LOCUS       CP125010                5125 bp    DNA     circular BCT 16-MAY-2023
DEFINITION  Escherichia coli strain KFS-D29 plasmid pKFS-D29_3, complete
            sequence.
ACCESSION   CP125010
VERSION     CP125010.1
DBLINK      BioProject: PRJNA956323
            BioSample: SAMN34598749
KEYWORDS    .
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 5125)
  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  JOURNAL   Unpublished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 5125)
  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..5125
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="KFS-D29"
                     /isolation_source="Fecal sludge"
                     /db_xref="taxon:562"
                     /plasmid="pKFS-D29_3"
                     /geo_loc_name="Uganda"
                     /lat_lon="0.19 N 32.35 E"
                     /collection_date="2018"
                     /collected_by="Hidenori Harada, Mai Tanaka"
     gene            complement(495..770)
                     /locus_tag="QL146_23760"
     CDS             complement(495..770)
                     /locus_tag="QL146_23760"
                     /inference="COORDINATES: protein motif:HMM:NF016875.2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="type II toxin-antitoxin system RelE/ParE family
                     toxin"
                     /protein_id="WHJ58444.1"
                     /translation="MIKSFKSKKLKQFNSGDTSKVAQAHKKKIEIILNALDTATSINDL
                     DLPGLDLHSYAEYTPTRWSLKVSANYRIFFEWDGANVRNVDYDDPH"
                     /name="type II toxin-antitoxin system RelE/ParE family
                     toxin"
     gene            1042..1383
                     /locus_tag="QL146_23765"
     CDS             1042..1383
                     /locus_tag="QL146_23765"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_018001973.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology. GO_function:
                     GO:0003677 - DNA binding [Evidence IEA]"
                     /codon_start=1
                     /transl_table=11
                     /product="HigA family addiction module antitoxin"
                     /protein_id="WHJ58445.1"
                     /translation="MFTLQKPMHPGEFIREVYLEPLELQIGTFAEKLGVDTSTVSRLVN
                     QKADLSYEMALRLSKALGRSADSWMKMQIAYGLYRAQDKVNLEEVEVVYRPRNLDAPEK
                     QVHEFYENI"
                     /name="HigA family addiction module antitoxin"
     gene            complement(3352..3894)
                     /locus_tag="QL146_23770"
     CDS             complement(3352..3894)
                     /locus_tag="QL146_23770"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001632013.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="stationary phase growth adaptation protein"
                     /protein_id="WHJ58443.1"
                     /translation="MNIDEVAKWRPFTDQDGNIWDLSFLDAHEVSYTHCSPGKPDIVYK
                     FTVSYSFHCFCKDYPEQTEEEKLSLMYDAGKDSRPFCKVRYALARDKLRAIIEGLGNAK
                     VIHAGYGSYAFVEITVDEGESEFYFVPFKVYRERKKLRLHVTSAYPVKERPSGKPVSFF
                     KIAHNLLRGKPLPKPHM"
                     /name="stationary phase growth adaptation protein"
     Typing          3..345
                     /name="rep_cluster_2358"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="82.597"
                     /coverage="94.0"
                     /evalue="1.47e-78"
     Typing          2356..2850
                     /name="rep_cluster_2335"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="88.258"
                     /coverage="97.0"
                     /evalue="1.6800000000000001e-167"
     Typing          4807..5125
                     /name="ColRNAI_rep_cluster_1987"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="91.304"
                     /coverage="95.0"
                     /evalue="2.93e-120"
ORIGIN
        1 gtctcattcc acgcctgaca ctcagttccg ggtaggcagt tcgctccaag ctggactgta
       61 tgcacgaacc ccccgttcag tccgactacc acgctctttt cggtaactat cgtcttgagt
      121 ccaacccgaa aaggcacgac aaatcgccat tggcggtagc cattggtaga gggtgtacaa
      181 gagattactg atgcagagtt cttgaagtta gagccagact gcggctaaac tagaaggacg
      241 attttggtgg cagcggtctt gtacaccctg ttaccacggt tcagaagttc cccaacttgc
      301 tgaaccttcg aaaaaccacc tccccaggtg gttttttcgt ttcaggatta aagatactct
      361 gcgtcccact caatctcaag aaattatctt taccaagcca ttgacttaat aaaaaaaaac
      421 catataatag cctcatgggc ttgaatcact ttagtgattc aagcccatgg cctaagtcgt
      481 tgatttaact gagattaatg tggatcgtcg taatccacat tacggacgtt ggcaccatcc
      541 cactcaaaga aaatacgata gttcgccgac acctttaatg accagcgggt tggggtatat
      601 tcagcatacg aatgaagatc caaaccagga aggtcaagat catttattga agtagcggta
      661 tctaaagcgt ttaagataat ctctattttc tttttatgcg cttgtgctac cttacttgta
      721 tcaccactgt taaattgttt tagttttttg gatttaaaac ttttaatcat tgaacttctc
      781 catatgaaaa tttttatgtt ttagaagttc ttcttgttta gtaaagtttc ttgactatgt
      841 tctatttata ggtagtattc tacgcctgcg aagctttaga actgccagat agtcactaca
      901 agaacaaaac agaagaacca aactgttaac gttaagaaaa aaaattaccc ttaactaatc
      961 cattttatca caaatagatt tattatgtca ataggtttgc gcgttgcgca aggcgcaaaa
     1021 tcagagtatt taggaggttg catgtttaca ttgcaaaaac ctatgcaccc cggcgagttt
     1081 atccgcgaag tatatttaga gccgttagag cttcaaatag gaacgtttgc agaaaagctt
     1141 ggtgttgata catcaaccgt tagccggtta gtaaaccaaa aagctgacct ttcttatgaa
     1201 atggcattac gcctatcaaa agccttaggg cgttctgctg actcttggat gaaaatgcaa
     1261 atagcatatg gtttatatcg tgctcaagat aaagtaaatc ttgaagaagt tgaggtggtt
     1321 taccgcccac ggaacttgga tgctcctgaa aaacaggtcc atgaatttta tgaaaatatc
     1381 taaaaacgat atttcattta ggtaaagaaa agctcctaac cataggggct ttttgtctct
     1441 acacctgtgt atttatgtga agacctaagg cagcatcgtt attcctgaag atgcttaaac
     1501 agcgggtgtt gagcctgtat caaccattga tagtgatctg tatatcctct tcactaaccc
     1561 caaacttcat agccagcccc cttctatgct tacctagaga atttaccata acatccgttg
     1621 cccgcaccgc ctcagaggcc ctcagggcgt ttctgcctcg tccggccgat ttccggcacc
     1681 tttccctatc ccaaacactg aaaaacgccc ctgatgattt ttgcgcagct gcatggctat
     1741 gcacagacat gcctggcctc cattttagcg gctaaaatcc ggcgagcgcc ctgaaagcca
     1801 tcatgaacca ccctgataac ggtgaacggg tgcgcagttt actgtgcggc cgtgaggcgt
     1861 tggccaggcc gtcaggcatg gcaggattta ttgctaaggg ggtcggattt aacctggggt
     1921 gatcagcgcg cagagatgaa cgggattcgg aaggggaacc cttgcggcgc ggcgatgtat
     1981 acatcgctaa cgtgcctgac tcttttcaca gcagagggta gcggtagcaa acaagtagca
     2041 aacagatagc aaacaagtag caaacagata gcaaacaggt agcaaaaaga tagcaaaaag
     2101 atagcaaaca tacggtttcg ggcggaacct gaccaggagt cattggcgtg ccggcgctac
     2161 tccaaaaaca catattgtcc cgctgttttg tgaataagcc agcatagctg tgggcacaaa
     2221 acatttcctg tccgctgctt taacctttgt aatccaggaa cgtcaggtga cgtcactttg
     2281 cggcgttagc cctatcctgc atcctatgaa aaaatgcagt tacggagtgt aaggtgccgg
     2341 acgtgaggcc gaagatattc cgcttcctcg ctcactgact cgctgcgctc ggtcgttcgg
     2401 ctgcggcgag cggagggaac aggcacatca aaagatgaag ccatgaggga cgatgagagg
     2461 gaaaaaaacg ccgcggtgtt gccggttttc cataggctcc gcccccctga caagcatcac
     2521 agaatctgac gctcaaatca gtggtggcga aacccgacag gactataaag ataccaggcg
     2581 tttccccctg gtggctccct cgtgcgctct cctgttcctg cctttcggtt taccggtgtc
     2641 attccgctgt tatggccgcg tttatctcat tccacgcctg acactcagtt ccgggtaggc
     2701 agttcgctcc aagctggact gtatgcacga accccccgtt cagtccgacc gctgcgcctt
     2761 gtccggtaac tatcgtcttg agtccaaccc ggatagacac gactaatcgc cattggcaac
     2821 ggccactggt aagcaggatg tgcgagagat gtaacgagag ttcttgaagt ggcggcctaa
     2881 ctgaggctac actgaaagga cagtatttgg tgacatgtct cgcacaagac tgttaccacg
     2941 gttagagaat ctgccaggat taactaacct tcggaaaaac cacctgccag ggtggttttt
     3001 tcgtttctga gcaagagact acgacgagcc actgatgatc tcaagtgttc atttctgata
     3061 tccacagcag aataactgtt aggatatagg gtatctatag tcaggagctt caagaaagcc
     3121 agacacagca atggattccg gcattatcga gaaaaattag tatataggtt gcaaccaaaa
     3181 tgttggttgc aaatctacat cacactacct acaattgctt taaggatgca gcagactggt
     3241 aacaccagac atcccactac caataacaat gttggtcgag gccaagcccg gtaaaggtgt
     3301 tctgaatacc agaagaaatt tctggcgaag cccgcaacta agcgggcttt gttacatatg
     3361 aggtttaggt aatggcttcc cgcgcaggag attgtgagct atcttgaaaa agctaactgg
     3421 cttacctgac ggtctctcct tgacaggata agcacttgtt acatgcaagc gcagcttttt
     3481 acgctcacga tataccttaa aaggcacaaa gtagaactca ctttcacctt catctacagt
     3541 aatctctaca aaagcataac taccatatcc agcatggata accttcgcgt tacccaatcc
     3601 ttcaatgatg gctctcagct tgtctcgagc aagggcatat cggaccttac aaaatggcct
     3661 cgagtctttg cctgcatcat acatcaacga taatttttct tcctcagtct gctctggata
     3721 atccttgcaa aaacaatgaa atgagtaaga aacagtgaac ttatacacaa tatcaggttt
     3781 accaggagaa caatgagtat aagaaacctc atgtgcatca agaaatgaca gatcccatat
     3841 attgccatcc tgatccgtaa aaggacgcca cttagcaact tcatcaatgt tcacgaaaaa
     3901 acctcaatat ccggatggca gaatccgcac attctaccag agaagaaaca agcggaagga
     3961 gcgtggcaaa ataagagcta ggccttttac agaagacttc gccacaacct ttcatggata
     4021 cattggtaat gattaagtgt tatttaccat aacatccgtt gcgtgcaccg ccgcagaggc
     4081 cctcagcgcg tttctgaggc ctccgacctg aaacacacac ctttctgtgc ccatatcgag
     4141 aaaaaacgcc cctgatgatt ctggcgcgac tgcatggcta tgcacggaca tacctggccg
     4201 ggattttagc ggctaaaatc cgatgaacgc cctgaaagcc accacgaacc accccgataa
     4261 cgcctcacgg gtgcgcagtt tactgtgcgg ccgtgaggcg ttggccaggc cgtcaggcat
     4321 ggctggattt attgctaagg gggtcggatt taacgtggat gaatcagcac gcagtgatga
     4381 acgggattcg gaaggggcac ccttgcggcg cggcgatgta tacatcgcta acgtgccttg
     4441 gtcatttatt gcaagaaggg agaggtagca ttttgatagc aaaaaagtag caaaaggata
     4501 gcaaccgaaa gaccagaaga ctctggagat agcaaaaaag tagcaaaatg gtagcaaaaa
     4561 gatagcaaaa agatagcaaa catgcgggag ctaaccagga gtctttagcg ggccggcggt
     4621 actccaaaaa cacatcttgt cccgctgttt tgtgaataag ccagcatagc tgtgggcaca
     4681 aaacatttcc tgtccgctgc tttaaccttt gtaatccagg aacgtcaggt gacgtcactt
     4741 tgcggcgttc gccctatcct gcatcgtatt aaaaaatgca gctatggcgc gtacggtgcc
     4801 aaagagaagc ccgcagatat tccgcttcct cgctcactga ctcgctccgc tcggtcgttc
     4861 ggctgcggcg agcgttacct gcacacggat aaggacaaag gcatacggcg tgacaggcag
     4921 ggcaggaaaa ggatgcggcg ctgccgtttt tccataggct ccgcccccct gacaagcatc
     4981 acgaaatctg acgctcaaat cagtggtggc gaaacccgac aggactataa agataccagg
     5041 cgtttccccc tggtggctcc ctcgtgcgct ctcctgttcc tgcctttcgg tttaccggtg
     5101 tcattccgct gttatggccg cgttt
//
