LOCUS       CP125063                6200 bp    DNA     circular BCT 16-MAY-2023
DEFINITION  Escherichia coli strain KFS-B43 plasmid pKFS-B43_3, complete
            sequence.
ACCESSION   CP125063
VERSION     CP125063.1
DBLINK      BioProject: PRJNA956323
            BioSample: SAMN34598741
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  JOURNAL   Unpublished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 16:29:33
            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)                     :: 4,819
            CDSs (total)                      :: 4,697
            Genes (coding)                    :: 4,451
            CDSs (with protein)               :: 4,451
            Genes (RNA)                       :: 122
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 87
            ncRNAs                            :: 13
            Pseudo Genes (total)              :: 246
            CDSs (without protein)            :: 246
            Pseudo Genes (ambiguous residues) :: 0 of 246
            Pseudo Genes (frameshifted)       :: 71 of 246
            Pseudo Genes (incomplete)         :: 173 of 246
            Pseudo Genes (internal stop)      :: 46 of 246
            Pseudo Genes (multiple problems)  :: 46 of 246
            Pseudo Genes (short protein)      :: 4 of 246
            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-B43"
                     /isolation_source="Fecal sludge"
                     /db_xref="taxon:562"
                     /plasmid="pKFS-B43_3"
                     /geo_loc_name="Uganda"
                     /lat_lon="0.19 N 32.35 E"
                     /collection_date="2018"
                     /collected_by="Hidenori Harada, Mai Tanaka"
     gene            complement(join(5503..6200,1..133))
                     /locus_tag="QL135_24065"
     CDS             complement(join(5503..6200,1..133))
                     /locus_tag="QL135_24065"
                     /inference="COORDINATES: ab initio prediction:GeneMarkS-2+"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GeneMarkS-2+."
                     /codon_start=1
                     /transl_table=11
                     /product="APH(6)-I family aminoglycoside
                     O-phosphotransferase"
                     /protein_id="WHJ95986.1"
                     /translation="MPPVFPAHWHVSQPVLIADTFSSLVWKVSLPDGTPAIVKGLKPIE
                     DIADELRGADYLVWRNGRGAVRLLGRENNLMLLEYAGERMLSHIVAEHGDYQATEIAAE
                     LMAKLYAASEEPLPSALLPIRDRFAALFQRARDDQNAGCQTDYVHAAIIADQMMSNASE
                     LRGLHGDLHHENIMFSSRGWLVIDPVGLVGEVGFGAANMFYDPADRDDLCLDPRRIAQM
                     ADAFSRALDVDPRRLLDQAYAYGCLSAAWNADGEEEQRDLAIAAAIKQVRQTSY"
                     /name="APH(6)-I family aminoglycoside O-phosphotransferase"
     ARG             complement(140..897)
                     /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             complement(143..942)
                     /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(1003..1818)
                     /gene="sul2"
                     /locus_tag="QL135_24075"
     ARG             complement(1007..1818)
                     /name="sul2"
                     /gene="sul2"
                     /gene_name="sulfonamide-resistant dihydropteroate synthase
                     Sul2"
                     /tool="amrfinderplus"
                     /drug_class="SULFONAMIDE"
                     /identity="100.0"
                     /coverage="100.0"
     gene            3007..3156
                     /locus_tag="QL135_24080"
     CDS             3007..3156
                     /locus_tag="QL135_24080"
                     /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="WHJ95988.1"
                     /translation="MPSEYDEQLDSTDTQLPGEYDLFDLMAQVTEENLHAPVDFGSPVG
                     REAL"
                     /name="hypothetical protein"
     gene            complement(3901..4341)
                     /locus_tag="QL135_24085"
     CDS             complement(3901..4341)
                     /locus_tag="QL135_24085"
                     /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="WHJ95984.1"
                     /translation="MAWHTVQETLKLTGKSRSQLYRDMAKGLVSYRTGKNDRREFETSE
                     LIRAYGELRTSETPKRHKEGHSKSVVSQAENAQLDVIQQKLDALQQTVTLMLEDKMARE
                     AENRLRNEEREQLQAEISRLADALAQEKKRGFWSRLFRSGSE"
                     /name="entry exclusion protein 1"
     gene            4559..4948
                     /locus_tag="QL135_24090"
     CDS             4559..4948
                     /locus_tag="QL135_24090"
                     /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="WHJ95985.1"
                     /translation="MSTELNSGTVGGFGHMGPNDPYNDGHSGSGSSGGSFNGGGNGGHD
                     NSSGSSYTASFGLITGRHPITVPGTKNINSVDLSAVINNIIHHEGARNNMYLDTANNVR
                     VGVTGTGWQCLATAGISAEGKRTFR"
                     /name="hypothetical protein"
     gene            4992..5396
                     /locus_tag="QL135_24095"
                     /pseudo=""
     CDS             4992..5396
                     /locus_tag="QL135_24095"
                     /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"
     ARG             complement(5504..6198)
                     /name="APH(6)-Id"
                     /gene="APH(6)-Id"
                     /gene_name="APH(6)"
                     /tool="rgi"
                     /drug_class="aminoglycoside antibiotic"
                     /identity="99.57"
                     /coverage="83.09"
     Typing          2799..2972
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="99.429"
                     /coverage="100.0"
                     /evalue="1.19e-84"
     Typing          complement(2270..2875)
                     /name="rep_cluster_2335"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="89.593"
                     /coverage="99.0"
                     /evalue="0.0"
ORIGIN
        1 ctataggttt caatcccttg acgattgcag gagtcccgtc tggcaatgaa actttccaaa
       61 cgaggctgga aaaggtgtcc gcaatgagaa caggttgcga aacgtgccaa tgagcaggaa
      121 aaacaggcgg catgaacatc aaccccaagt cagagggtcc aatcgcagat agaaggcaag
      181 gcgttcgcgg tcgggggctt cgatccccaa tacattgaat aggacagcga aggcgcgctc
      241 tgcttcatct ggcgctgccc agttctcttc ggcgttagca atcatgagtg ccaaatcggc
      301 atagcgatct gctgttccga gccgcccaag gtcgatcaga cccgtgcatt gaagagtttt
      361 agggtccacc atgaagttcg gcatgcaggg atcaccatgg caaacaacca tatcggtgcg
      421 ctcttggtcg agccgcaccg gtagctctcg ttcgacacga gccaaaagat cgagctgcgg
      481 cgtactcttg tcctcgtccg gtaagaagtc gggattgacg gcattgcggg acaccacatc
      541 aacggcgcgt ccgaacattc gcgacagcct gcgctcaaac ggacattgat caaccgatag
      601 gctgtgaaca gcgccaagtt gctgccccat tgacggccac gctttgagca aatccgctcc
      661 agacagatca gccgccggta ctcccggaat tgccgttatc accaagcatg caccctcctg
      721 ttcctcctgc cagttgatga cctcggggca agccacacct cgacctttga gccaaatgag
      781 gcggtcacgc tctccagcga gctcaccgcg gcgggaagca ggtgcgattt tcgcgaaggc
      841 atgcccgtca ccacgtcgaa aaacaaaatc accagattct ccgcctctga caggcaacca
      901 gtcagaatgc gattcaccaa aaaaaatatt agttcgattt aatggaggtt ccttcagttt
      961 tctgatgaag cgcgaatata gagaaatatc ccgaatgtgc agttaacgaa ttcttgcggt
     1021 ttctttcagc gccgccaata ccgccagccc gtcgcgcaag gggcgcggct cgtgtgtgcg
     1081 gatgaagtca gctccacctg cggcggcggc aagctctgca gcgagtgtcg cggccccgac
     1141 atcccccgga ccacggcctg tgagcgcgcg cagaaaggat ttgcgcgaaa cagacagaag
     1201 caccggcaaa tcgaagcgca gccgcaattc atcgaaccgc gccagcaccg agagcgaggt
     1261 ttcgggagca gcccccagaa aaaaccccat gccgggatca aggacaaggc ggttgcgttt
     1321 gataccggca cccgtcagcg ccgcgatgcg cgcgtcaaag aacgccgcaa tgtgatccat
     1381 gatgtcgcca gcgggtgcct cgcgccgatc tgcctgcccg tcttgcaccg aatgcataac
     1441 gacgagtttg gcagatgatt tcgccaattg cggatagaac gcagcgtctg gaaaaccgcg
     1501 aatatcattg agataggcca caccacgcga caaggcatag gcttgcgtcg cgggttgata
     1561 actgtcgagc gagacgggaa tgccatctgc cttgagcgcg tccagcaccg gcgcgatacg
     1621 cgcgatttct gtgtcggacg aaacaggcgc ggcgtcggga ttgctggatg ccggaccgag
     1681 gtcgatcaca tctgccccct cggccatcag cttacgcgcc tgcgcaatgg ctgcgtctgg
     1741 cgccagatac cggcctccat cggagaaact gtccgaggtt atgttgacga tgccgaaaat
     1801 gatgagcgat ttattcatgg gggcttctat aataataata atcgagcatg agtctcatac
     1861 ggatgctcgg gtcgaaaggg aatccccagg cgagtaacct gtttgcggtg atccgtttca
     1921 tgatgatgta tctgtagcat tttggaaata aatatatcat ctctcaataa gtagatatat
     1981 ttatcttttt tgcttctttg gtgctgcaag tcaccaatac gagggaaacc tgttacggag
     2041 cggtttaacc gtaatcaaca gtgactggtg tcatgttcgg aagattaatt gatagtaatc
     2101 tacaaaggat cttcttgaga tccttttcaa tgaatcgtaa tctcttgctc tgtaaacgaa
     2161 aaaaccgcct ggggaggcgg tttgttcgaa ggttaagtca gttggggaac tgcttaaccc
     2221 ggtaacaggg ttcacgagac cgccattacc aaaactgttc tttcagtgta gccgcagtca
     2281 ggcctctact tcaagacctc ttaatctatc ttctcgtgca ctcctgttac taatggctgc
     2341 tgccagtggc gttttgtcgt gtctttccgg gttggactca agttgatagt taccggacaa
     2401 ggcgcagcgg tcggactgaa cggggggttc gtgcatacag tccagcttgg agcgaactgc
     2461 cttcacggaa ctgagtgtca ggcgtggaat gagaaaccgc ggccataaca gcggaatgac
     2521 accggtaaac cgaaaggcag gaacaggaga gcgcacgagg gagctaccag ggggaaacgc
     2581 ctgggatctt tatagtcctg tcgggtttcg ccaccactga tttgagcgtc agattttgcg
     2641 atgcttgtca ggggggcgga gcctatggaa aaacggcttc gccgtggcct tatctcttct
     2701 ttgctaagtg tcttcctggt atcttccagg aaatttccgt ccccgtccgt aagccggtac
     2761 cgctcgccgc agccgaacga ccgagcgtag cgagtcagtg agcgaggaag cggaatatct
     2821 cctgtatcgc atattctgct gacgcgccgg tgctgccttt tttctcctgc cacatgaagc
     2881 acttcactga ttttcgcaat cgtggcaaca tagtaagcca gtatacactc cgctagcgct
     2941 acatgactgg ttcagggctg cgccccgaaa cccgctaaca acctctcagc tactggatat
     3001 caccccatgc catctgaata tgatgaacaa ctggattcga ctgatacgca gcttcccggc
     3061 gaatatgacc tttttgattt aatggcgcag gttactgaag agaacctgca tgcccctgtg
     3121 gattttgggt cgcctgtcgg ccgggaagcg ttatagcttt ttcgcttgcc cgcgtacgtg
     3181 gtaatactcc ggtattacct tttatttctt tattttcatg taattacagt ggatttttaa
     3241 tacccgggta ttactcgtga aaacgaaata ttcctttttt ttcttttaat tcatgcagtt
     3301 gcgatgaaaa tcgcggctgc gttaggtgta tgaccatttt gaggttgaaa aataatcaac
     3361 catggcgggt gatttacgca ggttaagggg agatcgtgac aaaaaaagcg ttcctcactg
     3421 tatcgttcat gcctgcatga acgggttatt cttcctgact acagaattac atcgctcctt
     3481 cagttcatac atcactttta catcacttat acatcacttt tacatcattc cttcagctca
     3541 tacgtcactt tcatcctctg tgccatttgt acatcacccc cttcctgaac gtgctgacag
     3601 cgggttttcc ggctgcgccg gcaacgcttc acggccacgc aataaattgc gtccccgttc
     3661 accgttttcg gatgggaaga acgccggaaa caggacttac cccggctgaa tggtgtgaat
     3721 ttccgcgcta tgcacttgtg cgcatactca tgcatgccgt aaaaacagag cctgcgcgtt
     3781 tctggcgggt tttcgggtgg tttgttgcct gttttaccgg tttcccgtca gaaacgccct
     3841 gagggcctct caggcggtgc tgataacaga tgttatggta aatcagagtc acctgcactg
     3901 ttactctgaa ccggagcgaa acagccgcga ccagaatccc cgcttttttt cctgtgccag
     3961 cgcgtcagcc agacggctaa tttcggcctg tagttgttcc ctctcctcat ttcgcaggcg
     4021 gttttctgct tcccgcgcca tcttgtcttc aagcattagg gtaacagtct gctgcagagc
     4081 gtccagtttc tgctgaatga cgtctagctg agcattttcc gcctggctaa cgacagattt
     4141 ggagtgtccc tccttgtgcc tttttggtgt ctcagaagtg cgcagctcgc cataggcccg
     4201 aatcagttca ctggtctcga actcccggcg atcatttttt cctgtgcgat agctgacaag
     4261 gcctttagcc atgtcacgat ataattgcga gcgcgacttt cctgttaatt tcagtgtctc
     4321 ttgaactgtg tgccatgcca taaaagtgac agtgtctcct gtgtgtaccg tattgtaaca
     4381 gcagaacata ttactgtttt aacacaaaag gtctgaggct gcccgtgagg cgtgaaaaat
     4441 acacaaaaaa cctgttgacg gtgtggtttt gacgggcgta gtatttcgaa tactgtatat
     4501 aaacacattg ttataaatac agtttttgct gtttttaaaa gtcaaagagg ataattttat
     4561 gagtacagag ttaaatagcg gtactgtcgg tggttttggt cacatgggac caaatgaccc
     4621 ctacaatgat ggtcatagcg gctctggaag ttcgggaggt agttttaacg gtggtggtaa
     4681 tggtggccat gataatagta gtggttcatc ttatactgca tcctttggtc tcatcactgg
     4741 ccgacacccg ataactgtcc caggtacgaa gaatattaat tctgtcgatc tttctgctgt
     4801 cattaataac attatacatc atgaaggtgc acgcaataac atgtacctag atactgcgaa
     4861 caatgtaaga gtgggagtga cgggcactgg ctggcaatgt ctagcaacgg caggcatttc
     4921 ggctgagggt aaaagaactt tccgctaagc gatagactgt atgtaaacac agtattgcaa
     4981 ggacgcggaa catgcctcat gtggcggcca ggacggccag ccgggatcgg gatactggtc
     5041 gttaccagag ccaccgaccc gagcaaaccc ttctctatca gatcgttgac gagtattacc
     5101 cggcattcgc tgcgcttatg gcagagcagg gaaaggaatt gccgggctat gtgcaacggg
     5161 aatttgaaga atttctccaa tgcgggcggc tggagcatgg ctttctacgg gttcgctgcg
     5221 agtcttgcca cgccgagcac ctggtcgctt tcagctgtaa gcgtcgcggt ttctgcccga
     5281 gctgtggggc gcggcggatg gccgaaagtg ccgccttgct ggttgatgaa gtactgcctg
     5341 aacaacccat gcgtcagtgg gtgttgagct tcccgtttca gctgcgtttc ctgtttgggg
     5401 tcgtttgcgg gaaggggcgg aatcctacgc taaggctttg gccagcgata ttctccggtg
     5461 agattgatgt gttcccaggg gataggagaa gtcgcttgat atctagtatg acgtctgtcg
     5521 cacctgcttg atcgcggccg cgatagctag atcgcgttgc tcctcttctc catccgcgtt
     5581 ccaagctgcg gaaaggcacc cataagcgta cgcctggtcg agcaggcgac gcggatcgac
     5641 gtccagcgca cgagagaatg cgtccgccat ctgtgcaatg cgtctaggat cgagacaaag
     5701 gtcgtctctg tcagccggat cgtagaacat attggcggcg ccaaagccca cttcaccgac
     5761 cagaccgacg ggatctatca ccagccagcc gcgactggag aacatgatgt tttcatgatg
     5821 cagatcgcca tgtagcccac gcagttccga ggcattgctc atcatttgat cggctataat
     5881 cgccgcgtgg acgtagtcag tttgacaacc tgcgttttga tcatcgcgcg cccgctgaaa
     5941 caaagctgca aagcgatccc ggatcgggag aagggcagaa ggcaggggtt cctcagatgc
     6001 ggcatacagc ttcgccatta gttccgctgc aatttcggtc gcctggtagt cgccgtgctc
     6061 ggcaacgatg tgagagagca ttcgctcccc ggcatattcg agcaacatca gattgttctc
     6121 acgaccgagc aaccggactg ctcccctccc attgcgccat accagatagt cggccccgcg
     6181 cagttcatca gcaatgtctt
//
