LOCUS       CP125041                6200 bp    DNA     circular BCT 16-MAY-2023
DEFINITION  Escherichia coli strain KFS-D01 plasmid pKFS-D01_2, complete
            sequence.
ACCESSION   CP125041
VERSION     CP125041.1
DBLINK      BioProject: PRJNA956323
            BioSample: SAMN34598744
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  JOURNAL   Unpublished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 17:05:00
            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)                     :: 4,733
            CDSs (total)                      :: 4,610
            Genes (coding)                    :: 4,397
            CDSs (with protein)               :: 4,397
            Genes (RNA)                       :: 123
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 88
            ncRNAs                            :: 13
            Pseudo Genes (total)              :: 213
            CDSs (without protein)            :: 213
            Pseudo Genes (ambiguous residues) :: 0 of 213
            Pseudo Genes (frameshifted)       :: 72 of 213
            Pseudo Genes (incomplete)         :: 141 of 213
            Pseudo Genes (internal stop)      :: 39 of 213
            Pseudo Genes (multiple problems)  :: 38 of 213
            Pseudo Genes (short protein)      :: 4 of 213
            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="KFS-D01"
                     /isolation_source="Fecal sludge"
                     /db_xref="taxon:562"
                     /plasmid="pKFS-D01_2"
                     /geo_loc_name="Uganda"
                     /lat_lon="0.19 N 32.35 E"
                     /collection_date="2018"
                     /collected_by="Hidenori Harada, Mai Tanaka"
     gene            372..521
                     /locus_tag="QL140_23600"
     CDS             372..521
                     /locus_tag="QL140_23600"
                     /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="WHJ49805.1"
                     /translation="MPSEYDEQLDSTDTQLPGEYDLFDLMAQVTEENLHAPVDFGSPVG
                     REAL"
                     /name="hypothetical protein"
     gene            complement(1266..1706)
                     /locus_tag="QL140_23605"
     CDS             complement(1266..1706)
                     /locus_tag="QL140_23605"
                     /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="WHJ49806.1"
                     /translation="MAWHTVQETLKLTGKSRSQLYRDMAKGLVSYRTGKNDRREFETSE
                     LIRAYGELRTSETPKRHKEGHSKSVVSQAENAQLDVIQQKLDALQQTVTLMLEDKMARE
                     AENRLRNEEREQLQAEISRLADALAQEKKRGFWSRLFRSGSE"
                     /name="entry exclusion protein 1"
     gene            1924..2313
                     /locus_tag="QL140_23610"
     CDS             1924..2313
                     /locus_tag="QL140_23610"
                     /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="WHJ49807.1"
                     /translation="MSTELNSGTVGGFGHMGPNDPYNDGHSGSGSSGGSFNGGGNGGHD
                     NSSGSSYTASFGLITGRHPITVPGTKNINSVDLSAVINNIIHHEGARNNMYLDTANNVR
                     VGVTGTGWQCLATAGISAEGKRTFR"
                     /name="hypothetical protein"
     gene            2357..2761
                     /locus_tag="QL140_23615"
                     /pseudo=""
     CDS             2357..2761
                     /locus_tag="QL140_23615"
                     /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(2868..3704)
                     /locus_tag="QL140_23620"
     CDS             complement(2868..3704)
                     /locus_tag="QL140_23620"
                     /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="WHJ49808.1"
                     /translation="MFMPPVFPAHWHVSQPVLIADTFSSLVWKVSLPDGTPAIVKGLKP
                     IEDIADELRGADYLVWRNGRGAVRLLGRENNLMLLEYAGERMLSHIVAEHGDYQATEIA
                     AELMAKLYAASEEPLPSALLPIRDRFAALFQRARDDQNAGCQTDYVHAAIIADQMMSNA
                     SELRGLHGDLHHENIMFSSRGWLVIDPVGLVGEVGFGAANMFYDPADRDDLCLDPRRIA
                     QMADAFSRALDVDPRRLLDQAYAYGCLSAAWNADGEEEQRDLAIAAAIKQVRQTSY"
                     /name="aminoglycoside O-phosphotransferase APH(6)-Id"
     gene            complement(3704..4507)
                     /gene="aph(3'')-Ib"
                     /locus_tag="QL140_23625"
     ARG             complement(3708..4507)
                     /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            complement(4568..5383)
                     /gene="sul2"
                     /locus_tag="QL140_23630"
     ARG             complement(4572..5383)
                     /name="sul2"
                     /gene="sul2"
                     /gene_name="sulfonamide-resistant dihydropteroate synthase
                     Sul2"
                     /tool="amrfinderplus"
                     /drug_class="SULFONAMIDE"
                     /identity="100.0"
                     /coverage="100.0"
     ARG             complement(2872..3704)
                     /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          164..337
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="99.429"
                     /coverage="100.0"
                     /evalue="1.19e-84"
     Typing          complement(2..197)
                     /name="rep_cluster_2335"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="91.371"
                     /coverage="99.0"
                     /evalue="4.15e-69"
     Typing          complement(5894..6200)
                     /name="rep_cluster_2373"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="96.764"
                     /coverage="85.0"
                     /evalue="3.9e-143"
ORIGIN
        1 ttgcgatgct tgtcaggggg gcggagccta tggaaaaacg gcttcgccgt ggccttatct
       61 cttctttgct aagtgtcttc ctggtatctt ccaggaaatt tccgtccccg tccgtaagcc
      121 ggtaccgctc gccgcagccg aacgaccgag cgtagcgagt cagtgagcga ggaagcggaa
      181 tatctcctgt atcgcatatt ctgctgacgc gccggtgctg ccttttttct cctgccacat
      241 gaagcacttc actgattttc gcaatcgtgg caacatagta agccagtata cactccgcta
      301 gcgctacatg actggttcag ggctgcgccc cgaaacccgc taacaacctc tcagctactg
      361 gatatcaccc catgccatct gaatatgatg aacaactgga ttcgactgat acgcagcttc
      421 ccggcgaata tgaccttttt gatttaatgg cgcaggttac tgaagagaac ctgcatgccc
      481 ctgtggattt tgggtcgcct gtcggccggg aagcgttata gctttttcgc ttgcccgcgt
      541 acgtggtaat actccggtat taccttttat ttctttattt tcatgtaatt acagtggatt
      601 tttaataccc gggtattact cgtgaaaacg aaatattcct tttttttctt ttaattcatg
      661 cagttgcgat gaaaatcgcg gctgcgttag gtgtatgacc attttgaggt tgaaaaataa
      721 tcaaccatgg cgggtgattt acgcaggtta aggggagatc gtgacaaaaa aagcgttcct
      781 cactgtatcg ttcatgcctg catgaacggg ttattcttcc tgactacaga attacatcgc
      841 tccttcagtt catacatcac ttttacatca cttatacatc acttttacat cattccttca
      901 gctcatacgt cactttcatc ctctgtgcca tttgtacatc acccccttcc tgaacgtgct
      961 gacagcgggt tttccggctg cgccggcaac gcttcacggc cacgcaataa attgcgtccc
     1021 cgttcaccgt tttcggatgg gaagaacgcc ggaaacagga cttaccccgg ctgaatggtg
     1081 tgaatttccg cgctatgcac ttgtgcgcat actcatgcat gccgtaaaaa cagagcctgc
     1141 gcgtttctgg cgggttttcg ggtggtttgt tgcctgtttt accggtttcc cgtcagaaac
     1201 gccctgaggg cctctcaggc ggtgctgata acagatgtta tggtaaatca gagtcacctg
     1261 cactgttact ctgaaccgga gcgaaacagc cgcgaccaga atccccgctt tttttcctgt
     1321 gccagcgcgt cagccagacg gctaatttcg gcctgtagtt gttccctctc ctcatttcgc
     1381 aggcggtttt ctgcttcccg cgccatcttg tcttcaagca ttagggtaac agtctgctgc
     1441 agagcgtcca gtttctgctg aatgacgtct agctgagcat tttccgcctg gctaacgaca
     1501 gatttggagt gtccctcctt gtgccttttt ggtgtctcag aagtgcgcag ctcgccatag
     1561 gcccgaatca gttcactggt ctcgaactcc cggcgatcat tttttcctgt gcgatagctg
     1621 acaaggcctt tagccatgtc acgatataat tgcgagcgcg actttcctgt taatttcagt
     1681 gtctcttgaa ctgtgtgcca tgccataaaa gtgacagtgt ctcctgtgtg taccgtattg
     1741 taacagcaga acatattact gttttaacac aaaaggtctg aggctgcccg tgaggcgtga
     1801 aaaatacaca aaaaacctgt tgacggtgtg gttttgacgg gcgtagtatt tcgaatactg
     1861 tatataaaca cattgttata aatacagttt ttgctgtttt taaaagtcaa agaggataat
     1921 tttatgagta cagagttaaa tagcggtact gtcggtggtt ttggtcacat gggaccaaat
     1981 gacccctaca atgatggtca tagcggctct ggaagttcgg gaggtagttt taacggtggt
     2041 ggtaatggtg gccatgataa tagtagtggt tcatcttata ctgcatcctt tggtctcatc
     2101 actggccgac acccgataac tgtcccaggt acgaagaata ttaattctgt cgatctttct
     2161 gctgtcatta ataacattat acatcatgaa ggtgcacgca ataacatgta cctagatact
     2221 gcgaacaatg taagagtggg agtgacgggc actggctggc aatgtctagc aacggcaggc
     2281 atttcggctg agggtaaaag aactttccgc taagcgatag actgtatgta aacacagtat
     2341 tgcaaggacg cggaacatgc ctcatgtggc ggccaggacg gccagccggg atcgggatac
     2401 tggtcgttac cagagccacc gacccgagca aacccttctc tatcagatcg ttgacgagta
     2461 ttacccggca ttcgctgcgc ttatggcaga gcagggaaag gaattgccgg gctatgtgca
     2521 acgggaattt gaagaatttc tccaatgcgg gcggctggag catggctttc tacgggttcg
     2581 ctgcgagtct tgccacgccg agcacctggt cgctttcagc tgtaagcgtc gcggtttctg
     2641 cccgagctgt ggggcgcggc ggatggccga aagtgccgcc ttgctggttg atgaagtact
     2701 gcctgaacaa cccatgcgtc agtgggtgtt gagcttcccg tttcagctgc gtttcctgtt
     2761 tggggtcgtt tgcgggaagg ggcggaatcc tacgctaagg ctttggccag cgatattctc
     2821 cggtgagatt gatgtgttcc caggggatag gagaagtcgc ttgatatcta gtatgacgtc
     2881 tgtcgcacct gcttgatcgc ggccgcgata gctagatcgc gttgctcctc ttctccatcc
     2941 gcgttccaag ctgcggaaag gcacccataa gcgtacgcct ggtcgagcag gcgacgcgga
     3001 tcgacgtcca gcgcacgaga gaatgcgtcc gccatctgtg caatgcgtct aggatcgaga
     3061 caaaggtcgt ctctgtcagc cggatcgtag aacatattgg cggcgccaaa gcccacttca
     3121 ccgaccagac cgacgggatc tatcaccagc cagccgcgac tggagaacat gatgttttca
     3181 tgatgcagat cgccatgtag cccacgcagt tccgaggcat tgctcatcat ttgatcggct
     3241 ataatcgccg cgtggacgta gtcagtttga caacctgcgt tttgatcatc gcgcgcccgc
     3301 tgaaacaaag ctgcaaagcg atcccggatc gggagaaggg cagaaggcag gggttcctca
     3361 gatgcggcat acagcttcgc cattagttcc gctgcaattt cggtcgcctg gtagtcgccg
     3421 tgctcggcaa cgatgtgaga gagcattcgc tccccggcat attcgagcaa catcagattg
     3481 ttctcacgac cgagcaaccg gactgctccc ctcccattgc gccataccag atagtcggcc
     3541 ccgcgcagtt catcagcaat gtcttctata ggtttcaatc ccttgacgat tgcaggagtc
     3601 ccgtctggca atgaaacttt ccaaacgagg ctggaaaagg tgtccgcaat gagaacaggt
     3661 tgcgaaacgt gccaatgagc aggaaaaaca ggcggcatga acatcaaccc caagtcagag
     3721 ggtccaatcg cagatagaag gcaaggcgtt cgcggtcggg ggcttcgatc cccaatacat
     3781 tgaataggac agcgaaggcg cgctctgctt catctggcgc tgcccagttc tcttcggcgt
     3841 tagcaatcat gagtgccaaa tcggcatagc gatctgctgt tccgagccgc ccaaggtcga
     3901 tcagacccgt gcattgaaga gttttagggt ccaccatgaa gttcggcatg cagggatcac
     3961 catggcaaac aaccatatcg gtgcgctctt ggtcgagccg caccggtagc tctcgttcga
     4021 cacgagccaa aagatcgagc tgcggcgtac tcttgtcctc gtccggtaag aagtcgggat
     4081 tgacggcatt gcgggacacc acatcaacgg cgcgtccgaa cattcgcgac agcctgcgct
     4141 caaacggaca ttgatcaacc gataggctgt gaacagcgcc aagttgctgc cccattgacg
     4201 gccacgcttt gagcaaatcc gctccagaca gatcagccgc cggtactccc ggaattgccg
     4261 ttatcaccaa gcatgcaccc tcctgttcct cctgccagtt gatgacctcg gggcaagcca
     4321 cacctcgacc tttgagccaa atgaggcggt cacgctctcc agcgagctca ccgcggcggg
     4381 aagcaggtgc gattttcgcg aaggcatgcc cgtcaccacg tcgaaaaaca aaatcaccag
     4441 attctccgcc tctgacaggc aaccagtcag aatgcgattc accaaaaaaa atattagttc
     4501 gattcaatgg aggttccttc agttttctga tgaagcgcga atatagagaa atatcccgaa
     4561 tgtgcagtta acgaattctt gcggtttctt tcagcgccgc caataccgcc agcccgtcgc
     4621 gcaaggggcg cggctcgtgt gtgcggatga agtcagctcc acctgcggcg gcggcaagct
     4681 ctgcagcgag tgtcgcggcc ccgacatccc ccggaccacg gcctgtgagc gcgcgcagaa
     4741 aggatttgcg cgaaacagac agaagcaccg gcaaatcgaa gcgcagccgc aattcatcga
     4801 accgcgccag caccgagagc gaggtttcgg gagcagcccc cagaaaaaac cccatgccgg
     4861 gatcaaggac aaggcggttg cgtttgatac cggcacccgt cagcgccgcg atgcgcgcgt
     4921 caaagaacgc cgcaatgtga tccatgatgt cgccagcggg tgcctcgcgc cgatctgcct
     4981 gcccgtcttg caccgaatgc ataacgacga gtttggcaga tgatttcgcc aattgcggat
     5041 agaacgcagc gtctggaaaa ccgcgaatat cattgagata ggccacacca cgcgacaagg
     5101 cataggcttg cgtcgcgggt tgataactgt cgagcgagac gggaatgcca tctgccttga
     5161 gcgcgtccag caccggcgcg atacgcgcga tttctgtgtc ggacgaaaca ggcgcggcgt
     5221 cgggattgct ggatgccgga ccgaggtcga tcacatctgc cccctcggcc atcagcttac
     5281 gcgcctgcgc aatggctgcg tctggcgcca gataccggcc tccatcggag aaactgtccg
     5341 aggttatgtt gacgatgccg aaaatgatga gcgatttatt catgggggct tctataataa
     5401 taataatcga gcatgagtct catacggatg ctcgggtcga aagggaatcc ccaggcgagt
     5461 aacctgtttg cggtgatccg tttcatgatg atgtatctgt agcattttgg aaataaatat
     5521 atcatctctc aataagtaga tatatttatc ttttttgctt ctttggtgct gcaagtcacc
     5581 aatacgaggg aaacctgtta cggagcggtt taaccgtaat caacagtgac tggtgtcatg
     5641 ttcggaagat taattgatag taatctacaa aggatcttct tgagatcctt ttcaatgaat
     5701 cgtaatctct tgctctgtaa acgaaaaaac cgcctgggga ggcggtttgt tcgaaggtta
     5761 agtcagttgg ggaactgctt aacccggtaa cagggttcac gagaccgcca ttaccaaaac
     5821 tgttctttca gtgtagccgc agtcaggcct ctacttcaag acctcttaat ctatcttctc
     5881 gtgcactcct gttactaatg gctgctgcca gtggcgtttt gtcgtgtctt tccgggttgg
     5941 actcaagttg atagttaccg gacaaggcgc agcggtcgga ctgaacgggg ggttcgtgca
     6001 tacagtccag cttggagcga actgccttca cggaactgag tgtcaggcgt ggaatgagaa
     6061 accgcggcca taacagcgga atgacaccgg taaaccgaaa ggcaggaaca ggagagcgca
     6121 cgagggagct accaggggga aacgcctggg atctttatag tcctgtcggg tttcgccacc
     6181 actgatttga gcgtcagatt
//
