LOCUS       CP125037                5594 bp    DNA     circular BCT 16-MAY-2023
DEFINITION  Escherichia coli strain KFS-D08 plasmid pKFS-D08_4, complete
            sequence.
ACCESSION   CP125037
VERSION     CP125037.1
DBLINK      BioProject: PRJNA956323
            BioSample: SAMN34598745
KEYWORDS    .
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 5594)
  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  JOURNAL   Unpublished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 5594)
  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..5594
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="KFS-D08"
                     /isolation_source="Fecal sludge"
                     /db_xref="taxon:562"
                     /plasmid="pKFS-D08_4"
                     /geo_loc_name="Uganda"
                     /lat_lon="0.19 N 32.35 E"
                     /collection_date="2018"
                     /collected_by="Hidenori Harada, Mai Tanaka"
     gene            1..477
                     /locus_tag="QL137_24760"
     CDS             1..477
                     /locus_tag="QL137_24760"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000469298.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology. GO_function:
                     GO:0003677 - DNA binding [Evidence IEA]"
                     /codon_start=1
                     /transl_table=11
                     /product="helix-turn-helix domain-containing protein"
                     /protein_id="WHJ32009.1"
                     /translation="MFIDSEKRLKQLSDEAKKNTEDLEEAKKNSRFTQVSPKGWERVRE
                     LLKDSQGISALKLYSFLAEHLDPTCGAVVADQQFLAEKLGVSRSTIIRWLNYLESKNAL
                     VRIPVAGKVCAYALDPHEVWKGYNTTKNHAAFVTKTLVNKDGDIQRRIMAMFSN"
                     /name="helix-turn-helix domain-containing protein"
     gene            complement(1535..1870)
                     /locus_tag="QL137_24765"
                     /pseudo=""
     CDS             complement(1535..1870)
                     /locus_tag="QL137_24765"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:YP_005221104.1"
                     /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="replication initiation protein"
                     /name="replication initiation protein"
     gene            3532..4239
                     /locus_tag="QL137_24770"
     CDS             3532..4239
                     /locus_tag="QL137_24770"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001296720.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology. GO_function:
                     GO:0003887 - DNA-directed DNA polymerase activity [Evidence
                     IEA]; GO_process: GO:0006270 - DNA replication initiation
                     [Evidence IEA]"
                     /codon_start=1
                     /transl_table=11
                     /product="replication initiation protein"
                     /protein_id="WHJ32007.1"
                     /translation="MTSTPLIAYKSNALVEASYKLTLQEQRFLLLCISRLNSGTDVASP
                     ELQKTMTITAAEYFDSFPDMGRKNAEVQLQEAIDRLWDRSIILKDDEKREEFRWIQYRA
                     QYARGEGKAQITFSDAVMPYLTQLKGQFTRVVIKNISNLSRSYSIRIYEILQQFRSTGE
                     RIIALDDFKSSLMIDSKYKDFKTLNRDLIKPCVDELNKKSDLAVTVETIKKGRTVVALH
                     FRFKEDKQIKMTI"
                     /name="replication initiation protein"
     gene            complement(4399..4791)
                     /locus_tag="QL137_24775"
     CDS             complement(4399..4791)
                     /locus_tag="QL137_24775"
                     /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="WHJ32008.1"
                     /translation="MVGGRRPSVLQRWGAGVLPRRFPVALKTLPEPWQEKICDDARHGV
                     RKFIIAAAIDGTHKDLIVICEWLLTTRQEYFALTVEGIATIVLKNGKKIVEYSIAVGHS
                     ECEQYFVLFNIVLCSSRGMNARSTVI"
                     /name="hypothetical protein"
     gene            complement(5294..5359)
                     /locus_tag="QL137_24780"
                     /pseudo=""
     CDS             complement(5294..5359)
                     /locus_tag="QL137_24780"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:YP_005221104.1"
                     /note="incomplete; partial on complete genome; missing
                     N-terminus and C-terminus; Derived by automated
                     computational analysis using gene prediction method:
                     Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /name="hypothetical protein"
     Typing          995..1075
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="97.561"
                     /coverage="89.0"
                     /evalue="1.21e-31"
     Typing          complement(2635..2720)
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="95.402"
                     /coverage="93.0"
                     /evalue="1.57e-30"
     Typing          complement(5408..5516)
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="99.091"
                     /coverage="100.0"
                     /evalue="9.09e-49"
     Typing          3533..4238
                     /name="rep_cluster_1778"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="99.01"
                     /coverage="99.0"
                     /evalue="0.0"
ORIGIN
        1 atgtttattg attcagaaaa acgactgaaa caactttcag atgaggcaaa gaaaaacacc
       61 gaggatctcg aagaagcaaa gaagaattca aggtttacac aggtatcccc aaaaggttgg
      121 gaacgcgttc gagagctgct gaaggatagc caaggtatat cagcactgaa gctgtactca
      181 tttttagcgg agcatctcga tcctacgtgt ggcgctgtcg ttgcggatca gcaattccta
      241 gctgaaaaac ttggagttag cagaagcaca attattcggt ggctcaatta cttagaatca
      301 aaaaatgcat tagttagaat ccccgttgct ggtaaggttt gtgcgtatgc cctcgatcca
      361 catgaagtct ggaagggata taacactacg aaaaaccatg cagcgtttgt cactaaaaca
      421 ctggtcaaca aagacggtga tattcagcgc cgaatcatgg ccatgttttc aaattgagcc
      481 agcggcaggc ggacaatcag gggctacgtg ttaacgttct gaccatgatt gtctatcctg
      541 cattgctctt ttctcgacct caaattccct tgcatattga ataggaattg cattacaaga
      601 ttatttgagc gcgtttcttc acagtccctt gacccacatt gtccgtggtc cctgaaacgc
      661 gctcatcctc cgtcgtgttc tctgttacgg ttccggtagc gccttgagcg ctaccggaaa
      721 ccgtctgggg ttctccccag ccccccatcg ctgtagcatc gacggtctac gaccaccaac
      781 cagccgaata gctgcctgtg ccgtgcaaat gggctttgca gggggctggc gcggttcctg
      841 gcgactcatt cccgaaagaa tgacagcgga atcaccgaca acatgcgaga ggtgacaccg
      901 ctcgccgcag ccccagcgac cgaacgttag tgagcgagtg ggcgaggaag cggaagagaa
      961 ccagaagtca cattgagcac tgacgcacag atgcggggtg tcggggcgaa gccctgacca
     1021 ggtggtaatc gtatagccgt gcgtgcgcgg ttatacgatt gcacatcctg tcccgacaat
     1081 tcccgccgtt tctcggtttt ttgagcgtcg cagaccgcac gacaaacgaa acaaagtgaa
     1141 gtttgtataa gtacgcactt cgtgagattc cccgactgcc agtttgtcga tcgcgcggaa
     1201 cggctgcggc acaaaaacgg caaaatgatt tgctgtccgg tcgccagaat ttggcgcggc
     1261 ggtggcgatg gctgtacgga acgggaatga ccgcggggtg gggcgcgtgg tgtaagggct
     1321 tgttttgtgt cggaatatac ggcaaattgt gtggtgcggg tgcgcacatc cgcagaaatc
     1381 gaaaccgttt aatcatacga tatacttttc cccgccctct ccaggcgggt tttttttgag
     1441 cgcggacagg tcgcgctggg ctgcctgcaa acactgtata caacgcattt acaccacgca
     1501 atggcttgat tttgctgtat ttctgcgttt acagccattc cgggtggaac gggtttttgc
     1561 aaatcagtcc gctgtagttc acatcagcac aaagtttctc acacagcgaa cgttcaatcg
     1621 cggcgacata tttcagcgcc ttaaccgaac tgtccagcgc gggggcgttc cggtcgctcc
     1681 agtcaatcgc agccccctcg cggtcaacgt caaaaaccag ccagaactgc gcatgaggct
     1741 ggttctgctg gatgtaccgc gcaagcagcg cacgcccttt gccggagatg cgaagaccaa
     1801 aagcgagatc atccgtgtga tagggacggc ggggtaaatt ttcttcgaag tattgaagcg
     1861 cggcgctcat atgttacgat tccttcccgg ttatcgaccg acatcgcccc tgtattttcg
     1921 tgacagtctt ggcggataga aacgaatttc aggggcgttt gtttttcagt cgcttacact
     1981 acacccactg tcgttccttc ccgaaaaacc gatccattta ccataactcc cgttgcgcgc
     2041 acctctaaaa cgcgctgaac gcgattctgc cgcgaacacc gcaaaaagag atgttttccc
     2101 cggggtaaac cggaaaaatg cgtcaggatc gctttcagct cactgcatag ctatgcatga
     2161 aagtgaatgg cgatcggttt gggcgcatat ggtgcccatg agacacattt tcggacattt
     2221 tcagttcgtg aatccctgac tcattgctac atatctgaac agacacccct agcagcgccc
     2281 ccaggggcgt tatgtaaaaa aaggcgacgc gcccctaggg gcgcccctac attaattaac
     2341 tgttttttct acagatagtc agtactgacc ctaggtaggg tcgtcctagg gtcgtcgacg
     2401 acgcgctttt gtataaatct gaataagaaa atacattttt ttaaacataa caacctgatt
     2461 taaaaaagaa atcagcaaaa agttagtttt gcgtggggtg tgggcatttt aggcatgaga
     2521 acagactcgc gtttttccgg agtatcagcg ggattattga ttaagaaaca ctcgacgcag
     2581 agcgaaattt tatgcaacag cggctgcact gcacagggat tatttatcag ttgaaacagg
     2641 acaggatgtg caattgtaat accgtcacac gcgacgctat cacaattgcc atctggtcag
     2701 ggcatccgcc ccgacacccc tgtgcagtct gcgggcaaaa aaaaaccgcc aagagatggc
     2761 ggtaagcaaa aaattacatg tatgaacagc ttgaataatg tgagtgagtc aaattttgcc
     2821 gcaagccgac cggaaaaaca attcacccgt gacgcggtga gacgctctct gacgcgttaa
     2881 acgtagccag ggtaatacct gacacccctg aaacgaaaaa acgcgcctga gcgcgttcta
     2941 ggggccttaa aatcgatttt tgattatcat cgggcgatgc ggtcggctta ccgtatgatt
     3001 gaggtggtcg tgctcgccgc agccccagcg accgaacgtt agtgagcgag tgggcgagga
     3061 agcggaagtg aatcagtcgc caggttgggc acatacgcac ggtttttcgg caggtgatat
     3121 gcgctgaacc cgcatgaata ctggatttcc acagggttgg agggggagtt ttcggaactt
     3181 gcaattctgc tttcttgcaa catattgttt ttattggttt tttattttca gcaccccaag
     3241 ttatccacag actcgccgtt aagtttttag atcttgtttt taagatcttg tttttaatac
     3301 ttgttttagg gccgaaattc ctgattaaaa acaatgcgtt acacgtgtat aggtgaggag
     3361 atttaaggta aaggtgatat aatttaaggt gcttgggtga ggtaatttaa ggtaaaggtg
     3421 aggagattta aggtaatatt cacaggaaaa tggggggtga aaatataatt gctcaccaat
     3481 gctaaaggtg ataggttttt atctcacctc atttttggcc tggtggttaa aatgacatca
     3541 acccctctga tagcctataa gtccaatgcg ctggttgagg ccagttacaa gctaacttta
     3601 caagaacagc gtttcttatt gctctgcata agccgactta actccggtac tgacgtagct
     3661 tcacctgaat tgcaaaagac aatgaccatt acagctgcag aatattttga ttcattccct
     3721 gatatggggc ggaaaaatgc cgaggttcag ctacaggaag cgatcgatcg tttgtgggac
     3781 aggtcgatca ttctcaagga cgacgagaag cgcgaggagt tccgctggat tcagtatcgg
     3841 gcacagtatg cgaggggaga ggggaaagca caaatcactt tttctgacgc ggtaatgcct
     3901 tatctgacac agttgaaggg gcaattcacc agagtcgtca ttaaaaatat ttccaattta
     3961 tcaagaagtt acagcattag aatatacgaa attctccagc aattccgcag tactggggaa
     4021 cgtattatcg ccctcgatga ttttaaatca tcactgatga ttgatagtaa atataaagat
     4081 ttcaaaacgt taaacaggga tctaataaaa ccctgtgttg acgaactgaa caaaaaaagc
     4141 gacctggctg taacggttga gacgatcaaa aaggggcgca cggttgtagc cctgcatttt
     4201 cgcttcaagg aagacaaaca gatcaagatg acgatctaaa atcgatttta aggcacctaa
     4261 aacgctccct gtcgtgtttt tcttgtgtca ggaatgcgaa ggtactactg aagtgaaaag
     4321 ttgcgtcaga attgatttga ggggccataa aaagaacccc caattttttg ggggcggaaa
     4381 aacaaaacta tgtttgcgtt atatgactgt acttcttgca ttcatccctc tcgatgaaca
     4441 taacacgatg ttaaacaaaa caaaatattg ttcacattca ctgtgaccaa ccgcaatgct
     4501 gtactcgaca attttcttcc cgttcttcag aacgattgtt gcgatacctt ctacggtgag
     4561 agcaaaatat tcctgacggg tggttaacaa ccactcgcat atcacaatca aatccttatg
     4621 cgttccgtct atggcggctg cgatgatgaa tttgcgtact ccatgtctag catcatcgca
     4681 gattttttcc tgccacggtt ccggcagcgt cttgagcgca accggaaacc gtctggggag
     4741 aaccccagcc ccccatcgct gtaataccga cggtctacga ccacccacca accgagtctc
     4801 cgctagtgct acgtgactgg ttcagggctg cgctccgaaa cccgctaaca accatatttg
     4861 gttttgttta acatcgtgtt atgttcatcg atgtccatcg acatggatga atgcaagaag
     4921 cacacgcata acacaaatca actttatagt tttcccgccc ccaaaaattt gggggttctt
     4981 ttttcgctgc atcagtgcgt acgtgctcaa tgtggtttcc ggttccctgg tgcttcctcg
     5041 ctcattcgct cgctacgctc ggtcatgaga ctgcggcgag cacgaccacc tcaatcatgc
     5101 tgtaagcagc accattgcgg ggctgaaagg agaaaaccgc gggaaagccc acggctcaaa
     5161 aaaacgccaa aaaggcgctg ttatctgata taggcttatt tggtctactc tacgagacct
     5221 cgttttttca gttggtaata ccaggcgcga ctgatcccta atgcctccca cggtttcagc
     5281 gtgcgtgcag atgtagccac tgtgagaatg ctggccatcc ctgacgaatc gctctgtaag
     5341 cccatttacg cgttatttcg acccccaaag ggtgttgcgt cgcgcgcaac acccttgcct
     5401 agaatagatc ttttacgccg atttgtaagc tgttgttttt ttagtgtgtt ttttgtttac
     5461 ctgtcgcatc cagggtgaca caacgttgtc gcatcctgga tgcgacaaca cgcaacaagg
     5521 tgttgcatag atgtgtcatg atggcttaga tttgaaccaa cgttagtgca tgggattttc
     5581 agagggaaaa aatc
//
