LOCUS       CP125038                2856 bp    DNA     circular BCT 16-MAY-2023
DEFINITION  Escherichia coli strain KFS-D08 plasmid pKFS-D08_5, complete
            sequence.
ACCESSION   CP125038
VERSION     CP125038.1
DBLINK      BioProject: PRJNA956323
            BioSample: SAMN34598745
KEYWORDS    .
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 2856)
  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  JOURNAL   Unpublished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 2856)
  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 16:54:04
            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)                     :: 4,957
            CDSs (total)                      :: 4,831
            Genes (coding)                    :: 4,600
            CDSs (with protein)               :: 4,600
            Genes (RNA)                       :: 126
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 92
            ncRNAs                            :: 12
            Pseudo Genes (total)              :: 231
            CDSs (without protein)            :: 231
            Pseudo Genes (ambiguous residues) :: 0 of 231
            Pseudo Genes (frameshifted)       :: 78 of 231
            Pseudo Genes (incomplete)         :: 150 of 231
            Pseudo Genes (internal stop)      :: 47 of 231
            Pseudo Genes (multiple problems)  :: 42 of 231
            Pseudo Genes (short protein)      :: 4 of 231
            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..2856
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="KFS-D08"
                     /isolation_source="Fecal sludge"
                     /db_xref="taxon:562"
                     /plasmid="pKFS-D08_5"
                     /geo_loc_name="Uganda"
                     /lat_lon="0.19 N 32.35 E"
                     /collection_date="2018"
                     /collected_by="Hidenori Harada, Mai Tanaka"
     gene            complement(1628..2638)
                     /locus_tag="QL137_24785"
     CDS             complement(1628..2638)
                     /locus_tag="QL137_24785"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_006859061.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology. GO_function:
                     GO:0003677 - DNA binding [Evidence IEA]; GO_process:
                     GO:0006260 - DNA replication [Evidence IEA]"
                     /codon_start=1
                     /transl_table=11
                     /product="protein rep"
                     /protein_id="WHJ32010.1"
                     /translation="MKNPDSPILSLRDYSTQDSKWDSDRARADQVAKIYASDQQFSRRG
                     ERMFDCSQRLQFAPQSSRLTGEMRLALRHGEFCHVPFCPVCSRRRSLRWMRRLWEALPK
                     LLAEHPTARWLFLTLTVKNPPVGELRETLKQMNAAWERLTKRKEFAPVLGWLRSTEITY
                     GNVPGGCHPHFHVVLWVPSSWFKRDYVKHERWVEIWSECLRVDYAAGAHIKRVRPKRGS
                     VPEGASAAEVQRAALEAGVIETLKYTVKSSEIVRDPAWFLELARQTYGLRMIATGGRFR
                     EILQVEKPETDEDLIGADMPAKPDEFEEMAFWLAFDWRRDEKRYKRNPRADRRKD"
                     /name="protein rep"
     Typing          367..448
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="93.976"
                     /coverage="90.0"
                     /evalue="3.4000000000000004e-27"
     Typing          complement(928..1183)
                     /name="MOBF"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="94.574"
                     /coverage="89.0"
                     /evalue="2.65e-108"
ORIGIN
        1 tgggctgaac agggaaaacc aatcctcgag ttgttgccta tagtataaat acaaggatcg
       61 cgcgcgagat ttgcttgaat tttgagcggg attttcagta acccaaaacc tcccaacccc
      121 acccacttac acccatctca cccacagact ttcaccccga ttttgtgaac aacaaaaaac
      181 cgtcttgcag gtggttggcc tcactccgtg acaccaacca ccatccccag tgttttcccc
      241 gtgccgtcgt caatcacaaa atcggaaccc acgccagagg cgcggggccc cgcgattttc
      301 tgtttgacga gttcgggaac ggtgagcggt acgcggaatt ttttcgcggg ccgtgaggcg
      361 ttggcggggt gtcggggcgc agccctgacc aggtggtaat tgtgatagcg tcgcgtgtga
      421 cggtattaca attacacatc ctgtcccgaa aattcccgcc gtttctcggt tttttgagcg
      481 tcgcagaccg cacgacaaac gaaacgaagt gaagtttgta taagtgcgca cttcgtgaga
      541 ttccctgact gccagtttgt cgatcacgcg gaacggctgc ggcacaaaaa cggcaaaatg
      601 atttgctgtc cggtcgccag aatttggcgc gtcggtggcg atggctgtac ggaacgggaa
      661 cgaccgcggg gtggggcgcg tggtgtaagg acttgttacg cgcaccgcta aaacgcgctg
      721 aacgcgattc tgccgcgaac accgcaaaaa gggatgtttt ccccagggta aaccggaaaa
      781 atgcgtcagg aacgttttca gcgcgttgca tgactatgca tgaaactgaa tggcgatcgg
      841 tttgggcgca tacagtgccc atgagacata ttttcggaca ttttcaattc gtgaatccct
      901 gactcattgc tacatatctg aacagacacc cctagcagcg cccccagggg cgtcctgtaa
      961 aaaaacacac cgcgccgcta gcagcacccc taatataaaa ttatgttttt tatgaaaata
     1021 gtcagtacca cccctacaaa gcggtgtcgg cgcagctaca acaccgcgcc gacaccgctt
     1081 ttttaaatat cacaaagaga gcaagagaaa ctaatttgtc ataactctct atttataaag
     1141 aaaaatcagc aaaaaattgt ttttgcgtgg ggtgtgggca tttcaggcat gagaacagac
     1201 tcgcgttttt ccggagtatc agcggaattc ttgattaaga aacactcgac gcagagcgaa
     1261 attttatgca acagcggctg tactgcacag ggattattta tcagttgaaa caggacagga
     1321 tgtgtaattg taataccgtc gcacgcgacg ctatcacaat tgcccctggt cagggctgcg
     1381 ccccgacacc ctcgacaccg taccagagac acgttaaaac gacatacgcg cgtttttggc
     1441 aatcaacaga ccaaggggat ggtttgcgta gcatcaagcg ccagaaacgc gctcaaaacg
     1501 cttctgagcg ccttaaaacg aaaaaacggg caaatccttg cctgtttctg aaaatcacgt
     1561 tagaacactt ctgagcgcgt ttcacctcca ctgccgcacc atcccactat gcgcctcaga
     1621 aacgcgctca atccttccgc ctgtctgctc tgggattccg cttgtagcgt ttctcgtccc
     1681 gcctccagtc gaacgccagc cagaacgcca tctcctcgaa ctcgtccggc ttcgctggca
     1741 tgtccgcacc aatcaaatcc tcgtccgtct ccggcttctc gacctggagg atctcccgaa
     1801 accgtcctcc tgtggcaatc atccgcagcc cgtaggtctg ccgcgcaagc tccagaaacc
     1861 acgccggatc gcgcacaatt tccgaggatt tcaccgtgta tttcagtgtc tcgatcaccc
     1921 ccgcttccag cgccgcccgt tgcacctctg cagcgcttgc tccttccggt acactcccgc
     1981 gttttggccg cacgcgcttg atgtgcgccc ccgctgcata atccacccgc aggcactcgc
     2041 tccagatttc cacccagcgt tcatgcttca cgtaatcccg cttgaaccac gacgaaggaa
     2101 cccagagcac cacgtgaaag tggggatgac agccccctgg tacattcccg taggtgattt
     2161 ccgtactccg cagccagccc agaacaggcg caaattcttt acgcttggtt aaacgctccc
     2221 aagccgcatt catctgcttg agcgtctctc tcaactcacc aacggggggg ttttttacgg
     2281 tcagggtcag aaagagccat ctcgcggtag ggtgctcagc cagtagtttc ggtagcgcct
     2341 cccacaaacg acgcatccag cgtaacgagc ggcgacggct gcacaccgga cagaagggga
     2401 catgacagaa ttcaccatga cgcagcgcaa gccgcatctc gcctgtaaga cgggaacttt
     2461 gcggagcgaa ctgtaaacgc tgactgcaat caaacatcct ctcgccgcga cgggaaaact
     2521 gctggtctga cgcgtaaatc tttgccacct ggtcagccct cgcgcgatcg ctgtcccatt
     2581 ttgaatcctg cgtactgtag tcacgcagtg agaggatcgg actatctgga tttttcataa
     2641 cccgccccca gtgggcaggg gcagaaatct tgtgttagca tgttcttacc acctgtgttg
     2701 atctcatcga attttacctt tcaggtggtc acccccgggg tgttagcgca ctgccgggga
     2761 acctcaccaa cctgttgctc acacggtagc caaaaagccc cgcagacgca atcaaaacat
     2821 ccacaaacca aaaccccctc aaacccgcgc cagcac
//
