LOCUS       CP125024                6015 bp    DNA     circular BCT 16-MAY-2023
DEFINITION  Escherichia coli strain KFS-D21 plasmid pKFS-D21_4, complete
            sequence.
ACCESSION   CP125024
VERSION     CP125024.1
DBLINK      BioProject: PRJNA956323
            BioSample: SAMN34598747
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  JOURNAL   Unpublished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 16:46:04
            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)                     :: 5,133
            CDSs (total)                      :: 5,011
            Genes (coding)                    :: 4,790
            CDSs (with protein)               :: 4,790
            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)              :: 221
            CDSs (without protein)            :: 221
            Pseudo Genes (ambiguous residues) :: 0 of 221
            Pseudo Genes (frameshifted)       :: 81 of 221
            Pseudo Genes (incomplete)         :: 152 of 221
            Pseudo Genes (internal stop)      :: 38 of 221
            Pseudo Genes (multiple problems)  :: 46 of 221
            Pseudo Genes (short protein)      :: 4 of 221
            ##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-D21"
                     /isolation_source="Fecal sludge"
                     /db_xref="taxon:562"
                     /plasmid="pKFS-D21_4"
                     /geo_loc_name="Uganda"
                     /lat_lon="0.19 N 32.35 E"
                     /collection_date="2018"
                     /collected_by="Hidenori Harada, Mai Tanaka"
     gene            163..561
                     /locus_tag="QL133_25600"
     CDS             163..561
                     /locus_tag="QL133_25600"
                     /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="WHJ86892.1"
                     /translation="MRISNIEWLKKRIGFIRKLGEQTARQRQIIDLLDNEAGLTEQERK
                     LLHVLATAEKNDLQAQESERKQAVQKRIEGKKQRRERNHRLFLAAGLLIEAGLVDTKTG
                     ELCYKKDRILQALKEIKYDLETSPNPDA"
                     /name="hypothetical protein"
     gene            complement(755..1690)
                     /locus_tag="QL133_25605"
     CDS             complement(755..1690)
                     /locus_tag="QL133_25605"
                     /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="WHJ86893.1"
                     /translation="MSAALQYFEENLPLRPYHTDDLAFGLRISGKGRALLARYIQQNQP
                     HAQFWLVFDVDREGAAIDWSDLNAPAPNITIKNPVNGHAHLLYALNIAVRTAPDASVKA
                     LKYAAAIERALCEKLGADVNYSGLICKNPFHLEWQVMEWREEAYTLDELADYLDLSTSA
                     RRSIDKHYGMGRNCHLFEMTRKWAYRAIRQGWPAFSQWLDAVIQRVEMYNASLPVPLSP
                     PECRAIGKSIAKYTHRNFTAETFAQYVADTHTPEIQAKRGRKGGIAKGEAYDDKRFMAL
                     CMLENGYSQKAIAAMLEVSTRTIRNWKSGK"
                     /name="replication initiation protein"
     gene            complement(2188..2331)
                     /locus_tag="QL133_25610"
     CDS             complement(2188..2331)
                     /locus_tag="QL133_25610"
                     /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="WHJ86894.1"
                     /translation="MKKITGIILLLLAAIILAACQANYIRDVQGGTVSPSSSAELTGVE
                     TQ"
                     /name="colicin release lysis protein"
     gene            complement(2415..2672)
                     /locus_tag="QL133_25615"
     CDS             complement(2415..2672)
                     /locus_tag="QL133_25615"
                     /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="WHJ86895.1"
                     /translation="MGLKLHIHWFDKKNEEFKGGEYSKDFGDDGSVIERLGMPLKDNIN
                     NGWFDVEKRWVPILQPYFKNVIDISKFDYFVSFDYRDGDW"
                     /name="cloacin immunity family protein"
     gene            complement(2682..4319)
                     /locus_tag="QL133_25620"
     CDS             complement(2682..4319)
                     /locus_tag="QL133_25620"
                     /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="WHJ86896.1"
                     /translation="MSGGDGRDHNSGAHNTGGNINGGPTGLGGNGGASDGSGWSSENNP
                     WGGGSGSGVHWGGGSGNGNGGGNGNSGGGSNSSVAAVAFGFPALATPGAGTLGIAVSGE
                     ALSAAIADIFAALKGPFKFSAWGIALYGILPSEIAKDDPNMMSKIVTSLPAETVTNVQV
                     STLPLDQATVSVTKRVTDVVKDTRQHIAVVAGVPMSVPVVNAKPTRTPGVFHASFPGVP
                     SLTVSTVKGLPVSTTLPRGITEDKGRTAVPAGFTFGGGSHEAVIRFPKESGQKPVYVSV
                     TDVLTPAQVKQRQDEEKRLQQEWNDAHPVEVAERNYEQARAELNQANKDVARNQERQAK
                     AVQVYNSRKSELDAANKTLADAKAEIKQFERFAREPMAAGHRMWQMAGLKAQRAQTDVN
                     NKKAAFDAAAKEKSAADAALSSAMESRKKKEDKKRSAENKLNEEKNKRRKGTKDYGHDY
                     HPAPKTEDIKGLGELKEGRPKTPKQGGGGKRARWYGDKGRKIYEWDSQHGELEGYRASD
                     GQHLGSFDPKTGKQLKGPDPKRSIKKYL"
                     /name="colicin-like bacteriocin tRNase domain-containing
                     protein"
     gene            complement(4540..5073)
                     /locus_tag="QL133_25625"
     CDS             complement(4540..5073)
                     /locus_tag="QL133_25625"
                     /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="WHJ86890.1"
                     /translation="MASTEEKLLTLLLSVEHLQHTAMEQQKAVADSLAVARETLRGYRD
                     ISDGVAKQVRDEVRNEVQRLDVAGLIGERISQDFQRLEESVANMKANADALNRDIATIH
                     SNIVQEYNTLKGYSWKWLGGVSVAFLVMFSVLGWGMKTILDRNYNATAAVYQKVVTLED
                     KLVEKPVTGKSRKN"
                     /name="hypothetical protein"
     gene            complement(5076..6002)
                     /locus_tag="QL133_25630"
     CDS             complement(5076..6002)
                     /locus_tag="QL133_25630"
                     /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="WHJ86891.1"
                     /translation="MATYHLSVKFGGKGQAANHADYIERKEKYRDRQDLEYSAHGNMPE
                     WARDNPSHFWQAADQFERANGSTYRELEIALPRELTAEQRLELVQDFVRQEAGERHAWS
                     FAIHNPKASIDGGEQPHAHIMMSQRVNDGIERTPEQYFRRYNARYPERGGAKKDSGSLT
                     LTQQKEQLRELRKRWEVKHNEHMRKHGFERGFIDCRTLKEQGIERRPEVHLGFEAAGRL
                     DDAQRHDIMQKRSEPDYSRHLEQARTVGHDIREWLDTPVKQHELVRRLQHDVAREHGFD
                     MRDRVSRQNRTEPERVKSPSRGFSMGF"
                     /name="MobA/MobL family protein"
     BGC             1..6015
                     /name="RiPP-like"
                     /gene="RiPP-like"
                     /tool="antismash"
     Typing          complement(756..1690)
                     /name="Col156"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="94.338"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          complement(5080..6002)
                     /name="MOBQ"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="98.052"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 cgcaggagcg cactgtttct cgacgaagga gagaaacata taagtgcgct tccttctaat
       61 tttacgaatt agcacggaag ataccccctg cacccaccga ccgcaagcga tatactgcac
      121 gaccacaaca cacagcaaaa aacaccaggg agcaccacga acatgcgcat cagcaacatc
      181 gaatggctga agaaacggat cggattcatc aggaagctcg gagaacagac cgcacgacag
      241 agacagatta ttgacctgct cgacaacgaa gcaggactca cagaacagga acgcaaactc
      301 ctccacgtac tggcaacagc ggaaaaaaac gacttacagg cacaggagag cgaacgaaaa
      361 caggcggtcc aaaaacgaat cgagggaaaa aaacaacgac gagaacgcaa tcaccgactc
      421 tttctcgcgg ctgggctact gatcgaagca ggactggtag acacaaaaac aggcgagcta
      481 tgctataaaa aagacaggat attacaggca cttaaggaaa ttaagtacga tctggagaca
      541 tccccaaacc cagacgcgta agtgcctcca tccgtgttcc tgttccctgg tgcttcctcg
      601 ctcattcgct cgctacgctc ggtcatgaga ctgcggcgag cactaccagc acaatcatgc
      661 ggaaaacagc accattgcag ggctgaacgg ggaaaaacgg caaaagacct aaggctcaaa
      721 aaaacgccag aaaggcgctg ttatctgata taggctattt tccgcttttc cagtttcgaa
      781 tggttcgagt agaaacctcc aacatcgccg caatagcttt ctgagaatat ccattctcca
      841 gcatacatag cgccatgaaa cgcttgtcat cgtaggcttc gcctttagcg atgccacctt
      901 tcctgcctct cttggcctgt atttctggcg tgtgcgtatc agccacatac tgtgcgaaag
      961 tttccgccgt gaagttcctg tgcgtgtatt tcgcaatact cttgccaata gcccgacatt
     1021 caggaggtga aagcggaacg ggaagcgatg cgttgtacat ttcgacacgc tgaatcacgg
     1081 catcaagcca ctgtgagaat gctggccagc cctgacgaat cgccctgtaa gcccatttgc
     1141 gcgtcatttc gaacagatgg cagtttctcc ccattccgta atgtttatcg atgctacggc
     1201 gcgctgaagt gctcaaatcg agataatcag ccagttcatc gagggtatag gcttcctcac
     1261 gccactccat cacctgccat tccagatgga acggattttt gcaaatcagt ccgctgtagt
     1321 ttacatctgc gcccagtttt tcacacaacg cacgttcaat cgcggcggcg tatttcagcg
     1381 ccttaaccga agcatcaggc gcggttctca cggcgatatt gagtgcgtag agcaggtggg
     1441 cgtgaccgtt cacgggattt tttatggtga tgttcggtgc gggggcgttc aggtcgctcc
     1501 agtcaatcgc agccccctcg cggtcaacgt caaaaaccag ccagaactgc gcatgaggtt
     1561 ggttctgctg gatataccgt gcaagaagcg cgcgcccttt accggagata cgaaggccga
     1621 aagcgagatc atccgtgtga taggggcgga ggggtaaatt ttcttcgaag tattgaagcg
     1681 cggcgctcat gtgttacgat tccttccagg ttatcgaccg acctcgcccc tgtattctcg
     1741 tgacaatctt ggcggagaga cacgaatttc aggggcgttt gtttttcagt cgcttacact
     1801 acacccaacg gcaaatcctg tcgatccttc ccgaaaaccc gatccattta ccataactcc
     1861 cgttgtacgt accccttaaa acgccctcaa tcgctttctg gcgcaaaaaa cgcaaaaaga
     1921 caagaaaaca ccaggacaaa ccagaaaaac gcgtcagaat cgttttcagg gcgttgcata
     1981 actatgcacg aaagcgatgt gcgatcggtt tcgtgcgttc tgaacaccga acggctcaaa
     2041 acgaaaagtt ttctccctcc ggatggaagg ttctgcacgg agattttaga tcccatctcc
     2101 cacatggaat ttttgtggca cttcaacaaa aaaagcgcgt cagaatcagc ctgacacgct
     2161 ttgtccttgt caaatgagga ttgcaggtta ctgcgtttcc actccggtca gttcagcaga
     2221 ggatgacggt gatacagtcc cgccctgaac atcacggata tagtttgcct gacatgcagc
     2281 aagaataatg gctgcaagaa gcaacaaaat aatccctgtt attttcttca tacgattccc
     2341 tgtatatatg gattcaggaa ttcatccttg aacacctgaa tcaaacactt tattactcgt
     2401 ccctgatagt ttaattacca gtcaccatca cgataatcga aagaaacaaa gtaatcgaac
     2461 ttactaatat caataacatt tttaaagtat ggctgtaata ttggcaccca tctcttttca
     2521 acatcaaacc aaccgttatt aatattatcc tttaaaggca ttccaagacg ttcaataacc
     2581 gaaccatcat caccgaaatc ctttgaatac tcaccacctt taaattcctc attcttctta
     2641 tcaaaccaat gaatgtgtaa tttaagtccc ataacatcac cttaaagata ctttttaata
     2701 cttcgtttcg gatctggacc tttcaactgc ttaccggttt tagggtcaaa tgaaccaaga
     2761 tgctgaccat cactggctcg atagccctca agctcaccat gctgagagtc ccactcataa
     2821 attttacgcc ccttatctcc ataccatctg gcacgcttac ctccaccacc ttgctttgga
     2881 gtttttggcc tcccctcttt taattccccc aaacctttaa tatcctcagt tttaggagct
     2941 ggatgataat catggccata atctttagtg ccttttcggc gtttattttt ctcttcgttt
     3001 aatttatttt cagcactcct tttcttatct tctttcttct tcctgctttc catcgcagaa
     3061 ctcaatgcag catctgctgc tgacttctct tttgcggcag catcaaatgc agccttctta
     3121 ttatttacat ccgtctgtgc ccgctgggcc ttaagccctg ccatttgcca cattctgtga
     3181 ccagcagcca ttggttctcg ggcaaatcgc tcgaattgtt ttatttcagc ctttgcatca
     3241 gcaagagttt tattcgctgc atcaagttca cttttacgag aattataaac ctgaacagct
     3301 ttagcctgtc gttcctggtt tctggcaaca tctttattag cctgattcag ttctgcgcgg
     3361 gcctgttcat aattgcgttc agccacttcc accggatgtg cgtcattcca ttcctgctgg
     3421 aggcgttttt cctcatcctg acgttgtttt acctgtgctg gggtaagaac atctgtcact
     3481 gatacataaa ccggcttctg cccactttct ttcggaaagc gaatcaccgc ttcatgtgaa
     3541 ccaccaccaa aggtaaatcc cgcaggaacg gcagtccggc ctttatcctc cgtaatacca
     3601 cggggaaggg ttgttgacac cggaaggcct ttgacagtgc tgactgtcag agaagggaca
     3661 ccaggaaatg atgcgtgaaa tacacctgga gtacgtgttg gtttggcatt cacaacaggc
     3721 acactcatag gcacacctgc aactacggca atatgctgtc gtgtgtcctt cacaacatct
     3781 gtcacacgtt tcgtcacgct gacagttgcc tggtccagcg gaagtgtact gacctgaaca
     3841 ttcgtcactg tttctgccgg taatgacgtc acaatctttg acatcatatt cgggtcatct
     3901 tttgctattt cagatggcag aatgccgtaa agcgcaatac cccatgcgct gaatttaaac
     3961 gggcctttca gggctgcaaa gatatccgct attgccgcag ataaagcctc accagagacg
     4021 gcgataccca gcgttccggc accaggagtt gccaaagcag gaaaaccaaa tgccactgct
     4081 gctacggatg aattgctgcc accaccggaa ttaccattcc ccccgccatt accattgccg
     4141 gagccacctc cccagtgaac accactaccg gaaccgccac cccatgggtt attttccgaa
     4201 ctccatcctg aaccgtcaga agccccacca tttccaccaa gccccgtagg gccgccatta
     4261 atgttaccac ctgtgttatg tgcgccactg ttgtggtcgc gtccatctcc accgctcata
     4321 aaaattccct cttttaagcg ttaaaacaat tgattatata gttgatactg tacataaaac
     4381 cactggtttt atgcacagac caaaaagtac tcgccattat tttttctgtc aagtcagggg
     4441 gggatatttt ttggcagttc ggaggaatca ctcatgaaaa cggtgaacgg aacgcgaaat
     4501 cctttcgcgg gtcgtgaggc gttggacaag cgaagcgcgt cagtttttcc ggctcttacc
     4561 cgtgacaggt ttctccacca gtttatcttc cagtgtcaca actttctgat acaccgccgc
     4621 tgtggcgttg tagttcctgt cgagaattgt tttcatcccc catccgagca cactgaacat
     4681 aaccagaaag gccactgaca ccccacccag ccatttccag ctataccctt taagggtgtt
     4741 gtattcctgc acgatattgc tgtgaattgt cgcaatatcc ctgttcaggg catccgcgtt
     4801 tgccttcatg tttgcgactg actcttccag ccgctgaaaa tcctgactga tgcgctcacc
     4861 tatcagccct gcaacatcca gcctctgcac ttcgtttctg acttcatccc tgacctgttt
     4921 tgccacaccg tcagaaatat cccgatatcc gcgaagtgtt tcccttgcca cagccagaga
     4981 atcagcaaca gctttctgtt gctccattgc ggtatgttgc agatgctcca ccgataacag
     5041 gagcgtgagt aatttttctt ctgtgctggc catgttcaga atcccataga aaatccacgt
     5101 gacggtgatt taacccgttc aggttcagtt cggttctgtc tgctcactct gtctctcatg
     5161 tcaaagccat gctcccgcgc aacatcatgt tgcagccttc tgaccagttc atgttgctta
     5221 accggagtgt ccagccattc cctgatgtca tgcccgaccg ttcgcgcctg ttcaagatgg
     5281 cgggaatagt ccggttcaga ccgtttttgc atgatgtcat gacgctgggc atcatcaagc
     5341 cgtccggcag cttcaaaacc cagatgcact tcgggacgtc gttcaatgcc ctgttctttc
     5401 agcgtccggc agtcaatgaa gcccctttca aagccatgct ttctcatatg ttcgttgtgc
     5461 ttcacctccc agcgttttcg caattcccgc aactgctctt tttgctgagt gagagtcagg
     5521 cttccggaat cctttttcgc acctccccgc tcgggatacc tggcgttata gcgccggaaa
     5581 tactgttccg gtgtacgttc aatgccatca ttcacacgct ggctcatcat gatatgcgca
     5641 tgaggctgtt cgccgccgtc aatgctcgct ttcggattgt gaatggcaaa actccaggcg
     5701 tgccgttcgc cagcttcctg acgtacaaaa tcctgcacca gttcaaggcg ctgttccgct
     5761 gtcagttcac ggggtaatgc aatttcaagt tcccgatagg tcgaaccgtt cgcacgttca
     5821 aactggtcag ccgcctgcca gaaatgtgag ggattatctc gcgcccattc cggcatgttt
     5881 ccgtgtgcgg aatattccaa atcctgacgg tcgcggtatt tctctttgcg ctcgatgtaa
     5941 tcggcgtggt ttgcagcctg ccccttgcca ccaaatttaa cgctgaggtg ataggttgcc
     6001 acggtttcag ccctc
//
