LOCUS       NZ_AP022024             5669 bp    DNA     circular CON 02-DEC-2023
DEFINITION  Klebsiella sp. WP3-S18-ESBL-05 plasmid pWP3-S18-ESBL-05_4, complete
            sequence.
ACCESSION   NZ_AP022024
VERSION     NZ_AP022024.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMD00194424
            Sequence Read Archive: DRR199260
            Assembly: GCF_014168915.1
KEYWORDS    RefSeq.
SOURCE      Klebsiella sp. WP3-S18-ESBL-05
  ORGANISM  Klebsiella sp. WP3-S18-ESBL-05
            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 sp. WP3-S18-ESBL-05 isolated
            from wastewater treatment plant effluent
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 5669)
  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                   :: 334x
            Sequencing Technology             :: Sequel; NextSeq 500
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 12/02/2023 12:00:48
            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)                     :: 5,520
            CDSs (total)                      :: 5,397
            Genes (coding)                    :: 5,271
            CDSs (with protein)               :: 5,271
            Genes (RNA)                       :: 123
            rRNAs                             :: 9, 8, 8 (5S, 16S, 23S)
            complete rRNAs                    :: 9, 8, 8 (5S, 16S, 23S)
            tRNAs                             :: 90
            ncRNAs                            :: 8
            Pseudo Genes (total)              :: 126
            CDSs (without protein)            :: 126
            Pseudo Genes (ambiguous residues) :: 0 of 126
            Pseudo Genes (frameshifted)       :: 38 of 126
            Pseudo Genes (incomplete)         :: 94 of 126
            Pseudo Genes (internal stop)      :: 12 of 126
            Pseudo Genes (multiple problems)  :: 16 of 126
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            AP022024.1.
            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..5669
                     /organism="Klebsiella sp. WP3-S18-ESBL-05"
                     /mol_type="genomic DNA"
                     /strain="WP3-S18-ESBL-05"
                     /isolation_source="wastewater"
                     /db_xref="taxon:2675711"
                     /plasmid="pWP3-S18-ESBL-05_4"
                     /geo_loc_name="Japan:Tokyo"
                     /lat_lon="35.6684 N 139.4278 E"
                     /collection_date="2018-08-06"
     gene            complement(101..910)
                     /locus_tag="H7R64_RS27360"
                     /old_locus_tag="WP3S18E05_P40010"
     CDS             complement(101..910)
                     /locus_tag="H7R64_RS27360"
                     /old_locus_tag="WP3S18E05_P40010"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_010222407.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="endonuclease"
                     /protein_id="WP_151216522.1"
                     /translation="MSKDKKDRSKNRYHQLVEKIFFDKYVDGDLEVLFERLEINSAAKD
                     LGIDLPSNVGDVIYSIRFRTPMPESILLTQPEGKEWIIELAGRSKYRFRLVTISRILPN
                     PNMVAIKIPDNTPEIITGYSLDDEQALLAKVRYNRLIDIFLGITTYSLQNHLRTTVKGI
                     GQIEIDELYVGIDKYGCHYIIPVQAKGGTDQISMVQTSQDTAWCEQKYPNVRCRAISAQ
                     FVSSDLIALFELKIDEGQVKLIEERHYKLVPAKELDSSDISNYRMSV"
                     /name="endonuclease"
     gene            complement(903..2153)
                     /locus_tag="H7R64_RS27365"
                     /old_locus_tag="WP3S18E05_P40020"
     CDS             complement(903..2153)
                     /locus_tag="H7R64_RS27365"
                     /old_locus_tag="WP3S18E05_P40020"
                     /EC_number="2.1.1.37"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_010222406.1"
                     /GO_function="GO:0003886 - DNA
                     (cytosine-5-)-methyltransferase activity [Evidence IEA];
                     GO:0008168 - methyltransferase activity [Evidence IEA];
                     GO:1904047 - S-adenosyl-L-methionine binding [Evidence
                     IEA]"
                     /GO_process="GO:0006304 - DNA modification [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="DNA cytosine methyltransferase"
                     /protein_id="WP_182945347.1"
                     /translation="MTRPIAVDLFAGAGGLSLGFEQAGFDIMASVEIDPIHCSAHKYNF
                     PMCKTICRSVVDVTGKYVREVSGIGEKEIDVVIGGAPCQGFSLIGKRALDDDRNKLVYH
                     YVRLVLELKPKYFIFENVKGLTVGKHKQFLVEIMDAFKDGGYDVVSDYKVLNAADYGVP
                     QDRRRLFLMGGRKGITLPSYPEPLSIRTTVGDAIGDIPDAEKYPELWGRDWVDAKFGEQ
                     SLYSSYLHGVGKDPSDFSYPRIFNKDKLTCSLLTDHSDISRGRFVETLPDTVEPISRFK
                     KLSMNGLCNTLRAGTASDRGAFTSPRPIHPIYPRVITVREAARLHSYPDWFRFHVTKWH
                     GFRQVGNSVPPMLARSVGLQIMKVLGVTPKKPTKKIKLGDESLVAISMSDAASMFGVSS
                     NVIAKRIKNSNKEVVCE"
                     /name="DNA cytosine methyltransferase"
     gene            complement(2426..2944)
                     /locus_tag="H7R64_RS27370"
                     /old_locus_tag="WP3S18E05_P40030"
     CDS             complement(2426..2944)
                     /locus_tag="H7R64_RS27370"
                     /old_locus_tag="WP3S18E05_P40030"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_016246513.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_011017199.1"
                     /translation="MKCFWACSVSVVLVMSFTVASAENITHTKPLARSDLYLTCKGYQV
                     KGASVINVEKPSYLEGTGEQVEFAIISLGDASDGLKVFFDSWGFSPFGLIESHVMHEHW
                     SLVHVGGRVSVKGEKIDYSFVDNQPQEGGSYKPKTGVFLYGCINSDKRPSWVEKIYTRT
                     GVFRGGIED"
                     /name="hypothetical protein"
     gene            complement(3073..3288)
                     /locus_tag="H7R64_RS27375"
                     /old_locus_tag="WP3S18E05_P40040"
     CDS             complement(3073..3288)
                     /locus_tag="H7R64_RS27375"
                     /old_locus_tag="WP3S18E05_P40040"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000137421.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MbeD family mobilization/exclusion protein"
                     /protein_id="WP_058671277.1"
                     /translation="MTELEKQLLSALEQLQQDYSKRLDEWENAFAEWRTMSGLMQRENA
                     ALSERVTGLSRQVQSLSDQLRRLSKG"
                     /name="MbeD family mobilization/exclusion protein"
     gene            complement(3292..3777)
                     /locus_tag="H7R64_RS27380"
                     /old_locus_tag="WP3S18E05_P40050"
     CDS             complement(3292..3777)
                     /locus_tag="H7R64_RS27380"
                     /old_locus_tag="WP3S18E05_P40050"
                     /inference="COORDINATES: protein motif:HMM:NF016710.3"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MbeB family mobilization protein"
                     /protein_id="WP_023139312.1"
                     /translation="MNSLLTLAKDLEQKSKAQQQSTGEMLKAAFSEHEKSVRAELSESE
                     KRISAAILDHDRKLSSAMSQRTKGMVRMVSQTWLTIVLVSALLTASGASILWWQGQQIL
                     DNYTTIREQKRTQAMLSERNSGVQLSTCGEQRRRCVRVNPEAGRFGEDSSWMILAGK"
                     /name="MbeB family mobilization protein"
     gene            complement(<3812..4516)
                     /locus_tag="H7R64_RS27885"
                     /pseudo=""
     CDS             complement(<3812..4516)
                     /locus_tag="H7R64_RS27885"
                     /inference="COORDINATES: protein motif:HMM:NF015397.3"
                     /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="relaxase/mobilization nuclease domain-containing
                     protein"
                     /name="relaxase/mobilization nuclease domain-containing
                     protein"
     gene            complement(4455..4778)
                     /locus_tag="H7R64_RS27390"
                     /old_locus_tag="WP3S18E05_P40070"
     CDS             complement(4455..4778)
                     /locus_tag="H7R64_RS27390"
                     /old_locus_tag="WP3S18E05_P40070"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000957083.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MobC family plasmid mobilization relaxosome
                     protein"
                     /protein_id="WP_170874913.1"
                     /translation="MLTMWVTEDEHRRLLDRCDGKQLAAWMRQTCLDEKPARAGKLPSL
                     SPALLRQLAGMGNNLNQIARQVNAGGGSGHDRVQVVAALMAIDAGLERLRHAVLEKGAD
                     DDR"
                     /name="MobC family plasmid mobilization relaxosome protein"
     gene            5419..5550
                     /locus_tag="H7R64_RS27890"
     CDS             5419..5550
                     /locus_tag="H7R64_RS27890"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_005761324.1"
                     /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_097739839.1"
                     /translation="MHEPPVQSDCCAFSGNYRLESNPERHAKAPLAAATGNRIHGAE"
                     /name="replication initiation protein"
     Typing          complement(4880..5066)
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="85.864"
                     /coverage="87.0"
                     /evalue="5.83e-49"
     Typing          5043..5528
                     /name="ColRNAI_rep_cluster_1987"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="90.65"
                     /coverage="93.0"
                     /evalue="0.0"
     Typing          complement(2982..4465)
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="91.515"
                     /coverage="99.0"
                     /evalue="0.0"
ORIGIN
        1 ttccggcaaa cgaaccaccg ttggtagcgg tggttttttt gtttacggct taggagatta
       61 cggctagaac gaaaggatct caagaagatc ctctcagaaa tcatacagac atgcggtagt
      121 ttgagatgtc tgagctatct aactcttttg ccggaaccag tttgtaatgc ctttcctcaa
      181 tcaatttcac ttgtccttcg tctatcttta gctcaaacag tgcaatcaaa tcgctcgaaa
      241 caaactgagc ggaaatagct ctacatctaa catttgggta tttttgttca caccacgctg
      301 tatcttgcga tgtttgcacc attgatattt gatcggttcc accttttgct tgaactggta
      361 ttatataatg gcaaccgtac ttatctatac ctacataaag ctcatcgatc tctatttgac
      421 caatcccctt caccgtagtt cttaaatgat tctgtaaaga atatgtggtt atacctagaa
      481 atatatctat tagtcggtta tatctcacct tcgccagcaa agcctgctcg tcgtctagag
      541 aataacctgt aattatctcc ggggtattat ctggtatttt tattgccacc atattaggat
      601 ttggcaaaat cctactaata gttaccaatc taaatcgata ctttgacctg ccagccagct
      661 caataatcca ctccttacct tctggctgtg tcaacagaat actttctggc ataggcgttc
      721 taaatctgat tgaatatata acatccccaa cattagatgg gagatctata cctaaatctt
      781 ttgcagcact gtttatctct aacctttcaa acaaaacctc taagtcacca tcaacatatt
      841 tatcgaaaaa tatcttttct accaactgat ggtatctatt ttttgaccta tcttttttat
      901 ccttactcac aaacaacctc cttgttacta ttttttattc tcttagcaat tacatttgat
      961 gacacaccaa acatagatgc agcatcggac atagaaatag caactaaact ttcatcaccg
     1021 agtttgattt tcttcgttgg tttttttggc gtaacaccaa gaaccttcat aatctgcaag
     1081 ccaacacttc tagctagcat aggaggaaca ctattaccga cctgtctgaa tccatgccac
     1141 ttagtcacat gaaatctgaa ccaatcagga tatgaatgca gtcttgctgc ctctctgacc
     1201 gtgatgaccc taggatagat cggatgtata ggacgaggag atgtaaaagc acctctgtca
     1261 cttgctgttc ctgctcttaa agtattacat aacccattca tcgagagctt tttgaacctg
     1321 ctgattggtt ctaccgtgtc aggcaaagtt tcaacaaacc gccctctaga aatgtcagag
     1381 tgatctgtca gtaaagaaca cgttaatttg tctttattaa aaatccttgg gtagctaaaa
     1441 tcactagggt cttttcctac gccatgcaaa taggatgagt atagtgattg ctcaccaaat
     1501 ttagcatcaa cccaatctct accccatagc tcaggatatt tttccgcatc agggatatcc
     1561 ccaatagcgt ccccaaccgt tgttctaatg gataatggct cagggtatga tggtagagta
     1621 attcctttcc ttccccccat taagaaaaga cgacggcgat cttgaggaac tccataatca
     1681 gctgcattta gcactttata atcacttaca acgtcgtacc cgccatcttt aaatgcatcc
     1741 attatctcta ctaaaaactg cttatgctta ccaaccgtca gcccttttac attctcaaaa
     1801 ataaagtatt taggctttag ctcaagaacc agccgtacat agtgatagac aagtttgttt
     1861 ctatcatcat caagcgcgcg ctttcctatt aatgaaaagc cttggcatgg agcgccgccg
     1921 atcactacat caatctcttt ctcaccaatg cctgaaactt ccctaacgta tttcccggta
     1981 acatcgacaa cacttctaca tatcgttttg cacataggaa agttatattt gtgagcagag
     2041 caatgtattg ggtctatttc aactgatgcc attatatcaa agccagcctg ctcgaaaccg
     2101 agactcagtc cacccgctcc agcaaataaa tcaacagcaa tcggtctagt cattctttac
     2161 acccacgtta tataaaatca acgtgatgct atcagaaaat cgatcgcttt accgatcgct
     2221 tttctgatat cggttgaaca taacatctct tgggcgcacc gctcagacgc gctcagggcg
     2281 tttttccgtc ctaagccaca aaagagcccg tcttctcacc gaaaaccgcc cggaatcgcg
     2341 ctgataagtt ttgcgtgtat gcatagccat gcacgaaaat gaactaacac tctgttcaat
     2401 gaattttcat gctgtacgca gtattttagt cttctatgcc ccctcgaaac acgcctgttc
     2461 ttgtgtagat tttttcgacc caagatggcc ttttatcaga gttaatgcag ccatacagga
     2521 acacacctgt tttgggttta tagctcccac cctcctgtgg ctggttatct acaaatgaat
     2581 aatcaatctt ttcacccttg actgaaacac gccccccaac atgaactaaa gaccagtgct
     2641 catgcattac atgactttca atcaatccaa aaggagaaaa accccatgaa tcaaaaaaaa
     2701 ccttgagtcc atcagatgca tcaccgagag aaatgattgc aaactcaacc tgctcacctg
     2761 taccttcaag gtaagaaggt ttctcgacgt taattacaga cgcccccttc acctgataac
     2821 ctttacaggt aagatataag tcgctcctgg ctaacggttt tgtgtgtgta atgttctccg
     2881 cagaagcgac tgtaaatgac ataaccaaaa ctactgagac tgagcaagcc cagaaacact
     2941 tcataacgca tcccttttca ttgattaact acattccaag ctcaaaacct ttctgccgct
     3001 gcgatcgttc cagctccagc gttttctgat gctgcgccgc ccgctcctgc tgcctgtgtg
     3061 cttcaatcga gttcagcctt tcgacaaccg gcgcagctga tcgctcaaac tctgcacctg
     3121 cctgctcaag cccgtgacgc gctcgctcag cgccgcgttc tcccgttgca taagaccaga
     3181 catcgtccgc cattccgcga aggcgttctc ccactcgtcc agccttttcg agtagtcctg
     3241 ctgtagctgc tctaatgcgc tcagcaactg tttttccagc tccgtcatgt gctatttccc
     3301 cgccagtatc atccagctcg aatcctctcc gaaccgtccc gcttccgggt tcaccctcac
     3361 gcagcggcgt ctctgctctc cgcaggtcga gagctgcacg ccgctgttcc tctcggacag
     3421 catggcctgc gtgcgcttct gctcccggat ggtcgtgtaa ttgtcgagta tctgctgccc
     3481 ctgccaccac agaatgcttg cgcccgatgc tgtcagcagt gcagacacca ggacgatggt
     3541 cagccacgtc tggctgacca tacgcaccat gcctttcgtg cgctggctca tggctgagga
     3601 cagcttccgg tcgtggtcga ggatggcggc gctgattctc ttctcgcttt cgctcagttc
     3661 cgctctgaca gacttctcgt gctcgctgaa tgcggctttc agcatctcgc cggtactctg
     3721 ctgctgcgct ttcgatttct gctctaagtc ctttgccagc gttaaaagac tgttcataga
     3781 tggctccctt cagtcggatg tttcgccccc cgtccgggtc ggcaatgctg atgctgcttt
     3841 ttgtggtgcg taccacctca aaacctgcgc tttccagcgc ctcagtgacg tcctggcggg
     3901 ttttcagctc cccggacgag gctaaggaca gtaaaccccg tgtaattgcc tgagcggctt
     3961 cctgcttcgt ttccggcagc gcggacggcg tgaccagcgc ccgccggttt tcaggcgcgt
     4021 tcgggtcatg cagccccagc ctgccgttca cgatggtctg ccaggcatca atgcgcggac
     4081 ggtcggcgcg gtcgtaatac ggctggagac gcttaccggt cagcagctcc gtgttcggga
     4141 tcaggaagtt cagctccagc cgccccttat cctggtgctc aacccacagc acgctgtact
     4201 ggtctttatc gagcccgggc atcagaaccc gttcaaagct cgccatcagc ttttcgcgct
     4261 gcccgggcgg taaatccttt tcggcaaagg acaggacgcc ggatgtgtac ttttttgcgt
     4321 agggcgaggc gtcgataagc tccctgactt cttccggctt cccctgcaga acggtggcgc
     4381 cgtcgcgctg tcggtctttc cccagcagat aatccaccgg accggcgcca ccgccgcgcc
     4441 ctcgcgggtg aaacttaacg atcatcgtct gcaccctttt ccagcacagc atgccgcagc
     4501 cgctcgagtc cggcatctat ggccatcagc gcggcgacga cctgcacgcg gtcgtgcccg
     4561 ctgccaccac cggcgttaac ctgccgggca atctggttga ggttgttccc catgccggca
     4621 agctgacgaa gcagcgccgg cgagagcgag ggaagcttgc cggcgcgggc gggtttctcg
     4681 tccaggcacg tctggcgcat ccaggctgca agctgtttac cgtcgcagcg atccagcaga
     4741 cggcggtgct catcttcggt cacccacatc gtgagcattt tgctgcgttt gtctgccaat
     4801 ccggcctcct gataacgccg ggacgggcgg gaaatctttt cccggtcggc gcggtgttgg
     4861 acaagccgca ggcgcgtcag tggttttagc gggtttcggg gcgcagccct gaaccagtca
     4921 cgtagcgcta gcggagtgta tactggctta atatggtaaa tcgaagtggg aattcaggga
     4981 agtgcttcat gtggcagggg gaaaatgcgg cgacggtgcg taagtgcaga atgtcaggat
     5041 tggtgaaatg acgcctcctc gctcactcag tcgctgcgct cctgccgtga gactgtggcg
     5101 ggcgttaccg gctcacgaat ggcgagataa ggagaccgag cggaaatcag gaaagactag
     5161 aaaaggatgc ggagttgccg tttttccata ggctccgccc ccctgacgag tatcataaaa
     5221 tctgacgctc aaatcagtgg cggcgaaacc cgacaggact ataaagatcc caggcgtttc
     5281 cccctggtag ctccctcgtg cgctctcctg ttcctgcctt tcggtttacc ggtgtcattc
     5341 cgctgttatg gccgcgtttg tctcattcca cgcctgacac tcagttccgg gtaggcagtt
     5401 cgctccaagc tggactgtat gcacgaaccc cccgttcagt ccgactgctg cgccttttcc
     5461 ggtaactatc gtcttgagtc caacccggaa agacatgcaa aagcgccact ggcagcagcc
     5521 actggtaatc ggattcacgg agcggagtag agttatctac agagttcttg aagtggtggc
     5581 ctgactacgg ctacactgaa aggacagttt tggtatctgc gctccgtgaa agccagttac
     5641 cttcggaagg aagagttggt agctctaaa
//
