LOCUS       NZ_CP054466             3188 bp    DNA     circular CON 16-MAY-2024
DEFINITION  Salmonella enterica subsp. enterica serovar Typhimurium strain CVM
            28321-a plasmid p28321a-5, complete sequence.
ACCESSION   NZ_CP054466
VERSION     NZ_CP054466.1
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 3188)
  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  JOURNAL   Unpublished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 3188)
  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
            CP054466.1.
            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..3188
                     /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-5"
                     /geo_loc_name="USA:MO"
                     /collection_date="2002"
                     /collected_by="MO State Veterinary Diagnostic Lab"
     gene            497..691
                     /locus_tag="HFS61_RS25680"
                     /old_locus_tag="HFS61_25670"
     CDS             497..691
                     /locus_tag="HFS61_RS25680"
                     /old_locus_tag="HFS61_25670"
                     /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            1772..2359
                     /locus_tag="HFS61_RS25685"
                     /old_locus_tag="HFS61_25675"
     CDS             1772..2359
                     /locus_tag="HFS61_RS25685"
                     /old_locus_tag="HFS61_25675"
                     /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            2369..2866
                     /locus_tag="HFS61_RS25690"
                     /old_locus_tag="HFS61_25680"
     CDS             2369..2866
                     /locus_tag="HFS61_RS25690"
                     /old_locus_tag="HFS61_25680"
                     /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          complement(8..238)
                     /name="MOBF"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="97.854"
                     /coverage="80.0"
                     /evalue="2.05e-109"
     Typing          complement(363..461)
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="6.22e-45"
     Typing          complement(765..847)
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="3.79e-36"
     Typing          860..1414
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="94.434"
                     /coverage="99.0"
                     /evalue="0.0"
ORIGIN
        1 ggggcgtcct gtaaaaaaaa cacaccgcgc cgctagcagc acccctaata taaaatgatg
       61 ttttttatga aaatagtcag taccacccct aaaaagcggt gttggcgcag ctacaacacc
      121 gcgccgacac cgctttttta aatatcacaa agagagcaag aagaactaat ttgtcataac
      181 tctctattta taaagaaaaa tcagcaaaaa attgtttttg cgtggggtgt gggcatttca
      241 ggcatgagaa cagactcgcg tttttccgga gtatcagcgg aattattgat taagaaacac
      301 tcgacgcaga gcgaaatttt atgcaacagc ggctgcactg cacagggatt atttatcagt
      361 tgatatgctg tgccatgata cgtcctaaaa aaacaggaca ggatgtgcaa ttgtaatacc
      421 gtcgcccgca acgtcttaca attaccacct ggtcagggtc cacccgacac ccggtactga
      481 cggagaacaa cggaaggtga acaaacagca acaaactgcg ctgaatatgg cgcgatttat
      541 caaaagccag agcctgacac tgcttgaaaa actggatgct ctggatgccg acgaacaggc
      601 ggccatgtgc gaacgactgc acgaactcgc ggaagaactc cagaacagca tccaggttcg
      661 ctttgagacc gaaagtgaaa caggaacata acgaagctga cggaggcgct cacggcttgt
      721 ccgcgagcgt tttcggcagc agacaagccc gccagggcgc gtcagcgggt gtcggggcga
      781 agccctgacc cagtcacgta gcgatagcgg agtgtatact ggcttaacta tgcggcatca
      841 gtgcagattg tatgaaaagt gccccatggc gggtgtgaaa ttccgcacag atgcgtaagg
      901 agaaaatgcg cgtccaggcg cttttccgct tcctcgctca ctgactcgct acgctcggtc
      961 gttcggctgc ggcgagcggt actgacttac acaaaaacgg cagcacggtt atccacagaa
     1021 tcaggggata aggccggaaa gaacatgtga gcaaaagacc aagaacagga agaaggccgc
     1081 gccgcaggcg tttttccata ggctccgccc ccctgacgag catcacagaa atcgacgctc
     1141 aagtcagagg tggcgaaacc cgacaggact taaagatacc agacgtttcc ccctggtggc
     1201 tccctcgtgc gctctcctgt tccgaccctg ccgcttaccg gatacctgtc cgcctttctc
     1261 ccttcgggaa gcgtggcgct ttctcatagc tcacgctgta ggtatctcgg ttcagtgtag
     1321 gtcgttcgct ccaagctggg ctgtgtgcac gaaccccccg ttcagcccga ccgctgcgcc
     1381 ttatccggta actatcatct tgagtccaac ccggaaagac acgacaaagc gccactggca
     1441 gcagccactg gtaactgatt tagaggagtt agtcttgaag ttatgcgccg gttcaggcta
     1501 aactgaaagg acaagttttg gtgactgcgc tcctccaagc cagttacctc ggttcaaaga
     1561 gttggtagct ctgagaacct tcgaaaaacc gccctccaag gcggtttttt cgtttcgtgg
     1621 ttaagagatt acgactctcg cttaaggatc tcaagaagat ctgcccgcat cctttcaaaa
     1681 tccttttaaa aaagaatatc gtgtgcaaaa tggtttcggg aatacgatgt tttttcagtc
     1741 tctgttaaaa agaaaaaaat aggataacga tatgataagg aagatttttt ttgcttctgc
     1801 gatcgtagta gcgatctctg gctgtacagc aatggataaa ttggcgggaa tgggtgttgt
     1861 ttctcagcaa acatcaacct ttgataactc gactgtcata gaggtatctc caaattcgct
     1921 atacgatcct aacagcactt ggggaacacc acttcagttg ggcgcgatat ggtctagtgc
     1981 ctatccagaa gaggctggac taatcctttc ctacaactcg aatgtatcta gcggaaatgc
     2041 cgcatactta ggtttgacgg ggattgatat aaatgttgat ggtaaaatat ccagctataa
     2101 agcacagcaa caaactaatc taagcagcag ctcatataac tccgtatcca agacgatcta
     2161 tacctctagc aagaatacta tcgttatccc gtataaattg ctggagagca tggtatcagc
     2221 taaaaactgc cgcattcgca tacacacaag ccaaggaaat caagacatcg acttctcagc
     2281 acaaagtatc cccggaggta aagcgacagc gatcgtttcc attaaagagt tcttggccaa
     2341 agtcgaacgt tttaaataag gaggcgtcat gaagaagcag attcttgcac tcgctttgct
     2401 atcattgcca ctgattggca tggcaaagga ctctggttat ggcaataccg aatggggtat
     2461 gaccccaaat caggtcgttg cagcccagaa aggaaaagct catttaatcc cccctcaaaa
     2521 gtataaagac caatggggaa aagtgagcat tgaagacgtg aatataggta gtggaatata
     2581 tacagttacg tttatttttg acgcatcaga taaattagtc caaaccaacg ttgccagcaa
     2641 agaaaagaaa aacgagggaa tagcaaacaa ccaatttaac acattaaatc aattacttac
     2701 acaaaagtat ggcaaaccac agtttgtaag tgatgaaaaa gcaacatgga aaactgatac
     2761 tacaacaatt gagctaaata agatgatcat ctccggaatt atggctcaaa cactagttcg
     2821 ctacattcct aataagaccg tgatttctga cacgtctaac ctgtaataat tgtcgcctca
     2881 ctgagtgtct ctctcctgtt tctatacctg aggtgggaga ttgaacataa cgtcgcatta
     2941 cgcgcaccgc taaaacgcgc tgaacgcgat tctgccgcga acaccgcaaa aagagatgtt
     3001 ttaccaagcg aaaaccggaa aaatgcgtca ggatcgcttt cagctcactg catagctatg
     3061 catgaaagtg aatggcgatc ggtttgggcg catacggtgc ccatgagaca cattttcgga
     3121 cattttcagt tcgtgaatcc ctgactcatt gctacatatc tgaacagaca cccctagcag
     3181 cgccccca
//
