LOCUS       NZ_CP011334             2954 bp    DNA     circular CON 01-MAY-2024
DEFINITION  Escherichia coli O104:H4 str. C227-11 isolate 368 shch plasmid
            unnamed, complete sequence.
ACCESSION   NZ_CP011334
VERSION     NZ_CP011334.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN03856947
            Sequence Read Archive: SRR1980037, SRR1980038
            Assembly: GCF_000986765.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli O104:H4 str. C227-11
  ORGANISM  Escherichia coli O104:H4 str. C227-11
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 2954)
  AUTHORS   Beaulaurier,J.A., Zhang,X.-S., Zhu,S., Sebra,R., Rosenbluh,C.,
            Deikus,G., Shen,N., Munera,D., Waldor,M.K., Chess,A., Blaser,M.J.,
            Schadt,E. and Fang,G.
  TITLE     Single molecule-level detection and long read-based phasing of
            epigenetic variations in bacterial methylomes
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 2954)
  AUTHORS   Beaulaurier,J.A. and Fang,G.
  TITLE     Direct Submission
  JOURNAL   Submitted (27-APR-2015) Genetics and Genomic Sciences, Icahn School
            of Medicine at Mount Sinai, 1425 Madison Ave, New York, NY 10029,
            USA
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: HGAP v. 2.0
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 100.0x
            Sequencing Technology             :: PacBio
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_000986765.1-RS_2024_05_01
            Annotation Date                   :: 05/01/2024 02:09:23
            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)                     :: 5,400
            CDSs (total)                      :: 5,274
            Genes (coding)                    :: 4,958
            CDSs (with protein)               :: 4,958
            Genes (RNA)                       :: 126
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 95
            ncRNAs                            :: 9
            Pseudo Genes (total)              :: 316
            CDSs (without protein)            :: 316
            Pseudo Genes (ambiguous residues) :: 0 of 316
            Pseudo Genes (frameshifted)       :: 136 of 316
            Pseudo Genes (incomplete)         :: 195 of 316
            Pseudo Genes (internal stop)      :: 60 of 316
            Pseudo Genes (multiple problems)  :: 68 of 316
            Pseudo Genes (short protein)      :: 2 of 316
            CRISPR Arrays                     :: 1
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP011334.1.
            Source DNA is available from Dr. Matthew K. Waldor at Havard
            Medical School (mwaldor@research.bwh.harvard.edu).
            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..2954
                     /organism="Escherichia coli O104:H4 str. C227-11"
                     /mol_type="genomic DNA"
                     /strain="C227-11"
                     /isolate="368 shch"
                     /isolation_source="stool sample from a 64-year-old woman
                     from Hamburg who presented with bloody diarrhea and did not
                     develop hemolytic uremic syndrome (HUS)"
                     /host="Homo sapiens"
                     /db_xref="taxon:1048254"
                     /plasmid="unnamed"
                     /geo_loc_name="Denmark"
                     /collection_date="2011-05-18"
                     /note="also called BCG-1 (Russian)"
     gene            complement(join(<2951..2954,1..191))
                     /locus_tag="AAF13_RS27285"
                     /old_locus_tag="AAF13_27285"
                     /pseudo=""
     CDS             complement(join(<2951..2954,1..191))
                     /locus_tag="AAF13_RS27285"
                     /old_locus_tag="AAF13_27285"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_032489477.1"
                     /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="hypothetical protein"
                     /name="hypothetical protein"
     gene            complement(444..1711)
                     /locus_tag="AAF13_RS27295"
                     /old_locus_tag="AAF13_27295"
                     /pseudo=""
     CDS             complement(444..1711)
                     /locus_tag="AAF13_RS27295"
                     /old_locus_tag="AAF13_27295"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_031587700.1"
                     /GO_function="GO:0004803 - transposase activity [Evidence
                     IEA]"
                     /note="frameshifted; internal stop; Derived by automated
                     computational analysis using gene prediction method:
                     Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="IS1380 family transposase"
                     /name="IS1380 family transposase"
     gene            complement(<1909..2109)
                     /locus_tag="AAF13_RS27300"
                     /old_locus_tag="AAF13_27300"
                     /pseudo=""
     CDS             complement(<1909..2109)
                     /locus_tag="AAF13_RS27300"
                     /old_locus_tag="AAF13_27300"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_076611787.1"
                     /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="DUF4158 domain-containing protein"
                     /name="DUF4158 domain-containing protein"
     gene            2274..2827
                     /locus_tag="AAF13_RS31600"
                     /old_locus_tag="AAF13_27305"
                     /pseudo=""
     CDS             2274..2827
                     /locus_tag="AAF13_RS31600"
                     /old_locus_tag="AAF13_27305"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:YP_005221001.1"
                     /GO_function="GO:0003677 - DNA binding [Evidence IEA];
                     GO:0000150 - DNA strand exchange activity [Evidence IEA]"
                     /GO_process="GO:0006310 - DNA recombination [Evidence IEA]"
                     /note="frameshifted; Derived by automated computational
                     analysis using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="recombinase family protein"
                     /name="recombinase family protein"
     ARG             complement(4..191)
                     /name="CTX-M-216"
                     /gene="CTX-M-216"
                     /gene_name="CTX-M beta-lactamase"
                     /tool="rgi"
                     /drug_class="cephalosporin"
                     /identity="100.0"
                     /coverage="21.65"
ORIGIN
        1 cgataaagta tttgcgaatt atctgctgtg ttaatcaatg ccacacccag tctgcctccc
       61 gactgccgct ctaattcggc aagtttttgc tgtacgtccg ccgtttgcgc atacagcggc
      121 acacttccta acaacagcgt gacggttgcc gtcgccatca gcgtgaactg gcgcagtgat
      181 tttttaacca tgggattcct tattctggaa gatacgaaaa acaacaacat gaatagtccc
      241 taaattccac gtgtttttta ttagcttcaa aaatcactat ttcacgaaga atttagactg
      301 cttctcacac attgtaacat tatttacaac cacctttcaa tcatttttga taaatcattg
      361 atttcatctt tgctgcaatg atacttaata aactctgcaa gttatccaca gagcaacact
      421 caattttatt gatgatattc ttattatacc agacattttt cattacactc ccttgtacgg
      481 atagttttcc gacaacttca tgattacaat atcttgcggt tttgattatt tttgctgcaa
      541 gaaatacata cttcaaacga aaggtcttta tttgctgtct gtattctgaa gagtccaagg
      601 aatcaaactt gaacaacaaa aataggttat atgaaagcat catcatttga aacacggctt
      661 cattcgccca aaatgacttt agcaagagat gacccaccgc catgtcgtat ttggcttctt
      721 tgatatagtt tcagcattac cacgcttttc atagtatata actacttttt cagaaaagca
      781 aggtagtatt tgttacaaag aaaagtagtc gtattcggaa ccttctaaaa gtgataattg
      841 tgctctttct ttttctggtt tcagtacgcg agatacgaca aatcttctgt ctttttccat
      901 ttaactaatt ttgtatacag ttctgctagt ttctctacct tcttctcctt taacgaatac
      961 aattgatgaa ttcgttgctt gtgaggtgag tgtagaataa cttttggctt taattaaata
     1021 tttgcatcca agagattcta tcgtttcgat aattttttca tcaaaagtag ccactatcca
     1081 ttcgaaataa aatttcttaa atcgtctgat ttgatgttag caacaatttc ttttgatcat
     1141 ttccgcagca ccgtttgcag tgtaagtatt gccacttctt acaaatccgg taacatatgc
     1201 ttttaattcg tcgcaaaatg caaattggat attgtagcat cggtttccca gtttcttagg
     1261 attatatcct tttgacgcac cttcttgatg accttctacg ttaattacac tactatcaat
     1321 atcaatcgta atggatgtca atttactttt agtgagcagt tttttaaaga ctttaaaatt
     1381 aatgtctcta aacatttggg ttgtcttgaa gttgaagttt cctagaaacc gtgacactgt
     1441 ttcaggttct tttacggaaa tatcaaactc gttgacgagg ggatcatttt gaagtagctt
     1501 tagacgttct aacttatcaa tgccaatgaa gtgaccggca gagcatggtc tttatatgat
     1561 tcatcttgat tttatttgtt gagtcattat caaatacgag gtcattttca ataaaatcaa
     1621 aaatcccatt gctttttgca ttctcaagga gcagaaaaag acctgcattt gatgttagat
     1681 tcttagcttt gaaatcaatt ttattaatca taattagaac ccctttttac tacttttctt
     1741 actattattt taccatatat cgagtcataa aagctgataa tttaacatat ttttgagcac
     1801 ttttctttca cccaatgggt gaaagctgaa ttcgaaggaa tgcatattta tcaaggcttt
     1861 gattatgctt tttgaagtac tgacgtagaa tctaggtatg attcatatcg tgaggaaggt
     1921 gcccagaaaa cggacacatc caatttgcag ggcaatgccc agacggttgt gatcacctct
     1981 gctttttccg ataaattcct tgtctgcttc atcaaggtga aaatatcgtg ccagctgaag
     2041 ctcatccggt tcaccggtga atctgccata gctttcagtc tgctcagtgg tcagaaagtc
     2101 aacgggcata tcggcctccc tgcctgacgg gcatttagta acatttttcc aaccgtacga
     2161 aatgttataa attatcggac atcgtaaaac tgttacattt aatatgtcta ttaaatcgta
     2221 aatttgtaat aatagacatg agttgtccga tattcgattt aaggtacatt tttatgcgac
     2281 tttttggtta cgctcggtct caaccagtca gcagtctctt gatcttcagg tcagagcact
     2341 caaagacgca ggtgtgaaag caaaccgtat atttaccgat aaggcatccg gcagttcaac
     2401 agaccgggaa gggctggatt tgctgaggat gaaggtggag gaaggtgatg tcattctggt
     2461 taagaagctc gaccgtcttg gccgcgacac tgccgatatg atccaactga taaaggaatt
     2521 tgacgctcag ggcgtggcag tccggttcat tgatgacggg atcagtacga cggtgatatg
     2581 gggcaaatgg tgtcaccatc ctgtcggctg tggcacaggc tgaacgccgg aggatcctag
     2641 aacgcacgaa tgagggccga caggaagcaa agctgaaagg aatcaaattt ggccgcaggc
     2701 gtaccgtgga caggaacgtc gtgctgacgc ttcatcagaa gggcactggt gcaacggaaa
     2761 ttgctcatca gctcagtatt gcccgctcca cggtttataa attcttgaag acgaaagggc
     2821 ctcgtgatac gcctattttt ataggttaat gtcatgataa taatggtttc ttagacgtca
     2881 ggtggcactt ttcggggaaa tgtgcgcgga accctatttg tttatttttc taaatacatt
     2941 caaatatgta tccg
//
