LOCUS       AAGMXG010000106          704 bp    DNA     linear   BCT 11-JUL-2019
DEFINITION  Salmonella enterica subsp. enterica strain ADRDL-LA-86-2014
            SAMN03780346-rid5147803.denovo.108, whole genome shotgun sequence.
ACCESSION   AAGMXG010000106 AAGMXG010000000
VERSION     AAGMXG010000106.1
DBLINK      BioProject: PRJNA280335
            BioSample: SAMN03780346
            Sequence Read Archive: SRR2533653
KEYWORDS    WGS; GMI.
SOURCE      Salmonella enterica subsp. enterica
  ORGANISM  Salmonella enterica subsp. enterica
            Bacteria; Pseudomonadati; Pseudomonadota; Gammaproteobacteria;
            Enterobacterales; Enterobacteriaceae; Salmonella.
REFERENCE   1  (bases 1 to 704)
  CONSRTM   GenomeTrakr network: Whole genome sequencing for foodborne pathogen
            traceback
  TITLE     Direct Submission
  JOURNAL   Submitted (14-JUL-2018) Center for Food Safety and Applied
            Nutrition, US Food and Drug Administraion, 5100 Paint Branch Pkwy,
            College Park, MD, USA
COMMENT     This draft WGS assembly was generated by running SKESA to generate
            a de-novo assembly. The de-novo assembly was then concatenated with
            contigs generated using a guided assembler using antimicrobial
            resistance genes as baits to comprehensively catalog the set of
            resistance genes in the isolate. Note, some parts of the contigs
            derived from the guided assembler may overlap de-novo contigs, and
            other guided assembler contigs. De-novo contigs can be
            differentiated from guided assembler contigs by their names , which
            include either 'denovo' or 'guided'.
            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/
            
            ##Genome-Assembly-Data-START##
            Assembly Date         :: 14-JUL-2018
            Assembly Method       :: SKESA v. 2.2
            Assembly Name         :: PDT000085346.2
            Long Assembly Name    :: NCBI Pathogen Detection Assembly
                                     PDT000085346.2
            Genome Coverage       :: 67x
            Sequencing Technology :: ILLUMINA
            ##Genome-Assembly-Data-END##
            
            ##Genome-Annotation-Data-START##
            Annotation Date                   :: 07/07/2019 02:23:33
            Annotation Method                 :: Best-placed reference protein
                                                 set; GeneMarkS-2+
            Annotation Pipeline               :: NCBI Prokaryotic Genome
                                                 Annotation Pipeline (PGAP)
            Annotation Provider               :: NCBI
            Features Annotated                :: Gene; CDS; rRNA; tRNA; ncRNA;
                                                 repeat_region
            Annotation Software revision      :: 4.8
            Genes (total)                     :: 4,978
            CDSs (total)                      :: 4,884
            Genes (coding)                    :: 4,776
            CDSs (with protein)               :: 4,776
            Genes (RNA)                       :: 94
            rRNAs                             :: 6, 2, 1 (5S, 16S, 23S)
            complete rRNAs                    :: 4 (5S)
            partial rRNAs                     :: 2, 2, 1 (5S, 16S, 23S)
            tRNAs                             :: 73
            ncRNAs                            :: 12
            Pseudo Genes (total)              :: 108
            CDSs (without protein)            :: 108
            Pseudo Genes (ambiguous residues) :: 0 of 108
            Pseudo Genes (frameshifted)       :: 39 of 108
            Pseudo Genes (incomplete)         :: 67 of 108
            Pseudo Genes (internal stop)      :: 31 of 108
            Pseudo Genes (multiple problems)  :: 27 of 108
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
FEATURES             Location/Qualifiers
     source          1..704
                     /organism="Salmonella enterica subsp. enterica"
                     /mol_type="genomic DNA"
                     /submitter_seqid="SAMN03780346-rid5147803.denovo.108"
                     /strain="ADRDL-LA-86-2014"
                     /isolation_source="bovine liver abscess"
                     /host="Bos taurus"
                     /sub_species="enterica"
                     /db_xref="taxon:59201"
                     /geo_loc_name="USA: CO"
                     /collection_date="2014"
                     /collected_by="ADRDL"
     gene            <1..>704
                     /locus_tag="AGR40_24855"
     CDS             <1..>704
                     /locus_tag="AGR40_24855"
                     /inference="COORDINATES: protein motif:HMM:PF00509.16"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=3
                     /transl_table=11
                     /product="hemagglutinin"
                     /protein_id="EBP8252082.1"
                     /translation="FQNVNKVTYGKCPKYIRQNTLKLATGMRNVPEKQIRGIFGAIAG
                     FIENGWEGMVDGWYGFRYQNSEGTGQAADLKSTQAAIDQINGKLNRVIERTNEKFHQI
                     EKEFSEVEGRIQDLEKYVEDTKIDLWSYNAELLVALENQHTIDLTDAEMNKLFERTRR
                     QLRENAEDMGGGCFKIYHKCNNACIGSIRNGTYDHYIYRDEALNNRFQIKGVELKSGY
                     KDWILWISFAISCFLI"
ORIGIN      
        1 cattccaaaa tgtgaacaaa gttacatatg gaaaatgtcc caagtatatc agacaaaaca
       61 ctttaaagct ggccactggg atgaggaatg taccagaaaa gcaaatcaga ggaatctttg
      121 gggcaatagc gggattcatc gaaaacggct gggaaggaat ggttgatgga tggtatgggt
      181 tccgatacca aaactctgaa ggaacagggc aagctgcaga tctaaagagc actcaagcag
      241 ccatcgacca gatcaatgga aaattaaaca gagtgattga aagaaccaat gagaaattcc
      301 atcaaataga gaaggaattc tcagaagtag aaggaagaat tcaggacttg gagaaatatg
      361 tagaagacac caaaatagac ctatggtcct acaatgcaga attgctggtg gctctagaaa
      421 atcaacatac aattgactta acagatgcag aaatgaacaa attgtttgag agaactagac
      481 gccaattaag agaaaacgca gaagacatgg gaggtggatg tttcaagatt taccacaaat
      541 gtaataatgc atgcattgga tcaataagaa atgggacata tgaccattac atatacagag
      601 atgaagcatt aaacaaccga tttcagatca aaggtgtaga gttgaaatca ggctacaaag
      661 attggatact ctggatttca ttcgccatat catgcttctt aatt
//