LOCUS       NZ_CP074190             4906 bp    DNA     circular CON 13-MAY-2024
DEFINITION  Raoultella planticola strain JBIWA001 plasmid pJBIWA001_8, complete
            sequence.
ACCESSION   NZ_CP074190
VERSION     NZ_CP074190.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN18916998
            Assembly: GCF_019968885.1
KEYWORDS    RefSeq.
SOURCE      Raoultella planticola
  ORGANISM  Raoultella planticola
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Klebsiella/Raoultella group; Raoultella.
REFERENCE   1  (bases 1 to 4906)
  AUTHORS   Gomi,R., Matsumura,Y., Tanaka,M., Ihara,M., Sugie,Y., Matsuda,T. and
            Yamamoto,M.
  TITLE     Emergence of rare carbapenemases (FRI, GES-5, IMI, SFC and SFH-1) in
            Enterobacterales isolated from surface waters in Japan
  JOURNAL   J Antimicrob Chemother 77 (5), 1237-1246 (2022)
   PUBMED   35137119
REFERENCE   2  (bases 1 to 4906)
  AUTHORS   Gomi,R.
  TITLE     Direct Submission
  JOURNAL   Submitted (03-MAY-2021) Department of Environmental Engineering,
            Kyoto University, KyotoDaigakuKatsura, Nishikyo-ku, Kyoto-city
            615-8540, Japan
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: Unicycler v. 0.4.8
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 135x
            Sequencing Technology             :: DNBSEQ; Oxford Nanopore GridION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_019968885.1-RS_2024_05_13
            Annotation Date                   :: 05/13/2024 04:14:11
            Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline
            (PGAP)
            Annotation Method :: Best-placed reference protein set; GeneMarkS-2+
            Annotation Software revision      :: 6.7
            Features Annotated                :: Gene; CDS; rRNA; tRNA; ncRNA
            Genes (total)                     :: 5,989
            CDSs (total)                      :: 5,866
            Genes (coding)                    :: 5,727
            CDSs (with protein)               :: 5,727
            Genes (RNA)                       :: 123
            rRNAs                             :: 9, 8, 8 (5S, 16S, 23S)
            complete rRNAs                    :: 9, 8, 8 (5S, 16S, 23S)
            tRNAs                             :: 85
            ncRNAs                            :: 13
            Pseudo Genes (total)              :: 139
            CDSs (without protein)            :: 139
            Pseudo Genes (ambiguous residues) :: 0 of 139
            Pseudo Genes (frameshifted)       :: 46 of 139
            Pseudo Genes (incomplete)         :: 109 of 139
            Pseudo Genes (internal stop)      :: 34 of 139
            Pseudo Genes (multiple problems)  :: 44 of 139
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP074190.1.
            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..4906
                     /organism="Raoultella planticola"
                     /mol_type="genomic DNA"
                     /strain="JBIWA001"
                     /isolation_source="lake water"
                     /db_xref="taxon:575"
                     /plasmid="pJBIWA001_8"
                     /geo_loc_name="Japan: Shiga"
                     /lat_lon="35 N 136 E"
                     /collection_date="2020-02-05"
                     /collected_by="Kyoto University"
     gene            complement(85..978)
                     /locus_tag="KGP19_RS29855"
                     /old_locus_tag="KGP19_29715"
     CDS             complement(85..978)
                     /locus_tag="KGP19_RS29855"
                     /old_locus_tag="KGP19_29715"
                     /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_094158691.1"
                     /translation="MNNAVLELFNDRLPHKPYFSDDLHFGVRIAGKERAILAKYIQFNQ
                     PHAMFWLGFDVDRAGAAIDWSDRNAPAPTLTITNPENGHAHLLYALETSIRTAPDGKMK
                     PLRYAAAVENALRKKLEADAGYSGLICKNPNHGHWKIAVWQPELYTLDWLADFLDLNAA
                     NDKEIVADYGLGRNCTLFDKTRKWAYRAIRQGWPEYEQWLQACYERASAYNLQFAVPLD
                     DKEVNDIAKSIAKWTLKRLDESTFKQYVLDTHSPEIQSVRGKRSKRGASLCSERTLEPW
                     VELGISRRKYYYDKKK"
                     /name="replication initiation protein"
     gene            complement(1171..1455)
                     /gene="nadS"
                     /locus_tag="KGP19_RS29860"
                     /old_locus_tag="KGP19_29720"
     CDS             complement(1171..1455)
                     /gene="nadS"
                     /locus_tag="KGP19_RS29860"
                     /old_locus_tag="KGP19_29720"
                     /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            complement(1457..1789)
                     /locus_tag="KGP19_RS29865"
                     /old_locus_tag="KGP19_29725"
     CDS             complement(1457..1789)
                     /locus_tag="KGP19_RS29865"
                     /old_locus_tag="KGP19_29725"
                     /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_064184160.1"
                     /translation="MSHAIEFIETPMFTRQIKQIATDEELRELQKTLIESPDKGDLIQK
                     TGGLRKIRMATGNQGKSGSVRVIYFLATAEVIYLVMAYPKSTKDSLTDAEKAALKTLTQ
                     QLKNEV"
                     /name="type II toxin-antitoxin system RelE/ParE family
                     toxin"
     gene            complement(1945..2190)
                     /locus_tag="KGP19_RS29870"
                     /old_locus_tag="KGP19_29730"
     CDS             complement(1945..2190)
                     /locus_tag="KGP19_RS29870"
                     /old_locus_tag="KGP19_29730"
                     /inference="COORDINATES: protein motif:HMM:NF016769.4"
                     /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_306293335.1"
                     /translation="MTKTMTEMEKQLLSALESLQTSYEQQQQAWQDSYSSLQHMFEATS
                     QALTHSDRVCQHLSSQVESLRAQVESLSRNVSRLMR"
                     /name="MbeD family mobilization/exclusion protein"
     gene            complement(2239..2724)
                     /locus_tag="KGP19_RS29875"
                     /old_locus_tag="KGP19_29735"
     CDS             complement(2239..2724)
                     /locus_tag="KGP19_RS29875"
                     /old_locus_tag="KGP19_29735"
                     /inference="COORDINATES: protein motif:HMM:NF016710.4"
                     /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_095841943.1"
                     /translation="MSEILNLAKGFEEKSKQQAQDTEQSVKREFARLETSISAELQSSS
                     QSISNAIREQNGRLTGMLRASVSTAMAWIFICFALLIGILSGIIWFQGTIITSRLSEMD
                     SYSQQLESLKAKSGAGVAIYSDDKHRNTYMVVLPKQAHGVETYTSTTDNTVVKYTAK"
                     /name="MbeB family mobilization protein"
     gene            complement(<2771..3193)
                     /locus_tag="KGP19_RS29880"
                     /old_locus_tag="KGP19_29740"
                     /pseudo=""
     CDS             complement(<2771..3193)
                     /locus_tag="KGP19_RS29880"
                     /old_locus_tag="KGP19_29740"
                     /inference="COORDINATES: protein motif:HMM:NF015397.4"
                     /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(3402..3728)
                     /locus_tag="KGP19_RS29885"
                     /old_locus_tag="KGP19_29745"
     CDS             complement(3402..3728)
                     /locus_tag="KGP19_RS29885"
                     /old_locus_tag="KGP19_29745"
                     /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_042014476.1"
                     /translation="MEKRTKEIKIRLTETEHQRLLDRCDRTHLAEWLRQLGLGEHISRK
                     RRVPDVAPELLRQVSGIGNNLNQIARRLNQTDSLTPAERASLLVVLTSLDRQLGDLLEQ
                     NRDR"
                     /name="MobC family plasmid mobilization relaxosome protein"
     gene            complement(3944..4669)
                     /locus_tag="KGP19_RS29890"
                     /old_locus_tag="KGP19_29750"
     CDS             complement(3944..4669)
                     /locus_tag="KGP19_RS29890"
                     /old_locus_tag="KGP19_29750"
                     /EC_number="2.1.1.-"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_004193434.1"
                     /GO_function="GO:0003677 - DNA binding [Evidence IEA];
                     GO:0008170 - N-methyltransferase activity [Evidence IEA]"
                     /GO_process="GO:0009307 - DNA restriction-modification
                     system [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="site-specific DNA-methyltransferase"
                     /protein_id="WP_223526271.1"
                     /translation="MDLFNVDAVEWLKTLPSGSVDMVVTDPPYESLEKHRKIGTTTRLK
                     VSKSSSNEWFSIFPNDRFESLLSEIHRVLKNNRHFYIFCDQETMFLLKPIGEKVGFKFW
                     KPIVWDKKAIGMGYHYRAKYEFILFFEKGKRKLNNLGIPDILESKRIRNGYPTEKPVEL
                     LELLIQQSTERGELVIDPFFGSGSALKAALNQGRLCAGNDISASAHAYFRDTHLPDDLK
                     SAALTPALPVEQAARICTK"
                     /name="site-specific DNA-methyltransferase"
     Typing          3403..3595
                     /name="Col(Ye4449)"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="80.513"
                     /coverage="100.0"
                     /evalue="1.87e-33"
     Typing          complement(1854..3412)
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="97.51"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 gcaatgctta aatcaacacc acaacaggta caagaactca tataaacctc caaattaaca
       61 atgctgtgaa tcaaattaaa aacatcattt tttcttgtcg tagtagtatt ttctacgact
      121 aataccaagc tcaacccaag gctctaaagt tctttcagaa cataatgatg cgcctctttt
      181 cgacctcttt ccccttactg attgaatctc aggggaatga gtatctaata catactgctt
      241 aaaagtagac tcgtcgagtc ttttaagagt ccatttggcg atactctttg caatatcatt
      301 gacctcttta tcatccaaag gcacagcaaa ttgcagattg taggcgctgg cacgctcata
      361 gcaggcttgc agccactgct catactcagg ccagccctga cggatggcgc ggtatgccca
      421 cttgcgggtt ttgtcgaaca acgtgcagtt acggcctaag ccgtagtcgg caacgatttc
      481 tttgtcgttc gcagcgttca ggtcgagaaa gtcagccagc cagtccagtg tgtagagttc
      541 tggctgccac accgcaattt tccagtggcc gtggttcgga tttttgcaga ttaaccccga
      601 ataccccgcg tcagcctcta attttttacg cagcgcgttc tccacggcgg cagcgtagcg
      661 cagcggcttc attttcccgt caggtgcggt gcgtatcgag gtttccagcg cgtacagcag
      721 gtgcgcgtgt ccgttttccg ggttggtgat ggtcagcgtg ggcgcgggcg cgttgcgatc
      781 gctccagtcg atggcggcac cggcgcgatc gacgtcgaat cccagccaga acatggcgtg
      841 aggctgattg aactggatgt atttcgccaa aatggcgcgt tctttccctg caatgcgtac
      901 accaaagtgt aaatcatccg agaagtacgg cttgtgcggt aagcggtcgt tgaaaagttc
      961 gagtactgcg ttattcaatt cgccctgcgc ttatggcggg ctgttgtctg gcacgtttca
     1021 tgtgctaata tcctttcaag gtttcgacct ggccctggtt atcatgtgca tccgccaaga
     1081 ttgagcatga tttccggggc tttgtttttt ctgttgccgt taaattacac gcgaacggcc
     1141 tcgcctgtcg aatccttctg tcacaacggc ttagtgcgcc gccagttcct ggaagaattt
     1201 cgggttcgcc tggatggttg ccagtacctt cgccgccagt ccggtcgggt tacggcgtcc
     1261 ggtttcccag ctcttgatgg tgtcgaggct ggttcccagc acttttgcca tctcgctctg
     1321 agatacgttc agctgtgccc tgatggcttt cacgtctgcc agctcgtaac gggtgacgcg
     1381 ggcaggctct ctgacgccgt ttttgatttc aacggcttct tccagcgatg ctttcagctc
     1441 gtcaaaaaaa ctcatgtcac acctcgtttt tcagttgttg ggtcagcgtc ttcagcgcgg
     1501 ctttttccgc gtccgtcagg ctgtctttgg tgcttttcgg gtaggccatc accagataga
     1561 tcacctcggc ggtggccaga aagtaaatca ccctcacgct gccgcttttt ccctggttgc
     1621 ccgtcgccat cctgattttg cgcagcccgc cggttttctg aatgagatcg cctttgtccg
     1681 gcgactcaat cagcgtcttt tgcagttccc tgagttcttc atccgtggcg atctgtttta
     1741 tctgacgggt aaacatcggg gtctcgataa actcaatcgc gtgactcacg gctgtctcct
     1801 gtttttaacg gagtacatag tacacttaat tctgatttcg gaaaagcggt cacatcgagg
     1861 ggccatagta acgagtcgtt tttttctgcg gctccggctg ctgctcgcgc agcttctcct
     1921 cactggcgcg gtcatgctgt gcaatcagcg catcaagcgg ctgacgttcc tgctcaagct
     1981 ctcgacctgc gcgcgcaagc tctctacctg actgctcaag tgctgacaca cccggtcgct
     2041 gtgcgtcagc gcctgtgaag tagcctcgaa catgtgctgc aagctgctgt agctgtcctg
     2101 ccacgcctgc tgctgttgct cgtagcttgt ctgtaagctc tctaaggcgc tcagaagctg
     2161 tttttccatc tcggtcatcg ttttggtcat cctcggtgtt aaaaacgcgc tgtgtcgttt
     2221 cagggcgctc tgacggggtt atttcgccgt gtatttcact acggtgttgt cggtcgtcga
     2281 tgtataggtt tccacgccgt gcgcctgctt cggcagcacc accatgtagg tgttccggtg
     2341 cttgtcgtcg ctgtagatcg ccacgcccgc gccgcttttc gctttcaggc tctccagctg
     2401 ttggctgtag ctgtccatct cgctcaggcg cgaggtgatg atcgtgccct gaaaccagat
     2461 tatcccgctc aggatgccga tcagcagggc gaagcagatg aatatccacg ccatcgccgt
     2521 tgagacagag gctctgagca tgcccgtcag tctgccgttc tgctcgcgga tagcgttgct
     2581 gatgctctgc gagcttgatt gcagttccgc gctgatagac gtctccagcc tcgcgaactc
     2641 gcgcttcacg ctctgctcgg tatcctgcgc ctgctgcttc gatttctcct cgaagccctt
     2701 cgccaaattt aaaatctcgc tcataaatca ttcctttcag ccggatattt cggccgccgt
     2761 ccggatcggc aatgctgatg ctgcttttcg tttcccgcgc cacggtcagg ccgtagcttt
     2821 ccagctgcgt caccacgtcc tgccggctgc ggatcacgcc ctgctgcatc aggttcatca
     2881 ggccggcggt gattttctct gccgcctgct gtttgtcgcg gggcagatcg ctggcctgcg
     2941 tcagcggacg gcggtagatc gggtcgttcg ggtcgcgcag ccccagccgg tcgttggtca
     3001 gggtctgcca ggcgttgacg cggggacggt cggcgcggtc aaagtagggt tgcaggcgtt
     3061 ttccactctg caattcgatg ttcgggatga caaaattcag ctcaagccgt cccttgtcgc
     3121 gatgctctac ccacaggcag gcgtactggt cgcggtcgag gccggtcagc agcgtgtgct
     3181 cccattcgtc catcaggcgc gatttctcca cgtctgcaat gtcaggttcc tggaatgaaa
     3241 gcacgccgga agtataggcg cgggcaaagt cgcagccgtc gatcagctcc cgcacatgtt
     3301 caggattgcc gcgcagtacg gtggcctgtt cgcgctgccg gtcttttccc agcaggtaat
     3361 ccacaggacc gctacccgaa cccgcacccc gcgagtgaat tttaacgatc acggttctgc
     3421 tccagcaggt cgccaagctg acggtcaagg ctggtcagta cgacgagcag cgaggcacgt
     3481 tcagcaggcg tcagggaatc agtctgattc aggcgacggg cgatctggtt caggttattg
     3541 ccaatcccgc tgacctgtcg cagcagttcg ggcgccacat caggcacacg gcgcttgcgt
     3601 gagatgtgtt cacccagacc gagctgacgt aaccattcgg caaggtgagt acggtcacag
     3661 cggtcaagca gccgctgatg ctcagtttcg gtgagccgga ttttgatctc tttcgttcgc
     3721 ttttccatag gctccgctga gaaaaaattc gcaccaccgt gagaattttt cgcagtggat
     3781 gccgggggtt tcggggggcg gcgagccccc tgaaccagtc acggtggcac ctcgttagag
     3841 gggacgctgt gtgtactggc ttaggggaaa gtgcagtatg acagattcag tgctggttgc
     3901 aaaaaaaagc cctctgctag agagggctgt tatctgatat aggttatttg gtgcaaattc
     3961 tcgcagcctg ctcaacggga agcgctggag tgagtgctgc tgattttaga tcgtcaggga
     4021 gatgggtatc tctaaagtaa gcgtgtgccg atgctgatat atcattacca gcgcaaagac
     4081 gcccctgatt gagagctgct tttagtgctg agccggaccc aaagaaaggg tctatcacaa
     4141 gctctccacg ctctgtactt tgctgtatca atagctccag caactcgaca ggtttctccg
     4201 ttgggtaccc atttctaatt cttttacttt ctaatatatc tggtatccct aaattattta
     4261 gctttctttt acccttttca aaaaatagaa taaactcata cttcgctctg tagtgatagc
     4321 ccatcccgat agccttttta tcccaaacta taggcttcca aaatttaaat cctactttct
     4381 ctccaatggg ttttaaaaga aacattgttt cttggtcaca aaatatataa aaatgcctat
     4441 tatttttaag caccctatga atttcagaaa gcaacgattc aaacctatcg tttgggaaaa
     4501 tactgaacca ttcattgcta gatgatttac tcaccttaag ccttgttgta gtacctatct
     4561 tcctgtgttt ctctaacgat tcatacgggg ggtctgtgac caccatatcg acgctcccgc
     4621 tagggagcgt ctttaaccat tcaactgcat caacattaaa caaatcaatc acgctttagc
     4681 taccatattg cacttaatct catgagataa atcgacagaa gatggttcac caggcccttt
     4741 attacgacaa tcaatgcaat ggctatgtac accatctggg ttatttgccg ttactcgacg
     4801 gtcagtaaaa ccgaagtctt caacaagcct acgaaaaata tgaagtgaac cgtgagtttg
     4861 agaacaccta gggcatgatt ttaacgtatt atcagcactt ctaata
//
