LOCUS       NZ_CP033853             3257 bp    DNA     circular CON 18-JUN-2024
DEFINITION  Escherichia coli strain FDAARGOS_497 plasmid unnamed6, complete
            sequence.
ACCESSION   NZ_CP033853
VERSION     NZ_CP033853.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN10163173
            Assembly: GCF_003812945.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 3257)
  AUTHORS   Minogue,T., Wolcott,M., Wasieloski,L., Aguilar,W., Moore,D.,
            Jaissle,J., Tallon,L.J., Sadzewicz,L., Zhao,X., 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  JOURNAL   Unpublished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 3257)
  AUTHORS   Minogue,T., Wolcott,M., Wasieloski,L., Aguilar,W., Moore,D.,
            Jaissle,J., Tallon,L.J., Sadzewicz,L., Zhao,X., Vavikolanu,K.,
            Mehta,A., Aluvathingal,J., Nadendla,S., 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 :: SMRT v. 2.3.0, HGAP v. 3.0, SPAdes v. 3.6.0
            Genome Coverage                   :: 2600.73023781818x
            Sequencing Technology             :: PacBio; Illumina
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_003812945.1-RS_2024_06_18
            Annotation Date                   :: 06/18/2024 02:29:19
            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)                     :: 5,401
            CDSs (total)                      :: 5,282
            Genes (coding)                    :: 5,065
            CDSs (with protein)               :: 5,065
            Genes (RNA)                       :: 119
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 92
            ncRNAs                            :: 5
            Pseudo Genes (total)              :: 217
            CDSs (without protein)            :: 217
            Pseudo Genes (ambiguous residues) :: 0 of 217
            Pseudo Genes (frameshifted)       :: 83 of 217
            Pseudo Genes (incomplete)         :: 151 of 217
            Pseudo Genes (internal stop)      :: 41 of 217
            Pseudo Genes (multiple problems)  :: 51 of 217
            Pseudo Genes (short protein)      :: 1 of 217
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP033853.1.
            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..3257
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="FDAARGOS_497"
                     /isolation_source="UCC isolate"
                     /host="Homo sapiens"
                     /culture_collection="FDA:FDAARGOS_497"
                     /db_xref="taxon:562"
                     /plasmid="unnamed6"
                     /collected_by="USAMRIID"
     gene            82..276
                     /locus_tag="EGY17_RS27390"
                     /old_locus_tag="EGY17_27425"
     CDS             82..276
                     /locus_tag="EGY17_RS27390"
                     /old_locus_tag="EGY17_27425"
                     /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_001041633.1"
                     /translation="MNKQQQTALNMARFIKSQSLTLLEKLDALDADEQAAMCERLHELA
                     EELQNSIQVRFETESETGT"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            929..1041
                     /locus_tag="EGY17_RS28295"
                     /pseudo=""
     CDS             929..1041
                     /locus_tag="EGY17_RS28295"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_005761324.1"
                     /note="frameshifted; Derived by automated computational
                     analysis using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="replication initiation protein"
                     /name="replication initiation protein"
     gene            complement(1272..1568)
                     /locus_tag="EGY17_RS27405"
                     /old_locus_tag="EGY17_27440"
     CDS             complement(1272..1568)
                     /locus_tag="EGY17_RS27405"
                     /old_locus_tag="EGY17_27440"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000609270.1"
                     /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="HigA family addiction module antitoxin"
                     /protein_id="WP_000609270.1"
                     /translation="MINLVDPVHPGVFIREMFMEPFEISAADLSEKLHVSPSTLSRVLN
                     GKADLSVEMALRLSRVLGRSAESWINMQTQYSLNASRKSPNVIKELDELVPIF"
                     /name="HigA family addiction module antitoxin"
     gene            1914..2195
                     /locus_tag="EGY17_RS27410"
                     /old_locus_tag="EGY17_27445"
     CDS             1914..2195
                     /locus_tag="EGY17_RS27410"
                     /old_locus_tag="EGY17_27445"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000586174.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="type II toxin-antitoxin system RelE/ParE family
                     toxin"
                     /protein_id="WP_000586174.1"
                     /translation="MIINIKHKGLRKFAETGNNAGIPQQFTQRLKLILTALSTATNLQD
                     MMDLKALRCHPLKGDRQGEYSLEVNGNWRVVFKLEEPNVFDVDLEDYH"
                     /name="type II toxin-antitoxin system RelE/ParE family
                     toxin"
     Typing          complement(349..431)
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="3.79e-36"
     Typing          complement(2825..3080)
                     /name="MOBF"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="96.512"
                     /coverage="89.0"
                     /evalue="1.21e-116"
     Typing          444..998
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="94.434"
                     /coverage="99.0"
                     /evalue="0.0"
ORIGIN
        1 ataccgtcgc ccgcaacgtc ttacaattac cacctggtca gggtccaccc gacacccggt
       61 actgacggag aacaacggaa ggtgaacaaa cagcaacaaa ctgcgctgaa tatggcgcga
      121 tttatcaaaa gccagagcct gacactgctt gaaaaactgg atgctctgga tgccgacgaa
      181 caggcggcca tgtgcgaacg actgcacgaa ctcgcggaag aactccagaa cagcatccag
      241 gttcgctttg agaccgaaag tgaaacagga acataacgaa gctgacgcgc cctggcgggc
      301 ttgtctgctg ccgaaaacgc tcgcggacaa gcccgccagg gcgcgtcagc gggtgtcggg
      361 gcgaagccct gacccagtca cgtagcgata gcggagtgta tactggctta actatgcggc
      421 atcagtgcag attgtatgaa aagtgcccca tgccgggtgt gaaattccgc acagatgcgt
      481 aaggagaaaa tgcgcgtcca ggcgcttttc cgcttcctcg ctcactgact cgctacgctc
      541 ggtcgttcgg ctgcggcgag cggtactgac ttacacaaaa acggcagcac ggttatctac
      601 agaatcaggg gataaggccg gaaagaacat gtgagcaaaa gaccaagaac aggaagaagg
      661 ccgcgccgca ggcgtttttc cataggctcc gcccccctga cgagcatcac agaaatcgac
      721 gctcaagtca gaggtggcga aacccgacag gacttaaaga taccagacgt ttccccctgg
      781 tggctccctc gtgcgctctc ctgttccgac cctgccgctt accggatacc tgtccgcctt
      841 tctcccttcg ggaagcgtgg cgctttctca tagctcacgc tgtaggtatc tcggttcagt
      901 gtaggtcgtt cgctccaagc tgggctgtgt gcacgaaccc cccgttcagc ccgaccgctg
      961 cgccttatcc ggtaactatc atcttgagtc caacccggaa agacatgcaa aacaccattg
     1021 gcagcagcca ctggtaactg atttagagga gttagtcttg aagttatgcg ccagttaagg
     1081 ctaaactgaa agaacaagtt ttggtgactg cgctcctcca agccagttac cctggttcag
     1141 aaacttgccg gttactgaac cttcgaaaaa accaccttgc cgggtggttt tttcgtttac
     1201 gagaaacgat acgatccagt tgcctgagag tcaagacaga aaaaggccgc atatagcggc
     1261 cttttctttt ctcaaaatat aggaaccaat tcatctaatt ccttaatgac attaggtgac
     1321 ttcctgctcg cgttaagact gtattgagtc tgcatgttta tccacgactc ggcactgcga
     1381 ccaagaactc gagaaagcct taatgccatc tcaacactta aatcagcttt tccattcagc
     1441 actctactta gagtggaagg tgatacatgc agtttttcag acaggtccgc ggctgatatt
     1501 tcaaacggtt ccataaacat ctcacggata aaaacccctg gatgtactgg atcgacaaga
     1561 ttaatcatac cttcctctga agcctatatt agttttaaaa agataggcct attgcgtttt
     1621 cagattgcgc attgcgcata acgcaactca ttgttgacta aaaaaaaaga atgacattat
     1681 gatgcacatt ggtgcgtcta atcattcctt atgatgtggg tacttgatgt gaaattcaag
     1741 gccccggcat tgtacagcgc atcaaaccaa tgtcaacaga ttaaaatgcg acttggttaa
     1801 gtaaaaccta cgtcatttat tcaaatagag caaggggttt gcaatggaaa tacggatgaa
     1861 ccggaaaaat aaactgcgat gtttctatct aaacaaatat gggatggtga ttaatgatca
     1921 taaatatcaa gcataaaggt ttgcgtaagt ttgccgaaac aggtaacaac gcaggaattc
     1981 cgcaacagtt tactcaacgt ctgaagctga tcctaacagc cttaagcaca gcgacgaact
     2041 tgcaggatat gatggattta aaggcattgc gctgccatcc attgaaggga gaccgtcaag
     2101 gagagtattc gttagaggtc aatggaaact ggcgcgtagt gtttaagctc gaagaaccta
     2161 acgtctttga cgtggatctc gaggattatc actaagaagg tccttaaagc atcaaagtga
     2221 cagtatcgat gctttagggt ctcataaaaa agcaaaacct cggggtaagt tatatgaagt
     2281 attttctgta ccagatagtc cctatagcag ccatcattag cgcagcaatt ctagcgctaa
     2341 aaggtatcaa tggctggggg tggttcttaa ctgttgggtt cctgcttgca ggggcagata
     2401 cagtaaaggc tcagttatct aagtagtaat aaacactatc aatagtggtt ggataattgc
     2461 caaaaaagcc tctatctgtt ctgaaacaga caacaaggaa aaatcggtgt aagccacctc
     2521 cataggaggt ggtattgata tcaacataga taaaaccatc ccgtaaatca cagcatttac
     2581 cataacgtcg cattacgcgc accgctaaaa cgcgctgaac gcgattctgc cgcgaacacc
     2641 gcaaaaagag atgttttacc aagcgaaaac cggaaaaatg cgtcaggatc gctttcagct
     2701 cactgcatag ctatgcatga aagtgaatgg cgatcggttt gggcgcatac ggtgcccatg
     2761 agacacattt tcggacattt tcagttcgtg aatccctgac tcattgctac atatctgaac
     2821 agacacccct agcagcgccc ccaggggcgt cctgtaaaaa aacacaccgc gccgctagca
     2881 gcacccctaa tataaaatga tgttttttat gaaaatagtc agtaccaccc ctaaaaagcg
     2941 gtgttggcgc agctacaaca ccgcgccgac accgcttttt taaatatcac aaagagagca
     3001 agaagaacta atttgtcata actctctatt tataaagaaa aatcagcaaa aaattgtttt
     3061 tgcgtggggt gtgggcattt caggcatgag aacagactcg cgtttttccg gagtatcagc
     3121 ggaattattg attaagaaac actcgacgca gagcgaaatt ttatgcaaca gcggctgcac
     3181 tgcacaggga ttatttatca gttgatatgc tgtgccatga tacgtcctaa aaaaacagga
     3241 caggatgtgc aattgta
//
