LOCUS       NZ_CP038387             6069 bp    DNA     circular CON 14-NOV-2023
DEFINITION  Escherichia coli O55:H7 strain DEC5D plasmid pDEC5D-2, complete
            sequence.
ACCESSION   NZ_CP038387
VERSION     NZ_CP038387.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN11229485
            Assembly: GCF_013167975.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli O55:H7
  ORGANISM  Escherichia coli O55:H7
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 6069)
  AUTHORS   Bono,J.L.
  TITLE     Comparison of complete closed STEC O157:H7 genomes
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 6069)
  AUTHORS   Bono,J.L.
  TITLE     Direct Submission
  JOURNAL   Submitted (27-MAR-2019) Meat Safety and Quality Research Unit,
            United State Department of Agriculture, State Spur 18D, P.O. Box
            166, Clay Center, NE 68933, USA
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: HGAP v. 3
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 307x
            Sequencing Technology             :: PacBio RSII
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 11/14/2023 02:31:27
            Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline
            (PGAP)
            Annotation Method :: Best-placed reference protein set; GeneMarkS-2+
            Annotation Software revision      :: 6.6
            Features Annotated                :: Gene; CDS; rRNA; tRNA; ncRNA
            Genes (total)                     :: 5,129
            CDSs (total)                      :: 5,004
            Genes (coding)                    :: 4,758
            CDSs (with protein)               :: 4,758
            Genes (RNA)                       :: 125
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 96
            ncRNAs                            :: 7
            Pseudo Genes (total)              :: 246
            CDSs (without protein)            :: 246
            Pseudo Genes (ambiguous residues) :: 0 of 246
            Pseudo Genes (frameshifted)       :: 88 of 246
            Pseudo Genes (incomplete)         :: 135 of 246
            Pseudo Genes (internal stop)      :: 70 of 246
            Pseudo Genes (multiple problems)  :: 41 of 246
            Pseudo Genes (short protein)      :: 4 of 246
            CRISPR Arrays                     :: 1
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP038387.1.
            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..6069
                     /organism="Escherichia coli O55:H7"
                     /mol_type="genomic DNA"
                     /strain="DEC5D"
                     /serotype="O55:H7"
                     /host="Homo sapiens"
                     /db_xref="taxon:244320"
                     /plasmid="pDEC5D-2"
                     /geo_loc_name="Sri Lanka"
                     /collection_date="1965"
     gene            join(5259..6069,1..5)
                     /gene="sul2"
                     /locus_tag="E3157_RS24940"
                     /old_locus_tag="E3157_25490"
     ARG             5260..6068
                     /name="sul2"
                     /gene="sul2"
                     /gene_name="sulfonamide-resistant dihydropteroate synthase
                     Sul2"
                     /tool="amrfinderplus"
                     /drug_class="SULFONAMIDE"
                     /identity="100.0"
                     /coverage="99.63"
     gene            92..>334
                     /gene="glmM"
                     /locus_tag="E3157_RS24945"
                     /old_locus_tag="E3157_25495"
                     /pseudo=""
     CDS             92..>334
                     /gene="glmM"
                     /locus_tag="E3157_RS24945"
                     /old_locus_tag="E3157_25495"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_008891390.1"
                     /note="catalyzes the conversion of glucosamine-6-phosphate
                     to glucosamine-1-phosphate; 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="phosphoglucosamine mutase"
                     /name="glmM"
     gene            complement(570..2063)
                     /locus_tag="E3157_RS24955"
                     /old_locus_tag="E3157_25505"
     CDS             complement(570..2063)
                     /locus_tag="E3157_RS24955"
                     /old_locus_tag="E3157_25505"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001120888.1"
                     /GO_function="GO:0004803 - transposase activity [Evidence
                     IEA]"
                     /GO_process="GO:0006313 - DNA transposition [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="IS91-like element ISVsa3 family transposase"
                     /protein_id="WP_001120888.1"
                     /translation="MPHVAARTASRDRDTGRYQSHRPEQTLLYQIVDEYYPAFAALMAE
                     QGKELPGYVQREFEEFLQCGRLEHGFLRVRCESCHAEHLVAFSCKRRGFCPSCGARRMA
                     ESAALLVDEVLPEQPMRQWVLSFPFQLRFLFASRPEIMGWVLGIVYRVIATHLVKKAGH
                     THQVAKTGAVTLIQRFGSALNLNVHFHMLFLDGVYVEQSHGSARFRWVKAPTSPELTQL
                     THTIAHRVGRYLERQGLLERDVENSYLASDAVDDDPMTPLLGHSITYRIAVGSQAGRKV
                     FTLQTLPTSGDPFGDGIGKVAGSSLHAGVAARADERKKLERLCRYISRPAVSEKRLSLT
                     RGGNVRYQLKTPYRDGTTHVIFEPLDFIARLAALVPKPRVNLTRFHGVFAPNSRHRALV
                     TPAKRGRGNKVRVADEPATPAQRRASMTWAQRLKRVFNIDIETCSGCGGAMKVIACIED
                     PIVIKQILDHLKHKAETSGTRALPESRAPPAELLLGLFD"
                     /name="IS91-like element ISVsa3 family transposase"
     gene            complement(2107..2496)
                     /locus_tag="E3157_RS24960"
                     /old_locus_tag="E3157_25510"
     CDS             complement(2107..2496)
                     /locus_tag="E3157_RS24960"
                     /old_locus_tag="E3157_25510"
                     /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            2714..3154
                     /locus_tag="E3157_RS24965"
                     /old_locus_tag="E3157_25515"
     CDS             2714..3154
                     /locus_tag="E3157_RS24965"
                     /old_locus_tag="E3157_25515"
                     /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(3921..4070)
                     /locus_tag="E3157_RS24970"
     CDS             complement(3921..4070)
                     /locus_tag="E3157_RS24970"
                     /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            4641..4799
                     /locus_tag="E3157_RS26105"
                     /old_locus_tag="E3157_25525"
     CDS             4641..4799
                     /locus_tag="E3157_RS26105"
                     /old_locus_tag="E3157_25525"
                     /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"
     Typing          complement(4106..4279)
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="99.429"
                     /coverage="100.0"
                     /evalue="1.19e-84"
     Typing          4203..4808
                     /name="rep_cluster_2335"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="89.593"
                     /coverage="99.0"
                     /evalue="0.0"
ORIGIN
        1 gttaactgca cattcgggat atttctctat attcgcggtt cagcaggcat gtcccctttg
       61 agggcgaccc gacgacagga taatcgacct tatggtgcgc aaatatttcg gcacagacgg
      121 tattcgtggc aaagccaacg aaggcgcgat gacggcggaa accgccttgc gcgtcggcat
      181 ggcggctggc cgtgtctttc gtcgcggtga ccaccgccat cgtgtcgtga tcggcaagga
      241 tacgcgcctg tcgggctata tgcttgaacc cgcgctcaca gccggtttca cctcgatggg
      301 catggacgta ttcctttttg gcccgctgcc gacaacgtat aggaagaata aacgcccttt
      361 tcacccaagt ccaacagctt tggaccgcag ttgactcttt cgacacccct gcgatgcaac
      421 ccaatccggc tgacggggag ccagcaacgc tgaaaattta ccctcctctt tcccactagc
      481 ggctcctttt ccgacaacca gcacggcgga tccctgccgc ggcgctgtga acgcagcatt
      541 ttgattggta tcgttggcct tcaggctcgt cagtcaaaca gacccaggag cagctcagcc
      601 ggtggcgccc ggctttcggg taacgccctg gtcccgctgg tttcggcttt gtgcttcagg
      661 tgatcaagga tctgcttgat cactataggg tcttcaatgc aggcgatgac tttcatggcg
      721 ccgccgcagc cgctgcaggt ctcgatgtcg atattgaaaa cacgcttgag ccgttgcgcc
      781 catgtcatcg acgctcgccg ttgtgctggt gttgccggtt catcagccac cctgaccttg
      841 ttgcccctgc cccgttttgc cggcgtgacc aacgcccggt gccgactgtt gggtgcgaac
      901 accccgtgga agcgggttag gttgactctg ggcttcggta ccagggcggc cagccttgca
      961 atgaaatcca atggttcgaa aatgacgtgc gtggtgccgt cccggtacgg cgtcttgagc
     1021 tggtagcgca cgttgccgcc tcgtgttaac gacagccgct tctcggatac cgccgggcgg
     1081 ctgatgtacc ggcacagccg ttcgagcttc ttgcgttcat cggccctggc cgccacgccg
     1141 gcgtgcaggc tggacccggc taccttgcca atcccgtcac cgaacggatc accactggtc
     1201 ggcagagttt gcaaagtgaa cacctttcgc cccgcctgtg aaccgacagc gatacggtaa
     1261 gtgatcgagt gccccagcag gggtgtcatc gggtcgtcat ccaccgcatc cgaggccaga
     1321 tagctgtttt cgacatcccg ttccagcagg ccttgccgtt ccagatagcg acccacccgg
     1381 tgggcgatgg tgtgcgtcag ctgggtgagc tctgggctgg tcggcgcctt gacccagcgg
     1441 aaacgcgctg agccgtggga ttgctcgaca tacacaccgt cgagaaacag catgtggaag
     1501 tgaacattca gattgagcgc cgatccaaaa cgctggatca gggtgaccgc gcccgtcttg
     1561 gccacttggt gggtatggcc cgctttcttg accaggtgcg tggcaatgac gcggtaaacg
     1621 atgcccagca cccaccccat gatctcgggc cggctggcaa acaggaaacg cagctgaaac
     1681 gggaagctca acacccactg acgcatgggt tgttcaggca gtacttcatc aaccagcaag
     1741 gcggcacttt cggccatccg ccgcgcccca cagctcgggc agaaaccgcg acgcttacag
     1801 ctgaaagcga ccaggtgctc ggcgtggcaa gactcgcagc gaacccgtag aaagccatgc
     1861 tccagccgcc cgcattggag aaattcttca aattcccgtt gcacatagcc cggcaattcc
     1921 tttccctgct ctgccataag cgcagcgaat gccgggtaat actcgtcaac gatctgatag
     1981 agaagggttt gctcgggtcg gtggctctgg taacgaccag tatcccgatc ccggctggcc
     2041 gtcctggccg ccacatgagg catgttccgc gtccttgcaa tactgtgttt acatacagtc
     2101 tatcgcttag cggaaagttc ttttaccctc agccgaaatg cctgccgttg ctagacattg
     2161 ccagccagtg cccgtcactc ccactcttac attgttcgca gtatctaggt acatgttatt
     2221 gcgtgcacct tcatgatgta taatgttatt aatgacagca gaaagatcga cagaattaat
     2281 attcttcgta cctgggacag ttatcgggtg tcggccagtg atgagaccaa aggatgcagt
     2341 ataagatgaa ccactactat tatcatggcc accattacca ccaccgttaa aactacctcc
     2401 cgaacttcca gagccgctat gaccatcatt gtaggggtca tttggtccca tgtgaccaaa
     2461 accaccgaca gtaccgctat ttaactctgt actcataaaa ttatcctctt tgacttttaa
     2521 aaacagcaaa aactgtattt ataacaatgt gtttatatac agtattcgaa atactacgcc
     2581 cgtcaaaacc acaccgtcaa caggtttttt gtgtattttt cacgcctcac gggcagcctc
     2641 agaccttttg tgttaaaaca gtaatatgtt ctgctgttac aatacggtac acacaggaga
     2701 cactgtcact tttatggcat ggcacacagt tcaagagaca ctgaaattaa caggaaagtc
     2761 gcgctcgcaa ttatatcgtg acatggctaa aggccttgtc agctatcgca caggaaaaaa
     2821 tgatcgccgg gagttcgaga ccagtgaact gattcgggcc tatggcgagc tgcgcacttc
     2881 tgagacacca aaaaggcaca aggagggaca ctccaaatct gtcgttagcc aggcggaaaa
     2941 tgctcagcta gacgtcattc agcagaaact ggacgctctg cagcagactg ttaccctaat
     3001 gcttgaagac aagatggcgc gggaagcaga aaaccgcctg cgaaatgagg agagggaaca
     3061 actacaggcc gaaattagcc gtctggctga cgcgctggca caggaaaaaa agcggggatt
     3121 ctggtcgcgg ctgtttcgct ccggttcaga gtaacagtgc aggtgactct gatttaccat
     3181 aacatctgtt atcagcaccg cctgagaggc cctcagggcg tttctgacgg gaaaccggta
     3241 aaacaggcaa caaaccaccc gaaaacccgc cagaaacgcg caggctctgt ttttacggca
     3301 tgcatgagta tgcgcacaag tgcatagcgc ggaaattcac accattcagc cggggtaagt
     3361 cctgtttccg gcgttcttcc catccgaaaa cggtgaacgg ggacgcaatt tattgcgtgg
     3421 ccgtgaagcg ttgccggcgc agccggaaaa cccgctgtca gcacgttcag gaagggggtg
     3481 atgtacaaat ggcacagagg atgaaagtga cgtatgagct gaaggaatga tgtaaaagtg
     3541 atgtataagt gatgtaaaag tgatgtataa gtgatgtaaa agtgatgtat gaactgaagg
     3601 agcgatgtaa ttctgtagtc aggaagaata acccgttcat gcaggcatga acgatacagt
     3661 gaggaacgct ttttttgtca cgatctcccc ttaacctgcg taaatcaccc gccatggttg
     3721 attatttttc aacctcaaaa tggtcataca cctaacgcag ccgcgatttt catcgcaact
     3781 gcatgaatta aaagaaaaaa aaggaatatt tcgttttcac gagtaatacc cgggtattaa
     3841 aaatccactg taattacatg aaaataaaga aataaaaggt aataccggag tattaccacg
     3901 tacgcgggca agcgaaaaag ctataacgct tcccggccga caggcgaccc aaaatccaca
     3961 ggggcatgca ggttctcttc agtaacctgc gccattaaat caaaaaggtc atattcgccg
     4021 ggaagctgcg tatcagtcga atccagttgt tcatcatatt cagatggcat ggggtgatat
     4081 ccagtagctg agaggttgtt agcgggtttc ggggcgcagc cctgaaccag tcatgtagcg
     4141 ctagcggagt gtatactggc ttactatgtt gccacgattg cgaaaatcag tgaagtgctt
     4201 catgtggcag gagaaaaaag gcagcaccgg cgcgtcagca gaatatgcga tacaggagat
     4261 attccgcttc ctcgctcact gactcgctac gctcggtcgt tcggctgcgg cgagcggtac
     4321 cggcttacgg acggggacgg aaatttcctg gaagatacca ggaagacact tagcaaagaa
     4381 gagataaggc cacggcgaag ccgtttttcc ataggctccg cccccctgac aagcatcgca
     4441 aaatctgacg ctcaaatcag tggtggcgaa acccgacagg actataaaga tcccaggcgt
     4501 ttccccctgg tagctccctc gtgcgctctc ctgttcctgc ctttcggttt accggtgtca
     4561 ttccgctgtt atggccgcgg tttctcattc cacgcctgac actcagttcc gtgaaggcag
     4621 ttcgctccaa gctggactgt atgcacgaac cccccgttca gtccgaccgc tgcgccttgt
     4681 ccggtaacta tcaacttgag tccaacccgg aaagacacga caaaacgcca ctggcagcag
     4741 ccattagtaa caggagtgca cgagaagata gattaagagg tcttgaagta gaggcctgac
     4801 tgcggctaca ctgaaagaac agttttggta atggcggtct cgtgaaccct gttaccgggt
     4861 taagcagttc cccaactgac ttaaccttcg aacaaaccgc ctccccaggc ggttttttcg
     4921 tttacagagc aagagattac gattcattga aaaggatctc aagaagatcc tttgtagatt
     4981 actatcaatt aatcttccga acatgacacc agtcactgtt gattacggtt aaaccgctcc
     5041 gtaacaggtt tccctcgtat tggtgacttg cagcaccaaa gaagcaaaaa agataaatat
     5101 atctacttat tgagagatga tatatttatt tccaaaatgc tacagataca tcatcatgaa
     5161 acggatcacc gcaaacaggt tactcgcctg gggattccct ttcgacccga gcatccgtat
     5221 gagactcatg ctcgattatt attattatag aagcccccat gaataaatcg ctcatcattt
     5281 tcggcatcgt caacataacc tcggacagtt tctccgatgg aggccggtat ctggcgccag
     5341 acgcagccat tgcgcaggcg cgtaagctga tggccgaggg ggcagatgtg atcgacctcg
     5401 gtccggcatc cagcaatccc gacgccgcgc ctgtttcgtc cgacacagaa atcgcgcgta
     5461 tcgcgccggt gctggacgcg ctcaaggcag atggcattcc cgtctcgctc gacagttatc
     5521 aacccgcgac gcaagcctat gccttgtcgc gtggtgtggc ctatctcaat gatattcgcg
     5581 gttttccaga cgctgcgttc tatccgcaat tggcgaaatc atctgccaaa ctcgtcgtta
     5641 tgcattcggt gcaagacggg caggcagatc ggcgcgaggc acccgctggc gacatcatgg
     5701 atcacattgc ggcgttcttt gacgcgcgca tcgcggcgct gacgggtgcc ggtatcaaac
     5761 gcaaccgcct tgtccttgat cccggcatgg ggttttttct gggggctgct cccgaaacct
     5821 cgctctcggt gctggcgcgg ttcgatgaat tgcggctgcg cttcgatttg ccggtgcttc
     5881 tgtctgtttc gcgcaaatcc tttctgcgcg cgctcacagg ccgtggtccg ggggatgtcg
     5941 gggccgcgac actcgctgca gagcttgccg ccgccgcagg tggagctgac ttcatccgca
     6001 cacacgagcc gcgccccttg cgcgacgggc tggcggtatt ggcggcgctg aaagaaaccg
     6061 caagaattc
//
