LOCUS       NZ_CP041004             1245 bp    DNA     linear   CON 20-JUN-2024
DEFINITION  Escherichia coli strain FDAARGOS_772 plasmid unnamed3.
ACCESSION   NZ_CP041004
VERSION     NZ_CP041004.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN11056487
            Assembly: GCF_006364695.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 1245)
  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  JOURNAL   Unpublished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 1245)
  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. 1.4, SPAdes v. 3.11.1
            Genome Coverage                   :: 994.93x
            Sequencing Technology             :: Pacbio; Illumina
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_006364695.1-RS_2024_06_20
            Annotation Date                   :: 06/20/2024 02:37:46
            Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline
            (PGAP)
            Annotation Method :: Best-placed reference protein set; GeneMarkS-2+
            Annotation Software revision      :: 6.7
            Features Annotated                :: Gene; CDS; rRNA; tRNA; ncRNA
            Genes (total)                     :: 5,342
            CDSs (total)                      :: 5,213
            Genes (coding)                    :: 4,917
            CDSs (with protein)               :: 4,917
            Genes (RNA)                       :: 129
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 98
            ncRNAs                            :: 9
            Pseudo Genes (total)              :: 296
            CDSs (without protein)            :: 296
            Pseudo Genes (ambiguous residues) :: 0 of 296
            Pseudo Genes (frameshifted)       :: 110 of 296
            Pseudo Genes (incomplete)         :: 200 of 296
            Pseudo Genes (internal stop)      :: 58 of 296
            Pseudo Genes (multiple problems)  :: 64 of 296
            CRISPR Arrays                     :: 1
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP041004.1.
            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..1245
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="FDAARGOS_772"
                     /isolation_source="ATCC Isolate"
                     /host="NIST Mixed Microbial RM strain"
                     /culture_collection="ATCC:BAA 2309"
                     /db_xref="taxon:562"
                     /plasmid="unnamed3"
                     /geo_loc_name="USA: VA"
                     /collected_by="NIST<ATCC"
                     /note="NIST Mixed Microbial RM strain"
     gene            <1..218
                     /locus_tag="FIU16_RS27150"
                     /old_locus_tag="FIU16_27150"
                     /pseudo=""
     CDS             <1..218
                     /locus_tag="FIU16_RS27150"
                     /old_locus_tag="FIU16_27150"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000277654.1"
                     /note="incomplete; too short partial abutting assembly gap;
                     missing N-terminus; Derived by automated computational
                     analysis using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=3
                     /transl_table=11
                     /product="replication initiation protein"
                     /name="replication initiation protein"
     gene            380..>1245
                     /locus_tag="FIU16_RS27155"
                     /old_locus_tag="FIU16_27155"
     CDS             380..>1245
                     /locus_tag="FIU16_RS27155"
                     /old_locus_tag="FIU16_27155"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000492283.1"
                     /GO_function="GO:0022857 - transmembrane transporter
                     activity [Evidence IEA]"
                     /GO_process="GO:0055085 - transmembrane transport [Evidence
                     IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MFS transporter"
                     /protein_id="WP_139975132.1"
                     /translation="MFSLYKKFKGLFYSVLFWLCILSFFSVLNEMVLNVSLPDIANHFN
                     TTPGITNWVNTAYMLTFSIGTAVYGKLSDYINIKKLLIIGISLSCLGSLIAFIGHNHFF
                     ILIFGRLVQGVGSAAFPSLIMVVVARNITRKKQGKAFGFIGSIVALGEGLGPSIGGIIA
                     HYIHWSYLLILPMITIVTIPFLIKVMVPGKSTKNTLDIVGIVLMSISIICFMLFTTNYN
                     WTFLILFTIFFVIFIKHISRVSNPFINPKLGKNIPFMLGLFSGGLIFSIVAGFISMVPY
                     MMKTISHV"
                     /name="MFS transporter"
     ARG             381..1243
                     /name="tet(K)"
                     /gene="tet(K)"
                     /gene_name="major facilitator superfamily (MFS) antibiotic
                     efflux pump"
                     /tool="rgi"
                     /drug_class="tetracycline antibiotic"
                     /identity="99.65"
                     /coverage="62.75"
ORIGIN
        1 aacgcactgc ggatagagca atagttttta tgttattgag tgatgaagaa gaatggggaa
       61 agcttcacag aaattctaga acaaaatata agcatttgat aaaagaaatt tcgccagtcg
      121 atttaacgga cttaatgaaa tcgactttaa aagcgaacga aaaacaattg caaaaacaaa
      181 tcgatttttg gcaacatgaa tttaaatttt ggaaatagtg tacatattaa tattactgaa
      241 caaaaatgat atatttaaac tattctaatt taggaggatt tttttatgaa gtgtctattt
      301 aaaaatttgg ggaatttata tgaggtgaaa gaataattta cccctataaa ctttagtcac
      361 ctcaagtaaa gaggtaaaat tgtttagttt atataaaaaa tttaaaggtt tgttttatag
      421 cgttttattt tggctttgta ttctttcatt ttttagtgta ttaaatgaaa tggttttaaa
      481 tgtttcttta cctgatattg caaatcattt taatactact cctggaatta caaactgggt
      541 aaacacggca tatatgttaa ctttttcgat aggaacagca gtatatggaa aattatctga
      601 ttatataaat ataaaaaaat tgttaattat tggtattagt ttgagctgtc ttggttcatt
      661 gattgctttt attggtcaca atcacttttt tattttgatt tttggtaggt tagtacaagg
      721 agtaggatct gctgcattcc cttcactgat tatggtggtt gtagctagaa atattacaag
      781 aaaaaaacaa ggcaaagcct ttggttttat aggatcaatt gtagctttag gtgaagggtt
      841 aggtccttca atagggggaa taatagcaca ttatattcat tggtcttacc tacttatact
      901 tcctatgatt acaatagtaa ctataccttt tcttattaaa gtaatggtac ctggtaaatc
      961 aacaaaaaat acattagata tcgtaggtat tgttttaatg tctataagta ttatatgttt
     1021 tatgttattt acgacaaatt ataattggac ttttttaata ctcttcacaa tcttttttgt
     1081 gatttttatt aaacatattt caagagtttc taaccctttt attaatccta aactagggaa
     1141 aaacattccg tttatgcttg gtttgttttc tggtgggcta atattttcta tagtagctgg
     1201 ttttatatca atggtgcctt atatgatgaa aactatttct catgt
//
