LOCUS       CP125056                5631 bp    DNA     circular BCT 16-MAY-2023
DEFINITION  Escherichia coli strain KFS-C08 plasmid pKFS-C08_3, complete
            sequence.
ACCESSION   CP125056
VERSION     CP125056.1
DBLINK      BioProject: PRJNA956323
            BioSample: SAMN34598742
KEYWORDS    .
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 5631)
  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  JOURNAL   Unpublished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 5631)
  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 16:42:08
            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)                     :: 4,967
            CDSs (total)                      :: 4,850
            Genes (coding)                    :: 4,635
            CDSs (with protein)               :: 4,635
            Genes (RNA)                       :: 117
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 89
            ncRNAs                            :: 6
            Pseudo Genes (total)              :: 215
            CDSs (without protein)            :: 215
            Pseudo Genes (ambiguous residues) :: 0 of 215
            Pseudo Genes (frameshifted)       :: 83 of 215
            Pseudo Genes (incomplete)         :: 146 of 215
            Pseudo Genes (internal stop)      :: 34 of 215
            Pseudo Genes (multiple problems)  :: 45 of 215
            Pseudo Genes (short protein)      :: 4 of 215
            ##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..5631
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="KFS-C08"
                     /isolation_source="Fecal sludge"
                     /db_xref="taxon:562"
                     /plasmid="pKFS-C08_3"
                     /geo_loc_name="Uganda"
                     /lat_lon="0.19 N 32.35 E"
                     /collection_date="2018"
                     /collected_by="Hidenori Harada, Mai Tanaka"
     gene            complement(1062..1928)
                     /locus_tag="QL145_24770"
     CDS             complement(1062..1928)
                     /locus_tag="QL145_24770"
                     /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="WHJ91530.1"
                     /translation="MIKGMLFAFLAAFSWGAAIVMSKKGVEELDAGGVFFWQICSAVIL
                     SWIVLFIKRKKLPLNSKAILAYATGVFEPFLAYTFTLYGLYFISAGSASIIFSLESVFI
                     LVLSVLICSVKINSPQYFILFLIGAIVGSILVALPDISNGSNNIVGYCLVVAGVLSAAF
                     YVVISSRLIKSFEPITLLSGQLTFSLILSSLFIFISKSSIYLPLESVIIVFSSGILQYF
                     LAFCFYLNSLRWLPVHLAGIMLYFIPLVALFLSWLFLDEQFTFLQGVGFIVTVLSVYFL
                     NRKYSEE"
                     /name="DMT family transporter"
     gene            complement(1930..2982)
                     /locus_tag="QL145_24775"
     CDS             complement(1930..2982)
                     /locus_tag="QL145_24775"
                     /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="WHJ91531.1"
                     /translation="MNLQQRINKLPQLSSSFSFGKDIDNIHSFIFNETSKDKIEDLLRK
                     WVSGNQPCVFGKLASKKIKGLDFHLSIVNSPQLYNDDGHLFDFLRNERVRFKERARRGE
                     VSAHLIYFIHPQLAFARPSEELVDIQKYICSLHMPECYPIKEDVIYTESVPFQDKDGLK
                     IYEAGVNVFYSSAHRTRNHDRRIPGGILISVNAPGHFMRLAIEKGFYKDQEQALADIRN
                     MTIQSVGKGGYSHPEGISTTWHSESNLDRFGCPVHTGNSSYYSGFYHTDVLIPGELTKD
                     ERLLHEIENSDPMIFNWNVLFYVSLEEFPIDDPYYGEFIGIPVDDASMFFNSFQPRKFE
                     NKPLYEKEDD"
                     /name="hypothetical protein"
     gene            complement(3463..3696)
                     /locus_tag="QL145_24780"
     CDS             complement(3463..3696)
                     /locus_tag="QL145_24780"
                     /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="WHJ91526.1"
                     /translation="MTELERHLLNALEQLQQDYMQRLNEWENAFVELQKMFSLTQRDNA
                     MLNGRVMQLSQQVQHLSERTERLSQLYSENRR"
                     /name="MbeD family mobilization/exclusion protein"
     gene            complement(3703..4233)
                     /locus_tag="QL145_24785"
     CDS             complement(3703..4233)
                     /locus_tag="QL145_24785"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001673158.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MbeB family mobilization protein"
                     /protein_id="WHJ91527.1"
                     /translation="MSNLLQTGAEFEKKLKERAESTEKMLNDEFRKLEESVNRELTSNE
                     SLIRNAINDHTTALKELLERYQKTTVDTMDAHWKTVLKMSVKRWLWLIIVSVLMFATTG
                     SLLWYQGMKINANMNILREQKESLEKLNAKTWGVRYHEDSNGRFLVLPKGMKAETNWTK
                     DNGKLNAVRLVQE"
                     /name="MbeB family mobilization protein"
     gene            complement(4271..4702)
                     /locus_tag="QL145_24790"
                     /pseudo=""
     CDS             complement(4271..4702)
                     /locus_tag="QL145_24790"
                     /inference="COORDINATES: protein motif:HMM:NF015397.2"
                     /note="incomplete; partial on complete genome; missing
                     C-terminus; Derived by automated computational analysis
                     using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="relaxase/mobilization nuclease domain-containing
                     protein"
                     /name="relaxase/mobilization nuclease domain-containing
                     protein"
     gene            complement(4911..5234)
                     /locus_tag="QL145_24795"
     CDS             complement(4911..5234)
                     /locus_tag="QL145_24795"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000956000.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MobC family plasmid mobilization relaxosome
                     protein"
                     /protein_id="WHJ91528.1"
                     /translation="MLTIRVTDDEHARLLERCEGKQLAVWMRRVCLGEPVARSGKLPTL
                     APPLLRQLAAIGNNLNQTARKVNSGQWSSGDRVQVVAALMAIGDELRRLRLAVREQGAR
                     DDS"
                     /name="MobC family plasmid mobilization relaxosome protein"
     gene            5299..5490
                     /locus_tag="QL145_24800"
     CDS             5299..5490
                     /locus_tag="QL145_24800"
                     /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="WHJ91529.1"
                     /translation="MTKQEKTALNMARFIRGQTLTLLEKLNELDADEQADICESLHDHA
                     DELYRSCLARFGDDGENR"
                     /name="Rop family plasmid primer RNA-binding protein"
     Typing          complement(492..679)
                     /name="rep_cluster_2401"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="4.63e-94"
     Typing          complement(3360..4921)
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 tatactggct taaccattcg gcatcagtgc ggattgtatg aaaagtgcgc catgtccggt
       61 gtgaaatgcc gcacagatgc gtaaggagaa aatgccagtt caggcgctct tccgcttcct
      121 cgctcactga ctcgctacgc tcggtcgttc ggctgcggcg agcggactct cctttctcaa
      181 aaacgctaac cctgttatcc acagaacccg gggataaacc aggaaagaac atgtgcgcaa
      241 aaaacgaaac cccgggaaag gccgcgccgg aggcgctttt tccataggct ccgcccccct
      301 gacggacttc acaaaacaga cactttttcg gtgcatctgt gggagccttg cggctcaacc
      361 atgaaatccg ccagcggtgg cgaaacccga cgtggcttaa agatcatcac cgtttccggt
      421 gaatcgctcc ctcctgcgcc cccacgttcc cgccatatcg attaccggat accttttccg
      481 cctttctccc ttacgggaca cgtggcgctt tctcatagct cacgtcttct ggtatctcgg
      541 ggcgacttag gcagttcgct ccgggctggg ctgtatgcag gaaccccccg ttcagcccga
      601 ctgctgcgcc ttctccggta actgttctct tgggtccaac ccggaaaaga caccacaaag
      661 cgccactggc agcagccatt ggtaaaagtc atgtgcgaga tatttagaga gtacttgaag
      721 tggctgccgg agtgcggcta cactagaaga acaattttgg tgactcgtct cgcataagac
      781 agttacctgg ttaagcagtc tgcaagctga cttaaccttc gatcaaaccg ccctgcaagg
      841 cggttttttc gtttacaggc agcagattac gcgcagaaaa aaaggatctc aagaggatcc
      901 tttgatcttt ttgttacaaa cgtctctatt tgactcccct gagagcgttt tagcgcgcct
      961 ctgaccccct tggttacatt ccgacaccag aaacgctccc gttttttacg tgcatttggc
     1021 acggtatcga tggaggccgg ggggcaatcc tgaacagaat gttactcctc tgagtatttt
     1081 ctgttaagaa aatatacact tagcacagtt acaataaatc ctaccccctg taagaatgtg
     1141 aattgttcat ccaaaaacaa ccatgacaaa aataatgcaa ctagcggaat aaagtacaac
     1201 attatccctg ccaaatgaac tgggagccaa cgcaaggagt tcaagtaaaa acaaaaagct
     1261 aaaaaatatt gtaatattcc agatgaaaaa acaataatca cggattccaa cggaagataa
     1321 attgatgatt tagatataaa aataaagagc gatgacagta taagggagaa tgtcaactgt
     1381 ccgctcaata atgtgatagg ctcaaacgat ttaataaggc gagacgatat aacaacataa
     1441 aatgctgccg ataacacacc ggcaacaaca agacaatatc caacaatatt attcgatcca
     1501 ttactgatgt ctggcaaggc taccaaaata ctgccaacaa ttgcacctat aaggaacaat
     1561 ataaaatatt gcggggaatt aattttaact gagcaaataa gaacagacaa caccaatata
     1621 aacactgatt caagtgaaaa aataattgat gcgcttcctg ctgaaataaa ataaagtccg
     1681 tagagtgtaa aagtatacgc taagaatggt tcaaaaacgc ctgtcgcata agcaagtatc
     1741 gcttttgagt ttaatgggag tttttttctt tttataaaaa gaactatcca agatagtatt
     1801 actgcactac aaatctgcca gaaaaacacc cctccggcat ctagttcttc aactcctttt
     1861 ttgctcatta cgatagctgc cccccatgag aacgctgcta aaaaagcaaa aagcattcct
     1921 ttaatcatat taatcatcct ctttctcata aaggggtttg ttttcaaatt tccttggttg
     1981 aaaggagtta aaaaacatag atgcatcatc tacaggaata ccaataaact ctccataata
     2041 aggatcatct ataggaaact cttctaatga aacataaaac aatacattcc agttgaagat
     2101 cattggatca ctattttcta tttcatggag caatctttca tccttagtta attctcctgg
     2161 aattaataca tcagtatgat aaaaaccgct gtaataagaa ctattaccgg tgtgcactgg
     2221 gcatccaaaa cgatccaaat tagattctga atgccatgtt gtagaaatcc cttccggatg
     2281 tgaataccca cccttaccaa cagactgaat agtcatgtta cgaatatccg ctaacgcttg
     2341 ttcttgatct ttatagaaac ctttttctat cgccagcctc ataaaatgcc ccggggcatt
     2401 tacagaaata agtattcccc ctggtattct tctatcatga tttcttgttc tatgagcaga
     2461 agagtaaaaa acattaacac cagcctcata tatttttagc ccatctttat cctgaaatgg
     2521 tacgctttca gtataaataa catcctcttt tattggatag cactctggca tatgcagcga
     2581 acaaatatat ttttgtatgt ccactaactc ttctgatgga cgagcaaagg caagttgtgg
     2641 atgaataaaa taaatgagat gcgcactgac ctctcctctt cttgcgcgtt ctttaaaacg
     2701 aactctttca ttacgcaaaa aatcaaacaa atgaccatca tcattatata gttgggggct
     2761 atttacaata gataaatgga aatcaagccc tttaattttc ttgcttgcca atttaccaaa
     2821 tacacagggc tgattgcctg acacccattt tcttagtaaa tcttcaattt tatctttaga
     2881 agtttcgtta aagataaatg aatgaatatt atcaatatct tttccaaatg aaaaactgga
     2941 tgataattgt ggtagtttat ttatacgttg ttgaagattc atgaaagctc ccacaagaca
     3001 cctcatatat ttttttatat actgaaacta cattatattt attaccggcg taaaacgaaa
     3061 taatttatta tcgttaccga tattttaaaa aaatcattat ttgcacagtg ttcgagttgt
     3121 tagtatcact ccttcctgaa aatccgctcc atttaccata acgtcgcatt gtacgcaccg
     3181 ccaaaacgcg ttcggtgcga tcacggcagc agacaggtaa aaatggcaac aaaccacccg
     3241 aaaaactgcc gcgatcgcac ctgataaatt ttaaccgcat gaatacctat gcaaccagat
     3301 gctacaggcc acattagccc gccttaatcc actgaacacg tcatttttca tggtttcacc
     3361 atcccagcga agggccatcc agtgtccgct cctggatttc cggctgacgc tcccgctcca
     3421 gagataactc atgttcgcgt tcctgcatca gccgttcatc ccttatctcc tgttctcgct
     3481 gtataactgg ctcaagcgtt ctgtccgctc gctcaagtgc tgcacctgct gactcaactg
     3541 catgactcgc ccgttcagca tcgcgttgtc ccgttgcgta agcgaaaaca ttttctgcaa
     3601 ttccacgaag gcgttctccc attcgttcag ccgctgcata tagtcctgtt gcagttgctc
     3661 taatgcgttc agcaaatgtc tttccagctc cgtcatgctc tgtcactcct gcaccagtct
     3721 cactgcgttc agtttgccgt tgtccttcgt ccagttcgtt tcggctttca tccccttcgg
     3781 caacaccaga aaacgtccgt tgctgtcctc gtgataacgc acgccccatg tcttcgcgtt
     3841 cagcttctcc agactctctt tctgctcgcg gagaatattc atattcgcgt ttatcttcat
     3901 gccctggtac cacagcagac tcccggtcgt ggcaaacatc agtactgaga cgataatcag
     3961 ccacagccag cgtttcacgc tcattttcag tacggttttc cagtgcgcgt ccatcgtatc
     4021 gacggtcgtt ttctgatacc tctccagcag ttctttcagg gctgttgtat ggtcgttgat
     4081 agcgttcctg attaaagatt cgtttgaggt cagttccctg tttacagatt cttcgagctt
     4141 cctgaactcg tcgttcagca ttttctctgt agattcggct ctctctttca gctttttctc
     4201 gaactccgcg cccgtctgta aaagattgct cataaaacgc tcctttcagt ctgatattcc
     4261 tcccgccgtt cgggtctgca atgctgatac tgcttcgcgt caccctgacc acttcaagcc
     4321 ccgcctctgt gagcgcctga atcacatcct gacggccttt tatctctccg gcatggtaaa
     4381 gcgcgtctat cccgcgtgtg acgccctcag caagcgcctg tttcgtttcc ggcaggttat
     4441 caggaagggt cagcgtccgg cggttctccg gggcgttggg gtcatgcaga ccgtaatggt
     4501 gattcaccag cgtctgccag gcatcaattc tcggcctgtc tgcccggtcg tagtacggct
     4561 ggaggcgttt tccggtctgt agctccatgt tcggaatgac aaaattcagc tcaagccgtc
     4621 ccttgtcctg gtgctccacc cacaggatgc tgtactgatt tttctcgaga ccgggcatca
     4681 gtacacgctc aaagctcgcc atcacttttt cacgccctcc aggcggcagc tccttctccg
     4741 cgaacgacag aacacctgac gtgtatttct tcgcaaatgg cgtggcatcg atgagttccc
     4801 ggacctcttc cggattcccc tgaagcaccg ttgccccttc ccggttacgc tcccttccca
     4861 gcaggtaatc aaccggacca ctgccaccac cttttcccct ggcatgaaac ttaactatca
     4921 tcccgcgccc cctgttccct gaccgccaga cgcagccggc gcagctcatc cccgatggcc
     4981 atcagtgcgg ccaccacctg aacccggtca ccggaagacc actgcccgct gttcaccttc
     5041 ctcgctgtct ggttaaggtt attcccgatg gcggccagct gacgcagtaa cggcggtgcc
     5101 agtgtcggca gcttcccgga acgggcaacc ggctcaccca ggcagacccg ccgcatccat
     5161 accgccagtt gtttaccctc acagcgttcc agtaaccggg catgttcatc atcagtaacc
     5221 cgtatcgtga gcatcctctc gcgtttcatc ggtatcatta cccccatgaa cagaaccccc
     5281 ccttacacgg aggcatcagt gaccaaacag gaaaaaaccg cccttaacat ggcccgcttc
     5341 atcagaggcc agacattaac gctgctggag aagctcaacg aactggacgc ggatgaacag
     5401 gcagacatct gtgaatcgct tcacgaccac gccgatgagc tttaccgcag ttgcctcgca
     5461 cgcttcgggg atgacggtga aaaccgctga cacatgcagc tcccggagac ggtcacagct
     5521 tgtctgtgag cggatgccgg gagcagacaa gcccgccagg gcgcgtcagg ccgttgacct
     5581 ttggggtgtc ggggcgaagc cctgacccag tcacgtagcg atagcggagt g
//
