LOCUS       CP125017                6200 bp    DNA     circular BCT 16-MAY-2023
DEFINITION  Escherichia coli strain KFS-D24 plasmid pKFS-D24_3, complete
            sequence.
ACCESSION   CP125017
VERSION     CP125017.1
DBLINK      BioProject: PRJNA956323
            BioSample: SAMN34598748
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  JOURNAL   Unpublished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                   :: Flye v. v2.9.1-b1780
            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 16:50:12
            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)                     :: 5,137
            CDSs (total)                      :: 5,015
            Genes (coding)                    :: 4,789
            CDSs (with protein)               :: 4,789
            Genes (RNA)                       :: 122
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 94
            ncRNAs                            :: 6
            Pseudo Genes (total)              :: 226
            CDSs (without protein)            :: 226
            Pseudo Genes (ambiguous residues) :: 0 of 226
            Pseudo Genes (frameshifted)       :: 82 of 226
            Pseudo Genes (incomplete)         :: 157 of 226
            Pseudo Genes (internal stop)      :: 38 of 226
            Pseudo Genes (multiple problems)  :: 47 of 226
            Pseudo Genes (short protein)      :: 4 of 226
            ##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="KFS-D24"
                     /isolation_source="Fecal sludge"
                     /db_xref="taxon:562"
                     /plasmid="pKFS-D24_3"
                     /geo_loc_name="Uganda"
                     /lat_lon="0.19 N 32.35 E"
                     /collection_date="2018"
                     /collected_by="Hidenori Harada, Mai Tanaka"
     ARG             complement(3..451)
                     /name="APH(3'')-Ib"
                     /gene="APH(3'')-Ib"
                     /gene_name="APH(3'')"
                     /tool="rgi"
                     /drug_class="aminoglycoside antibiotic"
                     /identity="98.67"
                     /coverage="56.18"
     ARG             complement(5894..6198)
                     /name="APH(3'')-Ib"
                     /gene="APH(3'')-Ib"
                     /gene_name="APH(3'')"
                     /tool="rgi"
                     /drug_class="aminoglycoside antibiotic"
                     /identity="100.0"
                     /coverage="37.83"
     gene            complement(557..1372)
                     /gene="sul2"
                     /locus_tag="QL134_25615"
     ARG             complement(561..1372)
                     /name="sul2"
                     /gene="sul2"
                     /gene_name="sulfonamide-resistant dihydropteroate synthase
                     Sul2"
                     /tool="amrfinderplus"
                     /drug_class="SULFONAMIDE"
                     /identity="100.0"
                     /coverage="100.0"
     gene            2561..2710
                     /locus_tag="QL134_25620"
     CDS             2561..2710
                     /locus_tag="QL134_25620"
                     /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="WHJ82104.1"
                     /translation="MPSEYDEQLDSTDTQLPGEYDLFDLMAQVTEENLHAPVDFGSPVG
                     REAL"
                     /name="hypothetical protein"
     gene            complement(3455..3895)
                     /locus_tag="QL134_25625"
     CDS             complement(3455..3895)
                     /locus_tag="QL134_25625"
                     /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="WHJ82099.1"
                     /translation="MAWHTVQETLKLTGKSRSQLYRDMAKGLVSYRTGKNDRREFETSE
                     LIRAYGELRTSETPKRHKEGHSKSVVSQAENAQLDVIQQKLDALQQTVTLMLEDKMARE
                     AENRLRNEEREQLQAEISRLADALAQEKKRGFWSRLFRSGSE"
                     /name="entry exclusion protein 1"
     gene            4113..4502
                     /locus_tag="QL134_25630"
     CDS             4113..4502
                     /locus_tag="QL134_25630"
                     /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="WHJ82100.1"
                     /translation="MSTELNSGTVGGFGHMGPNDPYNDGHSGSGSSGGSFNGGGNGGHD
                     NSSGSSYTASFGLITGRHPITVPGTKNINSVDLSAVINNIIHHEGARNNMYLDTANNVR
                     VGVTGTGWQCLATAGISAEGKRTFR"
                     /name="hypothetical protein"
     gene            4546..4950
                     /locus_tag="QL134_25635"
                     /pseudo=""
     CDS             4546..4950
                     /locus_tag="QL134_25635"
                     /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(5057..5893)
                     /locus_tag="QL134_25640"
     CDS             complement(5057..5893)
                     /locus_tag="QL134_25640"
                     /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="WHJ82101.1"
                     /translation="MFMPPVFPAHWHVSQPVLIADTFSSLVWKVSLPDGTPAIVKGLKP
                     IEDIADELRGADYLVWRNGRGAVRLLGRENNLMLLEYAGERMLSHIVAEHGDYQATEIA
                     AELMAKLYAASEEPLPSALLPIRDRFAALFQRARDDQNAGCQTDYVHAAIIADQMMSNA
                     SELRGLHGDLHHENIMFSSRGWLVIDPVGLVGEVGFGAANMFYDPADRDDLCLDPRRIA
                     QMADAFSRALDVDPRRLLDQAYAYGCLSAAWNADGEEEQRDLAIAAAIKQVRQTSY"
                     /name="aminoglycoside O-phosphotransferase APH(6)-Id"
     ARG             complement(5061..5893)
                     /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          2353..2526
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="99.429"
                     /coverage="100.0"
                     /evalue="1.19e-84"
     Typing          complement(1824..2429)
                     /name="rep_cluster_2335"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="89.593"
                     /coverage="99.0"
                     /evalue="0.0"
ORIGIN
        1 ctcgttcgac acgagccaaa agatcgagct gcggcgtact cttgtcctcg tccggtaaga
       61 agtcgggatt gacggcattg cgggacacca catcaacggc gcgtccgaac attcgcgaca
      121 gcctgcgctc aaacggacat tgatcaaccg ataggctgtg aacagcgcca agttgctgcc
      181 ccattgacgg ccacgctttg agcaaatccg ctccagacag atcagccgcc ggtactcccg
      241 gaattgccgt tatcaccaag catgcaccct cctgttcctc ctgccagttg atgacctcgg
      301 ggcaagccac acctcgacct ttgagccaaa tgaggcggtc acgctctcca gcgagctcac
      361 cgcggcggga agcaggtgcg attttcgcga aggcatgccc gtcaccacgt cgaaaaacaa
      421 aatcaccaga ttctccgcct ctgacaggca accagtcaga atgcgattca ccaaaaaaaa
      481 tattagttcg atttaatgga ggttccttca gttttctgat gaagcgcgaa tatagagaaa
      541 tatcccgaat gtgcagttaa cgaattcttg cggtttcttt cagcgccgcc aataccgcca
      601 gcccgtcgcg caaggggcgc ggctcgtgtg tgcggatgaa gtcagctcca cctgcggcgg
      661 cggcaagctc tgcagcgagt gtcgcggccc cgacatcccc cggaccacgg cctgtgagcg
      721 cgcgcagaaa ggatttgcgc gaaacagaca gaagcaccgg caaatcgaag cgcagccgca
      781 attcatcgaa ccgcgccagc accgagagcg aggtttcggg agcagccccc agaaaaaacc
      841 ccatgccggg atcaaggaca aggcggttgc gtttgatacc ggcacccgtc agcgccgcga
      901 tgcgcgcgtc aaagaacgcc gcaatgtgat ccatgatgtc gccagcgggt gcctcgcgcc
      961 gatctgcctg cccgtcttgc accgaatgca taacgacgag tttggcagat gatttcgcca
     1021 attgcggata gaacgcagcg tctggaaaac cgcgaatatc attgagatag gccacaccac
     1081 gcgacaaggc ataggcttgc gtcgcgggtt gataactgtc gagcgagacg ggaatgccat
     1141 ctgccttgag cgcgtccagc accggcgcga tacgcgcgat ttctgtgtcg gacgaaacag
     1201 gcgcggcgtc gggattgctg gatgccggac cgaggtcgat cacatctgcc ccctcggcca
     1261 tcagcttacg cgcctgcgca atggctgcgt ctggcgccag ataccggcct ccatcggaga
     1321 aactgtccga ggttatgttg acgatgccga aaatgatgag cgatttattc atgggggctt
     1381 ctataataat aataatcgag catgagtctc atacggatgc tcgggtcgaa agggaatccc
     1441 caggcgagta acctgtttgc ggtgatccgt ttcatgatga tgtatctgta gcattttgga
     1501 aataaatata tcatctctca ataagtagat atatttatct tttttgcttc tttggtgctg
     1561 caagtcacca atacgaggga aacctgttac ggagcggttt aaccgtaatc aacagtgact
     1621 ggtgtcatgt tcggaagatt aattgatagt aatctacaaa ggatcttctt gagatccttt
     1681 tcaatgaatc gtaatctctt gctctgtaaa cgaaaaaacc gcctggggag gcggtttgtt
     1741 cgaaggttaa gtcagttggg gaactgctta acccggtaac agggttcacg agaccgccat
     1801 taccaaaact gttctttcag tgtagccgca gtcaggcctc tacttcaaga cctcttaatc
     1861 tatcttctcg tgcactcctg ttactaatgg ctgctgccag tggcgttttg tcgtgtcttt
     1921 ccgggttgga ctcaagttga tagttaccgg acaaggcgca gcggtcggac tgaacggggg
     1981 gttcgtgcat acagtccagc ttggagcgaa ctgccttcac ggaactgagt gtcaggcgtg
     2041 gaatgagaaa ccgcggccat aacagcggaa tgacaccggt aaaccgaaag gcaggaacag
     2101 gagagcgcac gagggagcta ccagggggaa acgcctggga tctttatagt cctgtcgggt
     2161 ttcgccacca ctgatttgag cgtcagattt tgcgatgctt gtcagggggg cggagcctat
     2221 ggaaaaacgg cttcgccgtg gccttatctc ttctttgcta agtgtcttcc tggtatcttc
     2281 caggaaattt ccgtccccgt ccgtaagccg gtaccgctcg ccgcagccga acgaccgagc
     2341 gtagcgagtc agtgagcgag gaagcggaat atctcctgta tcgcatattc tgctgacgcg
     2401 ccggtgctgc cttttttctc ctgccacatg aagcacttca ctgattttcg caatcgtggc
     2461 aacatagtaa gccagtatac actccgctag cgctacatga ctggttcagg gctgcgcccc
     2521 gaaacccgct aacaacctct cagctactgg atatcacccc atgccatctg aatatgatga
     2581 acaactggat tcgactgata cgcagcttcc cggcgaatat gacctttttg atttaatggc
     2641 gcaggttact gaagagaacc tgcatgcccc tgtggatttt gggtcgcctg tcggccggga
     2701 agcgttatag ctttttcgct tgcccgcgta cgtggtaata ctccggtatt accttttatt
     2761 tctttatttt catgtaatta cagtggattt ttaatacccg ggtattactc gtgaaaacga
     2821 aatattcctt ttttttcttt taattcatgc agttgcgatg aaaatcgcgg ctgcgttagg
     2881 tgtatgacca ttttgaggtt gaaaaataat caaccatggc gggtgattta cgcaggttaa
     2941 ggggagatcg tgacaaaaaa agcgttcctc actgtatcgt tcatgcctgc atgaacgggt
     3001 tattcttcct gactacagaa ttacatcgct ccttcagttc atacatcact tttacatcac
     3061 ttatacatca cttttacatc attccttcag ctcatacgtc actttcatcc tctgtgccat
     3121 ttgtacatca cccccttcct gaacgtgctg acagcgggtt ttccggctgc gccggcaacg
     3181 cttcacggcc acgcaataaa ttgcgtcccc gttcaccgtt ttcggatggg aagaacgccg
     3241 gaaacaggac ttaccccggc tgaatggtgt gaatttccgc gctatgcact tgtgcgcata
     3301 ctcatgcatg ccgtaaaaac agagcctgcg cgtttctggc gggttttcgg gtggtttgtt
     3361 gcctgtttta ccggtttccc gtcagaaacg ccctgagggc ctctcaggcg gtgctgataa
     3421 cagatgttat ggtaaatcag agtcacctgc actgttactc tgaaccggag cgaaacagcc
     3481 gcgaccagaa tccccgcttt ttttcctgtg ccagcgcgtc agccagacgg ctaatttcgg
     3541 cctgtagttg ttccctctcc tcatttcgca ggcggttttc tgcttcccgc gccatcttgt
     3601 cttcaagcat tagggtaaca gtctgctgca gagcgtccag tttctgctga atgacgtcta
     3661 gctgagcatt ttccgcctgg ctaacgacag atttggagtg tccctccttg tgcctttttg
     3721 gtgtctcaga agtgcgcagc tcgccatagg cccgaatcag ttcactggtc tcgaactccc
     3781 ggcgatcatt ttttcctgtg cgatagctga caaggccttt agccatgtca cgatataatt
     3841 gcgagcgcga ctttcctgtt aatttcagtg tctcttgaac tgtgtgccat gccataaaag
     3901 tgacagtgtc tcctgtgtgt accgtattgt aacagcagaa catattactg ttttaacaca
     3961 aaaggtctga ggctgcccgt gaggcgtgaa aaatacacaa aaaacctgtt gacggtgtgg
     4021 ttttgacggg cgtagtattt cgaatactgt atataaacac attgttataa atacagtttt
     4081 tgctgttttt aaaagtcaaa gaggataatt ttatgagtac agagttaaat agcggtactg
     4141 tcggtggttt tggtcacatg ggaccaaatg acccctacaa tgatggtcat agcggctctg
     4201 gaagttcggg aggtagtttt aacggtggtg gtaatggtgg ccatgataat agtagtggtt
     4261 catcttatac tgcatccttt ggtctcatca ctggccgaca cccgataact gtcccaggta
     4321 cgaagaatat taattctgtc gatctttctg ctgtcattaa taacattata catcatgaag
     4381 gtgcacgcaa taacatgtac ctagatactg cgaacaatgt aagagtggga gtgacgggca
     4441 ctggctggca atgtctagca acggcaggca tttcggctga gggtaaaaga actttccgct
     4501 aagcgataga ctgtatgtaa acacagtatt gcaaggacgc ggaacatgcc tcatgtggcg
     4561 gccaggacgg ccagccggga tcgggatact ggtcgttacc agagccaccg acccgagcaa
     4621 acccttctct atcagatcgt tgacgagtat tacccggcat tcgctgcgct tatggcagag
     4681 cagggaaagg aattgccggg ctatgtgcaa cgggaatttg aagaatttct ccaatgcggg
     4741 cggctggagc atggctttct acgggttcgc tgcgagtctt gccacgccga gcacctggtc
     4801 gctttcagct gtaagcgtcg cggtttctgc ccgagctgtg gggcgcggcg gatggccgaa
     4861 agtgccgcct tgctggttga tgaagtactg cctgaacaac ccatgcgtca gtgggtgttg
     4921 agcttcccgt ttcagctgcg tttcctgttt ggggtcgttt gcgggaaggg gcggaatcct
     4981 acgctaaggc tttggccagc gatattctcc ggtgagattg atgtgttccc aggggatagg
     5041 agaagtcgct tgatatctag tatgacgtct gtcgcacctg cttgatcgcg gccgcgatag
     5101 ctagatcgcg ttgctcctct tctccatccg cgttccaagc tgcggaaagg cacccataag
     5161 cgtacgcctg gtcgagcagg cgacgcggat cgacgtccag cgcacgagag aatgcgtccg
     5221 ccatctgtgc aatgcgtcta ggatcgagac aaaggtcgtc tctgtcagcc ggatcgtaga
     5281 acatattggc ggcgccaaag cccacttcac cgaccagacc gacgggatct atcaccagcc
     5341 agccgcgact ggagaacatg atgttttcat gatgcagatc gccatgtagc ccacgcagtt
     5401 ccgaggcatt gctcatcatt tgatcggcta taatcgccgc gtggacgtag tcagtttgac
     5461 aacctgcgtt ttgatcatcg cgcgcccgct gaaacaaagc tgcaaagcga tcccggatcg
     5521 ggagaagggc agaaggcagg ggttcctcag atgcggcata cagcttcgcc attagttccg
     5581 ctgcaatttc ggtcgcctgg tagtcgccgt gctcggcaac gatgtgagag agcattcgct
     5641 ccccggcata ttcgagcaac atcagattgt tctcacgacc gagcaaccgg actgctcccc
     5701 tcccattgcg ccataccaga tagtcggccc cgcgcagttc atcagcaatg tcttctatag
     5761 gtttcaatcc cttgacgatt gcaggagtcc cgtctggcaa tgaaactttc caaacgaggc
     5821 tggaaaaggt gtccgcaatg agaacaggtt gcgaaacgtg ccaatgagca ggaaaaacag
     5881 gcggcatgaa catcaacccc aagtcagagg gtccaatcgc agatagaagg caaggcgttc
     5941 gcggtcgggg gcttcgatcc ccaatacatt gaataggaca gcgaaggcgc gctctgcttc
     6001 atctggcgct gcccagttct cttcggcgtt agcaatcatg agtgccaaat cggcatagcg
     6061 atctgctgtt ccgagccgcc caaggtcgat cagacccgtg cattgaagag ttttagggtc
     6121 caccatgaag ttcggcatgc agggatcacc atggcaaaca accatatcgg tgcgctcttg
     6181 gtcgagccgc accggtagct
//
