LOCUS       CP125011                3346 bp    DNA     circular BCT 16-MAY-2023
DEFINITION  Escherichia coli strain KFS-D29 plasmid pKFS-D29_4, complete
            sequence.
ACCESSION   CP125011
VERSION     CP125011.1
DBLINK      BioProject: PRJNA956323
            BioSample: SAMN34598749
KEYWORDS    .
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 3346)
  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  JOURNAL   Unpublished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 3346)
  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 16:48:53
            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)                     :: 4,759
            CDSs (total)                      :: 4,635
            Genes (coding)                    :: 4,417
            CDSs (with protein)               :: 4,417
            Genes (RNA)                       :: 124
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 88
            ncRNAs                            :: 14
            Pseudo Genes (total)              :: 218
            CDSs (without protein)            :: 218
            Pseudo Genes (ambiguous residues) :: 0 of 218
            Pseudo Genes (frameshifted)       :: 67 of 218
            Pseudo Genes (incomplete)         :: 150 of 218
            Pseudo Genes (internal stop)      :: 45 of 218
            Pseudo Genes (multiple problems)  :: 41 of 218
            Pseudo Genes (short protein)      :: 4 of 218
            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..3346
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="KFS-D29"
                     /isolation_source="Fecal sludge"
                     /db_xref="taxon:562"
                     /plasmid="pKFS-D29_4"
                     /geo_loc_name="Uganda"
                     /lat_lon="0.19 N 32.35 E"
                     /collection_date="2018"
                     /collected_by="Hidenori Harada, Mai Tanaka"
     gene            69..1037
                     /gene="mobV"
                     /locus_tag="QL146_23775"
     CDS             69..1037
                     /gene="mobV"
                     /locus_tag="QL146_23775"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000852935.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology. GO_function:
                     GO:0003677 - DNA binding [Evidence IEA]; GO_process:
                     GO:0006310 - DNA recombination [Evidence IEA]"
                     /codon_start=1
                     /transl_table=11
                     /product="MobV family relaxase"
                     /protein_id="WHJ58447.1"
                     /translation="MANYAIMRCKKLTGMGSVASALQHCYRERETPNADADRTPENHCS
                     VSQSADEAMGKLRELLPEKRRKDAVLAVEYVMTASPEWWNEATPRQQAEFFARSEQWLE
                     NKYGKDRVVAAVVHRDEATPHLSAFVVPLTQDGRLSAKEFIGGRSKMRDDQSTYAESVK
                     KLGLERGIEGSRATHQTVQHYYESINRGTRSQVSISPEALEPRVLRKGIFTKDVEDQAA
                     IAKRLSQAVNDGFAGTIAMASQSAQNAKRARDLQKTMDSQQKRLQSVTEPFKGLSREQM
                     THILTMAQTFQQQNHDREKQRQLEREQERQQRQKTDRGISR"
                     /name="mobV"
     gene            1034..1228
                     /locus_tag="QL146_23780"
     CDS             1034..1228
                     /locus_tag="QL146_23780"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001558245.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="antitoxin VbhA family protein"
                     /protein_id="WHJ58448.1"
                     /translation="MSEKQRREGFRKAEASLRLEGMDPSGVPRYECLKTRIISGETSYE
                     QGRKEILDYYLRINHKGEE"
                     /name="antitoxin VbhA family protein"
     gene            complement(1245..1955)
                     /locus_tag="QL146_23785"
     CDS             complement(1245..1955)
                     /locus_tag="QL146_23785"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001556733.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WHJ58449.1"
                     /translation="MLYWKKMPSLWIGNRLTEFNSLETSHAIAAIKIYITFCLFGKEED
                     DGVRTVKLTFTEISEIASISRSLVNEGLKLLDNKKLIKYLSPASKRKKIYTVDVDGCIH
                     DGWCKLPMAGIVSEDRTISAFQSMHNRYHFELVALQLYLYLLYARDNFQEHVLARKQTI
                     CEKLACRNVDLNKAITYLIHIGLLKGIKQKAVESYPIELFHDSFYFYVKTGASNALTFK
                     KQPLVNPPEKEIPY"
                     /name="hypothetical protein"
     gene            complement(2300..2821)
                     /locus_tag="QL146_23790"
     CDS             complement(2300..2821)
                     /locus_tag="QL146_23790"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_010657475.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology. GO_process:
                     GO:0006260 - DNA replication [Evidence IEA]; GO_process:
                     GO:0006276 - plasmid maintenance [Evidence IEA]"
                     /codon_start=1
                     /transl_table=11
                     /product="replication/maintenance protein RepL"
                     /protein_id="WHJ58446.1"
                     /translation="MDNSQIGTPESHEQDNYNFVQVSRAYLKEWRALTRKSPIASEILM
                     YLIENMGRTTNAVVCSYTTLMEITGVSRASVARAVKILKEDRWMQAVKIGNATAYCVNA
                     KAFWQAGRNQKKYAIFQATVIASSSEQESDFLEKSQQDLRYIPFVDLKDRPIVGTDELP
                     PPDQTDLDLD"
                     /name="replication/maintenance protein RepL"
     Typing          61..932
                     /name="MOBV"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="95.189"
                     /coverage="86.0"
                     /evalue="0.0"
ORIGIN
        1 cccgccggag gcatcgcaat gcgatccccc gtctggccgg atggacgccg gaacgagggg
       61 ggggaagcat ggcgaactac gcgataatgc gctgtaaaaa gctgacggga atgggcagtg
      121 tggccagcgc gttacagcac tgctacaggg agagagaaac gccgaatgct gatgctgacc
      181 ggacaccaga aaaccactgc tctgtgtctc agtcggcaga tgaggcgatg ggaaagctgc
      241 gggagctgtt gccggaaaaa cgccgtaaag atgcggtact ggctgttgaa tacgttatga
      301 cagcaagccc tgagtggtgg aacgaggcca caccgcggca gcaggcggag tttttcgccc
      361 gttctgagca atggctggag aacaaatacg ggaaagatcg cgttgtggcg gcggtggttc
      421 acagggacga ggccaccccg cacctgtctg cgttcgtggt gccattgacg caggatgggc
      481 ggctgtccgc gaaagagttt attggcgggc ggtcaaagat gcgtgacgat cagagcacct
      541 acgctgaatc ggtaaaaaaa ctgggtcttg agcgcggcat cgagggaagc cgtgccacgc
      601 atcagacagt tcagcactac tacgaatcga taaaccgtgg cacccgtagc caggtatcga
      661 tctcaccgga ggcgctggag ccgcgtgtac tgcggaaggg tattttcacc aaagacgtgg
      721 aagatcaggc agccatagcc aaacgtttaa gccaggcagt gaacgatggc tttgcaggaa
      781 ccatcgctat ggcctctcag agcgcccaga atgccaaaag agcgcgcgat ctacagaaga
      841 ctatggattc gcagcaaaaa cgcctacaga gcgttacaga gccttttaaa ggactttccc
      901 gggagcagat gacccatatt ctgacgatgg cgcagacgtt ccagcaacag aatcacgatc
      961 gtgaaaaaca gcgccagctt gaacgggagc aggaacgcca gcaacgtcag aaaactgaca
     1021 gaggtattag ccgatgagtg aaaagcagcg ccgtgaaggg tttcgaaaag cggaagcatc
     1081 actaagactt gagggaatgg atcctagtgg agtacctcgt tatgaatgtt tgaaaacgag
     1141 gattatctct ggcgaaacaa gttatgaaca agggcgtaaa gaaatattgg attactacct
     1201 tagaataaat cataagggcg aggagtaatt cgccctcagg tatgtcagta cggaatttct
     1261 ttttctggag ggttaacaag aggttgcttt ttgaatgtaa gcgcattgct tgctcctgtt
     1321 tttacataaa aataaaatga atcatgaaaa agttctatgg gataagactc cactgccttt
     1381 tgtttaattc cttttaaaag acctatgtgt attaaatatg ttattgcttt atttaaatct
     1441 acattgcggc aagcaagctt ttcgcaaata gtttgttttc tagctaacac atgctcctgg
     1501 aagttatctc tggcatatag aaggtataaa tatagctgaa gcgctacaag ctcaaaatgg
     1561 tatctattat gcattgactg gaaggcgctg attgttctgt cttcgctaac gatgcctgcc
     1621 ataggcagct tacaccatcc gtcatgaatg cacccatcaa catccactgt atagattttc
     1681 tttctttttg acgcgggcga taggtattta attagttttt tattatcgag caatttgaga
     1741 ccttcattta ccaaagatcg gctgatagaa gctatttcgc ttatttctgt aaacgtaagt
     1801 tttacggttc gcactccatc atcctcttct tttccaaaga gacaaaaagt tatatatatc
     1861 tttatggcgg caatggcatg tgaagtctct aaactattaa actctgtcag tctattaccg
     1921 atccagagtg atggcatttt tttccaatat aacattagtg attcctttat gcggaaatga
     1981 aagtgaaata aatcataatt aacacacaaa tggccaatgc aagactagta agtgaccctg
     2041 ccacttttcc cagcctttca gcaagctcta caaatcgctc taagtcaccc attttgacct
     2101 ctgctcctgt ttaccgatat accgattatc ccagcaatcc gcgtatctgt atctatagga
     2161 gcaaaaatct atctagaaag atatgggaaa aattaatatg aatttttata attaaatcaa
     2221 aaagttaaca tcaaaaaatg gttatcaaat gaacttcaat atggttcacg gtgaaccata
     2281 tttgaaggtt ttcagaggct cagtcgagat ctagatctgt ttgatccgga ggcgggagtt
     2341 catcggtgcc aacaataggg cggtctttga gatcgacaaa aggaatatat cgaagatctt
     2401 gctgtgattt ttctaagaaa tcagactctt gctctgagga ggaggcaatc acggtagctt
     2461 ggaagattgc gtattttttt tgatttctac ctgcctgcca aaatgctttg gcattaacac
     2521 aatatgctgt ggcattacct atttttactg cctgcatcca tcgatcttcc ttcaggattt
     2581 taaccgccct tgctactgat gctctagaga ccccggttat ctccatcaaa gtcgtatagc
     2641 tgcaaacaac agcattagtt gtcctaccca tattctcaat caagtacata aggatttcag
     2701 aggcaatagg gcttttcctt gtcagcgcac gccattcctt gagatacgcg cggctaacct
     2761 ggacgaaatt atagttatcc tgctcatgag actctggagt gccaatctgt gaattatcca
     2821 ttgctctata gaccatttca atatcccatt tgataccggt tgtatcatta gagatgcaac
     2881 aggtcaactt gagtctcata gctagtgaga ctcataagtc tcatggctgg tgagactccc
     2941 ccttttttta acccaatata atcagcgatt tactgaaagc tccttttcta tatctattaa
     3001 gtccgtgcat acgtagccca atgtacgcct agtagacatt ccgcttcctc gttcaggctg
     3061 ttcgttcctc gctgcgctgc ggtacgcctc agcctgacct gcggcgagcg gcacgtgctc
     3121 tttcaaagac gactttgttg cctgacattc gtcaagggcg agcgtagcga gtgccattta
     3181 cccttgacga ctcaccggat aaaacaggct tggcagtggt ggggggtggc gcggagcgac
     3241 gccttccacc tgccagaccg ctgttgaact tgacctttag gcagcttgct gcccgaacga
     3301 ttttgtaaag caaagtctag tgagtacact atcatcctga tagtgg
//
