LOCUS       CP124984                3896 bp    DNA     circular BCT 16-MAY-2023
DEFINITION  Escherichia coli strain KSE-D31 plasmid pKSE-D31_7, complete
            sequence.
ACCESSION   CP124984
VERSION     CP124984.1
DBLINK      BioProject: PRJNA956323
            BioSample: SAMN34598758
KEYWORDS    .
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 3896)
  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  JOURNAL   Unpublished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 3896)
  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 16:43:15
            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)                     :: 5,034
            CDSs (total)                      :: 4,910
            Genes (coding)                    :: 4,652
            CDSs (with protein)               :: 4,652
            Genes (RNA)                       :: 124
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 89
            ncRNAs                            :: 13
            Pseudo Genes (total)              :: 258
            CDSs (without protein)            :: 258
            Pseudo Genes (ambiguous residues) :: 0 of 258
            Pseudo Genes (frameshifted)       :: 82 of 258
            Pseudo Genes (incomplete)         :: 177 of 258
            Pseudo Genes (internal stop)      :: 54 of 258
            Pseudo Genes (multiple problems)  :: 49 of 258
            Pseudo Genes (short protein)      :: 4 of 258
            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..3896
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="KSE-D31"
                     /isolation_source="Sewage"
                     /db_xref="taxon:562"
                     /plasmid="pKSE-D31_7"
                     /geo_loc_name="Uganda"
                     /lat_lon="0.19 N 32.35 E"
                     /collection_date="2018"
                     /collected_by="Hidenori Harada, Mai Tanaka"
     gene            complement(492..1640)
                     /locus_tag="QL154_25160"
     CDS             complement(492..1640)
                     /locus_tag="QL154_25160"
                     /EC_number="2.1.1.37"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_003801590.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology. GO_function:
                     GO:0003886 - DNA (cytosine-5-)-methyltransferase activity
                     [Evidence IEA]; GO_function: GO:0008168 - methyltransferase
                     activity [Evidence IEA]; GO_function: GO:1904047 -
                     S-adenosyl-L-methionine binding [Evidence IEA]; GO_process:
                     GO:0006304 - DNA modification [Evidence IEA]"
                     /codon_start=1
                     /transl_table=11
                     /product="DNA cytosine methyltransferase"
                     /protein_id="WHJ27409.1"
                     /translation="MRSLEIFSGAGGLAKGLELAGFQHVGFVELNKHACDSLRLNFDEE
                     KVFQGDIKNYDLSSLDKIDIVAGGPPCQPFSLGGKHKAHDDSRDMFPFAIKAIEVLQPK
                     AFIFENVKGLLRKSFADYFEYIILRLTYPCLSLSNVSDWRIHLDVLRKARKDKHCGCTY
                     DVSFKLINAADYGVPQIRERVIIVGVRSDLNKKWSFPSVTHTQEKLLWEQHVTGDYWRK
                     HNIDAVIDKGISERLMKRFGIFPPSGKSWVTVRDALKNVPQPYESHGIGDHIFKDGARV
                     YPGHTGSYIDLPSKTLKAGAHGVPGGENMIRYEDGTVRYFTVYEGKLLQTFPREFLIAG
                     AWGEAMRQIGNAVPVLLAQKIGQQLYNLLNEEVEPLLCSNFN"
                     /name="DNA cytosine methyltransferase"
     gene            complement(1640..2284)
                     /locus_tag="QL154_25165"
     CDS             complement(1640..2284)
                     /locus_tag="QL154_25165"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001529705.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology. GO_function:
                     GO:0004518 - nuclease activity [Evidence IEA]"
                     /codon_start=1
                     /transl_table=11
                     /product="Eco29kI family restriction endonuclease"
                     /protein_id="WHJ27410.1"
                     /translation="MHNKKFDRSEHVYRNDSFLELIKDAVRFFSGTPVHSLPPPERFQG
                     AGVYALYYTGHYSLYDEYSRINRLAYNLPIYVGKAVPAGWRQSRISDHETRAGSELSNR
                     IREHGRNIAKTSNLDLCDFSCRFVIFEATGSDMISTVEAALIKIYKPLWNTVVDGFGNH
                     TPGAGRFAQAKSDWDVIHPGREWAEKCTGVHSEPYFIEERIKQYFSKSNFT"
                     /name="Eco29kI family restriction endonuclease"
     gene            complement(2634..2762)
                     /locus_tag="QL154_25170"
     CDS             complement(2634..2762)
                     /locus_tag="QL154_25170"
                     /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="WHJ27408.1"
                     /translation="MTRQRVVGDLSMTQHTVALVFREGESPESREEKYWMTRRRLP"
                     /name="hypothetical protein"
     Typing          complement(3414..3498)
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="97.674"
                     /coverage="100.0"
                     /evalue="6.569999999999999e-34"
     Typing          complement(3..187)
                     /name="ColRNAI_rep_cluster_1857"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="97.849"
                     /coverage="93.0"
                     /evalue="1.08e-85"
     Typing          3518..3896
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="92.727"
                     /coverage="99.0"
                     /evalue="1.38e-153"
ORIGIN
        1 ctccgccttt ctcccttcgg gaagcgtggc gctttctcat agctcacgct gttggtatct
       61 cagttcggtg taggtcgttc gctccaagct gggctgtgtg cacgaacccc ccgttcagcc
      121 cgaccgctgc gccttatccg gtaactatcg tcttgagtcc aacccggtaa gacacgcctt
      181 aacgccactg gcagcagcca ttggtaactg gacaaggtgg attgagatat taagagttct
      241 tgaagtggtg gcctaactga ggctacacta gaaggacagt atttggtatc tgcgctccac
      301 caagccagtt accttcggga aaaagagttg gtagctcttg attccggcaa acgaaccacc
      361 gttggtagcg gtggtttttt tgtttacagg cagcagatta cgcgcagaaa aaaaggatct
      421 caagaagatc ctttgatctt tttttgcaaa ttgcctctat ggctgtatca ccaccataga
      481 gacacaaact tttaattgaa gttagagcac aataacggct caacctcttc attcaataag
      541 ttatacaatt gctgccctat cttctgagct agcaacacag gaactgcatt accaatctgc
      601 ctcatagcct ccccccaagc tcctgcaatc agaaactctc gaggaaaagt ctgaagaagc
      661 ttcccttcat aaaccgtaaa ataacgaaca gtcccatcct catacctaat catattttca
      721 cctccaggta cgccatgagc gccagcctta agtgtttttg aaggcaaatc gatataactt
      781 ccagtatgac caggataaac tcgagcgcca tctttaaaga tatgatctcc aataccatgt
      841 gactcatacg gttgaggaac attctttaat gcgtccctaa cagtaaccca gcttttcccc
      901 gatgggggga aaataccaaa acgtttcatt aaacgctcag aaataccttt atctataacc
      961 gcatcaatat tatgctttcg ccaatagtca ccagtaacat gctgttccca cagcaatttt
     1021 tcttgagtat gcgttacact tggaaaagac cattttttat tcaaatcact tcgaacacca
     1081 acaattatga cccgttccct aatttgtgga actccataat cagctgcatt gattaattta
     1141 aaactgacat catatgtaca cccacagtgt ttatccttgc gagcttttct taatacatct
     1201 agatgtattc tccaatcact tacattactt aacgataaac aaggataagt caaacgaaga
     1261 attatgtatt caaaatagtc cgcaaatgat tttctaagca accctttaac attttcaaaa
     1321 ataaaagctt ttggttgcaa tacttcaatt gcttttattg caaatggaaa catatcccta
     1381 gagtcatcat gagctttatg ttttccgccc aatgaaaatg gttggcaagg aggcccgcca
     1441 gcaacaatat ctattttatc tagagatgaa aggtcataat ttttaatatc tccctgaaat
     1501 accttctcct catcaaaatt aagtcgcaaa gaatcacatg catgcttgtt taactcaaca
     1561 aatcctacat gctgaaatcc tgccaactct agacctttag ccaagccgcc ggctcctgaa
     1621 aaaatctcta atgatctcat tatgtaaaat tactcttaga aaaatactgt ttaattctct
     1681 cctcaataaa gtatggctca gaatgaacac ctgtacattt ctcagcccac tccctgccag
     1741 gatgtattac atcccaatca gatttagctt gcgcaaatcg cccggcacca ggggtatgat
     1801 ttccaaagcc atcaacaacg gtattccaca aaggcttata aattttaata agagcggcct
     1861 caactgtact aatcatatca gaccccgtag cctcaaagat aacaaagcga catgaaaaat
     1921 cacacaaatc tagattcgat gtttttgcta tatttcggcc atgttctcta attctattag
     1981 atagttcaga accagcccta gtttcatgat cactaattct agactgacgc caaccagcag
     2041 gaacagcctt gccaacataa ataggaaggt tatatgccaa cctatttata cgagaatatt
     2101 catcatataa tgaataatgt cctgtatagt aaagagcata caccccagca ccttgaaacc
     2161 gttccggtgg tggtaatgaa tgaacaggcg taccactaaa aaaacgaacg gcatctttta
     2221 ttaactctag gaaagagtca tttctataaa catgctcaga tctatcaaat ttcttattgt
     2281 gcattatgtt ttccgaaagg tctttatatt aacactccta ctcaacatca cctatgatac
     2341 gatcataaag ctaatacccc aacccatacg catttaccat aacgtcgcat tgtacgcacc
     2401 gttaaaacgc gctcagcgcg cttctggcgc aaaaaccgta aaaatggatg ttttcccccg
     2461 ggtaaaccgg aaaaatgcgt caggaacgct ttcagcgcgt tgcatgacta tgcataaaac
     2521 tgaatggcga gcggtttggg cgcgtctgat gcccataagg cgtattttct gacgttttca
     2581 gccctgataa gaagaaatca gactgtagtt acagacgagt cgtgagcgat tcactacggg
     2641 agtcgtcggc gagtcatcca gtatttttcc tcgcgactct ctggcgactc gccttctctg
     2701 aacaccagag cgacagtgtg ttgagtcatc gataaatcac cgacgactcg ttgccgagtc
     2761 atccagtagt cgccgacgac ccgcttttgt ataaatctga ataagaaaat acatttttta
     2821 aaacataaca acctgattta aaaaagaaat cagcaaaaag ttagttttgc gtggggtgtg
     2881 ggcatccggg gcatgagaac agactcgcgt ttttctggag gaactgcggg gatttttgat
     2941 taaacagtac tcatcgcaga gcggaatttt atgcaacgcc ggctgtgctg cacggggatt
     3001 tttaatcccc cggcccgtta ttcatctcca cgggcgacgg ggatacataa acccgacagc
     3061 agaggacggg tgagcgcgaa tcccagagat gatgaaaaaa gaggcagaga aacgcgcccg
     3121 ggcacgtttt atcttattgc tgtggtgttg tccagggtgt cggggctgtg ccctgaccag
     3181 gtggcatttg tctgattgcg cgtgcgcggt ccgacaaatg cacatcctgc cccgtcctgt
     3241 acgtgttttt ttcaccagaa caacttcacg aagtggcgga tgaacgctac caacgttgcc
     3301 gggaacgctt cggcgatgat ggcataacgg gctgatacag gcagctcccg gagacggtca
     3361 cagcttgcct gtgagcggat gccgggagcc gacaagcccg tcagggcgcg tcagggggtt
     3421 tcggggcgaa gccctgaacc agtcacgtag cgatagcgga gtgtatactg gtttaaccat
     3481 gcggcatcag tgcagattgt aagaaaagag caccatatgc ggtgtgaaat gccgcacaga
     3541 tgcgtaagga gaaaatgcac gttccggcgc tcttccgctt cctcgctcac tgactcgctg
     3601 cgctcggtcg ttcggctgcg gcgagcggtg tcggctcact caaaagcgga gatgcggtta
     3661 tccacagaat caggggataa cgccaaaaga aacatgtgag caaaaaacga gaacccggaa
     3721 aaggccacgc cgctggcgtt tttccatagg ctccgccccc ctgacgagca tcacaaaaat
     3781 cgacgctcaa gtcagaggtg gcgaaacccg acaggactat aaagatacca ggcgtttccc
     3841 cctggaagct ccctcgtgcg ctctcctgtt ccgaccctgc cgcttaccgg atacct
//
