LOCUS       NZ_CP093463             5988 bp    DNA     circular CON 11-JUN-2024
DEFINITION  Klebsiella pneumoniae strain VA684 plasmid pVA684-6, complete
            sequence.
ACCESSION   NZ_CP093463
VERSION     NZ_CP093463.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN26642722
            Assembly: GCF_030061645.1
KEYWORDS    RefSeq.
SOURCE      Klebsiella pneumoniae
  ORGANISM  Klebsiella pneumoniae
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Klebsiella/Raoultella group; Klebsiella.
REFERENCE   1  (bases 1 to 5988)
  AUTHORS   Marcoleta,A.E., Hormazabal,J.C. and Araya,P.
  TITLE     Complete genome sequencing and analysis of carbapenem-resistant
            Klebsiella pneumoniae isolated in Chile
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 5988)
  AUTHORS   Marcoleta,A.E., Hormazabal,J.C. and Araya,P.
  TITLE     Direct Submission
  JOURNAL   Submitted (13-MAR-2022) Biology, Grupo de Microbiologia Integrativa,
            Facultad de Ciencias, Universidad de Chile, Las Palmeras 3425 Nunoa,
            Santiago, RM 780000, Chile
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method :: unicycler v. 0.4.9b; Canu v. 2.3
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 195X
            Sequencing Technology             :: Illumina; Oxford Nanopore
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_030061645.1-RS_2024_06_11
            Annotation Date                   :: 06/11/2024 06:17:40
            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)                     :: 5,638
            CDSs (total)                      :: 5,516
            Genes (coding)                    :: 5,352
            CDSs (with protein)               :: 5,352
            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)              :: 164
            CDSs (without protein)            :: 164
            Pseudo Genes (ambiguous residues) :: 0 of 164
            Pseudo Genes (frameshifted)       :: 63 of 164
            Pseudo Genes (incomplete)         :: 96 of 164
            Pseudo Genes (internal stop)      :: 36 of 164
            Pseudo Genes (multiple problems)  :: 28 of 164
            CRISPR Arrays                     :: 3
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP093463.1.
            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..5988
                     /organism="Klebsiella pneumoniae"
                     /mol_type="genomic DNA"
                     /strain="VA684"
                     /isolation_source="Isolated from catheter blood of an 15
                     years old female"
                     /host="Homo sapiens"
                     /db_xref="taxon:573"
                     /plasmid="pVA684-6"
                     /geo_loc_name="Chile: Metropolitan Region"
                     /collection_date="2019-04-25"
                     /collected_by="Instituto de Salud Pblica de Chile"
     gene            complement(join(5825..5988,1..154))
                     /locus_tag="MO416_RS28095"
                     /old_locus_tag="MO416_28060"
     CDS             complement(join(5825..5988,1..154))
                     /locus_tag="MO416_RS28095"
                     /old_locus_tag="MO416_28060"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_006395424.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_227631199.1"
                     /translation="MRVLSLGAILMAMSALPLTAISQVTLASDGSYVSGSEATLAPDGS
                     YVGGSEVTLAPDGSYVGGSEVTLAPDGSYVGGSEVTLAPDGSYVGGSEATLAPDGSYVG
                     N"
                     /name="hypothetical protein"
     gene            complement(289..480)
                     /locus_tag="MO416_RS28100"
                     /old_locus_tag="MO416_28065"
     CDS             complement(289..480)
                     /locus_tag="MO416_RS28100"
                     /old_locus_tag="MO416_28065"
                     /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_049106033.1"
                     /translation="MLKKDDIIFMKSCGNAKTIIFLRGVDEKLMINASFEEIKFAINNN
                     LQELPGVQAVAATLKIAT"
                     /name="hypothetical protein"
     gene            722..1832
                     /locus_tag="MO416_RS28105"
                     /old_locus_tag="MO416_28070"
                     /pseudo=""
     CDS             722..1832
                     /locus_tag="MO416_RS28105"
                     /old_locus_tag="MO416_28070"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_076611476.1"
                     /GO_function="GO:0004803 - transposase activity [Evidence
                     IEA]"
                     /note="frameshifted; internal stop; Derived by automated
                     computational analysis using gene prediction method:
                     Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="IS3 family transposase"
                     /name="IS3 family transposase"
     gene            complement(2202..2315)
                     /locus_tag="MO416_RS28250"
                     /pseudo=""
     CDS             complement(2202..2315)
                     /locus_tag="MO416_RS28250"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_007772075.1"
                     /note="internal stop; Derived by automated computational
                     analysis using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="replication initiation protein"
                     /name="replication initiation protein"
     gene            2728..2918
                     /locus_tag="MO416_RS28110"
                     /old_locus_tag="MO416_28075"
                     /pseudo=""
     CDS             2728..2918
                     /locus_tag="MO416_RS28110"
                     /old_locus_tag="MO416_28075"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000166328.1"
                     /note="frameshifted; Derived by automated computational
                     analysis using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="Rop family plasmid primer RNA-binding protein"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            2918..3157
                     /locus_tag="MO416_RS28115"
                     /old_locus_tag="MO416_28080"
     CDS             2918..3157
                     /locus_tag="MO416_RS28115"
                     /old_locus_tag="MO416_28080"
                     /inference="COORDINATES: protein motif:HMM:NF024139.4"
                     /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_283447409.1"
                     /translation="MARVSISEAARLTGKSRTTLHRLIKTGDLSTCSGERNAKMVDTSE
                     LLRVFGPFEQPKGEHHSDRSLNSVIQPLLTRVNR"
                     /name="helix-turn-helix domain-containing protein"
     gene            complement(3647..3763)
                     /locus_tag="MO416_RS28255"
                     /pseudo=""
     CDS             complement(3647..3763)
                     /locus_tag="MO416_RS28255"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_007772075.1"
                     /note="internal stop; Derived by automated computational
                     analysis using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="replication initiation protein"
                     /name="replication initiation protein"
     gene            4175..4366
                     /locus_tag="MO416_RS28120"
                     /old_locus_tag="MO416_28085"
     CDS             4175..4366
                     /locus_tag="MO416_RS28120"
                     /old_locus_tag="MO416_28085"
                     /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            4366..4767
                     /locus_tag="MO416_RS28125"
                     /old_locus_tag="MO416_28090"
     CDS             4366..4767
                     /locus_tag="MO416_RS28125"
                     /old_locus_tag="MO416_28090"
                     /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_064175096.1"
                     /translation="MARVSISEAARLTGKSRTTLHRLIKTGDLSTCSGERNAKMVDTSE
                     LLRVFGPFEQPKGEHHSGQVSEQRDTASADQSEQVIRHLKQEIEHLNTLLLSKDSHIDS
                     LKQAMLLLENHQAKLTESPTPWWKFWKKS"
                     /name="helix-turn-helix domain-containing protein"
     gene            complement(5510..5620)
                     /locus_tag="MO416_RS28260"
     CDS             complement(5510..5620)
                     /locus_tag="MO416_RS28260"
                     /inference="COORDINATES: protein motif:HMM:NF033853.2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="small membrane protein"
                     /protein_id="WP_139157850.1"
                     /translation="MDFFLLAIAIALLVVAVYSGISYYKEKKTISRTFRR"
                     /name="small membrane protein"
     Typing          complement(2203..2607)
                     /name="ColRNAI_rep_cluster_1987"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="93.888"
                     /coverage="99.0"
                     /evalue="3.5400000000000005e-173"
     Typing          complement(3648..4054)
                     /name="ColRNAI_rep_cluster_1987"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="94.132"
                     /coverage="99.0"
                     /evalue="2.12e-175"
ORIGIN
        1 cttccgaacc accaacgtat gagccatcag gtgctaaggt tgcttccgaa ccactaacgt
       61 acgatccatc agatgctaag gttacttggg atatcgcggt tagtggtaat gctgacatag
      121 ccattaaaat ggcaccaaga gataatactc tcatcactat tactcctgtt aatatcaaaa
      181 atagaattga atcgttcagc ggtgccgaac gccggttcca gccgcgggat tcgtgatcgg
      241 gatgttatag taaattgatc tcttgatttt gagtgccctt actcgaaatc aggttgctat
      301 tttcagtgtc gcggctactg cttgtacccc cggaagctcc tgaagattat tattgatagc
      361 aaactttatc tcttcaaagc tcgcgttaat catgagcttc tcatccacgc cacgtaaaaa
      421 tattattgtt tttgcattac cacatgattt cataaagata atatcatctt tttttagcat
      481 gatactgtcg ttacttagtg tagtgagata aagcatagcc actgtttttg tgtgtttttg
      541 ttaaggctgt taagattatt cctaaccact gattttgtac atatcatcaa aaaaaataaa
      601 aaaactaatg cccccgtggt gggtatataa caaatcacgg ggagcggagc tgacctgctc
      661 cccgttgatt aatacaccgc gatgttagta atgtcttcat aagccacatg aggacatcct
      721 catgaagaag cgtttttccg acgaacagat catcagtatt ctccgcgagg ccgaagccgg
      781 ggtttctgcc cgtgagctct gccgtaagca cgccatttcc gacgccatct tttacacctg
      841 gcgtaagaag tatggcggta tggaggtgcc cgaggttaag cgccttaagt cgcttgagga
      901 agagaacgcc agactcaaga aactgcttgc cgaagccatg ctggataagc aggcgcttca
      961 ggtggctctg gggcgaaagt actgacgaca gaccagaagc aggaagccgt tgagtttatg
     1021 tgtgatgcga ccggtctgtc gcaacgtagt gcctgcaggc ttacaggttt gcccctgtcg
     1081 acctgccgct atgaggctca gcgttcggcg gctgatgcgc atttatcact gagctggcac
     1141 tggagcgcag gcgttttggc taccgacgca tctggcagtt actgcgccgt gaaggccttc
     1201 atgttaatca caagcgcgtg taccgtcttt accaccttaa cgggctgggt gtaaaacgca
     1261 gacgacgtcg taaaggtctg gcaacagaac gtctgccgct gctccgcccg gaggcgccca
     1321 acctgacctg gccgatggat tttgtcatgg acgcgctggc caccggtcgc aggatcaagt
     1381 gcctgacctg cgtggacgac ttcacgaagg agtgtctgac aattaccgcc gtcttcggga
     1441 tttcaggcgt tcaggtcacg cgaattctgg acagcattgc actgtttcgc ggctatccgg
     1501 cgacgataag aactgaccag gggccggagt ttacctgcag agcactcgac cagtgggctt
     1561 atgagcatgg ggtggagcta cggcttatcc agccgggcag gccaacacag aacggattta
     1621 ttgaaagttt taacggacga ttcagggatg agtgcctcaa tgagcactgg ttcagcgata
     1681 tcgttcacgc caggaaaacg attaatgact ggcggcagga ttagagcgag tgtcgtccac
     1741 attcatcgct gaactaccag actccggctg aatttgcggc gggctggcga aacgggaaat
     1801 atgaagaaaa acgaaccgac attactaact gaaggttgta tctaatcctg ggggggcagg
     1861 tcaaccgcgt tggatgattg tggatcatga ttatatatgt ttttttctta tcagaaacaa
     1921 tgggttaaat agttttattt tgatggttgg tgtcgcggag tggtgctggt ttcacttcag
     1981 gggtaggcat atggaacagg atcctcttga gatcctttct ttagcatcgt aatctcttgc
     2041 tcagtaaacg aaaaaaccgc ccagcaaggc ggttttctcg aaggttctca gagcagcaac
     2101 tctttgaacc gaggtaactg gcttaaaggg agcgcagtca ccaaaactgt tcgtttagtt
     2161 tagccctaac tggcgtataa cttcaagact aactccctaa atcagttacc agtggctgct
     2221 gccagtggcg ctttgtcgtg tctttccggg ttggactcaa gacgatagtt accggattag
     2281 gcgcagcagt cggactgaac ggggggttcg tgcatacagt ccagcttgga gcgaactgcc
     2341 ttcccggaac tgagtgtcag gcgtggaatg agacaaacgc ggccataaca gcggaatgac
     2401 accggtaaac cgaaaggcag gaacaggaga gcgcacgagg gagccatcag gggaaacgcc
     2461 tggtatcttt atagtcctgt cgggtttcgc caccactgat ttgagcgtca gattctgtga
     2521 tgcttgtcag ggggcggagc ctatggaaaa aggccaccat gcggcctttc cttttcacca
     2581 tcacgcgact gttcggtttt ctcgagcttt tatgtgcatg ctcctgccgc tcgccgcagc
     2641 cgaacggcag gagcatagcg actgagtgag cgaggaagcg gaaaagagaa catccctaca
     2701 ctgagcactg acgctctgag gcctcttatg acgaaacaac agaaaacagc gctgaacatg
     2761 gctaaattca tccagaatca gtctctgctc ctgctggaga agcttaacga gcttgatctc
     2821 gatgtcgagg ccgaccttgt gagaaactcc acgatgatgc ggagcatctt ttccgtacac
     2881 tgtcctcgag actggatgca ttacaggatg gtaactgatg gccagagtgt ctattagtga
     2941 ggctgcccga ctgacgggta agagtagaac aacactgcac aggttaatta aaacaggtga
     3001 cctgtccacc tgtagtggtg agcgcaatgc aaaaatggta gatacttcag agcttttacg
     3061 tgtctttggt ccctttgagc aaccgaaggg tgaacaccat tctgacaggt ctctgaacag
     3121 cgtgatacag cctctgctga ccagagtgaa caggtgattc gtcatctgaa acaggagatt
     3181 gaacacctga acaccttact tttgtccaag gattcgcaca ttgacagcct gaaacaggcc
     3241 atgctccttc ttgaaaatca ccagcaaaat taactgaatc cccgacgcca tggtggaaat
     3301 tctgaaaaaa tcctgacccc gtcatgcttc agttttcctc tccggccatc ccgggagttc
     3361 ctgaaccttc ccaaaaatcg tcagatctct gaacgctcct caccactaaa aatacccaca
     3421 ccccacgcaa aattaaaatt ttgcagattc cttatttaca acaatgggtt aatgaaaaat
     3481 aaatgtgcgg tgatgtgtta caaagtgcag atccaagtcg tggacaactc tatggcgaat
     3541 cgctgacgat tgaaccgagg taaccggctt aaagggagcg cagtcaccaa aactgttcgt
     3601 ttagtttagc cctaactggc gtataacttc aagactaact cctaaatcag ttaccagtgg
     3661 ctgctgccag tggcgctttg tcgtgtcttt ccgggttgga ctcaagacga tagttaccgg
     3721 attaggcgca gcagtcggac tgaacggggg ttcgtgcata cagtccagct tggagcgaac
     3781 tgccttcccg gaactgagtg tcaggcgtgg aatgagacaa acgcggccat aacagcggaa
     3841 tgacaccggt aaaccgaaag gcaggaacag gagagcgcac gagggagcca tcagggggaa
     3901 acgcctggta tctttatagt cctgtcgggt ttcgccacca ctgatttgag cgtcagattc
     3961 tgtgatgctt gtcagggggg cggagcctat ggaaaaaagg ccaccatgcg gcctttcctt
     4021 ttcaccatca cgcgactgtt cggttttctc gagcttttat gtgcatgctc ctgccgctcg
     4081 ccgcagccga acggcaggag catagcgact gagtgagcga ggaagcggaa aagagaacat
     4141 ccctacactg agcactgacg ctctgaggcc tcttatgacg aaacaacaga aaacagcgct
     4201 gaacatggct aaattcatcc agaatcagtc tctgctcctg ctggagaagc ttaacgagct
     4261 tgatctcgat gtcgaggccg acctttgtga gaaactccac gatgatgcgg agcatctttt
     4321 ccgtacactg tcctcgagac tggatgcatt acaggatggt aactgatggc cagagtgtct
     4381 attagtgagg ctgcccgact gacgggtaag agtagaacaa cactgcacag gttaattaaa
     4441 acaggtgacc tgtccacctg tagtggtgag cgcaatgcaa aaatggtaga tacttcagag
     4501 cttttacgtg tctttggtcc ctttgagcaa ccgaagggtg aacaccattc tggacaggtc
     4561 tctgaacagc gtgatacagc ctctgctgac cagagtgaac aggtgattcg tcatctgaaa
     4621 caggagattg aacacctgaa caccttactt ttgtccaagg attcgcacat tgacagcctg
     4681 aaacaggcca tgctccttct tgaaaatcac caggcaaaat taactgaatc cccgacgcca
     4741 tggtggaaat tctggaaaaa atcctgaccc cgtcatgctt cagttttcct ctccggccat
     4801 cccggggagt tcctgaacct tcccaaaaat cgtcagatct ctgaacgctc ctcaccacta
     4861 aaaataccca caccccacgc aaaattaaaa ttttgcagat tccttattta caacaatggg
     4921 ttaatgaaaa ataaatgtgc ggtgatgtgt tacaaagtgc agatccaagt cgtggacaac
     4981 tctatggcga atcgctgacg aattgcccac gattcatatg tgaatcacgc tttattatca
     5041 tattgttatg atgaatcgac tcttgattca attcatcact ctgggttttt tttgttcatg
     5101 gtgactcttg attcaattca cgattcgaat cgccggtgaa tcgtgtggtg agtcgtccgg
     5161 cggcttgcca taacgtgatt gccggccgtc gacgaacccg attcctgaac gtgctgaaaa
     5221 ccggttttcc ggctgcgccg gcaacgcttc acggccacgc aataaattgc gtccccgttc
     5281 accgttttcg gataggaaga acgccggaaa caggacttac cctggctgaa tggcgtgaat
     5341 tttcgcgcta tgcacttgcg tgcatactca tgcatgccgt aaaaacagag cctgcgcgtt
     5401 tctggcgggt tttcgggtgg tttgttgcct gttttaccgg tttcccgtca gaaacgcctt
     5461 gaggccgttt ttgcggtgcg tacaagaagg gattatggta aatagggcgc tatcgcctaa
     5521 atgtacgact gattgttttt ttttctttgt agtatgagat tcctgagtag acagctacaa
     5581 caagtagagc aatggcgata gcaagtaaaa aaaagtccat aagtacttta ttaatctaat
     5641 aaaaacaacc tgttatgatt agttattgta agtggttttc attctttttt cattacactt
     5701 attgctttga gctaatggtt cctgaggacg cattgttcag tacacgtaag aagacgttat
     5761 gataaatcca aaaatgctgg cattcggaat tcagtatatc ggtacgcagc ataataatgg
     5821 ggggttaatt tccaacgtat gagccatcag gtgctaaggt tgcttccgaa ccaccaacgt
     5881 atgagccatc aggtgctaag gttacttccg aaccaccaac gtatgagcca tcaggtgcta
     5941 aggttacttc cgaaccacca acgtatgagc catcaggtgc taaggtta
//
