LOCUS       NZ_AP026528             5207 bp    DNA     circular CON 27-NOV-2023
DEFINITION  Klebsiella pneumoniae subsp. pneumoniae strain TUM9839 plasmid
            pMTY9839_NA1, complete sequence.
ACCESSION   NZ_AP026528
VERSION     NZ_AP026528.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMD00510808
            Assembly: GCF_025997695.1
KEYWORDS    RefSeq.
SOURCE      Klebsiella pneumoniae subsp. pneumoniae
  ORGANISM  Klebsiella pneumoniae subsp. pneumoniae
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Klebsiella/Raoultella group; Klebsiella.
REFERENCE   1
  AUTHORS   Ikegaya,K., Aoki,K., Komori,K., Ishii,Y. and Tateda,K.
  TITLE     Complete genome of blaCTX-M-2-producing Enterobacteriales
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 5207)
  AUTHORS   Aoki,K. and Ishii,Y.
  TITLE     Direct Submission
  JOURNAL   Submitted (17-JUL-2022) Contact:Kotaro Aoki Toho University,
            Department of Microbiology and Infectious Diseases Toho University
            School of Medicine; 5-21-16, Omori-nishi, Ota-ku, Tokyo 143-8540,
            Japan
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: Unicycler v. 0.4.8-beta
            Genome Coverage                   :: 117x
            Sequencing Technology             :: Illumina MiSeq; ONT MinION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 11/27/2023 03:07:20
            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)                     :: 5,364
            CDSs (total)                      :: 5,242
            Genes (coding)                    :: 5,144
            CDSs (with protein)               :: 5,144
            Genes (RNA)                       :: 122
            rRNAs                             :: 9, 8, 8 (5S, 16S, 23S)
            complete rRNAs                    :: 9, 8, 8 (5S, 16S, 23S)
            tRNAs                             :: 86
            ncRNAs                            :: 11
            Pseudo Genes (total)              :: 98
            CDSs (without protein)            :: 98
            Pseudo Genes (ambiguous residues) :: 0 of 98
            Pseudo Genes (frameshifted)       :: 50 of 98
            Pseudo Genes (incomplete)         :: 48 of 98
            Pseudo Genes (internal stop)      :: 17 of 98
            Pseudo Genes (multiple problems)  :: 16 of 98
            CRISPR Arrays                     :: 1
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            AP026528.1.
            Annotated by DFAST https://dfast.ddbj.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..5207
                     /organism="Klebsiella pneumoniae subsp. pneumoniae"
                     /mol_type="genomic DNA"
                     /strain="TUM9839"
                     /isolation_source="animal"
                     /sub_species="pneumoniae"
                     /db_xref="taxon:72407"
                     /plasmid="pMTY9839_NA1"
                     /geo_loc_name="Japan"
                     /collection_date="2010"
     gene            complement(406..747)
                     /locus_tag="OO859_RS26760"
                     /old_locus_tag="TUM9839_51650"
     CDS             complement(406..747)
                     /locus_tag="OO859_RS26760"
                     /old_locus_tag="TUM9839_51650"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_006122514.1"
                     /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_071599364.1"
                     /translation="MADKRNKMLTMWVTEDEHRRLLERCDGKQLAAWMRQTCLDEKPTR
                     AGRLPSISPALLRQLAGMGNNLNQIARKVNAGGAGHDRVQIVAALMAIDAGLERLRHAV
                     LEKGPDDDC"
                     /name="MobC family plasmid mobilization relaxosome protein"
     gene            1361..1492
                     /locus_tag="OO859_RS26765"
     CDS             1361..1492
                     /locus_tag="OO859_RS26765"
                     /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_072007956.1"
                     /translation="MHEPPVQSDCCALSGNYRLESNPKRHAKAPLAAATGNRIHGAE"
                     /name="replication initiation protein"
     gene            complement(1712..2521)
                     /locus_tag="OO859_RS26770"
                     /old_locus_tag="TUM9839_51660"
     CDS             complement(1712..2521)
                     /locus_tag="OO859_RS26770"
                     /old_locus_tag="TUM9839_51660"
                     /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="hypothetical protein"
                     /protein_id="WP_032446875.1"
                     /translation="MSKDKKERSKNRYHQLVEKIFFDKYVDGDLEVLFERLDINSAAKD
                     LGIELPSNVGDVIYSIRFRTPMPESILLTQPEGKEWIIELAGRSKYRFRLVTISRILPN
                     PNMVAIKIPDNTPEIITGYSLDDEQALLAKVRYNRLIDIFLGITTYSLQNHLRTTVKGI
                     GQIEIDELYVGIDKYGCHYIIPVQAKGGTDQISMVQTSQDTAWCEQKYPNVRCRAISAQ
                     FVSSDLIALFELKIDEGQVKLIEERHYKLVPVKELDSSDISNYRMSV"
                     /name="hypothetical protein"
     gene            complement(2514..3764)
                     /locus_tag="OO859_RS26775"
                     /old_locus_tag="TUM9839_51670"
     CDS             complement(2514..3764)
                     /locus_tag="OO859_RS26775"
                     /old_locus_tag="TUM9839_51670"
                     /EC_number="2.1.1.37"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_015160339.1"
                     /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_001584442.1"
                     /translation="MTRPIAVDLFAGAGGLSLGFEQAGFDIMASVEIDPIHCSAHKYNF
                     PMCKTICRSVVDVTGEYVREVSGIGEKEIDVVIGGAPCQGFSLIGKRALDDDRNKLVYH
                     YVRLVLELKPKYFVFENVKGLTVGKHKQFLVEIMDAFKDGGYDVVSDYKVLNAADYGVP
                     QDRRRLFLMGGRKGIALPSYPEPLSIRTTVGDAIGDIPDAEKYPELWGRDWVYAKFGEQ
                     SLYSSYLHGVGKDPSDFSYPRIFNKDKLTCSLLTDHSDISRGRFVETLPDTVEPISRFK
                     KLSMNGLCNTLRAGTASDRGAFTSPRPIHPIYPRVITVREAARLHSYPDWFRFHVTKWH
                     GFRQVGNSVPPMLARSVGLQIMKVLGVTPKKPTKKIKLGDESLVAISMSDAASMFGVSS
                     NVIAKRIKNSNKEVVCE"
                     /name="DNA cytosine methyltransferase"
     gene            complement(4216..4431)
                     /locus_tag="OO859_RS26780"
                     /old_locus_tag="TUM9839_51680"
     CDS             complement(4216..4431)
                     /locus_tag="OO859_RS26780"
                     /old_locus_tag="TUM9839_51680"
                     /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="MbeD family mobilization/exclusion protein"
                     /protein_id="WP_015328239.1"
                     /translation="MTELEKQLLSALEQLQQDYSRRLDEWESAFEEWRKMSGLMQRENA
                     ALSERVSGLSRQVQSLSEQLRRLSTG"
                     /name="MbeD family mobilization/exclusion protein"
     gene            complement(4438..4935)
                     /locus_tag="OO859_RS26785"
                     /old_locus_tag="TUM9839_51690"
     CDS             complement(4438..4935)
                     /locus_tag="OO859_RS26785"
                     /old_locus_tag="TUM9839_51690"
                     /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="MbeB family mobilization protein"
                     /protein_id="WP_015328238.1"
                     /translation="MSSLLTASRDFEEKSKAQQQLTEERLKAAFSKHENVVKSELNASA
                     KRINDAISAHEQGMNAAMQSNRLSVLRMVGRTWLTITMVSGLLFASLSGVLWYQGNRIA
                     ANLAEIRQQRDTLSKLHMQTWGVTYLENRNGRFLVLPEGMKAETGRTVDNKTRNAVKLV
                     RE"
                     /name="MbeB family mobilization protein"
     Typing          complement(832..1007)
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="90.449"
                     /coverage="81.0"
                     /evalue="5.74e-59"
     Typing          954..1470
                     /name="ColRNAI_rep_cluster_1987"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="90.076"
                     /coverage="99.0"
                     /evalue="0.0"
     Typing          complement(4..416)
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="99.0"
                     /evalue="1.69e-83"
     Typing          complement(413..726)
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="92.453"
                     /coverage="99.0"
                     /evalue="1.04e-58"
     Typing          complement(4101..5206)
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="99.0"
                     /evalue="0.0"
ORIGIN
        1 accactgtct gccacgcatc gatgcgtggc cggtcggcac gatcgtaata cggctggagg
       61 cgtttccccg tcagtaattc ggtattgggg atcagaaaat tcagctcaag acgacccttg
      121 tctgcgtgtt ccacccacag aatgctgtac tggtctttat cgagtccggg catcagaacc
      181 cgctcaaagc tggccatcag tttttcacgc tgacccggcg gcaggtccgc ctccgcgaat
      241 gacagcaccc cggaggtata ttttttcaca tacggcgacg catcaatcag ctcccggact
      301 tcttccggct tcccctgcag gacgctggca ccttcacgct gccggtcttt acccagaaga
      361 taatccacag gaccggcgcc cccgccgcga ccccggggat ggaatttaac aatcatcgtc
      421 cggccctttt tccagtacgg catgccgcaa ccgttccaga ccggcatcga tcgccatcag
      481 cgctgccacg atctgcaccc ggtcatgacc ggcaccaccg gcgttcactt tccgggcgat
      541 ctggttcagg ttattgccca tgccggcaag ctgacgcagc agcgcgggcg aaatcgaggg
      601 aagcctgccg gcgcgtgtcg gtttctcatc aaggcaggtc tggcgcatcc acgccgccag
      661 ttgttttccg tcgcaccgct caagcaaccg ccggtgttcg tcttccgtca cccacatcgt
      721 gagcatcttg ttgcgtttat ctgccagaat cgcctcctga taacgccgtg acggacggga
      781 aagcctttcc cggtcggcgc ggggttggac aagccgcagg cgcgtcagtg gggtttcggg
      841 gcgcagccct gaaccagtca cgtagcgcta gcggagtgta tactggctta gtatgttacg
      901 gcgagatgga gattcgggga agtgcttcat gtggcaaggg ggaaaatacg gctgcggggc
      961 gtaagtgcaa aatgcaggta acgatgaaat gacgcctcct cgctcactcg gtcgctgcgc
     1021 tcctgccgtg agactgcggc gggcgttacc agctcacgaa ggacgagata acgagatcgc
     1081 gctcaagtca ggaaagtcag gaaaaaggat gcggcgttgc cgtttttcca taggctccgc
     1141 ccccctgaca agcatcacaa aatctgacgc tcaaatcagt ggtggcgaaa cccgacagga
     1201 ctataaagat cccaggcgtt tccccctggt agctccctcg tgcgctctcc tgttcctgcc
     1261 tttcggttta ccggtgtcat tccgctgtta tggccgcgtt tgtctcattc cacgcctgac
     1321 actcagttcc gggtaggcag ttcgctccaa gctggactgt atgcacgaac cccccgttca
     1381 gtccgactgc tgcgccttgt ccggtaacta tcgtcttgag tccaacccga aaagacatgc
     1441 aaaagcgcca ctggcagcag ccactggtaa tcggattcac ggagcggagt agagttatct
     1501 acagagttct tgaagtggtg gcctgactac ggctacactg aaaggacagt tttggtatct
     1561 gcgctccgtg aaagccagtt accttcggaa gaaagagttg gtagctctaa attccggcaa
     1621 acgaaccacc gttggtagcg gtggtttttt tgtttacggc ttaggagatt acggctagaa
     1681 cgaaaggatc tcaagaagat cctctcagaa attatacaga catgcggtag tttgagatgt
     1741 cagagctatc taactctttt accggaacca gtttgtaatg cctttcctca atcaatttca
     1801 cttgtccttc gtctatcttt agctcaaaca gtgcaatcaa atcgctcgaa acaaactgag
     1861 cggaaatagc tctacatcta acatttgggt atttttgttc acaccacgct gtatcttgcg
     1921 atgtttgcac cattgatatt tgatctgtcc caccttttgc ttgaactggt attatataat
     1981 ggcaaccgta tttatctata cctacataaa gttcatcgat ctctatttga ccaattccct
     2041 tcaccgtagt tcttaaatga ttctgtaaag aatatgtggt tatacctaga aatatatcta
     2101 ttagccggtt atatctcacc ttcgccagca atgcctgctc gtcgtctaaa gaataacctg
     2161 taattatctc cggggtattg tctggaattt ttattgccac catattagga tttggcaaaa
     2221 tcctactaat agttactaat ctaaatcgat actttgacct accagccagc tcaataatcc
     2281 actccttacc ttctggctga gtcaacagaa tactttctgg cataggcgtt ctaaatctga
     2341 ttgaatatat aacatcacca acattagatg ggagttctat acctaaatct tttgcagcac
     2401 tgtttatatc taacctttca aacaaaacct ctaagtcacc atcaacatat ttatcgaaaa
     2461 atatcttttc taccaactga tggtatctat ttttggacct ttctttttta tccttactca
     2521 caaacaacct ccttgttact attttttatt ctcttagcaa ttacatttga tgacacacca
     2581 aacatagatg cagcatcgga catagaaata gcaaccaaac tttcatcacc gagtttgatt
     2641 ttcttcgttg gtttttttgg cgtaacacca agaaccttca taatctgcaa gccaacactt
     2701 ctagctagca taggaggaac actattaccg acctgtctaa atccatgcca cttagtcaca
     2761 tgaaatctga accaatcagg atatgaatgc agtcttgctg cctctctgac cgtgatgacc
     2821 ctaggataga tcggatgtat aggacgagga gatgtaaaag cacctctgtc acttgctgtt
     2881 cctgccctta aagtattaca tagcccattc atcgagagct ttttaaacct gctgattggt
     2941 tctaccgtgt caggcaaagt ttcaacaaac cgccctctag aaatgtcaga gtgatctgtc
     3001 agtaaagaac acgttaattt gtctttatta aaaatccttg ggtagctaaa atcactagga
     3061 tcttttccta cgccatgcaa ataggatgag tatagtgatt gctcaccaaa tttagcataa
     3121 acccaatctc taccccatag ctcaggatat ttttccgcat caggaatatc cccaatagcg
     3181 tccccaaccg ttgttctaat ggataatggc tcagggtatg atggcagagc aattcctttc
     3241 cttcccccca ttaagaaaag acgacggcga tcttgaggaa ctccataatc agctgcgttt
     3301 agcactttat aatcgcttac aacgtcgtac ccgccatctt taaatgcatc cattatctct
     3361 actaaaaact gcttatgctt accaaccgtc aaccctttta cattttcaaa aacaaagtat
     3421 ttaggcttta gctcaagaac cagccgtaca tagtgataga ccagtttgtt tctatcatca
     3481 tcaagcgcgc gttttcctat taatgaaaag ccttggcagg gagcgcctcc gatcactaca
     3541 tcaatctctt tctcaccaat acctgaaact tccctaacgt attctccggt aacatcaaca
     3601 acacttctac atatcgtttt gcacatagga aagttatatt tgtgagcaga gcaatgtatt
     3661 ggatctattt caactgatgc cattatatca aagccagctt gctcgaaacc gagactcagc
     3721 ccacccgctc cagcaaataa atcaacagca atcggtctag tcattcttta cacccacgtt
     3781 atataaaatc aacatgatgc tatcagaaaa acgatcgctt taccgatcgt ttttctgatt
     3841 tcgattgaac ataacatctc ttacccgcac cgcgccggag gcactcaggg cgtttctgat
     3901 ggctgacggg caaaaggtgg tggcaagtac accgaaaacc accagaaacg cacctgattt
     3961 attttacgca tatgcatcac ttattcacat cactgcatag ccggtgattt cggttaaaaa
     4021 agactctctg tgtgctgaaa tcgcagaaaa tggccatgat ccccgtcacg ctcaggccac
     4081 ctgagacggg cgtttatcag tctccatact ccctgtcacc atgagataat gtgcgttgcc
     4141 gttccggtac cagatctgct gtcttctctg gttccttttc cgttgtttgc ccgtatcgct
     4201 gttgctcaat ctcattcagc ctgtcgataa ccggcgcagc tgctcgctca aactctgcac
     4261 ctgcctgctc aagcccgaca cgcgctcgct cagcgccgcg ttctcccgtt gcataagacc
     4321 agacatcttc cgccattcct cgaaggcgct ctcccactcg tccagccttc tcgagtagtc
     4381 ctgctgtagc tgctctaacg cgctcagcaa ttgtttttcc agttccgtca ttctgctcta
     4441 ctcccgtacc agcttcaccg cgttccgcgt cttgttgtcc accgtccggc ccgtttcggc
     4501 tttcatcccc tccggcagca ccagaaaccg tccgttgcgg ttctccagat aggtcacgcc
     4561 ccacgtctgc atgtgcagtt tcgacagcgt atctctctgc tgcctgattt ccgccaggtt
     4621 cgccgctatc cggttcccct ggtaccacag caccccgctc aggctggcga acagcagccc
     4681 tgacaccatg gtgatggtca gccacgtccg cccgaccatt cgcagcacgc tcagccggtt
     4741 cgactgcatc gccgcgttca tcccctgttc gtgggcgctg atggcgtcgt tgattctctt
     4801 cgcgcttgcg ttcagttccg atttgacaac gttctcgtgc ttgctgaatg cggctttcag
     4861 cctctcttcg gtaagctgct gctgtgcttt cgatttctcc tcgaagtccc tcgaggccgt
     4921 taaaagactg ctcataaatg gctcccctca gtcggatatt tcgccccccg tccgggtcgg
     4981 caatgctgat actgtttttt gtggttctga ccacctcaaa accggccgct gtgagcgccc
     5041 ctgtgacgtc atcacgcgtt ttcagctctc ctgatgaggc taacatcagc aaaccccgtg
     5101 taatcgtctc tgcggcttcc tgcttcgttt ctggcagtcc tgaaggcgtg accagcgccc
     5161 gccggttctc cgggtcgttc ggatcatgta gccccagcct gccgttg
//
