LOCUS       CP088809                6328 bp    DNA     circular BCT 09-DEC-2021
DEFINITION  Escherichia coli strain B16EC0268 plasmid pB16EC0268-2, complete
            sequence.
ACCESSION   CP088809
VERSION     CP088809.1
DBLINK      BioProject: PRJNA782071
            BioSample: SAMN23391558
KEYWORDS    .
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 6328)
  AUTHORS   Yoon,E.-J., Choi,Y.J., Kim,D., Won,D., Choi,J.R. and Jeong,S.H.
  TITLE     Chromosomal integration and amplification of group 9 blaCTX-M genes
            in Escherichia coli expand the spectrum of resistance under
            antimicrobial pressure
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 6328)
  AUTHORS   Yoon,E.-J., Choi,Y.J., Kim,D., Won,D., Choi,J.R. and Jeong,S.H.
  TITLE     Direct Submission
  JOURNAL   Submitted (26-NOV-2021) Research Institute of Bacterial Resistance,
            Yonsei University College of Medicine, Gangnam Severance Hospital,
            Yonsei, Seoul 06273, South Korea
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: other: SMRTLink v. v9.0
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 245x
            Sequencing Technology             :: PacBio Sequel
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI
            Annotation Date                   :: 12/02/2021 13:57:04
            Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline
            (PGAP)
            Annotation Method :: Best-placed reference protein set; GeneMarkS-2+
            Annotation Software revision      :: 5.3
            Features Annotated :: Gene; CDS; rRNA; tRNA; ncRNA; repeat_region
            Genes (total)                     :: 4,995
            CDSs (total)                      :: 4,881
            Genes (coding)                    :: 4,690
            CDSs (with protein)               :: 4,690
            Genes (RNA)                       :: 114
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 87
            ncRNAs                            :: 5
            Pseudo Genes (total)              :: 191
            CDSs (without protein)            :: 191
            Pseudo Genes (ambiguous residues) :: 0 of 191
            Pseudo Genes (frameshifted)       :: 78 of 191
            Pseudo Genes (incomplete)         :: 130 of 191
            Pseudo Genes (internal stop)      :: 40 of 191
            Pseudo Genes (multiple problems)  :: 48 of 191
            ##Genome-Annotation-Data-END##
            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/
FEATURES             Location/Qualifiers
     source          1..6328
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="B16EC0268"
                     /isolation_source="blood"
                     /host="Homo sapiens"
                     /db_xref="taxon:562"
                     /plasmid="pB16EC0268-2"
                     /geo_loc_name="South Korea"
                     /lat_lon="37.68 N 126.77 E"
                     /collection_date="2016"
                     /collected_by="Kor-GLASS"
     gene            join(5937..6328,1..16)
                     /locus_tag="LQT63_23890"
     CDS             join(5937..6328,1..16)
                     /locus_tag="LQT63_23890"
                     /inference="COORDINATES: ab initio prediction:GeneMarkS-2+"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GeneMarkS-2+."
                     /codon_start=1
                     /transl_table=11
                     /product="class I SAM-dependent methyltransferase"
                     /protein_id="UGJ51787.1"
                     /translation="MPGQSKLLAQSLKPGGIMLIGEPYWRQLPATDEIAQACGVSSTTD
                     FLTLPGLVSAFDDLGYDVVEMVLADQEGWDRYEAAKWLTMRRWLEANPDDDFAAEVRAE
                     LNISPKRHVTYAREYFGWGVFALIARYSCRF"
                     /name="class I SAM-dependent methyltransferase"
     gene            12..707
                     /locus_tag="LQT63_23895"
                     /pseudo=""
     CDS             12..707
                     /locus_tag="LQT63_23895"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000290541.1"
                     /note="frameshifted; incomplete; partial on complete
                     genome; missing N-terminus; Derived by automated
                     computational analysis using gene prediction method:
                     Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="phage tail protein"
                     /name="phage tail protein"
     gene            789..1214
                     /locus_tag="LQT63_23900"
     CDS             789..1214
                     /locus_tag="LQT63_23900"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001373091.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="IS66 family insertion sequence hypothetical
                     protein"
                     /protein_id="UGJ51788.1"
                     /translation="MELQDWRKEPRKNYSNEFKLRMVELASQPGACVAQIARENGVNDN
                     VIFKWLRLWQNEGRVSRRLPVTTSSDTGVELLPVEITPDEQKEPVAAIAPSLSTSTQTR
                     VSASSCKVEFRHGNMTLENPSPELLTVLIRELTGRGR"
                     /name="IS66 family insertion sequence hypothetical protein"
     gene            1211..1560
                     /gene="tnpB"
                     /locus_tag="LQT63_23905"
                     /pseudo=""
     CDS             1211..1560
                     /gene="tnpB"
                     /locus_tag="LQT63_23905"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:NP_311895.1"
                     /note="TnpB, as the term is used for proteins encoded by
                     IS66 family insertion elements, is considered an accessory
                     protein, since TnpC, encoded by a neighboring gene, is a
                     DDE family transposase.; frameshifted; Derived by automated
                     computational analysis using gene prediction method:
                     Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="IS66 family insertion sequence element accessory
                     protein TnpB"
                     /name="tnpB"
     gene            1591..3201
                     /locus_tag="LQT63_23910"
                     /pseudo=""
     CDS             1591..3201
                     /locus_tag="LQT63_23910"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000080195.1"
                     /note="frameshifted; Derived by automated computational
                     analysis using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="IS66-like element ISEc23 family transposase"
                     /name="IS66-like element ISEc23 family transposase"
     gene            complement(3238..3964)
                     /locus_tag="LQT63_23915"
                     /pseudo=""
     CDS             complement(3238..3964)
                     /locus_tag="LQT63_23915"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_176259710.1"
                     /note="frameshifted; incomplete; partial on complete
                     genome; missing N-terminus and C-terminus; Derived by
                     automated computational analysis using gene prediction
                     method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="AAA domain-containing protein"
                     /name="AAA domain-containing protein"
     gene            4041..4361
                     /locus_tag="LQT63_23920"
     CDS             4041..4361
                     /locus_tag="LQT63_23920"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001332034.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="GNAT family N-acetyltransferase"
                     /protein_id="UGJ51785.1"
                     /translation="MLGVLTLARDIQLAIVNKMTQVLIGDIYLRQQCDVFWLGYTISPA
                     YTRQGYAIEAITATIDWIKENGFSLIKAGVNPENTLSKKLLIRIGFNFSSIEDGEHIYV
                     LD"
                     /name="GNAT family N-acetyltransferase"
     gene            4715..4970
                     /locus_tag="LQT63_23925"
                     /pseudo=""
     CDS             4715..4970
                     /locus_tag="LQT63_23925"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:YP_588477.1"
                     /note="frameshifted; Derived by automated computational
                     analysis using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="YjhX family toxin"
                     /name="YjhX family toxin"
     gene            4982..5525
                     /locus_tag="LQT63_23930"
                     /pseudo=""
     CDS             4982..5525
                     /locus_tag="LQT63_23930"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_004131893.1"
                     /note="frameshifted; Derived by automated computational
                     analysis using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="N-acetyltransferase"
                     /name="N-acetyltransferase"
     gene            5581..5886
                     /locus_tag="LQT63_23935"
     CDS             5581..5886
                     /locus_tag="LQT63_23935"
                     /inference="COORDINATES: ab initio prediction:GeneMarkS-2+"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GeneMarkS-2+."
                     /codon_start=1
                     /transl_table=11
                     /product="class I SAM-dependent methyltransferase"
                     /protein_id="UGJ51786.1"
                     /translation="MDIPRIFTISESEHRIHNPFTEEKYATLGRVLRMKPETRILDLGS
                     GSGEMLCTWARDHGITRTGIDMSSLFTAQARRRAEELGVSERVHFIHNDAAGLRRQ"
                     /name="class I SAM-dependent methyltransferase"
ORIGIN
        1 ctcatgccgt ttttaaaaca gaacgacagg taaggttacg tatacggttt gatagtatga
       61 tggtagtgca acaacttttt cttggcgatg cgtacattga tacgcaaacg cttgaaatta
      121 atatgacagg tggtgctgcc ggcagaatta cggcacgagt caggaaggat aagaccacgg
      181 gctggatttt tgcagaggca acgattcagg caattgatgg tgagttaaaa ataggctctc
      241 agatacagta ttctcctgag gcagggtggg gcaacagtat ctggtgacta tatttatctt
      301 gccacccacc acagtagaaa tggccgtgtg tatcatcatt tattatttca ggaggcagcg
      361 caacgacaag ccagtgattt ggttagtatc cccaccaaat aatctttata agttaccatt
      421 tactttttta cttgagattc ataaaactgg gatattgcac caacgccgca ccccgcgtgt
      481 gggatatagc agccaatacc gggcaatcag caattgcagc aatcaacgag gtagtggtag
      541 ttatatatga gtctgtcaaa cccttcaggc tcgtatgtta atagcgcagc gacagatgta
      601 tttgcagaga aaaccacatt tgatgtattg caaaagctga tggtcacttt catgtggtga
      661 caaatggtaa agcggttaat gaagtttatt gtgaatataa tgggtaagcg taaactgacc
      721 gccgtatgta gccatcagac gagaattggt aacttagacg cccatctgat atagacggac
      781 atctaagtat ggaattacag gactggcgaa aagaacctcg taaaaactat tcgaatgaat
      841 tcaaacttcg tatggtggaa ctggcatcac aacctggagc ttgtgttgca cagattgcac
      901 gtgaaaatgg cgtcaatgat aatgttattt tcaaatggct caggctctgg cagaacgaag
      961 ggcgtgtttc gcggcgtctt ccggtaacga cctcttctga cactggcgtt gaattattac
     1021 ctgtagaaat aacgccggat gagcagaaag aacctgtggc ggccattgcg ccgtctttat
     1081 ccacttccac tcagaccaga gtcagtgcca gttcctgcaa ggtggaattc cgtcacggta
     1141 acatgacgct ggaaaatcca tcgccagagc tgctcacagt gttgatccgt gaactgaccg
     1201 ggaggggaag atgatctcac tcccatcagg tacccgtatc tggctcgttg ccggcgttac
     1261 cgatatgcgt aatccttcaa cggactggga gaacaggtac aacatgtgct gaatgataat
     1321 cccttctccg gtcacctgtt tatcttccgt ggccgacggg gtgacaccgt caaaattctt
     1381 tgggctgatg ctgatggtct gtgcctgttc accaaacgcc tggaggaagg ccagtttatc
     1441 tggcctgcgg tacgtgacgg caaggtatcc attacccgct cgcaactggc aatgctcctc
     1501 gataagctgg actggcgtca gccaaaaaca tccagccgta actcactgac aatgttgtaa
     1561 aaaactcctg accgcattat aaaaacggtc atgagtcaga aatacctcat tcgcatcgca
     1621 gagctggaaa ggttgctctc tgagcaggct gaagccctcc gtcagaaaga ccagcaactg
     1681 agtctggttg aagagacgga agccttcctg cgctctgcac tgacacgtgc cgaagaaaag
     1741 atcgaagaag atgaacggga aatagaacat ctgcgggctc agatagaaaa ctgcgccgga
     1801 tgctgttcgg tacccgttct gaaaaactgc gtcgtgaagt tgaactggct gaggctctgc
     1861 tgaaacaacg tgaacaggac agcgatcgtt acagtgggcg ggaagacgat cctcaggttc
     1921 cccgccagtt gcgacagtcg cgccatcgtc gtccgttacc ggcacacctt ccccgtgaaa
     1981 tacaccgcct ggagccagaa gaaagctgtt gcccggagtg tggcggtgag ctggattatc
     2041 tgggggaagt cagcgctgaa cagctggaac tggtgagcag tgccctgaaa gtgatccgca
     2101 cagaacgggt aaaaaaagcc tgtacaaaat gtgactgtat tgttgaagca ccggcgccgt
     2161 cccgcccgat agagcgtggt atcgcgggcc ccggattact tgcccgcgtg ttaacgggaa
     2221 aatactgcga acatctgcca ctgtatcgtc agagtgaaat ctttgcccgc cagggtgtcg
     2281 aactgagccg ggccttactc tccaactggg ttgacgcgtg ctgccagtta atgacaccgg
     2341 tgaatgatgc cctgtaccgt tatgtaatga atacccgcaa ggttcacact gatgacacac
     2401 cggtaaaggt actggcaccg ggtcagaaaa aggcgaaaac agggcgtatc tggacgtatg
     2461 tccgggatga tcgcaatgtg ggttcgtcat ctcctccagc ggtctggttc gcgtactcgc
     2521 cgaaccggca ggggaaacac ccggagcaac acctccgccc cttccggggt atcctgcagg
     2581 cggatgcgtt cacagttacg acaggttgtt cagtgcagaa cgtgaaggtg gtgcactgac
     2641 agaagttgcg tgctgggccc atgcccggcg aaaaatccac gatgtataca tcagcagcaa
     2701 aagtgcgacg gcagaagaag ccctgaagcg aatcagtgaa ctgtacgcca tcgaggatga
     2761 aatacgggga ttaccggagt cagagcgtct tgccgtcagg cagcagcgaa gcaaagtgtt
     2821 actgacgtcg ctgcatgaat ggatggtgga gaagaatggt acgctgtcga aaaaatccag
     2881 actgggcgaa gcgttcagct atgtactgaa tcagtgggat gccctctgtt attacagtga
     2941 tgacggtctg gcggaggcgg ataataatgc tgcggaaaga gcgcttcgtg cagtctgtct
     3001 cggaaagaaa aactttatgt tctttggcag cgatcacggc ggcgagcgtg gagcactgtt
     3061 gtacgggctg atcggcacct gccgtctgaa cggtatcgat ccggaagcgt atctgcgcct
     3121 atcctgagcg tactgccgga atggccttcc aaccgagttg acgaactcct gccatggaac
     3181 gtagtactca ccaataaata agcgtcaata cggtgctccg ttgacgctta cattaaaatc
     3241 ctgtcgtttc tgaaactcaa attgcaacgc attattatct gaagaaaaga gatattttgc
     3301 ccaataaccc tcgcggcgaa aatgcgggct gcatctcgat aaggtccata tcgccaaata
     3361 ccagaaaact atctttagcg cgtgagacag caacattgag gatactgctg ttgctatcaa
     3421 gaaacctgcc atcttcatgt tttgagtaga caggagaaaa gagaacaatc gccctttccg
     3481 ccccctgcaa ggagtgcaca gtccccactg tcagtgaacc ctgctcgtct ttgccattaa
     3541 tttccagctt acgcaatgac gtttgatagc attaacctgc gccgaaaatg gcgtcacaac
     3601 accaacaact ttgtacagtg gttccccgta atggcgctct atatcatcct tatgtgccac
     3661 cagccatgct gctattgttt cagcttcaag agggttataa cggcttcctc catttggctt
     3721 catgcctcta ccatcaatat gtaaatatcc cattgcgggg aaaatcgtcc ctttttccat
     3781 ccctctttta ggctgcaact taccgtgata gcaaagtgag ttacagtagc cgatgatgtt
     3841 attgaaacag cgacgatgct catacagata cattccgcgc tcgaacttgg gatcatactg
     3901 gtagtgagag ttgaaactgg gctacctgca ttacgctgcc agatgctgca ctttttccag
     3961 acccattatt atcgaatacg gtgaccgcct gagcggccac ctttaatcgt gggcagttac
     4021 acagaattat ttacagggcc ttgctgggag ttcttacact tgctcgcgat attcaattgg
     4081 ccattgtcaa caagatgacg caggttttga ttggtgatat ctatttacgt cagcaatgcg
     4141 atgtgttttg gctcggctat accatcagtc ccgcttatac tcgccaggga tatgcaattg
     4201 aagcaattac cgccacgatt gactggataa aagagaacgg tttttcactc atcaaagccg
     4261 gtgtgaatcc ggaaaatacc ctttcaaaaa aattacttat caggattggc ttcaattttt
     4321 cgagcatcga agatggtgag catatttatg ttctggatta aacaaaagga gaataatctc
     4381 ccgaagggaa aagccgatga ggccatttca ggcgtacttc aacatgcatt cgtcagtgtc
     4441 atctgccttt tccagtaaat ttggcattca atttccaaag tacatcacac ttttctactg
     4501 aaacatatcc cctctcctat aactacgtgt tatattcgct ccgtaaatat accttcaact
     4561 caacccgagg ctttgatgct ggagaatgta atcatccgat aatcagctta ccgacctttc
     4621 aggccggact gattatcaaa tgcgccgaaa tcgaatgcgg acaccgcggt gtgtttgcac
     4681 gttttgcaca tgatgattaa acaggttctt cagtatgaat ttatcccgtc aggaacaacg
     4741 tacgttacac gttctcgcta aaggtggacg tattgcgcac gtccgcgatt cttcagccgc
     4801 gtcacttccg ttgaatgcta cagccgcgaa gggctgttgc tgaccgactg cacgctcgcc
     4861 gtcttcaaaa aactcaaacc aaaaaactta tcaagtccgt caatggtcag ccctatcgaa
     4921 tcaacactac cgggctgaat aacgttcgcg ctcagctcga taatcgctaa ggagagtttc
     4981 gatgacagca caccacttca cttttcaaat cacagatgaa agtgatgcca gtgatatccg
     5041 gaagtcgaaa cccgcgcatt tggcttcagc aaagaagccg atttaacggc ctctttactt
     5101 gaggatgaaa gcgcgcgccc tgcgttatcg ctgctggccc gacatgaagg caaagccgtc
     5161 gggcatattt tatttacccg ggcaaccttc aaaggggaaa tggattcacc gctgatgcat
     5221 atcctcgctc ccctggcagt cataccggaa taccagggga tgggcgtgga ggcgttgata
     5281 cgcactggca tcgagcacct gaggttatgg gctgccagac ggtttttgtt ctcggccacg
     5341 ccacctatta cccccgacat gggttcgaac cctgtgccgg agacaaaggc tatccggcac
     5401 cttatcccat cccggaggag cacaaagcct gctggatgat gcaagcactc acccgctcag
     5461 cccatgaacg tgaccggcca catccagtgc gcgcaggccc tgatgaaacc ggagcactgg
     5521 cgtgaataac aatcttgttg tgcccttttt aatgcttaac ccaataacag gaattaacta
     5581 atggatattc cacgtatttt taccatcagt gaaagcgaac accgcatcca caacccgttc
     5641 accgaagaga agtacgccac gctgggtcgc gtgctgcgca tgaaaccaga gacccgaatt
     5701 ctggacctcg gcagcggctc gggcgagatg ctctgcacct gggcccggga tcatggcatt
     5761 acgaggactg gaatcgacat gagttcgctc ttcaccgcgc aggccagacg ccgcgcggaa
     5821 gaactcggcg tcagcgaacg cgtacatttt attcataatg atgcggcggg tttacgtcgc
     5881 caatgaaaaa tgtgacgtag cagcctgcgt tggcgcgacc tggattgccg gaggctttgc
     5941 cgggacagtc gaaactgctg gcgcagagcc ttaaaccggg cgggatcatg ctcatcggtg
     6001 aaccttactg gcgtcagctt ccggcaacgg acgagatagc ccaggcctgt ggcgtcagct
     6061 cgacgaccga ttttctgacg ctaccagggc ttgtcagcgc gtttgacgac ctcggctacg
     6121 acgtggtgga aatggtactg gcggaccagg aaggctggga ccgatatgag gccgcgaaat
     6181 ggctgaccat gcgccgctgg ctggaggcca atcctgacga tgacttcgcc gccgaagtca
     6241 gggccgagct aaacatctcg ccgaaacgcc acgtaacgta cgcgcgggaa tactttggct
     6301 ggggcgtgtt cgcactcatc gctaggta
//
