LOCUS       NC_017658               6211 bp    DNA     circular CON 27-MAR-2024
DEFINITION  Escherichia coli O55:H7 str. RM12579 plasmid p12579_4, complete
            sequence.
ACCESSION   NC_017658
VERSION     NC_017658.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN02604278
            Assembly: GCF_000245515.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli O55:H7 str. RM12579
  ORGANISM  Escherichia coli O55:H7 str. RM12579
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 6211)
  AUTHORS   Kyle,J.L., Cummings,C.A., Parker,C.T., Quinones,B., Vatta,P.,
            Newton,E., Huynh,S., Swimley,M., Degoricija,L., Barker,M.,
            Fontanoz,S., Nguyen,K., Patel,R., Fang,R., Tebbs,R., Petrauskene,O.,
            Furtado,M. and Mandrell,R.E.
  TITLE     Escherichia coli serotype O55:H7 diversity supports parallel
            acquisition of bacteriophage at Shiga toxin phage insertion sites
            during evolution of the O157:H7 lineage
  JOURNAL   J Bacteriol 194 (8), 1885-1896 (2012)
   PUBMED   22328665
REFERENCE   2  (bases 1 to 6211)
  AUTHORS   Kyle,J.L., Cummings,C.A., Parker,C.T., Quinones,B., Vatta,P.,
            Newton,E., Huynh,S., Swimley,M.S., Degoricija,L., Barker,M.,
            Fontanoz,S., Nguyen,K., Patel,R., Fang,R., Tebbs,R., Petrauskene,O.,
            Furtado,M. and Mandrell,R.E.
  TITLE     Direct Submission
  JOURNAL   Submitted (09-NOV-2011) Western Regional Research Center / Produce
            Safety and Microbiology Research Unit, United States Department of
            Agriculture / Agricultural Research Service, 800 Buchanan Street,
            Albany, CA 94710, USA
COMMENT     ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_000245515.1-RS_2024_03_27
            Annotation Date                   :: 03/27/2024 17:42:45
            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)                     :: 5,362
            CDSs (total)                      :: 5,231
            Genes (coding)                    :: 4,984
            CDSs (with protein)               :: 4,984
            Genes (RNA)                       :: 131
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 102
            ncRNAs                            :: 7
            Pseudo Genes (total)              :: 247
            CDSs (without protein)            :: 247
            Pseudo Genes (ambiguous residues) :: 0 of 247
            Pseudo Genes (frameshifted)       :: 95 of 247
            Pseudo Genes (incomplete)         :: 131 of 247
            Pseudo Genes (internal stop)      :: 73 of 247
            Pseudo Genes (multiple problems)  :: 45 of 247
            Pseudo Genes (short protein)      :: 4 of 247
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP003113.1.
            Genome was manually curated based on annotation generated by the
            NCBI Prokaryotic Genomes Automatic Annotation Pipeline Group.
            Information about the Pipeline can be found here:
            http://www.ncbi.nlm.nih.gov/genomes/static/Pipeline.html.
            Bacteria available from Dr. Robert Mandrell
            (robert.mandrell@ars.usda.gov).
            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 O55:H7 str. RM12579"
                     /mol_type="genomic DNA"
                     /strain="RM12579"
                     /serotype="O55:H7"
                     /isolation_source="urine from child < 5 years old"
                     /host="Homo sapiens"
                     /db_xref="taxon:1048689"
                     /plasmid="p12579_4"
                     /geo_loc_name="USA: California"
                     /collection_date="1974-12"
     gene            141..956
                     /gene="sul2"
                     /locus_tag="ECO55CA74_RS27430"
                     /old_locus_tag="ECO55CA74_26384"
     ARG             142..953
                     /name="sul2"
                     /gene="sul2"
                     /gene_name="sulfonamide-resistant dihydropteroate synthase
                     Sul2"
                     /tool="amrfinderplus"
                     /drug_class="SULFONAMIDE"
                     /identity="100.0"
                     /coverage="100.0"
     gene            1017..1820
                     /gene="aph(3'')-Ib"
                     /locus_tag="ECO55CA74_RS27435"
                     /old_locus_tag="ECO55CA74_26389"
     ARG             1018..1817
                     /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            1820..2656
                     /locus_tag="ECO55CA74_RS27440"
                     /old_locus_tag="ECO55CA74_26394"
     CDS             1820..2656
                     /locus_tag="ECO55CA74_RS27440"
                     /old_locus_tag="ECO55CA74_26394"
                     /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(<2763..3167)
                     /locus_tag="ECO55CA74_RS27445"
                     /old_locus_tag="ECO55CA74_26399"
                     /pseudo=""
     CDS             complement(<2763..3167)
                     /locus_tag="ECO55CA74_RS27445"
                     /old_locus_tag="ECO55CA74_26399"
                     /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"
     gene            complement(3211..3600)
                     /locus_tag="ECO55CA74_RS29910"
     CDS             complement(3211..3600)
                     /locus_tag="ECO55CA74_RS29910"
                     /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            3818..4258
                     /locus_tag="ECO55CA74_RS27450"
                     /old_locus_tag="ECO55CA74_26404"
     CDS             3818..4258
                     /locus_tag="ECO55CA74_RS27450"
                     /old_locus_tag="ECO55CA74_26404"
                     /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            complement(5014..5163)
                     /locus_tag="ECO55CA74_RS32080"
                     /old_locus_tag="ECO55CA74_26409"
     CDS             complement(5014..5163)
                     /locus_tag="ECO55CA74_RS32080"
                     /old_locus_tag="ECO55CA74_26409"
                     /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            5734..5892
                     /locus_tag="ECO55CA74_RS32830"
     CDS             5734..5892
                     /locus_tag="ECO55CA74_RS32830"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_007772075.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_032287700.1"
                     /translation="MHEPPVQSDRCALSGNYQLESNPERHDKTPLAAAISNRSAREDRL
                     RGLEVEA"
                     /name="hypothetical protein"
     ARG             1821..2653
                     /name="aph(6)-Id"
                     /gene="aph(6)-Id"
                     /gene_name="aminoglycoside O-phosphotransferase APH(6)-Id"
                     /tool="amrfinderplus"
                     /drug_class="AMINOGLYCOSIDE"
                     /identity="100.0"
                     /coverage="100.0"
     Typing          complement(5199..5372)
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="99.429"
                     /coverage="100.0"
                     /evalue="1.19e-84"
     Typing          5296..5901
                     /name="rep_cluster_2335"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="89.593"
                     /coverage="99.0"
                     /evalue="0.0"
ORIGIN
        1 gatatattta tttccaaaat gctacagata catcatcatg aaacggatca ccgcaaacag
       61 gttactcgcc tggggattcc ctttcgaccc gagcatccgt atgagactca tgctcgatta
      121 ttattattat agaagccccc atgaataaat cgctcatcat tttcggcatc gtcaacataa
      181 cctcggacag tttctccgat ggaggccggt atctggcgcc agacgcagcc attgcgcagg
      241 cgcgtaagct gatggccgag ggggcagatg tgatcgacct cggtccggca tccagcaatc
      301 ccgacgccgc gcctgtttcg tccgacacag aaatcgcgcg tatcgcgccg gtgctggacg
      361 cgctcaaggc agatggcatt cccgtctcgc tcgacagtta tcaacccgcg acgcaagcct
      421 atgccttgtc gcgtggtgtg gcctatctca atgatattcg cggttttcca gacgctgcgt
      481 tctatccgca attggcgaaa tcatctgcca aactcgtcgt tatgcattcg gtgcaagacg
      541 ggcaggcaga tcggcgcgag gcacccgctg gcgacatcat ggatcacatt gcggcgttct
      601 ttgacgcgcg catcgcggcg ctgacgggtg ccggtatcaa acgcaaccgc cttgtccttg
      661 atcccggcat ggggtttttt ctgggggctg ctcccgaaac ctcgctctcg gtgctggcgc
      721 ggttcgatga attgcggctg cgcttcgatt tgccggtgct tctgtctgtt tcgcgcaaat
      781 cctttctgcg cgcgctcaca ggccgtggtc cgggggatgt cggggccgcg acactcgctg
      841 cagagcttgc cgccgccgca ggtggagctg acttcatccg cacacacgag ccgcgcccct
      901 tgcgcgacgg gctggcggta ttggcggcgc tgaaagaaac cgcaagaatt cgttaactgc
      961 acattcggga tatttctcta tattcgcgct tcatcagaaa actgaaggaa cctccattga
     1021 atcgaactaa tatttttttt ggtgaatcgc attctgactg gttgcctgtc agaggcggag
     1081 aatctggtga ttttgttttt cgacgtggtg acgggcatgc cttcgcgaaa atcgcacctg
     1141 cttcccgccg cggtgagctc gctggagagc gtgaccgcct catttggctc aaaggtcgag
     1201 gtgtggcttg ccccgaggtc atcaactggc aggaggaaca ggagggtgca tgcttggtga
     1261 taacggcaat tccgggagta ccggcggctg atctgtctgg agcggatttg ctcaaagcgt
     1321 ggccgtcaat ggggcagcaa cttggcgctg ttcacagcct atcggttgat caatgtccgt
     1381 ttgagcgcag gctgtcgcga atgttcggac gcgccgttga tgtggtgtcc cgcaatgccg
     1441 tcaatcccga cttcttaccg gacgaggaca agagtacgcc gcagctcgat cttttggctc
     1501 gtgtcgaacg agagctaccg gtgcggctcg accaagagcg caccgatatg gttgtttgcc
     1561 atggtgatcc ctgcatgccg aacttcatgg tggaccctaa aactcttcaa tgcacgggtc
     1621 tgatcgacct tgggcggctc ggaacagcag atcgctatgc cgatttggca ctcatgattg
     1681 ctaacgccga agagaactgg gcagcgccag atgaagcaga gcgcgccttc gctgtcctat
     1741 tcaatgtatt ggggatcgaa gcccccgacc gcgaacgcct tgccttctat ctgcgattgg
     1801 accctctgac ttggggttga tgttcatgcc gcctgttttt cctgctcatt ggcacgtttc
     1861 gcaacctgtt ctcattgcgg acaccttttc cagcctcgtt tggaaagttt cattgccaga
     1921 cgggactcct gcaatcgtca agggattgaa acctatagaa gacattgctg atgaactgcg
     1981 cggggccgac tatctggtat ggcgcaatgg gaggggagca gtccggttgc tcggtcgtga
     2041 gaacaatctg atgttgctcg aatatgccgg ggagcgaatg ctctctcaca tcgttgccga
     2101 gcacggcgac taccaggcga ccgaaattgc agcggaacta atggcgaagc tgtatgccgc
     2161 atctgaggaa cccctgcctt ctgcccttct cccgatccgg gatcgctttg cagctttgtt
     2221 tcagcgggcg cgcgatgatc aaaacgcagg ttgtcaaact gactacgtcc acgcggcgat
     2281 tatagccgat caaatgatga gcaatgcctc ggaactgcgt gggctacatg gcgatctgca
     2341 tcatgaaaac atcatgttct ccagtcgcgg ctggctggtg atagatcccg tcggtctggt
     2401 cggtgaagtg ggctttggcg ccgccaatat gttctacgat ccggctgaca gagacgacct
     2461 ttgtctcgat cctagacgca ttgcacagat ggcggacgca ttctctcgtg cgctggacgt
     2521 cgatccgcgt cgcctgctcg accaggcgta cgcttatggg tgcctttccg cagcttggaa
     2581 cgcggatgga gaagaggagc aacgcgatct agctatcgcg gccgcgatca agcaggtgcg
     2641 acagacgtca tactagatat caagcgactt ctcctatccc ctgggaacac atcaatctca
     2701 ccggagaata tcgctggcca aagccttagc gtaggattcc gccccttccc gcaaacgacc
     2761 ccaaacagga aacgcagctg aaacgggaag ctcaacaccc actgacgcat gggttgttca
     2821 ggcagtactt catcaaccag caaggcggca ctttcggcca tccgccgcgc cccacagctc
     2881 gggcagaaac cgcgacgctt acagctgaaa gcgaccaggt gctcggcgtg gcaagactcg
     2941 cagcgaaccc gtagaaagcc atgctccagc cgcccgcatt ggagaaattc ttcaaattcc
     3001 cgttgcacat agcccggcaa ttcctttccc tgctctgcca taagcgcagc gaatgccggg
     3061 taatactcgt caacgatctg atagagaagg gtttgctcgg gtcggtggct ctggtaacga
     3121 ccagtatccc gatcccggct ggccgtcctg gccgccacat gaggcatgtt ccgcgtcctt
     3181 gcaatactgt gtttacatac agtctatcgc ttagcggaaa gttcttttac cctcagccga
     3241 aatgcctgcc gttgctagac attgccagcc agtgcccgtc actcccactc ttacattgtt
     3301 cgcagtatct aggtacatgt tattgcgtgc accttcatga tgtataatgt tattaatgac
     3361 agcagaaaga tcgacagaat taatattctt cgtacctggg acagttatcg ggtgtcggcc
     3421 agtgatgaga ccaaaggatg cagtataaga tgaaccacta ctattatcat ggccaccatt
     3481 accaccaccg ttaaaactac ctcccgaact tccagagccg ctatgaccat cattgtaggg
     3541 gtcatttggt cccatgtgac caaaaccacc gacagtaccg ctatttaact ctgtactcat
     3601 aaaattatcc tctttgactt ttaaaaacag caaaaactgt atttataaca atgtgtttat
     3661 atacagtatt cgaaatacta cgcccgtcaa aaccacaccg tcaacaggtt ttttgtgtat
     3721 ttttcacgcc tcacgggcag cctcagacct tttgtgttaa aacagtaata tgttctgctg
     3781 ttacaatacg gtacacacag gagacactgt cacttttatg gcatggcaca cagttcaaga
     3841 gacactgaaa ttaacaggaa agtcgcgctc gcaattatat cgtgacatgg ctaaaggcct
     3901 tgtcagctat cgcacaggaa aaaatgatcg ccgggagttc gagaccagtg aactgattcg
     3961 ggcctatggc gagctgcgca cttctgagac accaaaaagg cacaaggagg gacactccaa
     4021 atctgtcgtt agccaggcgg aaaatgctca gctagacgtc attcagcaga aactggacgc
     4081 tctgcagcag actgttaccc taatgcttga agacaagatg gcgcgggaag cagaaaaccg
     4141 cctgcgaaat gaggagaggg aacaactaca ggccgaaatt agccgtctgg ctgacgcgct
     4201 ggcacaggaa aaaaagcggg gattctggtc gcggctgttt cgctccggtt cagagtaaca
     4261 gtgcaggtga ctctgattta ccataacatc tgttatcagc accgcctgag aggccctcag
     4321 ggcgtttctg acgggaaacc ggtaaaacag gcaacaaacc acccgaaaac ccgccagaaa
     4381 cgcgcaggct ctgtttttac ggcatgcatg agtatgcgca caagtgcata gcgcggaaat
     4441 tcacaccatt cagccggggt aagtcctgtt tccggcgttc ttcccatccg aaaacggtga
     4501 acggggacgc aatttattgc gtggccgtga agcgttgccg gcgcagccgg aaaacccgct
     4561 gtcagcacgt tcaggaaggg ggtgatgtac aaatggcaca gaggatgaaa gtgacgtatg
     4621 agctgaagga atgatgtaaa agtgatgtaa aagtgatgta taagtgatgt aaaagtgatg
     4681 tatgaactga aggagcgatg taattctgta gtcaggaaga ataacccgtt catgcaggca
     4741 tgaacgatac agtgaggaac gctttttttg tcacgatctc cccttaacct gcgtaaatca
     4801 cccgccatgg ttgattattt ttcaacctca aaatggtcat acacctaacg cagccgcgat
     4861 tttcatcgca actgcatgaa ttaaaagaaa aaaaaggaat atttcgtttt cacgagtaat
     4921 acccgggtat taaaaatcca ctgtaattac atgaaaataa agaaataaaa ggtaataccg
     4981 gagtattacc acgtacgcgg gcaagcgaaa aagctataac gcttcccggc cgacaggcga
     5041 cccaaaatcc acaggggcat gcaggttctc ttcagtaacc tgcgccatta aatcaaaaag
     5101 gtcatattcg ccgggaagct gcgtatcagt cgaatccagt tgttcatcat attcagatgg
     5161 catggggtga tatccagtag ctgagaggtt gttagcgggt ttcggggcgc agccctgaac
     5221 cagtcatgta gcgctagcgg agtgtatact ggcttactat gttgccacga ttgcgaaaat
     5281 cagtgaagtg cttcatgtgg caggagaaaa aaggcagcac cggcgcgtca gcagaatatg
     5341 cgatacagga gatattccgc ttcctcgctc actgactcgc tacgctcggt cgttcggctg
     5401 cggcgagcgg taccggctta cggacgggga cggaaatttc ctggaagata ccaggaagac
     5461 acttagcaaa gaagagataa ggccacggcg aagccgtttt tccataggct ccgcccccct
     5521 gacaagcatc gcaaaatctg acgctcaaat cagtggtggc gaaacccgac aggactataa
     5581 agatcccagg cgtttccccc tggtagctcc ctcgtgcgct ctcctgttcc tgcctttcgg
     5641 tttaccggtg tcattccgct gttatggccg cggtttctca ttccacgcct gacactcagt
     5701 tccgtgaagg cagttcgctc caagctggac tgtatgcacg aaccccccgt tcagtccgac
     5761 cgctgcgcct tgtccggtaa ctatcaactt gagtccaacc cggaaagaca cgacaaaacg
     5821 ccactggcag cagccattag taacaggagt gcacgagaag atagattaag aggtcttgaa
     5881 gtagaggcct gactgcggct acactgaaag aacagttttg gtaatggcgg tctcgtgaac
     5941 cctgttaccg ggttaagcag ttccccaact gacttaacct tcgaacaaac cgcctcccca
     6001 ggcggttttt tcgtttacag agcaagagat tacgattcat tgaaaaggat ctcaagaaga
     6061 tcctttgtag attactatca attaatcttc cgaacatgac accagtcact gttgattacg
     6121 gttaaaccgc tccgtaacag gtttccctcg tattggtgac ttgcagcacc aaagaagcaa
     6181 aaaagataaa tatatctact tattgagaga t
//
