LOCUS       NZ_CP151196             5742 bp    DNA     circular CON 17-APR-2024
DEFINITION  Klebsiella variicola strain KVTMDU plasmid p9_KVTMDU, complete
            sequence.
ACCESSION   NZ_CP151196
VERSION     NZ_CP151196.1
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 5742)
  AUTHORS   Ota,Y.
  TITLE     Emergence of KPC-2-producing Klebsiella variicola from hospital
            sewage
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 5742)
  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
            CP151196.1.
            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..5742
                     /organism="Klebsiella variicola"
                     /mol_type="genomic DNA"
                     /strain="KVTMDU"
                     /isolation_source="sewage"
                     /db_xref="taxon:244366"
                     /plasmid="p9_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(join(<5557..5742,1..48))
                     /locus_tag="LQ252_RS30450"
                     /old_locus_tag="LQ252_30455"
                     /pseudo=""
     CDS             complement(join(<5557..5742,1..48))
                     /locus_tag="LQ252_RS30450"
                     /old_locus_tag="LQ252_30455"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_076612230.1"
                     /GO_process="GO:0006313 - DNA transposition [Evidence IEA]"
                     /note="incomplete; partial in the middle of a contig;
                     missing C-terminus; Derived by automated computational
                     analysis using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="IS1 family transposase"
                     /name="IS1 family transposase"
     gene            205..648
                     /locus_tag="LQ252_RS30455"
                     /old_locus_tag="LQ252_30460"
     CDS             205..648
                     /locus_tag="LQ252_RS30455"
                     /old_locus_tag="LQ252_30460"
                     /inference="COORDINATES: protein motif:HMM:NF024064.4"
                     /GO_process="GO:0006355 - regulation of DNA-templated
                     transcription [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="ribbon-helix-helix protein, CopG family"
                     /protein_id="WP_064188129.1"
                     /translation="MIAVSLPDELLQKLDNAVAKTGKKRSYLIRESIQMYLNQIENTHE
                     KKEIILNTSKPFYEILIEEFQVEKELMTEARKTEFTMFSDNGKLYVVNSKGNTRKLEAV
                     YVNNFFEEYKKTGSMSPSSYQDITFNSSYLLAALKYLIEKELI"
                     /name="ribbon-helix-helix protein, CopG family"
     gene            complement(720..992)
                     /locus_tag="LQ252_RS30460"
                     /old_locus_tag="LQ252_30465"
     CDS             complement(720..992)
                     /locus_tag="LQ252_RS30460"
                     /old_locus_tag="LQ252_30465"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_004897311.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_019405140.1"
                     /translation="MATDAQVKEINALIKKYPDSCSICHEVYDEDDVTYTVFGYDRKGK
                     IQVTTGCCAGMLTEPVLLGVCGCFDPEERDEIMQNHPMAKQFFTE"
                     /name="hypothetical protein"
     gene            complement(1798..2220)
                     /locus_tag="LQ252_RS30465"
                     /old_locus_tag="LQ252_30470"
     CDS             complement(1798..2220)
                     /locus_tag="LQ252_RS30465"
                     /old_locus_tag="LQ252_30470"
                     /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_061500298.1"
                     /translation="MARVSISEAARLVKVSRPTIYKMINSGKLSYTSVVKHGKGIKVID
                     TSELIRVFGSLDGVIDTVKYDVKSDAESTGINSVGLHDLQHRIALLEAENDGLKGAVKA
                     RDEHIDSLRQAMQLLEHKHEPSSPPHSPWWKFWKKS"
                     /name="helix-turn-helix domain-containing protein"
     gene            complement(2220..2411)
                     /locus_tag="LQ252_RS30470"
                     /old_locus_tag="LQ252_30475"
     CDS             complement(2220..2411)
                     /locus_tag="LQ252_RS30470"
                     /old_locus_tag="LQ252_30475"
                     /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_032421723.1"
                     /translation="MTKQQKTALNMAKFIQNQSLLLLEKLNELDLDAEADLCEKLHDDA
                     EHLFRTLSSRLDELQDGN"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            complement(2882..3073)
                     /locus_tag="LQ252_RS30475"
                     /old_locus_tag="LQ252_30480"
     CDS             complement(2882..3073)
                     /locus_tag="LQ252_RS30475"
                     /old_locus_tag="LQ252_30480"
                     /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"
     gene            complement(3967..4665)
                     /locus_tag="LQ252_RS30480"
                     /old_locus_tag="LQ252_30485"
                     /pseudo=""
     CDS             complement(3967..4665)
                     /locus_tag="LQ252_RS30480"
                     /old_locus_tag="LQ252_30485"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_076612230.1"
                     /GO_function="GO:0004803 - transposase activity [Evidence
                     IEA]"
                     /note="frameshifted; Derived by automated computational
                     analysis using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="IS1 family transposase"
                     /name="IS1 family transposase"
     gene            4914..5546
                     /locus_tag="LQ252_RS30485"
                     /old_locus_tag="LQ252_30490"
     CDS             4914..5546
                     /locus_tag="LQ252_RS30485"
                     /old_locus_tag="LQ252_30490"
                     /inference="COORDINATES: protein motif:HMM:NF027277.4"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="DUF4755 domain-containing protein"
                     /protein_id="WP_139137146.1"
                     /translation="MKIYYALKRIAYIAGALSIGCGSLPMIFSKTPALQYWVLGAFLIF
                     IGYCVSKLEFDKSKYIKYLNEKNDGIYIYYAKFGGEEHEIKINTKNKTIELKSGKNSAT
                     LNFDNIKSWRYNVSGISKVNVIGSTNSVMGNFTALSQASAINNQAGYSAWDNNGFFIHT
                     DALANPVWHIKIIPKDVAINLKSDKFWKSVAGECEVWMNVMNRAINK"
                     /name="DUF4755 domain-containing protein"
     Typing          2949..3574
                     /name="rep_cluster_2327"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="84.627"
                     /coverage="99.0"
                     /evalue="1.1900000000000001e-169"
ORIGIN
        1 gccttcagta gcggagcagg aaggacatct gatggaaatg gaagccacgc aagcacctta
       61 aaatcaccat catacactaa atcagtaagt tggcagtatt acccacacat agttgattaa
      121 aaaagaggcc tcacccattg acgaacatct aattttatat aaaattagat gaatcgaata
      181 gacgttaact atagaggcat ccaaatgata gcagtatcac ttcctgacga attactgcaa
      241 aaactagata acgctgtagc taaaacaggc aaaaaacgct cttatttaat cagggaatca
      301 atacagatgt atttgaatca aatagaaaat acacatgaaa aaaaagagat tatcctgaac
      361 acctcaaaac cgttctatga gatcctaatt gaggaatttc aagttgaaaa agaactgatg
      421 actgaggcca gaaagactga gttcacgatg tttagtgata acggaaaact ctatgtggta
      481 aattcgaaag gaaatacacg caagttagaa gccgtctacg taaataattt ctttgaagag
      541 tataagaaaa caggaagcat gagcccatcc agctatcaag atataacctt caactcatct
      601 tatcttttag cagcgctaaa gtacctgata gaaaaagaac tgatttaaca taaaccctca
      661 tttcacgcag atatgaaaaa gcccgcacaa ggcgggcttc agactcaaca gatacggaat
      721 cactctgtga aaaactgctt tgccatgggg tgattctgca tgatctcgtc acgttcttcc
      781 gggtcaaagc acccacagac acccagcaga accggctctg tcagcattcc ggcacagcat
      841 cccgtggtga cctgtatttt acctttccgg tcatacccaa aaacggtgta ggtcacatca
      901 tcctcatcat agacttcatg acagatggag catgagtctg ggtatttttt gatgagtgca
      961 ttaatttctt ttacctgagc gtcagtagcc aaaacatctc cctgagtcac tgattatcac
     1021 aatccgctga ctctaacaca gactcaggca tccgccgttg atttaccata acgtcccatt
     1081 acgcgcaccg cgaaaacggc ctcagggcgt ttctgacggg aaaccggtaa aacaggcaac
     1141 aacccccccg aaaacccgcc agaaacgcgc aggctctgtt tttacggcat gcatgagtat
     1201 gcgcgcaagt gcatagcgcg gaaattcacg ccattcagcc ggggtaagtc ctgtttccga
     1261 tgttcttctt acccgaaaac ggtgaacggg gacgcaattt attgcgtggc cgtgaagcgt
     1321 tgccggcgca gccggaaaac cggttttcag cacgttcagg aatcgggttc gtcgacggcc
     1381 ggcaatcacg ttatggcaag tcgccggacg actcaccaca cgattcaccg gcgattcgac
     1441 tcgtgacttg actctagagt caccacggtc ataaaaacgc caaagcgacg attcgactct
     1501 agagtcaagt cgtcataagt tactgatagt gtggagtgag tcgtcgatga ctctatgacg
     1561 agtcgtcggc aagtcgtaca cgaatcaccg acgacttgga ttgaccttac agaaggtaat
     1621 actgcgtaat ttaataaaac ctaaccaact gataataagg agttatctgc aaaattttaa
     1681 ttttgcgtgg tgtgtgggta ttttttttgg tgaggagtgt tcccggatct ggcgattttt
     1741 gggaaggttc aggaacgccc cgggatggcc ggagaggaaa actcaagcat ggcgggatca
     1801 ggattttttc cagaatttcc accacgggga atggggtggt gaagaaggtt cgtgcttgtg
     1861 ctccagaagc tgcatagcct gacgaaggga atcaatatgc tcatctcgag ccttaacagc
     1921 ccctttaaga ccatcgtttt cagcttcaag taaagcgatt ctatgttgta aatcatgtaa
     1981 accaacgctg ttaatacctg tagattctgc gtcacttttt acatcatatt ttacagtatc
     2041 gatgacacca tcaagagaac caaacactct aataagctct gatgtatcaa taactttaat
     2101 acccttcccg tgctttacaa cagaggtgta acttaactta ccactgttaa tcatcttgta
     2161 aatagtaggg cgactaacct taacaagccg tgctgcttca ctaatagaca ctctggccat
     2221 cagttaccat cctgtaattc atccagtctc gaggacagtg tacggaaaag atgctccgca
     2281 tcatcgtgga gtttctcaca aaggtcggcc tcagcatcga gatcaagctc gttaagcttc
     2341 tccagcagga gcagagactg attctggatg aatttagcca tgttcagcgc tgttttctgt
     2401 tgtttcgtca taagggacct cagagcatca gtgctcagtg taaaaccggt aagggggtcg
     2461 gatgtacgaa tggttcagag aacggatctg aggtaatcct gtagttattt tgtagtttat
     2521 ctgtagtcat cgcactaaaa atcaggatta agtcatcagc ttttgtagtc tttctgtagt
     2581 ttacctgtag tccggaaaaa taatccgttc atgcgagcat gaacgaggtc gttaatgacg
     2641 tttttttgtc accgacgccc cttaacctgc gtaaatcacc cgccatggtt gattattttt
     2701 caacctcaaa atggtcatac acctaacgca gccgcgattt tcatcgcaac ttcatgaaaa
     2761 ataaataaaa aagaaaaaat aaagggattc tgggtattac cggggtaata atattaagcg
     2821 ccaagacaat gaaaattaag gcgatgccgg tattactccg gtaataccca caacggagcc
     2881 attacgcacc gtcctgctgc tcattcaggc gcgctgacag gcttcggtaa aggcgttccg
     2941 catcctcatg gagtttctcg cagaaatcag cctcatgatc cagatccagc tcattaagcc
     3001 tgtccagaag aagcagggac tgatcctgga tgaatttagc catgttaacg gcagtctttt
     3061 gttgtttgtt catgaaggcc ccggcgcgaa agtgcttact gtacgttctg atggttttcc
     3121 gcttcctcgc tcattcgctc actccgttcg gtcatgagtc tgcggcgagc ggaggaagat
     3181 gagcagataa cgtaacggta agcataacga aagctaagga caagggcgaa aaggccacgc
     3241 cccgccgggg cgcttttcca taggctccgc ccccctgaca agcatcacga aatctgacgc
     3301 tcaaatcagt ggtggcgaaa cccgacagga ctataaagat accaggcgtt tccccctggt
     3361 ggctccctcg tgcgctctcc tgttcctgcc tttcggttta ccggtgtcat tccgctgtta
     3421 tggccgcgtt tgtctcattc cacgcctgac actcagttcc gggaaggcag ttcgctccaa
     3481 gctggactgt atgcacgaac cccccgttca gtccgaccgc tgcgccttat ccggtaacta
     3541 tcgtcttgag tccaatccgg aaagacacga cttatcgcca ctggcagcag ccactggtaa
     3601 caggattcac ggagcagagt agtagagtgc ttctacagag ttcttgaagt ggtggcctga
     3661 ctgcggctac actggaagga cagttttggt atctgcgctc cgtgaaagcc agttaccttc
     3721 ggaaaaaaga gttggtagct cttgattccg gcaaacgaac caccgttggt agcggtggtt
     3781 tttttgtttg caggacatga gattacgacg caacagaaag gatctcaaga agttccttgc
     3841 tgtattgcta ctatcctaga gatctgcccc attaggggca ttatcagatg acggccttgt
     3901 aatccacgat aaaaaaccca gaaaccagaa gagttggccc agcgacatat gggtaatgct
     3961 gccaacttac tgatagtgtt ttatgttcag atagtgtccg atgactttgt catgcagctc
     4021 caccgatttt gagaacgaca gtgacttccg tcccagcctt gccagatgtt gtctcagatt
     4081 caggttatgt cgctcaatgc gctgagtata acgcttgctg ataacgtggc agctttccct
     4141 tcaggcgtga ttcatacagc ggccagccat ccgtcatcca taccacgacc tcaaaggccg
     4201 acagcaggcc aagaagacgc tccagcgtgg ccaacgtgcg ttcaccgaat acgtgcgcca
     4261 caaccgtcct ccgtatcctg tcatacgcgt aaaacagcca gcgctgacgt gatttagcac
     4321 cgacgtagcc ccactgttcg tccatttcag cgcagacaat cacatcactg cccggctgta
     4381 tgcgcgaggt taccgactgc ggcctgagtt ttttaagtga cgtaaaatcg tgttgaggcc
     4441 aacgcccata atgcgggcgg ttgcccggca tccaacacca ttcatggcca tatcaatgat
     4501 tttctggtgc gtaccgggtt gagaagcggt gtaagtgaac tgcagttgcc atgttttacg
     4561 gcagtgagag cagagatagc gctgatgtcc ggcagtgctt ttgccgttac gcaccacccc
     4621 gtcagtagct gaacaggagg gacaactgat agaaatagaa gccactggag aacctcaaaa
     4681 acaccatcat acactaaatc agtaagttgg tatcatcacc tcaaagccat taggttcgat
     4741 ttgaatataa acaattttca ttaaactgat atttatcacc aaattccgag ccaaaagatt
     4801 acatcatatt taaatgtaat cttaaataac tcagtgtata attcaattgc acaataagaa
     4861 ttaacagtgt atttttagcc aggaaatatg atttctaaaa cggagattta aaagtgaaaa
     4921 tatattacgc attaaaaaga atagcgtata ttgcaggtgc tttatctatt ggttgcggct
     4981 cactaccaat gattttcagc aaaacacccg ctcttcaata ctgggtgctc ggggcttttt
     5041 taattttcat tgggtattgc gtatcaaagc ttgagttcga taagtctaaa tacatcaagt
     5101 acctaaatga aaagaacgat gggatttata tttattatgc aaaatttggt ggcgaagagc
     5161 acgaaataaa aatcaacaca aaaaacaaaa caatcgaact aaagtcaggg aaaaattccg
     5221 ccacactaaa ctttgataac atcaaatcat ggagatataa cgtatctggc attagcaagg
     5281 ttaatgtcat tggttccact aacagcgtaa tgggtaattt cacagcttta tctcaagcca
     5341 gtgcaatcaa caaccaagca gggtacagcg cgtgggataa taatggattc tttattcaca
     5401 cagatgcatt ggcaaatcct gtctggcata taaagataat accaaaagat gtcgcaataa
     5461 accttaagtc tgacaagttt tggaaaagtg tcgctggcga atgcgaagtc tggatgaacg
     5521 taatgaaccg agccattaat aaatagaagt cttactgttg aggccagcgc ccgtgatacg
     5581 ggcactggca cagcacccaa taccattcac gggcatatca atgattttct ggtgcgcacc
     5641 gggctgagag gcggtgtaag tgaactgtag ttgccatgtt ttacggcaat gagagcagag
     5701 atagcgctga tgtccggcag tgcttttgcc gttacgcacc ac
//
