LOCUS       NZ_CP028317             2096 bp    DNA     circular CON 05-JUN-2024
DEFINITION  Salmonella enterica subsp. enterica serovar Typhimurium var. 5-
            strain CFSAN067217 plasmid pSC-31-3, complete sequence.
ACCESSION   NZ_CP028317
VERSION     NZ_CP028317.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN08737533
            Assembly: GCF_003986655.1
KEYWORDS    RefSeq.
SOURCE      Salmonella enterica subsp. enterica serovar Typhimurium var. 5-
  ORGANISM  Salmonella enterica subsp. enterica serovar Typhimurium var. 5-
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Salmonella.
REFERENCE   1  (bases 1 to 2096)
  AUTHORS   Hoffman,M., Sanchez,M., Keefer,A., Figler,H. and Dudley,E.
  TITLE     Whole genome sequencing of cultured foodborne pathogen
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 2096)
  AUTHORS   Hoffman,M., Sanchez,M., Keefer,A., Figler,H. and Dudley,E.
  TITLE     Direct Submission
  JOURNAL   Submitted (22-MAR-2018) CFSAN-ORS-DM-MMSB, US Food and Drug
            Administration, 5100 Paint Branch Parkway, College Park, MD 20740,
            USA
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: HGAP v. 3.0
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 421.0x
            Sequencing Technology             :: PacBio
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_003986655.1-RS_2024_06_05
            Annotation Date                   :: 06/05/2024 01:20:33
            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)                     :: 4,980
            CDSs (total)                      :: 4,858
            Genes (coding)                    :: 4,722
            CDSs (with protein)               :: 4,722
            Genes (RNA)                       :: 122
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 85
            ncRNAs                            :: 15
            Pseudo Genes (total)              :: 136
            CDSs (without protein)            :: 136
            Pseudo Genes (ambiguous residues) :: 0 of 136
            Pseudo Genes (frameshifted)       :: 48 of 136
            Pseudo Genes (incomplete)         :: 102 of 136
            Pseudo Genes (internal stop)      :: 23 of 136
            Pseudo Genes (multiple problems)  :: 31 of 136
            CRISPR Arrays                     :: 3
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP028317.1.
            Bacteria and source DNA available from Bacterial culture available
            from Dwayne Roberson, FDA College Park Campus, 5001 Campus Drive,
            College Park, MD 20740.
            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..2096
                     /organism="Salmonella enterica subsp. enterica serovar
                     Typhimurium var. 5-"
                     /mol_type="genomic DNA"
                     /strain="CFSAN067217"
                     /serovar="Typhimurium var. 5-"
                     /host="Homo sapiens"
                     /sub_species="enterica"
                     /db_xref="taxon:1620419"
                     /plasmid="pSC-31-3"
                     /geo_loc_name="USA:PA"
                     /collection_date="2010"
                     /collected_by="Dudley Lab/Penn State/PADOH"
     gene            complement(join(1134..2096,1..27))
                     /locus_tag="C7X12_RS25760"
                     /old_locus_tag="C7X12_26325"
     CDS             complement(join(1134..2096,1..27))
                     /locus_tag="C7X12_RS25760"
                     /old_locus_tag="C7X12_26325"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001362017.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="protein rep"
                     /protein_id="WP_024136759.1"
                     /translation="MKNPDLQNLTDYSPSDAPWDAHRSVSDDVGGIYLLAAEYERYGAR
                     MALCGGLLRFGWSTLKETGETRLRLREAHFCRVRHCPVCQWRRSLMWQARFYQSLPRIV
                     ADYPDARWMFLTLTVRNCAIGELGEMLNRMNAAFQRMKVRKEFRPVQGWIRTTEVTRGS
                     DGSAHPHFHTLMMVPPGMLNGKSYVRHERWVELWRECLRVDYDPNVDVRAVKPRKPKGG
                     ESLACATAELVRGAVAETLKYSTKPADMVADPEWFLELTRQTHKRRFVATGGALKDVLK
                     LDQETDADMVIGDDISEGDDDGSRIAFEWKTEVRKYRRSPTKDKTESG"
                     /name="protein rep"
     Typing          complement(1051..1132)
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="93.976"
                     /coverage="90.0"
                     /evalue="3.4000000000000004e-27"
     Typing          1217..1408
                     /name="ColpVC"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="98.964"
                     /coverage="100.0"
                     /evalue="6.14e-93"
ORIGIN
        1 gaggttctgg agatcagggt ttttcatgcg caccacccga tagtgggcga tggctcatct
       61 gacgtgttat cattgccata tcacctgttg tgttagtcgt atcaccaatt cgaattccta
      121 caggtggtca cacccccgaa cgattgccct cgttgcgggg gtcgctttta atgcgaccac
      181 tcccgacaga ataactccaa aaccattttc cgacaaatcc cccttcaggc cttgcggcac
      241 aagggctgga ggcgaatttg aatcctagag ttatccctta agtataaata caaggatcgc
      301 gcgcgagatt cgcttgaatt ttgagcggga ttttcagtca cccaaaacac ccaaccccac
      361 ccacttacac ccatctcatc cacagacttt caccccgatt ttgtgaacaa caaaaaaaac
      421 cgtcttgcag gtggttggcc tcactgcgtg acaccaacca ccatccccag tgtttttccc
      481 gtgccgtcgt caatcacaaa atcggaaccc acgccggagg cgcgggcccc cgcgattttc
      541 tgtttgacga atcagggaac ggtgaacggt acgcggaatt ttttcgcgta ccgtgaggcg
      601 ttggcggggt gtcggggcgc agtcctgacc aggttcgtag aaccgcacag ggttgcaaag
      661 gggtgtcccc tttggcacaa gcgacggagc gaaacgcccc gttttgtgta cgccgcttat
      721 cgtgcctgtg ttttaggaga acaaaaaaat gccgtgcata cagcccacac aatgacccac
      781 ataatcaccc acaactcaaa acacacagcc cacacaatca cccacacttt aacccacaaa
      841 aaagaccaca accccattga caccccacaa aacaacccac acaaacggcg agtaaatcat
      901 tttgccgttt tcgtgccgca gccgttccgc gcaatcgaca aactggcagt cagggaatct
      961 cacgaagtgc gcacttatac aaactcacct taggttcgtt tgtcgtgcgg tctgcgacgc
     1021 tcaaaaaacc gagaaacggc gggaattttc gggacaggat gtgtaattgt aataccgtca
     1081 cacgcgacgc tatcacaatt gccatctggt caggggtgca ccccgacacc ccgctagcct
     1141 gattcagttt tatctttcgt cggtgagcga cggtactttc tgacctcggt tttccactcg
     1201 aacgcgattc gtgaaccgtc atcgtcgccc tcggaaatat catcaccgat caccatgtcg
     1261 gcgtcagttt cctgatcgag tttcagcacg tctttgagtg cgccgccggt cgccacaaag
     1321 cggcgcttgt gcgtctggcg ggtcagttcg aggaaccatt caggatcggc caccatgtca
     1381 gccggcttcg tggaatattt cagggtttcg gccaccgcac cgcgcaccag ttcggcggtc
     1441 gcgcaggcca gcgattcgcc gcccttcggc ttacgaggtt tcactgcccg gacatcaaca
     1501 ttcgggtcat aatcgacccg cagacactcc cgccagagtt caacccagcg ttcatgcctg
     1561 acgtaacttt tcccatttag catgccaggc ggcaccatca tcagggtgtg gaagtgcggg
     1621 tgtgcgctgc cgtcgctccc gcgggtgact tccgtggtac gtatccagcc ctgcacaggc
     1681 cggaactcct tgcgaacctt catgcgctga aaagctgcat tcatccggtt cagcatctcg
     1741 cccagctccc cgatcgcaca gttgcgcacg gtcagagtca ggaacatcca gcgggcatcg
     1801 ggataatccg ccacgatacg cggcagggac tggtagaaac gggcttgcca catcagggag
     1861 cgcctccact ggcagacagg acaatgccgg acacggcaga aatgcgcctc acgcagcctc
     1921 agacgcgttt ctccggtttc cttgagggta gaccacccga aacgcagtaa accaccacag
     1981 agagccatac gcgccccgta gcgctcatat tcggctgcaa gcaggtaaat ccctcccacg
     2041 tcatcagaaa cgcttctgtg agcgtcccag ggcgcatctg agggggaata gtccgt
//
