LOCUS       NZ_AP022415             6423 bp    DNA     circular CON 28-NOV-2023
DEFINITION  Klebsiella quasipneumoniae strain STW0522-39 plasmid pSTW0522-39-3,
            complete sequence.
ACCESSION   NZ_AP022415
VERSION     NZ_AP022415.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMD00195879
            Sequence Read Archive: DRR199684
            Assembly: GCF_015135515.1
KEYWORDS    RefSeq.
SOURCE      Klebsiella quasipneumoniae
  ORGANISM  Klebsiella quasipneumoniae
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Klebsiella/Raoultella group; Klebsiella.
REFERENCE   1
  AUTHORS   Sekizuka,T., Katagiri,M., Asai,K. and Kuroda,M.
  TITLE     complete genome sequences of Klebsiella quasipneumoniae str.
            STW0522-39 isolated from hospital sewage
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 6423)
  AUTHORS   Sekizuka,T., Katagiri,M., Asai,K. and Kuroda,M.
  TITLE     Direct Submission
  JOURNAL   Submitted (03-FEB-2020) 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 v. 2.5; minimap v. 0.2-r124; racon v. 1.1.0;
            circlator v. 1.5.3; Pilon v. 1.18; SPAdes v. 3.11.1; A5-miseq v.
            20140604
            Genome Coverage                   :: 288x
            Sequencing Technology             :: Sequel; NextSeq 500
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 11/28/2023 10:03:20
            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)                     :: 5,526
            CDSs (total)                      :: 5,415
            Genes (coding)                    :: 5,260
            CDSs (with protein)               :: 5,260
            Genes (RNA)                       :: 111
            rRNAs                             :: 9, 8, 8 (5S, 16S, 23S)
            complete rRNAs                    :: 9, 8, 8 (5S, 16S, 23S)
            tRNAs                             :: 78
            ncRNAs                            :: 8
            Pseudo Genes (total)              :: 155
            CDSs (without protein)            :: 155
            Pseudo Genes (ambiguous residues) :: 0 of 155
            Pseudo Genes (frameshifted)       :: 63 of 155
            Pseudo Genes (incomplete)         :: 82 of 155
            Pseudo Genes (internal stop)      :: 38 of 155
            Pseudo Genes (multiple problems)  :: 23 of 155
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            AP022415.1.
            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..6423
                     /organism="Klebsiella quasipneumoniae"
                     /mol_type="genomic DNA"
                     /strain="STW0522-39"
                     /isolation_source="sewage"
                     /db_xref="taxon:1463165"
                     /plasmid="pSTW0522-39-3"
                     /geo_loc_name="Japan:Tokyo"
                     /collection_date="2018-05-22"
     gene            complement(102..977)
                     /locus_tag="JLF46_RS27380"
                     /old_locus_tag="STW0522KLE39_P30010"
     CDS             complement(102..977)
                     /locus_tag="JLF46_RS27380"
                     /old_locus_tag="STW0522KLE39_P30010"
                     /EC_number="3.5.2.6"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_032489170.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="extended-spectrum class A beta-lactamase CTX-M-2"
                     /protein_id="WP_025368620.1"
                     /translation="MMTQSIRRSMLTVMATLPLLFSSATLHAQANSVQQQLEALEKSSG
                     GRLGVALINTADNSQILYRADERFAMCSTSKVMAAAAVLKQSESDKHLLNQRVEIKKSD
                     LVNYNPIAEKHVNGTMTLAELGAAALQYSDNTAMNKLIAHLGGPDKVTAFARSLGDETF
                     RLDRTEPTLNTAIPGDPRDTTTPLAMAQTLKNLTLGKALAETQRAQLVTWLKGNTTGSA
                     SIRAGLPKSWVVGDKTGSGDYGTTNDIAVIWPENHAPLVLVTYFTQPEQKAESRRDILA
                     AAAKIVTHGF"
                     /name="extended-spectrum class A beta-lactamase CTX-M-2"
     gene            complement(1234..2496)
                     /locus_tag="JLF46_RS27385"
                     /old_locus_tag="STW0522KLE39_P30030"
     CDS             complement(1234..2496)
                     /locus_tag="JLF46_RS27385"
                     /old_locus_tag="STW0522KLE39_P30030"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_031587700.1"
                     /GO_function="GO:0004803 - transposase activity [Evidence
                     IEA]"
                     /GO_process="GO:0006313 - DNA transposition [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="IS1380-like element ISEcp1 family transposase"
                     /protein_id="WP_000608644.1"
                     /translation="MINKIDFKAKNLTSNAGLFLLLENAKSNGIFDFIENDLVFDNDST
                     NKIKMNHIKTMLCGHFIGIDKLERLKLLQNDPLVNEFDISVKEPETVSRFLGNFNFKTT
                     QMFRDINFKVFKKLLTKSKLTSITIDIDSSVINVEGHQEGASKGYNPKKLGNRCYNIQF
                     AFCDELKAYVTGFVRSGNTYTANGAAEMIKEIVANIKSDDLEILFRMDSGYFDEKIIET
                     IESLGCKYLIKAKSYSTLTSQATNSSIVFVKGEEGRETTELYTKLVKWEKDRRFVVSRV
                     LKPEKERAQLSLLEGSEYDYFFFVTNTTLLSEKVVIYYEKRGNAENYIKEAKYDMAVGH
                     LLLKSFWANEAVFQMMMLSYNLFLLFKFDSLDSSEYRQQIKTFRLKYVFLAAKIIKTAR
                     YVIMKLSENYPYKGVYEKCLV"
                     /name="IS1380-like element ISEcp1 family transposase"
     gene            complement(2649..3227)
                     /locus_tag="JLF46_RS27390"
                     /old_locus_tag="STW0522KLE39_P30040"
     CDS             complement(2649..3227)
                     /locus_tag="JLF46_RS27390"
                     /old_locus_tag="STW0522KLE39_P30040"
                     /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_200928096.1"
                     /translation="MALMVTRRYLLGGEYPSEEFVQASLEKYFFRQGFDIDTGSYIDLI
                     CRDKESRDVVWHIEVKGKTSQPGLDFRTCLGQLVQRMTKDNINYAIAVPRIKQYERLIE
                     ETSILAVSKLNLHWIFVGPDGSVTIKEPDSSTMKNGNGNGNGNGNGREVSLVNGGFKRF
                     ITGDFMPTCSYGKAPVVFNLDSTSVLQKA"
                     /name="hypothetical protein"
     gene            complement(3427..3597)
                     /locus_tag="JLF46_RS27395"
     CDS             complement(3427..3597)
                     /locus_tag="JLF46_RS27395"
                     /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_157771094.1"
                     /translation="MATATNFDAWLDDVDGDYEEVMALYDSVQNVSDMGLYQCVEGGRG
                     DAWVVSSNHHP"
                     /name="hypothetical protein"
     gene            complement(4448..4849)
                     /locus_tag="JLF46_RS27400"
                     /old_locus_tag="STW0522KLE39_P30060"
     CDS             complement(4448..4849)
                     /locus_tag="JLF46_RS27400"
                     /old_locus_tag="STW0522KLE39_P30060"
                     /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_048270303.1"
                     /translation="MARVSISEAARLTGKSRTTLHRLIKTGDLSTCSGERNAKMVDTSE
                     LLRVFGPFEQPKGEHHSGQVSEQRDTASADQSEQVIRHLKQEIEHLNILLLSKDSHIDS
                     LKQAMLLLENHQAKLTESPAPWWKFWKKS"
                     /name="helix-turn-helix domain-containing protein"
     gene            complement(4849..5040)
                     /locus_tag="JLF46_RS27405"
                     /old_locus_tag="STW0522KLE39_P30070"
     CDS             complement(4849..5040)
                     /locus_tag="JLF46_RS27405"
                     /old_locus_tag="STW0522KLE39_P30070"
                     /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_049139654.1"
                     /translation="MTKQQKTALNMAKFIQNQSLLLLEKLNELDLDVEADLCEELHDDA
                     EHLFRTLSSRLDALQDGN"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            5474..>5554
                     /locus_tag="JLF46_RS27755"
                     /pseudo=""
     CDS             5474..>5554
                     /locus_tag="JLF46_RS27755"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001333247.1"
                     /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="replication initiation protein"
                     /name="replication initiation protein"
     ARG             complement(106..977)
                     /name="blaCTX-M-2"
                     /gene="blaCTX-M-2"
                     /gene_name="extended-spectrum class A beta-lactamase
                     CTX-M-2"
                     /tool="amrfinderplus"
                     /drug_class="BETA-LACTAM"
                     /identity="100.0"
                     /coverage="100.0"
     Typing          5217..5601
                     /name="rep_cluster_2370"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="92.487"
                     /coverage="89.0"
                     /evalue="2.97e-154"
ORIGIN
        1 cggaatgata gaaagagatg agggttcgtt gcaagacaag actgaagttc aggagcacat
       61 ttttaacgta aatggagcga tacctcgctc catttattgc atcagaaacc gtgggttacg
      121 attttcgccg ccgcagccag aatatcccga cggctttccg ccttctgctc cggttgggta
      181 aagtaggtca ccagaaccag cggtgcgtgg ttttccggcc agataaccgc gatatcgttg
      241 gtggtgccat aatctccgct gccggtttta tcgcccacta cccatgattt cggcagaccc
      301 gcccgaatgc tcgcgctacc ggtagtattg cccttaagcc acgtcaccaa ctgtgcccgc
      361 tgagtttccg ccagcgcttt acccagcgtc agatttttca gggtctgcgc catcgcgagc
      421 ggcgtggtgg tatcacgcgg gtcgcctgga atggcggtat tgagcgtggg ctcggttctg
      481 tccagacgga aggtctcatc acccaacgag cgagcaaacg ccgtcacttt atcgggacca
      541 cccagatggg caatcagctt attcatggca gtattgtcgc tatactgcag cgccgctgcg
      601 ccaagctcag ccagcgtcat cgtgccgtta acgtgtttct ccgcaatggg attgtagtta
      661 accaggtcgc tcttcttgat ttcaacgcgc tgatttagca ggtgcttatc gctctcgctc
      721 tgtttaagca ccgccgcggc cgccatcacc ttactggtac tgcacatcgc aaaacgttca
      781 tcggcacggt agagaatctg cgaattatcg gcggtgttaa tcagcgcaac gccaagccga
      841 cctcccgaac ttttctccag ggcttccagc tgctgttgca cgctgttcgc ctgcgcatgc
      901 agcgttgcgc tgctaaatag caggggtagc gtcgccatca ccgttaacat tgagcggcga
      961 atgctctgag tcatcattaa aaatcctcta ttagtattat cccttggcct tcaagtattc
     1021 attgaaccta aattccacgt gtgtttttta ttagcttcaa aaatcactat ttcacgaaga
     1081 atttagactg cttctcacac attgtaacat tatttacaac cacctttcaa tcatttttga
     1141 taaatcattg atttcatctt tgctgcaatg atacttaata aactctgcaa gttatccaca
     1201 gagcaacact caattttatt gatgatattc ttattatacc agacattttt catacactcc
     1261 cttgtacgga tagttttccg acaacttcat gattacatat cttgcggttt tgattatttt
     1321 tgctgcaaga aatacatact tcaaacgaaa ggtctttatt tgctgtctgt attctgaaga
     1381 gtccaaggaa tcaaacttga acaacaaaaa taggttatat gaaagcatca tcatttgaaa
     1441 cacggcttca ttcgcccaaa atgactttag caagagatga cccaccgcca tgtcgtattt
     1501 ggcttctttg atatagtttt cagcattacc acgcttttca tagtatataa ctactttttc
     1561 agaaagcaag gtagtatttg ttacaaagaa aaagtagtcg tattcggaac cttctaaaag
     1621 tgataattgt gctctttctt tttctggttt cagtacgcga gatacgacaa atcttctgtc
     1681 tttttcccat ttaactaatt ttgtatacag ttctgtagtt tctctacctt cttctccttt
     1741 aacgaataca attgatgaat tcgttgcttg tgaggtgagt gtagaataac ttttggcttt
     1801 aattaaatat ttgcatccaa gagattctat cgtttcgata attttttcat caaagtagcc
     1861 actatccatt cgaaataaaa tttctaaatc gtctgatttg atgttagcaa caatttcttt
     1921 gatcatttcc gcagcaccgt ttgcagtgta agtattgcca cttcttacaa atccggtaac
     1981 atatgctttt aattcgtcgc aaaatgcaaa ttggatattg tagcatcggt ttcccagttt
     2041 cttaggatta tatccttttg acgcaccttc ttgatgacct tctacgttaa ttacactact
     2101 atcaatatca atcgtaatgg atgtcaattt acttttagtg agcagttttt taaagacttt
     2161 aaaattaatg tctctaaaca tttgggttgt cttgaagttg aagtttccta gaaaccgtga
     2221 cactgtttca ggttctttta cggaaatatc aaactcgttg acgaggggat cattttgaag
     2281 tagctttaga cgttctaact tatcaatgcc aatgaagtga ccgcagagca tggtctttat
     2341 atgattcatc ttgattttat ttgttgagtc attatcaaat acgaggtcat tttcaataaa
     2401 atcaaaaatc ccattgcttt ttgcattctc aaggagcaga aaaagacctg catttgatgt
     2461 tagattctta gctttgaaat caattttatt aatcataatt agaacccctt tttactactt
     2521 ttcttactat tattttacca tatatcgagt cataaaagct gataatttaa catatttttg
     2581 agcacttttc tttcacccaa tgggtgaaag ctgaatttcg aaggaatgca tatttatcaa
     2641 ggctttgatt atgctttttg aagtactgac gtagaatcta ggttaaatac aacaggagct
     2701 ttcccatatg agcaagttgg cataaaatcc cccgtaataa atcttttaaa ccccccattc
     2761 acaagagaaa cttctcttcc attaccatta ccattaccat taccattacc atttttcatc
     2821 gtagagctat caggttcctt aattgtcaca ctgccatcag gcccaacaaa tatccagtgt
     2881 aaattcaatt tactaacagc aagaatgctc gtttcttcta ttaatctttc atactgtttt
     2941 attcttggaa cagcaatagc ataattaata ttatcttttg tcattctctg cactaattgt
     3001 ccaagacaag ttcgaaaatc caaccccggc tgtgatgttt ttccttttac ttcaatatgc
     3061 cacacaacat ccctagattc tttatcacga caaataaggt caatataaga acccgtatct
     3121 atatcgaacc cttgtcgaaa aaaatatttt tctaaagaag cttgaacaaa ttcctcggag
     3181 ggatattcac cacctagtaa gtaccttctc gtcaccataa gagccacaac ccctacgcat
     3241 cctatttact ataacgtcat attttaagag ttcccacaag gggaactctc tgtacgatta
     3301 cgagtgatca ttcgatatat ttcgttgaaa tccataccat gaatcaacat cttcgccgcc
     3361 acatagcctt tctctaatca atttgaggaa agtatcccta gccacagctg atgctagaaa
     3421 aagagcttat ggatgatgat tagagctcac gacccaagca tcaccccgac caccctcaac
     3481 acactgatac aaccccatat cacttacatt ctgaacggaa tcataaagag ccataacctc
     3541 ctcataatcg ccatcaacat catctaacca cgcatcaaaa ttagtagcag tcgccatgcc
     3601 aatcctccat tttttagttt tcaggagtta atttacatag tgataggggc tgttaagcaa
     3661 ataagttttt accttttttg cctcatgctc taaaagtgag caagacaggc atttaccata
     3721 acgtcccatt gtacgcaccg ctaaaacggc ctcagggcgt ttctgacggg aaaccggtaa
     3781 aacaggcaac aaaccacccg aaaacccgcc agaaacgcgc aggctctgtt tttacggcat
     3841 gcatgagtat gcacgcaagt gcatagcgcg aaaattcacg ccattcagcc agggtaagtc
     3901 ctgtttccgg cgtacttccc atccgaaaac ggtgaacggg gacgcaattt attgcgtggc
     3961 cgtgaagcgt tgccggcgca gccggaaaac cggttttcag cacgttcagg aatccggttc
     4021 gtcgacggcc ggcaatcacg ttatggcaag tcaccgaacg actcaccaca cgattcaccg
     4081 gcgactcttc actagagtcg tacccagagt cgccacgcct aaaaaacaac caaacgggga
     4141 gtcgggtcta gagtcgggtc gttattaact cattgttttt atagtcctga gtcgttaccg
     4201 actctatgac gactcgccgg ggactctatg acgagtcgtc atagagtcgg atctatataa
     4261 atcaaattta aaaaacgaaa ttttacagac ttaaactact gatattaaat acaaatccgc
     4321 aaaattttaa ttttgcgtag tgtgtggata tttttagtgg tgaggagcgt tcagaaatcc
     4381 ggcgattttt tggaaggttc aggaactccc cgggatggcc ggagaggaaa acggaagcat
     4441 gacggggtca ggattttttc cagaatttcc accatggcgc cggggattca gttaattttg
     4501 cctggtgatt ttcaagaagg agcatggcct gtttcaggct gtcaatgtgc gaatccttgg
     4561 acaaaagtaa gatattcagg tgttcaatct cctgtttcag atgacgaatc acctgttcac
     4621 tctggtcagc agaggctgta tcacgctgtt cggagacctg tccagaatgg tgttcaccct
     4681 tcggttgctc aaagggacca aagacacgta aaagctctga agtatctacc atttttgcat
     4741 tgcgctcacc actacaggtg gacaggtcac ctgttttaat taacctgtgc agtgttgttc
     4801 tactcttacc cgtcagtcgg gcagcctcac taatagacac tctggccatc agttaccatc
     4861 ctgtaatgca tccagtctcg aggacagtgt acggaaaaga tgctccgcat catcgtggag
     4921 ttcctcacaa aggtcggcct cgacatcgag atcaagctcg ttaagcttct ccagcaggag
     4981 cagagactga ttctggatga atttagccat gttcagcgct gttttctgtt gtttcgtcat
     5041 aagaggcctc agagcgtcag tgctcaatgt agggatgttc tcttttccgc ttcctcgctc
     5101 actcagtcgc tacgctcctg ccgttcggct gcggcgagcg gcaggagcat gcgtataaaa
     5161 gctcgagaaa accgagcgat cgcgtgatgg ggagaaggag aggccgcaca gcggccgttt
     5221 ttccataggc tccgcccccc ctgacaagca tcacagaaac tgacgctcaa atcagtggtg
     5281 gcgaaacccg acaggactat aaagatatca ggcgtttccc cctgatggct ccctcgtgcg
     5341 ctctcctgtt ccgaccctgc cgcttaccag atacctgtcc gcctttctcc cttcgggaag
     5401 cgtggcgctt tctcatagct cacgctgttg gtatctcagt tcggtgtagg tcgttcgctc
     5461 caagctgggc tgtgtgcacg aaccccccgt tcagcccgac cgctgcgcct tatccggtaa
     5521 ctatcgtctt gagtccaacc cggtaagaca cgactaatcg ccattgacaa cggccactgg
     5581 tagacaggat gtgcgagaga tgtatcgaga gttcttgaag tggtggcctg actgcggcta
     5641 cactgaaagg acagatttgg tgacatgtct cgcacaagac tgttaccacg gttcagaagt
     5701 tccccaactt actgaacctt cgaaaaacca cctccccagg tggttttttc gttttccgag
     5761 aaagagatta cgctttgagc gaatgaatct caagaagatc atggcatttg atgaacaaat
     5821 gagtaagcta ctcagattga tagaaaaaat gccccttata caagtgatat attttccaaa
     5881 actgatactc tattttaaca ttagaaagcg tccatttccc actccgcgat tcagcctctt
     5941 ttttaatatc agcaatactt gggatcaccc catttgaaat aacaaaatcg tccaaccaat
     6001 cccacatttc tcgccgagat gatttaaagc cggaaactgc gggactgacc ggagcgacag
     6061 gccacccccc tccctgctag cccgccgcca cgcggccggt tacaggggac actgagaaag
     6121 cagaaagcca acaaacacta tatatagcgt tcgttggcag ctgaagcagc actacatata
     6181 gtagagtacc tgtaaaactt gccaacctga ccataacagc gatactgtat aagtaaacag
     6241 tgatttggaa gatcgctatg aaggtcgatt aggaatactg caagtgtaaa tcagataatt
     6301 acaataaaaa caaacaacct aataattaaa tgccttaaac attatttaaa ataaaatagt
     6361 ttacataaga aattgttatc tattaccttc ctgaagctaa gatatttggt ccagaaaaaa
     6421 gag
//
