LOCUS       CP125016                5165 bp    DNA     circular BCT 16-MAY-2023
DEFINITION  Escherichia coli strain KFS-D24 plasmid pKFS-D24_5, complete
            sequence.
ACCESSION   CP125016
VERSION     CP125016.1
DBLINK      BioProject: PRJNA956323
            BioSample: SAMN34598748
KEYWORDS    .
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 5165)
  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  JOURNAL   Unpublished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 5165)
  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..5165
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="KFS-D24"
                     /isolation_source="Fecal sludge"
                     /db_xref="taxon:562"
                     /plasmid="pKFS-D24_5"
                     /geo_loc_name="Uganda"
                     /lat_lon="0.19 N 32.35 E"
                     /collection_date="2018"
                     /collected_by="Hidenori Harada, Mai Tanaka"
     gene            complement(join(4483..5165,1..244))
                     /locus_tag="QL134_25585"
     CDS             complement(join(4483..5165,1..244))
                     /locus_tag="QL134_25585"
                     /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="WHJ82096.1"
                     /translation="MATYHLSVKFGGKGQAANHADYIERKEKYRDRQDLEYSAHGNMPE
                     WARDNPSHFWQAADQFERANGSTYRELEIALPRELTPEQRLELVQDFVRQEAGERHAWS
                     FAIHNPKASIDGGEQPHAHIMMSQRVNDGIERTPEQYFRRYNARYPERGGAKKDSGSLT
                     FTQQKEQLRELRKRWEVKHNEHMRKHGFERGFIDCRTLKEQGIERRPEVHLGFEAAGRL
                     DDAQRHDIMQKRSEPDYSRHLEQARTVGHDIREWLDTPVKQHELVRRLQHDVAREHGFD
                     MRDRVSRQNRTAPERVKSPSRGFSMGF"
                     /name="MobA/MobL family protein"
     gene            421..819
                     /locus_tag="QL134_25590"
     CDS             421..819
                     /locus_tag="QL134_25590"
                     /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="WHJ82097.1"
                     /translation="MRISNIEWLKKRIGFIRKLGEQTARQRQIIDLIDNEAGLTEQERK
                     LLHVLATAEKNDLQAQESERKQAVQKRIEGKKQRRERNHRLFLAAGLLIEAGLVDTKTG
                     ELCYKKDRILQALKELKYDLETSPNPDA"
                     /name="hypothetical protein"
     gene            complement(1023..1937)
                     /locus_tag="QL134_25595"
     CDS             complement(1023..1937)
                     /locus_tag="QL134_25595"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001738986.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="replication initiation protein"
                     /protein_id="WHJ82098.1"
                     /translation="MSAALQYFEENLPHRPYHTDDLAFGLRISGKGRALLARYIQQNQP
                     HAQFWLVFDVDREGAAIDWSDRNAPAPNITVKNPVNGHAHLLYALNIAVRTAPDASVKA
                     LKYAAAVERSLCEKLCADVNYSGLICKNPFHLEWLVMEWREEAYTLDELADYLDLSASE
                     RRSIDKHYGMGRNCHLFEMTRKWAYRAIRQGWPAFSQWLEAVIQRVEMYNASLPVPLSL
                     AECRAIGKSIAKYTHRNFTPETFAQYVADTHTPEIQAARGRKGGSKSKRSTVATSARTL
                     KPWEALGISRAWYYQLKKRGLVE"
                     /name="replication initiation protein"
     gene            3672..3881
                     /locus_tag="QL134_25600"
     CDS             3672..3881
                     /locus_tag="QL134_25600"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001618649.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WHJ82094.1"
                     /translation="MAKLGENTPHIIDATVDFMASSQAFREYLKKLPPDNTIPPALTDE
                     HVPLYIRRLEYYRLLYRPKQTESY"
                     /name="hypothetical protein"
     gene            complement(3947..4480)
                     /locus_tag="QL134_25605"
     CDS             complement(3947..4480)
                     /locus_tag="QL134_25605"
                     /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="WHJ82095.1"
                     /translation="MASTEEKLLTLLLSVEHLQHTAMEQQKAVADSLAVARETLRGYRD
                     ISDGVAKQVRDEVRNEVQKLDVAGLIGERISQDFQRLEESVANMKANADALNRDIATIH
                     SNIVQEYNTLKGYSWKWLGGVSVAFLVMFCVLGWGMKTILDRNYNATAAVYQKVVTLED
                     KLVEKPVTGKSRKN"
                     /name="hypothetical protein"
     Typing          complement(1024..1937)
                     /name="rep_cluster_2131"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="91.909"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          complement(3..244)
                     /name="MOBQ"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="98.765"
                     /coverage="99.0"
                     /evalue="1.31e-45"
     Typing          complement(4487..5163)
                     /name="MOBQ"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="97.788"
                     /coverage="99.0"
                     /evalue="6.71e-146"
ORIGIN
        1 gtgtcagttc acggggtaat gcaatttcaa gttccctata ggtcgaaccg ttcgcacgtt
       61 caaactggtc agccgcctgc cagaaatggg aaggattatc cctggcccat tccggcatgt
      121 ttccgtgtgc ggaatattcc aaatcctgac ggtcgcggta tttctctttg cgctcgatgt
      181 aatcggcgtg gtttgcagcc tgccccttgc caccaaattt aacgctgagg tgataggttg
      241 ccacggtttc agccctctgc aggagcgcac tgtttctcga cgaaggagag aaacatataa
      301 gtgcgcttcc ttctaatttt acgaattagc acggaagata ccccctgcac ccgccgaccg
      361 caagcgatat actgcacgac cacaacacac cgcaaaaaaa caccagggag catcacgaac
      421 atgcgcatca gcaacatcga atggctgaag aaacggatcg gattcatcag gaagctcgga
      481 gaacagaccg cacgacagag acagattatt gacctgatcg acaacgaagc cggactcaca
      541 gaacaggaac gcaaacttct ccacgtactg gcaacagcgg aaaaaaacga cttacaggca
      601 caggagagcg aacgaaaaca ggcggtccaa aaacgaatcg agggaaaaaa acaacgacgg
      661 gaacgcaatc accggctctt tctcgcggct gggctactga tcgaagcagg actggtagac
      721 acaaaaacag gcgagctatg ctataaaaaa gacaggatat tacaagcact taaggaactt
      781 aagtacgatc tggagacatc cccaaaccca gacgcgtaag tgcctccatc cgtgttccga
      841 ttccctggtg cttcctcgct cattcgctcg ctacgctcgg tcatgagact gcggcgagca
      901 ctaccaccac aatcacgcgg aaagccgcgc cattgcaggg ctgaacgggg aaaaacggca
      961 aaaaacctgc tgctcaaaaa gacgccagaa aggcgctgtt atctgatata ggcttatttg
     1021 gtctactcta cgagacctcg ttttttcagt tggtaatacc aggcgcgact gatccctaat
     1081 gcctcccacg gtttcagcgt gcgtgcagat gtagctactg tgctgcgctt agacttagaa
     1141 ccgcccttgc gaccgcgtgc agcctgaatt tctggcgtgt gcgtatcagc cacatactgt
     1201 gcgaaagttt ccggcgtgaa gttcctgtgc gtgtatttcg caatgctctt gccaatagcc
     1261 cgacattcag ccagtgaaag cggaacggga agcgatgcat tgtacatttc gacacgctgg
     1321 atcaccgctt caagccactg tgagaacgct ggccagccct gacgaatcgc cctgtaagcc
     1381 catttgcgcg tcatttcgaa caggtggcag tttcgcccca tcccgtaatg tttatcgatg
     1441 ctacgacgct ctgaggcgct caaatcgaga taatcagcca gttcatcgag ggtataggct
     1501 tcctcgcgcc actccatcac cagccattcc aggtggaacg gatttttgca aatcaggccg
     1561 ctgtagttca catccgcaca aagtttctca cacagcgaac gttcaaccgc tgcggcatat
     1621 ttcagcgcct taaccgaggc atcaggcgcg gttctcacgg cgatgttgag tgcgtagagc
     1681 aggtgagcgt gtccgttcac aggattttta acggtgatgt tcggcgcggg agcgttccgg
     1741 tcgctccagt caatcgcagc cccctcgcgg tcaacgtcaa aaaccagcca gaactgtgca
     1801 tgaggctggt tctgctggat ataccgtgca agaagcgcgc gccctttgcc ggagatacga
     1861 aggccgaaag cgagatcatc cgtgtgatag ggacggtggg gtaaattttc ttcgaagtat
     1921 tgaagcgcgg cgctcatgtg ttacgattcc ttccaggtta tcgaccgaca tcgcccctgt
     1981 attttcgtga aagtcttggc ggatagacac gaatttcagg ggcgtttgtt tttcagtcgc
     2041 ttacactaca cccaacggca aatcctgtcg atccttcccg aaaaaccgat ccatttacca
     2101 taactcccgt tgtacgtacc atgtaaaacg ccatcaatcg ctttctggcg caaaaaacgc
     2161 aaaaagacaa gaaaacacca ggccaaacca gaaaaacgcg tcagaatcgt tttcagggcg
     2221 ttgcataact atgcacgaaa gcgatgtgcg atcggtttcg tgcgttctga acaccgaacg
     2281 gctcaaaacg acaagttttc tcccctggtg cgtggcgctc tgacggggtt tcctgtttcc
     2341 aaacttcaca tctcgccagg acaaaaaaaa accgacctgg ggtcggtggc aagaatcaga
     2401 gtctatggga aatattttag ttatcggatg ctcaatattc acaaacgcaa aaaatgcctc
     2461 agtgatgccc taaaacaacc tttccagaag gagtccgcgc tttacgatgc acggaagaga
     2521 taaaaaaccc cacaaaagtg gggaaccaag agaaacaaca attacaggtt gttggttgtg
     2581 ttcgaacaac gatgaagtag ctacgctaaa taataattac cgtacaggcc ctacatattc
     2641 aacactaaat ttaagatcct gacgaaggat ttataaatgc acgaaaacac acagacagac
     2701 aaattcacta aattcataca caaaaacaag tgtagttttc taagtaaatt agattcgaca
     2761 accaattagt ttatccacat cgcattccac tcttgctaca ccaatcacat ttcttgatat
     2821 gtaatagcag aaaaaataaa accagacacc aatagaccaa aaaacaaaca ttcaacaaga
     2881 aacattttga acaatatcac aaaactgtca caaccatcat cagactattg aaaaaaactg
     2941 gttgctgttt tataaaagcg actgtaacaa cctccactct atagttccat tagtttaaag
     3001 tgtcacacaa actgagcatc catttgtttt ccttactttt gcccctgtat tccaaggggt
     3061 ttttttataa cttaaagatt agcacaccac acaaaaacaa taaaaaaaaa cgacaagtta
     3121 tacaataaaa ccagtactat ccatacagct aattacatat aaatactatt aaaccatctg
     3181 gacattaaaa ataaactctt ataacataaa attaatgcgg ttccggtacc atatgtcagg
     3241 gataatgtgc aaatggaggt atcggaactg catttcagtt cattattaat taatgacaaa
     3301 aaaaacctct gcgagcgcag agggggtaag gaatgttccc ggtcataata tgtcgatagt
     3361 gtttatatac atacagaaca agaacaacaa ccagccaact aataaatatt ttatttttta
     3421 gagctgaaac cttaaagctc acttccattc catacattgt tataaacctt atgttgaaaa
     3481 ctgaaagtaa gtacggcaga cttattaagt tgcgtgcagt cttttcacgt tatacaaaca
     3541 agaacacctg cgaagttatt tctccttaca tatcccccta tgccaacggg ggattttttc
     3601 tggttcacta acgcataaat aatagtgaca ccctatcatt cacaaaccgt gataatataa
     3661 ggattatcat catggcaaaa ttaggtgaaa acaccccaca tattatcgat gctactgtag
     3721 attttatggc atcaagccag gcatttcgtg agtatctgaa aaaacttccc cctgataaca
     3781 caataccgcc agctcttact gatgagcacg taccgttata tatacgaagg ctggaatact
     3841 atcgtctgct ttatcgacca aagcagacag aatcatattg aaaaaaacgg tgaacggttc
     3901 gcgaaatcct ttcgcgggtc gtgaggcgtt ggacaagcga agcgcgtcag tttttccggc
     3961 tcttccccgt gacaggtttc tccaccagtt tatcttccag tgtcacaact ttctgataca
     4021 ccgccgctgt ggcgttgtag ttcctgtcga gtattgtttt cattccccat ccgagcacac
     4081 agaacataac cagaaaagcc actgacaccc cacccagcca tttccagcta taccctttaa
     4141 gggtgttgta ttcctgcacg atattgctgt gaattgtcgc aatatccctg ttcagggcat
     4201 ccgcgtttgc cttcatgttt gcgactgact cttccagccg ctgaaaatcc tggctgatgc
     4261 gctcacctat cagtcctgcc acgtccagct tctgcacctc atttctgact tcatccctga
     4321 cctgttttgc cacaccgtca gaaatatccc gatatccgcg aagagtttcc cttgccacag
     4381 ccagagaatc agcaacagct ttctgttgct ccattgcggt atgttgcaga tgctccaccg
     4441 ataacaggag cgtgagtaat ttttcttctg tgctggccat gttcagaatc ccatagaaaa
     4501 tccacgtgac ggtgatttaa cccgttcagg tgcagttcgg ttctgtctgc tcactctgtc
     4561 tctcatgtca aagccatgct cccgcgcaac atcatgttgc agccttctga ccagttcatg
     4621 ttgcttaacc ggagtgtcca gccattccct gatgtcatgc ccgaccgttc gcgcctgttc
     4681 aagatggcgg gaatagtccg gttcagaccg tttttgcatg atgtcatgac gctgggcatc
     4741 atcaagccgt ccggcagctt caaaacccag atgcacttcg ggacgtcgtt caatgccctg
     4801 ttctttcagc gtccggcagt caatgaagcc cctttcaaag ccatgctttc tcatatgttc
     4861 gttgtgcttc acctcccagc gttttcgcaa ttcccgcaac tgctcttttt gctgagtgaa
     4921 agtcaggctt ccggaatcct ttttcgcacc tccccgctcg ggatacctgg cgttatagcg
     4981 ccggaaatac tgttccggtg tacgttcaat gccatcattc acacgctgac tcatcatgat
     5041 atgcgcatga ggctgttcgc cgccgtcaat gctcgctttc ggattgtgaa tggcaaaact
     5101 ccaggcgtgc cgttcgccag cttcctgacg tacaaaatcc tgcaccagtt caaggcgctg
     5161 ttccg
//
