LOCUS       NZ_CP151200             3268 bp    DNA     circular CON 17-APR-2024
DEFINITION  Klebsiella variicola strain KVTMDU plasmid p13_KVTMDU, complete
            sequence.
ACCESSION   NZ_CP151200
VERSION     NZ_CP151200.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN23446385
            Assembly: GCF_038178705.1
KEYWORDS    RefSeq.
SOURCE      Klebsiella variicola
  ORGANISM  Klebsiella variicola
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Klebsiella/Raoultella group; Klebsiella.
REFERENCE   1  (bases 1 to 3268)
  AUTHORS   Ota,Y.
  TITLE     Emergence of KPC-2-producing Klebsiella variicola from hospital
            sewage
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 3268)
  AUTHORS   Ota,Y.
  TITLE     Direct Submission
  JOURNAL   Submitted (26-NOV-2021) Molecular Microbiology, Tokyo Medical and
            Dental University, 1-5-45, Yushima, Bunkyo-ku 113-8510, Japan
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: Unicycler v. July-2021
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 168.3x
            Sequencing Technology             :: Illumina MiSeq; Oxford Nanopore
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_038178705.1-RS_2024_04_17
            Annotation Date                   :: 04/17/2024 11:53:20
            Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline
            (PGAP)
            Annotation Method :: Best-placed reference protein set; GeneMarkS-2+
            Annotation Software revision      :: 6.7
            Features Annotated                :: Gene; CDS; rRNA; tRNA; ncRNA
            Genes (total)                     :: 6,118
            CDSs (total)                      :: 5,998
            Genes (coding)                    :: 5,805
            CDSs (with protein)               :: 5,805
            Genes (RNA)                       :: 120
            rRNAs                             :: 9, 8, 8 (5S, 16S, 23S)
            complete rRNAs                    :: 9, 8, 8 (5S, 16S, 23S)
            tRNAs                             :: 86
            ncRNAs                            :: 9
            Pseudo Genes (total)              :: 193
            CDSs (without protein)            :: 193
            Pseudo Genes (ambiguous residues) :: 0 of 193
            Pseudo Genes (frameshifted)       :: 68 of 193
            Pseudo Genes (incomplete)         :: 125 of 193
            Pseudo Genes (internal stop)      :: 32 of 193
            Pseudo Genes (multiple problems)  :: 29 of 193
            CRISPR Arrays                     :: 1
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP151200.1.
            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/
            COMPLETENESS: full length.
FEATURES             Location/Qualifiers
     source          1..3268
                     /organism="Klebsiella variicola"
                     /mol_type="genomic DNA"
                     /strain="KVTMDU"
                     /isolation_source="sewage"
                     /db_xref="taxon:244366"
                     /plasmid="p13_KVTMDU"
                     /geo_loc_name="Japan"
                     /lat_lon="35.7014 N 139.7642 E"
                     /collection_date="2021-06"
                     /collected_by="Tokyo Medical and Dental Hospital"
     gene            complement(312..767)
                     /locus_tag="LQ252_RS30575"
                     /old_locus_tag="LQ252_30580"
     CDS             complement(312..767)
                     /locus_tag="LQ252_RS30575"
                     /old_locus_tag="LQ252_30580"
                     /inference="COORDINATES: ab initio prediction:GeneMarkS-2+"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GeneMarkS-2+."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_061350436.1"
                     /translation="MTTKFNKFELHSAFRDGKLNEKHFVDLPYLKEEQLRALASFLGAI
                     TREEPLPGKNKPSWLDDDSIKISGTDAYEDGNYWHYHCGPYPESVKLRSMTFNLGMNVA
                     GLTSAEVIHYQKLNDGTVFVVGFSPTHEPFPKSDAPHYNPLFTESDD"
                     /name="hypothetical protein"
     gene            1164..1742
                     /locus_tag="LQ252_RS30580"
                     /old_locus_tag="LQ252_30585"
     CDS             1164..1742
                     /locus_tag="LQ252_RS30580"
                     /old_locus_tag="LQ252_30585"
                     /inference="COORDINATES: protein motif:HMM:NF025107.4"
                     /GO_function="GO:0003677 - DNA binding [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="helix-turn-helix domain-containing protein"
                     /protein_id="WP_123906182.1"
                     /translation="MKSEIELKKTEHLSVEIPERILAIWGRSILNSGWTSVPNELLKNQ
                     SKLGIGNTELVLLINLISFMHHSDARVYPSISLLCERMNQDRRTIQRNLNKLVEMDILR
                     IKIRSTGKNSKGMTNLYDLTPLMLKLINLKIPSLNTPDEKHTCPKCGKIAISREEITKE
                     FGFRTDTNGKMRTQSWCKDCRGKKVADLP"
                     /name="helix-turn-helix domain-containing protein"
     gene            complement(2514..2663)
                     /locus_tag="LQ252_RS30585"
                     /old_locus_tag="LQ252_30590"
     CDS             complement(2514..2663)
                     /locus_tag="LQ252_RS30585"
                     /old_locus_tag="LQ252_30590"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_017880354.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_001417847.1"
                     /translation="MPSEYDEQRDANDTQLPGEYDLFDLMAQVTEENLHAPVDFGPPVG
                     REAL"
                     /name="hypothetical protein"
     Typing          complement(2698..2870)
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="93.103"
                     /coverage="100.0"
                     /evalue="9.410000000000001e-66"
     Typing          3..265
                     /name="rep_cluster_2358"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="80.0"
                     /coverage="95.0"
                     /evalue="4.3e-44"
     Typing          2841..3267
                     /name="rep_cluster_2335"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="93.939"
                     /coverage="81.0"
                     /evalue="0.0"
ORIGIN
        1 ttccggtaac tatcaacttg agtccaaccc ggaaagacac gacaaagcgc cactggcagc
       61 agccactggt aaacaggatg tgcgagagat gtatcgagag ttcttgaagt ggtggcctga
      121 ctgcggctac actgaaagga cagatttggt gacatgtctc gcacaagact gttaccacgg
      181 ttagagaatc tgccaggatt aactaacctt cgaaaaacca cctgccaggg tggttttttc
      241 gtttcaggaa aagagactac agctgagaga aaaaaatctc aacatatcct taccagccac
      301 tattcagata tttaatcatc tgattcggtg aagagagggt tgtaatgcgg cgcatcagac
      361 ttagggaagg gctcatgtgt aggggagaag cctacgacaa acaccgtgcc atcgttgagt
      421 ttttgatagt ggatcacttc tgcggaggtt agtccagcaa cgttcatacc caagttaaaa
      481 gtcatcgatc taagtttgac cgattctgga tatggaccgc aatgataatg ccagtagttc
      541 ccgtcttcgt aagcatcagt accggaaatt ttaatggaat catcatcaag ccatgaaggc
      601 ttgtttttcc ctggaagagg ctcttcacga gttatcgcac ccaagaaaga ggctaatgcc
      661 cggagttgtt cttctttgag gtagggtaaa tctacgaaat gcttttcatt cagcttcccg
      721 tctcggaaag ctgaatgaag ctcaaactta ttgaatttgg ttgtcatcaa acactttcca
      781 cttaccttac tgagtaagca gatagcatat caaagatcga ttcatcagac ttcggagaat
      841 cgcattttaa cgcttcatgc gtctgattct tgtatgaacg cgagagcagc acttcgtcag
      901 cacgagattt gtactgctga cgacgttctg tatcgcagct gtgattatca aatcgtacgt
      961 ttgccaacat gtcagtccta tgtttgaaga aatctgggaa gataaaatct tgctcaattc
     1021 gatggtaaga gaggtctttc cccggtgcta gacattaggc ctttttggtc aaatacaagg
     1081 gcggcattga tgccgcccga ataattaatc ataataacaa tacctatata tataggtatt
     1141 gttattatga ttggtggccg aagttgaaat cagaaatcga actaaaaaaa acagaacact
     1201 tatcagtaga gatccccgaa agaatcttag ccatatgggg gcgcagcatt ttaaactctg
     1261 gctggacgtc cgttcccaat gaactattaa aaaaccaatc taagctagga ataggaaaca
     1321 cagagcttgt acttttgatt aacctgatct ctttcatgca tcattctgac gcaagagtgt
     1381 acccatcaat ttcgcttcta tgcgaaagaa tgaatcaaga cagacgaaca attcagagaa
     1441 atttaaacaa gttagtagaa atggacattc tgaggataaa aatacgttcc accggtaaaa
     1501 actccaaagg aatgactaac ttgtatgacc tcaccccttt aatgctgaag ctaatcaacc
     1561 taaaaatacc atctttaaat acgcccgatg aaaaacatac gtgtccaaaa tgcgggaaaa
     1621 tagccatatc aagagaagaa ataacaaaag agtttggatt cagaactgac actaatggga
     1681 agatgagaac gcaaagttgg tgcaaagatt gtcgaggcaa gaaagttgcg gatttaccat
     1741 aacatccgtt gcgtgcaccg ccgcagaggc cctcagcgcg tttctgaggc ctccggcctg
     1801 aaacacacac ctttctgtgc ccatatcgag aaaaaacgcc cctgatgatt ctggcgcgac
     1861 tgcatggcta tgcacggaca tacctggccg ggattttagc ggctaaaatc cgatgaacgc
     1921 cctgaaagcc accacgaacc accccgataa cggtgaacgg atgcgcaatt tattgcgtgg
     1981 ccgtgaggcg ttgccggcac agccggaaaa accattttca gcacgtgcag gaggcccagg
     2041 aagaggggcg gatgtacgaa tagttcagag gtcagatctg acgtaaaaat gatgtaaaag
     2101 tgacgtaaaa gtgatgtaat tttgatgtac ttttgatgta attctgttgt acacccgcga
     2161 tctgacgtaa aagtgatgta attttgatgt acttttgatg taattctgta gtcaggaaga
     2221 ataacccgtt catgcaggca tgaacgatac agtgaggaac gctttttttg tcacgatctc
     2281 cccttaacct gcgtaaatca ccctccatgg ttgattattt ttcaacctca aaatggtcat
     2341 acaccatacg caaccgcgat tttcatcgca attgcatgaa ttaaaaggta aaaactgaat
     2401 ttcccgttta tttatgtaat acacaacgta ttacaaccac ctgtaatcac atgaaaataa
     2461 agaaataaga tgtaataccg gcgtattaca cgtacgctga ccagcgaaaa aagttataac
     2521 gcttccctgc cgacaggcgg cccaaaatcc accggggcgt gcaggttctc ttcagtaacc
     2581 tgcgccatta aatcaaaaag gtcatattcg ccgggaagct gcgtatcatt cgcatcccgt
     2641 tgttcatcat actcagatgg catgttgtga tatccagtag ctgaggggtg ttagcgggtt
     2701 tcggggcgca gccctgaacc agtcacgcag cgctagcgga gtgtatactg gcttactatg
     2761 ttggcacggg tgcgggaatc tgtgaagcgc ttcatgtggc aggagaaaaa tgcagcagcg
     2821 gagcgtaagc ggaatatatg agacaggata tattccgctt cctcgctcac tgactcgctg
     2881 cgctcggtcg ttcggctgcg gcgagcggtg cgggcttacg aatagggcgg aagtttcctg
     2941 gtaaatgccc ggaaggaact taacagggaa atgagaaggc cgcggcgaag ccgtttttcc
     3001 ataggctccg cccccctgac aagcatcacg aaatctgacg ctcaaatcag tggtggcgaa
     3061 acccgacagg acttaaagat accaggcgtt tccccctggt ggctccctcg tgcgctctcc
     3121 tgttcctgcc tttcggttta ccggtgtcat tccgctgtta tggccgcgtt tatctcattc
     3181 cacgcctgac actcgattcc gggaaggcag ttcgctccaa gctggactgt atgcacgaac
     3241 cccccgttca gtccgactgc tgcgcctt
//
