LOCUS       CP082414                1888 bp    DNA     circular BCT 11-JAN-2022
DEFINITION  Salmonella enterica subsp. enterica serovar Derby strain
            FSIS11704880 plasmid pF18S034-3, complete sequence.
ACCESSION   CP082414
VERSION     CP082414.1
DBLINK      BioProject: PRJNA292666
            BioSample: SAMN08025063
KEYWORDS    .
SOURCE      Salmonella enterica subsp. enterica serovar Derby
  ORGANISM  Salmonella enterica subsp. enterica serovar Derby
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Salmonella.
REFERENCE   1  (bases 1 to 1888)
  AUTHORS   Li,C., Tyson,G.H., Hsu,C.H., Harrison,L., Strain,E., Tran,T.T.,
            Tillman,G.E., Dessai,U., McDermott,P.F. and Zhao,S.
  TITLE     Long-Read Sequencing Reveals Evolution and Acquisition of
            Antimicrobial Resistance and Virulence Genes in Salmonella enterica
  JOURNAL   Front Microbiol 12, 777817 (2021)
   PUBMED   34867920
  REMARK    Publication Status: Online-Only
REFERENCE   2  (bases 1 to 1888)
  CONSRTM   NARMS: The National Antimicrobial Resistance Monitoring System
  TITLE     Direct Submission
  JOURNAL   Submitted (27-JUL-2018) Center for Veterinary Medicine, US Food and
            Drug Administration, 8401 Muirkirk Rd, Laurel, MD, USA
REFERENCE   3  (bases 1 to 1888)
  AUTHORS   Li,C.
  TITLE     Direct Submission
  JOURNAL   Submitted (26-AUG-2021) CVM/OR, FDA-CVM, 8401 Muirkirk Rd, MOD2,
            Laurel, MD 20708, USA
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Date                     :: 01-JUN-2020
            Assembly Method :: SMRTLink Microbial Assembly v. SMRTLink9.0
            Assembly Name                     :: F18S034
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 601x
            Sequencing Technology             :: PacBio Sequel
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI
            Annotation Date                   :: 09/02/2021 11:00:03
            Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline
            (PGAP)
            Annotation Method :: Best-placed reference protein set; GeneMarkS-2+
            Annotation Software revision      :: 5.2
            Features Annotated :: Gene; CDS; rRNA; tRNA; ncRNA; repeat_region
            Genes (total)                     :: 4,746
            CDSs (total)                      :: 4,628
            Genes (coding)                    :: 4,534
            CDSs (with protein)               :: 4,534
            Genes (RNA)                       :: 118
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 84
            ncRNAs                            :: 12
            Pseudo Genes (total)              :: 94
            CDSs (without protein)            :: 94
            Pseudo Genes (ambiguous residues) :: 0 of 94
            Pseudo Genes (frameshifted)       :: 41 of 94
            Pseudo Genes (incomplete)         :: 53 of 94
            Pseudo Genes (internal stop)      :: 21 of 94
            Pseudo Genes (multiple problems)  :: 18 of 94
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            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/
FEATURES             Location/Qualifiers
     source          1..1888
                     /organism="Salmonella enterica subsp. enterica serovar
                     Derby"
                     /mol_type="genomic DNA"
                     /strain="FSIS11704880"
                     /serovar="Derby"
                     /isolation_source="animal-swine-market swine"
                     /sub_species="enterica"
                     /db_xref="taxon:28144"
                     /plasmid="pF18S034-3"
                     /geo_loc_name="USA:IA"
                     /collection_date="2017"
                     /collected_by="USDA-FSIS"
     gene            255..491
                     /locus_tag="CVB56_023725"
     CDS             255..491
                     /locus_tag="CVB56_023725"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001676031.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="UAF25092.1"
                     /translation="MNRLTNLTPAEKKFLDDAIAAAERASGKKLNQPNRHIVLNRARAQ
                     IESQRYADRQRALREDERQQSEFAWSRPRAPRR"
                     /name="hypothetical protein"
     gene            complement(1333..1446)
                     /locus_tag="CVB56_023730"
     CDS             complement(1333..1446)
                     /locus_tag="CVB56_023730"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_007772075.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="replication initiation protein"
                     /protein_id="UAF25091.1"
                     /translation="MHEPPVQSDCCACSGNYRLESNPERHAKAPLAAATGN"
                     /name="replication initiation protein"
     Typing          complement(1338..1821)
                     /name="rep_cluster_2335"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="95.277"
                     /coverage="80.0"
                     /evalue="0.0"
ORIGIN
        1 gctatgcctg atgtttctgc gatgttacat tttaagccag tatacactcc gctagcgcta
       61 tgtgactggt tcagggctgc gccccgaaac ccgctaaaac cactgacgcg cctgcggctt
      121 gcccaacgtc tcacgtcacc ggattaaaat ccgctcccgt tcaccgtttc tggctgtctt
      181 tcagcaccgc cagcgcttca tcggttctgc tgtgtctggc agactgtgcg gagttattct
      241 gacgggagaa tgctatgaac agactgacaa acctgacacc tgcagagaaa aaatttcttg
      301 atgatgctat tgccgcagct gagagagcgt caggcaaaaa gctaaatcag ccgaaccggc
      361 atatcgtcct gaacagagcg cgtgcgcaga ttgagtcgca gcgttacgcc gaccgccagc
      421 gtgcattacg tgaggatgag cggcagcagt ccgagtttgc ctggtcacgt ccgcgcgcgc
      481 cgcgccgctg attgcgcctt ttggcggttt agtggtgctg acactccgaa atcgtctgcc
      541 attcacccgc gtgcatagcc atgcagtcgc gcagaaatca tcaggtgcgt ttttcagggt
      601 tatggccagg gaaaggtgct ggaaatggct aactcgttac agagtggcgc tgagggcctc
      661 tcaggcggtg cgggcaacgg atgttatggt aaatagagcg ttttggtgac tcgcccgcca
      721 catctttagc tgtgatataa ttttacagaa ggatgaaagg gcaaaaaaaa agaatccgta
      781 aggattcttt ttctcgcctc agtcagcgac tgcgaatcgc tgactgctac ccgaaaacat
      841 gtaccgaagc tcacgttgtc gttacttatc acaaagtaat tttacccctg gggtgaatct
      901 acgtcaattg agccggtatt cctttctatc aatatgaagg aataaacgta tggccgaact
      961 gcttacggcg tttattaaag caccacttat aagccaggtg ctgaccatca ttctgtgtct
     1021 gatctttgta gtacacagtc ttttaaattg atgtaccacc cataaaaaaa gccacttatg
     1081 tggctttttt tatgaatcga gagataggta tctgttgaat atcacagatg atcttcttga
     1141 gatccttttc gttgcgtcgt aatctcttgc tctggaaacg aaaaaaaccg cccagcaagg
     1201 cggtttttcg aaggttctca gagcagcaac tctttgaacc gcggtaactg gcttaagagg
     1261 agcgcagtaa ccaaatctgt cctttcagtt tagccttaac tggcacataa cttcaagact
     1321 aactcctcta aatcagttac cagtggctgc tgccagtggc gcttttgcat gtctttccgg
     1381 gttggactca agtcgatagt taccggaaca ggcgcagcag tcggactgaa cggggggttc
     1441 gtgcatacag tccagcttgg agcgaactgc cttcccggaa ctgagtgtca ggcgtggaat
     1501 gagagaccgc ggccataaca gcggaatgac accggtaaac cgaaaggcag gaacaggaga
     1561 gcgcacgagg gagccaccag ggggaaacgc ctggtatctt taagtcctgt cgggtttcgc
     1621 caccactgat ttgagcgtca gatttcgtga tgcttgtcag gggggcggag cctatggaaa
     1681 aacggctttg ccgcggcctt atggtttccc tgttaagttt cttcctggca tccactagga
     1741 aatttccgcc ccattagtaa gcctgcaccg ctcgccgcag ccgaacgacc gagcggagcg
     1801 agtcagtgag cgaggaagcg gcatttctcc ggcagtgcat cttctgctga cgcatacgaa
     1861 tctcattttt cacctgcttt atgtggca
//
