LOCUS       CP124999                2462 bp    DNA     circular BCT 16-MAY-2023
DEFINITION  Escherichia coli strain KSE-C11 plasmid pKSE-C11_4, complete
            sequence.
ACCESSION   CP124999
VERSION     CP124999.1
DBLINK      BioProject: PRJNA956323
            BioSample: SAMN34598752
KEYWORDS    .
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 2462)
  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  JOURNAL   Unpublished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 2462)
  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                   :: Unicycler v. v0.5.0
            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 16:33:08
            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)                     :: 4,823
            CDSs (total)                      :: 4,701
            Genes (coding)                    :: 4,488
            CDSs (with protein)               :: 4,488
            Genes (RNA)                       :: 122
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 87
            ncRNAs                            :: 13
            Pseudo Genes (total)              :: 213
            CDSs (without protein)            :: 213
            Pseudo Genes (ambiguous residues) :: 0 of 213
            Pseudo Genes (frameshifted)       :: 62 of 213
            Pseudo Genes (incomplete)         :: 154 of 213
            Pseudo Genes (internal stop)      :: 37 of 213
            Pseudo Genes (multiple problems)  :: 40 of 213
            Pseudo Genes (short protein)      :: 4 of 213
            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..2462
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="KSE-C11"
                     /isolation_source="Sewage"
                     /db_xref="taxon:562"
                     /plasmid="pKSE-C11_4"
                     /geo_loc_name="Uganda"
                     /lat_lon="0.19 N 32.35 E"
                     /collection_date="2018"
                     /collected_by="Hidenori Harada, Mai Tanaka"
     gene            541..1083
                     /locus_tag="QL136_24100"
     CDS             541..1083
                     /locus_tag="QL136_24100"
                     /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="WHJ62935.1"
                     /translation="MNIDEVAKWRPFTDQDGNIWDLSFLDAHEVSYTHCSPGKPDIVYK
                     FTVSYSFHCFCKDYPEQTEEEKLSLMYDAGKDSRPFCKVRYALARDKLRAIIEGLGNAK
                     VIHAGYGSYAFVEITVDEGESEFYFVPFKVYRERKKLRLHVTSAYPVKERPSGKPVSFF
                     KIAHNLLRGKPLPKPHM"
                     /name="stationary phase growth adaptation protein"
     Typing          complement(1604..2091)
                     /name="ColRNAI_rep_cluster_1987"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="92.073"
                     /coverage="95.0"
                     /evalue="0.0"
ORIGIN
        1 acgttagcga tgtatacatc gccgcgccgc aagggtgccc cttccgaatc ccgttcatca
       61 ctgcgtgctg attcatccac gttaaatccg acccccttag caataaatcc agccatgcct
      121 gacggcctgg ccaacgcctc acggccgcac agtaaactgc gcacccgtga ggcgttatcg
      181 gggtggttcg tggtggcttt cagggcgttc atcggatttt agccgctaaa atcccggcca
      241 ggtatgtccg tgcatagcca tgcagtcgcg ccagaatcat caggggcgtt ttttctcgat
      301 atgggcacag aaaggtgtgt gtttcaggtc ggaggcctca gaaacgcgct gagggcctct
      361 gcggcggtgc acgcaacgga tgttatggta aataacactt aatcattacc aatgtatcca
      421 tgaaaggttg tggcgaagtc ttctgtaaaa ggcctagctc ttattttgcc acgctccttc
      481 cgcttgtttc ttctctggta gaatgtgcgg attctgccat ccggatattg aggttttttc
      541 gtgaacattg atgaagttgc taagtggcgt ccttttacgg atcaggatgg caatatatgg
      601 gatctgtcat ttcttgatgc acatgaggtt tcttatactc attgttctcc tggtaaacct
      661 gatattgtgt ataagttcac tgtttcttac tcatttcatt gtttttgcaa ggattatcca
      721 gagcagactg aggaagaaaa attatcgttg atgtatgatg caggcaaaga ctcgaggcca
      781 ttttgtaagg tccgatatgc ccttgctcga gacaagctga gagccatcat tgaaggattg
      841 ggtaacgcga aggttatcca tgctggatat ggtagttatg cttttgtaga gattactgta
      901 gatgaaggtg aaagtgagtt ctactttgtg ccttttaagg tatatcgtga gcgtaaaaag
      961 ctgcgcttgc atgtaacaag tgcttatcct gtcaaggaga gaccgtcagg taagccagtt
     1021 agctttttca agatagctca caatctcctg cgcgggaagc cattacctaa acctcatatg
     1081 taacaaagcc cgcttagttg cgggcttcgc cagaaatttc ttctggtatt cagaacacct
     1141 ttaccgggct tggcctcgac caacattgtt attggtagtg ggatgtctgg tgttaccagt
     1201 ctgctgcatc cttaaagcaa ttgtaggtag tgtgatgtag atttgcaacc aacattttgg
     1261 ttgcaaccta tatactaatt tttctcgata atgccggaat ccattgctgt gtctggcttt
     1321 cttgaagctc ctgactatag ataccctata tcctaacagt tattctgctg tggatatcag
     1381 aaatgaacac ttgagatcat cagtggctcg tcgtagtctc ttgctcagaa acgaaaaaac
     1441 caccctggca ggtggttttt ccgaaggtta gttaatcctg gcagattctc taaccgtggt
     1501 aacagtcttg tgcgagacat gtcaccaaat actgtccttt cagtgtagcc tcagttaggc
     1561 cgccacttca agaactctcg ttacatctct cgcacatcct gcttaccagt ggccgttgcc
     1621 aatggcgatt agtcgtgtct atccgggttg gactcaagac gatagttacc ggacaaggcg
     1681 cagcggtcgg actgaacggg gggttcgtgc atacagtcca gcttggagcg aactgcctac
     1741 ccggaactga gtgtcaggcg tggaatgaga taaacgcggc cataacagcg gaatgacacc
     1801 ggtaaaccga aaggcaggaa caggagagcg cacgagggag ccaccagggg gaaacgcctg
     1861 gtatctttat agtcctgtcg ggtttcgcca ccactgattt gagcgtcaga tttcgtgatg
     1921 cttgtcaggg gggcggagcc tatggaaaaa cggcagcgcc gcatcctttt cctgccctgc
     1981 ctgtcacgcc gtatgccttt gtccttatcc gtgtgcaggt aacgctcgcc gcagccgaac
     2041 gaccgagcgg agcgagtcag tgagcgagga agcggaatat ctgcgggctt ctctttggca
     2101 ccgtacgcgc catagctgca ttttttaata cgatgcagga tagggcgaac gccgcaaagt
     2161 gacgtcacct gacgttcctg gattacaaag gttaaagcag cggacaggaa atgttttgtg
     2221 cccacagcta tgctggctta ttcacaaaac agcgggacaa gatgtgtttt tggagtaccg
     2281 ccggcccgct aaagactcct ggttagctcc cgcatgtttg ctatcttttt gctatctttt
     2341 tgctaccatt ttgctacttt tttgctatct ccagagtctt ctggtctttc ggttgctatc
     2401 cttttgctac ttttttgcta tcaaaatgct acctctccct tcttgcaata aatgaccaag
     2461 gc
//
