LOCUS       NZ_AP021958             4380 bp    DNA     circular CON 05-JAN-2024
DEFINITION  Klebsiella quasipneumoniae strain WP3-W18-CRE-02 plasmid
            pWP3-W18-CRE-02_8, complete sequence.
ACCESSION   NZ_AP021958
VERSION     NZ_AP021958.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMD00194404
            Sequence Read Archive: DRR199240
            Assembly: GCF_014170655.1
KEYWORDS    RefSeq.
SOURCE      Klebsiella quasipneumoniae
  ORGANISM  Klebsiella quasipneumoniae
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Klebsiella/Raoultella group; Klebsiella.
REFERENCE   1
  AUTHORS   Sekizuka,T., Itokawa,K., Yatsu,K., Inamine,Y. and Kuroda,M.
  TITLE     complete genome sequences of Klebsiella quasipneumoniae str.
            WP3-W18-CRE-02 isolated from wastewater treatment plant effluent
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 4380)
  AUTHORS   Sekizuka,T., Itokawa,K., Yatsu,K., Inamine,Y. and Kuroda,M.
  TITLE     Direct Submission
  JOURNAL   Submitted (04-DEC-2019) Contact:Tsuyoshi Sekizuka National Institute
            of Infectious Diseases, Pathogen Genomics Center; 1-23-1 Toyama,
            Shinjuku-ku, Tokyo 162-8640, Japan
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method :: flye v2.5; minimap v0.2-r124; racon v1.1.0;
            circlator v1.5.3; Pilon v1.18; SPAdes v3.11.1; A5-miseq v20140604
            Genome Coverage                   :: 300x
            Sequencing Technology             :: Sequel; NextSeq 500
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 01/05/2024 07:15:30
            Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline
            (PGAP)
            Annotation Method :: Best-placed reference protein set; GeneMarkS-2+
            Annotation Software revision      :: 6.6
            Features Annotated                :: Gene; CDS; rRNA; tRNA; ncRNA
            Genes (total)                     :: 6,226
            CDSs (total)                      :: 6,101
            Genes (coding)                    :: 5,865
            CDSs (with protein)               :: 5,865
            Genes (RNA)                       :: 125
            rRNAs                             :: 9, 8, 8 (5S, 16S, 23S)
            complete rRNAs                    :: 9, 8, 8 (5S, 16S, 23S)
            tRNAs                             :: 93
            ncRNAs                            :: 7
            Pseudo Genes (total)              :: 236
            CDSs (without protein)            :: 236
            Pseudo Genes (ambiguous residues) :: 0 of 236
            Pseudo Genes (frameshifted)       :: 76 of 236
            Pseudo Genes (incomplete)         :: 151 of 236
            Pseudo Genes (internal stop)      :: 39 of 236
            Pseudo Genes (multiple problems)  :: 28 of 236
            CRISPR Arrays                     :: 1
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            AP021958.1.
            Annotated by DFAST v.1.2.3 (https://dfast.nig.ac.jp).
            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..4380
                     /organism="Klebsiella quasipneumoniae"
                     /mol_type="genomic DNA"
                     /strain="WP3-W18-CRE-02"
                     /isolation_source="wastewater"
                     /db_xref="taxon:1463165"
                     /plasmid="pWP3-W18-CRE-02_8"
                     /geo_loc_name="Japan:Tokyo"
                     /lat_lon="35.6684 N 139.4278 E"
                     /collection_date="2018-02-13"
     gene            complement(473..874)
                     /locus_tag="H7R86_RS30845"
                     /old_locus_tag="WP3W18C02_P80010"
     CDS             complement(473..874)
                     /locus_tag="H7R86_RS30845"
                     /old_locus_tag="WP3W18C02_P80010"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_009310048.1"
                     /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_086893472.1"
                     /translation="MARVSISEAARLTGKSRTTLHRLIKAGDLSICSGERNAKMVDTSE
                     LLRVFGPFEQPKGEHHSGQVSGQRDTASADQSEQVIRHLKQEIEHLNTLLLSKDSHIDS
                     LKQAMLLLENHQAKLTESPAPWWKFWKKS"
                     /name="helix-turn-helix domain-containing protein"
     gene            complement(874..1074)
                     /locus_tag="H7R86_RS30850"
     CDS             complement(874..1074)
                     /locus_tag="H7R86_RS30850"
                     /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_225368679.1"
                     /translation="MFRCSRNPKTALNMAKFIQNQSLLLLEKLNELDLDVEADLCEKLH
                     DDAEHLFRTLTSRLDALQDGN"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            2142..2384
                     /locus_tag="H7R86_RS30855"
     CDS             2142..2384
                     /locus_tag="H7R86_RS30855"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_012575772.1"
                     /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 transcriptional regulator"
                     /protein_id="WP_086893475.1"
                     /translation="MQPFDDDFSNIKTVLSENIKRYRNKNNLSQEDLAELSGLHRTYIG
                     SVERKERNVTLSTLIFIASALKTSVPDLLRKKEDE"
                     /name="helix-turn-helix transcriptional regulator"
     gene            2377..3117
                     /locus_tag="H7R86_RS30860"
                     /old_locus_tag="WP3W18C02_P80020"
     CDS             2377..3117
                     /locus_tag="H7R86_RS30860"
                     /old_locus_tag="WP3W18C02_P80020"
                     /inference="COORDINATES: protein motif:HMM:NF036585.4"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_086893474.1"
                     /translation="MSREHELLKLWRQLNETQQDNFLKWMKAYEIEKIYVNHNKGYFNQ
                     KFIDNFGDRLITHYFNSNRPLTKTLFEHAFNDSLNESGMQSQLAESRTNPGYDITIQNI
                     KASLKTEAARNISQKNIHVSKWMELGKGKWVLEELLARFLAHLNNYDKIFTLRYIKPTY
                     LTFKYQLIEIPKTLLLESKNAHLVVMENSTQDPKPGYGYVFDQNGEKKFSLYFDGGSER
                     KLQIKHLNVSLCIIHAEWCYTLPS"
                     /name="hypothetical protein"
     gene            complement(3106..3954)
                     /locus_tag="H7R86_RS30865"
                     /old_locus_tag="WP3W18C02_P80030"
     CDS             complement(3106..3954)
                     /locus_tag="H7R86_RS30865"
                     /old_locus_tag="WP3W18C02_P80030"
                     /EC_number="2.1.1.-"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_011346608.1"
                     /GO_function="GO:0003677 - DNA binding [Evidence IEA];
                     GO:0008170 - N-methyltransferase activity [Evidence IEA]"
                     /GO_process="GO:0006306 - DNA methylation [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_225368678.1"
                     /translation="MFGEDLNFSKANNNCEIVIGDSREVIKTLGDKVFDCIVTSPPYWG
                     LRDYGVGNQIGAEINIDDYIFDLVSLFKEAKRTLKDDGTLWVNIGDSYTSGGRTWRDKD
                     DKNKGRAMSYRPPTPEGLKPKDLIGVPWKLAFALQQDGWYLRSDIIWNKPNCQPESVKD
                     RPTRSHEYIFLFSKNKKYHYDSDAIKEPSMDKKQGKKNRRTVWNINTEPYPGSHFAVYP
                     REMARLCVLAGSRPGGLVLDPFFGSGTTGVVCNSLGRKCVGIELNEDYAKLAKERILSG
                     R"
                     /name="site-specific DNA-methyltransferase"
     Typing          1444..1851
                     /name="ColRNAI_rep_cluster_1987"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="95.355"
                     /coverage="99.0"
                     /evalue="0.0"
ORIGIN
        1 ggcgcagccg gaaaaccggt tttcagcacg ttcaggaatc gggttcgtcg acggccggca
       61 atcacgttat ggcaagtcgc cggacgactc accacacgat tcaccggcga ttcgaatcgt
      121 gaattgaatc aagagtcacc atgaacaaaa aacgcccaaa ttgatgaatt gaatcaagag
      181 tcgattcatc ataacaacat gataataaag cgtgattcac atatgaatcg tgggcaattc
      241 gtaaacgatt cgccatagag tcgtccacga cttggatctg cactttgtaa cacatcactg
      301 cacattaatt tttcattaac caattgtttt aaataaggaa tatgcaaaat tttaattttg
      361 cgtagtgtgt gggtattttt agtcgtgagg agcgttcaga gatctgacga tttttgggaa
      421 ggttcaggaa ctccccggga tggccggaga ggaaaactga agcatgacgg ggtcaggatt
      481 ttttccagaa tttccaccat ggcgccgggg attccgttaa ttttgcctgg tgattttcaa
      541 gaaggagcat ggcctgtttc aggctgtcaa tgtgcgaatc cttggacaaa agtaaggtgt
      601 tcaggtgttc aatctcctgt ttcagatgac gaatcacctg ttcactctgg tcagcagagg
      661 ctgtatcacg ctgtccagag acctgtccag aatggtgttc acccttcggt tgctcaaagg
      721 gaccaaagac acgtaaaagc tctgaagtat ctaccatttt tgcattacgc tcaccgctac
      781 agatggacag gtcacctgct ttaattaacc tgtgcagtgt tgttctactc ttacccgtca
      841 gtcgggcagc ctcactaata gacactctgg ccatcagtta ccatcctgta atgcatccag
      901 tctcgaggtc agtgtacgga aaagatgctc tgcatcatcg tggagtttct cacaaaggtc
      961 ggcctcgaca tcgagatcaa gctcgttaag cttctccagc aggagcagag actgattctg
     1021 gatgaattta gccatgttca gcgctgtttt ggggtttcgg gagcaacgga acagtaaacg
     1081 cccttaagcg gttattttaa atggccaaaa atcaaccggc caatttacat cgtgaattta
     1141 ctcttttggc tatctcgttt gcggtagcca aattggctct actcatcttg gccgtttgca
     1201 gagcaactta cgcagttgaa ctcaagagat tgatttacct gttattgacc attcaattga
     1261 accgcttaac tgtcttttgg gttccactac tccccaaacc ccgttttctg ttgtttcgtc
     1321 ataagaggcc tcagagcgtc agtgctcagt gtggggatgt tctcttttcc gcttcctcgc
     1381 tcactcagtc gctacgctcc tgccgttcgg ctgcggcgag cggcaggagc atgcgtataa
     1441 aagctcggga aagccgagca atcgcgtgat ggggaaaagg aaaggccgca ccgcggcggt
     1501 ttttccatag gctccgcccc cctgacaagc atcacagaat ttgacgctca aatcagtggt
     1561 ggcgaaaccc gacaggactt taaagatacc aggcgtttcc ccctgatggc tccctcgtgc
     1621 gctctcctgt tcctgccttt cggtttaccg gtgtcattcc gctgttatgg ccgcgtttat
     1681 ctcattccac gcctgacact cagttccggg aaggcagttc gctccaagct ggactgtatg
     1741 cacgaacccc ccgttcagtc cgactgctgc gccttatccg gtaactatca tcttgagtcc
     1801 aacccggtaa gacatgcaaa agcgccactg gcagcagcca ctggtaactg attagaggag
     1861 ttgagtcttg aacttatgta cctgttaagg ctacactgag agaacgagat ttggtgactg
     1921 tgctcctcta ctagccagtt acctcggatc agtcagttcc ccaacttact gatccctcga
     1981 aaaaaccgcc tcaccaggcg gttttttcgt tttaaaacaa gcagaacata cctcattttc
     2041 ttttcatcct caagctcgtt aaagaacaaa agctacttat agtctgtcga ctcataatca
     2101 tcatgcattt ataaattaat ttatttacag gcaaataaga aatgcaaccc tttgatgatg
     2161 atttttcaaa tataaaaaca gtactttctg aaaatatcaa aagatataga aataaaaata
     2221 atttatcaca agaagattta gcggagcttt ctggactcca ccgtacatat attggttcag
     2281 ttgaaagaaa ggaaagaaat gtaaccctca gcactttaat ttttattgct agcgcgctta
     2341 aaacatcggt accggattta ttaaggaaaa aagaagatga gtagagagca tgaattactt
     2401 aagctatgga gacagctaaa tgaaacgcag caagataatt tcttaaaatg gatgaaagcg
     2461 tatgaaatcg aaaaaatata tgttaaccac aataaaggtt atttcaatca aaaatttatt
     2521 gataattttg gcgacaggct aataactcat tatttcaaca gcaacagacc attaaccaag
     2581 acattattcg agcatgcttt caatgattct ttaaacgaat ctgggatgca atctcaacta
     2641 gctgaaagtc gaactaatcc ggggtacgat ataacgatac aaaacattaa agctagttta
     2701 aaaacagagg cagccaggaa tataagtcaa aaaaacattc atgtaagcaa atggatggaa
     2761 cttggtaaag gaaagtgggt tttagaagaa ttactagcga gattcttagc gcatttaaat
     2821 aactacgata aaatattcac actccggtat attaaaccaa cctatcttac atttaaatat
     2881 cagcttattg agataccaaa aacactactt ttggagtcaa aaaatgcaca tctagttgta
     2941 atggaaaata gtactcaaga cccaaaacca ggatatggtt acgtttttga tcaaaatggt
     3001 gaaaaaaagt tttctctcta ctttgatggg ggctcagaga gaaaacttca aataaaacat
     3061 ctaaatgtaa gtttgtgcat aattcacgct gaatggtgtt acacactacc ttcctgatag
     3121 gatacgctct ttggcaagct tagcgtaatc ttcatttagc tcaatcccaa cgcattttct
     3181 acccaaggaa ttacacacaa cacctgtagt accagaacca aagaaaggat caagaaccaa
     3241 acctccaggt cttgatccag ctaaaacaca taaccttgcc atttctcttg gataaactgc
     3301 aaaatgacta cctgggtaag gctctgtatt tatattccaa actgtcctcc gatttttttt
     3361 tccttgtttt ttgtccatgg atggttcttt tatggcatcg gaatcataat ggtatttttt
     3421 gtttttagaa aagagaaata tatactcatg agaccttgta ggcctatctt ttacactttc
     3481 aggctggcaa tttggtttat tccatataat atcagatcgt aggtaccatc catcttgctg
     3541 taaagcaaat gcaagcttcc aaggaacgcc aattaaatcc ttcggcttta gcccttcagg
     3601 tgtaggaggc ctatatgaca tagccctacc tttattttta tcatccttat ctctccaggt
     3661 tcttcctcca gatgtataac tatcaccaat gttaacccaa agagtaccat cgtcttttaa
     3721 tgttcttttt gcttctttaa aaagagagac aagatcaaat atataatcat caatatttat
     3781 ctcagcacct atttgatttc caacaccata atctcgcaag ccccagtatg gaggtgaagt
     3841 tacgatgcaa tcaaacacct tatcacctag tgtttttatt acttctcttg aatcaccaat
     3901 aactatttcg caattattat tagctttaga aaagtttaaa tcttctccaa acaaatctaa
     3961 ctctgtgcag tttttgtaca tatacacact atttatttaa tgactgatgc tacttatagt
     4021 attcaaaaaa acataaaaag acaacaagct gacttaagca acgtatctat tcatcaagag
     4081 catcagaaca gtagtagcaa cctcatactt tgacttattt accataacat ccgttatcag
     4141 caccgcctga gaggccctca gggcgtttct gacgggaaac cggtaaaaca ggcaacaaac
     4201 cacccgaaaa cccgccagaa acgcgcaggc tctgttttta cggcatgcat gagtatgcgc
     4261 gcaagtgcat agcgcggaaa ttcacgccat tcagccaggg taagtcctgt ttccggcgtt
     4321 cttctgatcc gaaaacggtg aacggggacg caatttattg cgtggccgtg aggcgttgcc
//
