LOCUS       CP124981                5874 bp    DNA     circular BCT 16-MAY-2023
DEFINITION  Escherichia coli strain KSE-D31 plasmid pKSE-D31_4, complete
            sequence.
ACCESSION   CP124981
VERSION     CP124981.1
DBLINK      BioProject: PRJNA956323
            BioSample: SAMN34598758
KEYWORDS    .
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 5874)
  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  JOURNAL   Unpublished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 5874)
  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..5874
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="KSE-D31"
                     /isolation_source="Sewage"
                     /db_xref="taxon:562"
                     /plasmid="pKSE-D31_4"
                     /geo_loc_name="Uganda"
                     /lat_lon="0.19 N 32.35 E"
                     /collection_date="2018"
                     /collected_by="Hidenori Harada, Mai Tanaka"
     gene            312..842
                     /locus_tag="QL154_25075"
     CDS             312..842
                     /locus_tag="QL154_25075"
                     /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="MbeB family mobilization protein"
                     /protein_id="WHJ27394.1"
                     /translation="MSNLLQTGAEFEKKLKERAESTEKMLNDEFRKLEESVNRELTSNE
                     SLIRNAINDHTTALKELLERYQKTTVDTMDAHWKTVLKMSVKRWLWLIIVSVLMFATTG
                     SLLWYQGMKINANMNILREQKESLEKLNAKTWGVRYHEDSNGRFLVLPKGMKAETNWTK
                     DNGKLNAVRLVQE"
                     /name="MbeB family mobilization protein"
     gene            849..1082
                     /locus_tag="QL154_25080"
     CDS             849..1082
                     /locus_tag="QL154_25080"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000137438.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MbeD family mobilization/exclusion protein"
                     /protein_id="WHJ27395.1"
                     /translation="MTELERHLLNALEQLQQDYMQRLNEWENAFVELQKMFSLTQRDNA
                     MLNGRVMQLSQQVQHLSERTERLSQLYSENWR"
                     /name="MbeD family mobilization/exclusion protein"
     gene            1802..2854
                     /locus_tag="QL154_25085"
     CDS             1802..2854
                     /locus_tag="QL154_25085"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001557502.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WHJ27396.1"
                     /translation="MNLQQRINKLPQLSSSFSFGKDIDNIHSFIFNETSKDKIEDLLRK
                     WVSGNQPCVFGKLASKKIKGLDFHLSIVNSPQLYNDDGHLFDFLRNERVRFKERARRGE
                     VSAHLIYFIHPQLAFARPSEELVDIQKYICSLHMPECYPIKEDVIYTESVPFQDKDGLK
                     IYKAGVNVFYSSAHRTRNHDRRIPGGILISVNAPGHFMRLAIEKGFYKDQEQALADIRN
                     MTIQSVGNGGYSHPEGISTTWHSESKLDRFGCPVHTGNSSYYSGFYHTDVLIPGELTKD
                     ERLLHEIDNSDPMIFNWNVLFYVSLEEFPIDDPYYGEFIGVPVDDASMFFNSFQPRKFE
                     NNPLYEKEDD"
                     /name="hypothetical protein"
     gene            2856..3722
                     /locus_tag="QL154_25090"
     CDS             2856..3722
                     /locus_tag="QL154_25090"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001335763.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology. GO_function:
                     GO:0005215 - transporter activity [Evidence IEA];
                     GO_process: GO:0055085 - transmembrane transport [Evidence
                     IEA]"
                     /codon_start=1
                     /transl_table=11
                     /product="DMT family transporter"
                     /protein_id="WHJ27397.1"
                     /translation="MIKGMLFAFLAAFSWGAAIVMSKKGVEELDAGGVFFWQICSAVIL
                     SWIVLFIKRKKLPLNSKAILAYATGVFEPFLAYTFTLYGLYFISAGSASIIFSLESVFI
                     LVLSVLICSVKINSPQYFILFLIGAIVGSILVALPDISNGSNNIVGYCLVVAGVLSAAF
                     YVVISSRLIKSFEPITLLSGQLTFSLILSSLFIFISKSSIYLPLESVIIVFSSGILQYF
                     LAFCFYLNSLRWLPVHLAGIMLYFIPLVALFLSWLFLDEQFTFLQGVGFIVTVLSVYFL
                     NRKYSEE"
                     /name="DMT family transporter"
     gene            complement(4928..5119)
                     /locus_tag="QL154_25095"
     CDS             complement(4928..5119)
                     /locus_tag="QL154_25095"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000165975.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="Rop family plasmid primer RNA-binding protein"
                     /protein_id="WHJ27392.1"
                     /translation="MTKQEKTALNMVRFIRSQTLTLLEKLNELDADEQADICESLHDHA
                     DELYRSCLARFGDDGENR"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            5152..5508
                     /locus_tag="QL154_25100"
     CDS             5152..5508
                     /locus_tag="QL154_25100"
                     /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="MobC family plasmid mobilization relaxosome
                     protein"
                     /protein_id="WHJ27393.1"
                     /translation="MGVMIPMKRERMLTIRVTDDEHARLLERCEGKQLAAWMRRVCLGE
                     PVARSGKLPTLAPPLLRQLAAIGNNLNQTARKVNSGQWSSGDRVQVVAALIAIGDELRR
                     LRLAVREQGARDDS"
                     /name="MobC family plasmid mobilization relaxosome protein"
     Typing          4753..4834
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="98.795"
                     /coverage="100.0"
                     /evalue="6.23e-34"
     Typing          4109..4296
                     /name="rep_cluster_2401"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="4.63e-94"
     Typing          3..1186
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="98.987"
                     /coverage="99.0"
                     /evalue="0.0"
     Typing          5499..5872
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="99.2"
                     /coverage="93.0"
                     /evalue="7.690000000000001e-77"
ORIGIN
        1 ggcagacagg ccgagaattg atgcctggca gacgctggtg aatcaccatt acggtctgca
       61 tgaccccaac gccccggaga accgccggac gctgaccctt cctgataacc tgccggaaac
      121 gaaacaggcg cttgctgagg gcgtcacacg cgggatagac gcgctttacc atgccggaga
      181 gataaaaggc cgtcaggatg tgattcaggc gctcacagag gcggggcttg aagtggtcag
      241 ggtgacgcga agcagtatca gcattgcaga cccgaacggc gggaggaata tcagactgaa
      301 aggagcgttt tatgagcaat cttttacaga cgggcgcgga gttcgagaaa aagctgaaag
      361 agagagccga atctacagag aaaatgctga acgacgagtt caggaagctc gaagaatctg
      421 taaacaggga actgacctca aacgaatctt taatcaggaa cgctatcaac gaccatacaa
      481 cagccctgaa agaactgctg gagaggtatc agaaaacgac cgtcgatacg atggacgcgc
      541 actggaaaac cgtactgaaa atgagcgtga aacgctggct gtggctgatt atcgtctcag
      601 tactgatgtt tgccacgacc gggagtctgc tgtggtacca gggcatgaag ataaacgcga
      661 atatgaatat tctccgcgag cagaaagaga gtctggagaa gctgaacgcg aagacatggg
      721 gcgtgcgtta tcacgaggac agcaacggac gttttctggt gttgccgaag gggatgaaag
      781 ccgaaacgaa ctggacgaag gacaacggca aactgaacgc agtgagactg gtgcaggagt
      841 gacagagcat gacggagctg gaaagacatt tgctgaacgc attagagcaa ctgcaacagg
      901 actatatgca gcggctgaac gaatgggaga acgccttcgt ggaattgcag aaaatgtttt
      961 cgcttacgca acgggacaac gcgatgctga acgggcgagt catgcagttg agtcagcagg
     1021 tgcagcactt gagcgagcgg acagaacgct tgagccagtt atacagcgag aactggagat
     1081 aagggatgag cggctgatac aggagcgcga atatgcgtta tccctggagc gggagcgcca
     1141 gccggaaatt caggaacgga cactggatgg cccttcgctg ggatggtaac cagagacagg
     1201 ctaaaatgtt ggcagcgcgt ttccggtgca ttttttggga taatggttgg ttcgggggca
     1261 ccgggaacgc gcttcagtca gagcttgctg aaaacacagg aacgcgttaa aacgcatgcg
     1321 ggcgcgattc tggtgtgtct ttgttgctgt gttttgccgt tattgccaga tcgcgctcat
     1381 tcccatgaat ttctgttttt ccgctccggt tccgtcttct gcctttccga aagtatgaaa
     1441 aaaatccgtt tcagcagtct ctggctggca attcctgcgt gattcacatg gctgcatagc
     1501 tatgcatgtg gttaaaattt atcgggtgcg atcgcggcag tttttcgggt ggtttgttgc
     1561 catttttacc tgtctgctgc cgtgatcgca ccgaacgcgt tttggcggtg cgtacaatgc
     1621 gacgttatgg taaatggagc ggattttcag gaaggagtga tactaacaac tcgaacactg
     1681 tgcaaataat gattttttaa aatatcggta acgataataa attatttcgt tttacgtcgg
     1741 taataaatat aatgtagttt cagtatataa aaaatatatg aggtgtcttg tgggagcttt
     1801 catgaatctt caacaacgta taaataaact accacaatta tcatccagtt tttcatttgg
     1861 aaaagatatt gataatattc attcatttat ctttaacgaa acttctaaag ataaaattga
     1921 agatttacta agaaaatggg tgtcaggcaa tcagccctgt gtatttggta aattggcaag
     1981 caagaaaatt aaagggcttg atttccattt atctattgta aatagccccc aactatataa
     2041 tgatgatggt catttgtttg attttttgcg taatgaaaga gttcgtttta aagaacgcgc
     2101 aagaagagga gaggtcagtg cgcatctcat ttattttatt catccacaac ttgcatttgc
     2161 tcgtccatca gaagagttag tggacataca aaaatatatt tgttcgctgc atatgccaga
     2221 gtgctatcca ataaaagagg atgttattta tactgaaagc gtaccatttc aggataaaga
     2281 tgggctaaaa atatataagg ctggtgttaa tgttttttac tcttctgctc atagaacaag
     2341 aaatcatgat agaagaatac cggggggaat acttatttct gtaaatgccc cggggcattt
     2401 tatgaggctg gcgatagaaa aaggtttcta taaagatcaa gaacaagcgt tagcggatat
     2461 tcgtaacatg actattcagt ctgttggtaa cggtgggtat tcacatccgg aagggatttc
     2521 tacaacatgg cattcagaat ctaaattgga tcgttttgga tgcccagtgc acaccggtaa
     2581 tagttcttat tacagcggtt tttatcatac tgatgtatta attccaggag aattaactaa
     2641 ggatgaaaga ttgctccatg aaatagataa tagtgatcca atgatcttca actggaatgt
     2701 attgttttat gtttcattag aagagtttcc tatagatgat ccttattatg gagagtttat
     2761 tggtgttcct gtagatgatg catctatgtt ttttaactcc tttcaaccaa ggaaatttga
     2821 aaacaacccc ctttatgaga aagaggatga ttaatatgat taaaggaatg ctttttgctt
     2881 ttttagcagc gttctcatgg ggggcagcta tcgtaatgag caaaaaagga gttgaagaac
     2941 tagatgccgg aggggtgttt ttctggcaga tttgtagtgc agtaatacta tcttggatag
     3001 ttctttttat aaaaagaaaa aaactcccat taaactcaaa agcgatactt gcttatgcga
     3061 caggcgtttt tgaaccattc ttagcgtata cttttacact ctacggactt tattttattt
     3121 cagcaggaag cgcatcaatt attttttcac ttgaatcagt gtttatattg gtgttgtctg
     3181 ttcttatttg ctcagttaaa attaattccc cgcaatattt tatattgttc cttataggtg
     3241 caattgttgg cagtattttg gtagccttgc cagacatcag taatggatcg aataatattg
     3301 ttggatattg tcttgttgtt gccggtgtgt tatcggcagc attttatgtt gttatatcgt
     3361 ctcgccttat taaatcgttt gagcctatca cattattgag cggacagttg acattctccc
     3421 ttatactgtc atcgctcttt atttttatat ctaaatcctc aatttatctt ccgttggaat
     3481 ccgtgattat tgttttttca tctggaatat tacaatattt tttagctttt tgtttttact
     3541 tgaactcctt gcgttggctc ccagttcatt tggcagggat aatgttgtac tttattccgc
     3601 tagttgcatt atttttgtca tggttgtttt tggatgaaca attcacattc ttacaggggg
     3661 taggatttat tgtaactgtg ctaagtgtat attttcttaa cagaaaatac tcagaggagt
     3721 aacattcttt tcaggattgc cccccccggc ctccatcgat accgtgccaa atgcacgtaa
     3781 aaaacgggag cgtttctggt gtcggaatgt aaccaagggg gggcagaggc gcgctaaaac
     3841 gctctcaggg gagtcaaata gagacgtttg taacaaaaag atcaaaggat cctcttgaga
     3901 tccttttttt ctgcgcgtaa tctgctgcct gtaaacgaaa aaaccgcctt gcagggcggt
     3961 ttgatcgaag gttaagtcag cttgcagact gcttaaccag gtaactgtct tatgcgagac
     4021 gagtcaccaa aattgttctt ctagtgtagc cgcactccgg cagccacttc aagtactctc
     4081 taaatatctc gcacatgact tttaccaatg gctgctgcca gtggcgcttt gtggtgtctt
     4141 ttccgggttg gacccaagag aacagttacc ggagaaggcg cagcagtcgg gctgaacggg
     4201 gggttcctgc atacagccca gcccggagcg aactgcctaa gtcgccccga gataccagaa
     4261 gacgtgagct atgagaaagc gccacgtgtc ccgtaaggga gaaaggcgga aaaggtatcc
     4321 ggtaatcgat atggcgggaa cgtgggggcg caggagggag cgattcaccg gaaacggtga
     4381 tgatctttaa gccacgtcgg gtttcgccac cgctggcgga tttcatggtt gagccgcaag
     4441 gctcccacag atgcaccgaa aaagtgtctg ttttgtgaag tccgtcaggg gggcggagcc
     4501 tatggaaaaa gcgcctccgg cgcggccttt tccggggttt cgttttttgc gcacatgttc
     4561 tttcctggtt tatccccggg ttctgtggat aacagggtta gcgtttttga gaaaggagag
     4621 tccgctcgcc gcagccgaac gaccgagcgt agcgagtcag tgagcgagga agcggaagag
     4681 cgcctgaact ggcattttct ccttacgcat ctgtgcggca tttcacaccc gacatggcgc
     4741 acttttcata caatccgcac tgatgccgaa tgattaagcc agtatacact ccgctatcgc
     4801 tacgtgactg ggtcagggct tcgccccgac accccaaagg tcaacggcct gacgcgccct
     4861 ggcgggcttg tctgctcccg gcatccgctc acagacaagc tgtgaccgtc tccgggagct
     4921 gcatgtgtca gcggttttca ccgtcatccc cgaagcgtgc gaggcaactg cggtaaagct
     4981 catcggcgtg gtcgtgaagc gattcacaga tgtctgcctg ttcatccgcg tccagttcgt
     5041 tgagcttctc cagcagcgtt aatgtctggc ttctgataaa gcggaccatg ttaagggcgg
     5101 ttttttcctg tttagtcact ggatgcctcc gtgtaagggg gatttctgtt catgggggta
     5161 atgataccga tgaaacgcga gaggatgctc acgatacggg tgactgatga tgagcatgcc
     5221 cgtttactgg aacgctgtga gggtaaacaa ctggcggcat ggatgcggcg ggtctgcctg
     5281 ggtgagcctg ttgcccgttc cgggaagctg ccgacactgg caccgccgtt actgcgtcag
     5341 ctggccgcta tcgggaataa ccttaaccag acagcgagga aggtgaacag cgggcagtgg
     5401 tcttccggtg accgggttca ggtggtggcc gcactgatag ccatcgggga tgagctgcgc
     5461 cggctgcgtc tggcggtcag ggaacagggg gcgcgggatg atagttaagt ttcatgccag
     5521 gggaaaaggt ggtggcagtg gtccggttga ttacctgctg ggaagggagc gtaaccggga
     5581 aggggcaacg gtgcttcagg ggaatccgga agaggtccgg gaactcatcg atgccacgcc
     5641 atttgcgaag aaatacacgt caggtgttct gtcgttcgcg gagaaggagc tgccgcctgg
     5701 agggcgtgaa aaagtgatgg cgagctttga gcgtgtactg atgcccggtc tcgagaaaaa
     5761 tcagtacagc atcctgtggg tggagcacca ggacaaggga cggcttgagc tgaattttgt
     5821 cattccgaac atggagctac agaccggaaa acgcctccag ccgtactacg accg
//
