LOCUS       NZ_AP022025             5064 bp    DNA     circular CON 02-DEC-2023
DEFINITION  Klebsiella sp. WP3-S18-ESBL-05 plasmid pWP3-S18-ESBL-05_5, complete
            sequence.
ACCESSION   NZ_AP022025
VERSION     NZ_AP022025.1
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  JOURNAL   Unpublished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 5064)
  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
            AP022025.1.
            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..5064
                     /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_5"
                     /geo_loc_name="Japan:Tokyo"
                     /lat_lon="35.6684 N 139.4278 E"
                     /collection_date="2018-08-06"
     gene            101..427
                     /locus_tag="H7R64_RS27395"
                     /old_locus_tag="WP3S18E05_P50010"
     CDS             101..427
                     /locus_tag="H7R64_RS27395"
                     /old_locus_tag="WP3S18E05_P50010"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_006674374.1"
                     /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_166687868.1"
                     /translation="MEKRTKEIKIRLTETEHQRLLDRCDRTHLAEWLRQLGLGEHTSRR
                     RRVPEVAPELLRQVSGIGNNLNQIARRLNQTDSLTPSERASLLVVLTSLDRQLGDLLEQ
                     NRDR"
                     /name="MobC family plasmid mobilization relaxosome protein"
     gene            636..>1058
                     /locus_tag="H7R64_RS27400"
                     /pseudo=""
     CDS             636..>1058
                     /locus_tag="H7R64_RS27400"
                     /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            1105..1590
                     /locus_tag="H7R64_RS27405"
                     /old_locus_tag="WP3S18E05_P50020"
     CDS             1105..1590
                     /locus_tag="H7R64_RS27405"
                     /old_locus_tag="WP3S18E05_P50020"
                     /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_139565498.1"
                     /translation="MSEILNLAKGFEEKSKQQAQDTEQSVKREFARLETSISAELQSSA
                     QSISNAIREQNGRLTGMLRKSVSTAMAWIFICFALLIGIMGGIIWFQGTIITSRLSEMD
                     SYSQQLASLKAKSGAGVTIYSDEKNRNTYLAVLPKQAHGVETYTSQAGNTVVKYTAK"
                     /name="MbeB family mobilization protein"
     gene            1660..1884
                     /locus_tag="H7R64_RS27410"
                     /old_locus_tag="WP3S18E05_P50030"
     CDS             1660..1884
                     /locus_tag="H7R64_RS27410"
                     /old_locus_tag="WP3S18E05_P50030"
                     /inference="COORDINATES: protein motif:HMM:NF016769.3"
                     /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_227652882.1"
                     /translation="MEKQLLSALESLQAGYEQQQQAWQDSYSSLQHMFEATSQALTHSD
                     RVCQHLSSQVDSLRAQVESLSRNVSRLMR"
                     /name="MbeD family mobilization/exclusion protein"
     gene            2040..2372
                     /locus_tag="H7R64_RS27415"
                     /old_locus_tag="WP3S18E05_P50040"
     CDS             2040..2372
                     /locus_tag="H7R64_RS27415"
                     /old_locus_tag="WP3S18E05_P50040"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_015873600.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="type II toxin-antitoxin system RelE/ParE family
                     toxin"
                     /protein_id="WP_001715142.1"
                     /translation="MSHTIEFIETPMFTRQIKQIATDEELRELQKTLIESPDKGDLIQK
                     TGGLRKVRMATGNQGKSGSARVIYFLATAEVIYLVMAYPKSTKDSLTDAEKAALKTLTQ
                     QLKDEV"
                     /name="type II toxin-antitoxin system RelE/ParE family
                     toxin"
     gene            2374..2658
                     /gene="nadS"
                     /locus_tag="H7R64_RS27420"
                     /old_locus_tag="WP3S18E05_P50050"
     CDS             2374..2658
                     /gene="nadS"
                     /locus_tag="H7R64_RS27420"
                     /old_locus_tag="WP3S18E05_P50050"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000007431.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="NadS family protein"
                     /protein_id="WP_001697687.1"
                     /translation="MSFFDELKASLEEAVEIKNGVREPARVTRYELADVKAIRAQLNVS
                     QSEMAKVLGTSLDTIKSWETGRRNPTGLAAKVLATIQANPKFFQELAAH"
                     /name="nadS"
     gene            2852..3754
                     /locus_tag="H7R64_RS27425"
                     /old_locus_tag="WP3S18E05_P50060"
     CDS             2852..3754
                     /locus_tag="H7R64_RS27425"
                     /old_locus_tag="WP3S18E05_P50060"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001517860.1"
                     /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_139565497.1"
                     /translation="MHNAALTLFNDRLPHKPYFSDDLHFGVRIAGKERAILAKYIQFNQ
                     PHAMFWLGFDVDRAGAAIDWSDRNAPAPTLTITNPDNGHAHLLYALKTSIRTAPDGKIK
                     PLRYAAAVENALRKKLEADAGYSGLICKNPNHGHWKIAVWQPELYTLDWLADFLDLNAA
                     NDKEIVADYGLGRNCTLFDRTRKWAYRAIRQGWPEYDQWLQACYERASAYNLQFAAPLD
                     DNEVNGIAKSIAKWTSIKITESSFKEYVEKTHTSDIQSLRGKKSKGGGRPFNPESLTSK
                     KPWLSMGISRSTYYRQLKR"
                     /name="replication initiation protein"
     gene            3757..4932
                     /locus_tag="H7R64_RS27430"
                     /old_locus_tag="WP3S18E05_P50070"
     CDS             3757..4932
                     /locus_tag="H7R64_RS27430"
                     /old_locus_tag="WP3S18E05_P50070"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_011217640.1"
                     /GO_function="GO:0005525 - GTP binding [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="GTPase"
                     /protein_id="WP_166687869.1"
                     /translation="MASSYEDFLGDSYDYNSQTFDADKAKQEAEEKKERFNIILFGATG
                     VGKSSLVNAVFGEEIVKSGVGKPVTQHLSKIKVPKKGIVLWDTKGIESKDYEETINQLK
                     KEIKSSFDNYSHLDDVPHLGWMCIDASGARVEPRDIELIGILKEYDIPIVIVFTKTLED
                     DTDEFVREAINEIDSHHGSYVSGNYVCVNSRERKIGKFTVPVSGLDELVDSSFKCLPEA
                     KRGAKQALKKAQMVKMGERLEAMKSGARNIVHGASAAAGAVGASPIPGSDAPLIAAVQS
                     GMIYKINSEFELDTSTSTTTSVVAGILGITAVAQVGKAVVSNALKFIPGVGSLIGGAIS
                     AATAVALTQAVGHAYIQVLVSYYNKETGIVELPESTTSILSVFKEHFSFKK"
                     /name="GTPase"
     Typing          complement(236..427)
                     /name="Col(Ye4449)"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="81.443"
                     /coverage="99.0"
                     /evalue="3.1e-36"
     Typing          418..1976
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="92.72"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 gccaccgtga ctggttcagg gggctcgccg ccccccgaaa cccctggcat ccactgcgaa
       61 aaattctcac ggtggtgcga attttttctc agcggagcct atggaaaagc gaacgaaaga
      121 gatcaaaatc cgtcttactg aaactgagca tcagcgactg cttgatcgct gcgaccggac
      181 tcatcttgcg gagtggctgc gtcagcttgg tttgggagaa cacacctcac gcaggcgccg
      241 tgtgcccgag gttgcgcccg aactgctgcg acaggtcagc gggattggca acaacctgaa
      301 ccagatagcc cgccgcctga accagactga ctccctgacg ccgtctgaac gtgcctcgct
      361 gcttgtcgta ctgaccagcc ttgaccggca gcttggcgac ctgctggagc agaaccgtga
      421 tcgttaaaat tcactcacgc ggtgcgggtt ccggcagtgg tccggtggat tacctgctgg
      481 gtaaagaccg gcagcgcgaa caggccagcg tactgcgcgg caaccctgaa catgtgcgcg
      541 aactgatcga cggctgcgac tttgcccgcg cctacacctc cggcgtgctg tcattccagg
      601 aacctgacat tgcagacgcg gagaaatcgc gcctgatgga tgaatgggag cacacgctgc
      661 tgaccggcct cgaccgcgac cagtacacct gcctgtgggt ggagcaccgc gacaagggac
      721 ggcttgagct gaattttgtc atcccgaaca tcgaattgca gagcggcaaa cgcctgcaac
      781 cctactttga ccgcgctgac cgcccccgtg tcaatgcctg gcagaccctg accaacgacc
      841 ggctggggct gcgcgacccg aacgacccga cttaccgccg cccgctgacg caggccagtg
      901 atctgccccg cgacaaacag caggcggcag agaaaatcac cgccggcctg atgaacctga
      961 tgcagcaggg cgtgatccgc agccggcagg acgtggtgac gcagctggaa agctacggcc
     1021 tgaccgtggc gcgggaaact aaaagcagta tcagcattgc cgatccggac ggcggccgaa
     1081 atatccggct gaaaggaatg atctatgagc gagattttaa atttggcgaa gggcttcgag
     1141 gagaaatcga agcagcaggc gcaggatacc gagcagagcg tgaagcgcga gttcgcgagg
     1201 ctggagacgt ctatcagcgc ggaactgcaa tcaagcgcgc agagcatcag caacgctatc
     1261 cgcgagcaga acggcaggct gacgggcatg ctcaggaagt cagtctcaac agcaatggcg
     1321 tggatattca tctgcttcgc cctgctgatc ggcatcatgg gcgggataat ctggtttcag
     1381 ggcacgatca tcacctcacg cctgagcgag atggacagct acagccagca gctggcgagc
     1441 ctgaaagcga aaagcggcgc gggcgtgacg atttacagcg acgaaaagaa ccggaacacc
     1501 tacctggcgg tgctgccgaa gcaggcgcac ggcgtggaaa cctacacctc gcaggccggg
     1561 aataccgtgg tgaaatacac ggcgaaataa cctcatcaga gcgccctgaa acgccacagc
     1621 acgtttttaa caccgaggat gaccaaaacc atgaccgaga tggaaaaaca gcttctgagc
     1681 gccttagaga gcttacaggc aggctacgag caacagcagc aggcgtggca ggacagctac
     1741 agcagtttgc agcacatgtt cgaggctacc tcacaggcgc tgacgcacag cgaccgggtg
     1801 tgtcagcact tgagcagtca ggtggacagc ttgcgcgcgc aggtcgagag cttgagcagg
     1861 aacgtcagcc gcttgatgcg ctgattgcgc agcatgaccg cgcccgtgcg gaaaagctgc
     1921 gcgagcaaca gccggagccg cagaaaaagc cgacccggta ctatggcccc tcgatgtgac
     1981 ctcttttccg gaatcagaat taagtgtact atgtactccg ttaaatacag gagacaaccg
     2041 tgagtcacac gattgaattt atcgagaccc cgatgtttac ccgtcagata aaacagatcg
     2101 ccacggatga agagctcagg gagctgcaaa agacgctgat tgagtcgccg gacaaaggcg
     2161 atctcatcca gaaaaccggc gggctgcgaa aagtcagaat ggcgacgggc aaccagggaa
     2221 aaagcggcag cgcgagggtg atttattttc tggccaccgc cgaggtgatt tatctggtga
     2281 tggcctaccc gaaaagcacc aaagacagcc tgacggacgc ggagaaagcc gcgctgaaga
     2341 cactgaccca acaactgaaa gacgaggtgt gacatgagtt tttttgacga gctgaaagca
     2401 tcgctggaag aagccgttga aatcaaaaac ggcgtcagag agcctgcccg cgtcacccgt
     2461 tacgagctgg cagacgtgaa ggctatcagg gcacaactga acgtttcaca gagtgagatg
     2521 gcgaaagtgc tgggaaccag cctcgacacc ataaaaagct gggaaaccgg acgccgtaat
     2581 ccgaccggac tggcggcgaa ggtgctggca accatccagg cgaacccgaa attcttccag
     2641 gagctggcgg cgcactaagc cgttgtgaca gaaggattcg acaggcgagg ccgttcgcgt
     2701 gtaatttaac ggcaacagaa aaaacaaagc cccggcatca tgctcaaatc ttggcggatc
     2761 cgcatgataa ccagggccag gtacgaaacc ttgaaaggat attagcacat gaaacgtgcc
     2821 agacaacagc ccgccataag cgcagggcgc attgcataac gccgcactca cactcttcaa
     2881 cgaccgctta ccgcacaagc cgtacttttc ggacgatctg cattttggtg tacggattgc
     2941 cggtaaggaa cgcgccattc tggcgaaata catccagttt aatcagcctc acgccatgtt
     3001 ctggctggga ttcgacgtcg atcgcgccgg tgccgccatc gactggagcg atcgcaacgc
     3061 ccccgcgcct acgttgacca tcaccaaccc cgacaacgga catgcgcacc tgctgtacgc
     3121 gttgaaaacc tcgatacgca ccgcaccgga cggaaaaata aagccattgc gctacgccgc
     3181 cgccgttgag aacgcgctac gcaaaaaatt agaggctgac gcggggtatt cggggctaat
     3241 ctgcaaaaat ccgaaccacg gccactggaa aattgccgta tggcaacctg aactttacac
     3301 gctggactgg ctggctgact ttctcgacct gaatgcggcg aacgacaaag aaatcgttgc
     3361 tgactacggt ttaggccgta actgcaccct gttcgacaga acccgcaagt gggcataccg
     3421 cgctatccgt cagggctggc ctgagtatga ccagtggctt caagcctgct acgaacgcgc
     3481 cagtgcctat aacctgcaat ttgcagcacc actggatgat aatgaggtga acggtattgc
     3541 taaaagcatt gctaagtgga cgagtataaa aataacagaa tcatctttta aagagtatgt
     3601 agaaaaaaca catacatccg atatccagtc tttacggggt aaaaagagta aaggtggtgg
     3661 acgacctttt aatcctgagt ccttaacatc aaaaaaacca tggctaagca tggggataag
     3721 tagaagcacg tattatcgac aattaaagag gtaactatgg ctagttctta tgaagacttt
     3781 ttaggcgatt cttatgacta caactcacaa actttcgatg ctgacaaagc aaaacaggaa
     3841 gcagaagaaa aaaaagaaag atttaatatt atattgttcg gtgccactgg cgttgggaaa
     3901 agctccttag ttaatgctgt ttttggggag gaaatagtca agtctggagt gggtaaacca
     3961 gttactcagc atctgagtaa aattaaagtt cccaaaaaag gaattgtatt atgggacact
     4021 aaagggattg aatctaaaga ttatgaagaa acaataaatc aattaaaaaa agaaattaaa
     4081 tctagctttg ataactactc acacttggat gatgttcctc accttggttg gatgtgcatt
     4141 gatgcttctg gcgccagagt tgaaccaaga gatatagagc ttatcgggat attaaaagaa
     4201 tatgacatac ctattgtaat tgtattcact aaaactcttg aagatgacac tgatgaattt
     4261 gtgcgcgagg ctatcaatga aattgatagc catcatggaa gttatgtttc tggtaactat
     4321 gtttgtgtta attcaagaga aagaaaaata gggaagttta ctgttccagt aagtggtttg
     4381 gatgagttag ttgactcgag ttttaaatgt cttccagaag ctaagagagg tgcaaagcaa
     4441 gccttaaaaa aggctcaaat ggttaagatg ggagaacggc ttgaagccat gaaaagtggc
     4501 gcgagaaaca tcgttcatgg agcgtcagca gcagctggag ctgtcggagc ttctcctatt
     4561 ccggggtctg atgcgccgtt aattgcagct gtacaaagtg gaatgatata taaaataaac
     4621 tctgagtttg aattggacac atctacatca acaactacat ctgttgtagc aggcattctt
     4681 ggtattacag ctgttgctca agtaggcaag gctgttgttt ctaatgcgtt aaaatttatt
     4741 cctggtgtag gttcccttat tggtggtgcc atttctgcag ctactgctgt agctcttacc
     4801 caagccgtag gtcatgctta catccaagtt ctggtttcct actacaacaa agaaaccggg
     4861 atcgtcgagt tgccggaaag taccacttca atactctctg tctttaaaga gcatttttcc
     4921 ttcaaaaaat agcgttgaga caataacaac ctatatcaga taacagcccc gtataagcgg
     4981 ggcttttttt ttgcagccag cacagaatct gacatactgc attactcttt aagccagtac
     5041 acacagcgtc ccctctatcg aggt
//
