LOCUS       NZ_CP033763             3272 bp    DNA     circular CON 18-JUN-2024
DEFINITION  Escherichia coli strain FDAARGOS_536 plasmid unnamed2, complete
            sequence.
ACCESSION   NZ_CP033763
VERSION     NZ_CP033763.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN10163231
            Assembly: GCF_003812625.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 3272)
  AUTHORS   Campos,J., Goldberg,B., Tallon,L., Sadzewicz,L., Zhao,X.,
            Vavikolanu,K., Mehta,A., Aluvathingal,J., Nadendla,S., Geyer,C.,
            Nandy,P., 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  JOURNAL   Unpublished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 3272)
  AUTHORS   Campos,J., Goldberg,B., Tallon,L., Sadzewicz,L., Zhao,X.,
            Vavikolanu,K., Mehta,A., Aluvathingal,J., Nadendla,S., Geyer,C.,
            Nandy,P., Yan,Y. and Sichtig,H.
  TITLE     Direct Submission
  JOURNAL   Submitted (13-NOV-2018) 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                   :: CA v. 8.2, SPAdes v. 3.6.0
            Genome Coverage                   :: 637.91065372549x
            Sequencing Technology             :: PacBio; Illumina
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_003812625.1-RS_2024_06_18
            Annotation Date                   :: 06/18/2024 02:02:53
            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)                     :: 5,010
            CDSs (total)                      :: 4,893
            Genes (coding)                    :: 4,661
            CDSs (with protein)               :: 4,661
            Genes (RNA)                       :: 117
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 89
            ncRNAs                            :: 6
            Pseudo Genes (total)              :: 232
            CDSs (without protein)            :: 232
            Pseudo Genes (ambiguous residues) :: 0 of 232
            Pseudo Genes (frameshifted)       :: 83 of 232
            Pseudo Genes (incomplete)         :: 168 of 232
            Pseudo Genes (internal stop)      :: 40 of 232
            Pseudo Genes (multiple problems)  :: 52 of 232
            Pseudo Genes (short protein)      :: 1 of 232
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP033763.1.
            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..3272
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="FDAARGOS_536"
                     /isolation_source="Peripheral blood"
                     /host="Homo sapiens"
                     /culture_collection="FDA:FDAARGOS_536"
                     /db_xref="taxon:562"
                     /plasmid="unnamed2"
                     /collection_date="2016-04-02"
                     /collected_by="Children's National Hospital"
     gene            complement(441..635)
                     /locus_tag="EGX93_RS25395"
                     /old_locus_tag="EGX93_25410"
     CDS             complement(441..635)
                     /locus_tag="EGX93_RS25395"
                     /old_locus_tag="EGX93_25410"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001041627.1"
                     /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_001041631.1"
                     /translation="MNKQQQTALNMARFIKSQSLTLLEKLDALDADEQAAMCERLHELA
                     EELQNSIQIRFEAESETGT"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            complement(1746..2585)
                     /locus_tag="EGX93_RS25400"
                     /old_locus_tag="EGX93_25415"
     CDS             complement(1746..2585)
                     /locus_tag="EGX93_RS25400"
                     /old_locus_tag="EGX93_25415"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000546749.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="EcsC family protein"
                     /protein_id="WP_052924426.1"
                     /translation="MHLEEEDLRALERAVELLAQDTITETLTQLVGTPIDYLMSKLPKG
                     AEKKIYSLVEKSLNKAANAALWSLDNEPNRIASTKTNKFFAALSGAIGGAFGFSALAIE
                     LPVSTTIMLRSIADIARSEGFDLDRIDTKLECLAVFSFGGPSEDDDAVNTAYYATRNLT
                     AEIVQDLSKEISNITVKNAASTQTGKWLASLIEKVATRFGIVITEKMAAQAAPVIGALA
                     GATLNTMFTDYYQDMARGHFIVKRLERKYGDELIKAEYIKISDKLTNQNQRKHLNSN"
                     /name="EcsC family protein"
     gene            complement(2900..3058)
                     /locus_tag="EGX93_RS26365"
     CDS             complement(2900..3058)
                     /locus_tag="EGX93_RS26365"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_005761324.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="replication initiation protein"
                     /protein_id="WP_071529495.1"
                     /translation="MHEPPVQPDRCALSGNYRLESNPVRHDKAPLAAATGNWTRWIEIL
                     RVLEVVA"
                     /name="replication initiation protein"
     Typing          284..368
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="96.512"
                     /coverage="100.0"
                     /evalue="3.06e-32"
     Typing          672..770
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="98.0"
                     /coverage="100.0"
                     /evalue="1.35e-41"
     Typing          882..1150
                     /name="MOBF"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="89.668"
                     /coverage="93.0"
                     /evalue="3.5e-92"
     Typing          complement(2..264)
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="91.698"
                     /coverage="99.0"
                     /evalue="1.5e-98"
     Typing          complement(2950..3270)
                     /name="rep_cluster_2370"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="97.516"
                     /coverage="88.0"
                     /evalue="2.97e-154"
ORIGIN
        1 tttttgtgat gctcgtcagg ggggcggagc ctatggaaaa acgccagcgg cgcggccttt
       61 cgttgccttt tgcctttttg ctcacatgtt ctttccggcc ttatcccctg attctgtgga
      121 taaccgtatt accgcctttg agtgagccgg caccgctcgc cgcagccgaa cgaccgagcg
      181 tagcgagtca gtgagcgagg aagcggaaga gcgcctgatg cggcattttc tccttacgca
      241 tctgtgcggt atttcacatc gcatatggtg ctcttttctt ataatctgta ctgatgctac
      301 atagttaagc cagtatacac tccgctatcg ctacgtgact ggttcagggc ttcgccccga
      361 aaccccctga cgcgccctga cgggcttgtc tgctgacgaa aacgcccacg ggaaagccgt
      421 gaccgcctcc gtcagcttcg ttatgttcct gtttcacttt cggcctcaaa gcgaatctgg
      481 atgctgttct ggagttcttc tgcgagttcg tgcagtcgtt cgcacatggc cgcctgttcg
      541 tcggcatcca gagcatccag tttttcaagc agtgtcaggc tctggctttt gataaatcgc
      601 gccatattca gcgcagtttg ttgttgtttg ttcaccttcc gttgttctcc gtcagttccg
      661 ggtgtcgggg ggaccctgag caggtggtaa ttgtaagacg ttgcgggcga cggtattaca
      721 attgcacatc ctgtcctgtt tctttaggac gtatcatggc acagcatatc aactgataaa
      781 gaatccctgt gcagtgcagc cgctgttgca taaaatttcg ctctgcgtcg agtatttctt
      841 aatcaataat tccgctgata ctccggaaaa acgcgagtct gttctcatgc ccgaaatgcc
      901 cacaccccac gcaaaaacaa ttttttgctg atttttcttt ataaatagag agttatgaca
      961 aattagttct tcttgctctc tttgtgatat ttaaaaaagc ggtgttggcg cagctacaac
     1021 accgcgccga caccgctttt taggggtggt gctgactatt ttcataaaaa acatcatctt
     1081 atattagggg tgctgctagc tgcgcggtgt gtttttttac aggacgcccc tgggggcgct
     1141 gccaggggtg tctgttcaga tatgtagcaa tgagtcaggg attcacgaac tgaaaatgtc
     1201 cgaaaatgtg tctcatgggc actgtatgcg cccaaaccga tcgtcattca ctttcatgca
     1261 tagctatgca gtgagctgaa agcgagcctg acgcattttt tcggtttacc ccggggaaaa
     1321 catctctttt tgcggtgttt gcggcagaat cgcgttcagc gcgttttagc ggtgcgcgca
     1381 atacgggatt atggtaaata tgattgatat tcgtagatgc tgggttaact atttattttg
     1441 tgcgtggagt tgaaattggt aatgattaga atggctatga cctataaatg tttatcatgc
     1501 cattggtgta aaactgtgcc taaatgtagc gatgttttag ttgatggggg gaatgctttt
     1561 agtcagtgcc caaattgtga ctctgtttta gttgattcaa aaaaagccaa tttcattaat
     1621 gcagttgttg cgaatataat gtttaaaata aaatcataaa taattttgtt gtttgtgtga
     1681 ttgttcgtga gttgacaccc tccatagcac ctggccataa cggtgctatg cacttagtga
     1741 aaccgttagt tgctgttcaa atgcttccgt tggttctgat tggtgagttt atctgagatt
     1801 tttatatatt cagcctttat caattcatca ccatattttc tctcaagtct tttgacaata
     1861 aaatgacctc gagccatatc ttgataatag tcggtaaaca tcgtgtttaa tgtggctcca
     1921 gccagtgctc caataacagg agcagcttga gctgccattt tttctgtaat aactatacca
     1981 aatcttgtcg caactttttc tattaacgaa gctaaccatt ttcctgtttg tgttgaagca
     2041 gcgttcttga cagtaatgtt agaaatttct ttggataaat cttgtacgat ctcagcagtc
     2101 aaattccttg ttgcatagta tgcagtatta actgcatcat cgtcctcaga tggtcctccg
     2161 aaggaaaaca ccgctaaaca ctctagtttt gtatcaatcc tatctagatc aaaaccttca
     2221 cttcttgcta tgtccgcaat tgaacgaagc ataattgtcg ttgaaactgg taactcaatt
     2281 gctaatgcag aaaagccaaa agcaccacca atggctccag ataaggcagc aaagaactta
     2341 tttgtcttag ttgatgctat tcggttaggt tcattgtcta ggctccataa ggctgcatta
     2401 gcagctttgt tgagagattt ttctactagg ctataaattt tcttttctgc tcctttggga
     2461 agtttactca ttaagtaatc tattggggtt ccaactaatt gggttagtgt ttctgtaatt
     2521 gtatcttgtg ctaataattc tacggctctt tctaaagcgc gcagatcttc ttcttcaaga
     2581 tgcatgtaaa aatcccttat gaatcaatct gtagcctact ttttgtaagt ggtctgtttt
     2641 gggatcttac cttgggagaa ttcagtgatt caacgggcga gatgccgata tcattgttgt
     2701 ccgtgaagta ggagtgatga aaagatcaaa ggatcctctt gagatccttt ttttctgcgc
     2761 gtaatctgct gccagtaaac gaaaaaaccg cctggggagg cggtttagtc gaaggttaag
     2821 tcagttgggg actgcttaac cgggtaactg gcttggtgga gcacagatac caaatactgt
     2881 ccttctagtg tagccgcagt taggccacca cttcaagaac tcttaatatc tcaatccacc
     2941 ttgtccagtt accagtggct gctgccagtg gcgctttgtc gtgtcttacc gggttggact
     3001 caagacgata gttaccggat aaggcgcagc ggtcgggctg aacggggggt tcgtgcacac
     3061 agcccagctt ggagcgaacg acctacaccg aactgagata ccaacagcgt gagctatgag
     3121 aaagcgccac gcttcccgaa gggagaaagg cggacaggta tccggtaagc ggcagggtcg
     3181 gaacaggaga gcgcacgagg gagcttccag ggggaaacgc ctggtatctt tatagtcctg
     3241 tcgggtttcg ccacctctga cttgagcgtc ga
//
