LOCUS       NZ_CP093480             5584 bp    DNA     circular CON 12-JUN-2024
DEFINITION  Klebsiella pneumoniae strain VA569 plasmid pVA569-6, complete
            sequence.
ACCESSION   NZ_CP093480
VERSION     NZ_CP093480.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN26642719
            Assembly: GCF_030061715.1
KEYWORDS    RefSeq.
SOURCE      Klebsiella pneumoniae
  ORGANISM  Klebsiella pneumoniae
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Klebsiella/Raoultella group; Klebsiella.
REFERENCE   1  (bases 1 to 5584)
  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  JOURNAL   Unpublished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 5584)
  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                   :: 164X
            Sequencing Technology             :: Illumina; Oxford Nanopore
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_030061715.1-RS_2024_06_12
            Annotation Date                   :: 06/12/2024 05:22:26
            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)                     :: 5,710
            CDSs (total)                      :: 5,587
            Genes (coding)                    :: 5,458
            CDSs (with protein)               :: 5,458
            Genes (RNA)                       :: 123
            rRNAs                             :: 9, 8, 8 (5S, 16S, 23S)
            complete rRNAs                    :: 9, 8, 8 (5S, 16S, 23S)
            tRNAs                             :: 86
            ncRNAs                            :: 12
            Pseudo Genes (total)              :: 129
            CDSs (without protein)            :: 129
            Pseudo Genes (ambiguous residues) :: 0 of 129
            Pseudo Genes (frameshifted)       :: 45 of 129
            Pseudo Genes (incomplete)         :: 81 of 129
            Pseudo Genes (internal stop)      :: 17 of 129
            Pseudo Genes (multiple problems)  :: 13 of 129
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP093480.1.
            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..5584
                     /organism="Klebsiella pneumoniae"
                     /mol_type="genomic DNA"
                     /strain="VA569"
                     /isolation_source="Isolated from peritoneal fluid of a 79
                     years old male"
                     /host="Homo sapiens"
                     /db_xref="taxon:573"
                     /plasmid="pVA569-6"
                     /geo_loc_name="Chile: Metropolitan Region"
                     /collection_date="2019-04-06"
                     /collected_by="Instituto de Salud Pblica de Chile"
     gene            complement(392..1933)
                     /locus_tag="MO417_RS28485"
                     /old_locus_tag="MO417_28460"
     CDS             complement(392..1933)
                     /locus_tag="MO417_RS28485"
                     /old_locus_tag="MO417_28460"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000050481.1"
                     /GO_function="GO:0004803 - transposase activity [Evidence
                     IEA]"
                     /GO_process="GO:0006313 - DNA transposition [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="IS91-like element ISCR1 family transposase"
                     /protein_id="WP_000050481.1"
                     /translation="MSLARNATASQSPTQTNGYERHQPDQTLLYQLVEQHYPAFKASLE
                     AQGQHLPRYIQQEFNDLLQCGRLEYGFMRVRCEDCHHERLVAFSCKRRGFCPSCGARRM
                     AESAALLIDEVFPKEPIRQWVLSFPFQLRFLLARHPQLMGQVLSIVYRTLSTHLIKKAG
                     YTKASAQTGSVTLIQRFGSALNLNVHYHMLFLDGVYAEDDYGKQRFHRVKAPTYDELNT
                     LAHTLSHRIARCMEKRGILERDAENTWLTLEEGEDDTLTQLHGASVTYRIAVGPQQGRK
                     VFTLQTLPGREDKADSSSRVANHAGFSLHAGVMAEAHQRDKLERLCRYISRPAVSEKRL
                     ALTANGQVRYELKTPYRNGTTHVIFEPLDFIAKLAALVPKPRVNLTRFHGVFAPNSKHR
                     VQVTPAKRGKKPDKSEGLDTNWRDKSPAERHRAMTWMQRLKRVFNIDIEVCEHCGGHVK
                     VIASIEDPKVIEQILKHLKQKTAKANAAKQRELPPERAPPLTPSLFDPSQSRLFD"
                     /name="IS91-like element ISCR1 family transposase"
     gene            complement(2338..3177)
                     /gene="sul1"
                     /locus_tag="MO417_RS28490"
                     /old_locus_tag="MO417_28465"
     ARG             complement(2342..3177)
                     /name="sul1"
                     /gene="sul1"
                     /gene_name="sulfonamide-resistant dihydropteroate synthase
                     Sul1"
                     /tool="amrfinderplus"
                     /drug_class="SULFONAMIDE"
                     /identity="100.0"
                     /coverage="100.0"
     gene            complement(3171..3518)
                     /locus_tag="MO417_RS28495"
                     /old_locus_tag="MO417_28470"
     CDS             complement(3171..3518)
                     /locus_tag="MO417_RS28495"
                     /old_locus_tag="MO417_28470"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000679427.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="quaternary ammonium compound efflux SMR
                     transporter QacE delta 1"
                     /protein_id="WP_000679427.1"
                     /translation="MKGWLFLVIAIVGEVIATSALKSSEGFTKLAPSAVVIIGYGIAFY
                     FLSLVLKSIPVGVAYAVWSGLGVVIITAIAWLLHGQKLDAWGFVGMGLIIAAFLLARSP
                     SWKSLRRPTPW"
                     /name="quaternary ammonium compound efflux SMR transporter
                     QacE delta 1"
     gene            complement(4602..5477)
                     /locus_tag="MO417_RS28500"
                     /old_locus_tag="MO417_28475"
     CDS             complement(4602..5477)
                     /locus_tag="MO417_RS28500"
                     /old_locus_tag="MO417_28475"
                     /EC_number="3.5.2.6"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_032489170.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="extended-spectrum class A beta-lactamase CTX-M-2"
                     /protein_id="WP_025368620.1"
                     /translation="MMTQSIRRSMLTVMATLPLLFSSATLHAQANSVQQQLEALEKSSG
                     GRLGVALINTADNSQILYRADERFAMCSTSKVMAAAAVLKQSESDKHLLNQRVEIKKSD
                     LVNYNPIAEKHVNGTMTLAELGAAALQYSDNTAMNKLIAHLGGPDKVTAFARSLGDETF
                     RLDRTEPTLNTAIPGDPRDTTTPLAMAQTLKNLTLGKALAETQRAQLVTWLKGNTTGSA
                     SIRAGLPKSWVVGDKTGSGDYGTTNDIAVIWPENHAPLVLVTYFTQPEQKAESRRDILA
                     AAAKIVTHGF"
                     /name="extended-spectrum class A beta-lactamase CTX-M-2"
     ARG             complement(3175..3518)
                     /name="qacEdelta1"
                     /gene="qacEdelta1"
                     /gene_name="quaternary ammonium compound efflux SMR
                     transporter QacE delta 1"
                     /tool="amrfinderplus"
                     /drug_class="QUATERNARY AMMONIUM"
                     /identity="100.0"
                     /coverage="100.0"
     ARG             complement(4606..5477)
                     /name="blaCTX-M-2"
                     /gene="blaCTX-M-2"
                     /gene_name="extended-spectrum class A beta-lactamase
                     CTX-M-2"
                     /tool="amrfinderplus"
                     /drug_class="BETA-LACTAM"
                     /identity="100.0"
                     /coverage="100.0"
ORIGIN
        1 ttacatcgcg gcgaaaaagc aaaagtcaga gatcgctcac gaaaggagca gcacattttg
       61 cagcagcgga aaaaaggatg aggggtacgc aggtacggca aaattttttg acgtctgtcg
      121 caaaattagc cataaaatca atagggttta aagggcgagg ggtataggaa gtataaacca
      181 cctttttgct cctcatccga agtatcttac ctgaaattcc ctcactcgtt taccgctcaa
      241 gccccaattt taactgccgg tccagcctaa accgctctaa taaggttcga tttggcggta
      301 aaatctctag cctgatagct cgagagatac aaactgcccc accgccccgt ttaaaagttg
      361 gcagtgttga gcagtgttgg atttggggtc gtcagtcaaa gagacgactc tgtgatggat
      421 cgaacaggct gggagtcagt ggcggcgctc gttctggtgg cagctcacgc tgcttggcgg
      481 cattcgcctt ggctgttttc tgtttcagat gcttgagaat ctgctcaatg accttcggat
      541 cttcgatgct ggcaatcact ttgacgtgac cgccgcagtg ttcgcagact tcaatatcaa
      601 tattgaagac tcgcttgagg cgttgcatcc aggtcatggc gcggtggcgc tctgcaggac
      661 tcttgtcacg ccagttagta tcgagacctt ccgatttgtc gggcttcttg ccccgcttgg
      721 cgggtgttac ttgaactcgg tgtttgctgt tcggtgcaaa gacgccgtgg aagcgtgtga
      781 ggttgactcg cggcttaggt accaacgcag cgagtttggc gatgaagtcc agcggctcga
      841 agatcacatg ggtggtgcca ttgcggtacg gagttttgag ctcgtaacgc acctgcccat
      901 tggcggttaa tgccagacgt ttttctgaaa ccgctggccg actaatgtag cgacacaagc
      961 gctcaagctt atcccgctga tgcgcttcgg ccatcacacc ggcgtgtagc gagaaaccag
     1021 catggttggc tactcgactg cttgagtcgg ctttatcctc acgccctggc aaggtttgca
     1081 gggtgaagac tttgcgccct tgctgggggc cgacggcaat gcgatacgta accgaagcac
     1141 catgtaattg agtcagcgta tcgtcttcgc cctcttccag tgtcaaccac gtattctcgg
     1201 catcacgctc caaaatccca cgcttttcca tgcagcgagc gatgcgatgg ctgagggtgt
     1261 gagcgagcgt attcagctca tcgtaagtgg gtgccttgac acgatggaag cgttgcttgc
     1321 catagtcatc ttcggcatag acaccatcga gaaacagcat gtggtagtgg acattgagat
     1381 ttagcgcgga gccaaagcgt tggataagag tcactgagcc agtttgtgca gaggctttgg
     1441 tgtaaccggc ttttttgatc agatgagttg agagtgtacg atagacgata ctcaagacct
     1501 ggcccatcag ctggggatgg cgagccagca aaaagcgtag ctggaaagga aagctgagca
     1561 cccactggcg aatgggctcc ttggggaaga cttcgtctat cagcagcgcc gcactctcgg
     1621 ccatccggcg ggcaccgcag ctagggcaaa agccgcgtcg tttacagctg aaggcgacca
     1681 gacgctcgtg atgacaatcc tcgcagcgaa cccgcatgaa accatactcc agacggccac
     1741 attggaggag gtcgttgaat tcttgttgga tgtagcgagg caggtgttga ccttgggctt
     1801 cgagtgaggc tttgaaggct gggtagtgct gctcaaccag ctggtagagc agcgtctggt
     1861 cgggttggtg gcgttcgtaa ccgtttgttt gagtgggcga ttgactcgcc gtggcgttcc
     1921 ttgccagcga catgggtatc ctccgctgat actgtggtta tgtacagtat cagcggcttg
     1981 cgttcagacg tccagtctgg ccctagacat cgctaaatgc ttaacccgca atagccctca
     2041 cgagttgtta tcagccacta ccggttgagc gagaaggttt tgggttcagg gtgctattgc
     2101 tccaccaatc acaatactga agccccaact gttatcagtt ggggcttttt cttgtctgtt
     2161 tgcggcggtt gcgttttatc ggtagtcgtc gagctctgca ccatcccaca taagagctta
     2221 acggtgcgat cttcaacgcc atcacacaaa actttctttt tcacgcacag tcaacttatt
     2281 ggatgtttta ttaacaaccc aaaaggagat atttagcggg cggccggaag gtgaatgcta
     2341 ggcatgatct aaccctcggt ctctggcgtc gcgactgcga aatttcgcga gggtttccga
     2401 gaaggtgatt gcgcttcgca gatctccagg cgcgtgggtg cggacgtagt cagcgccatt
     2461 gccgatcgcg tgaagttccg ccgcaaggct cgctggaccc agatccttta caggaaggcc
     2521 aacggtggcg cccaagaagg atttccgcga caccgagacc aatagcggaa gccccaacgc
     2581 cgacttcagc ttttgaaggt tcgacagcac gtgcagcgat gtttccggtg cggggctcaa
     2641 gaaaaatccc atccccggat cgaggatgag ccggtcggca gcgaccccgc tccgtcgcaa
     2701 ggcggaaacc cgcgcctcga agaaccgcac aatctcgtcg agcgcgtctt cgggtcgaag
     2761 gtgaccggtg cgggtggcga tgccatcccg ctgcgctgag tgcataacca ccagcctgca
     2821 gtccgcctca gcaatatcgg gatagagcgc agggtcagga aatccttgga tatcgttcag
     2881 gtagcccacg ccgcgcttga gcgcatagcg ctgggtttcc ggttggaagc tgtcgattga
     2941 aacacggtgc atctgatcgg acagggcgtc taagagcggc gcaatacgtc tgatctcatc
     3001 ggccggcgat acaggcctcg cgtccggatg gctggcggcc ggtccgacat ccacgacgtc
     3061 tgatccgact cgcagcattt cgatcgccgc ggtgacagcg ccggcggggt ctagccgccg
     3121 gctctcatcg aagaaggagt cctcggtgag attcagaatg ccgaacaccg tcaccatggc
     3181 gtcggcctcc gcagcgactt ccacgatggg gatcgggcga gcaaaaaggc agcaattatg
     3241 agccccatac ctacaaagcc ccacgcatca agcttttgcc catgaagcaa ccaggcaatg
     3301 gctgtaatta tgacgacgcc gagtcccgac cagactgcat aagcaacacc gacagggatg
     3361 gatttcagaa ccagagaaag aaaataaaat gcgatgccat aaccgattat gacaacggcg
     3421 gaaggggcaa gcttagtaaa gccctcgcta gattttaatg cggatgttgc gattacttcg
     3481 ccaactattg cgataacaag aaaaagccag cctttcatga tatatctccc aatttgtgta
     3541 gggcttatta tgcacggcgt attgatatca gcacccattt tcttctccgc ccgtcgcttt
     3601 gcggcataca ccgcacggat atcaagatgg cgccccctgg ccagatggtt acaatcttca
     3661 cccgcaatca gtgcccccag gacatcgaac tcgagcgttg acagagatag tccatgaaaa
     3721 aacgcatctc tctgatagat aaatcttttc tttaatttat caccagcaga ctttaaatta
     3781 tcctgttgat aaataatcaa aaaaatatct ttgtgatgct tataccagta attagccaat
     3841 ggtctgaggt gcctatcgca aacgagaact atctttagtt ttgtttcgta taaatagtcc
     3901 aaccattttt tgtcagtaaa aaaacgcaga tagctaatag agaaatcaac aaaaacacac
     3961 ccaagataca ggtagtgata ttgctgttta aggagaccct ccatgatacc gagtgagaaa
     4021 tagcgactgg cttcaggcca ggtacaaaaa cagtattcct gacaaaatga aacccgtaga
     4081 gaggcatttg gcttaacttc acaatgagaa gggcagctca tacaggtaac tcttgcaaaa
     4141 ttattattga gcgacttcat tgtcccctcc ttatccatat tagaataatt tcattgaggt
     4201 aatttattgt caataagctt ttaagatggc tcttagttca actattaaaa ataaataaaa
     4261 ttcttaaagc ataaaaaacc attagaaaac aaccatgcag acagaaagga gatacggaag
     4321 gccgaaatta ttccagtgta aaaaaatagg aatactgcaa gtgtaaatca gataattaca
     4381 ataaaaacaa acaacctaat aattaaatgc cttaaacatt atttaaaata aaatagttta
     4441 cataagaaat tgttatctat taccttcctg aagctaagat atttggtcca gaaaaaagag
     4501 cggaatgata gaaagagatg agggttcgtt gcaagacaag actgaagttc aggagcacat
     4561 ttttaacgta aatggagcga tacctcgctc catttattgc atcagaaacc gtgggttacg
     4621 attttcgccg ccgcagccag aatatcccga cggctttccg ccttctgctc cggttgggta
     4681 aagtaggtca ccagaaccag cggtgcgtgg ttttccggcc agataaccgc gatatcgttg
     4741 gtggtgccat aatctccgct gccggtttta tcgcccacta cccatgattt cggcagaccc
     4801 gcccgaatgc tcgcgctacc ggtagtattg cccttaagcc acgtcaccaa ctgtgcccgc
     4861 tgagtttccg ccagcgcttt acccagcgtc agatttttca gggtctgcgc catcgcgagc
     4921 ggcgtggtgg tatcacgcgg gtcgcctgga atggcggtat tgagcgtggg ctcggttctg
     4981 tccagacgga aggtctcatc acccaacgag cgagcaaacg ccgtcacttt atcgggacca
     5041 cccagatggg caatcagctt attcatggca gtattgtcgc tatactgcag cgccgctgcg
     5101 ccaagctcag ccagcgtcat cgtgccgtta acgtgtttct ccgcaatggg attgtagtta
     5161 accaggtcgc tcttcttgat ttcaacgcgc tgatttagca ggtgcttatc gctctcgctc
     5221 tgtttaagca ccgccgcggc cgccatcacc ttactggtac tgcacatcgc aaaacgttca
     5281 tcggcacggt agagaatctg cgaattatcg gcggtgttaa tcagcgcaac gccaagccga
     5341 cctcccgaac ttttctccag ggcttccagc tgctgttgca cgctgttcgc ctgcgcatgc
     5401 agcgttgcgc tgctaaatag caggggtagc gtcgccatca ccgttaacat tgagcggcga
     5461 atgctctgag tcatcattaa aaatcctcta ttagtattat ccctcggcct tcaagtatac
     5521 attgaaaaaa caaaaagtaa aaacaaaacc tgccaatatc tccacaattg agcctggtcc
     5581 atgt
//
