LOCUS       NZ_CP039841             6200 bp    DNA     circular CON 14-NOV-2023
DEFINITION  Escherichia coli O55:H7 strain USDA5905 plasmid pUSDA5905_3,
            complete sequence.
ACCESSION   NZ_CP039841
VERSION     NZ_CP039841.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN11229503
            Assembly: GCF_013343615.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli O55:H7
  ORGANISM  Escherichia coli O55:H7
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 6200)
  AUTHORS   Bono,J.L.
  TITLE     Comparison of 54 complete closed STEC O157:H7 genomes
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 6200)
  AUTHORS   Bono,J.L.
  TITLE     Direct Submission
  JOURNAL   Submitted (26-APR-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. 3.0
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 299.0x
            Sequencing Technology             :: PacBio RSII
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 11/14/2023 02:24:46
            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)                     :: 5,597
            CDSs (total)                      :: 5,462
            Genes (coding)                    :: 5,177
            CDSs (with protein)               :: 5,177
            Genes (RNA)                       :: 135
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 106
            ncRNAs                            :: 7
            Pseudo Genes (total)              :: 285
            CDSs (without protein)            :: 285
            Pseudo Genes (ambiguous residues) :: 0 of 285
            Pseudo Genes (frameshifted)       :: 117 of 285
            Pseudo Genes (incomplete)         :: 153 of 285
            Pseudo Genes (internal stop)      :: 77 of 285
            Pseudo Genes (multiple problems)  :: 55 of 285
            Pseudo Genes (short protein)      :: 4 of 285
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP039841.1.
            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..6200
                     /organism="Escherichia coli O55:H7"
                     /mol_type="genomic DNA"
                     /strain="USDA5905"
                     /serotype="O55:H7"
                     /isolation_source="Food (meat)"
                     /db_xref="taxon:244320"
                     /plasmid="pUSDA5905_3"
                     /collection_date="1994"
     gene            86..901
                     /gene="sul2"
                     /locus_tag="E3175_RS26605"
                     /old_locus_tag="E3175_27255"
     ARG             87..898
                     /name="sul2"
                     /gene="sul2"
                     /gene_name="sulfonamide-resistant dihydropteroate synthase
                     Sul2"
                     /tool="amrfinderplus"
                     /drug_class="SULFONAMIDE"
                     /identity="100.0"
                     /coverage="100.0"
     gene            962..1765
                     /gene="aph(3'')-Ib"
                     /locus_tag="E3175_RS26610"
                     /old_locus_tag="E3175_27260"
     ARG             963..1762
                     /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            1765..2601
                     /locus_tag="E3175_RS26615"
                     /old_locus_tag="E3175_27265"
     CDS             1765..2601
                     /locus_tag="E3175_RS26615"
                     /old_locus_tag="E3175_27265"
                     /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(<2708..3112)
                     /locus_tag="E3175_RS26620"
                     /old_locus_tag="E3175_27270"
                     /pseudo=""
     CDS             complement(<2708..3112)
                     /locus_tag="E3175_RS26620"
                     /old_locus_tag="E3175_27270"
                     /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(3156..3545)
                     /locus_tag="E3175_RS26625"
                     /old_locus_tag="E3175_27275"
     CDS             complement(3156..3545)
                     /locus_tag="E3175_RS26625"
                     /old_locus_tag="E3175_27275"
                     /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            3763..4203
                     /locus_tag="E3175_RS26630"
                     /old_locus_tag="E3175_27280"
     CDS             3763..4203
                     /locus_tag="E3175_RS26630"
                     /old_locus_tag="E3175_27280"
                     /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(4948..5097)
                     /locus_tag="E3175_RS26635"
     CDS             complement(4948..5097)
                     /locus_tag="E3175_RS26635"
                     /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            5668..5826
                     /locus_tag="E3175_RS28465"
                     /old_locus_tag="E3175_27290"
     CDS             5668..5826
                     /locus_tag="E3175_RS28465"
                     /old_locus_tag="E3175_27290"
                     /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             1766..2598
                     /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(5133..5306)
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="99.429"
                     /coverage="100.0"
                     /evalue="1.19e-84"
     Typing          5230..5835
                     /name="rep_cluster_2335"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="89.593"
                     /coverage="99.0"
                     /evalue="0.0"
ORIGIN
        1 aacaggttac tcgcctgggg attccctttc gacccgagca tccgtatgag actcatgctc
       61 gattattatt attatagaag cccccatgaa taaatcgctc atcattttcg gcatcgtcaa
      121 cataacctcg gacagtttct ccgatggagg ccggtatctg gcgccagacg cagccattgc
      181 gcaggcgcgt aagctgatgg ccgagggggc agatgtgatc gacctcggtc cggcatccag
      241 caatcccgac gccgcgcctg tttcgtccga cacagaaatc gcgcgtatcg cgccggtgct
      301 ggacgcgctc aaggcagatg gcattcccgt ctcgctcgac agttatcaac ccgcgacgca
      361 agcctatgcc ttgtcgcgtg gtgtggccta tctcaatgat attcgcggtt ttccagacgc
      421 tgcgttctat ccgcaattgg cgaaatcatc tgccaaactc gtcgttatgc attcggtgca
      481 agacgggcag gcagatcggc gcgaggcacc cgctggcgac atcatggatc acattgcggc
      541 gttctttgac gcgcgcatcg cggcgctgac gggtgccggt atcaaacgca accgccttgt
      601 ccttgatccc ggcatggggt tttttctggg ggctgctccc gaaacctcgc tctcggtgct
      661 ggcgcggttc gatgaattgc ggctgcgctt cgatttgccg gtgcttctgt ctgtttcgcg
      721 caaatccttt ctgcgcgcgc tcacaggccg tggtccgggg gatgtcgggg ccgcgacact
      781 cgctgcagag cttgccgccg ccgcaggtgg agctgacttc atccgcacac acgagccgcg
      841 ccccttgcgc gacgggctgg cggtattggc ggcgctgaaa gaaaccgcaa gaattcgtta
      901 actgcacatt cgggatattt ctctatattc gcgcttcatc agaaaactga aggaacctcc
      961 attgaatcga actaatattt tttttggtga atcgcattct gactggttgc ctgtcagagg
     1021 cggagaatct ggtgattttg tttttcgacg tggtgacggg catgccttcg cgaaaatcgc
     1081 acctgcttcc cgccgcggtg agctcgctgg agagcgtgac cgcctcattt ggctcaaagg
     1141 tcgaggtgtg gcttgccccg aggtcatcaa ctggcaggag gaacaggagg gtgcatgctt
     1201 ggtgataacg gcaattccgg gagtaccggc ggctgatctg tctggagcgg atttgctcaa
     1261 agcgtggccg tcaatggggc agcaacttgg cgctgttcac agcctatcgg ttgatcaatg
     1321 tccgtttgag cgcaggctgt cgcgaatgtt cggacgcgcc gttgatgtgg tgtcccgcaa
     1381 tgccgtcaat cccgacttct taccggacga ggacaagagt acgccgcagc tcgatctttt
     1441 ggctcgtgtc gaacgagagc taccggtgcg gctcgaccaa gagcgcaccg atatggttgt
     1501 ttgccatggt gatccctgca tgccgaactt catggtggac cctaaaactc ttcaatgcac
     1561 gggtctgatc gaccttgggc ggctcggaac agcagatcgc tatgccgatt tggcactcat
     1621 gattgctaac gccgaagaga actgggcagc gccagatgaa gcagagcgcg ccttcgctgt
     1681 cctattcaat gtattgggga tcgaagcccc cgaccgcgaa cgccttgcct tctatctgcg
     1741 attggaccct ctgacttggg gttgatgttc atgccgcctg tttttcctgc tcattggcac
     1801 gtttcgcaac ctgttctcat tgcggacacc ttttccagcc tcgtttggaa agtttcattg
     1861 ccagacggga ctcctgcaat cgtcaaggga ttgaaaccta tagaagacat tgctgatgaa
     1921 ctgcgcgggg ccgactatct ggtatggcgc aatgggaggg gagcagtccg gttgctcggt
     1981 cgtgagaaca atctgatgtt gctcgaatat gccggggagc gaatgctctc tcacatcgtt
     2041 gccgagcacg gcgactacca ggcgaccgaa attgcagcgg aactaatggc gaagctgtat
     2101 gccgcatctg aggaacccct gccttctgcc cttctcccga tccgggatcg ctttgcagct
     2161 ttgtttcagc gggcgcgcga tgatcaaaac gcaggttgtc aaactgacta cgtccacgcg
     2221 gcgattatag ccgatcaaat gatgagcaat gcctcggaac tgcgtgggct acatggcgat
     2281 ctgcatcatg aaaacatcat gttctccagt cgcggctggc tggtgataga tcccgtcggt
     2341 ctggtcggtg aagtgggctt tggcgccgcc aatatgttct acgatccggc tgacagagac
     2401 gacctttgtc tcgatcctag acgcattgca cagatggcgg acgcattctc tcgtgcgctg
     2461 gacgtcgatc cgcgtcgcct gctcgaccag gcgtacgctt atgggtgcct ttccgcagct
     2521 tggaacgcgg atggagaaga ggagcaacgc gatctagcta tcgcggccgc gatcaagcag
     2581 gtgcgacaga cgtcatacta gatatcaagc gacttctcct atcccctggg aacacatcaa
     2641 tctcaccgga gaatatcgct ggccaaagcc ttagcgtagg attccgcccc ttcccgcaaa
     2701 cgaccccaaa caggaaacgc agctgaaacg ggaagctcaa cacccactga cgcatgggtt
     2761 gttcaggcag tacttcatca accagcaagg cggcactttc ggccatccgc cgcgccccac
     2821 agctcgggca gaaaccgcga cgcttacagc tgaaagcgac caggtgctcg gcgtggcaag
     2881 actcgcagcg aacccgtaga aagccatgct ccagccgccc gcattggaga aattcttcaa
     2941 attcccgttg cacatagccc ggcaattcct ttccctgctc tgccataagc gcagcgaatg
     3001 ccgggtaata ctcgtcaacg atctgataga gaagggtttg ctcgggtcgg tggctctggt
     3061 aacgaccagt atcccgatcc cggctggccg tcctggccgc cacatgaggc atgttccgcg
     3121 tccttgcaat actgtgttta catacagtct atcgcttagc ggaaagttct tttaccctca
     3181 gccgaaatgc ctgccgttgc tagacattgc cagccagtgc ccgtcactcc cactcttaca
     3241 ttgttcgcag tatctaggta catgttattg cgtgcacctt catgatgtat aatgttatta
     3301 atgacagcag aaagatcgac agaattaata ttcttcgtac ctgggacagt tatcgggtgt
     3361 cggccagtga tgagaccaaa ggatgcagta taagatgaac cactactatt atcatggcca
     3421 ccattaccac caccgttaaa actacctccc gaacttccag agccgctatg accatcattg
     3481 taggggtcat ttggtcccat gtgaccaaaa ccaccgacag taccgctatt taactctgta
     3541 ctcataaaat tatcctcttt gacttttaaa aacagcaaaa actgtattta taacaatgtg
     3601 tttatataca gtattcgaaa tactacgccc gtcaaaacca caccgtcaac aggttttttg
     3661 tgtatttttc acgcctcacg ggcagcctca gaccttttgt gttaaaacag taatatgttc
     3721 tgctgttaca atacggtaca cacaggagac actgtcactt ttatggcatg gcacacagtt
     3781 caagagacac tgaaattaac aggaaagtcg cgctcgcaat tatatcgtga catggctaaa
     3841 ggccttgtca gctatcgcac aggaaaaaat gatcgccggg agttcgagac cagtgaactg
     3901 attcgggcct atggcgagct gcgcacttct gagacaccaa aaaggcacaa ggagggacac
     3961 tccaaatctg tcgttagcca ggcggaaaat gctcagctag acgtcattca gcagaaactg
     4021 gacgctctgc agcagactgt taccctaatg cttgaagaca agatggcgcg ggaagcagaa
     4081 aaccgcctgc gaaatgagga gagggaacaa ctacaggccg aaattagccg tctggctgac
     4141 gcgctggcac aggaaaaaaa gcggggattc tggtcgcggc tgtttcgctc cggttcagag
     4201 taacagtgca ggtgactctg atttaccata acatctgtta tcagcaccgc ctgagaggcc
     4261 ctcagggcgt ttctgacggg aaaccggtaa aacaggcaac aaaccacccg aaaacccgcc
     4321 agaaacgcgc aggctctgtt tttacggcat gcatgagtat gcgcacaagt gcatagcgcg
     4381 gaaattcaca ccattcagcc ggggtaagtc ctgtttccgg cgttcttccc atccgaaaac
     4441 ggtgaacggg gacgcaattt attgcgtggc cgtgaagcgt tgccggcgca gccggaaaac
     4501 ccgctgtcag cacgttcagg aagggggtga tgtacaaatg gcacagagga tgaaagtgac
     4561 gtatgagctg aaggaatgat gtaaaagtga tgtataagtg atgtaaaagt gatgtatgaa
     4621 ctgaaggagc gatgtaattc tgtagtcagg aagaataacc cgttcatgca ggcatgaacg
     4681 atacagtgag gaacgctttt tttgtcacga tctcccctta acctgcgtaa atcacccgcc
     4741 atggttgatt atttttcaac ctcaaaatgg tcatacacct aacgcagccg cgattttcat
     4801 cgcaactgca tgaattaaaa gaaaaaaaag gaatatttcg ttttcacgag taatacccgg
     4861 gtattaaaaa tccactgtaa ttacatgaaa ataaagaaat aaaaggtaat accggagtat
     4921 taccacgtac gcgggcaagc gaaaaagcta taacgcttcc cggccgacag gcgacccaaa
     4981 atccacaggg gcatgcaggt tctcttcagt aacctgcgcc attaaatcaa aaaggtcata
     5041 ttcgccggga agctgcgtat cagtcgaatc cagttgttca tcatattcag atggcatggg
     5101 gtgatatcca gtagctgaga ggttgttagc gggtttcggg gcgcagccct gaaccagtca
     5161 tgtagcgcta gcggagtgta tactggctta ctatgttgcc acgattgcga aaatcagtga
     5221 agtgcttcat gtggcaggag aaaaaaggca gcaccggcgc gtcagcagaa tatgcgatac
     5281 aggagatatt ccgcttcctc gctcactgac tcgctacgct cggtcgttcg gctgcggcga
     5341 gcggtaccgg cttacggacg gggacggaaa tttcctggaa gataccagga agacacttag
     5401 caaagaagag ataaggccac ggcgaagccg tttttccata ggctccgccc ccctgacaag
     5461 catcgcaaaa tctgacgctc aaatcagtgg tggcgaaacc cgacaggact ataaagatcc
     5521 caggcgtttc cccctggtag ctccctcgtg cgctctcctg ttcctgcctt tcggtttacc
     5581 ggtgtcattc cgctgttatg gccgcggttt ctcattccac gcctgacact cagttccgtg
     5641 aaggcagttc gctccaagct ggactgtatg cacgaacccc ccgttcagtc cgaccgctgc
     5701 gccttgtccg gtaactatca acttgagtcc aacccggaaa gacacgacaa aacgccactg
     5761 gcagcagcca ttagtaacag gagtgcacga gaagatagat taagaggtct tgaagtagag
     5821 gcctgactgc ggctacactg aaagaacagt tttggtaatg gcggtctcgt gaaccctgtt
     5881 accgggttaa gcagttcccc aactgactta accttcgaac aaaccgcctc cccaggcggt
     5941 tttttcgttt acagagcaag agattacgat tcattgaaaa ggatctcaag aagatccttt
     6001 gtagattact atcaattaat cttccgaaca tgacaccagt cactgttgat tacggttaaa
     6061 ccgctccgta acaggtttcc ctcgtattgg tgacttgcag caccaaagaa gcaaaaaaga
     6121 taaatatatc tacttattga gagatgatat atttatttcc aaaatgctac agatacatca
     6181 tcatgaaacg gatcaccgca
//
