LOCUS       NZ_AP022011             4937 bp    DNA     circular CON 28-NOV-2023
DEFINITION  Klebsiella quasipneumoniae strain WP3-S18-CRE-02 plasmid
            pWP3-S18-CRE-02_7, complete sequence.
ACCESSION   NZ_AP022011
VERSION     NZ_AP022011.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMD00194418
            Sequence Read Archive: DRR199254
            Assembly: GCF_014168875.1
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-S18-CRE-02 isolated from wastewater treatment plant effluent
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 4937)
  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                   :: 347x
            Sequencing Technology             :: Sequel; NextSeq 500
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 11/28/2023 08:52:43
            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)                     :: 5,876
            CDSs (total)                      :: 5,753
            Genes (coding)                    :: 5,554
            CDSs (with protein)               :: 5,554
            Genes (RNA)                       :: 123
            rRNAs                             :: 9, 8, 8 (5S, 16S, 23S)
            complete rRNAs                    :: 9, 8, 8 (5S, 16S, 23S)
            tRNAs                             :: 89
            ncRNAs                            :: 9
            Pseudo Genes (total)              :: 199
            CDSs (without protein)            :: 199
            Pseudo Genes (ambiguous residues) :: 0 of 199
            Pseudo Genes (frameshifted)       :: 71 of 199
            Pseudo Genes (incomplete)         :: 121 of 199
            Pseudo Genes (internal stop)      :: 37 of 199
            Pseudo Genes (multiple problems)  :: 26 of 199
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            AP022011.1.
            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..4937
                     /organism="Klebsiella quasipneumoniae"
                     /mol_type="genomic DNA"
                     /strain="WP3-S18-CRE-02"
                     /isolation_source="wastewater"
                     /db_xref="taxon:1463165"
                     /plasmid="pWP3-S18-CRE-02_7"
                     /geo_loc_name="Japan:Tokyo"
                     /lat_lon="35.6684 N 139.4278 E"
                     /collection_date="2018-08-06"
     gene            101..502
                     /locus_tag="H7R71_RS29185"
                     /old_locus_tag="WP3S18C02_P60010"
     CDS             101..502
                     /locus_tag="H7R71_RS29185"
                     /old_locus_tag="WP3S18C02_P60010"
                     /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_064181835.1"
                     /translation="MTRVSISEAARLTGKSRTTLHRLIKTGELSTCSGERNAKMVDISE
                     LLRVFGPFDQPKSEHLTRQVPEQCDTAPADQSEHIIRQLKQQIEHLNILILSKDSHIDS
                     LKQAMLLLENHQAKLTESPAPWWKFWKKS"
                     /name="helix-turn-helix domain-containing protein"
     gene            complement(1303..1464)
                     /locus_tag="H7R71_RS29190"
     CDS             complement(1303..1464)
                     /locus_tag="H7R71_RS29190"
                     /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_162870772.1"
                     /translation="MAKHWSGQECPKTGTYGQYHDTDNSYAGSEYDRHVSKGDKFPPSK
                     NNHHFQEK"
                     /name="hypothetical protein"
     gene            1701..1946
                     /locus_tag="H7R71_RS29195"
                     /old_locus_tag="WP3S18C02_P60020"
     CDS             1701..1946
                     /locus_tag="H7R71_RS29195"
                     /old_locus_tag="WP3S18C02_P60020"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_012848468.1"
                     /GO_component="GO:0110001 - toxin-antitoxin complex
                     [Evidence IEA]"
                     /GO_function="GO:0003677 - DNA binding [Evidence IEA];
                     GO:0097351 - toxin sequestering activity [Evidence IEA]"
                     /GO_process="GO:0045927 - positive regulation of growth
                     [Evidence IEA]; 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="type II toxin-antitoxin system Phd/YefM family
                     antitoxin"
                     /protein_id="WP_025987695.1"
                     /translation="MHAINFTDARKHFAETMKRVTDDAEPVRVMRRDAPDIVMIDAGEY
                     EALIETVYLFSNPANAEHINESMKQAERGEFVEVEY"
                     /name="type II toxin-antitoxin system Phd/YefM family
                     antitoxin"
     gene            1927..2202
                     /locus_tag="H7R71_RS29200"
                     /old_locus_tag="WP3S18C02_P60030"
     CDS             1927..2202
                     /locus_tag="H7R71_RS29200"
                     /old_locus_tag="WP3S18C02_P60030"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_017412855.1"
                     /GO_process="GO:0008219 - cell death [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="Txe/YoeB family addiction module toxin"
                     /protein_id="WP_019725129.1"
                     /translation="MSKWNIKFTRNGADDLNYWRDTDKKKFERIRQLLLSIEADPLTGI
                     GKPERLRHHKDPALYSRRIDQSHRLVYSIQNGEIIIYAARYHYGDK"
                     /name="Txe/YoeB family addiction module toxin"
     gene            2450..3352
                     /locus_tag="H7R71_RS29205"
                     /old_locus_tag="WP3S18C02_P60040"
     CDS             2450..3352
                     /locus_tag="H7R71_RS29205"
                     /old_locus_tag="WP3S18C02_P60040"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_004088970.1"
                     /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_064181838.1"
                     /translation="MHNAALELFNERLPHKPYFSDDLHFGVRIAGKERAILAKYIQFNQ
                     PHAMFWLGFDVDRAGSAIDWSDRNAPAPTLTITNPENGHAHLLYALENSIRTAPDGKIK
                     PLRYAASVENALRKKLEADAGYSGLICKNPNHNHWKIAVWQPKLYTLDWLADFLDLNTG
                     NDKEIVADYGLGRNCTLFDKTRKWAYRAIRQGWPEYEQWLQACYERACAYNLQFARPLD
                     ENEVRGIAKSIAKWTSNKFSPEEFSKFVDITHSSEIQSKRGKKSGQSRRKGSLEEIKPW
                     VAMGISRRKYFYIKKKKVE"
                     /name="replication initiation protein"
     gene            3354..4061
                     /locus_tag="H7R71_RS29210"
                     /old_locus_tag="WP3S18C02_P60050"
     CDS             3354..4061
                     /locus_tag="H7R71_RS29210"
                     /old_locus_tag="WP3S18C02_P60050"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001258875.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_064181837.1"
                     /translation="MKTFVTLWTIAFLSFIAVMCTVDISNYIPSVYTVFSKNRPLVTGA
                     LSILLISVFIWLMVSLYLLKKYSVKVEKLSLGGVNILFNESATLYKKSVKNHLDSKRAI
                     FKLRKNVDAFDEVISSYYQTYQFIRDEMKILNPKKDREIYDFSNEMLMVLNRFLTNYQN
                     NYKRWYKYISDKDEVVDRVSGDVMRFHATSINKIQMQYYDYERILKGFKDVNRFFVNDV
                     KPKFGINTDKWNW"
                     /name="hypothetical protein"
     gene            complement(4098..4712)
                     /locus_tag="H7R71_RS29215"
                     /old_locus_tag="WP3S18C02_P60060"
     CDS             complement(4098..4712)
                     /locus_tag="H7R71_RS29215"
                     /old_locus_tag="WP3S18C02_P60060"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_019725132.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="TIR domain-containing protein"
                     /protein_id="WP_064181836.1"
                     /translation="MGKHKVFISYHHANDQYYKNALEKMNEQHEIFVNRSVSLGDIDED
                     EAPQKIREIIRDKYLRDTSVLILLVGTETKNRKHVDWELYSSMRDSTINKKSGILVVNL
                     PSTNTTYIRSTHGTNEKSEVHPTVTEWISIDKRSTYEERFPYMPARIIDNFMKSGSYIS
                     VVNWNQIENNPETLRKLIDMTYNDREKATYDMSREMRMHNS"
                     /name="TIR domain-containing protein"
ORIGIN
        1 ttcatcgcct ttccgaaaaa cacatcactt ctgggccgat atgtcgtaag ctgctggccc
       61 ctgtttcctt gagactgaat gcattaaagg atgataactg atgaccagag tgtctattag
      121 tgaggctgca cggctgacgg gtaagagccg gacaacgctg cacaggttaa tcaaaacagg
      181 tgaactgtcc acttgtagcg gtgaacgaaa tgcaaaaatg gtcgatattt ccgagctttt
      241 gcgtgttttc ggaccgtttg accaaccgaa gagtgaacac cttactcgac aagtacctga
      301 acagtgtgat acagcgcctg ctgaccagag tgaacatatc attcgtcaac tgaaacagca
      361 gattgaacac cttaacatat tgattttatc taaggattcg cacattgata gcttgaaaca
      421 ggccatgctc cttcttgaaa atcaccaggc aaaattaact gaatccccgg cgccgtggtg
      481 gaaattctgg aagaaatcct gaccccgtca tgcttcagtt ttcctctccg gccatcccgg
      541 ggagttcctg aaccttccca aaaatcgtca catctctgaa cgctcctcac cactaaaaat
      601 acccacacac tacgcaaaat taaaattttg cagatttgta tttaatatca atggtttact
      661 ttcctgaaat ttcgtttttt aaattttatt tatatagatc cgactctatg atgactcgtc
      721 atagagtccc cggcgagtcg tcatagagtc ggtaacgact caggactata aaaacaataa
      781 gttaataacg acccgactct agacacgact ccccgtttgg ttgtttttta gacgaggcga
      841 ctctgggtac gactctagtg aagagtcgcc ggtgaatcgt gtggtgagtc gtccggcgac
      901 ttgccatcac gtcattaccg gctatcggcg aacccgattc ctgaacgtgc tgaaaaccgg
      961 ttttccggct gcgccggcaa cgcttcacgg acacgcaata aattgcgtcc ccgttcaccg
     1021 ttttcggagg agaagaacgc cggaaacagg acttcccctg gctgaatggt gtcaatttcc
     1081 gcgctatgca cttgcgcgca tactcatgca tgccgtaaaa acagagcctg cgcgtttctg
     1141 gcgggttttc gggtggtttg ttgcctgttt taccggtttc ccgtcagaaa cgccctgagg
     1201 gcctctcagg cggtgctgat aacggatgtt atggtaaatc aagtgaatgg caggtacaaa
     1261 aaaagcccca gagggctttt agtttagact tctgaagata ttttattttt cttggaagtg
     1321 gtggttgttt ttgctcggag ggaacttatc acccttgctc acatggcgat catattcaga
     1381 accagcgtat gagttgtcgg tatcatgata ttgaccgtaa gtacctgttt ttggacattc
     1441 ttgcccagac caatgttttg ccatttactt ttcctttgct cgttttagga gcttagctcc
     1501 tagcggtacg aaattgtgcc gcacttcata aatgtaattg cttgaaatta tgcttcaatg
     1561 tattgacttg ttgtttttgt ggttattcga ttgagttcac attttgagct gatttggttg
     1621 tgggttgtta gggaaatacc tatatgtact tatttgcgta catgttctat gctaagcccc
     1681 aacaaatggg ggttaacaac atgcatgcaa tcaattttac tgatgcccgt aaacattttg
     1741 ccgagacgat gaagcgcgtc actgatgatg ctgaaccggt acgtgtcatg cgccgtgatg
     1801 cgcctgatat tgttatgatc gatgcgggag agtatgaggc gctaatcgaa acggtctatc
     1861 tgttcagcaa tccggcgaac gcagagcata tcaatgagtc aatgaaacag gcggagcgcg
     1921 gcgaatttgt cgaagtggaa tattaagttc actaggaatg gcgctgatga ccttaactat
     1981 tggcgtgata ctgacaaaaa gaagtttgag cgtatccggc aactgttgct cagcatcgag
     2041 gctgatccgc tgacaggtat aggaaaaccc gaacggctgc ggcaccacaa agatccggca
     2101 ctctactccc gcaggattga tcagagccac cgtctggtct attcaatcca gaacggagaa
     2161 atcatcatct acgcagcccg ttatcactat ggtgacaaat agcaaaagtc gatatagccc
     2221 gcttgatgcg ggcttttcat gcaaggcgta caacggatgt tagggtaagt cgctgtcaga
     2281 tcgacacaga ggcaaagtcg gtgtaacgtt agcctcagaa aaaacaaagc cccggaaatc
     2341 atgtcatatc ttggcggatc gcatgataac cagggctagg tcgaaacctt gaaaggatat
     2401 tagcacatga accgtgccag acaacagccc gccataagcg cagggcacat tgcataacgc
     2461 cgcactcgaa cttttcaacg aacgcttacc acacaagccg tacttttcgg acgatctgca
     2521 ctttggtgtc cgtatcgccg gtaaggaacg cgctattctg gcgaaatata tccagttcaa
     2581 tcagcctcac gccatgttct ggctgggatt tgacgttgac cgcgccggtt ccgccatcga
     2641 ctggagcgac cgcaacgcgc ctgcaccgac gctgaccata actaaccccg aaaacggaca
     2701 cgcgcacctg ctgtacgcgc tggaaaactc gatacgcacc gcgccggacg gcaaaataaa
     2761 accgttacgc tacgccgcct ccgtggagaa tgcgctacgt aaaaaattag aggctgacgc
     2821 tggatattcg gggctcatct gcaaaaatcc gaaccacaac cactggaaaa tcgccgtgtg
     2881 gcagccgaag ctctacactc tggactggct ggccgacttt ctcgatctga acacagggaa
     2941 tgacaaggaa atcgttgccg actacggctt aggccgtaac tgcacgttgt tcgacaaaac
     3001 ccgtaagtgg gcatatcgcg ccatccgtca gggctggcct gagtatgagc agtggctgca
     3061 agcctgctac gaacgcgctt gcgcatacaa cctgcaattt gcacggcctc tggatgaaaa
     3121 tgaggtaaga gggatagcta agagcattgc taaatggaca tcaaataaat tttcacctga
     3181 agagttcagt aaatttgttg atattactca ctcctctgaa attcaatcaa agagaggaaa
     3241 aaagtcagga cagtcaagga ggaaaggaag cctagaggaa ataaaacctt gggtagctat
     3301 gggaataagc aggcggaagt atttttatat caagaaaaaa aaggtggaat aagatgaaaa
     3361 ccttcgtaac tctttggact atagcttttt tatcatttat tgccgtgatg tgtactgttg
     3421 atatatctaa ttacattccg tctgtttaca cagtttttag taagaataga cctcttgtaa
     3481 ctggcgccct ttccattctt ttgatatctg tttttatttg gctgatggta tccctctact
     3541 tacttaaaaa gtattcggtt aaggttgaga aacttagtct tggtggagtg aatatacttt
     3601 tcaatgagag tgctacactt tacaaaaaaa gtgtaaaaaa tcacctagat tcaaaaagag
     3661 caattttcaa attaagaaaa aacgttgatg cctttgatga ggttatttca tcatattatc
     3721 agacttacca atttattcgt gatgaaatga agatactaaa ccctaaaaaa gatcgtgaga
     3781 tttatgattt cagcaatgag atgctcatgg tgttaaatag atttctaact aactaccaga
     3841 acaactacaa gcgttggtat aagtacatat cagacaagga tgaggttgtt gatagggtta
     3901 gcggtgatgt catgagattc catgcaacca gcataaataa aatacaaatg cagtattatg
     3961 attatgagcg tattttgaaa ggttttaaag atgttaatcg gttctttgtt aatgatgtga
     4021 agcctaagtt tggaatcaat acagataagt ggaactggta aattaaagga gtagccaagg
     4081 ctactccttg gatagtacta tgaattatgc attctcattt ctctcgacat atcatacgtt
     4141 gctttttctc tatcgttata agtcatgtct attaattttc tgagtgtttc tgggttgttt
     4201 tctatttgat tccagttgac cactgatata tacgacccgc tcttcatgaa gttgtctatt
     4261 attcttgcag gcatatatgg gaatctttcc tcataagttg agcgtttatc aatagaaatc
     4321 cattcagtta cggtaggatg aacttctgat ttttcattag ttccatgtgt tgaacgaatg
     4381 tacgtagtat ttgttgacgg gagattgacg actaaaattc ctgatttttt gttaatggta
     4441 ctatctctca tgctagagta aagttcccaa tctacgtgtt ttctgttttt tgtttcagtt
     4501 ccaacaagaa ggataagaac tgatgtatct ctaagatatt tatctcttat tatctctctt
     4561 attttttgtg gggcttcatc ttcatctata tcacctaaag atactgagcg attcacgaat
     4621 atttcatgtt gctcattcat tttttcaagt gcgtttttgt agtactgatc attcgcatgg
     4681 tggtagctaa tgaatacctt atgctttccc atttttattg tccttttttt gtttgtgtgc
     4741 actctatttt gcacttgaac ctatatcaga taacagctct cttttagagc tcccctaaac
     4801 gccttgagaa gatagctata acctcacttc gttcgtacgt accgctcgcc gcagtctcat
     4861 gaccgaacgt agtgagcgaa tgcgcgagga agcggaaagt catctgttgc ctgcattttc
     4921 cacggtcact cctgtgt
//
