LOCUS       CP082466                3629 bp    DNA     circular BCT 11-JAN-2022
DEFINITION  Salmonella enterica subsp. enterica serovar Brandenburg strain
            FSIS1607501 plasmid pF18S015-2, complete sequence.
ACCESSION   CP082466
VERSION     CP082466.1
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 3629)
  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 3629)
  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 3629)
  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..3629
                     /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="pF18S015-2"
                     /geo_loc_name="USA:CA"
                     /collection_date="2016"
                     /collected_by="USDA-FSIS"
     gene            524..1186
                     /locus_tag="BHE67_024060"
     CDS             524..1186
                     /locus_tag="BHE67_024060"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_010308590.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="UAE50549.1"
                     /translation="MPSNSIKASLSAARIGTYESILGGPAGVHRTEKALRLYMWNAQIS
                     AAFFMPLHVCEVITRNAVSEVLETVYGARWPWSIGFERSLPIPVHGYKPKDDLINGRRN
                     QPTTGKVIPELKFVFWQKMLTGRFDNRLWNNHILTAFPHAAAQGLNAAQLRQNLYNDLE
                     TVRKLRNRIAHHEPILNRNLEDDFATIKRIIAYRCQHSLEWMLKNQVLLPLLTLKPL"
                     /name="hypothetical protein"
     gene            complement(1222..2061)
                     /locus_tag="BHE67_024065"
     CDS             complement(1222..2061)
                     /locus_tag="BHE67_024065"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001354646.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="UAE50550.1"
                     /translation="MLTLIIFFVLLIAACFFCFAPPRRGYDRNEIIPYKIKLSINKYRL
                     YIYSSGKVRQYLLFLVILSLYYSIAEPFKSELIKNISYSLMAAFIFDTGLNFSKENITK
                     GVISTRWHNDLYSSFERMKAINKIYYPSNKEINTEGLSKAITSSLFNDDANSFAKRDFC
                     LMWDLSSEKYLSYKEIIIRKGDKLDAVCLRFINDDYKFLVNFNRDEEVFKYFPSIMQPS
                     LKTYRALSRLVNSIKDPSRFKFTTESLEMELLEYLELRNELFNDIEEVMGSYAQRAP"
                     /name="hypothetical protein"
     gene            complement(3058..3252)
                     /locus_tag="BHE67_024070"
     CDS             complement(3058..3252)
                     /locus_tag="BHE67_024070"
                     /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="UAE50548.1"
                     /translation="MNKQQQTALNMARFIKSQSLTLLEKLDALDADEQAAMCERLHELA
                     EELQNSIQVRFETESETGT"
                     /name="Rop family plasmid primer RNA-binding protein"
     Typing          2..118
                     /name="MOBF"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="94.068"
                     /coverage="82.0"
                     /evalue="1.0399999999999998e-42"
     Typing          2903..2985
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="3.79e-36"
     Typing          3289..3387
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="98.0"
                     /coverage="100.0"
                     /evalue="1.35e-41"
     Typing          3512..3628
                     /name="MOBF"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="97.479"
                     /coverage="82.0"
                     /evalue="2.23e-49"
     Typing          complement(2331..2890)
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="94.139"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 ccgcttttta ggggtggtac tgactatttt cataaaaaac atcatcttat attaggggtg
       61 ctgctagcgg cgcggtgtgt ttttttacag gacgcccctg ggggcgctgc taggggtgtc
      121 tgttcagata tgtagcaatg agtcagggat tcacgaactg aaaatgtccg aaaatgtgtc
      181 tcatgggtac tgtatgcgcc caaaccgatc gtcattcact ttcatgcata gctatgcagt
      241 gagctgaaag cgatcctgac gcatttttcc ggtttacccc ggggaaaaca tctctttttg
      301 cggtgtttgc ggcagaatcg cgttcagcgc gttttagcgg tgcgcgcaag gagacgttat
      361 ggtaaatacg gagtatttta aattgcggga attaaaacaa caaaggcccg ctgtactcta
      421 tacagcgggc ctttgttgta tatctctgtc gtttgtcctc ggggggaagc attactgcta
      481 acaagtcccg tggctagtaa cttcattata aggatcgttg acgatgccgt caaacagcat
      541 aaaggctagc ttgtctgctg ccagaatagg aacctatgaa agcattttag gtggaccggc
      601 aggcgttcac cggacggaaa aagctctgag gctttacatg tggaacgcgc agatatccgc
      661 tgctttcttt atgcccttgc atgtatgcga ggttatcacg cgaaatgctg tttcagaggt
      721 tctcgaaacg gtatacggag ctagatggcc ctggtccatt ggttttgaac gaagtcttcc
      781 tatccctgtt catggttata aacccaaaga tgacctcatc aatggacgac gaaaccaacc
      841 cacgacaggg aaagttattc ctgaacttaa gtttgttttc tggcagaaaa tgctgaccgg
      901 gagattcgat aaccgcctct ggaacaatca tatactgacg gcttttcctc atgcggctgc
      961 acagggattg aatgcagcac agttacggca gaatctctac aacgatctgg aaacggtgag
     1021 aaaactgcgc aatcgtattg cgcatcatga acctattctc aaccgcaatc tggaagatga
     1081 ttttgctacg ataaagagaa ttatcgcgta tcggtgtcag cattcattgg agtggatgct
     1141 gaaaaaccag gtgttactcc ctctacttac acttaaacct ctctaaaaat ataagtaagt
     1201 actatcgagg gctatcatga tctatggtgc cctctgagca tagctaccca ttacttcttc
     1261 tatatcattg aataattcat ttcttaactc taagtattct agtaactcca tttctaatga
     1321 ctctgtcgtg aacttaaatc tagaaggatc tttgattgag tttactagtc ttgataacgc
     1381 tctataagtt ttgagtgaag gttgcattat agaaggaaag tatttgaaaa cctcttcatc
     1441 tctgttgaaa ttaactaaaa acttgtagtc atcatttata aatctcaagc atacagcgtc
     1501 aagcttatcg ccttttctta ttattatttc tttgtaggaa agatattttt cagaagataa
     1561 gtcccacatc aagcaaaaat ctctctttgc gaacgagttc gcgtcatcat tgaaaagaga
     1621 tgatgtgatg gctttggata gaccttctgt gtttatctct ttgttggatg gatagtaaat
     1681 tttattaatt gctttcattc tctcaaatga tgaatatagg tcattatgcc accttgttga
     1741 aatcacccct ttagttatat tctccttgct aaaattaagc cctgtatcaa aaataaatgc
     1801 agccatcagt gagtatgata tgttttttat taactcagac ttaaatggtt ccgctatgga
     1861 gtagtacagc gataaaataa ctaaaaataa aaggtattgt cttacctttc ccgatgagta
     1921 tatgtaaagg cgatatttat ttattgatag ttttattttg tatggaatga tctcatttct
     1981 gtcatatcct cttcgtggtg gagcaaaaca aaagaaacat gcagcaatta ataaaacaaa
     2041 aaagatgatc agtgtaagca agttcggctc ctgtgtatgc tcactatgca tgattgtctt
     2101 gagatctaac gatcctgaag gtagtcttgt ccgtaaacga aaaaaccgcc cagcaaggcg
     2161 gcttttcgaa ggttctcaga gcagcaactc tttgaaccaa ggtaactggc ttggaggagc
     2221 acagccacca aatctgtcct ttcagtttag ccttaaccgg cgcataactt caagactaac
     2281 tcctctaaac ggttaccaat ggctgctgtc agtggcgttt ttacgtgtct ttccgggttg
     2341 gactcaagat gacagttacc ggataaggcg cagcggtcgg gctgaacggg gggttcgtgc
     2401 acacagccca gcttggagcg aacgacctac accgaactga gataccaaca gcgtgagcta
     2461 tgagaaagcg ccacgcttcc cgaagggaga aaggcggaga ggtatccggt aagcggcagg
     2521 gtcggaacag gagagcgcac gagggagctt ccagggggaa acgcctggta tctttatagt
     2581 cctgtcgggt ttcgccacct ctgacttgag cgtcgatttt tgtgatgctc gtcagggggg
     2641 cggagcctat ggaaaaacgc cagcggcgcg gccttttgtc ctggctttgc cttgttgctc
     2701 acatgttctt tccggcctta tcccctgatt ctgtggataa ctgtgttacc gtttttgtgt
     2761 gagtcagtac cgctcgccgc agccgaacga ccgagcgtag cgagtcagtg agcgaggaag
     2821 cggaaaagcg cctggacgcg cattttctcc ttacgcatct gtgcggaatt tcacacccgg
     2881 catggggcac ttttcataca atctgcactg atgccgcata gttaagccag tatacactcc
     2941 gctatcgcta cgtgactggg tcagggcttc gccccgacac ccgctgacgc gccctggcgg
     3001 gcttgtctgc tgccgaaaac gctcgcggac aagccgtgag cgcctccgtc agcttcgtta
     3061 tgttcctgtt tcactttcgg tctcaaagcg aacctggatg ctgttctgga gttcttccgc
     3121 gagttcgtgc agtcgttcgc acatggccgc ctgttcgtcg gcatccagag catccagttt
     3181 ttcaagcagt gtcaggctct ggcttttgat aaatcgcgcc atattcagcg cagtttgttg
     3241 ctgtttgttc accttccgtt gttctccgtc agtaccgggt gtcgggggga ccctgagcag
     3301 gtggtaattg taagatgttg cgggcgacgg tattacaatt gcacatcctg tcctgttttt
     3361 ttaggacgta tcatggcaca gcatatcaac tgataaataa tccctgtgca gtgcagccgc
     3421 tgttgcataa aatttcgctc tgcgtcgagt gtttcttaat caataattcc gctgatactc
     3481 cggaaaaacg cgagtctgtt ctcattcctg aaatgcccac accccacgca aaaacaagtt
     3541 tttgctgatt tttctttata aatagagagt tatgacaaat tagttcttct tgctctcttt
     3601 gtgatattta aaaaagcggt gttggcgca
//
