LOCUS       CP125012                1747 bp    DNA     circular BCT 16-MAY-2023
DEFINITION  Escherichia coli strain KFS-D29 plasmid pKFS-D29_5, complete
            sequence.
ACCESSION   CP125012
VERSION     CP125012.1
DBLINK      BioProject: PRJNA956323
            BioSample: SAMN34598749
KEYWORDS    .
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 1747)
  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  JOURNAL   Unpublished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 1747)
  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 16:48:53
            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)                     :: 4,759
            CDSs (total)                      :: 4,635
            Genes (coding)                    :: 4,417
            CDSs (with protein)               :: 4,417
            Genes (RNA)                       :: 124
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 88
            ncRNAs                            :: 14
            Pseudo Genes (total)              :: 218
            CDSs (without protein)            :: 218
            Pseudo Genes (ambiguous residues) :: 0 of 218
            Pseudo Genes (frameshifted)       :: 67 of 218
            Pseudo Genes (incomplete)         :: 150 of 218
            Pseudo Genes (internal stop)      :: 45 of 218
            Pseudo Genes (multiple problems)  :: 41 of 218
            Pseudo Genes (short protein)      :: 4 of 218
            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..1747
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="KFS-D29"
                     /isolation_source="Fecal sludge"
                     /db_xref="taxon:562"
                     /plasmid="pKFS-D29_5"
                     /geo_loc_name="Uganda"
                     /lat_lon="0.19 N 32.35 E"
                     /collection_date="2018"
                     /collected_by="Hidenori Harada, Mai Tanaka"
     gene            700..1689
                     /locus_tag="QL146_23795"
     CDS             700..1689
                     /locus_tag="QL146_23795"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001529700.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="protein rep"
                     /protein_id="WHJ58450.1"
                     /translation="MKNPELQNLTDYSPSDAPWDAHRSVSDDVGGIYLLAAEYERYGAR
                     MASCGGLLRFGWSTLKETGETRLRLREAHFCRVRHCPVCQWRRSLMWQARFYQSLPRIV
                     ADYPDSRWMFLTLTVRNCAIGDLGDTLSRMNTAFQRLKDRKEFRPVQGWIRTTEVTRGS
                     DGSAHPHFHTLMMVPPGMLNGKSYVKHARWVELWRECLRVSYDPNVDVRAVKPRKPKDG
                     ESLACATAELVRGAVAETLKYSTKPADMVADPEWFLELTRQTHKRRFVATGGALKDVLK
                     LDQETDADMVIGDDISEGDDDGSRIAFEWKIEVKKYRRSPTKDKTESE"
                     /name="protein rep"
     Typing          complement(1418..1607)
                     /name="ColpVC"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="96.859"
                     /coverage="99.0"
                     /evalue="3.7200000000000003e-85"
ORIGIN
        1 cgccgcgttc gcccagtgac ctgcagtcgg ctctggggtg tcggggctgc gccctgacct
       61 ggggttttgg attgcggcat cgtgatggcg gtaatacaaa acgcacggga caagatgtgt
      121 ttttggagta ccgccgacac gcgacggaca gtccaaaata tcttggtcag ggctgcgccc
      181 cgacaccctg ccaacacctc acgccgccag attaaaatct gccagcgttc gccgttcctg
      241 aaatcgtcaa acgctaaatc gtggggtccc gctggcttgc cagtgggttc cgatttagtg
      301 attgacgagc gcacccgtaa aacactgccg acaggtggtt gtgatcacgc agtgagcgca
      361 accacctgat aagcgttttt ggggtttgtg gggtccgatt taacgtggat tttgggggca
      421 aaaaatcgcg cgcgttcctt gtatttatac ttaagggata actctggcgt taaaaataag
      481 cctcagccct tgtgccgcaa gggtttcagc gtgatttgcc tgaaaatgac tttgaagtta
      541 ttctgtctgg agtggtcgcg ttaaaagcga cccccgcaac gacggccatc gttcgggggc
      601 gtgaccacct gtaggaattc tattttgcga cagacaacac aggtgatacg gcaatgataa
      661 cacgtcaagt gagccatcgc ccagtatggg gcggtgcgca tgaaaaatcc tgaactccag
      721 aacctcacgg actattcccc ctcagatgcg ccctgggacg ctcacagaag cgtttctgac
      781 gacgtgggag ggatttacct gcttgcggcc gaatatgagc gctacggggc gcgtatggcc
      841 tcctgcggcg gtttactgcg tttcgggtgg tctaccctca aagaaaccgg agaaacgcgc
      901 ctgaggctgc gtgaggcgca tttctgccgt gtccggcact gtcctgtctg ccagtggagg
      961 cgctccctga tgtggcaagc ccgtttctac cagtccctgc cgcgtatcgt ggcggattac
     1021 cccgattccc gctggatgtt cctgaccctg accgtgcgca actgtgcgat cggggatctg
     1081 ggcgatacgc tgagccggat gaacacggct ttccagcggc tgaaggatcg caaagagttc
     1141 agaccagttc agggatggat ccgcaccacg gaagtcaccc gcggcagtga cggcagcgca
     1201 cacccgcact tccacacact gatgatggtt ccgcctggca tgcttaacgg gaagagttac
     1261 gtcaaacatg cgcgctgggt tgagctgtgg cgggagtgcc ttcgggtcag ctacgatccg
     1321 aatgtcgatg tccgggcagt gaaaccccgg aagccgaagg acggcgaatc gctggcctgc
     1381 gcgaccgccg aactggtgcg cggcgcggtg gccgagaccc tgaaatattc cacgaagccg
     1441 gccgacatgg tcgccgatcc tgaatggttc ctcgaactga cccgccagac gcacaagcgc
     1501 cgctttgtgg cgaccggcgg cgcactcaaa gacgtattga aactcgatca ggaaaccgat
     1561 gccgacatgg tgatcgggga tgatatttcc gagggcgatg atgacggttc ccgcatcgcg
     1621 ttcgagtgga aaatcgaggt caaaaaatac cggcgttcgc cgacgaaaga taaaaccgaa
     1681 tcagagtaaa aacactgcga tgcaggatag ggcaaacgcc gcaaaatgac gtcatccgac
     1741 atcattc
//
