LOCUS       NZ_CP069554             2495 bp    DNA     circular CON 17-JUN-2023
DEFINITION  Escherichia coli strain FDAARGOS_1253 plasmid unnamed5, complete
            sequence.
ACCESSION   NZ_CP069554
VERSION     NZ_CP069554.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN16357395
            Assembly: GCF_016889865.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 2495)
  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  JOURNAL   Unpublished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 2495)
  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, SPAdes v. 3.14.1
            Genome Coverage                   :: 1090.86x
            Sequencing Technology             :: Pacbio; Illumina
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 06/17/2023 05:01:47
            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)                     :: 4,554
            CDSs (total)                      :: 4,441
            Genes (coding)                    :: 4,315
            CDSs (with protein)               :: 4,315
            Genes (RNA)                       :: 113
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 85
            ncRNAs                            :: 6
            Pseudo Genes (total)              :: 126
            CDSs (without protein)            :: 126
            Pseudo Genes (ambiguous residues) :: 0 of 126
            Pseudo Genes (frameshifted)       :: 49 of 126
            Pseudo Genes (incomplete)         :: 81 of 126
            Pseudo Genes (internal stop)      :: 27 of 126
            Pseudo Genes (multiple problems)  :: 27 of 126
            Pseudo Genes (short protein)      :: 3 of 126
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP069554.1.
            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/
            COMPLETENESS: full length.
FEATURES             Location/Qualifiers
     source          1..2495
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="FDAARGOS_1253"
                     /host="Homo sapiens"
                     /culture_collection="FDA:FDAARGOS_1253"
                     /db_xref="taxon:562"
                     /plasmid="unnamed5"
                     /geo_loc_name="USA: WA"
                     /collected_by="ARMADA"
     gene            complement(257..484)
                     /locus_tag="I6J83_RS22505"
                     /old_locus_tag="I6J83_22505"
     CDS             complement(257..484)
                     /locus_tag="I6J83_RS22505"
                     /old_locus_tag="I6J83_22505"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_010615788.1"
                     /GO_component="GO:0005886 - plasma membrane [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="YgdI/YgdR family lipoprotein"
                     /protein_id="WP_021243043.1"
                     /translation="MKKIFVSVFAAAVALSALTGCTRTSYAIHTNDGRTIVSDGKPKES
                     DSGLLGYTDANGVKQQINKTDVKEVSEIPH"
                     /name="YgdI/YgdR family lipoprotein"
     gene            complement(2201..2386)
                     /locus_tag="I6J83_RS22510"
                     /old_locus_tag="I6J83_22510"
     CDS             complement(2201..2386)
                     /locus_tag="I6J83_RS22510"
                     /old_locus_tag="I6J83_22510"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000165998.1"
                     /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="WP_013772937.1"
                     /translation="MTRQESAALNMAKFIRAQTLLLLERLEQMDLDEAAGCCEHLHDQA
                     EALYAMLNAQIGEENA"
                     /name="Rop family plasmid primer RNA-binding protein"
     Typing          2067..2154
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="6.86e-39"
     Typing          complement(900..1428)
                     /name="rep_cluster_2335"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="88.598"
                     /coverage="88.0"
                     /evalue="0.0"
ORIGIN
        1 tccggggtgg tttgttgtgg tttttgtcat ggtttcgtca ggaacgcgct gaacgcgtct
       61 caggcggtgc gggcaacgga tgttatggta aattcttggg ggcttgatta taaaataccg
      121 cacttcctct tatgtcttgt gctttttaga caaccctgaa agcttttagc tttggtgatg
      181 caatttgctg ggattttggc ggagaaccac aggtaaagaa aaaggccaca ttagcggcct
      241 ttttcggaga agatgctcag tgcggaattt cggagacttc tttaacgtcg gttttattga
      301 tctgctgttt gacaccattc gcgtctgtat agccaagcag gcctgagtct gattctttag
      361 gtttgccgtc gctgacaata gtgcgaccgt cattggtgtg tatggcatag cttgtgcgcg
      421 tgcagccggt gagggctgaa agcgcaactg ccgctgcgaa cactgaaaca aaaatctttt
      481 tcaaagccag ctccttttat ccatatcagt tttggtcact aaccatctaa ctataggtca
      541 ttttttatgt gaaaagaggc ttgatggtgg gctgtatatc gagttaggcg cgaggtgcta
      601 tggtcaaagt gtggtgtcag gcggggagga ggcttatatg agatgtaatc cggccgatac
      661 atataccaag atgatttaag tattcctctt tgtgaggttg gatgtctaat ttataaagga
      721 tcttcttgag atcctttttt tccgcgcgta atctcttgcc ctgtaaacga aaaaaccacc
      781 ctggcaggtg gtttttcgaa ggttaggtaa tcctggcaga tcccctaacc gtggtaacag
      841 tcttgtgcga gacatgtcac caaatttgtc ctttcagtgt agcctcacta aggccgccac
      901 ttcaagaact cttgagacat ctctcgcaca tcctgtttgc caatggccgt tgccaatggc
      961 gattagtcgt gtctttccgg gttggactca agttgatagt taccggataa ggcgcagcgg
     1021 tcggactgaa cggggggttc gtgcatacag tccatcctgg agcgaactgc cttcccggaa
     1081 ctgagtgtca ggcgtggaat gagaaaccgc ggccataaca gcggagtgac accggtaaac
     1141 cgaaaggcag gaatgcgggg gagcacgagg gagccaccag ggggaaacgc ctggtatctt
     1201 taagccgcat cgggtttcgc caccactgat ttgagcgtca gattctgtga tgcttgtcag
     1261 gggggcggag cctatggaaa aacggctttg gcgcggcctt atgctttctt cgttaagtat
     1321 cttcctggca tcccccagga aatttctgat ccatccgtaa gcccgtcccg ctcgccgcag
     1381 ccgaacgacc gagcggagcg agtcagtgag cgaggaagcg gaatatattc tgtatcacat
     1441 tttctcctga cgcgttttct ttcactttct gcgcctgtct tatgtggcat taatgctatg
     1501 tgttactgcc atgctacatc ttaagccagt atacactccg ctagtgctcc gtgactggtc
     1561 cggcgctgcg cccggaaccc gcctgtaccg gttcagcagc cgttccggcc tgactgcaat
     1621 tttttttttt tcatccctgc ccgctaccct gtaaaccttt cttctgcgtt gccgttaaca
     1681 gtaggtaagc catgtttggt ttttcttccg gagccctgat gactcttagt gatgatgagc
     1741 gacacctgct tgtgtccgtt gtttcggtct ggctacggcg tgccggaggg gatgccggag
     1801 ccatgatgct ggatgcatac cggcagattt tgtctgacac cgaaccggcc gtaaggactg
     1861 tcatgctcga atttcttgaa tccgttcgca ttcattacat ttcgtcctga gcattttctg
     1921 tatttctgtc catacttaaa cgaggcggcc gtcacggacg gtggtcgtcg ttccatgatg
     1981 ctgttatgga cgagtgagag taatctaatc taacttgatt gagttccggg cgtgccgccc
     2041 ggtttttttt gctgtttccc ggtgtccgtt ccgggacagg atgtgcattt gtaataccgc
     2101 gcacgcgccg gcatcacaaa taccctggtc agggctgcgc cccgacaccc cgccatcgcc
     2161 tcacggccgc gcactgaatt gcgcacccgt tcaccgattt tcacgcattt tcctcgccta
     2221 tctgtgcgtt cagcatggcg taaagcgctt cggcctgatc gtgcaggtgc tcacagcagc
     2281 cggcagcctc atccagatcc atctgctcga gccgctcaag gaggagaagt gtctgtgcgc
     2341 ggataaattt ggccatattg agggcggcgg attcctgtct ggtcactggt gattttcccc
     2401 gtctggtgat gatttttgcg tgaaaagagc atggcgtcat tctggtgcat agtcatgcat
     2461 gccgttaaaa tttaacaggc gcgtttctga cgggt
//
