LOCUS       CP125018                6015 bp    DNA     circular BCT 16-MAY-2023
DEFINITION  Escherichia coli strain KFS-D24 plasmid pKFS-D24_4, complete
            sequence.
ACCESSION   CP125018
VERSION     CP125018.1
DBLINK      BioProject: PRJNA956323
            BioSample: SAMN34598748
KEYWORDS    .
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 6015)
  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  JOURNAL   Unpublished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 6015)
  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 16:50:12
            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)                     :: 5,137
            CDSs (total)                      :: 5,015
            Genes (coding)                    :: 4,789
            CDSs (with protein)               :: 4,789
            Genes (RNA)                       :: 122
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 94
            ncRNAs                            :: 6
            Pseudo Genes (total)              :: 226
            CDSs (without protein)            :: 226
            Pseudo Genes (ambiguous residues) :: 0 of 226
            Pseudo Genes (frameshifted)       :: 82 of 226
            Pseudo Genes (incomplete)         :: 157 of 226
            Pseudo Genes (internal stop)      :: 38 of 226
            Pseudo Genes (multiple problems)  :: 47 of 226
            Pseudo Genes (short protein)      :: 4 of 226
            ##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..6015
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="KFS-D24"
                     /isolation_source="Fecal sludge"
                     /db_xref="taxon:562"
                     /plasmid="pKFS-D24_4"
                     /geo_loc_name="Uganda"
                     /lat_lon="0.19 N 32.35 E"
                     /collection_date="2018"
                     /collected_by="Hidenori Harada, Mai Tanaka"
     gene            join(5633..6015,1..151)
                     /locus_tag="QL134_25645"
     CDS             join(5633..6015,1..151)
                     /locus_tag="QL134_25645"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:YP_005221103.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WHJ82107.1"
                     /translation="MASTEEKLLTLLLSVEHLQHTAMEQQKAVADSLAVARETLRGYRD
                     ISDGVAKQVRDEVRNEVQRLDVAGLIGERISQDFQRLEESVANMKANADALNRDIATIH
                     SNIVQEYNTLKGYSWKWLGGVSVAFLVMFSVLGWGMKTILDRNYNATAAVYQKVVTLED
                     KLVEKPVTGKSRKN"
                     /name="hypothetical protein"
     gene            372..2009
                     /locus_tag="QL134_25650"
     CDS             372..2009
                     /locus_tag="QL134_25650"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000012964.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="colicin-like bacteriocin tRNase domain-containing
                     protein"
                     /protein_id="WHJ82108.1"
                     /translation="MSGGDGRDHNSGAHNTGGNINGGPTGLGGNGGASDGSGWSSENNP
                     WGGGSGSGVHWGGGSGNGNGGGNGNSGGGSNSSVAAVAFGFPALATPGAGTLGIAVSGE
                     ALSAAIADIFAALKGPFKFSAWGIALYGILPSEIAKDDPNMMSKIVTSLPAETVTNVQV
                     STLPLDQATVSVTKRVTDVVKDTRQHIAVVAGVPMSVPVVNAKPTRTPGVFHASFPGVP
                     SLTVSTVKGLPVSTTLPRGITEDKGRTAVPAGFTFGGGSHEAVIRFPKESGQKPVYVSV
                     TDVLTPAQVKQRQDEEKRLQQEWNDAHPVEVAERNYEQARAELNQANKDVARNQERQAK
                     AVQVYNSRKSELDAANKTLADAKAEIKQFERFAREPMAAGHRMWQMAGLKAQRAQTDVN
                     NKKAAFDAAAKEKSAADAALSSAMESRKKKEDKKRSAENKLNEEKNKRRKGTKDYGHDY
                     HPAPKTEDIKGLGELKEGRPKTPKQGGGGKRARWYGDKGRKIYEWDSQHGELEGYRASD
                     GQHLGSFDPKTGKQLKGPDPKRSIKKYL"
                     /name="colicin-like bacteriocin tRNase domain-containing
                     protein"
     gene            2019..2276
                     /locus_tag="QL134_25655"
     CDS             2019..2276
                     /locus_tag="QL134_25655"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_010891189.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="cloacin immunity family protein"
                     /protein_id="WHJ82109.1"
                     /translation="MGLKLHIHWFDKKNEEFKGGEYSKDFGDDGSVIERLGMPLKDNIN
                     NGWFDVEKRWVPILQPYFKNVIDISKFDYFVSFDYRDGDW"
                     /name="cloacin immunity family protein"
     gene            2360..2503
                     /locus_tag="QL134_25660"
     CDS             2360..2503
                     /locus_tag="QL134_25660"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000724569.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology. GO_component:
                     GO:0019867 - outer membrane [Evidence IEA]; GO_process:
                     GO:0019835 - cytolysis [Evidence IEA]"
                     /codon_start=1
                     /transl_table=11
                     /product="colicin release lysis protein"
                     /protein_id="WHJ82110.1"
                     /translation="MKKITGIILLLLAAIILAACQANYIRDVQGGTVSPSSSAELTGVE
                     TQ"
                     /name="colicin release lysis protein"
     gene            3001..3936
                     /locus_tag="QL134_25665"
     CDS             3001..3936
                     /locus_tag="QL134_25665"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_011666805.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="replication initiation protein"
                     /protein_id="WHJ82111.1"
                     /translation="MSAALQYFEENLPLRPYHTDDLAFGLRISGKGRALLARYIQQNQP
                     HAQFWLVFDVDREGAAIDWSDLNAPAPNITIKNPVNGHAHLLYALNIAVRTAPDASVKA
                     LKYAAAIERALCEKLGADVNYSGLICKNPFHLEWQVMEWREEAYTLDELADYLDLSTSA
                     RRSIDKHYGMGRNCHLFEMTRKWAYRAIRQGWPAFSQWLDAVIQRVEMYNASLPVPLSP
                     PECRAIGKSIAKYTHRNFTAETFAQYVADTHTPEIQAKRGRKGGIAKGEAYDDKRFMAL
                     CMLENGYSQKAIAAMLEVSTRTIRNWKSGK"
                     /name="replication initiation protein"
     gene            complement(4130..4528)
                     /locus_tag="QL134_25670"
     CDS             complement(4130..4528)
                     /locus_tag="QL134_25670"
                     /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="WHJ82105.1"
                     /translation="MRISNIEWLKKRIGFIRKLGEQTARQRQIIDLLDNEAGLTEQERK
                     LLHVLATAEKNDLQAQESERKQAVQKRIEGKKQRRERNHRLFLAAGLLIEAGLVDTKTG
                     ELCYKKDRILQALKEIKYDLETSPNPDA"
                     /name="hypothetical protein"
     gene            4704..5630
                     /locus_tag="QL134_25675"
     CDS             4704..5630
                     /locus_tag="QL134_25675"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:YP_005221102.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MobA/MobL family protein"
                     /protein_id="WHJ82106.1"
                     /translation="MATYHLSVKFGGKGQAANHADYIERKEKYRDRQDLEYSAHGNMPE
                     WARDNPSHFWQAADQFERANGSTYRELEIALPRELTAEQRLELVQDFVRQEAGERHAWS
                     FAIHNPKASIDGGEQPHAHIMMSQRVNDGIERTPEQYFRRYNARYPERGGAKKDSGSLT
                     LTQQKEQLRELRKRWEVKHNEHMRKHGFERGFIDCRTLKEQGIERRPEVHLGFEAAGRL
                     DDAQRHDIMQKRSEPDYSRHLEQARTVGHDIREWLDTPVKQHELVRRLQHDVAREHGFD
                     MRDRVSRQNRTEPERVKSPSRGFSMGF"
                     /name="MobA/MobL family protein"
     BGC             1..6015
                     /name="RiPP-like"
                     /gene="RiPP-like"
                     /tool="antismash"
     Typing          3002..3936
                     /name="Col156"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="94.338"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          4705..5627
                     /name="MOBQ"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="98.052"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 ctttctggtt atgttcagtg tgctcggatg ggggatgaaa acaattctcg acaggaacta
       61 caacgccaca gcggcggtgt atcagaaagt tgtgacactg gaagataaac tggtggagaa
      121 acctgtcacg ggtaagagcc ggaaaaactg acgcgcttcg cttgtccaac gcctcacgac
      181 ccgcgaaagg atttcgcgtt ccgttcaccg ttttcatgag tgattcctcc gaactgccaa
      241 aaaatatccc cccctgactt gacagaaaaa ataatggcga gtactttttg gtctgtgcat
      301 aaaaccagtg gttttatgta cagtatcaac tatataatca attgttttaa cgcttaaaag
      361 agggaatttt tatgagcggt ggagatggac gcgaccacaa cagtggcgca cataacacag
      421 gtggtaacat taatggcggc cctacggggc ttggtggaaa tggtggggct tctgacggtt
      481 caggatggag ttcggaaaat aacccatggg gtggcggttc cggtagtggt gttcactggg
      541 gaggtggctc cggcaatggt aatggcgggg ggaatggtaa ttccggtggt ggcagcaatt
      601 catccgtagc agcagtggca tttggttttc ctgctttggc aactcctggt gccggaacgc
      661 tgggtatcgc cgtctctggt gaggctttat ctgcggcaat agcggatatc tttgcagccc
      721 tgaaaggccc gtttaaattc agcgcatggg gtattgcgct ttacggcatt ctgccatctg
      781 aaatagcaaa agatgacccg aatatgatgt caaagattgt gacgtcatta ccggcagaaa
      841 cagtgacgaa tgttcaggtc agtacacttc cgctggacca ggcaactgtc agcgtgacga
      901 aacgtgtgac agatgttgtg aaggacacac gacagcatat tgccgtagtt gcaggtgtgc
      961 ctatgagtgt gcctgttgtg aatgccaaac caacacgtac tccaggtgta tttcacgcat
     1021 catttcctgg tgtcccttct ctgacagtca gcactgtcaa aggccttccg gtgtcaacaa
     1081 cccttccccg tggtattacg gaggataaag gccggactgc cgttcctgcg ggatttacct
     1141 ttggtggtgg ttcacatgaa gcggtgattc gctttccgaa agaaagtggg cagaagccgg
     1201 tttatgtatc agtgacagat gttcttaccc cagcacaggt aaaacaacgt caggatgagg
     1261 aaaaacgcct ccagcaggaa tggaatgacg cacatccggt ggaagtggct gaacgcaatt
     1321 atgaacaggc ccgcgcagaa ctgaatcagg ctaataaaga tgttgccaga aaccaggaac
     1381 gacaggctaa agctgttcag gtttataatt ctcgtaaaag tgaacttgat gcagcgaata
     1441 aaactcttgc tgatgcaaag gctgaaataa aacaattcga gcgatttgcc cgagaaccaa
     1501 tggctgctgg tcacagaatg tggcaaatgg cagggcttaa ggcccagcgg gcacagacgg
     1561 atgtaaataa taagaaggct gcatttgatg ctgccgcaaa agagaagtca gcagcagatg
     1621 ctgcattgag ttctgcgatg gaaagcagga agaagaaaga agataagaaa aggagtgctg
     1681 aaaataaatt aaacgaagag aaaaataaac gccgaaaagg cactaaagat tatggccatg
     1741 attatcatcc agctcctaaa actgaggata ttaaaggttt gggggaatta aaagagggga
     1801 ggccaaaaac tccaaagcaa ggtggtggag gtaagcgtgc cagatggtat ggagataagg
     1861 ggcgtaaaat ttatgagtgg gactctcagc atggtgagct tgagggctat cgagccagtg
     1921 atggtcagca tcttggttca tttgacccta aaaccggtaa gcagttgaaa ggtccagatc
     1981 cgaaacgaag tattaaaaag tatctttaag gtgatgttat gggacttaaa ttacacattc
     2041 attggtttga taagaagaat gaggaattta aaggtggtga gtattcaaag gatttcggtg
     2101 atgatggttc ggttattgaa cgtcttggaa tgcctttaaa ggataatatt aataacggtt
     2161 ggtttgatgt tgaaaagaga tgggtgccaa tattacagcc atactttaaa aatgttattg
     2221 atattagtaa gttcgattac tttgtttctt tcgattatcg tgatggtgac tggtaattaa
     2281 actatcaggg acgagtaata aagtgtttga ttcaggtgtt caaggatgaa ttcctgaatc
     2341 catatataca gggaatcgta tgaagaaaat aacagggatt attttgttgc ttcttgcagc
     2401 cattattctt gctgcatgtc aggcaaacta tatccgtgat gttcagggcg ggactgtatc
     2461 accgtcatcc tctgctgaac tgaccggagt ggaaacgcag taacctgcaa tcctcatttg
     2521 acaaggacaa agcgtgtcag gctgattctg acgcgctttt tttgttgaag tgccacaaaa
     2581 attccatgtg ggagatggga tctaaaatct ccgtgcagaa ccttccatcc ggagggagaa
     2641 aacttttcgt tttgagccgt tcggtgttca gaacgcacga aaccgatcgc acatcgcttt
     2701 cgtgcatagt tatgcaacgc cctgaaaacg attctgacgc gtttttctgg tttgtcctgg
     2761 tgttttcttg tctttttgcg ttttttgcgc cagaaagcga ttgagggcgt tttaaggggt
     2821 acgtacaacg ggagttatgg taaatggatc gggttttcgg gaaggatcga caggatttgc
     2881 cgttgggtgt agtgtaagcg actgaaaaac aaacgcccct gaaattcgtg tctctccgcc
     2941 aagattgtca cgagaataca ggggcgaggt cggtcgataa cctggaagga atcgtaacac
     3001 atgagcgccg cgcttcaata cttcgaagaa aatttacccc tccgccccta tcacacggat
     3061 gatctcgctt tcggccttcg tatctccggt aaagggcgcg cgcttcttgc acggtatatc
     3121 cagcagaacc aacctcatgc gcagttctgg ctggtttttg acgttgaccg cgagggggct
     3181 gcgattgact ggagcgacct gaacgccccc gcaccgaaca tcaccataaa aaatcccgtg
     3241 aacggtcacg cccacctgct ctacgcactc aatatcgccg tgagaaccgc gcctgatgct
     3301 tcggttaagg cgctgaaata cgccgccgcg attgaacgtg cgttgtgtga aaaactgggc
     3361 gcagatgtaa actacagcgg actgatttgc aaaaatccgt tccatctgga atggcaggtg
     3421 atggagtggc gtgaggaagc ctataccctc gatgaactgg ctgattatct cgatttgagc
     3481 acttcagcgc gccgtagcat cgataaacat tacggaatgg ggagaaactg ccatctgttc
     3541 gaaatgacgc gcaaatgggc ttacagggcg attcgtcagg gctggccagc attctcacag
     3601 tggcttgatg ccgtgattca gcgtgtcgaa atgtacaacg catcgcttcc cgttccgctt
     3661 tcacctcctg aatgtcgggc tattggcaag agtattgcga aatacacgca caggaacttc
     3721 acggcggaaa ctttcgcaca gtatgtggct gatacgcaca cgccagaaat acaggccaag
     3781 agaggcagga aaggtggcat cgctaaaggc gaagcctacg atgacaagcg tttcatggcg
     3841 ctatgtatgc tggagaatgg atattctcag aaagctattg cggcgatgtt ggaggtttct
     3901 actcgaacca ttcgaaactg gaaaagcgga aaatagccta tatcagataa cagcgccttt
     3961 ctggcgtttt tttgagcctt aggtcttttg ccgtttttcc ccgttcagcc ctgcaatggt
     4021 gctgttttcc gcatgattgt gctggtagtg ctcgccgcag tctcatgacc gagcgtagcg
     4081 agcgaatgag cgaggaagca ccagggaaca ggaacacgga tggaggcact tacgcgtctg
     4141 ggtttgggga tgtctccaga tcgtacttaa tttccttaag tgcctgtaat atcctgtctt
     4201 ttttatagca tagctcgcct gtttttgtgt ctaccagtcc tgcttcgatc agtagcccag
     4261 ccgcgagaaa gagtcggtga ttgcgttctc gtcgttgttt ttttccctcg attcgttttt
     4321 ggaccgcctg ttttcgttcg ctctcctgtg cctgtaagtc gtttttttcc gctgttgcca
     4381 gtacgtggag gagtttgcgt tcctgttctg tgagtcctgc ttcgttgtcg agcaggtcaa
     4441 taatctgtct ctgtcgtgcg gtctgttctc cgagcttcct gatgaatccg atccgtttct
     4501 tcagccattc gatgttgctg atgcgcatgt tcgtggtgct ccctggtgtt ttttgctgtg
     4561 tgttgtggtc gtgcagtata tcgcttgcgg tcggtgggtg cagggggtat cttccgtgct
     4621 aattcgtaaa attagaagga agcgcactta tatgtttctc tccttcgtcg agaaacagtg
     4681 cgctcctgcg gagggctgaa accgtggcaa cctatcacct cagcgttaaa tttggtggca
     4741 aggggcaggc tgcaaaccac gccgattaca tcgagcgcaa agagaaatac cgcgaccgtc
     4801 aggatttgga atattccgca cacggaaaca tgccggaatg ggcgcgagat aatccctcac
     4861 atttctggca ggcggctgac cagtttgaac gtgcgaacgg ttcgacctat cgggaacttg
     4921 aaattgcatt accccgtgaa ctgacagcgg aacagcgcct tgaactggtg caggattttg
     4981 tacgtcagga agctggcgaa cggcacgcct ggagttttgc cattcacaat ccgaaagcga
     5041 gcattgacgg cggcgaacag cctcatgcgc atatcatgat gagccagcgt gtgaatgatg
     5101 gcattgaacg tacaccggaa cagtatttcc ggcgctataa cgccaggtat cccgagcggg
     5161 gaggtgcgaa aaaggattcc ggaagcctga ctctcactca gcaaaaagag cagttgcggg
     5221 aattgcgaaa acgctgggag gtgaagcaca acgaacatat gagaaagcat ggctttgaaa
     5281 ggggcttcat tgactgccgg acgctgaaag aacagggcat tgaacgacgt cccgaagtgc
     5341 atctgggttt tgaagctgcc ggacggcttg atgatgccca gcgtcatgac atcatgcaaa
     5401 aacggtctga accggactat tcccgccatc ttgaacaggc gcgaacggtc gggcatgaca
     5461 tcagggaatg gctggacact ccggttaagc aacatgaact ggtcagaagg ctgcaacatg
     5521 atgttgcgcg ggagcatggc tttgacatga gagacagagt gagcagacag aaccgaactg
     5581 aacctgaacg ggttaaatca ccgtcacgtg gattttctat gggattctga acatggccag
     5641 cacagaagaa aaattactca cgctcctgtt atcggtggag catctgcaac ataccgcaat
     5701 ggagcaacag aaagctgttg ctgattctct ggctgtggca agggaaacac ttcgcggata
     5761 tcgggatatt tctgacggtg tggcaaaaca ggtcagggat gaagtcagaa acgaagtgca
     5821 gaggctggat gttgcagggc tgataggtga gcgcatcagt caggattttc agcggctgga
     5881 agagtcagtc gcaaacatga aggcaaacgc ggatgccctg aacagggata ttgcgacaat
     5941 tcacagcaat atcgtgcagg aatacaacac ccttaaaggg tatagctgga aatggctggg
     6001 tggggtgtca gtggc
//
