LOCUS       CP125043                2871 bp    DNA     circular BCT 16-MAY-2023
DEFINITION  Escherichia coli strain KFS-D01 plasmid pKFS-D01_4, complete
            sequence.
ACCESSION   CP125043
VERSION     CP125043.1
DBLINK      BioProject: PRJNA956323
            BioSample: SAMN34598744
KEYWORDS    .
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 2871)
  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  JOURNAL   Unpublished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 2871)
  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..2871
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="KFS-D01"
                     /isolation_source="Fecal sludge"
                     /db_xref="taxon:562"
                     /plasmid="pKFS-D01_4"
                     /geo_loc_name="Uganda"
                     /lat_lon="0.19 N 32.35 E"
                     /collection_date="2018"
                     /collected_by="Hidenori Harada, Mai Tanaka"
     gene            1931..2443
                     /locus_tag="QL140_23665"
     CDS             1931..2443
                     /locus_tag="QL140_23665"
                     /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="hypothetical protein"
                     /protein_id="WHJ49814.1"
                     /translation="MTKVTVDYPSSISRRKLSNLFNHSPFMLSLIHDMCDSQAIVFAAM
                     CEGKCVTSAGNRIEADYEVTKLAAVIDVLENKFYLPVSRVKIPTASDTGGGTIQAKYLI
                     TENDMQLLLEDPESVVLMRERLALSKLKSRDERCLKRLVSVHGYDEVFRTLQALDVAND
                     SFGRDCG"
                     /name="hypothetical protein"
     Typing          complement(2..148)
                     /name="rep_cluster_2373"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="98.649"
                     /coverage="83.0"
                     /evalue="1.5599999999999998e-67"
     Typing          complement(2659..2868)
                     /name="rep_cluster_2373"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="92.891"
                     /coverage="83.0"
                     /evalue="7.1e-81"
ORIGIN
        1 ggcaggaaca ggagagcgca cgagggagct accaggggga aacgcctggg atctttatag
       61 tcctgtcggg tttcgccacc actgatttga gcgtcagatt ctgtgatgct tgtcaggggg
      121 gcggagccta tggaaaaccg gcagcgcctc taccttcctc ggttggctca ctgtcctact
      181 tcatagcttt ctctccctag gtgtctgctc cctccgctcg ccgcagtcga acgaccgagc
      241 gtagcgagtc agtgagcgag gaagcggaat atcgctaggc ttatcttcgg caccgtacac
      301 gctatagctg catttcttaa tacgatgcag gatagggcga acgccgcaaa atgacgtcac
      361 ctaacgttct aaagtagcgg acaggaaatg ttttgtgtcc accgccatac tggcttattc
      421 acaaaacagc gggaaaagat gtgtctttgg agtaccgccc gaactccaaa acgctatgat
      481 caggctccgc ccgatacctt tagcgacgag tgtttgcagt ctgtctttaa tctgttggcc
      541 atgtgccccg catctgtttg ctgagtgttt gcaatgtgtc cctgatctgt ttactacgtg
      601 tttacgatgt gtccctgatc tgtttactac gggtttatag cctgtttttc ccctgattta
      661 ctgctcatga ccaaggcacg ttagcgatgt atacaccgcc gcgccgcaag ggtgcccctt
      721 ccgaatcccg ttacatcgct gtgcgctgat cactccaggt tacatccgac cccttggcaa
      781 taaatcctgc catgcctgac ggcctggcca acgcctcacg gccgcacagt aaactgcgca
      841 accgtgaggc gttatcggtg gggtttgtgg tggctttcag gacgttcgct ggattttagc
      901 cgctaaaatg gcggccattc gtttgtttgc atagccatgc acacgcgcag aaattaactg
      961 ggggttaaaa gcggttttta acggggttta accccggttt tcaggcagga gaccgcagaa
     1021 acgcactgag ggtgtctgag atggtgcggc caacagatgt tatggtaaat gtcacacgtt
     1081 ttgatgatga cttatggttc ctgcattttg ggtacaaagt tacttttccg cattgcatct
     1141 tcgtttcttt tgatgtggcg aatcacatga tgggccgata gatggtgcag tccaaagatc
     1201 ctcaccgatc cttccacttc aatttaacta attgttaatt aatcgctatt ttcaaatcta
     1261 taaattacac cgatcgatat aggtactttc aatagataaa aacactaaag aatttatatg
     1321 tgctttaaac ggctttaaac ggctttaaac ggctttaaat tattagtgag gtaatgcgat
     1381 ggctaatctg ttgatcgcgt cttagatggc gtttggtgcc gcgtaatgaa ggttttatag
     1441 atagctctcg atgttgctgt tggtctgatg gctggttttt taaacactgt ttacgggatc
     1501 tctcgttaga attactatcc ttggcgctgg ctgtggtggc tggcgatgaa aaatataggc
     1561 aggtagctgt ggtggctatt tgtcgaagct tgagatggct tctaaagaag gtgaaacctt
     1621 cacaatagaa cccgctaatc gtgaagaggc gggttttttt gtgtcaaaaa ttctctattc
     1681 atcagcccac taattgctct tcaatatgat gatcgtgtta gaataggcgc aacggcagac
     1741 ctaaccagtt tgcgagccta accagctcat gcaccgttag caaataacct taattttctt
     1801 cacggaccgc aaggtcaagg tgccaaaatg tgtaatgaaa tctcgatccc tcatcagggg
     1861 gatgtcagct atacctcctt cacgttccgc aaggttctgt ccgctatttt tcgtggcgtg
     1921 ggggtgaatc atgactaaag taactgtcga ttatccttct tccatctccc gccgtaagct
     1981 ttcaaatctg ttcaatcact ctccgtttat gctgtctctt atccatgaca tgtgtgactc
     2041 tcaagctatt gtttttgcgg ccatgtgtga aggtaagtgc gttacaagcg cggggaatcg
     2101 gattgaagca gactacgaag taactaagct agcggctgtc attgatgttc tggaaaataa
     2161 gttttacctg cctgtatcgc gcgtgaaaat tcctaccgcg tcggatactg gcggtggaac
     2221 catccaagct aagtatctta ttacggaaaa tgatatgcag ctgttgttgg aagacccgga
     2281 atcagtggtt ttgatgaggg aacgattggc tctttctaaa ctaaagagtc gagatgaacg
     2341 ttgcttgaaa cgtttggtgt ccgttcatgg ttatgatgaa gtttttcgaa cgctccaggc
     2401 attagatgta gctaatgatt cttttggtcg agattgcggg taatacctta agcggtaata
     2461 aattgacgtt taaggcatgg ccgtttaacg tctaacgcta gaaagaaaaa aagccacccg
     2521 gcaaggtggc tttttcaagg ttcaataaac gggcaagttt ttgaacctgg taactgtcgt
     2581 aagggcgacg agtcaccaaa acaagtatct ccagtttagc cgcaatatgg ctatcacatc
     2641 aagactcatc cctttgccca gttaccattg gccgctgcca ttggcgcttt gtcgtgtcta
     2701 tccggattgg attcaagtcg aaagttaccg gaataggcgc tgcggtcgga ctgaacgggg
     2761 ggttcgtgca tacagtccag cttggagcga actgcctacc cggaactgag tgtcaggcgt
     2821 ggaatgagac aaacgcggcc ataacagcgg aatgacaccg gtaaaccgca t
//
