LOCUS       NZ_CP151197             5665 bp    DNA     circular CON 17-APR-2024
DEFINITION  Klebsiella variicola strain KVTMDU plasmid p10KVTMDU, complete
            sequence.
ACCESSION   NZ_CP151197
VERSION     NZ_CP151197.1
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 5665)
  AUTHORS   Ota,Y.
  TITLE     Emergence of KPC-2-producing Klebsiella variicola from hospital
            sewage
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 5665)
  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
            CP151197.1.
            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..5665
                     /organism="Klebsiella variicola"
                     /mol_type="genomic DNA"
                     /strain="KVTMDU"
                     /isolation_source="sewage"
                     /db_xref="taxon:244366"
                     /plasmid="p10KVTMDU"
                     /geo_loc_name="Japan"
                     /lat_lon="35.7014 N 139.7642 E"
                     /collection_date="2021-06"
                     /collected_by="Tokyo Medical and Dental Hospital"
     gene            84..425
                     /locus_tag="LQ252_RS30490"
                     /old_locus_tag="LQ252_30495"
     CDS             84..425
                     /locus_tag="LQ252_RS30490"
                     /old_locus_tag="LQ252_30495"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_006122514.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MobC family plasmid mobilization relaxosome
                     protein"
                     /protein_id="WP_071599364.1"
                     /translation="MADKRNKMLTMWVTEDEHRRLLERCDGKQLAAWMRQTCLDEKPTR
                     AGRLPSISPALLRQLAGMGNNLNQIARKVNAGGAGHDRVQIVAALMAIDAGLERLRHAV
                     LEKGPDDDC"
                     /name="MobC family plasmid mobilization relaxosome protein"
     gene            634..>1062
                     /locus_tag="LQ252_RS30495"
                     /old_locus_tag="LQ252_30500"
                     /pseudo=""
     CDS             634..>1062
                     /locus_tag="LQ252_RS30495"
                     /old_locus_tag="LQ252_30500"
                     /inference="COORDINATES: protein motif:HMM:NF015397.4"
                     /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="relaxase/mobilization nuclease domain-containing
                     protein"
                     /name="relaxase/mobilization nuclease domain-containing
                     protein"
     gene            1103..1600
                     /locus_tag="LQ252_RS30500"
                     /old_locus_tag="LQ252_30505"
     CDS             1103..1600
                     /locus_tag="LQ252_RS30500"
                     /old_locus_tag="LQ252_30505"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_020325392.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MbeB family mobilization protein"
                     /protein_id="WP_015328238.1"
                     /translation="MSSLLTASRDFEEKSKAQQQLTEERLKAAFSKHENVVKSELNASA
                     KRINDAISAHEQGMNAAMQSNRLSVLRMVGRTWLTITMVSGLLFASLSGVLWYQGNRIA
                     ANLAEIRQQRDTLSKLHMQTWGVTYLENRNGRFLVLPEGMKAETGRTVDNKTRNAVKLV
                     RE"
                     /name="MbeB family mobilization protein"
     gene            1607..1822
                     /locus_tag="LQ252_RS30505"
                     /old_locus_tag="LQ252_30510"
     CDS             1607..1822
                     /locus_tag="LQ252_RS30505"
                     /old_locus_tag="LQ252_30510"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_015328239.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MbeD family mobilization/exclusion protein"
                     /protein_id="WP_015328239.1"
                     /translation="MTELEKQLLSALEQLQQDYSRRLDEWESAFEEWRKMSGLMQRENA
                     ALSERVSGLSRQVQSLSEQLRRLSTG"
                     /name="MbeD family mobilization/exclusion protein"
     gene            2328..2699
                     /locus_tag="LQ252_RS30510"
                     /old_locus_tag="LQ252_30515"
     CDS             2328..2699
                     /locus_tag="LQ252_RS30510"
                     /old_locus_tag="LQ252_30515"
                     /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_021314598.1"
                     /translation="MSKKNDLNLSESTLESLREYVDDFGMTVDDVVLKLINENKSLKES
                     LGQDFVLSGEKEAHHFKDYVIHKLPKGKILVTHNGLKASNMKKILIEAGRELGMDENEL
                     NPDFTTYEIGRFLFKHLHA"
                     /name="hypothetical protein"
     gene            complement(3109..3867)
                     /locus_tag="LQ252_RS30515"
                     /old_locus_tag="LQ252_30520"
     CDS             complement(3109..3867)
                     /locus_tag="LQ252_RS30515"
                     /old_locus_tag="LQ252_30520"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_013558434.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="PmeII family type II restriction endonuclease"
                     /protein_id="WP_065782962.1"
                     /translation="MIESRIISDFIESCIDEEFHQKKQEKIRAIKLSDITKRKNPYLFK
                     AKGLTSASDLIKSIMDATVSSGEETVFGNFMEKIAIFTCSQAFGGRKSSAVGIDLEFET
                     ESTKYLISIKSGPNWGNSSQKKKMQDNFIKAKKVLGTSGGINSKSITCIEGCCYGYDAR
                     PEKGTHIKLCGQDFWTFISNGNNELYSDIIEPIGKLADEKNKELIELTNAKLNLFTAEF
                     ISEYCNSDGSINWALFVARNSGSKSDYHSN"
                     /name="PmeII family type II restriction endonuclease"
     gene            complement(3860..4654)
                     /locus_tag="LQ252_RS30520"
                     /old_locus_tag="LQ252_30525"
     CDS             complement(3860..4654)
                     /locus_tag="LQ252_RS30520"
                     /old_locus_tag="LQ252_30525"
                     /EC_number="2.1.1.-"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_015164793.1"
                     /GO_function="GO:0003677 - DNA binding [Evidence IEA];
                     GO:0008170 - N-methyltransferase activity [Evidence IEA]"
                     /GO_process="GO:0009307 - DNA restriction-modification
                     system [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="site-specific DNA-methyltransferase"
                     /protein_id="WP_227818858.1"
                     /translation="MLQSDSIDLIVTSPPYADQRKKTYGGVSADKYVEWFTPIAKELLR
                     VTKSSGSFVLNIKERAINGERHTYVIELILMMRKLGWLWTEEYIWHKKNSYPGKWPNRF
                     RDSWERCIHFTKSKKFNMYQEEVMVPMGDWKNSRLKNMSDTDKKRDESKVGSGFGKKIE
                     NWVTRDLAYPTNVLHMATECGNRSHSAAFPESLPEWFIKLFTTEGDTVLDPFSGSGTTL
                     KVAKAMKRNAVGIEILDEYCEITANRVGLKKSSQKKYRYTND"
                     /name="site-specific DNA-methyltransferase"
     gene            complement(5006..5134)
                     /locus_tag="LQ252_RS30525"
                     /old_locus_tag="LQ252_30530"
     CDS             complement(5006..5134)
                     /locus_tag="LQ252_RS30525"
                     /old_locus_tag="LQ252_30530"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001505258.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="replication initiation protein"
                     /protein_id="WP_074440740.1"
                     /translation="MHEPPVQSDRCALSGNYRLESNPERHDKTPLAAANSKRVYKR"
                     /name="replication initiation protein"
     Typing          5489..5664
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="81.667"
                     /coverage="100.0"
                     /evalue="2.75e-31"
     Typing          complement(5033..5537)
                     /name="ColRNAI_rep_cluster_1987"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="90.551"
                     /coverage="97.0"
                     /evalue="0.0"
     Typing          416..1938
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 cactgacgcg cctgcggctt gtccaacccc gcgccgaccg ggaaaggctt tcccgtccgt
       61 cacggcgtta tcaggaggcg attctggcag ataaacgcaa caagatgctc acgatgtggg
      121 tgacggaaga cgaacaccgg cggttgcttg agcggtgcga cggaaaacaa ctggcggcgt
      181 ggatgcgcca gacctgcctt gatgagaaac cgacacgcgc cggcaggctt ccctcgattt
      241 cgcccgcgct gctgcgtcag cttgccggca tgggcaataa cctgaaccag atcgcccgga
      301 aagtgaacgc cggtggtgcc ggtcatgacc gggtgcagat cgtggcagcg ctgatggcga
      361 tcgatgccgg tctggaacgg ttgcggcatg ccgtactgga aaaagggccg gacgatgatt
      421 gttaaattcc atccccgggg tcgcggcggg ggcgccggtc ctgtggatta tcttctgggt
      481 aaagaccggc agcgtgaagg tgccagcgtc ctgcagggga agccggaaga agtccgggag
      541 ctgattgatg cgtcgccgta tgtgaaaaaa tatacctccg gggtgctgtc attcgcggag
      601 gcggacctgc cgccgggtca gcgtgaaaaa ctgatggcca gctttgagcg ggttctgatg
      661 cccggactcg ataaagacca gtacagcatt ctgtgggtgg aacacgcaga caagggtcgt
      721 cttgagctga attttctgat ccccaatacc gaattactga cggggaaacg cctccagccg
      781 tattacgatc gtgccgaccg gccgcgcatc gatgcgtggc agacagtggt caacggcagg
      841 ctggggctac atgatccgaa cgacccggag aaccggcggg cgctggtcac gccttcagga
      901 ctgccagaaa cgaagcagga agccgcagag acgattacac ggggtttgct gatgttagcc
      961 tcatcaggag agctgaaaac gcgtgatgac gtcacagggg cgctcacagc ggccggtttt
     1021 gaggtggtca gaaccacaaa aaacagtatc agcattgccg acccggacgg ggggcgaaat
     1081 atccgactga ggggagccat ttatgagcag tcttttaacg gcctcgaggg acttcgagga
     1141 gaaatcgaaa gcacagcagc agcttaccga agagaggctg aaagccgcat tcagcaagca
     1201 cgagaacgtt gtcaaatcgg aactgaacgc aagcgcgaag agaatcaacg acgccatcag
     1261 cgcccacgaa caggggatga acgcggcgat gcagtcgaac cggctgagcg tgctgcgaat
     1321 ggtcgggcgg acgtggctga ccatcaccat ggtgtcaggg ctgctgttcg ccagcctgag
     1381 cggggtgctg tggtaccagg ggaaccggat agcggcgaac ctggcggaaa tcaggcagca
     1441 gagagatacg ctgtcgaaac tgcacatgca gacgtggggc gtgacctatc tggagaaccg
     1501 caacggacgg tttctggtgc tgccggaggg gatgaaagcc gaaacgggcc ggacggtgga
     1561 caacaagacg cggaacgcgg tgaagctggt acgggagtag agcagaatga cggaactgga
     1621 aaaacaattg ctgagcgcgt tagagcagct acagcaggac tactcgagaa ggctggacga
     1681 gtgggagagc gccttcgagg aatggcggaa gatgtctggt cttatgcaac gggagaacgc
     1741 ggcgctgagc gagcgcgtgt cgggcttgag caggcaggtg cagagtttga gcgagcagct
     1801 gcgccggtta tcgacaggct gaatgagatt gagcaacagc gatacgggca aacaacggaa
     1861 aaggaaccag agaagacagc agatctggta ccggaacggc aacgcacatt atctcatggt
     1921 gacagggagt atggagactg ataaacgccc gtctcaggtg gcctgagcgt gacggggatc
     1981 atggccattt tctgcgattt cagcacacag agagtctttt ttaaccgaaa tcaccggcta
     2041 tgcagtgatg tgaataagtg atgcatatgc gtaaaataaa tcaggtgcgt ttctggtggt
     2101 tttcggtgta cttgccacca ccttttgccc gtcagccatc agaaacgccc tgagtgcctc
     2161 cggcgcggtg cgggtaagag atgttatggt aaatccagcg gtgtagctgt tctttttgaa
     2221 ccagcgatca gtgacttcta tgttatttgt tcaatactaa aaagcggtgt actataccac
     2281 ttatgttgtg ttttttcttt tctgacaact agcatggtgg tgattacatg agtaaaaaaa
     2341 acgatttaaa ccttagtgaa tcaacgttag aaagcctcag ggagtatgtc gatgacttcg
     2401 gtatgactgt tgatgatgtt gttctgaagt taattaatga gaataagtca ttgaaggaat
     2461 cacttggaca agactttgtg ttatctggcg aaaaggaagc gcaccacttt aaagattatg
     2521 tgattcataa actgcccaaa ggaaaaattc tggttaccca taatgggctt aaggccagca
     2581 acatgaagaa gatattgatt gaggcgggga gggagctagg catggatgaa aatgaactca
     2641 atccagattt cacaacctat gagatagggc gttttttgtt taagcaccta catgcgtaac
     2701 aatcctgcag gcctgaaggg caggcatcga acttcgctgc ccggatgtta tggtaaatat
     2761 gagtatttaa tctgatgcaa aaaaaaccgc ctaaaaggcg gctttttgct aaggtgtgtt
     2821 ggttattggt gtcagtcttt gtgcgacagc cccaccatta gcactcacat gtgtgactat
     2881 gttgttgtcg gttcgagtgt gtagctgtac gaagatatca aagcctgaac ttgcatgaac
     2941 atcacagatg taggcttcag tattgggtgc ccagattgca ctggtatcct ctctacggag
     3001 tcttacacca aagttgttag atgcatgatt ctggcaacca tttactatgc atgctggcat
     3061 ggagtgtcct tgtttttgtt gaggcatttc cccatttata ctcttctgtt agttgctatg
     3121 atagtctgat tttgaacctg agtttcttgc tacaaataaa gcccaattta ttgaaccatc
     3181 actattacaa tattctgaaa taaactcagc cgtaaaaaga tttagtttgg catttgttag
     3241 ttctatcagt tccttgtttt tttcgtctgc aagcttacca ataggctcaa ttatatcact
     3301 atataattcg ttgtttccgt tagatataaa tgtccagaag tcttggccgc atagttttat
     3361 gtgggttccc ttttcaggtc tggcgtcata accataacaa cacccctcga tgcaagttat
     3421 tgattttgaa ttaattccac cggatgtgcc taggactttt ttggctttaa tgaagttgtc
     3481 ttgcattttc tttttttgtg atgagttacc ccagtttggg ccggatttga tgcttattag
     3541 atattttgtg ctttcagttt cgaactcaag atctattcct accgcactgg attttcttcc
     3601 accaaatgct tgggaacatg tgaagattgc aatcttttcc atgaaattgc caaaaacggt
     3661 ctcctctcca gaggataccg ttgcatccat tattgacttt attaagtcac ttgctgatgt
     3721 tagccccttc gccttaaata aatatgggtt ttttcttttt gttatatctg ataattttat
     3781 cgcccttatt ttttcttgtt ttttttgatg gaactcttca tcaatgcaag attctataaa
     3841 atctgaaata atccgtgatt caatcatttg tataccggta ttttttttga gacgattttt
     3901 tcaaacctac tctatttgcc gttatctcgc aatattcatc taatatttca atacctacag
     3961 cgttcctttt cattgctttc gcaactttta atgtggttcc agaaccggaa aatggatcca
     4021 gaacggtgtc accttctgtg gtgaaaagtt tgatgaacca ttcaggtagg ctttcaggaa
     4081 aagctgcgct gtgactgcgg tttccacact ctgtagccat gtgtagcacg ttggttgggt
     4141 atgctagatc cctggtgacc cagttttcta tttttttacc gaaaccactc cctactttcg
     4201 attcatctct tttcttatct gtatcactca tgtttttaag tcgtgagttt ttccaatccc
     4261 ccataggcac cattacttcc tcttggtaca tgttgaattt tttacttttc gtaaagtgga
     4321 tgcatctttc ccaagagtct ctaaagcgat ttggccattt cccagggtaa ctattttttt
     4381 tatgccatat gtattcctct gtccataacc agcctaattt tcgcatcatt aaaattagct
     4441 ctattacata cgtatggcgc tcgccattaa tcgccctttc ctttatgttt agaacaaatg
     4501 agcctgatga ttttgtcact ctcagtagtt ctttggctat cggggtgaac cactcaacat
     4561 atttgtctgc acttactccg ccataggttt ttttcctttg gtctgcgtaa ggtggtgatg
     4621 taacgatcag atctattgaa tcgctttgaa gcatctttaa agcgattaaa caatcatcat
     4681 tgattagttc tatcgtctgt tttttttctt taacttcttg tttcattagc atttcttttg
     4741 tcgcattctg tgttcattat caggatatta cctccttttg ttttggaggt ccagtcttgc
     4801 tgatggttgt tgacctaagt ataagatgcg acgtaatatc ctcgtctgaa acgaaaaaac
     4861 cgcctgggga ggcggttttt tcgagggttc agtaagttgg ggaacttctg aaccgtggta
     4921 acagggtgta caagaccgct gaaaccaaat tctgtccttt cagtttagcc gtagttgggc
     4981 tgagacttca agaactctgc atcagttatc tcttgtacac cctcttactg ttggctgctg
     5041 ccagtggcgt tttgtcgtgt ctttccgggt tggactcaag acgatagtta ccggataagg
     5101 cgcagcggtc ggactgaacg gggggttcgt gcatacagtc cagcttggag cgaactgcct
     5161 acccggaact gagtgtcagg cgtggaatga gaaaccgcgg ccataacagc ggaatgacac
     5221 cggtaaaccg aaaggcagga acaggagagc gcacgaggga gccatcaggg ggaaacgcct
     5281 ggtatcttta tagtcctgtc gggtttcgcc accactgatt tgagcgtcag attctgtgat
     5341 gctcgtcagg ggggcggagc ctatggaaaa acggcaacgc cgcatccttt tcgtgccctt
     5401 ttctgactct agctccatct ctttatctcg tcactcgtga gcaggtaacg cccgccgcag
     5461 cctcacggca ggagcgtcag cgaccgagtg agcgaggagg cgtcatatcc ccggcactac
     5521 cattatctgc cttacgcacc ttcgctgcat gtcatccctg ccatatatag cactttcgct
     5581 gatacccata ccgatgccac catagtaagc cagtatacac tccgctagcg ctacgtgact
     5641 ggttcagggc tgcgccccga aaccc
//
