LOCUS       NZ_CP069546             6211 bp    DNA     circular CON 17-JUN-2023
DEFINITION  Escherichia coli strain FDAARGOS_1248 plasmid unnamed4, complete
            sequence.
ACCESSION   NZ_CP069546
VERSION     NZ_CP069546.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN16357390
            Assembly: GCF_016889845.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 6211)
  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  JOURNAL   Unpublished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 6211)
  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                   :: 947.14x
            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)                     :: 4,982
            CDSs (total)                      :: 4,860
            Genes (coding)                    :: 4,620
            CDSs (with protein)               :: 4,620
            Genes (RNA)                       :: 122
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 88
            ncRNAs                            :: 12
            Pseudo Genes (total)              :: 240
            CDSs (without protein)            :: 240
            Pseudo Genes (ambiguous residues) :: 0 of 240
            Pseudo Genes (frameshifted)       :: 68 of 240
            Pseudo Genes (incomplete)         :: 167 of 240
            Pseudo Genes (internal stop)      :: 52 of 240
            Pseudo Genes (multiple problems)  :: 43 of 240
            Pseudo Genes (short protein)      :: 4 of 240
            CRISPR Arrays                     :: 1
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP069546.1.
            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..6211
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="FDAARGOS_1248"
                     /host="Homo sapiens"
                     /culture_collection="FDA:FDAARGOS_1248"
                     /db_xref="taxon:562"
                     /plasmid="unnamed4"
                     /geo_loc_name="USA: WA"
                     /collected_by="ARMADA"
     gene            complement(join(6105..6211,1..730))
                     /locus_tag="I6J78_RS24455"
                     /old_locus_tag="I6J78_24460"
     CDS             complement(join(6105..6211,1..730))
                     /locus_tag="I6J78_RS24455"
                     /old_locus_tag="I6J78_24460"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000480972.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="aminoglycoside O-phosphotransferase APH(6)-Id"
                     /protein_id="WP_000480968.1"
                     /translation="MFMPPVFPAHWHVSQPVLIADTFSSLVWKVSLPDGTPAIVKGLKP
                     IEDIADELRGADYLVWRNGRGAVRLLGRENNLMLLEYAGERMLSHIVAEHGDYQATEIA
                     AELMAKLYAASEEPLPSALLPIRDRFAALFQRARDDQNAGCQTDYVHAAIIADQMMSNA
                     SELRGLHGDLHHENIMFSSRGWLVIDPVGLVGEVGFGAANMFYDPADRDDLCLDPRRIA
                     QMADAFSRALDVDPRRLLDQAYAYGCLSAAWNADGEEEQRDLAIAAAIKQVRQTSY"
                     /name="aminoglycoside O-phosphotransferase APH(6)-Id"
     gene            complement(730..1533)
                     /gene="aph(3'')-Ib"
                     /locus_tag="I6J78_RS24460"
                     /old_locus_tag="I6J78_24465"
     ARG             complement(734..1533)
                     /name="aph(3'')-Ib"
                     /gene="aph(3'')-Ib"
                     /gene_name="aminoglycoside O-phosphotransferase
                     APH(3'')-Ib"
                     /tool="amrfinderplus"
                     /drug_class="AMINOGLYCOSIDE"
                     /identity="100.0"
                     /coverage="100.0"
     gene            complement(1594..2409)
                     /gene="sul2"
                     /locus_tag="I6J78_RS24465"
                     /old_locus_tag="I6J78_24470"
     ARG             complement(1598..2409)
                     /name="sul2"
                     /gene="sul2"
                     /gene_name="sulfonamide-resistant dihydropteroate synthase
                     Sul2"
                     /tool="amrfinderplus"
                     /drug_class="SULFONAMIDE"
                     /identity="100.0"
                     /coverage="100.0"
     gene            3598..3747
                     /locus_tag="I6J78_RS24470"
                     /old_locus_tag="I6J78_24475"
     CDS             3598..3747
                     /locus_tag="I6J78_RS24470"
                     /old_locus_tag="I6J78_24475"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_017880354.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_001138880.1"
                     /translation="MPSEYDEQLDSTDTQLPGEYDLFDLMAQVTEENLHAPVDFGSPVG
                     REAL"
                     /name="hypothetical protein"
     gene            complement(4503..4943)
                     /locus_tag="I6J78_RS24475"
                     /old_locus_tag="I6J78_24480"
     CDS             complement(4503..4943)
                     /locus_tag="I6J78_RS24475"
                     /old_locus_tag="I6J78_24480"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_011161230.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_005119689.1"
                     /translation="MAWHTVQETLKLTGKSRSQLYRDMAKGLVSYRTGKNDRREFETSE
                     LIRAYGELRTSETPKRHKEGHSKSVVSQAENAQLDVIQQKLDALQQTVTLMLEDKMARE
                     AENRLRNEEREQLQAEISRLADALAQEKKRGFWSRLFRSGSE"
                     /name="hypothetical protein"
     gene            5161..5550
                     /locus_tag="I6J78_RS24480"
                     /old_locus_tag="I6J78_24485"
     CDS             5161..5550
                     /locus_tag="I6J78_RS24480"
                     /old_locus_tag="I6J78_24485"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000102614.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_000102614.1"
                     /translation="MSTELNSGTVGGFGHMGPNDPYNDGHSGSGSSGGSFNGGGNGGHD
                     NSSGSSYTASFGLITGRHPITVPGTKNINSVDLSAVINNIIHHEGARNNMYLDTANNVR
                     VGVTGTGWQCLATAGISAEGKRTFR"
                     /name="hypothetical protein"
     gene            5594..>5998
                     /locus_tag="I6J78_RS24485"
                     /old_locus_tag="I6J78_24490"
                     /pseudo=""
     CDS             5594..>5998
                     /locus_tag="I6J78_RS24485"
                     /old_locus_tag="I6J78_24490"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001120888.1"
                     /note="incomplete; partial in the middle of a contig;
                     missing C-terminus; Derived by automated computational
                     analysis using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="IS91 family transposase"
                     /name="IS91 family transposase"
     ARG             complement(3..730)
                     /name="APH(6)-Id"
                     /gene="APH(6)-Id"
                     /gene_name="APH(6)"
                     /tool="rgi"
                     /drug_class="aminoglycoside antibiotic"
                     /identity="100.0"
                     /coverage="87.41"
     Typing          3390..3563
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="99.429"
                     /coverage="100.0"
                     /evalue="1.19e-84"
     Typing          complement(2861..3466)
                     /name="rep_cluster_2335"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="89.593"
                     /coverage="99.0"
                     /evalue="0.0"
ORIGIN
        1 acgcctggtc gagcaggcga cgcggatcga cgtccagcgc acgagagaat gcgtccgcca
       61 tctgtgcaat gcgtctagga tcgagacaaa ggtcgtctct gtcagccgga tcgtagaaca
      121 tattggcggc gccaaagccc acttcaccga ccagaccgac gggatctatc accagccagc
      181 cgcgactgga gaacatgatg ttttcatgat gcagatcgcc atgtagccca cgcagttccg
      241 aggcattgct catcatttga tcggctataa tcgccgcgtg gacgtagtca gtttgacaac
      301 ctgcgttttg atcatcgcgc gcccgctgaa acaaagctgc aaagcgatcc cggatcggga
      361 gaagggcaga aggcaggggt tcctcagatg cggcatacag cttcgccatt agttccgctg
      421 caatttcggt cgcctggtag tcgccgtgct cggcaacgat gtgagagagc attcgctccc
      481 cggcatattc gagcaacatc agattgttct cacgaccgag caaccggact gctcccctcc
      541 cattgcgcca taccagatag tcggccccgc gcagttcatc agcaatgtct tctataggtt
      601 tcaatccctt gacgattgca ggagtcccgt ctggcaatga aactttccaa acgaggctgg
      661 aaaaggtgtc cgcaatgaga acaggttgcg aaacgtgcca atgagcagga aaaacaggcg
      721 gcatgaacat caaccccaag tcagagggtc caatcgcaga tagaaggcaa ggcgttcgcg
      781 gtcgggggct tcgatcccca atacattgaa taggacagcg aaggcgcgct ctgcttcatc
      841 tggcgctgcc cagttctctt cggcgttagc aatcatgagt gccaaatcgg catagcgatc
      901 tgctgttccg agccgcccaa ggtcgatcag acccgtgcat tgaagagttt tagggtccac
      961 catgaagttc ggcatgcagg gatcaccatg gcaaacaacc atatcggtgc gctcttggtc
     1021 gagccgcacc ggtagctctc gttcgacacg agccaaaaga tcgagctgcg gcgtactctt
     1081 gtcctcgtcc ggtaagaagt cgggattgac ggcattgcgg gacaccacat caacggcgcg
     1141 tccgaacatt cgcgacagcc tgcgctcaaa cggacattga tcaaccgata ggctgtgaac
     1201 agcgccaagt tgctgcccca ttgacggcca cgctttgagc aaatccgctc cagacagatc
     1261 agccgccggt actcccggaa ttgccgttat caccaagcat gcaccctcct gttcctcctg
     1321 ccagttgatg acctcggggc aagccacacc tcgacctttg agccaaatga ggcggtcacg
     1381 ctctccagcg agctcaccgc ggcgggaagc aggtgcgatt ttcgcgaagg catgcccgtc
     1441 accacgtcga aaaacaaaat caccagattc tccgcctctg acaggcaacc agtcagaatg
     1501 cgattcacca aaaaaaatat tagttcgatt caatggaggt tccttcagtt ttctgatgaa
     1561 gcgcgaatat agagaaatat cccgaatgtg cagttaacga attcttgcgg tttctttcag
     1621 cgccgccaat accgccagcc cgtcgcgcaa ggggcgcggc tcgtgtgtgc ggatgaagtc
     1681 agctccacct gcggcggcgg caagctctgc agcgagtgtc gcggccccga catcccccgg
     1741 accacggcct gtgagcgcgc gcagaaagga tttgcgcgaa acagacagaa gcaccggcaa
     1801 atcgaagcgc agccgcaatt catcgaaccg cgccagcacc gagagcgagg tttcgggagc
     1861 agcccccaga aaaaacccca tgccgggatc aaggacaagg cggttgcgtt tgataccggc
     1921 acccgtcagc gccgcgatgc gcgcgtcaaa gaacgccgca atgtgatcca tgatgtcgcc
     1981 agcgggtgcc tcgcgccgat ctgcctgccc gtcttgcacc gaatgcataa cgacgagttt
     2041 ggcagatgat ttcgccaatt gcggatagaa cgcagcgtct ggaaaaccgc gaatatcatt
     2101 gagataggcc acaccacgcg acaaggcata ggcttgcgtc gcgggttgat aactgtcgag
     2161 cgagacggga atgccatctg ccttgagcgc gtccagcacc ggcgcgatac gcgcgatttc
     2221 tgtgtcggac gaaacaggcg cggcgtcggg attgctggat gccggaccga ggtcgatcac
     2281 atctgccccc tcggccatca gcttacgcgc ctgcgcaatg gctgcgtctg gcgccagata
     2341 ccggcctcca tcggagaaac tgtccgaggt tatgttgacg atgccgaaaa tgatgagcga
     2401 tttattcatg ggggcttcta taataataat aatcgagcat gagtctcata cggatgctcg
     2461 ggtcgaaagg gaatccccag gcgagtaacc tgtttgcggt gatccgtttc atgatgatgt
     2521 atctgtagca ttttggaaat aaatatatca tctctcaata agtagatata tttatctttt
     2581 ttgcttcttt ggtgctgcaa gtcaccaata cgagggaaac ctgttacgga gcggtttaac
     2641 cgtaatcaac agtgactggt gtcatgttcg gaagattaat tgatagtaat ctacaaagga
     2701 tcttcttgag atccttttca atgaatcgta atctcttgct ctgtaaacga aaaaaccgcc
     2761 tggggaggcg gtttgttcga aggttaagtc agttggggaa ctgcttaacc cggtaacagg
     2821 gttcacgaga ccgccattac caaaactgtt ctttcagtgt agccgcagtc aggcctctac
     2881 ttcaagacct cttaatctat cttctcgtgc actcctgtta ctaatggctg ctgccagtgg
     2941 cgttttgtcg tgtctttccg ggttggactc aagttgatag ttaccggaca aggcgcagcg
     3001 gtcggactga acggggggtt cgtgcataca gtccagcttg gagcgaactg ccttcacgga
     3061 actgagtgtc aggcgtggaa tgagaaaccg cggccataac agcggaatga caccggtaaa
     3121 ccgaaaggca ggaacaggag agcgcacgag ggagctacca gggggaaacg cctgggatct
     3181 ttatagtcct gtcgggtttc gccaccactg atttgagcgt cagattttgc gatgcttgtc
     3241 aggggggcgg agcctatgga aaaacggctt cgccgtggcc ttatctcttc tttgctaagt
     3301 gtcttcctgg tatcttccag gaaatttccg tccccgtccg taagccggta ccgctcgccg
     3361 cagccgaacg accgagcgta gcgagtcagt gagcgaggaa gcggaatatc tcctgtatcg
     3421 catattctgc tgacgcgccg gtgctgcctt ttttctcctg ccacatgaag cacttcactg
     3481 attttcgcaa tcgtggcaac atagtaagcc agtatacact ccgctagcgc tacatgactg
     3541 gttcagggct gcgccccgaa acccgctaac aacctctcag ctactggata tcaccccatg
     3601 ccatctgaat atgatgaaca actggattcg actgatacgc agcttcccgg cgaatatgac
     3661 ctttttgatt taatggcgca ggttactgaa gagaacctgc atgcccctgt ggattttggg
     3721 tcgcctgtcg gccgggaagc gttatagctt tttcgcttgc ccgcgtacgt ggtaatactc
     3781 cggtattacc ttttatttct ttattttcat gtaattacag tggattttta atacccgggt
     3841 attactcgtg aaaacgaaat attccttttt tttcttttaa ttcatgcagt tgcgatgaaa
     3901 atcgcggctg cgttaggtgt atgaccattt tgaggttgaa aaataatcaa ccatggcggg
     3961 tgatttacgc aggttaaggg gagatcgtga caaaaaaagc gttcctcact gtatcgttca
     4021 tgcctgcatg aacgggttat tcttcctgac tacagaatta catcgctcct tcagttcata
     4081 catcactttt acatcacttt tacatcactt atacatcact tttacatcat tccttcagct
     4141 catacgtcac tttcatcctc tgtgccattt gtacatcacc cccttcctga acgtgctgac
     4201 agcgggtttt ccggctgcgc cggcaacgct tcacggccac gcaataaatt gcgtccccgt
     4261 tcaccgtttt cggatgggaa gaacgccgga aacaggactt accccggctg aatggtgtga
     4321 atttccgcgc tatgcacttg tgcgcatact catgcatgcc gtaaaaacag agcctgcgcg
     4381 tttctggcgg gttttcgggt ggtttgttgc ctgttttacc ggtttcccgt cagaaacgcc
     4441 ctgagggcct ctcaggcggt gctgataaca gatgttatgg taaatcagag tcacctgcac
     4501 tgttactctg aaccggagcg aaacagccgc gaccagaatc cccgcttttt ttcctgtgcc
     4561 agcgcgtcag ccagacggct aatttcggcc tgtagttgtt ccctctcctc atttcgcagg
     4621 cggttttctg cttcccgcgc catcttgtct tcaagcatta gggtaacagt ctgctgcaga
     4681 gcgtccagtt tctgctgaat gacgtctagc tgagcatttt ccgcctggct aacgacagat
     4741 ttggagtgtc cctccttgtg cctttttggt gtctcagaag tgcgcagctc gccataggcc
     4801 cgaatcagtt cactggtctc gaactcccgg cgatcatttt ttcctgtgcg atagctgaca
     4861 aggcctttag ccatgtcacg atataattgc gagcgcgact ttcctgttaa tttcagtgtc
     4921 tcttgaactg tgtgccatgc cataaaagtg acagtgtctc ctgtgtgtac cgtattgtaa
     4981 cagcagaaca tattactgtt ttaacacaaa aggtctgagg ctgcccgtga ggcgtgaaaa
     5041 atacacaaaa aacctgttga cggtgtggtt ttgacgggcg tagtatttcg aatactgtat
     5101 ataaacacat tgttataaat acagtttttg ctgtttttaa aagtcaaaga ggataatttt
     5161 atgagtacag agttaaatag cggtactgtc ggtggttttg gtcacatggg accaaatgac
     5221 ccctacaatg atggtcatag cggctctgga agttcgggag gtagttttaa cggtggtggt
     5281 aatggtggcc atgataatag tagtggttca tcttatactg catcctttgg tctcatcact
     5341 ggccgacacc cgataactgt cccaggtacg aagaatatta attctgtcga tctttctgct
     5401 gtcattaata acattataca tcatgaaggt gcacgcaata acatgtacct agatactgcg
     5461 aacaatgtaa gagtgggagt gacgggcact ggctggcaat gtctagcaac ggcaggcatt
     5521 tcggctgagg gtaaaagaac tttccgctaa gcgatagact gtatgtaaac acagtattgc
     5581 aaggacgcgg aacatgcctc atgtggcggc caggacggcc agccgggatc gggatactgg
     5641 tcgttaccag agccaccgac ccgagcaaac ccttctctat cagatcgttg acgagtatta
     5701 cccggcattc gctgcgctta tggcagagca gggaaaggaa ttgccgggct atgtgcaacg
     5761 ggaatttgaa gaatttctcc aatgcgggcg gctggagcat ggctttctac gggttcgctg
     5821 cgagtcttgc cacgccgagc acctggtcgc tttcagctgt aagcgtcgcg gtttctgccc
     5881 gagctgtggg gcgcggcgga tggccgaaag tgccgccttg ctggttgatg aagtactgcc
     5941 tgaacaaccc atgcgtcagt gggtgttgag cttcccgttt cagctgcgtt tcctgtttgg
     6001 ggtcgtttgc gggaaggggc ggaatcctac gctaaggctt tggccagcga tattctccgg
     6061 tgagattgat gtgttcccag gggataggag aagtcgcttg atatctagta tgacgtctgt
     6121 cgcacctgct tgatcgcggc cgcgatagct agatcgcgtt gctcctcttc tccatccgcg
     6181 ttccaagctg cggaaaggca cccataagcg t
//
