LOCUS       NZ_AP022147             5444 bp    DNA     circular CON 28-NOV-2023
DEFINITION  Klebsiella quasipneumoniae strain WP5-S18-ESBL-05 plasmid
            pWP5-S18-ESBL-05_5, complete sequence.
ACCESSION   NZ_AP022147
VERSION     NZ_AP022147.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMD00194531
            Sequence Read Archive: DRR199367
            Assembly: GCF_014169355.1
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.
            WP5-S18-ESBL-05 isolated from wastewater treatment plant effluent
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 5444)
  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                   :: 195x
            Sequencing Technology             :: Sequel; NextSeq 500
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 11/28/2023 10:17:57
            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)                     :: 5,988
            CDSs (total)                      :: 5,866
            Genes (coding)                    :: 5,626
            CDSs (with protein)               :: 5,626
            Genes (RNA)                       :: 122
            rRNAs                             :: 9, 8, 8 (5S, 16S, 23S)
            complete rRNAs                    :: 9, 8, 8 (5S, 16S, 23S)
            tRNAs                             :: 84
            ncRNAs                            :: 13
            Pseudo Genes (total)              :: 240
            CDSs (without protein)            :: 240
            Pseudo Genes (ambiguous residues) :: 0 of 240
            Pseudo Genes (frameshifted)       :: 79 of 240
            Pseudo Genes (incomplete)         :: 174 of 240
            Pseudo Genes (internal stop)      :: 45 of 240
            Pseudo Genes (multiple problems)  :: 48 of 240
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            AP022147.1.
            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..5444
                     /organism="Klebsiella quasipneumoniae"
                     /mol_type="genomic DNA"
                     /strain="WP5-S18-ESBL-05"
                     /isolation_source="wastewater"
                     /db_xref="taxon:1463165"
                     /plasmid="pWP5-S18-ESBL-05_5"
                     /geo_loc_name="Japan:Tokyo"
                     /lat_lon="35.6538 N 139.5126 E"
                     /collection_date="2018-08-06"
     gene            101..292
                     /locus_tag="H7R80_RS29605"
                     /old_locus_tag="WP5S18E05_P50010"
     CDS             101..292
                     /locus_tag="H7R80_RS29605"
                     /old_locus_tag="WP5S18E05_P50010"
                     /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_004187666.1"
                     /translation="MTKQQKTALNMAKFIQNQSLLLLEKLNELDLDVEADLCEKLHDDA
                     EHLFRTLSSRLDALQDGN"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            292..693
                     /locus_tag="H7R80_RS29610"
                     /old_locus_tag="WP5S18E05_P50020"
     CDS             292..693
                     /locus_tag="H7R80_RS29610"
                     /old_locus_tag="WP5S18E05_P50020"
                     /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_009310048.1"
                     /translation="MARVSISEAARLTGKSRTTLHRLIKAGDLSTCSGERNAKMVDTSE
                     LLRVFGPFEQPKGEHHSGQVSEQRDTASADQSEQVIRHLKQEIEHLNTLLLSKDSHIDS
                     LKQAMLLLENHQAKLTESPAPWWKFWKKS"
                     /name="helix-turn-helix domain-containing protein"
     gene            1285..2280
                     /locus_tag="H7R80_RS29615"
                     /old_locus_tag="WP5S18E05_P50030"
     CDS             1285..2280
                     /locus_tag="H7R80_RS29615"
                     /old_locus_tag="WP5S18E05_P50030"
                     /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_182940179.1"
                     /translation="MKFILKKSVVLGSSAIGITLLFIACFLSIQFGRYISLSDRISLTG
                     KTELENKLDEYMNDSYINEATNKVSELSGKLIMQGGNAASPESIQETKVKTEVLSKDKD
                     LDYNSYDSEFLGKKRVITYINLLSVEDSIYKILYPNVDCLGKTFSGTFEGDKPKSKKEC
                     ESEVIKIHKKDAENQRNTIAKIKEINDFIAGKIKPLKDEVIANGGAVKIWMPGPSIDTC
                     SEHTAMASEDIPEAYKTKNECISAINKKIKDIDEENARNEGVISFFPFIVILVVILLMP
                     AALKISSLIIKAALNLWLVFLEKSSESINKSEKKIKIDAKIEMREKKDKE"
                     /name="hypothetical protein"
     gene            complement(2385..2642)
                     /locus_tag="H7R80_RS29620"
     CDS             complement(2385..2642)
                     /locus_tag="H7R80_RS29620"
                     /inference="COORDINATES: protein motif:HMM:NF020291.3"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="primase C-terminal domain-containing protein"
                     /protein_id="WP_309487325.1"
                     /translation="MRQGWLEYDQWLQACYERASAYNLQFAPSLDENEVDGIAKSIAKW
                     TISKFSEDQFMDFVKATHTPEIQSKRGKKGGVKSRRAVGK"
                     /name="primase C-terminal domain-containing protein"
     gene            complement(3064..3219)
                     /locus_tag="H7R80_RS29625"
     CDS             complement(3064..3219)
                     /locus_tag="H7R80_RS29625"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_010251985.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="DUF1508 domain-containing protein"
                     /protein_id="WP_064761103.1"
                     /translation="MNDTWDFYTDGKGEWRWRRTASNGRIVGASSQGYVNRADCIANAR
                     RNGYTG"
                     /name="DUF1508 domain-containing protein"
     gene            3695..4462
                     /locus_tag="H7R80_RS29630"
                     /old_locus_tag="WP5S18E05_P50040"
     CDS             3695..4462
                     /locus_tag="H7R80_RS29630"
                     /old_locus_tag="WP5S18E05_P50040"
                     /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_053890738.1"
                     /translation="MRFLWRPLPYSRLRECDFLNCIDENDSSSWIAALKIFICIVIKSD
                     LDENGEYCAMITYPQIQKMTGMSRQLICCGFDKLRFYKIISSEGVRKKKHSLLTCEKGS
                     TRQKPLTKRFDGLSTGRWCKLPLKGLIDDDGVIPSFLAMSNRNINDLHALRLFIYLLSV
                     RRHGDVFIVVKAETLMKKLRLKRVQLTLALAHMSALGLIVKERYREGDFLSLNKTPAYA
                     FLLCGWDVLEWNHNRIKESNWRNDYLESFDNWA"
                     /name="hypothetical protein"
     gene            complement(4483..4656)
                     /locus_tag="H7R80_RS29635"
                     /old_locus_tag="WP5S18E05_P50050"
     CDS             complement(4483..4656)
                     /locus_tag="H7R80_RS29635"
                     /old_locus_tag="WP5S18E05_P50050"
                     /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_155765196.1"
                     /translation="MDIKTKLKRSLSSVESAISSLKRARGQTTDAYHEISKAIRELEDA
                     EYNIRKSIREME"
                     /name="hypothetical protein"
     Typing          complement(5032..5404)
                     /name="ColRNAI_rep_cluster_1987"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="95.722"
                     /coverage="91.0"
                     /evalue="2.76e-169"
ORIGIN
        1 cgctcgccgc agccgaacgg caggagcgta gcgactgagt gagcgaggaa gcggaaaaga
       61 gatctgtctg acattgagca ctgacgctct gaggcccttt atgacgaaac aacagaaaac
      121 agcgctgaac atggctaaat tcatccagaa tcagtctctg ctcctgctgg agaagcttaa
      181 cgagcttgat ctcgatgttg aggcggacct ttgtgagaaa ctccacgatg atgcggagca
      241 tcttttccgt acactgtcct cgagactgga tgcattacag gatggtaact gatggccaga
      301 gtgtctatta gtgaggctgc acgactgacg ggtaagagta gaacaacact gcacaggtta
      361 attaaagcag gtgacctgtc cacctgtagc ggtgaacgta atgcaaaaat ggtagatact
      421 tcagagcttt tacgtgtctt tggtcccttt gagcaaccga agggtgaaca ccattctgga
      481 caggtctctg aacagcgtga tacagcctct gctgaccaga gtgaacaggt gattcgtcat
      541 ctgaaacagg agattgaaca cctgaacacc ttacttttgt ccaaggattc gcacattgac
      601 agcctgaaac aggccatgct ccttcttgaa aatcaccagg caaaattaac tgaatccccg
      661 gcgccatggt ggaaattctg gaaaaaatcc tgaccccgtc atgcttcagt tttcctctcc
      721 ggtcattccg gggagttcct gaaccttccc aaaaatcgtc agatctctga atgctcctca
      781 ccactaaaaa tacccacacc ccacgcaaaa ttaaaatttt gaagataact cattaatatc
      841 agttagttgt gggttattaa attacgcagt attactttct gtaaggtgaa tccaagtcgt
      901 cggcgattcg tgtacgactt gccgacgact cgtcatagag tcatcgacga ctcacttaat
      961 actatcagta acttatgacg acttgactct agagtcgaat cgtcattttg gtgttttttt
     1021 gaccttggcg actctagagt caagtcacga gtcgaatcgc cggtgaatcg tgtggtgagt
     1081 cgtccggcga cttgccataa cgtcattgcc ggccgtcgac gaaccccctt cctgagtgtg
     1141 ctgaaaaccg gttgccggcg cagccggaaa accggttttc agcacactca ggaagggggg
     1201 cgatgtatgt ataggcttgt tctggtccac acgatcagat gttaagatgg tttatcgttt
     1261 cccttctgtt ggattcttct aaaaatgaaa tttattctaa agaaaagtgt cgttttaggt
     1321 tcctcggcaa taggtattac tttgctattt atagcttgtt ttttatcaat tcaattcggg
     1381 aggtatatct cactctcaga cagaattagt cttactggta agactgaatt agagaataag
     1441 ttagatgagt acatgaacga cagttatatc aatgaggcaa caaataaagt tagcgaatta
     1501 tctggtaagt taataatgca gggaggtaac gctgcatcac cagaaagcat tcaagagaca
     1561 aaagttaaaa cagaggtttt gtctaaggat aaagatcttg attacaacag ctatgattca
     1621 gaattcttag gcaagaagag agtgataact tatataaacc tattgtctgt ggaagatagc
     1681 atttataaga ttctttatcc gaatgttgat tgcttaggta aaacattttc aggaacattt
     1741 gagggtgaca aaccaaaatc aaagaaagaa tgtgagtctg aagtaataaa aatacataaa
     1801 aaagatgctg aaaaccaacg aaacactatc gctaaaatca aagaaattaa tgattttata
     1861 gctggtaaga taaaaccgct taaggacgag gtaatagcaa acggcggagc cgtaaaaata
     1921 tggatgcctg gcccatcaat cgacacctgt tcagagcaca ctgcaatggc atctgaagat
     1981 atacctgaag catataagac aaaaaatgaa tgcatatcgg caattaataa aaaaataaag
     2041 gatattgacg aagaaaatgc cagaaacgaa ggtgtgatta gtttttttcc ttttattgta
     2101 atccttgtgg taatacttct catgcctgct gcgttaaaaa tatcctcact aataatcaaa
     2161 gctgcactaa atctctggct tgttttttta gagaaaagct cagaatctat aaataaatct
     2221 gagaagaaaa taaaaataga tgcaaagata gaaatgagag aaaaaaaaga taaagagtaa
     2281 agttgtcggg gttagaaatt aaagccccga cttcaactta taataaatac ttctacttat
     2341 ccccatcgaa caccacggtt tactttgtct ctcacttcgt ggggttattt tcctaccgcc
     2401 cttcgacttt tcaccccgcc tttctttccc cttttagatt gaatttcagg agtatgggtg
     2461 gctttcacaa aatccataaa ttgatcttct gaaaattttg agatggtcca tttagcaata
     2521 cttttcgcta ttccatctac ctcattttca tccagagatg gtgcaaattg taaattatag
     2581 gcactggcac gttcatagca ggcttgcagc cattggtcgt actcaagcca gccctgacga
     2641 attgtgcggt atgcccactt tccggctgca ccggcaacgc ttcacggcca cgcaataaat
     2701 tgcgtccccg ttcaccgttt tcggatagga agaacgccgg aaacaggact taccccggct
     2761 gaatggcgtg aattttcgcg ctatgcactt gcgtgcatac tcatgcatgc cgtaaaaaca
     2821 gagcctgcgc gtttctggcg ggttttcggg tggtttgttg cctgttttac cggtttcccg
     2881 tcagaaatgc cctgaggccg ttctggcggt gcgtacaatc agggggttat gttaaatgac
     2941 agaagtaaaa aaagcccccg aagaggctta aggtttttct gtagggagga aaaactggtg
     3001 acctgtttga cagtacccgt taccgactga cagccacatt ccagtcgtat acctgatcca
     3061 agactagccg gtgtaaccat tgcggcgggc attagcgata caatccgctc ggtttacata
     3121 gccctgactg gatgcaccaa caatacgacc attgctggcc gttctgcgcc agcgccattc
     3181 gcctttacca tcagtataaa aatcccatgt atcgttcatt ctgtttttat cctgtgctgt
     3241 gtggggttcc ccaagattga tataaagcat ttctcctctt tttcaatcga tacgagtgtg
     3301 ttttgcgatg cgagtacgat aggaatttct gttacatgtt acccatgcaa tgccgtctca
     3361 ttaggtctaa aggcttcttg tgatgcacat agactatctt ggtatcttaa tagactatct
     3421 ttaattgtta ttttgttgat tttaaagctt tttatctttt tgtttattct agaaagatta
     3481 taataaaaag acttataagt ctttttatta tgtgtcatga ttttttcaag atttgagcag
     3541 aggtgttttc gggaggagag tgtcatgggt ctagaaaagt atgtgaagtt gctcgagaga
     3601 gttgcagcga tttctggtga gttaacccag cttgtaatct ctgtgacgtt attaataatt
     3661 tcttggtatc tttttaaata attaaggtga agctatgcgg tttttatgga ggcctttgcc
     3721 ttactctagg ttaagagaat gtgatttttt aaactgtatt gatgaaaatg attcgtcttc
     3781 atggatagct gcattgaaaa tattcatttg cattgttatt aaatctgatc tggatgagaa
     3841 tggagagtat tgtgcaatga ttacgtatcc acaaatccag aaaatgacag ggatgagtag
     3901 gcagttaata tgttgtggtt ttgataagtt gaggttttat aaaataatat ctagcgaagg
     3961 tgttaggaaa aaaaagcatt cattattaac ttgtgaaaaa ggctctacaa gacaaaaacc
     4021 tttgacgaaa aggtttgatg ggctgtcaac ggggcgatgg tgtaaactcc cgttaaaagg
     4081 attgattgat gatgatggtg taatcccttc gtttctggca atgagcaata gaaatattaa
     4141 cgaccttcat gcacttcggt tgtttatcta tttgttgtca gtgagacggc atggtgatgt
     4201 ttttattgtt gtaaaagcag aaacgctgat gaaaaaatta cgacttaaaa gagttcagct
     4261 aacattggct ttggctcata tgtcagcttt ggggttgata gttaaagagc gatataggga
     4321 gggcgatttt ttgagtttaa ataaaacacc tgcatatgct tttttattgt gtgggtggga
     4381 tgttcttgaa tggaatcaca atagaataaa agagagcaac tggagaaatg attatttaga
     4441 gtcgtttgat aactgggctt gaagcccagt tatctatata actcactcca tctcacgaat
     4501 ggatttcctt atgttgtact cggcatcctc aagttcacga attgctttgc ttatttcatg
     4561 gtatgcatcc gtagtttgcc ctcttgcacg ctttaaagat gaaattgcac tttccacaga
     4621 acttaaagaa cgtttaagct ttgtcttgat atccatattg aacctctgtt tttatctgct
     4681 gctagggtga ttgtgcaaca ccctaatgga tggattttat tccaataaaa tcaatgaaat
     4741 aagtcttttt ctgaggtcta ttggtgttgt taagtggtgc tggtttgggt ttgatttatg
     4801 tctatgtatc taacggattt gcttgtgatc ctttcctcgg cgtcgtagtc tcttgctctg
     4861 taaacgaaaa aaccacccgt caaggtggtt tttcgaaggt tcattaaccg gcaagtttat
     4921 gaaccgtggt aacagtcttg tgcgagacgt gtcaccaaat ccgtccttcc agtgtagcct
     4981 cagttaggtc ttcacttcaa gaactcaaat acatctctcg cacatcctgt ttaccagtgg
     5041 ctgctgccag tggcgctttg tcgtgtcttt ccgggttgga ctcaagatga tagttaccgg
     5101 ataagacgca gcagtcggac tgaacggggg gttcgtgcat acagtccagc ttggagcgaa
     5161 ctgcctaccc ggaactgagt gtcaggcgtg gaatgagaca aacgcggcca taacagcgga
     5221 atgacaccgg taaaccgaat ggcaggaaca ggagagcgca cgagggagcc atcaggggga
     5281 aacgcctggt atctttatag tcctgtcggg tttcgccacc actgatttga gcgtcaaatt
     5341 ctgtgatgct tgtcaggggg gcggagccta tggaaaaacg gccgctgtgc tgccttctcc
     5401 ctctccgagc tgtctgctct atgtcgttat gtgcgcgttg cgac
//
