LOCUS       NZ_CP151198             4922 bp    DNA     circular CON 17-APR-2024
DEFINITION  Klebsiella variicola strain KVTMDU plasmid p11_KVTMDU, complete
            sequence.
ACCESSION   NZ_CP151198
VERSION     NZ_CP151198.1
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 4922)
  AUTHORS   Ota,Y.
  TITLE     Emergence of KPC-2-producing Klebsiella variicola from hospital
            sewage
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 4922)
  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
            CP151198.1.
            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..4922
                     /organism="Klebsiella variicola"
                     /mol_type="genomic DNA"
                     /strain="KVTMDU"
                     /isolation_source="sewage"
                     /db_xref="taxon:244366"
                     /plasmid="p11_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            347..1282
                     /locus_tag="LQ252_RS30530"
                     /old_locus_tag="LQ252_30535"
     CDS             347..1282
                     /locus_tag="LQ252_RS30530"
                     /old_locus_tag="LQ252_30535"
                     /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_087777346.1"
                     /translation="MTAQDLINVLTILKANDSTSFSKIQRALKMSISQLEGIIDGLTAM
                     GIVYKSSFTSYSLTELTSKPVVSDGVRKAFEDIITNRGTYLSEELLQKVSTPFIPLMTH
                     EYKNAPVKVMIVGQETLGMEDAFSTIVSVDDYINESIESFNKFNFGEDLRNSHFWYAFD
                     EVVKYFNLPSRRHAYWTNLHKFQLIENDGDSVSISKLPSKDIMTMIHMQRELFLAEIKD
                     TKPDIIIYFTGGQTWVLDHYLNNGKKLAVKAIDERSHLGIIQTEFLHCPIAICTDHPSR
                     RGYTQAIVDHRANLLKYAADKFHASESARV"
                     /name="hypothetical protein"
     gene            <1311..1414
                     /locus_tag="LQ252_RS30535"
                     /old_locus_tag="LQ252_30540"
                     /pseudo=""
     CDS             <1311..1414
                     /locus_tag="LQ252_RS30535"
                     /old_locus_tag="LQ252_30540"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_086558297.1"
                     /GO_process="GO:0015074 - DNA integration [Evidence IEA]"
                     /note="frameshifted; incomplete; partial in the middle of a
                     contig; missing N-terminus; Derived by automated
                     computational analysis using gene prediction method:
                     Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="IS3 family transposase"
                     /name="IS3 family transposase"
     gene            complement(1992..2348)
                     /locus_tag="LQ252_RS30540"
                     /old_locus_tag="LQ252_30545"
     CDS             complement(1992..2348)
                     /locus_tag="LQ252_RS30540"
                     /old_locus_tag="LQ252_30545"
                     /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_025714790.1"
                     /translation="MAGNILDVFESCDLTNEKIDELISNKKTFVINNIPSSFFDQLLLR
                     IEKSIEDKSMKCRVYTEYRSAIFAAMTIPTGVTQIIGIASAIGVGIHNLVTYNPDYELA
                     KNLTSTKLGVIYKK"
                     /name="hypothetical protein"
     gene            complement(3131..3541)
                     /locus_tag="LQ252_RS30545"
                     /old_locus_tag="LQ252_30550"
     CDS             complement(3131..3541)
                     /locus_tag="LQ252_RS30545"
                     /old_locus_tag="LQ252_30550"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:YP_005229777.1"
                     /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_025714791.1"
                     /translation="MARVSISEAARLVKVSRPTIYKMINSGKLSYTSVVKHGKSIKVID
                     TSELIRVFGSLDGVIDDVKSDAESTGINSVGLHDLQHRIALLEAENDGLKGAVKARDEH
                     IDSLRQAMQLLEHKHEPSSPPHSPWWKFWKKS"
                     /name="helix-turn-helix domain-containing protein"
     gene            complement(3541..3732)
                     /locus_tag="LQ252_RS30550"
                     /old_locus_tag="LQ252_30555"
     CDS             complement(3541..3732)
                     /locus_tag="LQ252_RS30550"
                     /old_locus_tag="LQ252_30555"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000166328.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="Rop family plasmid primer RNA-binding protein"
                     /protein_id="WP_025714792.1"
                     /translation="MTKQQKTALNMAKFIQNQSLLLLEKLNELDLDAEADLCEKLHDDA
                     EHLFRTLSSRLDELLDGN"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            complement(4203..4394)
                     /locus_tag="LQ252_RS30555"
                     /old_locus_tag="LQ252_30560"
     CDS             complement(4203..4394)
                     /locus_tag="LQ252_RS30555"
                     /old_locus_tag="LQ252_30560"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001041614.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="Rop family plasmid primer RNA-binding protein"
                     /protein_id="WP_001041614.1"
                     /translation="MNKQQKTAVNMAKFIQDQSLLLLDRLNELDLDHEADFCEKLHEDA
                     ERLYRSLSARLNEQQDGA"
                     /name="Rop family plasmid primer RNA-binding protein"
     Typing          4270..4889
                     /name="rep_cluster_2327"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="84.772"
                     /coverage="99.0"
                     /evalue="1.1900000000000001e-169"
ORIGIN
        1 gcaggatgtg cgagagatgt agtaagagtt cttgaagtga tggcctgagt gcggctacac
       61 tgaaaggaca aatttggtga catgtctcgc acaagactgt tacctggtta agcagttccc
      121 caactgacct aaccttcgat caaaccacct ccccaggtgg ttttttcgtt tcttggagaa
      181 gagactacga cgacaaatga cggatctcaa gaagatcctt ttaacgtaca aaaatttccg
      241 ttctccaaag gtgatgctgc caacttactg atttagtgta ctgcgaccgt cagaatgagt
      301 taaacgcgta tctacattga agcagttcaa tatgaggaaa acaggaatga cagcacaaga
      361 tttaatcaac gttctcacta ttcttaaggc caacgactca accagtttta gcaagattca
      421 acgcgcgtta aagatgagta tttcgcagtt ggagggcatc attgatgggt taactgcaat
      481 gggaatagtg tataaatcat cattcacttc atacagcctt actgagttaa cctctaaacc
      541 tgttgttagt gacggtgtaa gaaaggcatt cgaagatatc attaccaatc gcggtactta
      601 cctgtcagaa gaactactac aaaaggtaag tacaccattc atcccactga tgacgcacga
      661 atacaaaaat gccccagtta aagtgatgat cgtggggcaa gaaactctgg gaatggaaga
      721 tgctttcagt accatcgttt cggtcgatga ctacattaat gagagcattg aatccttcaa
      781 taaattcaat tttggtgaag atttaaggaa tagccacttt tggtatgcat ttgatgaagt
      841 agtaaagtat tttaacctac catccagaag gcatgcttat tggactaatc ttcataagtt
      901 tcaattaatt gaaaatgatg gagatagtgt cagcatttcc aaactacctt caaaagatat
      961 catgacaatg attcatatgc agcgtgaatt attcttggct gaaattaaag ataccaagcc
     1021 agatatcatc atctacttca cgggtgggca aacctgggtg ttagatcatt atctaaacaa
     1081 tggtaaaaaa ttagcagtta aggcaataga tgaacgctcg catctgggga ttatccagac
     1141 agaatttttg cattgcccaa tcgctatatg taccgaccat cctagtagaa ggggatatac
     1201 tcaagccatc gtagatcata gagctaatct gcttaaatat gctgctgaca aatttcatgc
     1261 aagtgaatcg gcacgggttt aacagccccc cagagtcatt taagatcgct tacatcgaaa
     1321 tgttttataa cagtaacgtc ggcatggttc tagcgaacac atgtcaccga cagaatatga
     1381 aaaccagtat tatcaacggc tcggaagtgt ctagattatc cgtggcgatt caatttacca
     1441 taacatccgt tatcagcacc gcctgagagg ctctcagggc gtttctgacg ggaaaccggc
     1501 aaaacaggca acaaaccacc cgaaaacccg ccagaaacgc gcaggctctg tttttacggc
     1561 atgcatgagt atgcgcgcaa gtgcatagcg cggaaattca cgccattcag ccggggtaag
     1621 tcctgtttcc gatgttcttc ttacccgaaa acggtgaacg gggacgcaat ttattgcgtg
     1681 gccgtgaggc gttgccggca cagccggaaa ccccgtttca gcacgttcag gaatcgggtt
     1741 cgtcgacagc cggcaatcac gttatggcga gtcaccggac gacttaccac acgattcacc
     1801 ggcgattcga atcgtgaatt gactctagag tcgctatgaa caaaaaacac ccagaatgat
     1861 gaattgaatc tggattcaat tcatcataac aatatgataa taaagcgtga ttcacatatg
     1921 aatcgtgggc aattcgtcag cgattcacca tagagtcatc aacgaattgg attcatctta
     1981 aaagaaatca tttatttttt ataaataact ccaagttttg ttgatgttag atttttcgcc
     2041 aattcataat ctggattata agtaactaaa ttatgtattc caactcctat cgcagatgct
     2101 attccaatta tctgtgttac acctgtggga attgtcatgg ccgcaaaaat agcacttcta
     2161 tactctgtgt atacgcgaca tttcattgac ttatcttcaa ttgatttttc tattcgcagt
     2221 aataactggt caaaaaaaga tgaagggatg ttatttatga cgaaggtttt tttattacta
     2281 ataagctcat caatcttttc attagttaaa tcacaacttt caaaaacatc cagaatgtta
     2341 cctgccatat aacaacccct tgttttgtta aatatcagaa ccatgaaagt ttatataatt
     2401 aaaaagttac cataataccg cattacgtgc acgccctgag aggccctcag ggcgtttctg
     2461 acgggaaacc aacaaaaagg caacaaacca cccggaaacg cgcaggctct gtttttacgg
     2521 catgcatgag tatgcgcaca agtgcatagc gcgggaattg acaccattca gccagggtaa
     2581 gtcctgtttc cggcgttctt cccatccgaa aacggtgaac ggggacgcaa tctattgcgt
     2641 ggccgtgaag cgttgccggc gcagccggaa aaccggtttt cagcacgttc aggaattggg
     2701 ttcgtcgacg gccggcaatc acgttatggc aagtcgccgg acgactcacc acacgattca
     2761 ccggcgattc gactcgtgac ttgactctag agtcaccacg gtcaaaaaaa cgccaaagcg
     2821 acgattcgac tctagagtca agtcgtcata agttactgat agtgtggagt gagtcgtcga
     2881 tgactctatg acgagtcgtc ggtaagtcgt acacgaatca ccgacgactt ggattgacct
     2941 tacagaaggt aatactgcgt aatttaataa aacctaacca actgataata aggagttatc
     3001 tgcaaaattt taattttgcg tggtgtgtgg gtatttttcg tggtgaggag tgttcccgga
     3061 tctggcgatt tttgggaagg ttcaggaacg ccccgggatg gccggagagg aaaactcaag
     3121 catggcggga tcaggatttt ttccagaatt tccaccacgg ggaatggggt ggtgaagaag
     3181 gttcgtgctt gtgctccaga agctgcatag cctgacgaag ggaatcaata tgctcatctc
     3241 gagccttaac agccccttta agaccatcgt tttcagcttc aagtaaagcg attctatgtt
     3301 gtaaatcatg taaaccaacg ctgttaatac ctgtagattc tgcgtcactt tttacatcat
     3361 cgatgacacc atcaagagaa ccaaacaccc taataagctc tgatgtatca ataactttga
     3421 tactcttccc gtgctttaca acagaggtgt aacttaactt accactgtta atcatcttgt
     3481 aaatagttgg gcgactaacc ttcacaagcc gtgctgcttc actaatagac actctggcca
     3541 tcagttacca tccagtaatt catccagtct cgaggacagt gtacggaaaa gatgctccgc
     3601 atcatcgtgg agtttctcac aaaggtcggc ctcagcatcg agatcaagct cgttaagctt
     3661 ctccagcagg agcagagact gattctggat gaatttagcc atgttcagcg ctgttttctg
     3721 ttgtttcgtc ataagggacc tcagagcatc agtgctcagt gtaaaaccgg taagggggtc
     3781 ggatgtacga atggttcaga gaacggatct gaggtaatcc tgtagttatt ttgtagttta
     3841 tctgtagtca tcgcactaaa aatcaggatt aagtcatcag cttttgtagt ctttctgtag
     3901 tttacctgta gtccggaaaa ataatccgtt catgctcgca tgaacgaggt cgttaatgac
     3961 gtttttttgt caccgacgcc ccttaacctg cgtaaatcac ccgccatggt tgattatttt
     4021 tcaacctcaa aatggtcata cacctaacgc agctgcgatt ttcatcgcaa cttcatgaaa
     4081 aataaataaa aaagaaaaaa tacagggatt gtgggtatta ccggggtaat aatgttaagc
     4141 gccaagacaa tgaaaattaa ggcgatgccg gtattactcc ggtaataccc acaacggagc
     4201 cattacgcac cgtcctgctg ctcattcagg cgcgctgaca ggcttcggta aaggcgttcc
     4261 gcatcctcat ggagtttctc gcagaaatca gcctcatgat ccagatccag ctcattaagc
     4321 ctgtccagaa gaagcaggga ctgatcctgg atgaatttag ccatgttaac ggcagtcttt
     4381 tgttgtttgt tcatgaaggc cccggcgcga aagtgcttac tgtacgttct gatggttttc
     4441 cgcttcctcg ctcattcgct cactccgttc ggtcatgagt ctgcggcgag cggagggaag
     4501 ataagcagat aacgtaacgg taagcataac gaaagctaag gacaagggcg aaaaggccac
     4561 gccccgccgg ggcgtttttc cataggctcc gcccccctga caagcatcac gaaatctgac
     4621 gctcaaatca gtggtggcga aacccgacag gactataaag ataccaggcg tttccccctg
     4681 atggctccct cgtgcgctct cctgttcctg cctttcggtt taccggtgtc attccgctgt
     4741 tatggccgcg tttatctcat tccacgcctg acactcagtt ccgggtaggc agttcgctcc
     4801 aagctggact gtatgcacga accccccgtt cagtccgact gctgcgcctt atccggtaac
     4861 tatcgtcttg agtccaaccc ggaaagacat gcaaaagcgc cactggcagc agccactggt
     4921 aa
//
