LOCUS       CP124998                3346 bp    DNA     circular BCT 16-MAY-2023
DEFINITION  Escherichia coli strain KSE-C11 plasmid pKSE-C11_3, complete
            sequence.
ACCESSION   CP124998
VERSION     CP124998.1
DBLINK      BioProject: PRJNA956323
            BioSample: SAMN34598752
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  JOURNAL   Unpublished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                   :: 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..3346
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="KSE-C11"
                     /isolation_source="Sewage"
                     /db_xref="taxon:562"
                     /plasmid="pKSE-C11_3"
                     /geo_loc_name="Uganda"
                     /lat_lon="0.19 N 32.35 E"
                     /collection_date="2018"
                     /collected_by="Hidenori Harada, Mai Tanaka"
     gene            complement(join(2723..3346,1..345))
                     /gene="mobV"
                     /locus_tag="QL136_24080"
     CDS             complement(join(2723..3346,1..345))
                     /gene="mobV"
                     /locus_tag="QL136_24080"
                     /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="WHJ62933.1"
                     /translation="MANYAIMRCKKLTGMGSVASALQHCYRERETPNADADRTPENHCS
                     VSQSADEAMGKLRELLPEKRRKDAVLAVEYVMTASPEWWNEATPRQQAEFFARSEQWLE
                     NKYGKDRVVAAVVHRDEATPHLSAFVVPLTQDGRLSAKEFIGGRSKMRDDQSTYAESVK
                     KLGLERGIEGSRATHQTVQHYYESINRGTRSQVSISPEALEPRVLRKGIFTKDVEDQAA
                     IAKRLSQAVNDGFAGTIAMASQSAQNAKRARDLQKTMDSQQKRLQSVTEPFKGLSREQM
                     THILTMAQTFQQQNHDREKQRQLEREQERQQRQKTDRGISR"
                     /name="mobV"
     gene            939..1460
                     /locus_tag="QL136_24085"
     CDS             939..1460
                     /locus_tag="QL136_24085"
                     /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="WHJ62934.1"
                     /translation="MDNSQIGTPESHEQDNYNFVQVSRAYLKEWRALTRKSPIASEILM
                     YLIENMGRTTNAVVCSYTTLMEITGVSRASVARAVKILKEDRWMQAVKIGNATAYCVNA
                     KAFWQAGRNQKKYAIFQATVIASSSEQESDFLEKSQQDLRYIPFVDLKDRPIVGTDELP
                     PPDQTDLDLD"
                     /name="replication/maintenance protein RepL"
     gene            1805..2515
                     /locus_tag="QL136_24090"
     CDS             1805..2515
                     /locus_tag="QL136_24090"
                     /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="WHJ62931.1"
                     /translation="MLYWKKMPSLWIGNRLTEFNSLETSHAIAAIKIYITFCLFGKEED
                     DGVRTVKLTFTEISEIASISRSLVNEGLKLLDNKKLIKYLSPASKRKKIYTVDVDGCIH
                     DGWCKLPMAGIVSEDRTISAFQSMHNRYHFELVALQLYLYLLYARDNFQEHVLARKQTI
                     CEKLACRNVDLNKAITYLIHIGFLKGIKQKAVESYPIELFHDSFYFYVKTGASNALTFK
                     KQPLVNPPEKEIPY"
                     /name="hypothetical protein"
     gene            complement(2532..2726)
                     /locus_tag="QL136_24095"
     CDS             complement(2532..2726)
                     /locus_tag="QL136_24095"
                     /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="WHJ62932.1"
                     /translation="MSEKQRREGFRKAEASLRLEGMDPSGVPRYECLKTRIISGETSYE
                     QGRKEILDYYLRINHKGEE"
                     /name="antitoxin VbhA family protein"
     Typing          complement(2..354)
                     /name="MOBV"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="94.915"
                     /coverage="86.0"
                     /evalue="2.46e-68"
ORIGIN
        1 cgccgccaca acgcgatctt tcccgtattt gttctccagc cattgctcag aacgggcgaa
       61 aaactccgcc tgctgccgcg gtgtggcctc gttccaccac tcagggcttg ctgtcataac
      121 gtattcaaca gccagtaccg catctttacg gcgtttttcc ggcaacagct cccgcagctt
      181 tcccatcgcc tcatctgccg actgagacac agagcagtgg ttttctggtg tccggtcagc
      241 atcagcattc ggcgtttctc tctccctgta gcagtgctgt aacgcgctgg ccacactgcc
      301 cattcccgtc agctttttac agcgcattat cgcgtagttc gccatgcttc ccccccctcg
      361 ttccggcgtc catccggcca gacgggggat cgcattgcga tgcctccggc gggccactat
      421 caggatgata gtgtactcac tagactttgc tttacaaaat cgttcgggca gcaagctgcc
      481 taaaggtcaa gttcaacagc ggtctggcag gtggaaggcg tcgctccgcg ccacccccca
      541 ccactgccaa gcctgtttta tccggtgagt cgtcaagggt aaatggcact cgctacgctc
      601 gcccttgacg aatgtcaggc aacaaagtcg tctttgaaag agcacgtgcc gctcgccgca
      661 ggtcaggctg aggcgtaccg cagcgcagcg aggaacgaac agcctgaacg aggaagcgga
      721 atgtctacta ggcgtacatt gggctacgta tgcacggact taatagatat agaaaaggag
      781 ctttcagtaa atcgctgatt atattgggtt aaaaaaaggg ggagtctcac cagccatgag
      841 acttatgagt ctcactagct atgagactca agttgacctg ttgcatctct aatgatacaa
      901 ccggtatcaa atgggatatt gaaatggtct atagagcaat ggataattca cagattggca
      961 ctccagagtc tcatgagcag gataactata atttcgtcca ggttagccgc gcgtatctca
     1021 aggaatggcg tgcgctgaca aggaaaagcc ctattgcctc tgaaatcctt atgtacttga
     1081 ttgagaatat gggtaggaca actaatgctg ttgtttgcag ctatacgact ttgatggaga
     1141 taaccggggt ctctagagca tcagtagcaa gggcggttaa aatcctgaag gaagatcgat
     1201 ggatgcaggc agtaaaaata ggtaatgcca cagcatattg tgttaatgcc aaagcatttt
     1261 ggcaggcagg tagaaatcaa aaaaaatacg caatcttcca agctaccgtg attgcctcct
     1321 cctcagagca agagtctgat ttcttagaaa aatcacagca agatcttcga tatattcctt
     1381 ttgtcgatct caaagaccgc cctattgttg gcaccgatga actcccgcct ccggatcaaa
     1441 cagatctaga tctcgactga gcctctgaaa accttcaaat atggttcacc gtgaaccata
     1501 ttgaagttca tttgataacc attttttgat gttaactttt tgatttaatt ataaaaattc
     1561 atattaattt ttcccatatc tttctagata gatttttgct cctatagata cagatacgcg
     1621 gattgctggg ataatcggta tatcggtaaa caggagcaga ggtcaaaatg ggtgacttag
     1681 agcgatttgt agagcttgct gaaaggctgg gaaaagtggc agggtcactt actagtcttg
     1741 cattggccat ttgtgtgtta attatgattt atttcacttt catttccgca taaaggaatc
     1801 actaatgtta tattggaaaa aaatgccatc actctggatc ggtaatagac tgacagagtt
     1861 taatagttta gagacttcac atgccattgc cgccataaag atatatataa ctttttgtct
     1921 ctttggaaaa gaagaggatg atggagtgcg aaccgtaaaa cttacgttta cagaaataag
     1981 cgaaatagct tctatcagcc gatctttggt aaatgaaggt ctcaaattgc tcgataataa
     2041 aaaactaatt aaatacctat cgcccgcgtc aaaaagaaag aaaatctata cagtggatgt
     2101 tgatgggtgc attcatgacg gatggtgtaa gctgcctatg gcaggcatcg ttagcgaaga
     2161 cagaacaatc agcgccttcc agtcaatgca taatagatac cattttgagc ttgtagcgct
     2221 tcagctatat ttataccttc tatatgccag agataacttc caggagcatg tgttagctag
     2281 aaaacaaact atttgcgaaa agcttgcttg ccgcaatgta gatttaaata aagcaataac
     2341 atatttaata cacataggtt ttttaaaagg aattaaacaa aaggcagtgg agtcttatcc
     2401 catagaactt tttcatgatt cattttattt ttatgtaaaa acaggagcaa gcaatgcgct
     2461 tacattcaaa aagcaacctc ttgttaaccc tccagaaaaa gaaattccgt actgacatac
     2521 ctgagggcga attactcctc gcccttatga tttattctaa ggtagtaatc caatatttct
     2581 ttacgccctt gttcataact tgtttcgcca gagataatcc tcgttttcaa acattcataa
     2641 cgaggtactc cactaggatc cattccctca agtcttagtg atgcttccgc ttttcgaaac
     2701 ccttcacggc gctgcttttc actcatcggc taatacctct gtcagttttc tgacgttgct
     2761 ggcgttcctg ctcccgttca agctggcgct gtttttcacg atcgtgattc tgttgctgga
     2821 acgtctgcgc catcgtcaga atatgggtca tctgctcccg ggaaagtcct ttaaaaggct
     2881 ctgtaacgct ctgtaggcgt ttttgctgcg aatccatagt cttctgtaga tcgcgcgctc
     2941 ttttggcatt ctgggcgctc tgagaggcca tagcgatggt tcctgcaaag ccatcgttca
     3001 ctgcctggct taaacgtttg gctatggctg cctgatcttc cacgtctttg gtgaaaatac
     3061 ccttccgcag tacacgcggc tccagcgcct ccggtgagat cgatacctgg ctacgggtgc
     3121 cacggtttat cgattcgtag tagtgctgaa ctgtctgatg cgtggcacgg cttccctcga
     3181 tgccgcgctc aagacccagt ttttttaccg attcagcgta ggtgctctga tcgtcacgca
     3241 tctttgaccg cccgccaata aactctttcg cggacagccg cccatcctgc gtcaatggca
     3301 ccacgaacgc agacaggtgc ggggtggcct cgtccctgtg aaccac
//
