LOCUS       CP082467                3830 bp    DNA     circular BCT 11-JAN-2022
DEFINITION  Salmonella enterica subsp. enterica serovar Brandenburg strain
            FSIS1607501 plasmid pF18S015-3, complete sequence.
ACCESSION   CP082467
VERSION     CP082467.1
DBLINK      BioProject: PRJNA292666
            BioSample: SAMN05726932
KEYWORDS    .
SOURCE      Salmonella enterica subsp. enterica serovar Brandenburg
  ORGANISM  Salmonella enterica subsp. enterica serovar Brandenburg
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Salmonella.
REFERENCE   1  (bases 1 to 3830)
  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 3830)
  CONSRTM   NARMS: The National Antimicrobial Resistance Monitoring System
  TITLE     Direct Submission
  JOURNAL   Submitted (02-JUL-2019) Center for Veterinary Medicine, US Food and
            Drug Administration, 8401 Muirkirk Rd, Laurel, MD, USA
REFERENCE   3  (bases 1 to 3830)
  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                     :: F18S015
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 238x
            Sequencing Technology             :: PacBio Sequel
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI
            Annotation Date                   :: 09/02/2021 13:39:58
            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)                     :: 4,817
            CDSs (total)                      :: 4,696
            Genes (coding)                    :: 4,561
            CDSs (with protein)               :: 4,561
            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)              :: 135
            CDSs (without protein)            :: 135
            Pseudo Genes (ambiguous residues) :: 0 of 135
            Pseudo Genes (frameshifted)       :: 75 of 135
            Pseudo Genes (incomplete)         :: 68 of 135
            Pseudo Genes (internal stop)      :: 19 of 135
            Pseudo Genes (multiple problems)  :: 23 of 135
            CRISPR Arrays                     :: 1
            ##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..3830
                     /organism="Salmonella enterica subsp. enterica serovar
                     Brandenburg"
                     /mol_type="genomic DNA"
                     /strain="FSIS1607501"
                     /serovar="Brandenburg"
                     /isolation_source="animal-swine-market swine"
                     /sub_species="enterica"
                     /db_xref="taxon:149387"
                     /plasmid="pF18S015-3"
                     /geo_loc_name="USA:CA"
                     /collection_date="2016"
                     /collected_by="USDA-FSIS"
     gene            complement(join(2852..3830,1..926))
                     /locus_tag="BHE67_024075"
     CDS             complement(join(2852..3830,1..926))
                     /locus_tag="BHE67_024075"
                     /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="nitrate- and nitrite sensing domain-containing
                     protein"
                     /protein_id="UAE50552.1"
                     /translation="MSWAYRISMQMKLFIALFPLLLALVWFAGSGIVSRINTEQQMNTI
                     GQLTTLARSAGDVVHQLQSERGMSAGFIGARGQKFRDDLAAQRQLTDKVLATFKRLLTD
                     TNKDLLQGNIAAPLKTFNESIQFLDSTRTAISELTIDSPKASQFYTQTISDVLKFVGGM
                     GHLSTSGSMVNELAAYYSLLNLKEQAGVERALLSNIFSMDRFDDGQFSMFSDVVGQQDA
                     WLTAARSFSTPVQAAELDKSLQSAEATRALELRETAFNKAAEGGFGVNPTDWFNLQTQR
                     IETLRKVENRAVDALQEHAALLAHNARVDWQSFLVISLVALLIAIAFAVMVARSIQQQL
                     NGTLKTIAEMDGDLTRRLDVPGSDELSALNRAYNQAIENIQHIVQEIKSGAVVLRSASS
                     DIAAGNQDLAQRTDEQAASIVETAASMEQISTAITQTADNASEAERLIHSMERDVLEAN
                     RVSNEASQSMAEIRSSSEQISQIVASIDEISFQTNLLALNAAVEAARAGELGKGFAVVA
                     TEVRNLSQRCAREASQIRELINQNMDKIGEGVARVTASGTALKAAAENTGRMKQYVSDI
                     ARAANEQSLGVSQVHQALNQLEQVTQQNAALVSQAASASQMLDGQSEAMSTLVDRFIV"
                     /name="nitrate- and nitrite sensing domain-containing
                     protein"
     gene            2126..2326
                     /locus_tag="BHE67_024080"
     CDS             2126..2326
                     /locus_tag="BHE67_024080"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001046776.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="UAE50553.1"
                     /translation="MNLFPDERLLFVRMISAMLRRSGGDAGAVMFEAYRHIVSDTNQAR
                     RSCMLDLLESVRHDYVHGGYT"
                     /name="hypothetical protein"
     gene            complement(2374..2562)
                     /locus_tag="BHE67_024085"
     CDS             complement(2374..2562)
                     /locus_tag="BHE67_024085"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000165985.1"
                     /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="UAE50551.1"
                     /translation="MTKQESAALNMAKFIRAQSLLLLEKLDVLDLDDEAADCERMHEQA
                     EALYQKLSARFGIQDGE"
                     /name="Rop family plasmid primer RNA-binding protein"
     Typing          1744..1916
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="91.379"
                     /coverage="100.0"
                     /evalue="9.47e-61"
     Typing          complement(1223..1819)
                     /name="rep_cluster_2335"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="91.211"
                     /coverage="99.0"
                     /evalue="0.0"
ORIGIN
        1 acacgggcat tgtgggcaag cagcgcagca tgttcctgca aggcatccac cgcgcgattt
       61 tccacctttc gcagcgtttc aatacgctgg gtctgaaggt taaaccagtc agtcgggttg
      121 actccaaatc cgccttcggc ggctttatta aaagccgtct cccgcagttc aagagcacga
      181 gttgcttcag cggactgaag agatttgtcc agctcagccg cctgcacagg tgtgctaaag
      241 ctgcgagctg ccgtcagcca ggcatcctgc tggcctacca catcgctaaa catgctgaac
      301 tggccgtcgt caaagcgatc catcgagaag atattggaca gcagcgcacg ttctacacca
      361 gcctgctcct tcaaattcaa gagactataa taagccgcca gttcgttcac catcgagcct
      421 gaggtgctta aatgccccat cccgccgaca aacttcagca cgtcagagat ggtttgggta
      481 tagaactgac tcgcttttgg tgaatcgata gttaattcgc tgatggcggt acgggttgag
      541 tcgagaaact gaatactttc attaaacgtt ttcagggggg cggcaatatt tccctggagt
      601 aaatccttat tcgtatcggt cagcaaccgc ttaaatgttg ccagcacctt gtcggttaac
      661 tgccgctggg cagctaagtc atcgcgaaac ttttggccgc gcgcgccgat aaatccagcg
      721 ctcattccac gttcgctctg gagttgatgc accacatcac ccgcgctgcg ggcgagcgtg
      781 gtgagctgtc caatggtgtt catctgctgt tcggtattga tacggctgac aatacccgaa
      841 ccggcgaacc agaccaaggc aagcagtagc gggaataatg caataaacaa cttcatttgc
      901 attgaaatac gataagccca tgacatatcg atactttcct tactttcttg agggatcgca
      961 ggagtatcgg tagatacatg cataaacttt atagtttatt gttgggggaa cgggcaccac
     1021 attcggcagt ggcgctggta gcaatccata aaggatcttc ttgagatcct ttgacgatcg
     1081 tcgtaatctc ttgctctgta aacgaaaaaa ccacccttgc aggtggtttt tcgaaggtta
     1141 gataatcctg gcagattctc taaccgtggt aacagtcttg tgcgagacat gtcaccaaat
     1201 ttgtccttct agtgtagcct cagtcaggcc actacttcaa gaactctcga tacatctctc
     1261 gcacatcctg tttaccagtg gccgctgcca gtggcgattt ttcgtgtctt tccgggttgg
     1321 actcaagacg atagttaccg gaaaaggcgc agcagtcgga ctgaacgggg ggttcgtgca
     1381 tacagtccag cttggagcga actgccttcc cggaactgag tgtcaggcgt ggaatgagat
     1441 aaacgcggcc ataacagcgg aatgacaccg gtaaaccgaa aggcaggaac aggagagcgc
     1501 acgagggagc taccaggggg aaacgcctgg gatctttata gtcctgtcgg gtttcgccgc
     1561 cactgatttg agcgtcagat ttcgtgatgc ttgtcagggg ggcggagcct atggaaaaac
     1621 ggcttcgccg cggccttacc gtttccctgt taagtttctt cctggcatct cccaggaaat
     1681 ttccgcccca ttcgtaatcc cgcaccgctc gccgcagccg aacgaccgag cgcagcgagt
     1741 cagtgagcga ggaagcggaa tatctcctgt ctcatatatt ccgcttacgc tctgctgctg
     1801 cattttcctc ctgccacatg aagcacttca ctgattcccg cacccgtgcc tacataataa
     1861 gccagtatac actccgctag cgctacgtga ctggttcagg gctgcgcccc gacacccgct
     1921 aaaagcactg acgcgcctgc ggcttgccca accccgcgcc gtccgggaaa gaatttcccg
     1981 atcgacccga cgtttctgtt tacctgtgat gttaacgttt ggatcttttt cccgggttta
     2041 cctattttaa tgaagcgtaa tgaagcgttc acagctgacg ttaatagatg ggtgcttcat
     2101 gtttggtttt tcaccaggag aacttatgaa ccttttcccc gatgaacgtc tgctctttgt
     2161 gcggatgatt tccgctatgc ttcgccgttc gggcggtgat gcgggtgctg ttatgtttga
     2221 ggcgtatcgc catattgtgt ccgataccaa tcaagctcgt cgttcctgca tgctcgacct
     2281 gctcgaaagc gtcaggcatg actatgtaca cggtggatat acatagttgc cctggatacg
     2341 cttttcgtct aagtgagcgt tcttttcgtc tctttattcg ccgtcctgta taccgaagcg
     2401 tgcgctcagc ttctgataaa gcgcttctgc ctgttcgtgc attcgctcac agtcggctgc
     2461 ctcgtcatca agatcgagca cgtcgagttt ttcgagcagc agcagcgact gcgcccggat
     2521 aaattttgcc atgttcagtg cggctgattc ctgttttgtc atacggcttt ttcccggttt
     2581 tatggtgatc gcagactgaa atcttacttc attcacttga gtgcatagcc atgcaggtac
     2641 gcagaaatca tcaggggcgt tttttctcga tatgggcaca gaaaggtgta tgtttcaggt
     2701 cggagtcctc agaaacgctc tcagagcctc tcaggcggtg cacgcaacag atgttatggt
     2761 aaatcctagt tatttgcagg cataaaaaag ccgcctttta ggcggttttt tctgattgta
     2821 agttatcaag accggatgct gaacggcagt atcagacaat aaagcgatcg accagcgtgg
     2881 acatcgcttc agactggccg tccagcatct ggctggcgct cgccgcctga gagaccagcg
     2941 ctgcgttttg ctgagtgacc tgctccagct gattcagtgc ctgatgcacc tgcgacacgc
     3001 caagcgactg ctcattcgcc gcacgggcaa tatcgctcac gtactgtttc atccgcccgg
     3061 tattttccgc cgctgctttc agcgcggtgc cggacgcggt gactcgtgct accccttcgc
     3121 caatcttatc catattctgg ttaatcagct cacggatctg actggcctct cgtgcacagc
     3181 gctgggaaag gttacgcacc tccgtcgcca ctaccgcaaa gcctttgcca agctcaccgg
     3241 cacgtgccgc ttcaacggcg gcgttaagcg ccagcaagtt ggtctggaaa gaaatctcat
     3301 caattgacgc aacaatctgg gaaatctgct cgctggaaga acgaatttcc gccatgctct
     3361 gactggcctc gttagagacg cgattagctt ccagtacgtc ccgctccatc gaatgtatca
     3421 gacgctccgc ctcgctggcg ttatcggcgg tctgggtgat cgcagtagaa atctgctcca
     3481 tgctggcggc cgtttccaca atcgatgccg cctgttcatc cgtacgctgg gccagatcct
     3541 gattaccggc agcgatatca ctactggcgc tacgcaacac caccgcaccg gacttaattt
     3601 cttgcacgat atgctgaata ttctcaatcg cttggttata ggcacggttc agggctgaga
     3661 gctcgtcgct gccggggacg tcaagacgac gtgtcaggtc gccgtccatc tctgcgatgg
     3721 ttttcagcgt accgttcagt tgctgctgga tactgcgtgc caccatcacc gcaaaggcga
     3781 tagcaatcag tagggcaacc aggctgatta ccaggaagga ctgccagtcg
//
