LOCUS       NZ_CP041007             3360 bp    DNA     linear   CON 07-JAN-2024
DEFINITION  Salmonella enterica strain FDAARGOS_768 plasmid unnamed2.
ACCESSION   NZ_CP041007
VERSION     NZ_CP041007.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN11056483
            Assembly: GCF_006365335.1
KEYWORDS    RefSeq.
SOURCE      Salmonella enterica
  ORGANISM  Salmonella enterica
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Salmonella.
REFERENCE   1  (bases 1 to 3360)
  AUTHORS   Jackson,S., Kralj,J., Tallon,L., Sadzewicz,L., Vavikolanu,K.,
            Mehta,A., Aluvathingal,J., Nadendla,S., Yan,Y. and Sichtig,H.
  TITLE     FDA dAtabase for Regulatory Grade micrObial Sequences (FDA-ARGOS):
            Supporting development and validation of Infectious Disease Dx tests
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 3360)
  AUTHORS   Jackson,S., Kralj,J., Tallon,L., Sadzewicz,L., Vavikolanu,K.,
            Mehta,A., Aluvathingal,J., Nadendla,S., Yan,Y. and Sichtig,H.
  TITLE     Direct Submission
  JOURNAL   Submitted (11-JUN-2019) Center for Devices and Radiological Health,
            US Food and Drug Administration, 10903 New Hampshire Avenue, Silver
            Spring, MD 20993-0002, USA
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: canu v. 1.7, SPAdes v. 3.11.1
            Genome Coverage                   :: 623.76x
            Sequencing Technology             :: Pacbio; Illumina
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 01/07/2024 02:15:27
            Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline
            (PGAP)
            Annotation Method :: Best-placed reference protein set; GeneMarkS-2+
            Annotation Software revision      :: 6.6
            Features Annotated                :: Gene; CDS; rRNA; tRNA; ncRNA
            Genes (total)                     :: 4,839
            CDSs (total)                      :: 4,714
            Genes (coding)                    :: 4,612
            CDSs (with protein)               :: 4,612
            Genes (RNA)                       :: 125
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 86
            ncRNAs                            :: 17
            Pseudo Genes (total)              :: 102
            CDSs (without protein)            :: 102
            Pseudo Genes (ambiguous residues) :: 0 of 102
            Pseudo Genes (frameshifted)       :: 37 of 102
            Pseudo Genes (incomplete)         :: 77 of 102
            Pseudo Genes (internal stop)      :: 20 of 102
            Pseudo Genes (multiple problems)  :: 29 of 102
            Pseudo Genes (short protein)      :: 1 of 102
            CRISPR Arrays                     :: 3
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP041007.1.
            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..3360
                     /organism="Salmonella enterica"
                     /mol_type="genomic DNA"
                     /strain="FDAARGOS_768"
                     /isolation_source="ATCC Isolate"
                     /host="NIST Mixed Microbial RM strain"
                     /culture_collection="ATCC:700720"
                     /type_material="type strain of Salmonella enterica"
                     /db_xref="taxon:28901"
                     /plasmid="unnamed2"
                     /geo_loc_name="USA: VA"
                     /collected_by="NIST<ATCC"
                     /note="NIST Mixed Microbial RM strain"
     gene            4..1761
                     /gene="blaR1"
                     /locus_tag="FIU17_RS24320"
                     /old_locus_tag="FIU17_24315"
     ARG             5..1758
                     /name="blaR1"
                     /gene="blaR1"
                     /gene_name="beta-lactam sensor/signal transducer BlaR1"
                     /tool="amrfinderplus"
                     /drug_class="BETA-LACTAM"
                     /identity="99.66"
                     /coverage="100.0"
     gene            1751..2131
                     /gene="blaI"
                     /locus_tag="FIU17_RS24325"
                     /old_locus_tag="FIU17_24320"
     ARG             1752..2128
                     /name="blaI"
                     /gene="blaI"
                     /gene_name="penicillinase repressor BlaI"
                     /tool="amrfinderplus"
                     /drug_class="BETA-LACTAM"
                     /identity="100.0"
                     /coverage="100.0"
     gene            2395..2973
                     /locus_tag="FIU17_RS24330"
                     /old_locus_tag="FIU17_24325"
     CDS             2395..2973
                     /locus_tag="FIU17_RS24330"
                     /old_locus_tag="FIU17_24325"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000690624.1"
                     /GO_function="GO:0003677 - DNA binding [Evidence IEA];
                     GO:0000150 - DNA strand exchange activity [Evidence IEA]"
                     /GO_process="GO:0006310 - DNA recombination [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="recombinase family protein"
                     /protein_id="WP_000690625.1"
                     /translation="MKIGYARVSTGLQNLNLQEDQLNQYGCEKIFSDHISGSKSKRPGL
                     DKAIEFARAGDTIVVWRLDRLGRNMEDLITLVNELNNRGVSFHSLEENITMDKSSSTGQ
                     LLFHLFAAFAEFERNLILERSSAGRIAARARGRYGGRPEKLNKQDLKLLKTLYDNGTPI
                     KTIAEQWKVSRTTIYRYLNRLNNQENKDK"
                     /name="recombinase family protein"
     gene            3099..>3360
                     /locus_tag="FIU17_RS24335"
                     /old_locus_tag="FIU17_24330"
     CDS             3099..>3360
                     /locus_tag="FIU17_RS24335"
                     /old_locus_tag="FIU17_24330"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000583527.1"
                     /GO_function="GO:0003677 - DNA binding [Evidence IEA];
                     GO:0000150 - DNA strand exchange activity [Evidence IEA]"
                     /GO_process="GO:0006310 - DNA recombination [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="recombinase family protein"
                     /protein_id="WP_140192262.1"
                     /translation="MIIGYARVSSIDQNLERQLDNLKTFGVEKIFTEKQSGKSVENRPV
                     FQEALNFVRMGDRFVVESIDRLGRNYDEIIETVNYLKEKDVQ"
                     /name="recombinase family protein"
ORIGIN
        1 gaaatggcta agttattaat aatgagcata gtaagctttt gttttatatt tctattgtta
       61 ttatttttta ggtacatatt aaaacgctat tttaattata tgttaaatta taaagtttgg
      121 tatctaactc ttcttgcagg attaattcct ttcattccta ttaaattctc tctttttaaa
      181 tttaataatg tgaataatca agcgcccaca gttgaaagta agtcacacga cttgaaccat
      241 aacataaata ccaccaaacc tattcaagag ttcgcaacag atatccataa gtttaattgg
      301 gattcaattg ataatatctg cacagttatt tggatagttt tagttattat tttaagtttt
      361 aaatttttga aagccttatt atatcttaaa tatttaaaga aacagtcact ttatctaaac
      421 gaaaatgaaa aaaataaaat agatacgata cttttcaacc atcaatataa aaaaaatatt
      481 gtgattcgaa aagcagagac tattcaatct ccaataactt tttggtatgg gaaatatatt
      541 attttgattc ctagttcata ttttaaaagt gtaattgaca aaagactaaa atatataata
      601 ttgcatgaat atgctcatgt taaaaataga gatactttac atttaattat ctttaatatc
      661 ttctctatta ttatgagtta caatccatta gtacatattg taaaaagaaa gataattcat
      721 gacaatgaag tagaagccga tagatttgtc cttaataata ttaacaaaaa tgaatttaaa
      781 acttatgcgg aatctattat ggactccgta ttaaatgttc cattttttaa taaaaatata
      841 ttaagccatt catttaatgg taaaaagtca ttactcaaaa gaagattaat taatataaaa
      901 gaagccaatc tgaaaaaaca gtccaaatta attctaattt ttatttgtat ttttactttt
      961 ttgctcatgg taattcaaag ccagtttttg atggggcaat ccataactga ttataattat
     1021 aaaaagccct tacacaacga ttaccaaatt ttagataaaa gtaaaatttt tggttcaaat
     1081 agtggatctt tcgtcatgta cagcatgaag aaagacaaat actatattta taacgaaaaa
     1141 gaaagtagaa aaaggtattc tcctaattca acttataaaa tttatttagc tatgtttgga
     1201 cttgaccgac atattataaa tgatgaaaat tcacgtatgt catggaatca taagcattac
     1261 ccttttgatg cttggaataa ggaacaagat ttaaatacag caatgcaaaa ttcagttaat
     1321 tggtacttcg aacgtattag cgatcaaata ccaaagaact atactgcgac tcaactcaag
     1381 caattaaatt atggtaataa aaatttggga agttataaaa gctattggat ggaagatagt
     1441 ttgaaaatat ctaatcttga acaagtaata gtttttaaaa atatgatgga acaaaataac
     1501 cattttagta aaaaagcaaa gaatcaatta tcttcttcat tattgattaa gaaaaatgaa
     1561 aagtatgaac tgtatgggaa aacaggtaca ggtatagtaa acgggaagta taataatggg
     1621 tggtttgtag gttacgtaat tacaaatcat gataagtatt attttgctac acatttatca
     1681 gatggaaagc catctgggaa aaatgctgaa ttaatcagtg aaaaaatatt aaaagaaatg
     1741 ggtgttttaa atggccaata agcaagttga aatatctatg gctgaatggg atgttatgaa
     1801 tataatatgg ggtaaaaaat cagtatcagc taatgaaatt gtagttgaaa ttcaaaaata
     1861 taaagaagtt agcgataaaa cgattagaac attaatcaca agactatata aaaaagagat
     1921 tataaaacga tacaaatcag agaatattta tttttactca tcaaatatta aagaagacga
     1981 tattaaaatg aaaactgcta aaacctttct taataaactg tatggagggg acatgaaaag
     2041 tttagtgctg aattttgcga aaaatgaaga attaaataac aaagaaattg aagaattgcg
     2101 agacatttta aatgatatta gtaaaaagta attagagata tgtttcaaac ataatacata
     2161 tgtaaactat gcttgactct tattaaatta gttttgttaa taacatttaa aatatattat
     2221 taaagatgag agtgtacaga aaataaccat tttctataca ctctcttttt atgtctatat
     2281 atatagcgag tatacatatt ttagtgttca ataacccaac agaaaatcta tgttcataaa
     2341 tatggttaga attaagttat gatacaatga agatgtatat aggaggtttg tattttgaaa
     2401 ataggttatg caagagtttc aactggttta caaaatttaa atttgcagga agatcaatta
     2461 aatcaatatg gttgtgaaaa gatatttagc gaccacataa gtggatcaaa aagtaaacgt
     2521 cctggtttag ataaagccat tgaatttgcg agggcaggag atacgattgt tgtttggaga
     2581 ctagatagac tagggcgtaa tatggaagat ttaatcacat tagttaatga acttaataat
     2641 cgaggcgtga gttttcatag tttagaagaa aatataacaa tggataaatc aagttctaca
     2701 ggacaattgt tatttcattt attcgcagca tttgcagagt ttgaacgcaa cttaatttta
     2761 gaacgttctt cagcaggacg aattgccgct cgtgctagag gacgctatgg aggtcgtccc
     2821 gaaaaattaa ataaacaaga tttaaagtta ctcaaaacac tttatgataa tggaacacca
     2881 attaaaacta ttgcagaaca atggaaagtt tcacgtacca caatctatcg ttatctcaat
     2941 aggttaaata atcaagaaaa taaagataaa taatattact aagttttaag aaagataaaa
     3001 atagacagga cacaccctaa ccatacaaaa agaattgttg aaattataac aattaaaacg
     3061 tatgattagg gtgtatattt attatggagt gaagatgaat gattataggt tatgcgagag
     3121 tatcatcgat agatcaaaat ttagaaagac aattggataa tttaaagacg tttggtgtgg
     3181 agaaaatctt tacagagaaa cagtcgggaa agtcagtgga aaatagacct gtatttcaag
     3241 aagcactcaa ttttgtcaga atgggagatc gattcgttgt ggaatctatt gatcgtttag
     3301 gacgtaacta tgatgaaatt attgaaactg tgaattattt aaaagaaaaa gacgttcagt
//
