LOCUS       NZ_AP022141             3852 bp    DNA     circular CON 28-NOV-2023
DEFINITION  Klebsiella pneumoniae strain WP5-S18-ESBL-02 plasmid
            pWP5-S18-ESBL-02_2, complete sequence.
ACCESSION   NZ_AP022141
VERSION     NZ_AP022141.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMD00194529
            Sequence Read Archive: DRR199365
            Assembly: GCF_014169335.1
KEYWORDS    RefSeq.
SOURCE      Klebsiella pneumoniae
  ORGANISM  Klebsiella pneumoniae
            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 pneumoniae str.
            WP5-S18-ESBL-02 isolated from wastewater treatment plant effluent
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 3852)
  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                   :: 484x
            Sequencing Technology             :: Sequel; NextSeq 500
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 11/28/2023 08:46:40
            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)                     :: 5,216
            CDSs (total)                      :: 5,094
            Genes (coding)                    :: 4,976
            CDSs (with protein)               :: 4,976
            Genes (RNA)                       :: 122
            rRNAs                             :: 9, 8, 8 (5S, 16S, 23S)
            complete rRNAs                    :: 9, 8, 8 (5S, 16S, 23S)
            tRNAs                             :: 87
            ncRNAs                            :: 10
            Pseudo Genes (total)              :: 118
            CDSs (without protein)            :: 118
            Pseudo Genes (ambiguous residues) :: 0 of 118
            Pseudo Genes (frameshifted)       :: 54 of 118
            Pseudo Genes (incomplete)         :: 66 of 118
            Pseudo Genes (internal stop)      :: 21 of 118
            Pseudo Genes (multiple problems)  :: 20 of 118
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            AP022141.1.
            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..3852
                     /organism="Klebsiella pneumoniae"
                     /mol_type="genomic DNA"
                     /strain="WP5-S18-ESBL-02"
                     /isolation_source="wastewater"
                     /db_xref="taxon:573"
                     /plasmid="pWP5-S18-ESBL-02_2"
                     /geo_loc_name="Japan:Tokyo"
                     /lat_lon="35.6538 N 139.5126 E"
                     /collection_date="2018-08-06"
     gene            101..292
                     /locus_tag="H7R18_RS25935"
                     /old_locus_tag="WP5S18E02_P20010"
     CDS             101..292
                     /locus_tag="H7R18_RS25935"
                     /old_locus_tag="WP5S18E02_P20010"
                     /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_032421723.1"
                     /translation="MTKQQKTALNMAKFIQNQSLLLLEKLNELDLDAEADLCEKLHDDA
                     EHLFRTLSSRLDELQDGN"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            292..702
                     /locus_tag="H7R18_RS25940"
     CDS             292..702
                     /locus_tag="H7R18_RS25940"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:YP_005229777.1"
                     /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_048295909.1"
                     /translation="MARVSISEAARLVKVSRPTIYKMINSGKLSYTSVVKHGKGIKVID
                     TSELIRVFGSLDGVIDDVKSDAESTGINSVGLHDLQHRIALLEAENDGLKGAVKARDEH
                     IDSLRQAMQLLEHKHEPSSPPHSPWWKFWKKS"
                     /name="helix-turn-helix domain-containing protein"
     gene            1505..2344
                     /locus_tag="H7R18_RS25945"
                     /old_locus_tag="WP5S18E02_P20020"
     CDS             1505..2344
                     /locus_tag="H7R18_RS25945"
                     /old_locus_tag="WP5S18E02_P20020"
                     /inference="COORDINATES: protein motif:HMM:NF042851.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="HipA family kinase"
                     /protein_id="WP_048987779.1"
                     /translation="MHIEFKPSSDFNNVKINRAPDGAMAETFSCNINWGENLDSRSYVK
                     CFSDRKIMAISNEITGYILAKEAGLPVPEKCALIALPQEIKDEFKSRSGEECFEYGFAM
                     MMADGSTPNAIIKIHSPDGDFANSIFMDALNKWPQTARLIAFDEWVANEDRNLGNFIIT
                     PNNNIVVIDHSNLPCEMLWECDDLINEKAYTNKLVLIYELCKVKGRSYSIPDDAFINKE
                     ASHHALILTSSIAELEAWWDYLLDQPRKAKLKDFLNVRANKARTLPYNQQSGLRMTA"
                     /name="HipA family kinase"
     gene            2341..3192
                     /locus_tag="H7R18_RS25950"
                     /old_locus_tag="WP5S18E02_P20030"
     CDS             2341..3192
                     /locus_tag="H7R18_RS25950"
                     /old_locus_tag="WP5S18E02_P20030"
                     /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_048295908.1"
                     /translation="MINIQELLAASKAKENNQLVKGVWFLIQWSPDDYSQERFNIGVAF
                     SSERGEKQVKFTKSFKELSNWYGGNLTKQGDMVIKIATHTFIGKSLDKFSSGFFESGIH
                     YVPMGMAQGESIEKIMNVLFKDVVPMAQEKQNIARASYTTTRNIITVVREAISKNSVLK
                     DIMPENPMVETLSGISVKVPIQFRSNAGTIVSADYATSDTVENELLRSFRDIDLILNGN
                     DFDNVNSFLLLPASAKGEAKKISNLISDYTSSLKSKGVETISAHQPSSLVNKIDGWYKE
                     VA"
                     /name="hypothetical protein"
     Typing          complement(3431..3833)
                     /name="ColRNAI_rep_cluster_1987"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="88.78"
                     /coverage="99.0"
                     /evalue="4.8099999999999985e-137"
ORIGIN
        1 cgctcgccgc agccgaacgg caggagcgta gcgactgagt gagcgaggaa gcggaaaaga
       61 gaacatccct acattgagca ctgacgctct gaggcccctt atgacgaaac aacagaaaac
      121 agcgctgaac atggctaaat tcatccagaa tcagtctctg ctcctgctgg agaagcttaa
      181 cgagcttgat ctcgatgctg aggccgacct ttgtgagaaa ctccacgatg atgcggagca
      241 tcttttccgt acactgtcct cgagactgga tgaattacag gatggtaact gatggccaga
      301 gtgtctatta gtgaagcagc acggcttgtt aaggttagtc gccctactat ttacaagatg
      361 attaacagtg gtaagttaag ttacacctct gttgtaaagc acgggaaggg tattaaagtt
      421 attgatacat cagagcttat tagagtgttt ggttctcttg atggtgtcat cgatgatgta
      481 aaaagtgacg cagaatctac aggtattaac agcgttggtt tacatgattt acaacataga
      541 atcgctttac ttgaagctga aaacgatggt cttaaagggg ctgttaaggc tcgagatgag
      601 catattgatt cccttcgtca ggctatgcag cttctggagc acaagcacga accttcttca
      661 ccaccccatt ccccgtggtg gaaattctgg aaaaaatcct gatcccgcca tgcttgagtt
      721 ttcctctccg gccatcccgg ggcgttcctg aaccttccca aaaatcgcca gatccgggaa
      781 cactcctcac cacgaaaaat acccacacac cacgcaaaat taaaattttg cagataactc
      841 cttattatca gttggttagg ttttattaaa ttacgcagta ttaccttctg taaggtcaat
      901 ccaagtcgtc ggtgattcgt gtacgacttg ccgacgactc gtcatagagt catcgacgac
      961 tcactccaca ctatcagtaa cttatgacga cttgactcta gagtcgaatc gtcgctttgg
     1021 cgtttttttg accacggtga ctctagagtc aagtcacgag tcgaatcgcc ggtgagtcgt
     1081 ccggcgactt gccataacgt gattgccggc cgtcgacgaa cccgattcct gaacgtgctg
     1141 aaaaccggtt ttccggctgc gccggcaacg cttcacggcc acgcaataaa ttgcgtcccc
     1201 gttcaccgtt ttcggatggg aagaacgccg gaaacaggac ttaccccggc tgaatggcgt
     1261 gaatttccgc gctatgcact tgtgcgcata ctcatgcatg ccgtaaaaac agagcctgcg
     1321 cgtttctggc gggttttcgg gtggtttgtt gcctgttttg ccggtttccc gtcagaaacg
     1381 ccctgagggc ctctcaggcg gtgctgataa cggatgttat ggtaaatgtg aaaaacattt
     1441 cccttgataa aaaagctttc aagaaaaata atacagcaac cacaaacttt gatggaccag
     1501 agctatgcac atagaattta agccgtcatc tgactttaat aacgttaaaa ttaatagagc
     1561 tcctgacggc gctatggcag aaacttttag ctgcaatatt aactggggcg agaatcttga
     1621 cagcagaagc tatgtgaaat gctttagcga tcgcaagatt atggcaattt ccaacgaaat
     1681 aactggttat attttggcga aggaggcagg gctgcctgta cctgaaaaat gtgctttaat
     1741 agcattgcca caagaaataa aagatgaatt taaatccagg tctggcgaag agtgctttga
     1801 atacggattt gctatgatga tggccgacgg gagcacgcct aacgctatta taaaaattca
     1861 cagccctgat ggggattttg caaattccat ctttatggat gctttaaata aatggcctca
     1921 aacagctagg cttatagcgt ttgatgaatg ggttgccaat gaagatagga atttaggtaa
     1981 ctttattatt acgccaaata ataatattgt ggtcatagat catagtaatc tcccatgcga
     2041 aatgctatgg gagtgtgatg acttaataaa tgaaaaggca tacaccaata aattggtgtt
     2101 gatttatgaa ttatgtaagg taaaggggcg ttcatactcc attcctgatg atgcctttat
     2161 taataaagaa gctagccacc atgctttaat attaacttct tcaattgcag agcttgaagc
     2221 atggtgggat tatcttttag atcagccaag aaaagctaag ttgaaagatt ttttgaacgt
     2281 gcgtgccaac aaagcaagaa cattgcctta taaccagcag tctgggctaa ggatgacagc
     2341 atgataaaca tacaagagtt acttgccgca agcaaagcta aggaaaacaa tcagcttgtt
     2401 aaaggggttt ggttccttat tcaatggtca cctgatgact atagccaaga gcgttttaat
     2461 attggtgttg ctttttcatc agaaagaggc gagaaacaag ttaagttcac caaatccttc
     2521 aaggaattat ctaattggta tggtggtaac ttaacaaagc aaggtgatat ggttataaaa
     2581 atagctaccc atacttttat tgggaaaagc cttgataaat tttccagtgg gtttttcgag
     2641 agtggaattc attatgtccc tatgggtatg gctcaaggtg agtcgataga aaaaataatg
     2701 aatgtgctat ttaaagatgt agttcccatg gctcaagaaa agcaaaatat cgctagggct
     2761 agttatacaa caacacgaaa tattataact gttgttagag aagccatatc aaaaaatagc
     2821 gtgcttaaag acattatgcc tgagaatcca atggtggaaa cgctttcagg aatttcggtt
     2881 aaggttccta ttcaatttag aagtaatgca ggaactatag tgtcggctga ttacgctacg
     2941 agcgatacag tagaaaatga gttgcttagg tcttttagag atattgatct tatcttaaat
     3001 ggcaatgatt ttgataatgt aaatagcttt ctcttgttgc cagcatctgc caaaggggag
     3061 gctaaaaaaa ttagcaatct aattagtgat tatacatctt ctttaaaatc taagggcgtt
     3121 gaaactatta gtgctcatca gccatcatcc ctagtgaata aaattgatgg ttggtataaa
     3181 gaggttgcat aatctttata cgcatcctat ttcttgacgc tgaggattgg cgatcgtatc
     3241 ttagaggcca aacgaaaaaa accgccttgg cgggcggttt tttcgaaggt tcgcaagagt
     3301 tggcgctctt ttgaaccgtg gtaactggct ttaacggagc gcagtaacca aatctgtcct
     3361 tccagtgtag ccgtatttgg gctttcactt caagaactct gcgttaatac accttcgctc
     3421 cgtaaacctg ttaccagtgg ctaccaccag tggcaattcg ttgtgtcttc agagattgga
     3481 atcaagagta cagttgcttt gaaggcgtgg tagtcggact gaacgggggg ttcgtgcata
     3541 cagtccagct tggagcgaac tgcctacccg gaactgagtg tcaggcgtgg aatgagacaa
     3601 acgcggccat aacagcggaa tgacaccggt aaaccgaaag gcaggaacag gagagcgcac
     3661 gagggagcta ccagggggaa acgcctggga tctttatagt cctgtcgggt ttcgccacca
     3721 ctgatttgag cgtcagattt cgtgatgctt gtcagggggg cggagcctat ggaaaaacgg
     3781 ccgccatgcg gcctttcctt tttacatcac gcgaccgttc ggttttctcg agctttatac
     3841 gcatgctcct gc
//
