LOCUS       NZ_CP101297             6222 bp    DNA     circular CON 27-JUL-2023
DEFINITION  Escherichia coli strain 2003-3014 plasmid pO26-4, complete sequence.
ACCESSION   NZ_CP101297
VERSION     NZ_CP101297.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN24907326
            Assembly: GCF_024300685.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 6222)
  AUTHORS   Kalalah,A. and Eppinger,M.
  TITLE     Whole genome sequencing, comparative phylogenetic analysis, and
            phenotypic profiling of the non-O157 Big Six Shiga toxin-producing
            Escherichia coli strains obtained from ATCC
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 6222)
  AUTHORS   Kalalah,A. and Eppinger,M.
  TITLE     Direct Submission
  JOURNAL   Submitted (08-JUL-2022) Molecular Microbiology and Immunology, The
            University of Texas at San Antonio, One UTSA Circle, San Antonio, TX
            78249, USA
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Date                     :: JUN-2022
            Assembly Method :: Unicycler v. Galaxy Version 0.4.8.0
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 296x
            Sequencing Technology :: Oxford Nanopore MiniION; Illumina MiSeq
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 07/27/2023 05:39:48
            Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline
            (PGAP)
            Annotation Method :: Best-placed reference protein set; GeneMarkS-2+
            Annotation Software revision      :: 6.5
            Features Annotated                :: Gene; CDS; rRNA; tRNA; ncRNA
            Genes (total)                     :: 6,128
            CDSs (total)                      :: 5,990
            Genes (coding)                    :: 5,666
            CDSs (with protein)               :: 5,666
            Genes (RNA)                       :: 138
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 105
            ncRNAs                            :: 11
            Pseudo Genes (total)              :: 324
            CDSs (without protein)            :: 324
            Pseudo Genes (ambiguous residues) :: 0 of 324
            Pseudo Genes (frameshifted)       :: 132 of 324
            Pseudo Genes (incomplete)         :: 191 of 324
            Pseudo Genes (internal stop)      :: 73 of 324
            Pseudo Genes (multiple problems)  :: 66 of 324
            Pseudo Genes (short protein)      :: 3 of 324
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP101297.1.
            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..6222
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="2003-3014"
                     /serotype="O26:H11"
                     /host="Homo sapiens"
                     /culture_collection="ATCC:BAA-2196"
                     /db_xref="taxon:562"
                     /plasmid="pO26-4"
                     /collection_date="2021"
                     /note="ATCC lot#70005699"
     gene            652..1467
                     /gene="sul2"
                     /locus_tag="NMK58_RS30505"
                     /old_locus_tag="NMK58_30505"
     ARG             653..1464
                     /name="sul2"
                     /gene="sul2"
                     /gene_name="sulfonamide-resistant dihydropteroate synthase
                     Sul2"
                     /tool="amrfinderplus"
                     /drug_class="SULFONAMIDE"
                     /identity="100.0"
                     /coverage="100.0"
     gene            1528..2331
                     /gene="aph(3'')-Ib"
                     /locus_tag="NMK58_RS30510"
                     /old_locus_tag="NMK58_30510"
     ARG             1529..2328
                     /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            2331..3167
                     /locus_tag="NMK58_RS30515"
                     /old_locus_tag="NMK58_30515"
     CDS             2331..3167
                     /locus_tag="NMK58_RS30515"
                     /old_locus_tag="NMK58_30515"
                     /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(<3274..3678)
                     /locus_tag="NMK58_RS30520"
                     /old_locus_tag="NMK58_30520"
                     /pseudo=""
     CDS             complement(<3274..3678)
                     /locus_tag="NMK58_RS30520"
                     /old_locus_tag="NMK58_30520"
                     /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(3722..4111)
                     /locus_tag="NMK58_RS30525"
                     /old_locus_tag="NMK58_30525"
     CDS             complement(3722..4111)
                     /locus_tag="NMK58_RS30525"
                     /old_locus_tag="NMK58_30525"
                     /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            4329..4769
                     /locus_tag="NMK58_RS30530"
                     /old_locus_tag="NMK58_30530"
     CDS             4329..4769
                     /locus_tag="NMK58_RS30530"
                     /old_locus_tag="NMK58_30530"
                     /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(5536..5685)
                     /locus_tag="NMK58_RS30535"
                     /old_locus_tag="NMK58_30535"
     CDS             complement(5536..5685)
                     /locus_tag="NMK58_RS30535"
                     /old_locus_tag="NMK58_30535"
                     /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"
     ARG             2332..3164
                     /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(5721..5894)
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="99.429"
                     /coverage="100.0"
                     /evalue="1.19e-84"
     Typing          2..142
                     /name="rep_cluster_2373"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="95.775"
                     /coverage="85.0"
                     /evalue="1.5800000000000001e-57"
     Typing          5861..6219
                     /name="rep_cluster_2335"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="93.629"
                     /coverage="98.0"
                     /evalue="2.86e-150"
ORIGIN
        1 tccgtgaagg cagttcgctc caagctggac tgtatgcacg aaccccccgt tcagtccgac
       61 cgctgcgcct tgtccggtaa ctatcaactt gagtccaacc cggaaagaca cgacaaaacg
      121 ccactggcag cagccattag taacaggagt gcacgagaag atagattaag aggtcttgaa
      181 gtagaggcct gactgcggct acactgaaag aacagttttg gtaatggcgg tctcgtgaac
      241 cctgttaccg ggttaagcag ttccccaact gacttaacct tcgaacaaac cgcctcccca
      301 ggcggttttt tcgtttacag agcaagagat tacgattcat tgaaaaggat ctcaagaaga
      361 tcctttgtag attactatca attaatcttc cgaacatgac accagtcact gttgattacg
      421 gttaaaccgc tccgtaacag gtttccctcg tattggtgac ttgcagcacc aaagaagcaa
      481 aaaagataaa tatatctact tattgagaga tgatatattt atttccaaaa tgctacagat
      541 acatcatcat gaaacggatc accgcaaaca ggttactcgc ctggggattc cctttcgacc
      601 cgagcatccg tatgagactc atgctcgatt attattatta tagaagcccc catgaataaa
      661 tcgctcatca ttttcggcat cgtcaacata acctcggaca gtttctccga tggaggccgg
      721 tatctggcgc cagacgcagc cattgcgcag gcgcgtaagc tgatggccga gggggcagat
      781 gtgatcgacc tcggtccggc atccagcaat cccgacgccg cgcctgtttc gtccgacaca
      841 gaaatcgcgc gtatcgcgcc ggtgctggac gcgctcaagg cagatggcat tcccgtctcg
      901 ctcgacagtt atcaacccgc gacgcaagcc tatgccttgt cgcgtggtgt ggcctatctc
      961 aatgatattc gcggttttcc agacgctgcg ttctatccgc aattggcgaa atcatctgcc
     1021 aaactcgtcg ttatgcattc ggtgcaagac gggcaggcag atcggcgcga ggcacccgct
     1081 ggcgacatca tggatcacat tgcggcgttc tttgacgcgc gcatcgcggc gctgacgggt
     1141 gccggtatca aacgcaaccg ccttgtcctt gatcccggca tggggttttt tctgggggct
     1201 gctcccgaaa cctcgctctc ggtgctggcg cggttcgatg aattgcggct gcgcttcgat
     1261 ttgccggtgc ttctgtctgt ttcgcgcaaa tcctttctgc gcgcgctcac aggccgtggt
     1321 ccgggggatg tcggggccgc gacactcgct gcagagcttg ccgccgccgc aggtggagct
     1381 gacttcatcc gcacacacga gccgcgcccc ttgcgcgacg ggctggcggt attggcggcg
     1441 ctgaaagaaa ccgcaagaat tcgttaactg cacattcggg atatttctct atattcgcgc
     1501 ttcatcagaa aactgaagga acctccattg aatcgaacta atattttttt tggtgaatcg
     1561 cattctgact ggttgcctgt cagaggcgga gaatctggtg attttgtttt tcgacgtggt
     1621 gacgggcatg ccttcgcgaa aatcgcacct gcttcccgcc gcggtgagct cgctggagag
     1681 cgtgaccgcc tcatttggct caaaggtcga ggtgtggctt gccccgaggt catcaactgg
     1741 caggaggaac aggagggtgc atgcttggtg ataacggcaa ttccgggagt accggcggct
     1801 gatctgtctg gagcggattt gctcaaagcg tggccgtcaa tggggcagca acttggcgct
     1861 gttcacagcc tatcggttga tcaatgtccg tttgagcgca ggctgtcgcg aatgttcgga
     1921 cgcgccgttg atgtggtgtc ccgcaatgcc gtcaatcccg acttcttacc ggacgaggac
     1981 aagagtacgc cgcagctcga tcttttggct cgtgtcgaac gagagctacc ggtgcggctc
     2041 gaccaagagc gcaccgatat ggttgtttgc catggtgatc cctgcatgcc gaacttcatg
     2101 gtggacccta aaactcttca atgcacgggt ctgatcgacc ttgggcggct cggaacagca
     2161 gatcgctatg ccgatttggc actcatgatt gctaacgccg aagagaactg ggcagcgcca
     2221 gatgaagcag agcgcgcctt cgctgtccta ttcaatgtat tggggatcga agcccccgac
     2281 cgcgaacgcc ttgccttcta tctgcgattg gaccctctga cttggggttg atgttcatgc
     2341 cgcctgtttt tcctgctcat tggcacgttt cgcaacctgt tctcattgcg gacacctttt
     2401 ccagcctcgt ttggaaagtt tcattgccag acgggactcc tgcaatcgtc aagggattga
     2461 aacctataga agacattgct gatgaactgc gcggggccga ctatctggta tggcgcaatg
     2521 ggaggggagc agtccggttg ctcggtcgtg agaacaatct gatgttgctc gaatatgccg
     2581 gggagcgaat gctctctcac atcgttgccg agcacggcga ctaccaggcg accgaaattg
     2641 cagcggaact aatggcgaag ctgtatgccg catctgagga acccctgcct tctgcccttc
     2701 tcccgatccg ggatcgcttt gcagctttgt ttcagcgggc gcgcgatgat caaaacgcag
     2761 gttgtcaaac tgactacgtc cacgcggcga ttatagccga tcaaatgatg agcaatgcct
     2821 cggaactgcg tgggctacat ggcgatctgc atcatgaaaa catcatgttc tccagtcgcg
     2881 gctggctggt gatagatccc gtcggtctgg tcggtgaagt gggctttggc gccgccaata
     2941 tgttctacga tccggctgac agagacgacc tttgtctcga tcctagacgc attgcacaga
     3001 tggcggacgc attctctcgt gcgctggacg tcgatccgcg tcgcctgctc gaccaggcgt
     3061 acgcttatgg gtgcctttcc gcagcttgga acgcggatgg agaagaggag caacgcgatc
     3121 tagctatcgc ggccgcgatc aagcaggtgc gacagacgtc atactagata tcaagcgact
     3181 tctcctatcc cctgggaaca catcaatctc accggagaat atcgctggcc aaagccttag
     3241 cgtaggattc cgccccttcc cgcaaacgac cccaaacagg aaacgcagct gaaacgggaa
     3301 gctcaacacc cactgacgca tgggttgttc aggcagtact tcatcaacca gcaaggcggc
     3361 actttcggcc atccgccgcg ccccacagct cgggcagaaa ccgcgacgct tacagctgaa
     3421 agcgaccagg tgctcggcgt ggcaagactc gcagcgaacc cgtagaaagc catgctccag
     3481 ccgcccgcat tggagaaatt cttcaaattc ccgttgcaca tagcccggca attcctttcc
     3541 ctgctctgcc ataagcgcag cgaatgccgg gtaatactcg tcaacgatct gatagagaag
     3601 ggtttgctcg ggtcggtggc tctggtaacg accagtatcc cgatcccggc tggccgtcct
     3661 ggccgccaca tgaggcatgt tccgcgtcct tgcaatactg tgtttacata cagtctatcg
     3721 cttagcggaa agttctttta ccctcagccg aaatgcctgc cgttgctaga cattgccagc
     3781 cagtgcccgt cactcccact cttacattgt tcgcagtatc taggtacatg ttattgcgtg
     3841 caccttcatg atgtataatg ttattaatga cagcagaaag atcgacagaa ttaatattct
     3901 tcgtacctgg gacagttatc gggtgtcggc cagtgatgag accaaaggat gcagtataag
     3961 atgaaccact actattatca tggccaccat taccaccacc gttaaaacta cctcccgaac
     4021 ttccagagcc gctatgacca tcattgtagg ggtcatttgg tcccatgtga ccaaaaccac
     4081 cgacagtacc gctatttaac tctgtactca taaaattatc ctctttgact tttaaaaaca
     4141 gcaaaaactg tatttataac aatgtgttta tatacagtat tcgaaatact acgcccgtca
     4201 aaaccacacc gtcaacaggt tttttgtgta tttttcacgc ctcacgggca gcctcagacc
     4261 ttttgtgtta aaacagtaat atgttctgct gttacaatac ggtacacaca ggagacactg
     4321 tcacttttat ggcatggcac acagttcaag agacactgaa attaacagga aagtcgcgct
     4381 cgcaattata tcgtgacatg gctaaaggcc ttgtcagcta tcgtacagga aaaaatgatc
     4441 gccgggagtt cgagaccagt gaactgattc gggcctatgg cgagctgcgc acttctgaga
     4501 caccaaaaag gcacaaggag ggacactcca aatctgtcgt tagccaggcg gaaaatgctc
     4561 agctagacgt cattcagcag aaactggacg ctctgcagca gactgttacc ctaatgcttg
     4621 aagacaagat ggcgcgggaa gcagaaaacc gcctgcgaaa tgaggagagg gaacaactac
     4681 aggccgaaat tagccgtctg gctgacgcgc tggcacagga aaaaaagcgg ggattctggt
     4741 cgcggctgtt tcgctccggt tcagagtaac agtgcaggtg actctgattt accataacat
     4801 ctgttatcag caccgcctga gaggccctca gggcgtttct gacgggaaac cggtaaaaca
     4861 ggcaacaaac cacccgaaaa cccgccagaa acgcgcaggc tctgttttta cggcatgcat
     4921 gagtatgcgc acaagtgcat agcgcggaaa ttcacaccat tcagccgggg taagtcctgt
     4981 ttccggcgtt cttcccatcc gaaaacggtg aacggggacg caatttattg cgtggccgtg
     5041 aagcgttgcc ggcgcagccg gaaaacccgc tgtcagcacg ttcaggaagg gggtgatgta
     5101 caaatggcac agaggatgaa agtgacgtat gagctgaagg aatgatgtaa aagtgatgta
     5161 taagtgatgt aaaagtgatg tataagtgat gtaaaagtga tgtatgaact gaaggagcga
     5221 tgtaattctg tagtcaggaa gaataacccg ttcatgcagg catgaacgat acagtgagga
     5281 acgctttttt tgtcacgatc tccccttaac ctgcgtaaat cacccgccat ggttgattat
     5341 ttttcaacct caaaatggtc atacacctaa cgcagccgcg attttcatcg caactgcatg
     5401 aattaaaaga aaaaaaagga atatttcgtt ttcacgagta atacccgggt attaaaaatc
     5461 cactgtaatt acatgaaaat aaagaaataa aaggtaatac cggagtatta ccacgtacgc
     5521 gggcaagcga aaaagctata acgcttcccg gccgacaggc gacccaaaat ccacaggggc
     5581 atgcaggttc tcttcagtaa cctgcgccat taaatcaaaa aggtcatatt cgccgggaag
     5641 ctgcgtatca gtcgaatcca gttgttcatc atattcagat ggcatggggt gatatccagt
     5701 agctgagagg ttgttagcgg gtttcggggc gcagccctga accagtcatg tagcgctagc
     5761 ggagtgtata ctggcttact atgttgccac gattgcgaaa atcagtgaag tgcttcatgt
     5821 ggcaggagaa aaaaggcagc accggcgcgt cagcagaata tgcgatacag gagatattcc
     5881 gcttcctcgc tcactgactc gctacgctcg gtcgttcggc tgcggcgagc ggtaccggct
     5941 tacggacggg gacggaaatt tcctggaaga taccaggaag acacttagca aagaagagat
     6001 aaggccacgg cgaagccgtt tttccatagg ctccgccccc ctgacaagca tcgcaaaatc
     6061 tgacgctcaa atcagtggtg gcgaaacccg acaggactat aaagatccca ggcgtttccc
     6121 cctggtagct ccctcgtgcg ctctcctgtt cctgcctttc ggtttaccgg tgtcattccg
     6181 ctgttatggc cgcggtttct cattccacgc ctgacactca gt
//
