LOCUS       CP124972                6200 bp    DNA     circular BCT 16-MAY-2023
DEFINITION  Escherichia coli strain KSE-D40 plasmid pKSE-D40_2, complete
            sequence.
ACCESSION   CP124972
VERSION     CP124972.1
DBLINK      BioProject: PRJNA956323
            BioSample: SAMN34598759
KEYWORDS    .
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 6200)
  AUTHORS   Gomi,R., Matsumura,Y., Yamamoto,M., Matsuda,T. and Harada,H.
  TITLE     Genomic surveillance of antimicrobial-resistant Escherichia coli in
            fecal sludge and sewage in Uganda
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 6200)
  AUTHORS   Gomi,R., Matsumura,Y., Yamamoto,M., Matsuda,T. and Harada,H.
  TITLE     Direct Submission
  JOURNAL   Submitted (05-MAY-2023) Department of environmental engineering,
            Kyoto University, KyotoDaigakuKatsura, Nishikyo-ku, Kyoto-city
            615-8540, Japan
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: Unicycler v. v0.5.0
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 100x
            Sequencing Technology :: Illumina; Oxford Nanopore MinION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI
            Annotation Date                   :: 05/09/2023 16:34:32
            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)                     :: 4,970
            CDSs (total)                      :: 4,850
            Genes (coding)                    :: 4,603
            CDSs (with protein)               :: 4,603
            Genes (RNA)                       :: 120
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 87
            ncRNAs                            :: 11
            Pseudo Genes (total)              :: 247
            CDSs (without protein)            :: 247
            Pseudo Genes (ambiguous residues) :: 0 of 247
            Pseudo Genes (frameshifted)       :: 91 of 247
            Pseudo Genes (incomplete)         :: 160 of 247
            Pseudo Genes (internal stop)      :: 55 of 247
            Pseudo Genes (multiple problems)  :: 55 of 247
            Pseudo Genes (short protein)      :: 4 of 247
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            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/
FEATURES             Location/Qualifiers
     source          1..6200
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="KSE-D40"
                     /isolation_source="Sewage"
                     /db_xref="taxon:562"
                     /plasmid="pKSE-D40_2"
                     /geo_loc_name="Uganda"
                     /lat_lon="0.19 N 32.35 E"
                     /collection_date="2018"
                     /collected_by="Hidenori Harada, Mai Tanaka"
     gene            complement(join(5446..6200,1..61))
                     /gene="sul2"
                     /locus_tag="QL152_24805"
     ARG             complement(5450..6198)
                     /name="sul2"
                     /gene="sul2"
                     /gene_name="sulfonamide-resistant dihydropteroate synthase
                     Sul2"
                     /tool="amrfinderplus"
                     /drug_class="SULFONAMIDE"
                     /identity="100.0"
                     /coverage="92.25"
     gene            1250..1399
                     /locus_tag="QL152_24810"
     CDS             1250..1399
                     /locus_tag="QL152_24810"
                     /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="WHJ22753.1"
                     /translation="MPSEYDEQLDSTDTQLPGEYDLFDLMAQVTEENLHAPVDFGSPVG
                     REAL"
                     /name="hypothetical protein"
     gene            complement(2144..2584)
                     /locus_tag="QL152_24815"
     CDS             complement(2144..2584)
                     /locus_tag="QL152_24815"
                     /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="entry exclusion protein 1"
                     /protein_id="WHJ22754.1"
                     /translation="MAWHTVQETLKLTGKSRSQLYRDMAKGLVSYRTGKNDRREFETSE
                     LIRAYGELRTSETPKRHKEGHSKSVVSQAENAQLDVIQQKLDALQQTVTLMLEDKMARE
                     AENRLRNEEREQLQAEISRLADALAQEKKRGFWSRLFRSGSE"
                     /name="entry exclusion protein 1"
     gene            2802..3191
                     /locus_tag="QL152_24820"
     CDS             2802..3191
                     /locus_tag="QL152_24820"
                     /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="WHJ22755.1"
                     /translation="MSTELNSGTVGGFGHMGPNDPYNDGHSGSGSSGGSFNGGGNGGHD
                     NSSGSSYTASFGLITGRHPITVPGTKNINSVDLSAVINNIIHHEGARNNMYLDTANNVR
                     VGVTGTGWQCLATAGISAEGKRTFR"
                     /name="hypothetical protein"
     gene            3235..3639
                     /locus_tag="QL152_24825"
                     /pseudo=""
     CDS             3235..3639
                     /locus_tag="QL152_24825"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001120888.1"
                     /note="incomplete; partial on complete genome; 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(3746..4582)
                     /locus_tag="QL152_24830"
     CDS             complement(3746..4582)
                     /locus_tag="QL152_24830"
                     /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="WHJ22750.1"
                     /translation="MFMPPVFPAHWHVSQPVLIADTFSSLVWKVSLPDGTPAIVKGLKP
                     IEDIADELRGADYLVWRNGRGAVRLLGRENNLMLLEYAGERMLSHIVAEHGDYQATEIA
                     AELMAKLYAASEEPLPSALLPIRDRFAALFQRARDDQNAGCQTDYVHAAIIADQMMSNA
                     SELRGLHGDLHHENIMFSSRGWLVIDPVGLVGEVGFGAANMFYDPADRDDLCLDPRRIA
                     QMADAFSRALDVDPRRLLDQAYAYGCLSAAWNADGEEEQRDLAIAAAIKQVRQTSY"
                     /name="aminoglycoside O-phosphotransferase APH(6)-Id"
     gene            complement(4582..5385)
                     /gene="aph(3'')-Ib"
                     /locus_tag="QL152_24835"
     ARG             complement(4586..5385)
                     /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"
     ARG             complement(3750..4582)
                     /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          1042..1215
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="99.429"
                     /coverage="100.0"
                     /evalue="1.19e-84"
     Typing          complement(513..1118)
                     /name="rep_cluster_2335"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="89.593"
                     /coverage="99.0"
                     /evalue="0.0"
ORIGIN
        1 catcggagaa actgtccgag gttatgttga cgatgccgaa aatgatgagc gatttattca
       61 tgggggcttc tataataata ataatcgagc atgagtctca tacggatgct cgggtcgaaa
      121 gggaatcccc aggcgagtaa cctgtttgcg gtgatccgtt tcatgatgat gtatctgtag
      181 cattttggaa ataaatatat catctctcaa taagtagata tatttatctt ttttgcttct
      241 ttggtgctgc aagtcaccaa tacgagggaa acctgttacg gagcggttta accgtaatca
      301 acagtgactg gtgtcatgtt cggaagatta attgatagta atctacaaag gatcttcttg
      361 agatcctttt caatgaatcg taatctcttg ctctgtaaac gaaaaaaccg cctggggagg
      421 cggtttgttc gaaggttaag tcagttgggg aactgcttaa cccggtaaca gggttcacga
      481 gaccgccatt accaaaactg ttctttcagt gtagccgcag tcaggcctct acttcaagac
      541 ctcttaatct atcttctcgt gcactcctgt tactaatggc tgctgccagt ggcgttttgt
      601 cgtgtctttc cgggttggac tcaagttgat agttaccgga caaggcgcag cggtcggact
      661 gaacgggggg ttcgtgcata cagtccagct tggagcgaac tgccttcacg gaactgagtg
      721 tcaggcgtgg aatgagaaac cgcggccata acagcggaat gacaccggta aaccgaaagg
      781 caggaacagg agagcgcacg agggagctac cagggggaaa cgcctgggat ctttatagtc
      841 ctgtcgggtt tcgccaccac tgatttgagc gtcagatttt gcgatgcttg tcaggggggc
      901 ggagcctatg gaaaaacggc ttcgccgtgg ccttatctct tctttgctaa gtgtcttcct
      961 ggtatcttcc aggaaatttc cgtccccgtc cgtaagccgg taccgctcgc cgcagccgaa
     1021 cgaccgagcg tagcgagtca gtgagcgagg aagcggaata tctcctgtat cgcatattct
     1081 gctgacgcgc cggtgctgcc ttttttctcc tgccacatga agcacttcac tgattttcgc
     1141 aatcgtggca acatagtaag ccagtataca ctccgctagc gctacatgac tggttcaggg
     1201 ctgcgccccg aaacccgcta acaacctctc agctactgga tatcacccca tgccatctga
     1261 atatgatgaa caactggatt cgactgatac gcagcttccc ggcgaatatg acctttttga
     1321 tttaatggcg caggttactg aagagaacct gcatgcccct gtggattttg ggtcgcctgt
     1381 cggccgggaa gcgttatagc tttttcgctt gcccgcgtac gtggtaatac tccggtatta
     1441 ccttttattt ctttattttc atgtaattac agtggatttt taatacccgg gtattactcg
     1501 tgaaaacgaa atattccttt tttttctttt aattcatgca gttgcgatga aaatcgcggc
     1561 tgcgttaggt gtatgaccat tttgaggttg aaaaataatc aaccatggcg ggtgatttac
     1621 gcaggttaag gggagatcgt gacaaaaaaa gcgttcctca ctgtatcgtt catgcctgca
     1681 tgaacgggtt attcttcctg actacagaat tacatcgctc cttcagttca tacatcactt
     1741 ttacatcact tatacatcac ttttacatca ttccttcagc tcatacgtca ctttcatcct
     1801 ctgtgccatt tgtacatcac ccccttcctg aacgtgctga cagcgggttt tccggctgcg
     1861 ccggcaacgc ttcacggcca cgcaataaat tgcgtccccg ttcaccgttt tcggatggga
     1921 agaacgccgg aaacaggact taccccggct gaatggtgtg aatttccgcg ctatgcactt
     1981 gtgcgcatac tcatgcatgc cgtaaaaaca gagcctgcgc gtttctggcg ggttttcggg
     2041 tggtttgttg cctgttttac cggtttcccg tcagaaacgc cctgagggcc tctcaggcgg
     2101 tgctgataac agatgttatg gtaaatcaga gtcacctgca ctgttactct gaaccggagc
     2161 gaaacagccg cgaccagaat ccccgctttt tttcctgtgc cagcgcgtca gccagacggc
     2221 taatttcggc ctgtagttgt tccctctcct catttcgcag gcggttttct gcttcccgcg
     2281 ccatcttgtc ttcaagcatt agggtaacag tctgctgcag agcgtccagt ttctgctgaa
     2341 tgacgtctag ctgagcattt tccgcctggc taacgacaga tttggagtgt ccctccttgt
     2401 gcctttttgg tgtctcagaa gtgcgcagct cgccataggc ccgaatcagt tcactggtct
     2461 cgaactcccg gcgatcattt tttcctgtgc gatagctgac aaggccttta gccatgtcac
     2521 gatataattg cgagcgcgac tttcctgtta atttcagtgt ctcttgaact gtgtgccatg
     2581 ccataaaagt gacagtgtct cctgtgtgta ccgtattgta acagcagaac atattactgt
     2641 tttaacacaa aaggtctgag gctgcccgtg aggcgtgaaa aatacacaaa aaacctgttg
     2701 acggtgtggt tttgacgggc gtagtatttc gaatactgta tataaacaca ttgttataaa
     2761 tacagttttt gctgttttta aaagtcaaag aggataattt tatgagtaca gagttaaata
     2821 gcggtactgt cggtggtttt ggtcacatgg gaccaaatga cccctacaat gatggtcata
     2881 gcggctctgg aagttcggga ggtagtttta acggtggtgg taatggtggc catgataata
     2941 gtagtggttc atcttatact gcatcctttg gtctcatcac tggccgacac ccgataactg
     3001 tcccaggtac gaagaatatt aattctgtcg atctttctgc tgtcattaat aacattatac
     3061 atcatgaagg tgcacgcaat aacatgtacc tagatactgc gaacaatgta agagtgggag
     3121 tgacgggcac tggctggcaa tgtctagcaa cggcaggcat ttcggctgag ggtaaaagaa
     3181 ctttccgcta agcgatagac tgtatgtaaa cacagtattg caaggacgcg gaacatgcct
     3241 catgtggcgg ccaggacggc cagccgggat cgggatactg gtcgttacca gagccaccga
     3301 cccgagcaaa cccttctcta tcagatcgtt gacgagtatt acccggcatt cgctgcgctt
     3361 atggcagagc agggaaagga attgccgggc tatgtgcaac gggaatttga agaatttctc
     3421 caatgcgggc ggctggagca tggctttcta cgggttcgct gcgagtcttg ccacgccgag
     3481 cacctggtcg ctttcagctg taagcgtcgc ggtttctgcc cgagctgtgg ggcgcggcgg
     3541 atggccgaaa gtgccgcctt gctggttgat gaagtactgc ctgaacaacc catgcgtcag
     3601 tgggtgttga gcttcccgtt tcagctgcgt ttcctgtttg gggtcgtttg cgggaagggg
     3661 cggaatccta cgctaaggct ttggccagcg atattctccg gtgagattga tgtgttccca
     3721 ggggatagga gaagtcgctt gatatctagt atgacgtctg tcgcacctgc ttgatcgcgg
     3781 ccgcgatagc tagatcgcgt tgctcctctt ctccatccgc gttccaagct gcggaaaggc
     3841 acccataagc gtacgcctgg tcgagcaggc gacgcggatc gacgtccagc gcacgagaga
     3901 atgcgtccgc catctgtgca atgcgtctag gatcgagaca aaggtcgtct ctgtcagccg
     3961 gatcgtagaa catattggcg gcgccaaagc ccacttcacc gaccagaccg acgggatcta
     4021 tcaccagcca gccgcgactg gagaacatga tgttttcatg atgcagatcg ccatgtagcc
     4081 cacgcagttc cgaggcattg ctcatcattt gatcggctat aatcgccgcg tggacgtagt
     4141 cagtttgaca acctgcgttt tgatcatcgc gcgcccgctg aaacaaagct gcaaagcgat
     4201 cccggatcgg gagaagggca gaaggcaggg gttcctcaga tgcggcatac agcttcgcca
     4261 ttagttccgc tgcaatttcg gtcgcctggt agtcgccgtg ctcggcaacg atgtgagaga
     4321 gcattcgctc cccggcatat tcgagcaaca tcagattgtt ctcacgaccg agcaaccgga
     4381 ctgctcccct cccattgcgc cataccagat agtcggcccc gcgcagttca tcagcaatgt
     4441 cttctatagg tttcaatccc ttgacgattg caggagtccc gtctggcaat gaaactttcc
     4501 aaacgaggct ggaaaaggtg tccgcaatga gaacaggttg cgaaacgtgc caatgagcag
     4561 gaaaaacagg cggcatgaac atcaacccca agtcagaggg tccaatcgca gatagaaggc
     4621 aaggcgttcg cggtcggggg cttcgatccc caatacattg aataggacag cgaaggcgcg
     4681 ctctgcttca tctggcgctg cccagttctc ttcggcgtta gcaatcatga gtgccaaatc
     4741 ggcatagcga tctgctgttc cgagccgccc aaggtcgatc agacccgtgc attgaagagt
     4801 tttagggtcc accatgaagt tcggcatgca gggatcacca tggcaaacaa ccatatcggt
     4861 gcgctcttgg tcgagccgca ccggtagctc tcgttcgaca cgagccaaaa gatcgagctg
     4921 cggcgtactc ttgtcctcgt ccggtaagaa gtcgggattg acggcattgc gggacaccac
     4981 atcaacggcg cgtccgaaca ttcgcgacag cctgcgctca aacggacatt gatcaaccga
     5041 taggctgtga acagcgccaa gttgctgccc cattgacggc cacgctttga gcaaatccgc
     5101 tccagacaga tcagccgccg gtactcccgg aattgccgtt atcaccaagc atgcaccctc
     5161 ctgttcctcc tgccagttga tgacctcggg gcaagccaca cctcgacctt tgagccaaat
     5221 gaggcggtca cgctctccag cgagctcacc gcggcgggaa gcaggtgcga ttttcgcgaa
     5281 ggcatgcccg tcaccacgtc gaaaaacaaa atcaccagat tctccgcctc tgacaggcaa
     5341 ccagtcagaa tgcgattcac caaaaaaaat attagttcga ttcaatggag gttccttcag
     5401 ttttctgatg aagcgcgaat atagagaaat atcccgaatg tgcagttaac gaattcttgc
     5461 ggtttctttc agcgccgcca ataccgccag cccgtcgcgc aaggggcgcg gctcgtgtgt
     5521 gcggatgaag tcagctccac ctgcggcggc ggcaagctct gcagcgagtg tcgcggcccc
     5581 gacatccccc ggaccacggc ctgtgagcgc gcgcagaaag gatttgcgcg aaacagacag
     5641 aagcaccggc aaatcgaagc gcagccgcaa ttcatcgaac cgcgccagca ccgagagcga
     5701 ggtttcggga gcagccccca gaaaaaaccc catgccggga tcaaggacaa ggcggttgcg
     5761 tttgataccg gcacccgtca gcgccgcgat gcgcgcgtca aagaacgccg caatgtgatc
     5821 catgatgtcg ccagcgggtg cctcgcgccg atctgcctgc ccgtcttgca ccgaatgcat
     5881 aacgacgagt ttggcagatg atttcgccaa ttgcggatag aacgcagcgt ctggaaaacc
     5941 gcgaatatca ttgagatagg ccacaccacg cgacaaggca taggcttgcg tcgcgggttg
     6001 ataactgtcg agcgagacgg gaatgccatc tgccttgagc gcgtccagca ccggcgcgat
     6061 acgcgcgatt tctgtgtcgg acgaaacagg cgcggcgtcg ggattgctgg atgccggacc
     6121 gaggtcgatc acatctgccc cctcggccat cagcttacgc gcctgcgcaa tggctgcgtc
     6181 tggcgccaga taccggcctc
//
