LOCUS       CP082379                3071 bp    DNA     circular BCT 25-APR-2023
DEFINITION  Salmonella enterica subsp. enterica serovar Bredeney strain
            FSIS1702037 plasmid pF18S044-4, complete sequence.
ACCESSION   CP082379
VERSION     CP082379.2
DBLINK      BioProject: PRJNA292666
            BioSample: SAMN07283941
KEYWORDS    .
SOURCE      Salmonella enterica subsp. enterica serovar Bredeney
  ORGANISM  Salmonella enterica subsp. enterica serovar Bredeney
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Salmonella.
REFERENCE   1  (bases 1 to 3071)
  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 3071)
  CONSRTM   NARMS: The National Antimicrobial Resistance Monitoring System
  TITLE     Direct Submission
  JOURNAL   Submitted (25-JUL-2018) Center for Veterinary Medicine, US Food and
            Drug Administration, 8401 Muirkirk Rd, Laurel, MD, USA
REFERENCE   3  (bases 1 to 3071)
  AUTHORS   Li,C.
  TITLE     Direct Submission
  JOURNAL   Submitted (26-AUG-2021) CVM/OR, FDA-CVM, 8401 Muirkirk Rd, MOD2,
            Laurel, MD 20708, USA
REFERENCE   4  (bases 1 to 3071)
  AUTHORS   Li,C.
  TITLE     Direct Submission
  JOURNAL   Submitted (02-MAR-2023) CVM/OAS, FDA-CVM, 8401 Muirkirk Rd, MOD2,
            Laurel, MD 20708, USA
  REMARK    Nucleotide sequence updated by submitter
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Date                     :: 24-SEP-2021
            Assembly Method                   :: HGAP v. 4
            Assembly Name                     :: Microbial assembly
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 313x
            Sequencing Technology             :: PacBio Sequel
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI
            Annotation Date                   :: 04/21/2023 11:55:33
            Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline
            (PGAP)
            Annotation Method :: Best-placed reference protein set; GeneMarkS-2+
            Annotation Software revision      :: 6.5
            Features Annotated                :: Gene; CDS; rRNA; tRNA; ncRNA
            Genes (total)                     :: 4,822
            CDSs (total)                      :: 4,706
            Genes (coding)                    :: 4,547
            CDSs (with protein)               :: 4,547
            Genes (RNA)                       :: 116
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 83
            ncRNAs                            :: 11
            Pseudo Genes (total)              :: 159
            CDSs (without protein)            :: 159
            Pseudo Genes (ambiguous residues) :: 0 of 159
            Pseudo Genes (frameshifted)       :: 68 of 159
            Pseudo Genes (incomplete)         :: 110 of 159
            Pseudo Genes (internal stop)      :: 15 of 159
            Pseudo Genes (multiple problems)  :: 31 of 159
            Pseudo Genes (short protein)      :: 1 of 159
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            On Apr 25, 2023 this sequence version replaced CP082379.1.
            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/
FEATURES             Location/Qualifiers
     source          1..3071
                     /organism="Salmonella enterica subsp. enterica serovar
                     Bredeney"
                     /mol_type="genomic DNA"
                     /strain="FSIS1702037"
                     /serovar="Bredeney"
                     /isolation_source="animal-swine-market swine"
                     /sub_species="enterica"
                     /db_xref="taxon:134047"
                     /plasmid="pF18S044-4"
                     /geo_loc_name="USA:IL"
                     /collection_date="2017"
                     /collected_by="USDA-FSIS"
     gene            complement(join(2565..3071,1..138))
                     /locus_tag="CFC63_000015"
     CDS             complement(join(2565..3071,1..138))
                     /locus_tag="CFC63_000015"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_017900990.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="quinolone resistance pentapeptide repeat protein
                     QnrB19"
                     /protein_id="UAF61238.1"
                     /translation="MTLALVGEKIDRNRFTGEKVENSTFFNCDFSGADLSGTEFIGCQF
                     YDRESQKGCNFSRAMLKDAIFKSCDLSMADFRNVSALGIEIRHCRAQGADFRGASFMNM
                     ITTRTWFCSAYITNTNLSYANFSKVVLEKCELWENRWMGTQVLGATFSGSDLSGGEFST
                     FDWRAANFTHCDLTNSELGDLDIRGVDLQGVKLDSYQASLLMERLGIAVIG"
                     /name="quinolone resistance pentapeptide repeat protein
                     QnrB19"
     gene            complement(232..387)
                     /locus_tag="CFC63_000010"
                     /pseudo=""
     CDS             complement(232..387)
                     /locus_tag="CFC63_000010"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:NP_309907.2"
                     /note="incomplete; partial on complete genome; missing
                     N-terminus; Derived by automated computational analysis
                     using gene prediction method: Protein Homology.
                     GO_function: GO:0043565 - sequence-specific DNA binding
                     [Evidence IEA]"
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="helix-turn-helix domain-containing protein"
                     /name="helix-turn-helix domain-containing protein"
     gene            1325..1474
                     /locus_tag="CFC63_000005"
     CDS             1325..1474
                     /locus_tag="CFC63_000005"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_017880354.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="UAF61239.1"
                     /translation="MPSEYDEQRGSTDTQLPGEYDLFDLMAKVTEEILHAPVDSGPPVG
                     REAL"
                     /name="hypothetical protein"
     ARG             complement(2..174)
                     /name="QnrB10"
                     /gene="QnrB10"
                     /gene_name="quinolone resistance protein (qnr)"
                     /tool="rgi"
                     /drug_class="fluoroquinolone antibiotic"
                     /identity="98.28"
                     /coverage="25.66"
     ARG             complement(2566..3071)
                     /name="QnrB19"
                     /gene="QnrB19"
                     /gene_name="quinolone resistance protein (qnr)"
                     /tool="rgi"
                     /drug_class="fluoroquinolone antibiotic"
                     /identity="100.0"
                     /coverage="78.5"
     Typing          1117..1290
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="2.5600000000000002e-86"
     Typing          complement(647..1138)
                     /name="rep_cluster_2335"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="92.51"
                     /coverage="81.0"
                     /evalue="0.0"
ORIGIN
        1 atagaactgg cagccgataa attcagtgcc gctcaggtcg gcacctgaaa aatcgcagtt
       61 aaaaaatgta ctattttcaa ctttctcacc ggtgaagcga tttctgtcaa ttttttcgcc
      121 aactaatgcc agagtcatat ctatgcctgt gtttttatac agtaatgacg ccatggtaaa
      181 ccttatgacg ttatgcgtca aacccgccag tatgacacct gcaaatgcgt attagatctg
      241 gtgtttcttc agcaaggcac gtagctgatg ataagtcaga cccagtaatt cagcggcttt
      301 tttctggtta aatttagcct gctgtaagct ggtttgtaga aagtctttct cttgctgctg
      361 ctggaattca cgcagatcca gcgttataac gatgtgtatc ctatgtgctc ggattggata
      421 gatttccatt acggtgaagg atcttcttga gatcctttct gtggcgtcgt aatctcttgc
      481 tctgtaaacg aaaaaaccgc cctgcaaggc ggtttttcga aggttctcag agcagcaact
      541 ctttgaaccg tggtaactgg cttacgagga gcgcagtaac caaatctgtt ctttcagttt
      601 agccttaaca ggcgcataac ttcaagacta actcctctaa atcagttacc agtggctgct
      661 gccagtggcg ataagtcgtg tctttccggg ttggactcaa gatgatagtt accggataag
      721 gcgcagcagt cggactgaac ggggggttcg tgcatacagt ccatccagga gcgaactgcc
      781 ttcgcggaac tgagtgtcag gcgtggaatg agataaacgc ggccataaca gcggaatgac
      841 accggtaaac cgaaaggcag gaatgcgggg gagcacgagg gagccaccag ggggaaacgc
      901 ctggtatctt taagccgcat cgggtttcgc caccactgat ttgagcgtca gatttcatga
      961 tgtttgtcag gggggcggag cctatggaaa aacggcttcg ccgcggcctt atctcttccc
     1021 tgttaagctc cttcctggta tctcccagga aatttccgcc ccgcctgtaa gccggcaccg
     1081 ctcgccgcag ccgaacgacc gagcgcagcg agtcagtgag cgaggaagcg gaatatatcc
     1141 tgtactacat atcctgctga cgcgctggtg ccgccttttt tctcctgcta catgaagcac
     1201 ttcactgatt tccacatccg tgccaacata gtcagccagt atacactccg ctagcgctac
     1261 gtgactggtt cagggctgcg ccccgaaacc cgctaacaac ctctctgcta ctggatatca
     1321 ccccatgcca tctgaatatg atgaacaacg gggttcgact gatacgcagc ttcccggcga
     1381 atatgacctt tttgatttaa tggcgaaggt tactgaagag atcctgcatg cccctgtgga
     1441 ttctgggccg cctgtcggcc gggaagcgtt atagcttttt cgcttgcccg cgtacgtggt
     1501 aatacgccgg tattaccttt tatttcttta ttttcatgta attacagtgg gtttttaata
     1561 cctgggtatt actcgtgaaa acgaaacatt actttttttt cttttaattc atgcagttgc
     1621 gatgaaaatc gcggctgcgt taggtgtatg accattttga ggttgaaaaa taatcaacca
     1681 tggcgggtga tttacgcagg ttaaggggag atcgtgacaa aaaaaagcgt tcctcactgt
     1741 atcgttcatg caggcatgaa cgggttattc ttcctgacta cagaattaca tcgctccttc
     1801 agttcataca tcacttttac aacactttta caacactcct tcggcctgta catcactttt
     1861 acaacacttt tgcatcactt ttacatcatt tatacatcac ttttacatca ttccttcagc
     1921 tcatacgtca ctttcatcct ctgtgccatt tgtacatcac ccccttcctg aacgtgctga
     1981 cagcgggttt tccggctgcg ccggcaacgc ttcacggcca cgcaataaat tgcgtccccg
     2041 ttcaccgttt tcggatggga agaacgccgg aaacaggact tcccctggct gaatggtgtg
     2101 aatttccgcg ctatgcactt gcgcgcatac tcatgcatgc cgtaaaaaca gagcctgcgc
     2161 gtttctggcg ggttttcggg tggtttgttg cctgttttac cggtttcccg tcagaaacgc
     2221 cctcagagcc tctcaggcgg tgcacgcaag ggatgttatg tttaatcggt ctgaccgtca
     2281 ggtacaaaaa aaagccctta gggggctttt tttttgctat gagttagcca tattttcgtt
     2341 aagacatggc ttcatgattc gggagtggtt attcgttgtt ctcgcgaaaa tgaattggtt
     2401 agatattcat caaattcctg tccagaatgc agcattagat ggcatgtcgt tgatgcggta
     2461 ggtcaggata ttcgtccact ggagaaaacg tttcacaatg cttgccagga gtcgtactgg
     2521 ttaaaagtaa atcgtcaaac gcatctcccg gtgtaaacgc tgaactaacc aatcacagcg
     2581 atgccaagcc gctccatgag caacgatgcc tggtagctgt ctaacttaac gccttgtaaa
     2641 tcaacacccc gaatatctaa gtcacctaac tccgaattgg tcagatcgca atgtgtgaag
     2701 tttgctgctc gccagtcgaa agtcgaaaac tcgccgccgg agagatctga accactgaac
     2761 gtcgcaccca gtacctgagt ccccatccag cggttttccc acagctcaca cttttccaac
     2821 acgactttcg aaaaattggc gtagcttaga ttagtattag tgatatatgc gctgcaaaac
     2881 caggtgcgcg tggtgatcat attcataaag cttgcaccgc ggaaatctgc gccttgtgcg
     2941 cggcagtggc gaatttcaat gcccaaggca ctgacgttgc ggaaatctgc cattgataaa
     3001 tcacagcttt tgaaaatggc atctttcagc attgcgcgac taaaattgca ccctttctga
     3061 ctttcgcgat c
//
