LOCUS       CP125046                6222 bp    DNA     circular BCT 16-MAY-2023
DEFINITION  Escherichia coli strain KFS-C10 plasmid pKFS-C10_2, complete
            sequence.
ACCESSION   CP125046
VERSION     CP125046.1
DBLINK      BioProject: PRJNA956323
            BioSample: SAMN34598743
KEYWORDS    .
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 6222)
  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  JOURNAL   Unpublished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 6222)
  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 16:59:26
            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)                     :: 4,998
            CDSs (total)                      :: 4,876
            Genes (coding)                    :: 4,619
            CDSs (with protein)               :: 4,619
            Genes (RNA)                       :: 122
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 88
            ncRNAs                            :: 12
            Pseudo Genes (total)              :: 257
            CDSs (without protein)            :: 257
            Pseudo Genes (ambiguous residues) :: 0 of 257
            Pseudo Genes (frameshifted)       :: 86 of 257
            Pseudo Genes (incomplete)         :: 177 of 257
            Pseudo Genes (internal stop)      :: 48 of 257
            Pseudo Genes (multiple problems)  :: 52 of 257
            Pseudo Genes (short protein)      :: 4 of 257
            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..6222
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="KFS-C10"
                     /isolation_source="Fecal sludge"
                     /db_xref="taxon:562"
                     /plasmid="pKFS-C10_2"
                     /geo_loc_name="Uganda"
                     /lat_lon="0.19 N 32.35 E"
                     /collection_date="2018"
                     /collected_by="Hidenori Harada, Mai Tanaka"
     gene            complement(join(5966..6222,1..148))
                     /locus_tag="QL142_24840"
                     /pseudo=""
     CDS             complement(join(5966..6222,1..148))
                     /locus_tag="QL142_24840"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001120888.1"
                     /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="IS91 family transposase"
                     /name="IS91 family transposase"
     gene            complement(192..581)
                     /locus_tag="QL142_24845"
     CDS             complement(192..581)
                     /locus_tag="QL142_24845"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000102614.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WHJ45393.1"
                     /translation="MSTELNSGTVGGFGHMGPNDPYNDGHSGSGSSGGSFNGGGNGGHD
                     NSSGSSYTASFGLITGRHPITVPGTKNINSVDLSAVINNIIHHEGARNNMYLDTANNVR
                     VGVTGTGWQCLATAGISAEGKRTFR"
                     /name="hypothetical protein"
     gene            799..1239
                     /locus_tag="QL142_24850"
     CDS             799..1239
                     /locus_tag="QL142_24850"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_011161230.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="entry exclusion protein 1"
                     /protein_id="WHJ45394.1"
                     /translation="MAWHTVQETLKLTGKSRSQLYRDMAKGLVSYRTGKNDRREFETSE
                     LIRAYGELRTSETPKRHKEGHSKSVVSQAENAQLDVIQQKLDALQQTVTLMLEDKMARE
                     AENRLRNEEREQLQAEISRLADALAQEKKRGFWSRLFRSGSE"
                     /name="entry exclusion protein 1"
     gene            complement(2006..2155)
                     /locus_tag="QL142_24855"
     CDS             complement(2006..2155)
                     /locus_tag="QL142_24855"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_017880354.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WHJ45395.1"
                     /translation="MPSEYDEQLDSTDTQLPGEYDLFDLMAQVTEENLHAPVDFGSPVG
                     REAL"
                     /name="hypothetical protein"
     gene            3344..4159
                     /gene="sul2"
                     /locus_tag="QL142_24860"
     ARG             3345..4156
                     /name="sul2"
                     /gene="sul2"
                     /gene_name="sulfonamide-resistant dihydropteroate synthase
                     Sul2"
                     /tool="amrfinderplus"
                     /drug_class="SULFONAMIDE"
                     /identity="100.0"
                     /coverage="100.0"
     gene            4220..5023
                     /gene="aph(3'')-Ib"
                     /locus_tag="QL142_24865"
     ARG             4221..5020
                     /name="aph(3'')-Ib"
                     /gene="aph(3'')-Ib"
                     /gene_name="aminoglycoside O-phosphotransferase
                     APH(3'')-Ib"
                     /tool="amrfinderplus"
                     /drug_class="AMINOGLYCOSIDE"
                     /identity="100.0"
                     /coverage="100.0"
     gene            5023..5859
                     /locus_tag="QL142_24870"
     CDS             5023..5859
                     /locus_tag="QL142_24870"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000480972.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="aminoglycoside O-phosphotransferase APH(6)-Id"
                     /protein_id="WHJ45392.1"
                     /translation="MFMPPVFPAHWHVSQPVLIADTFSSLVWKVSLPDGTPAIVKGLKP
                     IEDIADELRGADYLVWRNGRGAVRLLGRENNLMLLEYAGERMLSHIVAEHGDYQATEIA
                     AELMAKLYAASEEPLPSALLPIRDRFAALFQRARDDQNAGCQTDYVHAAIIADQMMSNA
                     SELRGLHGDLHHENIMFSSRGWLVIDPVGLVGEVGFGAANMFYDPADRDDLCLDPRRIA
                     QMADAFSRALDVDPRRLLDQAYAYGCLSAAWNADGEEEQRDLAIAAAIKQVRQTSY"
                     /name="aminoglycoside O-phosphotransferase APH(6)-Id"
     ARG             5024..5856
                     /name="aph(6)-Id"
                     /gene="aph(6)-Id"
                     /gene_name="aminoglycoside O-phosphotransferase APH(6)-Id"
                     /tool="amrfinderplus"
                     /drug_class="AMINOGLYCOSIDE"
                     /identity="100.0"
                     /coverage="100.0"
     Typing          complement(2191..2364)
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="99.429"
                     /coverage="100.0"
                     /evalue="1.19e-84"
     Typing          2288..2893
                     /name="rep_cluster_2335"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="89.593"
                     /coverage="99.0"
                     /evalue="0.0"
ORIGIN
        1 attcctttcc ctgctctgcc ataagcgcag cgaatgccgg gtaatactcg tcaacgatct
       61 gatagagaag ggtttgctcg ggtcggtggc tctggtaacg accagtatcc cgatcccggc
      121 tggccgtcct ggccgccaca tgaggcatgt tccgcgtcct tgcaatactg tgtttacata
      181 cagtctatcg cttagcggaa agttctttta ccctcagccg aaatgcctgc cgttgctaga
      241 cattgccagc cagtgcccgt cactcccact cttacattgt tcgcagtatc taggtacatg
      301 ttattgcgtg caccttcatg atgtataatg ttattaatga cagcagaaag atcgacagaa
      361 ttaatattct tcgtacctgg gacagttatc gggtgtcggc cagtgatgag accaaaggat
      421 gcagtataag atgaaccact actattatca tggccaccat taccaccacc gttaaaacta
      481 cctcccgaac ttccagagcc gctatgacca tcattgtagg ggtcatttgg tcccatgtga
      541 ccaaaaccac cgacagtacc gctatttaac tctgtactca taaaattatc ctctttgact
      601 tttaaaaaca gcaaaaactg tatttataac aatgtgttta tatacagtat tcgaaatact
      661 acgcccgtca aaaccacacc gtcaacaggt tttttgtgta tttttcacgc ctcacgggca
      721 gcctcagacc ttttgtgtta aaacagtaat atgttctgct gttacaatac ggtacacaca
      781 ggagacactg tcacttttat ggcatggcac acagttcaag agacactgaa attaacagga
      841 aagtcgcgct cgcaattata tcgtgacatg gctaaaggcc ttgtcagcta tcgcacagga
      901 aaaaatgatc gccgggagtt cgagaccagt gaactgattc gggcctatgg cgagctgcgc
      961 acttctgaga caccaaaaag gcacaaggag ggacactcca aatctgtcgt tagccaggcg
     1021 gaaaatgctc agctagacgt cattcagcag aaactggacg ctctgcagca gactgttacc
     1081 ctaatgcttg aagacaagat ggcgcgggaa gcagaaaacc gcctgcgaaa tgaggagagg
     1141 gaacaactac aggccgaaat tagccgtctg gctgacgcgc tggcacagga aaaaaagcgg
     1201 ggattctggt cgcggctgtt tcgctccggt tcagagtaac agtgcaggtg actctgattt
     1261 accataacat ctgttatcag caccgcctga gaggccctca gggcgtttct gacgggaaac
     1321 cggtaaaaca ggcaacaaac cacccgaaaa cccgccagaa acgcgcaggc tctgttttta
     1381 cggcatgcat gagtatgcgc acaagtgcat agcgcggaaa ttcacaccat tcagccgggg
     1441 taagtcctgt ttccggcgtt cttcccatcc gaaaacggtg aacggggacg caatttattg
     1501 cgtggccgtg aagcgttgcc ggcgcagccg gaaaacccgc tgtcagcacg ttcaggaagg
     1561 gggtgatgta caaatggcac agaggatgaa agtgacgtat gagctgaagg aatgatgtaa
     1621 aagtgatgta taagtgatgt aaaagtgatg tataagtgat gtaaaagtga tgtatggact
     1681 gaaggagcga tgtaattctg tagtcaggaa gaataacccg ttcatgcagg catgaacgat
     1741 acagtgagga acgctttttt tgtcacgatc tccccttaac ctgcgtaaat cacccgccat
     1801 ggttgattat ttttcaacct caaaatggtc atacacctaa cgcagccgcg attttcatcg
     1861 caactgcatg aattaaaaga aaaaaaagga atatttcgtt ttcacgagta atacccgggt
     1921 attaaaaatc cactgtaatt acatgaaaat aaagaaataa aaggtaatac cggagtatta
     1981 ccacgtacgc gggcaagcga aaaagctata acgcttcccg gccgacaggc gacccaaaat
     2041 ccacaggggc atgcaggttc tcttcagtaa cctgcgccat taaatcaaaa aggtcatatt
     2101 cgccgggaag ctgcgtatca gtcgaatcca gttgttcatc atattcagat ggcatggggt
     2161 gatatccagt agctgagagg ttgttagcgg gtttcggggc gcagccctga accagtcatg
     2221 tagcgctagc ggagtgtata ctggcttact atgttgccac gattgcgaaa atcagtgaag
     2281 tgcttcatgt ggcaggagaa aaaaggcagc accggcgcgt cagcagaata tgcgatacag
     2341 gagatattcc gcttcctcgc tcactgactc gctacgctcg gtcgttcggc tgcggcgagc
     2401 ggtaccggct tacggacggg gacggaaatt tcctggaaga taccaggaag acacttagca
     2461 aagaagagat aaggccacgg cgaagccgtt tttccatagg ctccgccccc ctgacaagca
     2521 tcgcaaaatc tgacgctcaa atcagtggtg gcgaaacccg acaggactat aaagatccca
     2581 ggcgtttccc cctggtagct ccctcgtgcg ctctcctgtt cctgcctttc ggtttaccgg
     2641 tgtcattccg ctgttatggc cgcggtttct cattccacgc ctgacactca gttccgtgaa
     2701 ggcagttcgc tccaagctgg actgtatgca cgaacccccc gttcagtccg accgctgcgc
     2761 cttgtccggt aactatcaac ttgagtccaa cccggaaaga cacgacaaaa cgccactggc
     2821 agcagccatt agtaacagga gtgcacgaga agatagatta agaggtcttg aagtagaggc
     2881 ctgactgcgg ctacactgaa agaacagttt tggtaatggc ggtctcgtga accctgttac
     2941 cgggttaagc agttccccaa ctgacttaac cttcgaacaa accgcctccc caggcggttt
     3001 tttcgtttac agagcaagag attacgattc attgaaaagg atctcaagaa gatcctttgt
     3061 agattactat caattaatct tccgaacatg acaccagtca ctgttgatta cggttaaacc
     3121 gctccgtaac aggtttccct cgtattggtt acttgcagca ccaaagaagc aaaaaagata
     3181 aatatatcta cttattgaga gatgatatat ttatttccaa aatgctacag atacatcatc
     3241 atgaaacgga tcaccgcaaa caggttactc gcctggggat tccctttcga cccgagcatc
     3301 cgtatgagac tcatgctcga ttattattat tatagaagcc cccatgaata aatcgctcat
     3361 cattttcggc atcgtcaaca taacctcgga cagtttctcc gatggaggcc ggtatctggc
     3421 gccagacgca gccattgcgc aggcgcgtaa gctgatggcc gagggggcag atgtgatcga
     3481 cctcggtccg gcatccagca atcccgacgc cgcgcctgtt tcgtccgaca cagaaatcgc
     3541 gcgtatcgcg ccggtgctgg acgcgctcaa ggcagatggc attcccgtct cgctcgacag
     3601 ttatcaaccc gcgacgcaag cctatgcctt gtcgcgtggt gtggcctatc tcaatgatat
     3661 tcgcggtttt ccagacgctg cgttctatcc gcaattggcg aaatcatctg ccaaactcgt
     3721 cgttatgcat tcggtgcaag acgggcaggc agatcggcgc gaggcacccg ctggcgacat
     3781 catggatcac attgcggcgt tctttgacgc gcgcatcgcg gcgctgacgg gtgccggtat
     3841 caaacgcaac cgccttgtcc ttgatcccgg catggggttt tttctggggg ctgctcccga
     3901 aacctcgctc tcggtgctgg cgcggttcga tgaattgcgg ctgcgcttcg atttgccggt
     3961 gcttctgtct gtttcgcgca aatcctttct gcgcgcgctc acaggccgtg gtccggggga
     4021 tgtcggggcc gcgacactcg ctgcagagct tgccgccgcc gcaggtggag ctgacttcat
     4081 ccgcacacac gagccgcgcc ccttgcgcga cgggctggcg gtattggcgg cgctgaaaga
     4141 aaccgcaaga attcgttaac tgcacattcg ggatatttct ctatattcgc gcttcatcag
     4201 aaaactgaag gaacctccat tgaatcgaac taatattttt tttggtgaat cgcattctga
     4261 ctggttgcct gtcagaggcg gagaatctgg tgattttgtt tttcgacgtg gtgacgggca
     4321 tgccttcgcg aaaatcgcac ctgcttcccg ccgcggtgag ctcgctggag agcgtgaccg
     4381 cctcatttgg ctcaaaggtc gaggtgtggc ttgccccgag gtcatcaact ggcaggagga
     4441 acaggagggt gcatgcttgg tgataacggc aattccggga gtaccggcgg ctgatctgtc
     4501 tggagcggat ttgctcaaag cgtggccgtc aatggggcag caacttggcg ctgttcacag
     4561 cctatcggtt gatcaatgtc cgtttgagcg caggctgtcg cgaatgttcg gacgcgccgt
     4621 tgatgtggtg tcccgcaatg ccgtcaatcc cgacttctta ccggacgagg acaagagtac
     4681 gccgcagctc gatcttttgg ctcgtgtcga acgagagcta ccggtgcggc tcgaccaaga
     4741 gcgcaccgat atggttgttt gccatggtga tccctgcatg ccgaacttca tggtggaccc
     4801 taaaactctt caatgcacgg gtctgatcga ccttgggcgg ctcggaacag cagatcgcta
     4861 tgccgatttg gcactcatga ttgctaacgc cgaagagaac tgggcagcgc cagatgaagc
     4921 agagcgcgcc ttcgctgtcc tattcaatgt attggggatc gaagcccccg accgcgaacg
     4981 ccttgccttc tatctgcgat tggaccctct gacttggggt tgatgttcat gccgcctgtt
     5041 tttcctgctc attggcacgt ttcgcaacct gttctcattg cggacacctt ttccagcctc
     5101 gtttggaaag tttcattgcc agacgggact cctgcaatcg tcaagggatt gaaacctata
     5161 gaagacattg ctgatgaact gcgcggggcc gactatctgg tatggcgcaa tgggagggga
     5221 gcagtccggt tgctcggtcg tgagaacaat ctgatgttgc tcgaatatgc cggggagcga
     5281 atgctctctc acatcgttgc cgagcacggc gactaccagg cgaccgaaat tgcagcggaa
     5341 ctaatggcga agctgtatgc cgcatctgag gaacccctgc cttctgccct tctcccgatc
     5401 cgggatcgct ttgcagcttt gtttcagcgg gcgcgcgatg atcaaaacgc aggttgtcaa
     5461 actgactacg tccacgcggc gattatagcc gatcaaatga tgagcaatgc ctcggaactg
     5521 cgtgggctac atggcgatct gcatcatgaa aacatcatgt tctccagtcg cggctggctg
     5581 gtgatagatc ccgtcggtct ggtcggtgaa gtgggctttg gcgccgccaa tatgttctac
     5641 gatccggctg acagagacga cctttgtctc gatcctagac gcattgcaca gatggcggac
     5701 gcattctctc gtgcgctgga cgtcgatccg cgtcgcctgc tcgaccaggc gtacgcttat
     5761 gggtgccttt ccgcagcttg gaacgcggat ggagaagagg agcaacgcga tctagctatc
     5821 gcggccgcga tcaagcaggt gcgacagacg tcatactaga tatcaagcga cttctcctat
     5881 cccctgggaa cacatcaatc tcaccggaga atatcgctgg ccaaagcctt agcgtaggat
     5941 tccgcccctt cccgcaaacg accccaaaca ggaaacgcag ctgaaacggg aagctcaaca
     6001 cccactgacg catgggttgt tcaggcagta cttcatcaac cagcaaggcg gcactttcgg
     6061 ccatccgccg cgccccacag ctcgggcaga aaccgcgacg cttacagctg aaagcgacca
     6121 ggtgctcggc gtggcaagac tcgcagcgaa cccgtagaaa gccatgctcc agccgcccgc
     6181 attggagaaa ttcttcaaat tcccgttgca catagcccgg ca
//
