LOCUS       NZ_CP069458             2495 bp    DNA     circular CON 17-JUN-2023
DEFINITION  Escherichia coli strain FDAARGOS_1254 plasmid unnamed5, complete
            sequence.
ACCESSION   NZ_CP069458
VERSION     NZ_CP069458.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN16357396
            Assembly: GCF_016889105.1
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  JOURNAL   Unpublished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                   :: 740.26x
            Sequencing Technology             :: Pacbio; Illumina
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 06/17/2023 05:32:33
            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)                     :: 4,781
            CDSs (total)                      :: 4,667
            Genes (coding)                    :: 4,515
            CDSs (with protein)               :: 4,515
            Genes (RNA)                       :: 114
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 86
            ncRNAs                            :: 6
            Pseudo Genes (total)              :: 152
            CDSs (without protein)            :: 152
            Pseudo Genes (ambiguous residues) :: 0 of 152
            Pseudo Genes (frameshifted)       :: 58 of 152
            Pseudo Genes (incomplete)         :: 107 of 152
            Pseudo Genes (internal stop)      :: 26 of 152
            Pseudo Genes (multiple problems)  :: 35 of 152
            Pseudo Genes (short protein)      :: 3 of 152
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP069458.1.
            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_1254"
                     /host="Homo sapiens"
                     /culture_collection="FDA:FDAARGOS_1254"
                     /db_xref="taxon:562"
                     /plasmid="unnamed5"
                     /geo_loc_name="USA: WA"
                     /collected_by="ARMADA"
     gene            complement(join(2341..2495,1..73))
                     /locus_tag="I6J84_RS23645"
                     /old_locus_tag="I6J84_23645"
     CDS             complement(join(2341..2495,1..73))
                     /locus_tag="I6J84_RS23645"
                     /old_locus_tag="I6J84_23645"
                     /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(1790..1975)
                     /locus_tag="I6J84_RS23650"
                     /old_locus_tag="I6J84_23650"
     CDS             complement(1790..1975)
                     /locus_tag="I6J84_RS23650"
                     /old_locus_tag="I6J84_23650"
                     /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          1656..1743
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="6.86e-39"
     Typing          complement(489..1017)
                     /name="rep_cluster_2335"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="88.598"
                     /coverage="88.0"
                     /evalue="0.0"
ORIGIN
        1 ttgtgcgcgt gcagccggtg agggctgaaa gcgcaactgc cgctgcgaac actgaaacaa
       61 aaatcttttt caaagccagc tccttttatc catatcagtt ttggtcacta accatctaac
      121 tataggtcat tttttatgtg aaaagaggct tgatggtggg ctgtatatcg agttaggcgc
      181 gaggtgctat ggtcaaagtg tggtgtcagg cggggaggag gcttatatga gatgtaatcc
      241 ggccgataca tataccaaga tgatttaagt attcctcttt gtgaggttgg atgtctaatt
      301 tataaaggat cttcttgaga tccttttttt ccgcgcgtaa tctcttgccc tgtaaacgaa
      361 aaaaccaccc tggcaggtgg tttttcgaag gttaggtaat cctggcagat cccctaaccg
      421 tggtaacagt cttgtgcgag acatgtcacc aaatttgtcc tttcagtgta gcctcactaa
      481 ggccgccact tcaagaactc ttgagacatc tctcgcacat cctgtttgcc aatggccgtt
      541 gccaatggcg attagtcgtg tctttccggg ttggactcaa gttgatagtt accggataag
      601 gcgcagcggt cggactgaac ggggggttcg tgcatacagt ccatcctgga gcgaactgcc
      661 ttcccggaac tgagtgtcag gcgtggaatg agaaaccgcg gccataacag cggagtgaca
      721 ccggtaaacc gaaaggcagg aatgcggggg agcacgaggg agccaccagg gggaaacgcc
      781 tggtatcttt aagccgcatc gggtttcgcc accactgatt tgagcgtcag attctgtgat
      841 gcttgtcagg ggggcggagc ctatggaaaa acggctttgg cgcggcctta tgctttcttc
      901 gttaagtatc ttcctggcat cccccaggaa atttctgatc catccgtaag cccgtcccgc
      961 tcgccgcagc cgaacgaccg agcggagcga gtcagtgagc gaggaagcgg aatatattct
     1021 gtatcacatt ttctcctgac gcgttttctt tcactttctg cgcctgtctt atgtggcatt
     1081 aatgctatgt gttactgcca tgctacatct taagccagta tacactccgc tagtgctccg
     1141 tgactggtcc ggcgctgcgc ccggaacccg cctgtaccgg ttcagcagcc gttccggcct
     1201 gactgcaatt tttttttttt catccctgcc cgctaccctg taaacctttc ttctgcgttg
     1261 ccgttaacag taggtaagcc atgtttggtt tttcttccgg agccctgatg actcttagtg
     1321 atgatgagcg acacctgctt gtgtccgttg tttcggtctg gctacggcgt gccggagggg
     1381 atgccggagc catgatgctg gatgcatacc ggcagatttt gtctgacacc gaaccggccg
     1441 taaggactgt catgctcgaa tttcttgaat ccgttcgcat tcattacatt tcgtcctgag
     1501 cattttctgt atttctgtcc atacttaaac gaggcggccg tcacggacgg tggtcgtcgt
     1561 tccatgatgc tgttatggac gagtgagagt aatctaatct aacttgattg agttccgggc
     1621 gtgccgcccg gttttttttg ctgtttcccg gtgtccgttc cgggacagga tgtgcatttg
     1681 taataccgcg cacgcgccgg catcacaaat accctggtca gggctgcgcc ccgacacccc
     1741 gccatcgcct cacggccgcg cactgaattg cgcacccgtt caccgatttt cacgcatttt
     1801 cctcgcctat ctgtgcgttc agcatggcgt aaagcgcttc ggcctgatcg tgcaggtgct
     1861 cacagcagcc ggcagcctca tccagatcca tctgctcgag ccgctcaagg aggagaagtg
     1921 tctgtgcgcg gataaatttg gccatattga gggcggcgga ttcctgtctg gtcactggtg
     1981 attttccccg tctggtgatg atttttgcgt gaaaagagca tggcgtcatt ctggtgcata
     2041 gtcatgcatg ccgttaaaat ttaacaggcg cgtttctgac gggttccggg gtggtttgtt
     2101 gtggtttttg tcatggtttc gtcaggaacg cgctgaacgc gtctcaggcg gtgcgggcaa
     2161 cggatgttat ggtaaattct tgggggcttg attataaaat accgcacttc ctcttatgtc
     2221 ttgtgctttt tagacaaccc tgaaagcttt tagctttggt gatgcaattt gctgggattt
     2281 tggcggagaa ccacaggtaa agaaaaaggc cacattagcg gcctttttcg gagaagatgc
     2341 tcagtgcgga atttcggaga cttctttaac gtcggtttta ttgatctgct gtttgacacc
     2401 attcgcgtct gtatagccaa gcaggcctga gtctgattct ttaggtttgc cgtcgctgac
     2461 aatagtgcga ccgtcattgg tgtgtatggc atagc
//
