LOCUS       CP125050                3348 bp    DNA     circular BCT 16-MAY-2023
DEFINITION  Escherichia coli strain KFS-C10 plasmid pKFS-C10_6, complete
            sequence.
ACCESSION   CP125050
VERSION     CP125050.1
DBLINK      BioProject: PRJNA956323
            BioSample: SAMN34598743
KEYWORDS    .
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 3348)
  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  JOURNAL   Unpublished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 3348)
  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 16:59:26
            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)                     :: 4,998
            CDSs (total)                      :: 4,876
            Genes (coding)                    :: 4,619
            CDSs (with protein)               :: 4,619
            Genes (RNA)                       :: 122
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 88
            ncRNAs                            :: 12
            Pseudo Genes (total)              :: 257
            CDSs (without protein)            :: 257
            Pseudo Genes (ambiguous residues) :: 0 of 257
            Pseudo Genes (frameshifted)       :: 86 of 257
            Pseudo Genes (incomplete)         :: 177 of 257
            Pseudo Genes (internal stop)      :: 48 of 257
            Pseudo Genes (multiple problems)  :: 52 of 257
            Pseudo Genes (short protein)      :: 4 of 257
            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..3348
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="KFS-C10"
                     /isolation_source="Fecal sludge"
                     /db_xref="taxon:562"
                     /plasmid="pKFS-C10_6"
                     /geo_loc_name="Uganda"
                     /lat_lon="0.19 N 32.35 E"
                     /collection_date="2018"
                     /collected_by="Hidenori Harada, Mai Tanaka"
     gene            complement(join(3075..3348,1..191))
                     /locus_tag="QL142_24950"
     CDS             complement(join(3075..3348,1..191))
                     /locus_tag="QL142_24950"
                     /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="helix-turn-helix domain-containing protein"
                     /protein_id="WHJ45411.1"
                     /translation="MENKNNLSSEVKNHVSKWGKTNISAGWTIIPNALLENQSRLGLSC
                     IDTMVLINLIMHWWEKDNPPRPSKKRLANMLGVSLKTVQRSFIHLEQCGAIKRIPRYKE
                     GKDNARTTNHYDLNGLVDLLEGFSKELIEEREANRKSEVNRPKKRGNPKS"
                     /name="helix-turn-helix domain-containing protein"
     gene            473..1039
                     /locus_tag="QL142_24955"
     CDS             473..1039
                     /locus_tag="QL142_24955"
                     /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="WHJ45412.1"
                     /translation="MAVFRQCEIREKYLAIYKESFDEVITYLEKAGALEPGVLRLTTID
                     DNAIRAWKSQWKGRSRKHAHGAWDWQNLVSKRARSCKRFDVAVWGEDVLCGLSVGKLTR
                     GKKTVRMDYLEACPTAHPLEKRITMIVVAVALSVAKKVGAQHVAIFNPIKDKEEKVLKH
                     YQSYGFTQRMLYGRFLKNVLYKEVV"
                     /name="hypothetical protein"
     gene            complement(1043..1213)
                     /locus_tag="QL142_24960"
     CDS             complement(1043..1213)
                     /locus_tag="QL142_24960"
                     /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="WHJ45413.1"
                     /translation="MSYVSERKSELVKAQQRKMDPSSPDSAPINQGLMDFILLAMKVDD
                     GFVQRGRIHGA"
                     /name="hypothetical protein"
     gene            complement(1486..1630)
                     /locus_tag="QL142_24965"
                     /pseudo=""
     CDS             complement(1486..1630)
                     /locus_tag="QL142_24965"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001717510.1"
                     /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            2174..2374
                     /locus_tag="QL142_24970"
     CDS             2174..2374
                     /locus_tag="QL142_24970"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001558245.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="antitoxin VbhA family protein"
                     /protein_id="WHJ45410.1"
                     /translation="MTDDRTLQLRLTGFRKAEASLRLEGMDPSGPPLYESVKTRILSGD
                     ITFDEGRTEIRAHYQKRANSN"
                     /name="antitoxin VbhA family protein"
     Typing          complement(1523..2123)
                     /name="rep_cluster_2324"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="94.05"
                     /coverage="92.0"
                     /evalue="0.0"
ORIGIN
        1 gggttatctt tttcccacca atgcattatg aggtttatga gaaccatcgt atcaatacag
       61 ctaagaccca acctggactg attttccagt aaggcatttg ggataatcgt ccatcctgca
      121 gaaatgtttg tcttccccca cttgcttacg tggttcttta cttcgctcga caggttattt
      181 ttgttttcca taaaacatgc atcctgtggt catctgaggc tagagggcat tttatatatt
      241 gaacgtttta ccgttcacct tgcgtcattg tcttaacgta ttgtcccact atatcttttt
      301 ctgtgtggtc aaatcagacc ataccctatg gtttttaaag tccacagggt ggggtttaaa
      361 tgtaccatag gatatggtct ttgttgacca ctaaccaaaa tgttagcaaa tgatttaaag
      421 tggttttttt atggcaaaat gtttactggt caaggtcagg agggagacga gcgtggcggt
      481 ttttagacaa tgcgaaatta gagaaaaata tctcgcgatt tacaaagagt cattcgatga
      541 agttataact tatcttgaga aggcaggtgc tttagagccc ggcgttttaa ggctcactac
      601 aatcgatgac aatgctattc gtgcatggaa gagccaatgg aaaggcaggt ctcgtaagca
      661 cgctcatggt gcttgggatt ggcagaacct tgtatcaaag agagctcgtt cttgtaaaag
      721 atttgatgtg gctgtttggg gagaggatgt gctttgtggg ctttcagttg gaaagctaac
      781 ccgtggtaaa aagacagtta gaatggatta tctagaggct tgtccaacag ctcatccgtt
      841 ggagaaacga atcacaatga ttgtggttgc tgtggctctg tcagtagcta aaaaagtagg
      901 ggcacagcac gtagccatat tcaatccgat aaaagacaaa gaagaaaaag tgttaaaaca
      961 ctaccagtct tacgggttta cacaaagaat gttgtatgga cgctttttga aaaacgtgct
     1021 gtacaaagaa gttgtttgat agctatgcgc cgtgaatacg accacgttga acaaagccgt
     1081 catctacttt catagcaagc aggatgaagt ccataagacc ctgattgatt ggagctgaat
     1141 caggagagga tggatccatt ttgcgttgct gtgcctttac cagctcactt ttgcgctcag
     1201 atacataact catcttgtga ctctctgtct tgtatgggga tgtagacact ataacaagtg
     1261 gataaaaaaa taacgagatc tctatatttt caaaaagaga tgactgttgt tgactcgcct
     1321 cttctgcaaa gcgtactctt ttctttcaaa agaaaaaaac cgcctttgcg gggcggtttt
     1381 tttccagttc attgagtttg cggctctttg aacctaggta acagtcttgt gcgagacgtg
     1441 tcaccaaatc tgtccttcca gtgtagctgt agtcaggctt taacttcaag aactctcgat
     1501 acacctctcg cactcactgc taccaatggc taccgccagt ggcgctttgt cgtgtctttc
     1561 agggttggat tcaagagtac agttacctga taaagacgtg gtagtcgggc tgaacgggga
     1621 gttcgtgcat acagcccagc ttggagcgaa ccacctacaa ggaacccagt tgcacgggta
     1681 ggaatgagaa aacgccacct tacggcggac tgcaacgggt aaacctcagg gtgggaacag
     1741 gagagcgcac gagggagcga cccatcggaa acggtgggga tctttaagtc ctgtcaggtt
     1801 tcgccacttc tgatttgagc gccggaaatc acctgatttc tgtgaagctt gtcaggaggg
     1861 cgaagcctat ggaaaaccgg caatccccag aacctcctta tggccttctg cctgagcagg
     1921 taacgctcgc cgcagtgtca tgaccgaacg aagtgagcga atgaccgagg aagcgtaatg
     1981 tctgtaatgc tgaacaggga tcgtgtcgct cggtacacac gtttcctccc tgattacaca
     2041 cccggctgca acagtttcct gtcgttttcc acttttccct gcacagctat acaacggcaa
     2101 catccgggca ggacatgtaa agttagctaa ctttacgcct gccttattcg catgactgct
     2161 caaaggaaaa accatgactg atgatcggac actgcaactg cgcctgacag ggttccgtaa
     2221 agcggaggcc tctctcaggc ttgaagggat ggatccatca ggacccccgc tttatgaatc
     2281 ggtaaagaca aggattcttt ccggtgacat caccttcgat gaaggccgca ctgagatacg
     2341 ggctcattac cagaagcggg cgaacagtaa ctgacgcgga caggaaatgt cttgtcatta
     2401 ccgccgcttt gcgccagtga caacatcagc gggacaagat gtgtttttgg agtaccgccg
     2461 acactccaga atgtttcatc aggcgccgcc cgatacgctg agtttcgtgc gtacgaaatt
     2521 tctctgctgt tgagatctag ggcaggattc gcaaagtgct ggcgtttgta cccaccggaa
     2581 gctgccgcgc ctggcggctt ggccaacgcc tcacggccgc acagtcaact gtgcacccgt
     2641 tcaccgttac cagatcccct gattccggcc gggcctgcct gcactggcca aagccctaaa
     2701 actgcgcaat cagcagcgcg ggggcagttg ataaccactt tttactgtca tacttatttg
     2761 ccggctctct gatcggtacc ggctgactgt ttgtgcaaat tttgtcggac atcctgaccc
     2821 tcgatgtccg ttttttttgt tcaaaattcg cctttagtgc cagcattcgt ccgaaaccgg
     2881 ccgccattca cttccgtgca tagccatgca ggcgcgcaga aatcatcagg cgcgtttttt
     2941 cacgatatgg acagggaaag gtgccggaaa cggcccgcac gcggcagaaa cgcgctgagg
     3001 gcctctgcgg cggtgcacgc aagagatgtt atggtaaatt ggactctcta caggagagtg
     3061 tgtttgtcag cctattaact tttcggatta ccgcgcttct taggtctatt aacttcactt
     3121 tttcgattcg cctctctttc ttcgataagc tctttcgaaa aaccttccag caggtctacc
     3181 agtccgttca gatcgtaatg gtttgttgtt ctggcattgt ctttcccttc tttgtatcga
     3241 ggtatccgct tgatggcacc acactgttcc aaatgaataa aacttctttg aacggttttt
     3301 agtgaaacgc ccagcatgtt cgccagtctc tttttcgaag gtcttggg
//
