ctgaggtgct
      961 taaatgcccc atcccgccga caaacttcag cacgtcagag atggtttggg tatagaactg
     1021 actcgctttt ggtgaatcga tagttaattc gctgatggcg gtacgggttg agtcgagaaa
     1081 ctgaatactt tcattaaacg ttttcagggg ggcggcaata tttccctgga gtaaatcctt
     1141 attcgtatcg gtcagcaacc gcttaaatgt tgccagcacc ttgtcggtta actgccgctg
     1201 ggcagctaag tcatcgcgaa acttttggcc gcgcgcgccg ataaatccag cgctcattcc
     1261 acgttcgctc tggagttgat gcaccacatc acccgcgctg cgggcgagcg tggtgagctg
     1321 tccaatggtg ttcatctgct gttcggtatt gatacggctg acaatacccg aaccggcgaa
     1381 ccagaccaag gcaagcagta gcgggaataa tgcaataaac aacttcattt gcattgaaat
     1441 acgataagcc catgacatat cgatactttc cttactttct tgagggatcg caggagtatc
     1501 ggtagataca tgcataaact ttatagttta ttgttggggg aacgggcacc acattcggca
     1561 gtggcgctgg tagcaatcca taaaggatct tcttgagatc ctttgacgat cgtcgtaatc
     1621 tcttgctctg taaacgaaaa accacccttg caggtggttt ttcgaaggtt agataatcct
     1681 ggcagattct ctaaccgtgg taacagtctt gtgcgagaca tgtcaccaaa tttgtccttc
     1741 tagtgtagcc tcagtcaggc cactacttca agaactctcg atacatctct cgcacatcct
     1801 gtttaccagt ggccgctgcc agtggcgatt tttcgtgtct ttccgggttg gactcaagac
     1861 gatagttacc ggaaaaggcg cagcagtcgg actgaacggg gggttcgtgc atacagtcca
     1921 gcttggagcg aactgccttc ccggaactga gtgtcaggcg tggaatgaga taaacgcggc
     1981 cataacagcg gaatgacacc ggtaaaccga aaggcaggaa caggagagcg cacgagggag
     2041 ctaccagggg gaaacgcctg ggatctttat agtcctgtcg ggtttcgccg ccactgattt
     2101 gagcgtcaga tttcgtgatg cttgtcaggg gggcggagcc tatggaaaaa cggcttcgcc
     2161 gcggccttac cgtttccctg ttaagtttct tcctggcatc tcccaggaaa tttccgcccc
     2221 attcgtaatc ccgcaccgct cgccgcagcc gaacgaccga gcgcagcgag tcagtgagcg
     2281 aggaagcgga atatctcctg tctcatatat tccgcttacg ctctgctgct gcattttcct
     2341 cctgccacat gaagcacttc actgattccc gcacccgtgc ctacataata agccagtata
     2401 cactccgcta gcgctacgtg actggttcag ggctgcgccc cgacacccgc taaaagcact
     2461 gacgcgcctg cggcttgccc aaccccgcgc cgtccgggaa agaatttccc gatcgacccg
     2521 acgtttctgt ttacctgtga tgttaacgtt tggatctttt tcccgggttt acctatttta
     2581 atgaagcgta atgaagcgtt cacagctgac gttaatagat gggtgcttca tgtttggttt
     2641 ttcaccagga gaacttatga acctttgccc cgatgaacgt ctgctctttg tgcggatgat
     2701 ttccgctatg cttcgccgtt cgggcggtga tgcgggtgct gttatgtttg aggcgtatcg
     2761 ccatattgtg tccgatacca atcaagctcg tcgttcctgc atgctcgacc tgctcgaaag
     2821 cgtcaggcat gactatgtac acggtggata tacatagttg ccctggatac gcttttcgtc
     2881 taagtgagcg ttcttttcgt ctctttattc gccgtcctgt ataccgaagc gtgcgctcag
     2941 cttctgataa agcgcttctg cctgttcgtg cattcgctca cagtcggctg cctcgtcatc
     3001 aagatcgagc acgtcgagtt tttcgagcag cagcagcgac tgcgcccgga taaattttgc
     3061 catgttcagt gcggctgatt cctgttttgt catacggctt tttcccggtt ttatggtgat
     3121 cgcagactga aatcttactt cattcacttg agtgcatagc catgcaggta cgcagaaatc
     3181 atcaggggcg ttttttctcg atatgggcac agaaaggtgt atgtttcagg tcggagtcct
     3241 cagaaacgct ctcagagcct ctcaggcggt gcacgcaaca gatgttatgg taaatcctag
     3301 ttatttgcag gcataaaaaa gccgcctttt aggcggtttt ttctgattgt aagttatcaa
     3361 gaccggatgc tgaacggcag tatcagacaa taaagcgatc gaccagcgtg gacatcgctt
     3421 cagactggcc gtccagcatc tggctggcgc tcgccgcctg agagaccagc gctgcgtttt
     3481 gctgagtgac ctgctccagc tgattcagtg cctgatgcac ctgcgacacg ccaagcgact
     3541 gctcattcgc cgcacgggca atatcgctca cgtactgttt catccgcccg gtattttccg
     3601 ccgctgcttt cagcgcggtg ccggacgcgg tgactcgtgc taccccttcg ccaatcttat
     3661 ccatattctg gttaatcagc tcacggatct gactggcctc tcgtgcacag cgctgggaaa
     3721 ggttacgcac ctccgtcgcc actaccgcaa agcctttgcc aagctcaccg gcacgtgccg
     3781 cttcaacggc ggcgttaagc gccagcaagt tggtctggaa agaaatctc
//
