LOCUS       CP125023                6200 bp    DNA     circular BCT 16-MAY-2023
DEFINITION  Escherichia coli strain KFS-D21 plasmid pKFS-D21_3, complete
            sequence.
ACCESSION   CP125023
VERSION     CP125023.1
DBLINK      BioProject: PRJNA956323
            BioSample: SAMN34598747
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  JOURNAL   Unpublished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 16:46:04
            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)                     :: 5,133
            CDSs (total)                      :: 5,011
            Genes (coding)                    :: 4,790
            CDSs (with protein)               :: 4,790
            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)              :: 221
            CDSs (without protein)            :: 221
            Pseudo Genes (ambiguous residues) :: 0 of 221
            Pseudo Genes (frameshifted)       :: 81 of 221
            Pseudo Genes (incomplete)         :: 152 of 221
            Pseudo Genes (internal stop)      :: 38 of 221
            Pseudo Genes (multiple problems)  :: 46 of 221
            Pseudo Genes (short protein)      :: 4 of 221
            ##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-D21"
                     /isolation_source="Fecal sludge"
                     /db_xref="taxon:562"
                     /plasmid="pKFS-D21_3"
                     /geo_loc_name="Uganda"
                     /lat_lon="0.19 N 32.35 E"
                     /collection_date="2018"
                     /collected_by="Hidenori Harada, Mai Tanaka"
     gene            join(5424..6200,1..60)
                     /locus_tag="QL133_25565"
     CDS             join(5424..6200,1..60)
                     /locus_tag="QL133_25565"
                     /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="WHJ86885.1"
                     /translation="MFMPPVFPAHWHVSQPVLIADTFSSLVWKVSLPDGTPAIVKGLKP
                     IEDIADELRGADYLVWRNGRGAVRLLGRENNLMLLEYAGERMLSHIVAEHGDYQATEIA
                     AELMAKLYAASEEPLPSALLPIRDRFAALFQRARDDQNAGCQTDYVHAAIIADQMMSNA
                     SELRGLHGDLHHENIMFSSRGWLVIDPVGLVGEVGFGAANMFYDPADRDDLCLDPRRIA
                     QMADAFSRALDVDPRRLLDQAYAYGCLSAAWNADGEEEQRDLAIAAAIKQVRQTSY"
                     /name="aminoglycoside O-phosphotransferase APH(6)-Id"
     gene            complement(167..571)
                     /locus_tag="QL133_25570"
                     /pseudo=""
     CDS             complement(167..571)
                     /locus_tag="QL133_25570"
                     /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(615..1004)
                     /locus_tag="QL133_25575"
     CDS             complement(615..1004)
                     /locus_tag="QL133_25575"
                     /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="WHJ86886.1"
                     /translation="MSTELNSGTVGGFGHMGPNDPYNDGHSGSGSSGGSFNGGGNGGHD
                     NSSGSSYTASFGLITGRHPITVPGTKNINSVDLSAVINNIIHHEGARNNMYLDTANNVR
                     VGVTGTGWQCLATAGISAEGKRTFR"
                     /name="hypothetical protein"
     gene            1222..1662
                     /locus_tag="QL133_25580"
     CDS             1222..1662
                     /locus_tag="QL133_25580"
                     /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="WHJ86887.1"
                     /translation="MAWHTVQETLKLTGKSRSQLYRDMAKGLVSYRTGKNDRREFETSE
                     LIRAYGELRTSETPKRHKEGHSKSVVSQAENAQLDVIQQKLDALQQTVTLMLEDKMARE
                     AENRLRNEEREQLQAEISRLADALAQEKKRGFWSRLFRSGSE"
                     /name="entry exclusion protein 1"
     gene            complement(2407..2556)
                     /locus_tag="QL133_25585"
     CDS             complement(2407..2556)
                     /locus_tag="QL133_25585"
                     /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="WHJ86888.1"
                     /translation="MPSEYDEQLDSTDTQLPGEYDLFDLMAQVTEENLHAPVDFGSPVG
                     REAL"
                     /name="hypothetical protein"
     gene            3745..4560
                     /gene="sul2"
                     /locus_tag="QL133_25590"
     ARG             3746..4557
                     /name="sul2"
                     /gene="sul2"
                     /gene_name="sulfonamide-resistant dihydropteroate synthase
                     Sul2"
                     /tool="amrfinderplus"
                     /drug_class="SULFONAMIDE"
                     /identity="100.0"
                     /coverage="100.0"
     ARG             4667..5424
                     /name="APH(3'')-Ib"
                     /gene="APH(3'')-Ib"
                     /gene_name="APH(3'')"
                     /tool="rgi"
                     /drug_class="aminoglycoside antibiotic"
                     /identity="99.21"
                     /coverage="94.38"
     ARG             4622..5421
                     /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             5425..6200
                     /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="93.17"
     Typing          complement(2592..2765)
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="99.429"
                     /coverage="100.0"
                     /evalue="1.19e-84"
     Typing          2689..3294
                     /name="rep_cluster_2335"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="89.593"
                     /coverage="99.0"
                     /evalue="0.0"
ORIGIN
        1 gagcaacgcg atctagctat cgcggccgcg atcaagcagg tgcgacagac gtcatactag
       61 atatcaagcg acttctccta tcccctggga acacatcaat ctcaccggag aatatcgctg
      121 gccaaagcct tagcgtagga ttccgcccct tcccgcaaac gaccccaaac aggaaacgca
      181 gctgaaacgg gaagctcaac acccactgac gcatgggttg ttcaggcagt acttcatcaa
      241 ccagcaaggc ggcactttcg gccatccgcc gcgccccaca gctcgggcag aaaccgcgac
      301 gcttacagct gaaagcgacc aggtgctcgg cgtggcaaga ctcgcagcga acccgtagaa
      361 agccatgctc cagccgcccg cattggagaa attcttcaaa ttcccgttgc acatagcccg
      421 gcaattcctt tccctgctct gccataagcg cagcgaatgc cgggtaatac tcgtcaacga
      481 tctgatagag aagggtttgc tcgggtcggt ggctctggta acgaccagta tcccgatccc
      541 ggctggccgt cctggccgcc acatgaggca tgttccgcgt ccttgcaata ctgtgtttac
      601 atacagtcta tcgcttagcg gaaagttctt ttaccctcag ccgaaatgcc tgccgttgct
      661 agacattgcc agccagtgcc cgtcactccc actcttacat tgttcgcagt atctaggtac
      721 atgttattgc gtgcaccttc atgatgtata atgttattaa tgacagcaga aagatcgaca
      781 gaattaatat tcttcgtacc tgggacagtt atcgggtgtc ggccagtgat gagaccaaag
      841 gatgcagtat aagatgaacc actactatta tcatggccac cattaccacc accgttaaaa
      901 ctacctcccg aacttccaga gccgctatga ccatcattgt aggggtcatt tggtcccatg
      961 tgaccaaaac caccgacagt accgctattt aactctgtac tcataaaatt atcctctttg
     1021 acttttaaaa acagcaaaaa ctgtatttat aacaatgtgt ttatatacag tattcgaaat
     1081 actacgcccg tcaaaaccac accgtcaaca ggttttttgt gtatttttca cgcctcacgg
     1141 gcagcctcag accttttgtg ttaaaacagt aatatgttct gctgttacaa tacggtacac
     1201 acaggagaca ctgtcacttt tatggcatgg cacacagttc aagagacact gaaattaaca
     1261 ggaaagtcgc gctcgcaatt atatcgtgac atggctaaag gccttgtcag ctatcgcaca
     1321 ggaaaaaatg atcgccggga gttcgagacc agtgaactga ttcgggccta tggcgagctg
     1381 cgcacttctg agacaccaaa aaggcacaag gagggacact ccaaatctgt cgttagccag
     1441 gcggaaaatg ctcagctaga cgtcattcag cagaaactgg acgctctgca gcagactgtt
     1501 accctaatgc ttgaagacaa gatggcgcgg gaagcagaaa accgcctgcg aaatgaggag
     1561 agggaacaac tacaggccga aattagccgt ctggctgacg cgctggcaca ggaaaaaaag
     1621 cggggattct ggtcgcggct gtttcgctcc ggttcagagt aacagtgcag gtgactctga
     1681 tttaccataa catctgttat cagcaccgcc tgagaggccc tcagggcgtt tctgacggga
     1741 aaccggtaaa acaggcaaca aaccacccga aaacccgcca gaaacgcgca ggctctgttt
     1801 ttacggcatg catgagtatg cgcacaagtg catagcgcgg aaattcacac cattcagccg
     1861 gggtaagtcc tgtttccggc gttcttccca tccgaaaacg gtgaacgggg acgcaattta
     1921 ttgcgtggcc gtgaagcgtt gccggcgcag ccggaaaacc cgctgtcagc acgttcagga
     1981 agggggtgat gtacaaatgg cacagaggat gaaagtgacg tatgagctga aggaatgatg
     2041 taaaagtgat gtataagtga tgtaaaagtg atgtatgaac tgaaggagcg atgtaattct
     2101 gtagtcagga agaataaccc gttcatgcag gcatgaacga tacagtgagg aacgcttttt
     2161 ttgtcacgat ctccccttaa cctgcgtaaa tcacccgcca tggttgatta tttttcaacc
     2221 tcaaaatggt catacaccta acgcagccgc gattttcatc gcaactgcat gaattaaaag
     2281 aaaaaaaagg aatatttcgt tttcacgagt aatacccggg tattaaaaat ccactgtaat
     2341 tacatgaaaa taaagaaata aaaggtaata ccggagtatt accacgtacg cgggcaagcg
     2401 aaaaagctat aacgcttccc ggccgacagg cgacccaaaa tccacagggg catgcaggtt
     2461 ctcttcagta acctgcgcca ttaaatcaaa aaggtcatat tcgccgggaa gctgcgtatc
     2521 agtcgaatcc agttgttcat catattcaga tggcatgggg tgatatccag tagctgagag
     2581 gttgttagcg ggtttcgggg cgcagccctg aaccagtcat gtagcgctag cggagtgtat
     2641 actggcttac tatgttgcca cgattgcgaa aatcagtgaa gtgcttcatg tggcaggaga
     2701 aaaaaggcag caccggcgcg tcagcagaat atgcgataca ggagatattc cgcttcctcg
     2761 ctcactgact cgctacgctc ggtcgttcgg ctgcggcgag cggtaccggc ttacggacgg
     2821 ggacggaaat ttcctggaag ataccaggaa gacacttagc aaagaagaga taaggccacg
     2881 gcgaagccgt ttttccatag gctccgcccc cctgacaagc atcgcaaaat ctgacgctca
     2941 aatcagtggt ggcgaaaccc gacaggacta taaagatccc aggcgtttcc ccctggtagc
     3001 tccctcgtgc gctctcctgt tcctgccttt cggtttaccg gtgtcattcc gctgttatgg
     3061 ccgcggtttc tcattccacg cctgacactc agttccgtga aggcagttcg ctccaagctg
     3121 gactgtatgc acgaaccccc cgttcagtcc gaccgctgcg ccttgtccgg taactatcaa
     3181 cttgagtcca acccggaaag acacgacaaa acgccactgg cagcagccat tagtaacagg
     3241 agtgcacgag aagatagatt aagaggtctt gaagtagagg cctgactgcg gctacactga
     3301 aagaacagtt ttggtaatgg cggtctcgtg aaccctgtta ccgggttaag cagttcccca
     3361 actgacttaa ccttcgaaca aaccgcctcc ccaggcggtt ttttcgttta cagagcaaga
     3421 gattacgatt cattgaaaag gatctcaaga agatcctttg tagattacta tcaattaatc
     3481 ttccgaacat gacaccagtc actgttgatt acggttaaac cgctccgtaa caggtttccc
     3541 tcgtattggt gacttgcagc accaaagaag caaaaaagat aaatatatct acttattgag
     3601 agatgatata tttatttcca aaatgctaca gatacatcat catgaaacgg atcaccgcaa
     3661 acaggttact cgcctgggga ttccctttcg acccgagcat ccgtatgaga ctcatgctcg
     3721 attattatta ttatagaagc ccccatgaat aaatcgctca tcattttcgg catcgtcaac
     3781 ataacctcgg acagtttctc cgatggaggc cggtatctgg cgccagacgc agccattgcg
     3841 caggcgcgta agctgatggc cgagggggca gatgtgatcg acctcggtcc ggcatccagc
     3901 aatcccgacg ccgcgcctgt ttcgtccgac acagaaatcg cgcgtatcgc gccggtgctg
     3961 gacgcgctca aggcagatgg cattcccgtc tcgctcgaca gttatcaacc cgcgacgcaa
     4021 gcctatgcct tgtcgcgtgg tgtggcctat ctcaatgata ttcgcggttt tccagacgct
     4081 gcgttctatc cgcaattggc gaaatcatct gccaaactcg tcgttatgca ttcggtgcaa
     4141 gacgggcagg cagatcggcg cgaggcaccc gctggcgaca tcatggatca cattgcggcg
     4201 ttctttgacg cgcgcatcgc ggcgctgacg ggtgccggta tcaaacgcaa ccgccttgtc
     4261 cttgatcccg gcatggggtt ttttctgggg gctgctcccg aaacctcgct ctcggtgctg
     4321 gcgcggttcg atgaattgcg gctgcgcttc gatttgccgg tgcttctgtc tgtttcgcgc
     4381 aaatcctttc tgcgcgcgct cacaggccgt ggtccggggg atgtcggggc cgcgacactc
     4441 gctgcagagc ttgccgccgc cgcaggtgga gctgacttca tccgcacaca cgagccgcgc
     4501 cccttgcgcg acgggctggc ggtattggcg gcgctgaaag aaaccgcaag aattcgttaa
     4561 ctgcacattc gggatatttc tctatattcg cgcttcatca gaaaactgaa ggaacctcca
     4621 ttaaatcgaa ctaatatttt ttttggtgaa tcgcattctg actggttgcc tgtcagaggc
     4681 ggagaatctg gtgattttgt ttttcgacgt ggtgacgggc atgccttcgc gaaaatcgca
     4741 cctgcttccc gccgcggtga gctcgctgga gagcgtgacc gcctcatttg gctcaaaggt
     4801 cgaggtgtgg cttgccccga ggtcatcaac tggcaggagg aacaggaggg tgcatgcttg
     4861 gtgataacgg caattccggg agtaccggcg gctgatctgt ctggagcgga tttgctcaaa
     4921 gcgtggccgt caatggggca gcaacttggc gctgttcaca gcctatcggt tgatcaatgt
     4981 ccgtttgagc gcaggctgtc gcgaatgttc ggacgcgccg ttgatgtggt gtcccgcaat
     5041 gccgtcaatc ccgacttctt accggacgag gacaagagta cgccgcagct cgatcttttg
     5101 gctcgtgtcg aacgagagct accggtgcgg ctcgaccaag agcgcaccga tatggttgtt
     5161 tgccatggtg atccctgcat gccgaacttc atggtggacc ctaaaactct tcaatgcacg
     5221 ggtctgatcg accttgggcg gctcggaaca gcagatcgct atgccgattt ggcactcatg
     5281 attgctaacg ccgaagagaa ctgggcagcg ccagatgaag cagagcgcgc cttcgctgtc
     5341 ctattcaatg tattggggat cgaagccccc gaccgcgaac gccttgcctt ctatctgcga
     5401 ttggaccctc tgacttgggg ttgatgttca tgccgcctgt ttttcctgct cattggcacg
     5461 tttcgcaacc tgttctcatt gcggacacct tttccagcct cgtttggaaa gtttcattgc
     5521 cagacgggac tcctgcaatc gtcaagggat tgaaacctat agaagacatt gctgatgaac
     5581 tgcgcggggc cgactatctg gtatggcgca atgggagggg agcagtccgg ttgctcggtc
     5641 gtgagaacaa tctgatgttg ctcgaatatg ccggggagcg aatgctctct cacatcgttg
     5701 ccgagcacgg cgactaccag gcgaccgaaa ttgcagcgga actaatggcg aagctgtatg
     5761 ccgcatctga ggaacccctg ccttctgccc ttctcccgat ccgggatcgc tttgcagctt
     5821 tgtttcagcg ggcgcgcgat gatcaaaacg caggttgtca aactgactac gtccacgcgg
     5881 cgattatagc cgatcaaatg atgagcaatg cctcggaact gcgtgggcta catggcgatc
     5941 tgcatcatga aaacatcatg ttctccagtc gcggctggct ggtgatagat cccgtcggtc
     6001 tggtcggtga agtgggcttt ggcgccgcca atatgttcta cgatccggct gacagagacg
     6061 acctttgtct cgatcctaga cgcattgcac agatggcgga cgcattctct cgtgcgctgg
     6121 acgtcgatcc gcgtcgcctg ctcgaccagg cgtacgctta tgggtgcctt tccgcagctt
     6181 ggaacgcgga tggagaagag
//
