LOCUS       CP125067                5631 bp    DNA     circular BCT 16-MAY-2023
DEFINITION  Escherichia coli strain KFS-B24 plasmid pKFS-B24_3, complete
            sequence.
ACCESSION   CP125067
VERSION     CP125067.1
DBLINK      BioProject: PRJNA956323
            BioSample: SAMN34598740
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  JOURNAL   Unpublished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 16:46:15
            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)                     :: 5,120
            CDSs (total)                      :: 5,003
            Genes (coding)                    :: 4,789
            CDSs (with protein)               :: 4,789
            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)              :: 214
            CDSs (without protein)            :: 214
            Pseudo Genes (ambiguous residues) :: 0 of 214
            Pseudo Genes (frameshifted)       :: 81 of 214
            Pseudo Genes (incomplete)         :: 148 of 214
            Pseudo Genes (internal stop)      :: 39 of 214
            Pseudo Genes (multiple problems)  :: 50 of 214
            Pseudo Genes (short protein)      :: 4 of 214
            ##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-B24"
                     /isolation_source="Fecal sludge"
                     /db_xref="taxon:562"
                     /plasmid="pKFS-B24_3"
                     /geo_loc_name="Uganda"
                     /lat_lon="0.19 N 32.35 E"
                     /collection_date="2018"
                     /collected_by="Hidenori Harada, Mai Tanaka"
     gene            complement(1..192)
                     /locus_tag="QL139_25490"
     CDS             complement(1..192)
                     /locus_tag="QL139_25490"
                     /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="WHK00759.1"
                     /translation="MTKQEKTALNMARFIRGQTLTLLEKLNELDADEQADICESLHDHA
                     DELYRSCLARFGDDGENR"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            257..580
                     /locus_tag="QL139_25495"
     CDS             257..580
                     /locus_tag="QL139_25495"
                     /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="WHK00763.1"
                     /translation="MLTIRVTDDEHARLLERCEGKQLAVWMRRVCLGEPVARSGKLPTL
                     APPLLRQLAAIGNNLNQTARKVNSGQWSSGDRVQVVAALMAIGDELRRLRLAVREQGAR
                     DDS"
                     /name="MobC family plasmid mobilization relaxosome protein"
     gene            789..1220
                     /locus_tag="QL139_25500"
                     /pseudo=""
     CDS             789..1220
                     /locus_tag="QL139_25500"
                     /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            1258..1788
                     /locus_tag="QL139_25505"
     CDS             1258..1788
                     /locus_tag="QL139_25505"
                     /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="WHK00760.1"
                     /translation="MSNLLQTGAEFEKKLKERAESTEKMLNDEFRKLEESVNRELTSNE
                     SLIRNAINDHTTALKELLERYQKTTVDTMDAHWKTVLKMSVKRWLWLIIVSVLMFATTG
                     SLLWYQGMKINANMNILREQKESLEKLNAKTWGVRYHEDSNGRFLVLPKGMKAETNWTK
                     DNGKLNAVRLVQE"
                     /name="MbeB family mobilization protein"
     gene            1795..2028
                     /locus_tag="QL139_25510"
     CDS             1795..2028
                     /locus_tag="QL139_25510"
                     /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="WHK00761.1"
                     /translation="MTELERHLLNALEQLQQDYMQRLNEWENAFVELQKMFSLTQRDNA
                     MLNGRVMQLSQQVQHLSERTERLSQLYSENRR"
                     /name="MbeD family mobilization/exclusion protein"
     gene            2509..3561
                     /locus_tag="QL139_25515"
     CDS             2509..3561
                     /locus_tag="QL139_25515"
                     /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="WHK00762.1"
                     /translation="MNLQQRINKLPQLSSSFSFGKDIDNIHSFIFNETSKDKIEDLLRK
                     WVSGNQPCVFGKLASKKIKGLDFHLSIVNSPQLYNDDGHLFDFLRNERVRFKERARRGE
                     VSAHLIYFIHPQLAFARPSEELVDIQKYICSLHMPECYPIKEDVIYTESVPFQDKDGLK
                     IYKAGVNVFYSSAHRTRNHDRRIPGGILISVNAPGHFMRLAIEKGFYKDQEQALADIRN
                     MTIQSVGKGGYSHPEGISTTWHSESNLDRFGCPVHTGNSSYYSGFYHTDVLIPGELTKD
                     ERLLHEIENSDPMIFNWNVLFYVSLEEFPIDDPYYGEFIGIPVDDASMFFNSFQPRKFE
                     NKPLYEKEDD"
                     /name="hypothetical protein"
     gene            3563..4429
                     /locus_tag="QL139_25520"
     CDS             3563..4429
                     /locus_tag="QL139_25520"
                     /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="WHK00758.1"
                     /translation="MIKGMLFAFLAAFSWGAAIVMSKKGVEELDAGGVFFWQICSAVIL
                     SWIVLFIKRKKLPLNSKAILAYATGVFEPFLAYTFTLYGLYFISAGSASIIFSLESVFI
                     LVLSVLICSVKINSPQYFILFLIGAIVGSILVALPDISNGSNNIVGYCLVVAGVLSAAF
                     YVVISSRLIKSFEPITLLSGQLTFSLILSSLFIFISKSSIYLPLESVIIVFSSGILQYF
                     LAFCFYLNSLRWLPVHLAGIMLYFIPLVALFLSWLFLDEQFTFLQGVGFIVTVLSVYFL
                     NRKYSEE"
                     /name="DMT family transporter"
     Typing          5457..5538
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="98.795"
                     /coverage="100.0"
                     /evalue="6.23e-34"
     Typing          4813..5000
                     /name="rep_cluster_2401"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="4.63e-94"
     Typing          571..2132
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 tcagcggttt tcaccgtcat ccccgaagcg tgcgaggcaa ctgcggtaaa gctcatcggc
       61 gtggtcgtga agcgattcac agatgtctgc ctgttcatcc gcgtccagtt cgttgagctt
      121 ctccagcagc gttaatgtct ggcctctgat gaagcgggcc atgttaaggg cggttttttc
      181 ctgtttggtc actgatgcct ccgtgtaagg gggggttctg ttcatggggg taatgatacc
      241 gatgaaacgc gagaggatgc tcacgatacg ggttactgat gatgaacatg cccggttact
      301 ggaacgctgt gagggtaaac aactggcggt atggatgcgg cgggtctgcc tgggtgagcc
      361 ggttgcccgt tccgggaagc tgccgacact ggcaccgccg ttactgcgtc agctggccgc
      421 catcgggaat aaccttaacc agacagcgag gaaggtgaac agcgggcagt ggtcttccgg
      481 tgaccgggtt caggtggtgg ccgcactgat ggccatcggg gatgagctgc gccggctgcg
      541 tctggcggtc agggaacagg gggcgcggga tgatagttaa gtttcatgcc aggggaaaag
      601 gtggtggcag tggtccggtt gattacctgc tgggaaggga gcgtaaccgg gaaggggcaa
      661 cggtgcttca ggggaatccg gaagaggtcc gggaactcat cgatgccacg ccatttgcga
      721 agaaatacac gtcaggtgtt ctgtcgttcg cggagaagga gctgccgcct ggagggcgtg
      781 aaaaagtgat ggcgagcttt gagcgtgtac tgatgcccgg tctcgagaaa aatcagtaca
      841 gcatcctgtg ggtggagcac caggacaagg gacggcttga gctgaatttt gtcattccga
      901 acatggagct acagaccgga aaacgcctcc agccgtacta cgaccgggca gacaggccga
      961 gaattgatgc ctggcagacg ctggtgaatc accattacgg tctgcatgac cccaacgccc
     1021 cggagaaccg ccggacgctg acccttcctg ataacctgcc ggaaacgaaa caggcgcttg
     1081 ctgagggcgt cacacgcggg atagacgcgc tttaccatgc cggagagata aaaggccgtc
     1141 aggatgtgat tcaggcgctc acagaggcgg ggcttgaagt ggtcagggtg acgcgaagca
     1201 gtatcagcat tgcagacccg aacggcggga ggaatatcag actgaaagga gcgttttatg
     1261 agcaatcttt tacagacggg cgcggagttc gagaaaaagc tgaaagagag agccgaatct
     1321 acagagaaaa tgctgaacga cgagttcagg aagctcgaag aatctgtaaa cagggaactg
     1381 acctcaaacg aatctttaat caggaacgct atcaacgacc atacaacagc cctgaaagaa
     1441 ctgctggaga ggtatcagaa aacgaccgtc gatacgatgg acgcgcactg gaaaaccgta
     1501 ctgaaaatga gcgtgaaacg ctggctgtgg ctgattatcg tctcagtact gatgtttgcc
     1561 acgaccggga gtctgctgtg gtaccagggc atgaagataa acgcgaatat gaatattctc
     1621 cgcgagcaga aagagagtct ggagaagctg aacgcgaaga catggggcgt gcgttatcac
     1681 gaggacagca acggacgttt tctggtgttg ccgaagggga tgaaagccga aacgaactgg
     1741 acgaaggaca acggcaaact gaacgcagtg agactggtgc aggagtgaca gagcatgacg
     1801 gagctggaaa gacatttgct gaacgcatta gagcaactgc aacaggacta tatgcagcgg
     1861 ctgaacgaat gggagaacgc cttcgtggaa ttgcagaaaa tgttttcgct tacgcaacgg
     1921 gacaacgcga tgctgaacgg gcgagtcatg cagttgagtc agcaggtgca gcacttgagc
     1981 gagcggacag aacgcttgag ccagttatac agcgagaaca ggagataagg gatgaacggc
     2041 tgatgcagga acgcgaacat gagttatctc tggagcggga gcgtcagccg gaaatccagg
     2101 agcggacact ggatggccct tcgctgggat ggtgaaacca tgaaaaatga cgtgttcagt
     2161 ggattaaggc gggctaatgt ggcctgtagc atctggttgc ataggtattc atgcggttaa
     2221 aatttatcag gtgcgatcgc ggcagttttt cgggtggttt gttgccattt ttacctgtct
     2281 gctgccgtga tcgcaccgaa cgcgttttgg cggtgcgtac aatgcgacgt tatggtaaat
     2341 ggagcggatt ttcaggaagg agtgatacta acaactcgaa cactgtgcaa ataatgattt
     2401 ttttaaaata tcggtaacga taataaatta tttcgtttta cgccggtaat aaatataatg
     2461 tagtttcagt atataaaaaa atatatgagg tgtcttgtgg gagctttcat gaatcttcaa
     2521 caacgtataa ataaactacc acaattatca tccagttttt catttggaaa agatattgat
     2581 aatattcatt catttatctt taacgaaact tctaaagata aaattgaaga tttactaaga
     2641 aaatgggtgt caggcaatca gccctgtgta tttggtaaat tggcaagcaa gaaaattaaa
     2701 gggcttgatt tccatttatc tattgtaaat agcccccaac tatataatga tgatggtcat
     2761 ttgtttgatt ttttgcgtaa tgaaagagtt cgttttaaag aacgcgcaag aagaggagag
     2821 gtcagtgcgc atctcattta ttttattcat ccacaacttg cctttgctcg tccatcagaa
     2881 gagttagtgg acatacaaaa atatatttgt tcgctgcata tgccagagtg ctatccaata
     2941 aaagaggatg ttatttatac tgaaagcgta ccatttcagg ataaagatgg gctaaaaata
     3001 tataaggctg gtgttaatgt tttttactct tctgctcata gaacaagaaa tcatgataga
     3061 agaataccag ggggaatact tatttctgta aatgccccgg ggcattttat gaggctggcg
     3121 atagaaaaag gtttctataa agatcaagaa caagcgttag cggatattcg taacatgact
     3181 attcagtctg ttggtaaggg tgggtattca catccggaag ggatttctac aacatggcat
     3241 tcagaatcta atttggatcg ttttggatgc ccagtgcaca ccggtaatag ttcttattac
     3301 agcggttttt atcatactga tgtattaatt ccaggagaat taactaagga tgaaagattg
     3361 ctccatgaaa tagaaaatag tgatccaatg atcttcaact ggaatgtatt gttttatgtt
     3421 tcattagaag agtttcctat agatgatcct tattatggag agtttattgg tattcctgta
     3481 gatgatgcat ctatgttttt taactccttt caaccaagga aatttgaaaa caaacccctt
     3541 tatgagaaag aggatgatta atatgattaa aggaatgctt tttgcttttt tagcagcgtt
     3601 ctcatggggg gcagctatcg taatgagcaa aaaaggagtt gaagaactag atgccggagg
     3661 ggtgtttttc tggcagattt gtagtgcagt aatactatct tggatagttc tttttataaa
     3721 aagaaaaaaa ctcccattaa actcaaaagc gatacttgct tatgcgacag gcgtttttga
     3781 accattctta gcgtatactt ttacactcta cggactttat tttatttcag caggaagcgc
     3841 atcaattatt ttttcacttg aatcagtgtt tatattggtg ttgtctgttc ttatttgctc
     3901 agttaaaatt aattccccgc aatattttat attgttcctt ataggtgcaa ttgttggcag
     3961 tattttggta gccttgccag acatcagtaa tggatcgaat aatattgttg gatattgtct
     4021 tgttgttgcc ggtgtgttat cggcagcatt ttatgttgtt atatcgtctc gccttattaa
     4081 atcgtttgag cctatcacat tattgagcgg acagttgaca ttctccctta tactgtcatc
     4141 gctctttatt tttatatcta aatcatcaat ttatcttccg ttggaatccg tgattattgt
     4201 tttttcatct ggaatattac aatatttttt agctttttgt ttttacttga actccttgcg
     4261 ttggctccca gttcatttgg cagggataat gttgtacttt attccgctag ttgcattatt
     4321 tttgtcatgg ttgtttttgg atgaacaatt cacattctta cagggggtag gatttattgt
     4381 aactgtgcta agtgtatatt ttcttaacag aaaatactca gaggagtaac attctgttca
     4441 ggattgcccc ccggcctcca tcgataccgt gccaaatgca cgtaaaaaac gggagcgttt
     4501 ctggtgtcgg aatgtaacca agggggtcag aggcgcgcta aaacgctctc aggggagtca
     4561 aatagagacg tttgtaacaa aaagatcaaa ggatcctctt gagatccttt ttttctgcgc
     4621 gtaatctgct gcctgtaaac gaaaaaaccg ccttgcaggg cggtttgatc gaaggttaag
     4681 tcagcttgca gactgcttaa ccaggtaact gtcttatgcg agacgagtca ccaaaattgt
     4741 tcttctagtg tagccgcact ccggcagcca cttcaagtac tctctaaata tctcgcacat
     4801 gacttttacc aatggctgct gccagtggcg ctttgtggtg tcttttccgg gttggaccca
     4861 agagaacagt taccggagaa ggcgcagcag tcgggctgaa cggggggttc ctgcatacag
     4921 cccagcccgg agcgaactgc ctaagtcgcc ccgagatacc agaagacgtg agctatgaga
     4981 aagcgccacg tgtcccgtaa gggagaaagg cggaaaaggt atccggtaat cgatatggcg
     5041 ggaacgtggg ggcgcaggag ggagcgattc accggaaacg gtgatgatct ttaagccacg
     5101 tcgggtttcg ccaccgctgg cggatttcat ggttgagccg caaggctccc acagatgcac
     5161 cgaaaaagtg tctgttttgt gaagtccgtc aggggggcgg agcctatgga aaaagcgcct
     5221 ccggcgcggc ctttcccggg gtttcgtttt ttgcgcacat gttctttcct ggtttatccc
     5281 cgggttctgt ggataacagg gttagcgttt ttgagaaagg agagtccgct cgccgcagcc
     5341 gaacgaccga gcgtagcgag tcagtgagcg aggaagcgga agagcgcctg aactggcatt
     5401 ttctccttac gcatctgtgc ggcatttcac accggacatg gcgcactttt catacaatcc
     5461 gcactgatac cgaatggtta agccagtata cactccgcta tcgctacgtg actgggtcag
     5521 ggcttcgccc cgacacccca aaggtcaacg gcctgacgcg ccctggcggg cttgtctgct
     5581 cccggcatcc gctcacagac aagctgtgac cgtctccggg agctgcatgt g
//
