LOCUS       CP125042                3414 bp    DNA     circular BCT 16-MAY-2023
DEFINITION  Escherichia coli strain KFS-D01 plasmid pKFS-D01_3, complete
            sequence.
ACCESSION   CP125042
VERSION     CP125042.1
DBLINK      BioProject: PRJNA956323
            BioSample: SAMN34598744
KEYWORDS    .
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 3414)
  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  JOURNAL   Unpublished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 3414)
  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..3414
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="KFS-D01"
                     /isolation_source="Fecal sludge"
                     /db_xref="taxon:562"
                     /plasmid="pKFS-D01_3"
                     /geo_loc_name="Uganda"
                     /lat_lon="0.19 N 32.35 E"
                     /collection_date="2018"
                     /collected_by="Hidenori Harada, Mai Tanaka"
     gene            198..310
                     /locus_tag="QL140_23635"
                     /pseudo=""
     CDS             198..310
                     /locus_tag="QL140_23635"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_005761324.1"
                     /note="frameshifted; 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            540..1022
                     /locus_tag="QL140_23640"
     CDS             540..1022
                     /locus_tag="QL140_23640"
                     /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="WHJ49812.1"
                     /translation="MDKKQTAKSSVPPSQFILQLEKCKKVKDIKITNSDTKSGVSAIGG
                     TFNLYDDKAHFFYSESVSFVAINVRSIYKLENTKKSSELSLLRAINKYNEGSFGTKVCL
                     LSSNDESFNIELNVESILNPGNTKSLPIEPMIMILARSINEIDTSIESLLINNQEG"
                     /name="hypothetical protein"
     gene            1088..1573
                     /locus_tag="QL140_23645"
     CDS             1088..1573
                     /locus_tag="QL140_23645"
                     /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="WHJ49813.1"
                     /translation="MQNWLVPWLETIGMPDWITKSPAPIAFLFVFATLVNMWFVGKFTP
                     KEPNKLAENEKKKIVRREGSKHKRAVDSLQKKHKKEVEAECNAVRRELGTRISSLNEEC
                     SRKQITIDVLSAELTKARQEQSSSPHANVKKPSSGHIETGRHQPQIPDLFATLKENS"
                     /name="hypothetical protein"
     gene            complement(1840..2061)
                     /locus_tag="QL140_23650"
     CDS             complement(1840..2061)
                     /locus_tag="QL140_23650"
                     /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="WHJ49809.1"
                     /translation="MKKWLATLIDDLKFLGAEFKREFSDLGITPVTAEQHQQRIAEMRR
                     STVAGKLSRGVLQIRDGVLTFYGMKTKW"
                     /name="hypothetical protein"
     gene            complement(2569..3000)
                     /locus_tag="QL140_23655"
     CDS             complement(2569..3000)
                     /locus_tag="QL140_23655"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000135004.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="helix-turn-helix domain-containing protein"
                     /protein_id="WHJ49810.1"
                     /translation="MARVSISEAARLASVSRPTIYKLLKSGELSYTSVVKHGKSVKAID
                     TTELIRVFGSLSFDSGRDNGVVKFDEHSTGVNSNFLQDLQHQVALLQAENAGLKDAVNA
                     RDEHINSLRQAMQLLEHKQDTADPQHVPAKSWWQFWKSR"
                     /name="helix-turn-helix domain-containing protein"
     gene            complement(3000..3191)
                     /locus_tag="QL140_23660"
     CDS             complement(3000..3191)
                     /locus_tag="QL140_23660"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000166328.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="Rop family plasmid primer RNA-binding protein"
                     /protein_id="WHJ49811.1"
                     /translation="MTKQQKTALNMAKFIQGQTLLLLEKLNELDLDVEADLCEKLHEDA
                     EQLCRTLTIRLDGHQGDL"
                     /name="Rop family plasmid primer RNA-binding protein"
     Typing          21..486
                     /name="rep_cluster_2358"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="85.571"
                     /coverage="94.0"
                     /evalue="8.13e-136"
ORIGIN
        1 atcgacgctc aagtcagaag tggcgaaacc cgacaggact ataaagatac caggcgtttc
       61 cccctggcgg ctccctcgtg cgctctcctg ttcccgcctt tcggtttacc gatgtcattc
      121 cgctgttatg gccgcggttt ctcattccac gcctgacact cagttccggg aaggcagttc
      181 gctccaagct ggactgtatg cacgaacccc ccgttcagtc cgactgctgc gcctattccg
      241 gtaactatca cttgagtcca acccgaaaag acatgcaaaa gcgccaatgg cagcagccac
      301 tggtaactga tttagaggag ttagtcttga agtcatgcgc cagttaaggc taaactgaaa
      361 gaacaatttt ggtgactgcg ctcctccaag ccagttaccg cggttcagaa acttgccggt
      421 tgctgaacct tcgaaaaaac caccttgccg ggtggttttt tcgtttacaa accagacgat
      481 acagctaaaa atgtccaatt tcaataactc acattttaag atataaacgg attgtcaaag
      541 tggacaaaaa gcaaacagca aaatctagcg tacctccctc acaattcatt ttgcagctag
      601 agaagtgcaa gaaagttaaa gatataaaaa taaccaacag cgacaccaag agtggcgtga
      661 gcgcaattgg aggcacgttc aatctgtatg atgataaagc tcacttcttt tatagtgaat
      721 cagtttcttt tgtagctata aatgtaaggt caatatacaa actagaaaac actaagaaat
      781 ccagcgagct atctctcctt cgagcaataa ataaatacaa tgaaggcagt tttgggacaa
      841 aggtttgctt attaagcagc aatgatgaat cctttaatat tgaactgaat gtcgaatcaa
      901 ttcttaaccc aggaaacacc aaatcattac cgatagagcc gatgataatg atcctggcta
      961 gatcaattaa tgaaatagac acatctattg agagtctact cataaataac caagaggggt
     1021 aaccatgacc ctcactagag ctttcatata cttgatatca tcaatcttta tgttccttgc
     1081 aggaaacatg cagaactggc tggtaccatg gttagaaaca attggaatgc cagattggat
     1141 aactaaatct ccagcaccga tagcatttct tttcgttttt gcgacattag tcaatatgtg
     1201 gttcgtaggg aagttcacac caaaagaacc gaataaatta gctgaaaacg agaagaaaaa
     1261 aatagtgcga agagaaggca gcaaacacaa aagagctgta gattcacttc agaaaaaaca
     1321 taagaaggaa gtagaggccg agtgtaatgc cgtcagaaga gagttaggaa ctcgtatatc
     1381 ttcacttaac gaagaatgtt caagaaagca aattacaatt gatgttcttt cggcagagct
     1441 aacgaaagcc cgccaagagc agagcagcag cccacatgca aatgtcaaaa agccatcaag
     1501 tggtcacatt gaaacagggc gacaccaacc tcaaatccca gatttatttg caacacttaa
     1561 agaaaactca taataataag gccgctaatc cggcctttta cattcacatt taccataacg
     1621 cctcattacg cgcaccgctg aaacgcgctg agtgcgattt cggcgcgaag acgatgaaaa
     1681 ccacagctta tccggcaaaa acgcgccaga atcgatctga gcgcgtttac ggcctgtgaa
     1741 tgattatgca gcgcagtgaa tgagctcagg cctggcacaa aaaagctggt gaaaccgcga
     1801 tttttcccgg ttttcctgac cggatttccg ggcggaagcc taccatttcg ttttcatgcc
     1861 ataaaaggtc agtaccccgt ccctgatttg caaaacaccc cgggataact tcccggctac
     1921 ggtggaacgg cgcatttcag ctattctctg ctgatgttgc tcggccgtca caggggtgat
     1981 acccagatcc gaaaactctc tcttaaactc agcccccaga aacttcaggt catcgataag
     2041 ggtcgcaagc cattttttca ccgttctgcc tcacatcatt taagttattc agataacagt
     2101 ctggcacaga ctggagaaag aaagcggtga acgggcacgc aatttattgc ggggtcgtga
     2161 ggcgctggca ggatcgtcta gcaaatttag caacgggaaa agtcatgcac gtcgaacagg
     2221 taaaaataat aattaaaatc aacacgttat atgaataaaa taagagaaac atcatgcagg
     2281 gggggcatga tgccgcgaac gcctgtaact ctgggctttc agtccaattt cataaaaaaa
     2341 tgcatgacat ttgcacattg ggtgtcatgc ccccccaaag ccagtctcag cacggctttg
     2401 ggctttgcat tgcataatgc gtggggtgtg acacgatttt atggcctttc tcagccatca
     2461 ggagtcaaac atgcaggaaa atcagcagga caaaagagta caaaaatcca tatccggcag
     2521 aaactgagtg gcaggacgaa cgctatggcc ggaatgcgtg gtaatgactc agcgggattt
     2581 ccagaactgc caccaggact tagcagggac atgctgcgga tcagcagtgt cctgtttatg
     2641 ctccagcagc tgcatggcct ggcgaagtga gttgatatgt tcatcccggg cattcactgc
     2701 atctttcagc ccggcgtttt ctgcctgcaa aagtgccacc tgatgctgta aatcctgtaa
     2761 aaaattactg ttaacacctg tagagtgttc gtcaaatttt acaacgccat tgtcacgtcc
     2821 actgtcaaaa ctaagagaac caaaaacacg aataagctct gtagtatcaa tggcttttac
     2881 agattttcca tgctttacaa cagaggtgta acttaactca ccagatttga gtaacttgta
     2941 aatagtcgga cgactgacac tggcaaggcg tgccgcttcg ctaatagata cccgagccat
     3001 tataaatccc cctgatgacc atccagacga atagtcagag tacgacagag ttgttccgca
     3061 tcctcatgga gcttttcaca aagatccgcc tcaacatcga gatcgagttc attaagcttt
     3121 tccaacaaaa gcagggtctg cccctggata aacttcgcca tattaagcgc agttttctgt
     3181 tgtttcgtca tcacagcgtc agtgctccat gttaactctg gttcttttcc gcttcctcga
     3241 ccgttcgctc gctacgctcg gtcacttgtc tgcggcgagc gtagcgagcg ttctaaaaga
     3301 caagcaagaa agaaagagga taaccgtaag aggaagcagc caaaaagcca aaagaaggcc
     3361 acgccccctg ggcgttttac cataggcttc gcccccctga cgagcatcac aaaa
//
