LOCUS       CP125055                5753 bp    DNA     circular BCT 16-MAY-2023
DEFINITION  Escherichia coli strain KFS-C08 plasmid pKFS-C08_2, complete
            sequence.
ACCESSION   CP125055
VERSION     CP125055.1
DBLINK      BioProject: PRJNA956323
            BioSample: SAMN34598742
KEYWORDS    .
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 5753)
  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  JOURNAL   Unpublished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 5753)
  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..5753
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="KFS-C08"
                     /isolation_source="Fecal sludge"
                     /db_xref="taxon:562"
                     /plasmid="pKFS-C08_2"
                     /geo_loc_name="Uganda"
                     /lat_lon="0.19 N 32.35 E"
                     /collection_date="2018"
                     /collected_by="Hidenori Harada, Mai Tanaka"
     gene            join(5308..5753,1..73)
                     /locus_tag="QL145_24720"
                     /pseudo=""
     CDS             join(5308..5753,1..73)
                     /locus_tag="QL145_24720"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_009310049.1"
                     /note="frameshifted; Derived by automated computational
                     analysis using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /name="hypothetical protein"
     gene            70..633
                     /locus_tag="QL145_24725"
     CDS             70..633
                     /locus_tag="QL145_24725"
                     /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="WHJ91521.1"
                     /translation="MNDMKAVRHRYKQRYDFAASEVVGAFDELRSLDWSLEIASLSDVE
                     MSKRWIGAVDPNGVARLPPNGGWDWVKLYNGYLKNPSAFVCAIKSEGKLCALIGGGVSD
                     SKVVTKLHYLESAPYDTALSGYALDISVTYVVTVANAMGSEYSAIYEPNSKVREIAIND
                     YGFSEDNLFGTSKDFALYLPMSRI"
                     /name="hypothetical protein"
     gene            complement(643..795)
                     /locus_tag="QL145_24730"
     CDS             complement(643..795)
                     /locus_tag="QL145_24730"
                     /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="WHJ91522.1"
                     /translation="MLAHVVELKKATEPCSSGTAGAFRQRVKARRAEQGRSNQQPEKLY
                     GVLVG"
                     /name="hypothetical protein"
     gene            complement(1091..1237)
                     /locus_tag="QL145_24735"
     CDS             complement(1091..1237)
                     /locus_tag="QL145_24735"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001354639.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="replication initiation protein"
                     /protein_id="WHJ91523.1"
                     /translation="MHEPPVQSDCCALSGNYHLESNPERHAKAPLAAANGKRMYKRLLT
                     QSS"
                     /name="replication initiation protein"
     gene            1466..1669
                     /locus_tag="QL145_24740"
     CDS             1466..1669
                     /locus_tag="QL145_24740"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001347451.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WHJ91524.1"
                     /translation="MEKRQRRILFQPFLISAKSLYPAIRELATPAAVSRQERSDRVSEE
                     ASYHRNLHFLLYALQLHFSPAT"
                     /name="hypothetical protein"
     gene            1878..2201
                     /locus_tag="QL145_24745"
     CDS             1878..2201
                     /locus_tag="QL145_24745"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000957083.1"
                     /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="WHJ91525.1"
                     /translation="MLTMWVTEDEHRRLLERCDGKQLAAWMRQTCLDEKPARAGKLPSI
                     SPALLRQLAGMGNNLNQIARQVNAGGGSGHDRVQVVAALMAIDAGLERLRHAVLEKGAD
                     DDR"
                     /name="MobC family plasmid mobilization relaxosome protein"
     gene            2410..2844
                     /locus_tag="QL145_24750"
                     /pseudo=""
     CDS             2410..2844
                     /locus_tag="QL145_24750"
                     /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            2879..3364
                     /locus_tag="QL145_24755"
     CDS             2879..3364
                     /locus_tag="QL145_24755"
                     /inference="COORDINATES: protein motif:HMM:NF016710.2"
                     /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="WHJ91518.1"
                     /translation="MNSLLTLAKDLEQKSKAQQQSTGEMLKAAFSEHEKSVRAELSESE
                     KRISAAILDHDRKLSSAMSQRTKGMMRMVSQTWLTIVLVSTLLTASGASILWWQGQQIL
                     DNYTIIREQKSTQAMLSERNSGVQLSTCGEQRRRCVRVNPEAGRFGEDSSWMILAGK"
                     /name="MbeB family mobilization protein"
     gene            3368..3583
                     /locus_tag="QL145_24760"
     CDS             3368..3583
                     /locus_tag="QL145_24760"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000137421.1"
                     /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="WHJ91519.1"
                     /translation="MTELEKQLLSALEQLQQDYSKRLDEWENAFAEWRTMSGLMQRENA
                     ALSERVTGLSRQVQSLSEQLRRLSQG"
                     /name="MbeD family mobilization/exclusion protein"
     gene            complement(3782..4333)
                     /locus_tag="QL145_24765"
     CDS             complement(3782..4333)
                     /locus_tag="QL145_24765"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000654246.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WHJ91520.1"
                     /translation="MKDMKAVVVFTGKDLNIMRTEGGSGYWHARTDRLNDADYLIAVRN
                     RRETWAVKDLEHGTAFLIAKITGCFKSPDYDDRNVITFDEYAEIHTPKAWKMLTDGQRY
                     PVAYLSAQEAFLRIGVTPEQLEWKKFHPSSPSVPNTVIPGLAEEKTEKLSLNEAIERAK
                     KDISNATGIDSSAITISIKI"
                     /name="hypothetical protein"
     Typing          1590..1774
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="86.702"
                     /coverage="86.0"
                     /evalue="1.25e-50"
     Typing          complement(1129..1644)
                     /name="ColRNAI_rep_cluster_1987"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="90.211"
                     /coverage="99.0"
                     /evalue="0.0"
     Typing          2192..3687
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="92.385"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 tggatgggca agggatgagc gttacaacgc tctattttct aggatgcagg aagtgggggc
       61 ggagtgggaa tgaacgacat gaaagctgtt cgtcaccgat ataagcagag atatgatttt
      121 gctgcgtcag aagtagtggg ggcgtttgat gaacttagaa gtttggattg gagtttagaa
      181 atcgcatctt taagtgacgt ggaaatgtca aagagatgga ttggggctgt tgatcctaac
      241 ggtgttgcaa gactaccacc taacggtgga tgggactggg ttaagctcta caacggctat
      301 ttgaagaacc ctagcgcatt cgtctgtgcc attaaatcag aaggcaagct atgcgctctg
      361 attggtggcg gggtttctga tagtaaagtg gtaactaagc tgcattacct tgaatcagcc
      421 ccttatgaca cggctctttc aggatatgca ctggatattt ctgttacgta tgttgttact
      481 gtcgcgaatg cgatgggaag cgaatactca gccatctatg agccaaatag caaagtcaga
      541 gagatagcta taaatgatta tggatttagc gaggacaact tgtttgggac aagtaaagat
      601 ttcgctctgt atctaccaat gagccggatt taaccggctc atttatccta ccagtacgcc
      661 gtagagtttt tctggctgtt ggtttgatcg gccttgctct gctcgtcttg ctttcacgcg
      721 ctggcgaaat gctccggctg tgccagaaga gcatggttcc gtcgcttttt taagttcgac
      781 cacgtgagct aacatattat ttccgttttt tcgtgagtta gtacaaagca tatgaggtga
      841 cggatacgtc aacttcatag taactgtact gtattgtaga agagatgcgc aagtcgcaga
      901 attaatgcga cccttcattg acgaggcgaa gagtaaacgc gtatcttctt tgaaaacgaa
      961 aaaaccaccc ggcaaggtgg tttttcgaag gttcattaaa ccggcaagtt tatgaaccgt
     1021 ggtaacaggg tgtacaagac cactgccacc aaattcgtcc ttccagttta gccgtagttg
     1081 ggctgatact tcaagaactc tgcgttagta atctcttgta catcctctta ccgttggctg
     1141 ctgccagtgg cgcttttgca tgtctttccg ggttggactc aagatgatag ttaccggata
     1201 aggcgcagca gtcggactga acggggggtt cgtgcataca gtccagcttg gagcgaactg
     1261 cctacccgga actgagtgtc aggcgtggaa tgagaaaccg cggccataac agcggagtga
     1321 caccggtaaa ccgaaaggca ggaacaggag agcgcacgag ggagctacca gggggaaacg
     1381 cctgggatct ttatagtcct gtcgggtttc gccgcctctg atttgagcgt cagatttcgt
     1441 gatgcttgtc aggggggcgg agcctatgga aaaacggcaa cgccgcatcc tttttcagcc
     1501 cttcctgatt tccgctaagt ctctttatcc agccattcgt gagctggcaa cgcccgccgc
     1561 agtctcacgg caggagcgca gcgaccgagt gagcgaggag gcgtcatatc accgtaacct
     1621 ccattttctc ctgtacgccc tgcagctgca tttttcccct gccacatgaa gcactttcat
     1681 taagtgttac tccgccgtaa catattgagc cagtatacac tccgctagcg ctacgtgact
     1741 ggttcagggc tgcgccccga aacctgctaa aaccactgac gcgcctgcgg cttgtccaac
     1801 accgcgccga ccgggaaaag atttcccgcc cgtcccggcg ttatcaggag gctggattgg
     1861 cagacaaacg cagtaaaatg ctcacgatgt gggtgaccga agatgagcac cgccgtctgt
     1921 tggaacgctg cgacggtaaa cagcttgcag cctggatgcg ccagacgtgc ttggacgaga
     1981 aacccgcccg cgccggcaag cttccctcga tctcgccggc gctgcttcgt cagcttgccg
     2041 gcatggggaa caacctcaac cagattgccc ggcaggttaa cgccggtggt ggcagcgggc
     2101 acgaccgcgt gcaggtcgtc gccgcgctga tggccataga tgccggactc gagcggctgc
     2161 ggcatgccgt gctggaaaag ggtgcagacg atgatcgtta agtttcaccc gcgagggcgc
     2221 ggcggtggcg ccggtccggt ggattatctg ctggggaaag accgacagcg cgacggcgcc
     2281 accgttttgc aggggaagcc ggaagaagtc agggagctta tcgacgcctc gccctacgca
     2341 aaaaagtaca catccggcgt cctgtccttt gccgaaaagg atttaccgcc cgggcagcgc
     2401 gaaaagctga tggcgagctt tgaacgggtt ctgatgcccg gactcgataa agaccagtac
     2461 agcgtgctgt gggttgagca ccaggataag gggcggctgg agctgaactt cctgatcccg
     2521 aacatggagc tgctgactgg caggcgtctc cagccgtatt acgaccgcgc cgaccgtccg
     2581 cgcattgatg cctggcagac catcgtgaac ggcaggctgg ggctgcatga cccgaacgcg
     2641 cctgaaaacc ggcgggcgct ggtcacgccg tccgcgctgc cgaaaacgaa gcaggaagcc
     2701 gctcaggcaa ttacacgggg tttactggcc ttagcctcgt ccggggagct gaaaacccgc
     2761 caggacgtca ctgaggcgct ggaaagcgca ggttttgagg tggtacgcac cacaaaaagc
     2821 agcatcagca ttgccgaccc ggacgggggg cgaaacatcc gactgaaggg agccatctat
     2881 gaacagtctt ttaacgctgg caaaggactt agagcagaaa tcgaaagcgc agcagcagag
     2941 taccggcgag atgctgaaag ccgcattcag cgagcacgag aagtctgtca gagcggaact
     3001 gagcgaaagc gagaagagaa tcagcgccgc catcctcgac cacgaccgga agctgtcctc
     3061 agccatgagc cagcgcacga aaggcatgat gcgtatggtc agccagacgt ggctgaccat
     3121 cgtcctggtg tctacactgc tgacagcatc gggcgcaagc attctatggt ggcaggggca
     3181 gcagatactc gacaattaca cgatcatccg ggagcagaag agcacgcagg ccatgctgtc
     3241 cgagaggaac agcggcgtgc agctctcgac ctgcggagag cagagacgcc gctgcgtgag
     3301 ggtgaacccg gaagcgggac ggttcggaga ggattcgagc tggatgatac tggcggggaa
     3361 atagcacatg acggagctgg aaaaacagtt gctgagcgca ttagagcagc tacagcagga
     3421 ctactcgaaa aggctggacg agtgggagaa cgccttcgcg gaatggcgga cgatgtctgg
     3481 tcttatgcaa cgggagaacg cggcgctgag cgagcgcgtc acgggcttga gcaggcaggt
     3541 gcagagtttg agcgagcagc tgcgccggtt gtcacaaggc tgaacgtgat agaggcacat
     3601 cgtgagcagg aacgggcggc gcagcatcag aaagcgctgg agctggaacg atctcagcga
     3661 cagcgaacgt acaacggtcc gtcactttga atctgtgcgc cggaaaagca tgggcttgct
     3721 gtttctggcg tacaggttca gttctagaac atgaggctgc tatcttgttg ttcacgcttc
     3781 atcagatctt gatgcttatt gttatggctg agctatcaat ccctgttgcg ttgctaatat
     3841 cctttttggc tctttcaatt gcctcgttaa gggagagttt ttctgttttc tcttcagcca
     3901 gaccaggaat cactgtatta ggaaccgatg gggatgaagg atggaatttc ttccattcca
     3961 gttgttccgg tgttacccca atacgtaaaa aagcttcctg tgcgctcagg taagcaaccg
     4021 gatagcgctg accatcggtt agcattttcc atgcttttgg cgtgtgaatt tctgcgtatt
     4081 catcaaaggt tatgacgttc ctgtcgtcgt aatcagggct tttaaaacac ccggtaattt
     4141 tggcgatcag gaatgctgtg ccgtgttcta ggtcttttac tgcccacgtt tcccttctgt
     4201 ttcttactgc tatgaggtaa tcggcatcgt tgagcctgtc tgttctggca tgccagtagc
     4261 ctgacccccc ctcagttctc attatgttca aatccttccc ggtaaaaacc acaacagctt
     4321 tcatatcttt catatagaaa cccttaatag gtgagtaaat ttcatttttt atgaaatcta
     4381 tacgatagaa ttcgtgttgt aaatgttttt tatacgataa aatacagccc cctacctctt
     4441 ttactgttag tggtaaggct ttctgtttga ttttttgata aaccggttaa aacaggggct
     4501 tggacgagga tatacattga aagcatgagc cattcacgtg gctgcatggc tatgcagtcg
     4561 cgtgaaattt atcaggcgca gaatgcgcgg tttagcgggg agtttactgc cggttttacc
     4621 gggctaacgc cgctttcacg ctgaacccgt ccggagcggt gcgggcaagg gatgttatgg
     4681 taaatggttt ctgaggtgta agcgaaaact cgagttttga cgccattctg agtaggtaat
     4741 ttgcagacgg aataaatact ggcgagcaat aagctcatca acaaaaaatg gagatcctaa
     4801 gatggataga gaaaccctat acctactcaa aacgttagac cataacaatg ccttgcttga
     4861 cgatattatc cgaagaaaga tgggtaggta ctacaacacg aagattttgc gtgattcctg
     4921 tgatgctatt gaagccgaac tacgacgtcg aggaatcatt taaaaagacg aagcccgctt
     4981 atgtgggctt tttcattgcg cattcagggc accccttccc ccccttaaac cccctaagaa
     5041 ccccattcag cacagcgagc acaacgatta cattagagta cattgagaac agcgagtaca
     5101 aaatagcgca taactaattg aaaaataaaa ccgtaattgt aaaaaatatt acatctcaat
     5161 atttgtattg acaaaaaaaa agaatcatat caaatgagat gttggttaat gatgtgcttg
     5221 gtttttgtgt tattacacat aactcattga atataatagg ttttttgttg ataatatttt
     5281 catgttgaat tgacttttgg gggataaatg tcagagaagg caaaaaaagt aggtaggcgc
     5341 tctctatcaa aaagaagaga aagtctaata aaagagcttt ggggggatga gctttccgaa
     5401 cttaatatat ggaacaggaa agaacacgat ggatttacaa caatcccaag aacattgaat
     5461 tatatcaata ggataatcga ttaccttgct ggcgctggat ctcctgtgtc acagacatac
     5521 ctcagtttat ggtgtcgagt ttttgacgag ggattcgtcg aaattaggga taaagatgct
     5581 ctggcatttg agtcagggtt tagtgggcag cgagcggtga ctacttggct aggaagaatg
     5641 aaaaagctac gggagctggg actgatatca acgaagcctg gtacttctgg cgagtttcat
     5701 tatgtaatca tgttgaatcc actttacgta attaaaaagt catatgaatc aaa
//
