LOCUS       CP125031                4066 bp    DNA     circular BCT 16-MAY-2023
DEFINITION  Escherichia coli strain KFS-D13 plasmid pKFS-D13_4, complete
            sequence.
ACCESSION   CP125031
VERSION     CP125031.1
DBLINK      BioProject: PRJNA956323
            BioSample: SAMN34598746
KEYWORDS    .
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 4066)
  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  JOURNAL   Unpublished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 4066)
  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 17:09:07
            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)                     :: 5,445
            CDSs (total)                      :: 5,326
            Genes (coding)                    :: 5,075
            CDSs (with protein)               :: 5,075
            Genes (RNA)                       :: 119
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 91
            ncRNAs                            :: 6
            Pseudo Genes (total)              :: 251
            CDSs (without protein)            :: 251
            Pseudo Genes (ambiguous residues) :: 0 of 251
            Pseudo Genes (frameshifted)       :: 91 of 251
            Pseudo Genes (incomplete)         :: 177 of 251
            Pseudo Genes (internal stop)      :: 39 of 251
            Pseudo Genes (multiple problems)  :: 53 of 251
            Pseudo Genes (short protein)      :: 4 of 251
            ##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..4066
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="KFS-D13"
                     /isolation_source="Fecal sludge"
                     /db_xref="taxon:562"
                     /plasmid="pKFS-D13_4"
                     /geo_loc_name="Uganda"
                     /lat_lon="0.19 N 32.35 E"
                     /collection_date="2018"
                     /collected_by="Hidenori Harada, Mai Tanaka"
     gene            join(3658..4066,1..1745)
                     /gene="mobQ"
                     /locus_tag="QL144_27205"
     CDS             join(3658..4066,1..1745)
                     /gene="mobQ"
                     /locus_tag="QL144_27205"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001029350.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MobQ family relaxase"
                     /protein_id="WHJ77321.1"
                     /translation="MAIYHLSMKIISRSNGYSAVASAAYRSGSLMLDERTGLTHDYTRK
                     SGVAEAVILTPATAPAWCTNRAELWNAVEKAERRKNSQLAREIELAIPRELPQDAARET
                     VLAFVRENFVSQGMIADVAFHHMDKTNPHAHIMLTTRAVGPAGFGGKVRDWNDRTHAET
                     WRASWADHANRALANAGYQEEIDHRSYERQGLEKTPGIHLGKSACAMETRGIETERGEQ
                     NRLINRLNLEIQISRTELRNSGLTEPARRVADLLNIGLPDNATSYTLRDIIEALPEDSN
                     AAWKLTSNAMSMMADMQATRRRWEELNTERKEAMSHAASLKKSSPFSSGFSRIPLMQWA
                     APEYRSEQGKIQSLSQQMEKLRQHYRKVEKQDIPASQTAFEKQWQQWGESGLAALRSQL
                     LKREEELRRKELEDTERSRAEQLRKNDNAVMDSGVLRAVVTGYGEAPMPGNGEMTCYLL
                     LHNRNGEYTLWGNELEKYRTRIFESVDLMRDRSGYICDRSEIGQHPPLQRVYSSATFEQ
                     LLTQVCQTWPQHTRNLRQPKTWPESFCLGEDRQPAMPSLAARKVDFTQGRLPPTLMPVM
                     SSVDRETRQLQLLLVMGVDDSLGGVVRLNGTLYPAFAVPSADNSQLVISALTDKGLRYA
                     GYGVAVNHDADSHISPAPELMEFHLKTREAPLFAVVNTPEKQPDHLFRSLGFNRTWDEW
                     RREEDARTHATERRPDRGWSQGM"
                     /name="mobQ"
     gene            complement(1987..2694)
                     /locus_tag="QL144_27210"
     CDS             complement(1987..2694)
                     /locus_tag="QL144_27210"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001296720.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology. GO_function:
                     GO:0003887 - DNA-directed DNA polymerase activity [Evidence
                     IEA]; GO_process: GO:0006270 - DNA replication initiation
                     [Evidence IEA]"
                     /codon_start=1
                     /transl_table=11
                     /product="replication initiation protein"
                     /protein_id="WHJ77322.1"
                     /translation="MTSNPLIAYKSNALVEASYKLTLQEQRFLLLCISRLNSGTDVASP
                     ELQKTMTITAAEYFDSFPDMGRKNAEVQLQEAIDRLWDRSIILKDDEKREEFRWIQYRA
                     QYARGEGKAQITFSDAVMPYLTQLKGQFTRVVIKNISNLSRSYSIRIYEILQQFRSTGE
                     RIIALDDFKSSLMLDGKYKDFKTLNRDLIKPCVDELNKKSDLAVTVETIKKGRTVVALH
                     FRFKEDKQIKMTI"
                     /name="replication initiation protein"
     gene            complement(3225..3479)
                     /gene="mobC"
                     /locus_tag="QL144_27215"
     CDS             complement(3225..3479)
                     /gene="mobC"
                     /locus_tag="QL144_27215"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000091747.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="relaxase accessory protein MobC"
                     /protein_id="WHJ77320.1"
                     /translation="MSRTLEQKIAEAEARLQRLKAKSRSLDTAQKVIVGAALLAKVRKP
                     EEVQLRAWLLQFLKAEVTRQADVTRILPLINELEALPEQ"
                     /name="mobC"
     Typing          complement(3484..3657)
                     /name="MOBQ"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="98.286"
                     /coverage="98.0"
                     /evalue="2.6299999999999998e-81"
     Typing          3658..4016
                     /name="MOBQ"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="97.222"
                     /coverage="100.0"
                     /evalue="3.97e-172"
     Typing          complement(1988..2694)
                     /name="rep_cluster_1778"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          4..1736
                     /name="MOBQ"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="97.423"
                     /coverage="99.0"
                     /evalue="0.0"
ORIGIN
        1 tgctgaccac gagggctgtc ggacctgctg ggttcggcgg aaaggtcagg gactggaacg
       61 accggacaca tgccgagacg tggcgtgcat catgggctga ccatgcaaac agggcactgg
      121 cgaacgccgg ttatcaggaa gagatagacc atcgttcata cgagcgacag gggcttgaga
      181 aaacgcctgg tattcacctc ggaaagtctg cctgtgcgat ggaaacacgc ggtatcgaaa
      241 cagaacgcgg cgaacagaat cgtctgatta acaggcttaa cctggaaata cagatttccc
      301 gcaccgaact caggaacagc gggctgacag agcctgcccg ccgtgtggct gaccttctga
      361 atatcgggct tcctgacaac gcaacttcgt acacactacg tgacatcatc gaagcgttgc
      421 cggaggacag taacgcggca tggaaactca ccagtaacgc catgtcgatg atggcagata
      481 tgcaggcgac gcgcagacgc tgggaagagc tgaacaccga acgaaaggaa gcgatgagcc
      541 atgctgccag cctgaaaaaa tcatcgccgt tttcgtccgg tttttcccgt attcccctga
      601 tgcaatgggc tgcaccggaa taccgtagtg agcagggaaa aatccagtct ctgagccagc
      661 aaatggaaaa attgcgacag cattaccgga aggtggagaa acaggacatt cccgcgagtc
      721 agacggcatt tgaaaaacag tggcagcagt ggggggaatc cggccttgca gctctcagat
      781 cccagttgct taaacgtgaa gaggaattgc gccggaagga gctggaggat acagaacgta
      841 gtcgcgcgga gcagctcaga aaaaatgaca atgccgttat ggattcaggg gtgctgagag
      901 cagtcgttac ggggtatggc gaggctccca tgcctggtaa cggggaaatg acctgttacc
      961 ttctgcttca caaccggaac ggagaatata cgctctgggg gaacgagctg gagaaatacc
     1021 gcaccaggat ctttgagagt gttgatttaa tgcgtgacag gagtggttat atctgtgacc
     1081 gaagcgaaat cggtcaacat ccaccactgc aacgtgttta ttcctctgcg acctttgagc
     1141 aacttctgac gcaggtttgc cagacatggc cgcaacatac ccgcaatctc cgccaaccga
     1201 agacatggcc ggagtctttc tgtcttggag aagaccgcca gccagccatg ccatcactgg
     1261 cagcaaggaa ggtggatttt acgcagggac gtctgccacc gacgctgatg ccggtcatga
     1321 gttctgtcga ccgggaaacc cgccagcttc agcttttgct ggtcatgggc gtggatgact
     1381 ctctgggcgg tgttgtccgg cttaatggta cgctgtatcc cgcgtttgcc gttccctcag
     1441 ccgataacag ccagctggtc atcagtgcac tgaccgataa ggggttacgg tatgcagggt
     1501 atggtgttgc cgtaaatcac gatgcagaca gccacatatc acctgcgccg gaacttatgg
     1561 agtttcatct gaaaacccgt gaggcaccgc tttttgctgt cgtcaacaca ccagaaaaac
     1621 agccggatca tctgttccgc tcgctgggtt tcaatcgtac ctgggacgaa tggcggcgcg
     1681 aggaagatgc acgaacacac gccaccgaga ggagacctga tcgcggttgg tcacagggaa
     1741 tgtgaacaat attttgtttt gtttaacatc gtgttatgtt cgtcgatgtt catcgacagg
     1801 gatgaatgca agaagcacac tcacatagcg caaacatagt tttgtttttc cgcccccaaa
     1861 aattgggggt tctttttttg ctgcatcaga gcgtttttga cgcaactttt cacttcaata
     1921 gtaccttcgc attcctgaca caagaaaaac gcgacagtga gcgttttagg tgccttaaaa
     1981 tcgattctag atcgtcatct tgatctgttt gtcttccttg aagcgaaaat gcagggctac
     2041 aaccgtgcgc ccctttttga tcgtctcaac cgttacagcc aggtcgcttt ttttgttcag
     2101 ttcgtcaaca cagggtttta ttagatccct gtttaacgtt ttgaaatctt tatatttacc
     2161 atcaagcatc agtgatgatt taaaatcatc gagggcgata atacgttccc cagtactgcg
     2221 gaattgctgg agaatttcgt atattcttat gctgtaactt cttgataaat tagaaatatt
     2281 tttaatgacg actctggtga attgcccctt caactgtgtc agataaggca ttaccgcgtc
     2341 agaaaaagtg atttgtgctt tcccctctcc cctcgcgtac tgtgcccgat actgaatcca
     2401 gcggaactcc tcgcgcttct cgtcgtcctt gagaatgatc gacctgtccc acaaacgatc
     2461 gatcgcttcc tgtagctgaa cctcggcatt tttccgcccc atatcaggga atgaatcaaa
     2521 atattccgca gctgtaatgg tcattgtctt ttgcaattca ggtgaagcta cgtcagtacc
     2581 ggagttaagt cggcttatgc agagcaataa gaaacgctgt tcttgtaaag ttagcttgta
     2641 actggcctca accagcgcat tggacttata ggctatcaga gggtttgatg tcattttaac
     2701 caccaggcca aaaatgaggt gaaataaaaa cctatcacct ttagcattgg tgagcaatta
     2761 tattttcacc ccccatttcc ctgtgaatat taccttaaat ctcctcacct ttaccttaaa
     2821 ttacctcacc caagcacctt aaattatatc acctttacct taaattcccc cacctatgca
     2881 cgtgtaacgc attgttttta atcaggaatt tcgaccctaa aacaagtatt aaaaacaaga
     2941 tcttaaaaac aagatctaaa aacttaacgg cgagcctgtg gataacttgg ggtgctgaaa
     3001 ataaaaatca aataaaaaca atgtattgca aaaaatcagg attgaaaatt ccgaatacac
     3061 cccctccaac cctgtggaaa tccagtattc atgcgggttc agcgcatatc acctgtcgaa
     3121 aaaccgtgcg tatgtgctca acctggcgac tgattcactt ccgcttcctc gcccactcgc
     3181 tcgctaacgt tcggtcgctg ggctgcggcg agcggacgat acaatcactg ctctggcagc
     3241 gcctccagct cgttaatcag cggcagtatt cgcgtcacat cagcctgccg tgtcacctct
     3301 gccttcagga actggagtaa ccaagctcgc aactgcactt cctccggctt tctgaccttt
     3361 gccagcaatg ctgcacccac aatgaccttc tgcgctgtgt ccaggctccg gctcttcgcc
     3421 ttcaggcgct gtaatctggc ctcagcttcg gcaatcttct gttcgagtgt tctgctcatt
     3481 tcgtgactcc gtgcgcggtg aaaaatcgca ttttagcgcg tcactggtag tttaaaaact
     3541 gagctggcat aatgcacggc aaatcacgaa gtgcgcactt atacaatctc cactccgttt
     3601 cgattgtgtg cgccctgcgg ggctgaaaga aaactgcaaa aaggcattac ggcagaaatg
     3661 gcgatttatc atctcagtat gaaaatcatc tccagaagca acggctacag cgccgttgct
     3721 tctgctgcct atcgttctgg ttcactaatg cttgatgagc gtaccggact gactcacgac
     3781 tacacccgca aaagcggtgt ggctgaggct gtgattctga cccccgcgac agcccctgcc
     3841 tggtgtacga accgtgccga actctggaat gccgttgaga aggccgaacg ccggaagaac
     3901 tcacaacttg cgcgggaaat tgaactcgct atcccccgtg aactgccgca ggatgccgca
     3961 cgggaaaccg ttctcgcctt tgtcagagaa aactttgtca gtcagggcat gattgctgat
     4021 gtggcgttcc atcacatgga taaaacaaat ccccatgcgc acatca
//
