LOCUS       NZ_CP069986             2544 bp    DNA     linear   CON 17-JUN-2023
DEFINITION  Escherichia coli strain FDAARGOS_1291 plasmid unnamed6.
ACCESSION   NZ_CP069986
VERSION     NZ_CP069986.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN16357433
            Assembly: GCF_016903855.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 2544)
  AUTHORS   Sokurenko,E., Tallon,L., Sadzewicz,L., Zhao,X., Boylan,J., Ott,S.,
            Bowen,H., 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  JOURNAL   Unpublished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 2544)
  AUTHORS   Sokurenko,E., Tallon,L., Sadzewicz,L., Zhao,X., Boylan,J., Ott,S.,
            Bowen,H., Vavikolanu,K., Mehta,A., Aluvathingal,J., Nadendla,S.,
            Yan,Y. and Sichtig,H.
  TITLE     Direct Submission
  JOURNAL   Submitted (05-FEB-2021) Institute for Genome Sciences, University of
            Maryland School of Medicine, BioPark II, 801 W. Baltimore St., Suite
            619, Baltimore, MD 21201, USA
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: SMRT v. 8.0.0, HGAP v. 4
            Genome Coverage                   :: 1725.19x
            Sequencing Technology             :: Pacbio; Illumina
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 06/17/2023 05:14:06
            Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline
            (PGAP)
            Annotation Method :: Best-placed reference protein set; GeneMarkS-2+
            Annotation Software revision      :: 6.5
            Features Annotated                :: Gene; CDS; rRNA; tRNA; ncRNA
            Genes (total)                     :: 5,142
            CDSs (total)                      :: 5,021
            Genes (coding)                    :: 4,807
            CDSs (with protein)               :: 4,807
            Genes (RNA)                       :: 121
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 90
            ncRNAs                            :: 9
            Pseudo Genes (total)              :: 214
            CDSs (without protein)            :: 214
            Pseudo Genes (ambiguous residues) :: 0 of 214
            Pseudo Genes (frameshifted)       :: 53 of 214
            Pseudo Genes (incomplete)         :: 163 of 214
            Pseudo Genes (internal stop)      :: 38 of 214
            Pseudo Genes (multiple problems)  :: 38 of 214
            Pseudo Genes (short protein)      :: 4 of 214
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP069986.1.
            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..2544
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="FDAARGOS_1291"
                     /host="Homo sapiens"
                     /culture_collection="FDA:FDAARGOS_1291"
                     /db_xref="taxon:562"
                     /plasmid="unnamed6"
                     /geo_loc_name="USA: WA"
                     /collected_by="ARMADA"
     gene            complement(91..567)
                     /locus_tag="I6K21_RS25315"
                     /old_locus_tag="I6K21_25325"
     CDS             complement(91..567)
                     /locus_tag="I6K21_RS25315"
                     /old_locus_tag="I6K21_25325"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000469298.1"
                     /GO_function="GO:0003677 - DNA binding [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="helix-turn-helix domain-containing protein"
                     /protein_id="WP_000469298.1"
                     /translation="MFIDSEKRLKQLSDEAKKNTEDLEEAKKNSRFTQVSPKGWERVRE
                     LLKDSQGISALKLYSFLAEHIDPTCGAVVADQQFLAEKLGVSRSTIIRWLNYLESKNAL
                     VRIPVAGKVCAYALDPHEVWKGYNTTKNHAAFVTKTLVNKDGDIQRRIMAMFSN"
                     /name="helix-turn-helix domain-containing protein"
     gene            complement(1659..1877)
                     /locus_tag="I6K21_RS25320"
                     /old_locus_tag="I6K21_25330"
     CDS             complement(1659..1877)
                     /locus_tag="I6K21_RS25320"
                     /old_locus_tag="I6K21_25330"
                     /inference="COORDINATES: ab initio prediction:GeneMarkS-2+"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GeneMarkS-2+."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_141071555.1"
                     /translation="MNTEDKLMLKVDRLLSHDALNQRNILNNWERQFLTSVLAIYRRIN
                     KYSLVGLSPKQKNATYNILKKYKFHTD"
                     /name="hypothetical protein"
     gene            complement(1896..2420)
                     /locus_tag="I6K21_RS25325"
                     /old_locus_tag="I6K21_25335"
     CDS             complement(1896..2420)
                     /locus_tag="I6K21_RS25325"
                     /old_locus_tag="I6K21_25335"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000893324.1"
                     /GO_process="GO:0006260 - DNA replication [Evidence IEA];
                     GO:0006276 - plasmid maintenance [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="replication/maintenance protein RepL"
                     /protein_id="WP_045145680.1"
                     /translation="MLEQRFEDFEQQKRRDHKAQDQAQNTKQKRDRLNPPDWSQVTKAG
                     WNMLDAISEKVPRAFRLYSFFAQNIDKSCGAVVCDQKFLADYFGVSLRTIQYWIGDLER
                     IGAIVKIPVGIYYAYALDPYQVWRGYNKSKKYAAFNAKTLTQKDGVIDRKLRLMLSRRE
                     EFESSLKPSKS"
                     /name="replication/maintenance protein RepL"
     Typing          647..755
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="98.182"
                     /coverage="100.0"
                     /evalue="4.23e-47"
     Typing          complement(951..1049)
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="6.22e-45"
     Typing          1149..1409
                     /name="Col(MG828)"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="91.603"
                     /coverage="100.0"
                     /evalue="8.62e-98"
ORIGIN
        1 ggattttgag gcggcaaaag agcaatgcag gatagacaat catggtcaga acgttaacac
       61 gtagcccctg attgtccgcc tgccgctagc tcaatttgaa aacatggcca tgattcggcg
      121 ctgaatatca ccgtctttgt tgaccagtgt tttagtgaca aacgctgcat ggtttttcgt
      181 agtgttgtat cccttccaaa cttcatgtgg atcgagggca tacgcacaaa ccttaccagc
      241 aacggggatt ctaactaatg cattttttga ttctaagtaa ttgagccacc gaataattgt
      301 gcttctgcta actccaagtt tttcagctag gaattgctga tccgcaacga cagcgccaca
      361 cgtaggatcg atatgctccg ctaaaaatga gtacagcttc agtgctgata tgccttggct
      421 atccttcagc agctctcgaa cacgttccca accttttggg gatacctgtg taaaccttga
      481 atttttcttt gcttcttcga gatcctcggt gtttttcttt gcctcatctg aaagttgttt
      541 cagtcgtttt tctgaatcaa taaacatgat tttttccctc tgaaaatccc atgcactaac
      601 gttggttcaa atctaagcca tcatgacaca tctgtgcaac accttgttgc gtgttgtcgc
      661 atccaggatg cgacaacgtt gtgtcatcct ggatgcgaca ggtaaataaa aaacacacta
      721 aaaaaacaac cacttataaa tcggcgtaaa agatctattc taggcaaggg tgttgcgtgc
      781 aacgcaacgc cctttggggg tgtcggggcg aagccctgac ccagtcacgt agcgatagcg
      841 gagtgtatac tggcttactc ctatgcaagc ctcgccagcc gtgatttttg ccagatttcg
      901 tggttttcac gttcaacagc tccatcgtgt ttttgccgtc cgttcaccgt taaaacgcct
      961 cagaaatcgg gacaggatgt gtaatcgtat aaccgcgcat gcacgccgat acgattacca
     1021 cttggtcagg gcttcacccc gacaccccgc atcagtgcgt aagtgctcaa tgtggcttcc
     1081 ggttctcttc cgcttcctcg tcgattcgct cgctacgctc ggtcatcgac ttgcggcgag
     1141 cgggatcacc tctcgcatgt tgtcggtgat cccggtgctg ttcttttggg gatgagtcgc
     1201 cagatagccc ctcaaacgcg ctcaaaagct ctcagacgca cgaaacgggt tttagatgcc
     1261 cgccagggca tggaaggcgc gaaaaacgct tacagaggct ctcaggaggt caagcgcgcc
     1321 gataccccta accaggggct ttcaggtcgc caggaaccgc gccagccccc tgcaaagccc
     1381 atttgcacgg aacaggcagc catgcggttg gtaggtggtc gtagaccgtc ggtgttgcag
     1441 cgatgggggt ctggggttct ccccagacgg tttccggtag cgctcaaggc gctgccggaa
     1501 ccgtggcggc tcggtttttt ctggagaacg gggagcaaaa acacgcaaag gattttgagg
     1561 cggcaaaaga gcaatgcagg atagacaatc atggtcagaa cgttaacacg tagcccctga
     1621 ttgtccgcct gccgctagct ctttaaaata tttcactttt aatcagtatg aaatttatat
     1681 ttttttaaaa tgttatacgt tgcatttttc tgttttggtg atagcccaac taaagaatat
     1741 ttattgatcc tcctatagat agctaaaaca cttgttaaaa attgtctttc ccaattattt
     1801 aaaatattgc gttgatttaa cgcatcatga ctaagtaatc gatcaacttt tagcattagc
     1861 ttatcttcag tattcatcta gacctccaag actagtcatg atttagaggg cttgagtgag
     1921 ctttcaaact cttctcttct agagagcatg agccgcaact tacgatcaat aacaccatct
     1981 ttttgagtta atgtttttgc gttaaatgct gcatattttt tagatttatt atatccacgc
     2041 catacctgat aaggatctaa agcataagca taataaatac ctactggtat ttttactatt
     2101 gcaccaatac gttctaaatc tccgatccaa tattgaattg tccttaaact aaccccgaaa
     2161 taatcagcta ggaatttttg atcacataca acagctccac acgatttatc tatattttga
     2221 gcaaaaaaag aatatagcct aaatgcccta ggaaccttct cggatatagc gtccaacata
     2281 ttccaaccag ccttagtgac ttgtgaccag tcaggtggat tcaaccgatc tcgtttttgc
     2341 ttagtgtttt gggcttgatc ttgtgccttg tgatctcgcc gtttttgctg ttcaaagtct
     2401 tcaaatcgct gttccagcat acttgcatcc ttacctgcaa caatctttcg taccttacga
     2461 aatttatatc gtacagtacg aaacaacaca cgcaaacatg gttgcgtata cacatgcaaa
     2521 taacgtttcg tatgatgggg tcat
//
