LOCUS       NZ_CP107019             5596 bp    DNA     circular CON 06-NOV-2023
DEFINITION  Klebsiella pneumoniae strain K30821 plasmid punamed2, complete
            sequence.
ACCESSION   NZ_CP107019
VERSION     NZ_CP107019.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN30826912
            Assembly: GCF_025725705.1
KEYWORDS    RefSeq.
SOURCE      Klebsiella pneumoniae
  ORGANISM  Klebsiella pneumoniae
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Klebsiella/Raoultella group; Klebsiella.
REFERENCE   1  (bases 1 to 5596)
  AUTHORS   Pu,D.
  TITLE     A 1.5-Year Within-Patient Resistance evolution of a fatal ST11
            carbapenem-resistant hypervirulent Klebsiella pneumoniae
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 5596)
  AUTHORS   Pu,D.
  TITLE     Direct Submission
  JOURNAL   Submitted (03-OCT-2022) China-Japan Friendship Hospital, Peking
            Union Medical College, No.2 Yinghua dong Avenue, Beijing 100020,
            China
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method :: SPAdes v. v3.15.5; Unicycler v. v0.4.8
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 196.5x
            Sequencing Technology             :: PacBio
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 11/06/2023 04:58:10
            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)                     :: 5,919
            CDSs (total)                      :: 5,798
            Genes (coding)                    :: 5,586
            CDSs (with protein)               :: 5,586
            Genes (RNA)                       :: 121
            rRNAs                             :: 9, 8, 8 (5S, 16S, 23S)
            complete rRNAs                    :: 9, 8, 8 (5S, 16S, 23S)
            tRNAs                             :: 85
            ncRNAs                            :: 11
            Pseudo Genes (total)              :: 212
            CDSs (without protein)            :: 212
            Pseudo Genes (ambiguous residues) :: 0 of 212
            Pseudo Genes (frameshifted)       :: 73 of 212
            Pseudo Genes (incomplete)         :: 153 of 212
            Pseudo Genes (internal stop)      :: 29 of 212
            Pseudo Genes (multiple problems)  :: 41 of 212
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP107019.1.
            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..5596
                     /organism="Klebsiella pneumoniae"
                     /mol_type="genomic DNA"
                     /strain="K30821"
                     /isolation_source="bronchoalveolar lavage fluid"
                     /host="Homo sapiens"
                     /db_xref="taxon:573"
                     /plasmid="punamed2"
                     /geo_loc_name="China:Beijing"
                     /collection_date="2020-07-03"
     gene            198..422
                     /locus_tag="OF890_RS29480"
                     /old_locus_tag="OF890_29480"
     CDS             198..422
                     /locus_tag="OF890_RS29480"
                     /old_locus_tag="OF890_29480"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000879771.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="DUF6290 family protein"
                     /protein_id="WP_000879771.1"
                     /translation="MLAIRLSDEIESRLDSLAKQTGRTKTFYAREAILAHLEDLEDYYL
                     SAETAARVRRGDEAVHSSEDVRKSLGLDD"
                     /name="DUF6290 family protein"
     gene            406..672
                     /locus_tag="OF890_RS29485"
                     /old_locus_tag="OF890_29485"
     CDS             406..672
                     /locus_tag="OF890_RS29485"
                     /old_locus_tag="OF890_29485"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000262326.1"
                     /GO_function="GO:0008657 - DNA topoisomerase type II
                     (double strand cut, ATP-hydrolyzing) inhibitor activity
                     [Evidence IEA]; GO:0042803 - protein homodimerization
                     activity [Evidence IEA]"
                     /GO_process="GO:0030541 - plasmid partitioning [Evidence
                     IEA]; GO:0051290 - protein heterotetramerization [Evidence
                     IEA]"
                     /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_004197762.1"
                     /translation="MVWTINYSDRALKSLRKMDKQNARRIVDFMSLRIAVAADPRQSGK
                     PLKGELGEFWRYRVGDYRVLCEIRDDELVILAATIGHRREVYD"
                     /name="type II toxin-antitoxin system RelE/ParE family
                     toxin"
     gene            complement(742..1092)
                     /locus_tag="OF890_RS29490"
                     /old_locus_tag="OF890_29490"
     CDS             complement(742..1092)
                     /locus_tag="OF890_RS29490"
                     /old_locus_tag="OF890_29490"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_004197756.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_004197756.1"
                     /translation="MYWLIAFLAFIFPGRSFADGYTAYYRCNGTQEASLTVKDNKLSMV
                     VGLSKFNRQLDTYRFKEKGIEVVMQRAASDDNSEAIMSFIMPDVNNMTLLVKNNGYIIV
                     KTTCWLTKTDKQ"
                     /name="hypothetical protein"
     gene            complement(1158..1703)
                     /locus_tag="OF890_RS29495"
                     /old_locus_tag="OF890_29495"
     CDS             complement(1158..1703)
                     /locus_tag="OF890_RS29495"
                     /old_locus_tag="OF890_29495"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_004197758.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_023317533.1"
                     /translation="MFFKRYLTEKEIYKAALPIVRLQGRVNTSLRFLSKYSDVNKNGLI
                     ALHLNLLHFISYNIHGVESLKITQAGINKAVQQSPHADEIKNIAQAIGRKGPEYIEGLI
                     RNPWGKKNDNPLIFIMSIEESIKETLNSGYMLYRVAPITEGEAAAFMDVLKQLLLFEDN
                     FRLFGRDLVYKIEKLKIR"
                     /name="hypothetical protein"
     gene            complement(1729..2055)
                     /locus_tag="OF890_RS29500"
                     /old_locus_tag="OF890_29500"
     CDS             complement(1729..2055)
                     /locus_tag="OF890_RS29500"
                     /old_locus_tag="OF890_29500"
                     /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_050516389.1"
                     /translation="MRERTNIMLDIGLKQSLQRLSNKTKMSLSDLINQRLSGSLSVEER
                     IGEKPEWMRNLDPYLANHFSNIELPLPSPLKEYQEKMDEIDSIINDMMVLKEYFRAKFY
                     DEIK"
                     /name="hypothetical protein"
     gene            complement(2413..2571)
                     /locus_tag="OF890_RS29655"
     CDS             complement(2413..2571)
                     /locus_tag="OF890_RS29655"
                     /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_071596352.1"
                     /translation="MHEPPVQPDCCALSGNYHLESNPDGHAKTPLAAAIGNWIYTREIL
                     RGLEVGA"
                     /name="replication initiation protein"
     gene            3211..3387
                     /locus_tag="OF890_RS29505"
                     /old_locus_tag="OF890_29505"
     CDS             3211..3387
                     /locus_tag="OF890_RS29505"
                     /old_locus_tag="OF890_29505"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_004197757.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_004197757.1"
                     /translation="MQKPKKKPLVVKKRSWHPAVMANLMRQAQEEDYRREQMAELERSA
                     RSHFADIGGEDGG"
                     /name="hypothetical protein"
     gene            3377..3721
                     /locus_tag="OF890_RS29510"
                     /old_locus_tag="OF890_29510"
     CDS             3377..3721
                     /locus_tag="OF890_RS29510"
                     /old_locus_tag="OF890_29510"
                     /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_062955149.1"
                     /translation="MAVKRTRFLGIRVTDGEYQQLLERCNGRQLAVWMRETCLDTRPAR
                     SLRLPSIDPVLLRQLAGMGNNLNQIARKINGGQWSGADRVQVVAALMAIDAELERLRHA
                     VLEKGADDDR"
                     /name="MobC family plasmid mobilization relaxosome protein"
     gene            3930..>4364
                     /locus_tag="OF890_RS29515"
                     /old_locus_tag="OF890_29515"
                     /pseudo=""
     CDS             3930..>4364
                     /locus_tag="OF890_RS29515"
                     /old_locus_tag="OF890_29515"
                     /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            4399..4908
                     /locus_tag="OF890_RS29520"
                     /old_locus_tag="OF890_29520"
     CDS             4399..4908
                     /locus_tag="OF890_RS29520"
                     /old_locus_tag="OF890_29520"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_020325392.1"
                     /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_032433972.1"
                     /translation="MNSLLTLAKDLEQKSKAQQQSTGEMLKAAFSEHEKSVRAELSESG
                     KRISAAIRAHEQGMSAAMQSNRLSVMRMVGRTWLTITMVSGLLFASLSGVLWYQGSLIA
                     SNLAEIDRQNAALSKLNAKTWGVTYLEDSNGRFLVLPKGTAVDRTQSWTVGNGRSKQNA
                     LRLVKE"
                     /name="MbeB family mobilization protein"
     gene            4915..5127
                     /locus_tag="OF890_RS29525"
                     /old_locus_tag="OF890_29525"
     CDS             4915..5127
                     /locus_tag="OF890_RS29525"
                     /old_locus_tag="OF890_29525"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000137423.1"
                     /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_021527181.1"
                     /translation="MTELEKQLLSALEQLQQDYSKRLDEWESAFGEWRKMSGLMQRENA
                     ALSERVTRLSQQVERLSGQLQRLSR"
                     /name="MbeD family mobilization/exclusion protein"
     Typing          3046..3125
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="90.361"
                     /coverage="97.0"
                     /evalue="1.1100000000000001e-21"
     Typing          complement(2463..2860)
                     /name="rep_cluster_2370"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="89.526"
                     /coverage="91.0"
                     /evalue="3.03e-139"
     Typing          3712..5243
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="99.804"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 tcggcaattc gtttcggacc cggcttaaga cccataatcg ttatcctttc aatagttaag
       61 aggaaagccc tcaagctaga tatattgacc gcgttacgga ttatcaagag gggctaacaa
      121 gattattttt tgttctttta ggttgattgt ggtactgttg atatacatgt atagcaaatg
      181 gtgttcggga ggtttatatg cttgctatcc ggttatctga tgagattgag tcccgtctgg
      241 actcgctggc gaagcaaacc ggcagaacaa agacgtttta tgcgcgggaa gcaatactgg
      301 cgcatctgga agacctggag gattattatc tttcagcaga aactgctgca cgcgttcgcc
      361 gtggtgatga agcagtgcat tcgtctgaag acgtgaggaa gtcacttggt ctggacgatt
      421 aactattccg atcgggcgct caaatcgtta cgcaagatgg acaaacagaa cgcacgacgg
      481 attgtggatt ttatgagttt acgcattgca gttgctgccg atcctcgcca gtcagggaag
      541 ccgctcaaag gtgagctggg cgagttctgg cgctatcggg tgggagatta tcgcgttctg
      601 tgtgagatcc gagatgacga gcttgttatc cttgccgcca cgattggaca tcgccgcgaa
      661 gtttacgact gaagcccgct atgcgggctt ttttgatgcc gacaacaggt attatggtaa
      721 atactcgact aactacgtgt tctactgttt gtcggtttta gttaaccagc aggttgtctt
      781 aacgataatg tagccgttat ttttaactaa taaggtcata ttgttaacgt caggcataat
      841 aaaagacatt atggcctcag agttatcatc agaagcagct ctctgcatta ctacttcgat
      901 tcccttttct ttgaatctat aagtatccag ttgcctatta aacttagaaa gacctacaac
      961 catacttagt ttgttatctt taacagtaag agatgcttcc tgagtaccat tacatcggta
     1021 gtaagcggtg taaccgtcag caaaagatcg accggggaat ataaatgcta ggaacgcaat
     1081 taaccaatac atagttgaga atcttggtat tacacatttc actatcctct ctttcatttt
     1141 tcgttcacca tactttgtta tctgattttt aatttttcta ttttataaac caagtctcta
     1201 ccaaaaaggc gaaaattatc ctcaaataat aataattgtt taagaacatc catgaaagca
     1261 gctgcttcac cctcagttat gggagctact ctatataaca tataacctga gttaagggtt
     1321 tcttttatac tttcttcaat gctcattata aatattagtg gattatcatt tttcttcccc
     1381 catgggtttc taattaatcc ttcgatgtac tcaggtcctt tgcgtcctat tgcctgcgca
     1441 atatttttta tttcatctgc gtgagggctt tgttgtacag ctttgtttat gcctgcttga
     1501 gtgattttca gagactctac accgtgtatg ttgtatgaga taaaatgtaa taaattaaga
     1561 tgcaatgcaa ttaatccatt tttgtttaca tctgagtatt tggataaaaa acgtaatgaa
     1621 gtgttaactc tcccttgaag cctaacaatt gggagtgctg ccttgtatat ttccttctcc
     1681 gttaaatacc gtttaaaaaa cataattctc cgcctccgta tagcgtgcct attttatttc
     1741 gtcgtaaaac ttagctctga aatattcctt tagaaccatc atgtcattaa taattgaatc
     1801 tatctcatcc attttttctt ggtattcttt taatggtgaa gggagcggta actcaatatt
     1861 tgaaaagtga ttggcgagat agggatcaag gtttctcatc cattcaggct tttcgccaat
     1921 gcgttcttca actgaaagtg aacctgataa tctctggtta ataagatcac ttagactcat
     1981 tttggtttta ttcgaaagcc gttgtaagga ttgctttaat cctatatcta gcatgatatt
     2041 tgttctttct ctcattaccc ccccttgcta ttgcgttttt tgttgcgcac aaagctacca
     2101 ttgcgcatta agaaacgcaa taaaaaagga gggagggagt ggtttgtaca tgatgtgcag
     2161 tgcgctgagg gcatcagtgg cgggtgtttt tccgtgggat ggatggagct ccggggataa
     2221 cagaactgac gatcatttaa aggatcttct tgagatcctt tttttctgcg cgtaatctct
     2281 tgcactgtaa acgaaaaaac cgcctgggga ggcggtttga tcgaaggtta agtcagttgg
     2341 ggaactgctt aaccgggtaa ctgggtatac gagaccgcag ataccaaaac tgttctttca
     2401 gtgtagccgc agttaggcac ccacttcaag acctctcaat atctctctcg tatatatcca
     2461 gttaccaatg gctgctgcca gtggcgtttt tgcgtgtccg tccgggttgg actcaagatg
     2521 atagttaccg gaaagggcgc agcagtcggg ctgaacgggg ggttcgtgca tacagcccag
     2581 cttggagcga acgacctaaa ccgagccgag ataccagcag cgtgagctat gagaaagcgc
     2641 cacgcttccc gaaagggaaa aaggcggaac aggtatccgg taaacggcag ggtcggaaca
     2701 ggagagcgca cgagggagcc gccggagaga aatcaccggc atctttaagt cctgtcgggt
     2761 ttcgtcctcc tctgacttga gcgtccattt ctgtgatgct cgtcagggga ggcggagcct
     2821 atggaaaaac ggcaacgccg catccttttc tccggccctt tctgatttga gcgcctttgc
     2881 tttatcccgt tatccgtgag tcggtcacgc ccgccgcagc cgaacggcag gagcgcagct
     2941 accgagtgag cgaggaggcg tcatttcatc tgtccgtgca tggtattgcg gacgctcctg
     3001 agccacatat cacacctgcc acatgaggca ctttcatgaa tcgtgctctc atgccaacat
     3061 agtaagccag tatacacagc gtaaacgctg tgactggttc agggctgcgc cccgaaaccc
     3121 gctaacacca ctgacgcgct ggcgcttgtc caacgccgga gcgacccgga aaacttttcc
     3181 gtgccgtccg gcgtttgcga aggagggata atgcagaagc cgaagaagaa gccgctcgtc
     3241 gtaaaaaaaa gatcctggca tccggcagtg atggcaaatc tgatgcgtca ggcacaggag
     3301 gaagattacc gccgggagca gatggcagag cttgagcgtt cagcccggtc acattttgcg
     3361 gatatcggag gagaggatgg cggttaagcg tacccgtttt ttaggtatcc gggtgaccga
     3421 tggggagtac cagcagctgc tggagcgctg caatggaagg caactggcgg tgtggatgcg
     3481 ggaaacctgt ctcgatacgc gcccggcgcg gtcgttgcgg ctgccgtcca tcgatccggt
     3541 tttgctgcgc cagcttgccg ggatggggaa caacctcaac cagatcgccc ggaaaattaa
     3601 cggcggccag tggtcaggcg ctgaccgggt tcaggtggtg gccgcgctga tggccattga
     3661 tgccgaactc gagcggctgc ggcatgccgt gctggaaaag ggggcagacg atgatcgtta
     3721 agtttcatcc gcgagggcga ggcggcggtg ccgggccggt ggattatctg ctggggaaag
     3781 accgccagcg cgacggggcc atcgtcctgc agggaaagcc ggaggaggtc cgggagctta
     3841 tcgacgcctc gccctacgcc aaaaagtaca cctccggcgt cctgtctttt gctgaacagg
     3901 atttaccgcc cggccagcgt gaaaagctga tggcgagctt cgagcgggtt ctgatgcccg
     3961 gactcgataa agaccagtac agcgtgctgt gggttgaaca ccgggacaag gggcggctgg
     4021 aactgaattt tctggtaccg aacacggaac tgctgaccgg caggcgtctc cagccgtact
     4081 acgaccgggc agaccgtccg cgcatcgatg cgtggcagac cgtggtgaac gggcgactgg
     4141 ggctgcacga cccgaacgca ccggagaacc ggcgcgcgct ggtgacgcca tcttcgttac
     4201 ccaaaacgaa gcaggaagcc gcagaggcta ttacgcgggg cttactggcc ctcgcctcgt
     4261 caggggagct taaaacgcgt caggacgtca ctgaggcgct ggaaagcgca ggttttgagg
     4321 tcgtgcgcac cacaaagagc agcatcagca ttgccgaccc ggacggaggg cgaaacatcc
     4381 gacttaaggg agccatctat gaacagtctt ttaacgctgg cgaaggactt agagcagaaa
     4441 tcgaaagcgc agcagcagag taccggcgaa atgctgaaag ccgcattcag cgagcacgag
     4501 aagtctgtca gagcggaact gagcgaaagc gggaagagaa tcagcgccgc catccgcgcc
     4561 cacgagcagg gtatgagcgc ggccatgcag tcgaaccgcc tgagcgtgat gcgtatggtc
     4621 gggcggacat ggctgaccat cacgatggtg tcaggactgc tgttcgccag cctgagcggg
     4681 gtgttgtggt atcaggggag cttgatagcg tcaaatctgg ccgaaatcga ccggcagaac
     4741 gcagcgctgt cgaagctgaa cgcgaagacc tggggcgtga cgtacctgga agacagcaac
     4801 ggacgttttc tggtgctgcc gaaggggacg gccgtagaca ggacgcagag ctggacggtc
     4861 gggaacgggc ggtcgaagca gaacgcgctg agactggtga aggagtaagt gccgatgacc
     4921 gagctggaaa aacagttgct gagcgcatta gagcagctac agcaggacta ctcgaaaagg
     4981 ctggacgagt gggagagcgc cttcggggaa tggcggaaaa tgtcagggct tatgcaacgg
     5041 gagaacgcgg cgctgagcga gcgcgtgacg cgcttgagtc agcaggtgga acgcttgagc
     5101 gggcaactgc agcgtttgag ccggtagtgc agcgtcatga gatggccgtg gccgcagaac
     5161 gggcgcacga gcaacggcag cacgaaaagg aactgacgga agcgcgttcc cggcagcgaa
     5221 gctatgacgg tccgtcgctg ggctgaaatg caggaaaaca gggttctcat cgggcattta
     5281 cgctgaaacc ggatgtcatt cacctggctg catggctatg cagccaggta aaatttatct
     5341 gtcgcgaacg gggcggttta tcgggtggtt tgttgccggt tttacctgac tgccaccccg
     5401 ttcgcggcga acccgtccgg ggcggtgcgg gcaacgggtg ttatgtttaa tcagcgtgaa
     5461 cggcagatac aaaaaagccc cggagggctt ttaactactg acttattttt ttgaagattt
     5521 gctgggtttc aatttgtcag tatttcccgg cgttttttta ttgtcacgct ggcgtttatc
     5581 aggttcccct gttgaa
//
