LOCUS       NZ_CP003995             5065 bp    DNA     circular CON 03-MAR-2024
DEFINITION  Klebsiella pneumoniae subsp. pneumoniae Kp13 plasmid pKP13c,
            complete sequence.
ACCESSION   NZ_CP003995
VERSION     NZ_CP003995.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN02641520
            Assembly: GCF_000512165.1
KEYWORDS    RefSeq.
SOURCE      Klebsiella pneumoniae subsp. pneumoniae Kp13
  ORGANISM  Klebsiella pneumoniae subsp. pneumoniae Kp13
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Klebsiella/Raoultella group; Klebsiella.
REFERENCE   1  (bases 1 to 5065)
  AUTHORS   Ramos,P.I., Picao,R.C., Almeida,L.G., Lima,N.C., Girardello,R.,
            Vivan,A.C., Xavier,D.E., Barcellos,F.G., Pelisson,M., Vespero,E.C.,
            Medigue,C., Vasconcelos,A.T., Gales,A.C. and Nicolas,M.F.
  TITLE     Comparative analysis of the complete genome of KPC-2-producing
            Klebsiella pneumoniae Kp13 reveals remarkable genome plasticity and
            a wide repertoire of virulence and resistance mechanisms
  JOURNAL   BMC Genomics 15, 54 (2014)
   PUBMED   24450656
  REMARK    Publication Status: Online-Only
REFERENCE   2  (bases 1 to 5065)
  AUTHORS   Perreira,P.I., Picao,R.C., Almeida,L.G.P., Vespero,E.C.,
            Pelisson,M., Vivan,A.C.P., Zuleta,L.F.G., Barcellos,F.G.,
            Lima,N.C.B., Xavier,D.E., Girardello,R., Medigue,C.,
            Vasconcelos,A.T.R., Gales,A.C. and Nicolas,M.F.
  TITLE     Direct Submission
  JOURNAL   Submitted (14-DEC-2012) Labinfo, LNCC - Laboratorio Nacional de
            Computacao Cientifica, Rua Getulio Vargas 333, Petropolis, RJ
            25651070, Brazil
COMMENT     ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 03/03/2024 06:16:00
            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)                     :: 5,644
            CDSs (total)                      :: 5,523
            Genes (coding)                    :: 5,383
            CDSs (with protein)               :: 5,383
            Genes (RNA)                       :: 121
            rRNAs                             :: 9, 8, 8 (5S, 16S, 23S)
            complete rRNAs                    :: 9, 8, 8 (5S, 16S, 23S)
            tRNAs                             :: 86
            ncRNAs                            :: 10
            Pseudo Genes (total)              :: 140
            CDSs (without protein)            :: 140
            Pseudo Genes (ambiguous residues) :: 0 of 140
            Pseudo Genes (frameshifted)       :: 63 of 140
            Pseudo Genes (incomplete)         :: 77 of 140
            Pseudo Genes (internal stop)      :: 22 of 140
            Pseudo Genes (multiple problems)  :: 19 of 140
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP003995.1.
            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..5065
                     /organism="Klebsiella pneumoniae subsp. pneumoniae Kp13"
                     /mol_type="genomic DNA"
                     /strain="Kp13"
                     /isolation_source="blood"
                     /host="Homo sapiens"
                     /sub_species="pneumoniae"
                     /db_xref="taxon:1123862"
                     /plasmid="pKP13c"
                     /geo_loc_name="Brazil"
                     /collection_date="2009"
     gene            <1..441
                     /locus_tag="KP13_RS00025"
                     /pseudo=""
     CDS             <1..441
                     /locus_tag="KP13_RS00025"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_076612230.1"
                     /GO_function="GO:0004803 - transposase activity [Evidence
                     IEA]"
                     /GO_process="GO:0006313 - DNA transposition [Evidence IEA]"
                     /note="incomplete; partial in the middle of a contig;
                     missing N-terminus; Derived by automated computational
                     analysis using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="IS1-like element IS1B family transposase"
                     /name="IS1-like element IS1B family transposase"
     gene            complement(435..845)
                     /locus_tag="KP13_RS00030"
                     /old_locus_tag="KP13_06779"
     CDS             complement(435..845)
                     /locus_tag="KP13_RS00030"
                     /old_locus_tag="KP13_06779"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_009310048.1"
                     /GO_function="GO:0003677 - DNA binding [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="helix-turn-helix domain-containing protein"
                     /protein_id="WP_025367739.1"
                     /translation="MARVSISEAARLTGKSRTTLHRLIKAGDLSTCSGERNAKMVDTSE
                     LLRVFGPFEQPKGEHHSGQVSGQRDTASADQSEQVIRHLKQEIEHLNTLLLSKDSHIDS
                     LKQAMLLLENHQAKLTESPAPWWKFWVMTPTY"
                     /name="helix-turn-helix domain-containing protein"
     gene            complement(845..1036)
                     /locus_tag="KP13_RS00035"
                     /old_locus_tag="KP13_06780"
     CDS             complement(845..1036)
                     /locus_tag="KP13_RS00035"
                     /old_locus_tag="KP13_06780"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000166328.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="Rop family plasmid primer RNA-binding protein"
                     /protein_id="WP_004187666.1"
                     /translation="MTKQQKTALNMAKFIQNQSLLLLEKLNELDLDVEADLCEKLHDDA
                     EHLFRTLSSRLDALQDGN"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            1452..1565
                     /locus_tag="KP13_RS33010"
     CDS             1452..1565
                     /locus_tag="KP13_RS33010"
                     /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_071886188.1"
                     /translation="MHEPPVQSDCCALSGNYRLESNPERHDKAPLAAATGN"
                     /name="replication initiation protein"
     gene            1908..2051
                     /locus_tag="KP13_RS32695"
     CDS             1908..2051
                     /locus_tag="KP13_RS32695"
                     /inference="COORDINATES: protein motif:HMM:NF024573.4"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="AAA family ATPase"
                     /protein_id="WP_227502461.1"
                     /translation="MIKEISLKNFKCFNELYLKQLKTLNIIAGKNNYGKTSILDAIFVF
                     MM"
                     /name="AAA family ATPase"
     gene            2096..2479
                     /locus_tag="KP13_RS32700"
                     /old_locus_tag="KP13_32112"
     CDS             2096..2479
                     /locus_tag="KP13_RS32700"
                     /old_locus_tag="KP13_32112"
                     /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_227502462.1"
                     /translation="MAEINKNKPFWVSYFHDMDTSQKMSIVIRDERSEVTQTYETETNQ
                     RLESSLSLNVDTVLSNQNIPRQTIGSQATVNSLKINVTETPNAKNRVSNKLFSMQLKED
                     GVEIKSEIKTKGMGLIINLRQQQ"
                     /name="hypothetical protein"
     gene            2675..3019
                     /locus_tag="KP13_RS32705"
                     /old_locus_tag="KP13_32113"
     CDS             2675..3019
                     /locus_tag="KP13_RS32705"
                     /old_locus_tag="KP13_32113"
                     /inference="COORDINATES: protein motif:HMM:NF024573.4"
                     /GO_function="GO:0005524 - ATP binding [Evidence IEA];
                     GO:0016887 - ATP hydrolysis activity [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="AAA family ATPase"
                     /protein_id="WP_025367740.1"
                     /translation="MLGEGISRALSFISSVLVQENSIILIDEIENGIHYSVIKDIIKSL
                     ISSAKQNNNQIFATTHSQDVIRAINEIDSKNEDIAYIRLGREKNSLKPTAVQFNMDDFS
                     YSVENDWEVR"
                     /name="AAA family ATPase"
     gene            3019..3522
                     /locus_tag="KP13_RS00045"
                     /old_locus_tag="KP13_32114"
     CDS             3019..3522
                     /locus_tag="KP13_RS00045"
                     /old_locus_tag="KP13_32114"
                     /inference="COORDINATES: protein motif:HMM:NF022971.4"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="DUF3226 domain-containing protein"
                     /protein_id="WP_025367741.1"
                     /translation="MKDINNSKKIIFVEGDDDFHFLCNLLEIQGITDVFVEKINGKSKL
                     KQALRAFKNIDSFDEKESIFIILDADTSFSDTERSIIATLRELQISSPSSHNEIAMNGN
                     TKISFFIMPGKDKQGAIEDLIIEHASTRALYEYIIEFFEKLKIIKMTSQRVTKSTLIQQ
                     TKKS"
                     /name="DUF3226 domain-containing protein"
     gene            4015..4257
                     /locus_tag="KP13_RS31305"
     CDS             4015..4257
                     /locus_tag="KP13_RS31305"
                     /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_098963735.1"
                     /translation="MHSAEIHTIQPGEVLFPAFFSSENGERGRNLLRGREALPAQPENR
                     FSAPSGIGFVDGRQSRYGKSPDDSPHDSPAIRIVN"
                     /name="hypothetical protein"
     gene            4679..>5064
                     /locus_tag="KP13_RS00050"
                     /old_locus_tag="KP13_32116"
                     /pseudo=""
     CDS             4679..>5064
                     /locus_tag="KP13_RS00050"
                     /old_locus_tag="KP13_32116"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001743396.1"
                     /GO_function="GO:0004803 - transposase activity [Evidence
                     IEA]"
                     /GO_process="GO:0006313 - DNA transposition [Evidence IEA]"
                     /note="frameshifted; 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="IS1-like element IS1B family transposase"
                     /name="IS1-like element IS1B family transposase"
     Typing          1158..1565
                     /name="ColRNAI_rep_cluster_1987"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="93.643"
                     /coverage="99.0"
                     /evalue="1.27e-172"
ORIGIN
        1 ctcaggccgc agtcggtaac ctcgcgcata cagccgggca gtgacgtcat cgtctgcgcg
       61 gaaatggacg aacagtgggg atacgtcggg gctaaatcgc gccagcgctg gctgttttac
      121 gcgtatgaca ggctccggaa gacggttgtt gcgcacgtat tcggtgaacg cactatggcg
      181 acgctggggc gtcttatgag cctgctgtca ccctttgacg tggtgatatg gatgacggat
      241 ggctggccgc tgtatgaatc ccgcctgaag ggaaagctgc acgtaatcag caagcgatat
      301 acgcagcgaa ttgagcggca taacctgaat ctgaggcagc acctggcacg gctgggacgg
      361 aagtcgctgt cgttctcaaa atcggtggag ctgcatgaca aagtcatcgg gcattatctg
      421 aacataaaac actatcaata agttggagtc attacccaga atttccacca tggcgccggg
      481 gattcagtta attttgcctg gtgattttca agaaggagca tggcctgttt caggctgtca
      541 atgtgcgaat ccttggacaa aagtaaggtg ttcaggtgtt caatctcctg tttcagatga
      601 cggatcacct gttcactctg gtcagcagag gctgtatcac gctgtccaga gacctgtcca
      661 gaatggtgtt cacccttcgg ttgctcaaag gggccaaaga cacgtaaaag ctctgaagta
      721 tctaccattt ttgcattgcg ctcaccgcta caggtggaca ggtcacctgc tttaattaac
      781 ctgtgcagtg ttgttctact cttacccgtc agtcgggcag cctcactaat agacactctg
      841 gccatcagtt accatcctgt aatgcatcca gtctcgagga cagtgtacgg aaaagatgct
      901 ccgcatcatc gtggagtttc tcacaaaggt cggcctcgac atcgagatca agctcgttaa
      961 gcttctccag caggagcaga gactgattct ggatgaattt agccatattc agcgctgttt
     1021 tctgttgttt cgtcataaga ggcctcagag cgtcagtggt cagtgtaggg atctcctctt
     1081 ttccgcttcc tcgctcactc agtcgctacg ctcctgccgt tcggctgcgg cgagcggcag
     1141 gagcatgcgt agaaacgctc gagaaaaccg agtaatcgca tggaggaaag aaggaaaggc
     1201 cgcacagcgg ccgtttttcc ataggctccg cccccctgac gagcatcacg gaatctgacg
     1261 ctcaaatcag tggtggcgaa acccgacagg actataaaga taccaggcgt ttccccctga
     1321 tggctccctc gtgcgctctc ctgttcctgc ctttcggttt accggtgtca ttccgctgtt
     1381 atggccgcgt ttgtctcatt ccacgcctga cactcagttc cgggtaggca gttcgctcca
     1441 agctggactg tatgcacgaa ccccccgttc agtccgactg ctgcgcctta tccggtaact
     1501 atcgtcttga gtccaacccg gaaagacacg acaaagcgcc actggcagca gccactggta
     1561 actgatttag ggagttagtc ttgaagttat acgccagtta aagctaaact aaacgaacag
     1621 ttttggtgac tgcgctccct ttaagccagt tacctcggtt catagagcgc caactctact
     1681 gaacctttcg aaaaaaccgc ccgccaaggc ggttttttcg ttcacagccg gaagcttacg
     1741 gctgctgcca gataatctca agaagaaagt aaaaaaatcg attaaaacac aagcaatcaa
     1801 agttaatctt tgacataaag tctagctaat cacaatgaaa gctgtacatt ttattaaggt
     1861 actaacaaat cgtatggcat ataacaaaaa cacgaacaga ggctatcatg ataaaggaaa
     1921 taagtttaaa gaacttcaaa tgcttcaatg agctatatct aaagcaatta aagactttaa
     1981 atatcatagc tgggaaaaac aactacggga aaacatctat actggatgct atttttgttt
     2041 ttatgatgta aaaaacccgg ctgttttgtt aaacattcaa gcattcagaa aagaaatggc
     2101 agaaataaac aaaaacaagc cattttgggt tagttacttt catgatatgg acacatcaca
     2161 aaagatgtcc atagtcattc gagatgaacg ctctgaagta acacaaacat atgaaacaga
     2221 aacaaatcag agattagaat caagtttgtc tctaaacgtt gacaccgtac tatctaacca
     2281 aaacatacct cgtcaaacta tcggttctca ggccacagta aactctttaa aaataaatgt
     2341 gaccgagaca cccaatgcga aaaacagggt ttccaataag cttttctcta tgcaattgaa
     2401 agaagatggc gtagaaataa aatccgaaat aaaaacgaaa gggatgggat taattataaa
     2461 tttaagacag caacaataat aacaacatcc agaaagataa acaaagaggc aacaattaca
     2521 aatgtatcta gcctactaac acaaaaaagg aaaaagacat actagaaaac ttaaaaaaat
     2581 agatgacaga attgtagata tagcaatatc tgcgataggt aacaataagg aaatatattt
     2641 agacattgga tttagtgagc taaatgaaat atcaatgctt ggcgagggta tcagtcgagc
     2701 attatctttt atcagctcag tgctggtaca ggaaaactca attattctta ttgatgaaat
     2761 cgagaacgga atacattact cagtaattaa agacataata aaatcattaa tttcatctgc
     2821 aaaacaaaac aacaatcaaa tatttgcaac aactcatagt caagatgtga tacgagcaat
     2881 aaacgaaata gatagcaaaa atgaagatat cgcttatatt agactaggaa gagaaaagaa
     2941 ctccctaaaa ccaacagccg tacaattcaa tatggatgat ttctcctact cagttgagaa
     3001 cgactgggag gtaagataat gaaagacata aataatagca aaaagatcat tttcgttgag
     3061 ggtgatgatg attttcattt tctatgcaac ctacttgaaa tacaaggcat taccgatgtt
     3121 tttgtcgaaa aaataaatgg aaaatcaaaa ttaaaacaag cacttagagc attcaaaaac
     3181 attgattctt tcgatgaaaa agaaagtatt tttattatat tagatgctga cacatcattt
     3241 tctgacacag aaagatcaat aattgccaca ttgcgagaac tacaaatctc ctcccccagc
     3301 tcgcataacg agatagctat gaatggcaat acaaaaattt ctttctttat aatgccagga
     3361 aaagacaagc aaggtgccat tgaagatctg ataattgaac acgcaagcac tcgagcgtta
     3421 tatgaataca taatagaatt tttcgaaaaa ttaaaaataa taaagatgac atctcagcga
     3481 gtgacaaaga gtacacttat ccaacaaacg aaaaaaagct aaggtacaag tctatcttag
     3541 ctgcaataga gaatccgact caagaatagg aatatccatg aaaaatggaa taataaacac
     3601 agcagacaat tgctttgatg aaataaaaga ttttatttca aaaatataaa tccaaatcaa
     3661 gccagccctt cacgggctgg cttatcacca gggtgttatt aaacgccgga taacgtatag
     3721 aaagcatcat acactttagt tatcagcaat ctcaaacgtc ctaaagacat caccagatgc
     3781 caaaacaatg attgtgcaga tctaatgtaa aagacccagc acaagatgct cccttaagtt
     3841 atattctctc tattcactta aaacaattta acataaaatc ataattgtac gcaccgctaa
     3901 aacggactca ggacgtttct gacgggaaac cggtaaaaca ggcaacaaac cacccgaaaa
     3961 cccgccagaa acgcgcaggc tctgttttta cggcatgcat gagtatgcgc gcaagtgcat
     4021 agcgcggaaa ttcacaccat tcagccaggg gaagtcctgt ttccggcgtt cttctcctcc
     4081 gaaaacggtg aacggggacg caatttattg cgtggccgtg aagcgttgcc ggcgcagccg
     4141 gaaaaccggt tttcagcacc ttcaggaatc gggttcgtcg acggccggca atcacgttat
     4201 ggcaagtcgc cggacgactc accacacgat tcaccggcga ttcgaatcgt gaattgaatc
     4261 aagagtcacc atgagcaaaa aacacccaaa gtgatgaatt gaatcaagag tcgattcatc
     4321 ataacaatat gataataaag cgtgattcac atatgaatcg tgggcaattc gtcagcgatt
     4381 cgccatagag tcgtccacga cttggatctg cactttgtaa cacatcaccg cacatttatt
     4441 tttcattaac ccattgttgt aaataaggaa tctgcaaaat tttaattttg cgtggggtgt
     4501 gggtattttt agtggtgagg agcgttcaga gatctgacga tttttgggaa ggttcaggaa
     4561 ctccctggga tggccggaga ggaaaactga agcatgacgg ggtcaggatt ttttccagaa
     4621 tttggtgatg ctgccaactt actgatttag tgtatgatgg tgtttttgag gtgctccagt
     4681 ggcttctgtt tctatcagct gtccctcctg ttcagctact gacggggtgg tgcgtaacgg
     4741 caaaagcacc gccggacatc agcgctatct ctgctctcac tgccgtaaaa catggcaact
     4801 gcagttcact tacaccgctt ctcaacccgg tacgcaccag aaaatcattg atatggccat
     4861 gaatggcgtt ggatgccggg caaccgcccg cattatgggc gttggcctca acacgatttt
     4921 ccgccattta aaaaactcag gccgcagtcg gtaacctcgc gcatacagcc gggcagtgac
     4981 gtcatcgtct gcgcggaaat ggacgaacag tggggatacg tcggggctaa atcgcgccag
     5041 cgctggctgt tttacgcgta tgaca
//
