LOCUS       NZ_CP084821             4773 bp    DNA     circular CON 10-JAN-2024
DEFINITION  Klebsiella quasipneumoniae subsp. quasipneumoniae strain 18A069
            plasmid pKqq_18A069_3, complete sequence.
ACCESSION   NZ_CP084821
VERSION     NZ_CP084821.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN22024801
            Assembly: GCF_020525805.1
KEYWORDS    RefSeq.
SOURCE      Klebsiella quasipneumoniae subsp. quasipneumoniae
  ORGANISM  Klebsiella quasipneumoniae subsp. quasipneumoniae
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Klebsiella/Raoultella group; Klebsiella.
REFERENCE   1  (bases 1 to 4773)
  AUTHORS   Hawkey,J., Vezina,B., Monk,J.M., Judd,L.M., Harshegyi,T., Brisse,S.,
            Holt,K.E. and Wyres,K.L.
  TITLE     A curated collection of Klebsiella metabolic models reveals variable
            substrate usage and gene essentiality
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 4773)
  AUTHORS   Hawkey,J., Vezina,B., Monk,J.M., Judd,L.M., Harshegyi,T., Brisse,S.,
            Holt,K.E. and Wyres,K.L.
  TITLE     Direct Submission
  JOURNAL   Submitted (04-OCT-2021) Infectious Diseases, Monash University, 85
            Commercial Rd, Melbourne, VIC 3004, Australia
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Date                     :: 01-JAN-2021
            Assembly Method :: Trycycler; Medaka; Pilon v. 0.3.3; 1.3.3; 1.23
            Assembly Name :: Klebsiella quasipneumoniae subsp. quasipneumoniae
            18A069
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 50x
            Sequencing Technology :: Minion (Oxford Nanopore) and NextSeq
            500/550 (Illumina)
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 01/10/2024 04:28:27
            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)                     :: 5,397
            CDSs (total)                      :: 5,264
            Genes (coding)                    :: 5,141
            CDSs (with protein)               :: 5,141
            Genes (RNA)                       :: 133
            rRNAs                             :: 9, 8, 8 (5S, 16S, 23S)
            complete rRNAs                    :: 9, 8, 8 (5S, 16S, 23S)
            tRNAs                             :: 88
            ncRNAs                            :: 20
            Pseudo Genes (total)              :: 123
            CDSs (without protein)            :: 123
            Pseudo Genes (ambiguous residues) :: 0 of 123
            Pseudo Genes (frameshifted)       :: 50 of 123
            Pseudo Genes (incomplete)         :: 71 of 123
            Pseudo Genes (internal stop)      :: 28 of 123
            Pseudo Genes (multiple problems)  :: 21 of 123
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP084821.1.
            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..4773
                     /organism="Klebsiella quasipneumoniae subsp.
                     quasipneumoniae"
                     /mol_type="genomic DNA"
                     /strain="18A069"
                     /isolation_source="blood"
                     /host="Homo sapiens"
                     /sub_species="quasipneumoniae"
                     /db_xref="taxon:1667327"
                     /plasmid="pKqq_18A069_3"
                     /geo_loc_name="Spain"
                     /collection_date="1997"
     gene            complement(join(4404..4773,1..53))
                     /locus_tag="LGM21_RS26935"
                     /old_locus_tag="LGM21_26935"
     CDS             complement(join(4404..4773,1..53))
                     /locus_tag="LGM21_RS26935"
                     /old_locus_tag="LGM21_26935"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:YP_005229777.1"
                     /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_048290308.1"
                     /translation="MARVSISEAARLVKVSRPTIYKMINSGKLSYTSVVKHGKHTKVID
                     TSELIRVFGSLYGGDDTVKHDVKGDAGATAVNILGLHDLQHKIALLEAENDGLKGAVKA
                     RDEHIDSLRQAMQLLEHKHEPSPQVHSPWWKFWKKS"
                     /name="helix-turn-helix domain-containing protein"
     gene            complement(53..244)
                     /locus_tag="LGM21_RS26940"
                     /old_locus_tag="LGM21_26940"
     CDS             complement(53..244)
                     /locus_tag="LGM21_RS26940"
                     /old_locus_tag="LGM21_26940"
                     /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_032421723.1"
                     /translation="MTKQQKTALNMAKFIQNQSLLLLEKLNELDLDAEADLCEKLHDDA
                     EHLFRTLSSRLDELQDGN"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            660..773
                     /locus_tag="LGM21_RS26945"
                     /old_locus_tag="LGM21_26945"
     CDS             660..773
                     /locus_tag="LGM21_RS26945"
                     /old_locus_tag="LGM21_26945"
                     /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_071997595.1"
                     /translation="MHEPPVQSDCCACFGNYRLESNPKRHDKTPLAAATGN"
                     /name="replication initiation protein"
     gene            complement(988..1212)
                     /locus_tag="LGM21_RS26950"
                     /old_locus_tag="LGM21_26950"
     CDS             complement(988..1212)
                     /locus_tag="LGM21_RS26950"
                     /old_locus_tag="LGM21_26950"
                     /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_197986819.1"
                     /translation="MKIKLLDSVYNVEPKTDIMAWDNHWNYQWSGRTSGITKDAIKWRK
                     ESDGQFIVCDETGAVWLVDQNELDNLLAA"
                     /name="hypothetical protein"
     gene            1349..2239
                     /locus_tag="LGM21_RS26955"
                     /old_locus_tag="LGM21_26955"
     CDS             1349..2239
                     /locus_tag="LGM21_RS26955"
                     /old_locus_tag="LGM21_26955"
                     /inference="COORDINATES: protein motif:HMM:NF015983.4"
                     /GO_function="GO:0051539 - 4 iron, 4 sulfur cluster binding
                     [Evidence IEA]; GO:0003824 - catalytic activity [Evidence
                     IEA]; GO:1904047 - S-adenosyl-L-methionine binding
                     [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="radical SAM protein"
                     /protein_id="WP_048290309.1"
                     /translation="MFELKSPLLLVIDITNECNLSCNYCFQDFRSDTKNSINLGTITEI
                     LSEAKDMGIFEINICGGEPFKHKDIINIISEVKRVGFNLSIVTNGTLINKKTALLLNEL
                     DVIKNMQISFDSHIDSIHNKLRGGYHQAIRGLDYLLSYDSPPPSIGIVISKENVNHINE
                     TIDFFSRKGIRRFHIMNLLGNKELSCSDAELNEATKRINESFLQSRDGDKKLIISNLDF
                     KEKKDYQYKDVHINCLAGYTTLVLTSSLNIIPCDMVNYIIKKWKKKGDLRDGFELSKKQ
                     WLGLKESWCKGCFKC"
                     /name="radical SAM protein"
     gene            complement(2774..3064)
                     /locus_tag="LGM21_RS26960"
                     /old_locus_tag="LGM21_26960"
     CDS             complement(2774..3064)
                     /locus_tag="LGM21_RS26960"
                     /old_locus_tag="LGM21_26960"
                     /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_226554717.1"
                     /translation="MVRLIKDDRLRTLATFDGKTLKDDRLRTLATFDGKTLKDDRLRTL
                     ATFDGKTLKDDRLRTLATFDGKTLKDDRLRTLATVDGSVSIVIIAFAARIF"
                     /name="hypothetical protein"
     gene            complement(3182..3595)
                     /locus_tag="LGM21_RS26965"
                     /old_locus_tag="LGM21_26965"
     CDS             complement(3182..3595)
                     /locus_tag="LGM21_RS26965"
                     /old_locus_tag="LGM21_26965"
                     /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_071997596.1"
                     /translation="MTIPKIKSFPEVGSRREEQAHFVWIALTSWCLFNKNKTITYGELA
                     KLIGYPAQAGRTLAEALGTVSLYCLYNDLPPLSCIVVAKNTNHPGWEGMIPSNSSLEKE
                     QNKVWETSWNLYRTPSVGTLRRAREELNWDEFI"
                     /name="hypothetical protein"
     Typing          366..773
                     /name="ColRNAI_rep_cluster_1987"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="91.484"
                     /coverage="99.0"
                     /evalue="1.3e-157"
ORIGIN
        1 gggcgactaa ccttaacaag ccgtgccgct tcactaatag acactctggc catcaattac
       61 catcctgtaa ttcatccagt ctcgaggaca gtgtacggaa aagatgctcc gcatcatcgt
      121 ggagtttctc acaaaggtcg gcctcagcat caagatcaag ctcgttaagc ttctccagca
      181 ggagcagaga ctgattctgg atgaatttag ccatgttcag cgctgttttc tgttgtttcg
      241 tcataagagg cctcacagcg tcagtgctca gtgtagggat gttctctttt ccgcttcctc
      301 gctcactcag tcgctatgct cctgccgttc ggctgcggcg agcggcagga gcatgcgtgt
      361 aaaagctcga gaaaaccgag cggtcgcgtg acggggaaaa ggaaaggccg ctaagcggcc
      421 gtttttccat aggctccgcc cccctgacaa gcatcacgaa atctgacact caaatcagtg
      481 gtggcgaaac ccgacaggac tataaagata cctatcattt ctgataggcg gctccctcgt
      541 gcgctctcct gttcctgcct ttcggtttac cggtgtcact ccgctgttat ggccgcgttt
      601 atctcattcc acgcctgaca ctcagttccg ggtaggcagt tcgctccaag ctggactgta
      661 tgcacgaacc ccccgttcag tccgactgct gcgcctgttt cggtaactat cgacttgagt
      721 ccaacccgaa aagacacgac aaaacgccac tggcagcagc cactggtaac tgatttagag
      781 gagttagtct tgaagtcata cgccagttaa ggctaaacta aacgaacagt tttggttact
      841 gcgctcctcc aagccagtta cctcggttca aagagttgct gctcagagaa cctttgaaaa
      901 accgccttgc tgggcggttt ttctctttca ggggagaaga ttacgatggg aaggtgagga
      961 tctcaagtaa atactagaaa tatggcgtta tgcagcgagc aagttatcca actcattctg
     1021 atctactagc cagacagctc ctgtctcatc acaaacaata aactgcccat cagactcttt
     1081 cctccactta atggcatcct tcgtaattcc cgatgtacgg ccactccatt gataattcca
     1141 atgattatcc cacgccatga tatccgtttt aggctctacg ttataaaccg aatctaacag
     1201 cttgattttc accgcaatta cctctcaaga aaaaatctag aactacagat gagcatataa
     1261 aatactgaat cgaattttat tgactaccgt caagactaat caattaattg aaaaatataa
     1321 taaaaaccaa aaacacaggg taacgattat gttcgaattg aaatcaccat tgctattggt
     1381 cattgatata accaatgagt gtaatttatc atgcaattat tgcttccaag atttcagatc
     1441 ggatactaaa aacagcatca acttaggtac aatcaccgaa atattatcag aagcaaaaga
     1501 tatgggtatt tttgagataa acatatgtgg cggagaacca tttaagcaca aagatattat
     1561 aaatataata tctgaagtaa agagagttgg gtttaattta tccattgtaa ctaacggtac
     1621 attgatcaat aaaaaaacag cattactact caatgaactt gacgttataa aaaacatgca
     1681 gattagtttt gatagccata tagattccat tcacaacaag ttaagaggag gttaccatca
     1741 agcaattaga gggttagact acttgctttc ttatgattcc cctcccccat caataggcat
     1801 agttataagt aaagaaaatg ttaatcatat aaatgaaact atagattttt tttccaggaa
     1861 gggaatacgc agatttcaca taatgaacct actgggtaac aaagagctat catgttcaga
     1921 tgctgaatta aacgaagcaa caaaaagaat aaatgaatca tttttacaat caagagatgg
     1981 cgataaaaaa ttaataatat ccaacttaga ttttaaagaa aagaaagact atcaatataa
     2041 agatgtgcac atcaactgcc ttgccggata cactacgtta gtcttgacat catctttaaa
     2101 tataatacct tgcgatatgg ttaattatat tataaaaaaa tggaaaaaaa aaggtgattt
     2161 gcgtgatggc tttgaacttt caaaaaaaca atggcttgga ttaaaggaat catggtgtaa
     2221 gggttgtttt aaatgctaag tgtattaaca tgtaaatgcg agtaaaatag ttttccacta
     2281 ctctatactg aatactaaaa atctttttaa tggggtttga tggccaaccg tacgaaaacg
     2341 tacggtaaga ggaaaattat cgtctgaaaa atcgatttat agacaagcct gtccgttaaa
     2401 tgccaatttt cgattaaaaa gacaccgttt tgagggcgtt tttcaatgtc cattatgttt
     2461 cgatatatca gacacttact taactaacgt acgtttccgt tccattggac ttcatacccg
     2521 tggtacggtt tctttggcaa acgcagactg aatagatcaa tggcatggct agtcaatgta
     2581 gcatgagctt atggcgggct gttgtttggc gcatttcatg cgctaatatc cttttaggtt
     2641 ttgtacctgc gccctagtaa ttgggaatct accgccaagt tgagtccacg atttctgggg
     2701 cgttgttttt tttacaaaaa aatcatactc atttataaca cctgtagata taagtacttt
     2761 tttataaaaa aagtcaaaag atgcgggcgg caaaagcgat aattacaata cttaccgaac
     2821 catctacagt tgctaaggtt cttagcctgt catccttgag ggtcttgcca tcaaaggtcg
     2881 ccaaagttct tagcctgtca tccttgaggg tcttaccatc aaaggtcgcc aaagttctta
     2941 acctgtcatc cttgagagtc ttgccatcaa aggtcgccaa agttcttaac ctgtcatcct
     3001 tgagagtttt accatcaaag gtcgccaagg ttcttagtct gtcatccttg atgagtctta
     3061 ccatcaaagg tcgctaaagt tcttaacctg tcatctttta tagttatagt catatacatc
     3121 ccctattaga aattcatttt tctcaggttt ggattaattc tgaatattac ttttcataaa
     3181 attaaataaa ttcatcccaa ttaagttcct ctctcgctct tcttaacgtt ccaaccgatg
     3241 gtgtcctata tagattccac gatgtttccc ataccttatt ttgttctttt tctaatgatg
     3301 aatttgaagg gatcattcct tcccatccgg gatgattggt atttttggca acaacaatgc
     3361 aacttaaggg gggaagatcg ttatataaac aatacagtga gactgtacct aaagcctcag
     3421 ctaaagtgcg tcctgcttgc gcaggatacc caataagttt cgcaagttct ccatatgtga
     3481 ttgttttatt cttattgaac aaacaccatg acgtcaaagc gatccacaca aaatgagcct
     3541 gctcttctct tcttgaacca acttctggaa atgattttat ttttggaatt gtcattgtta
     3601 aaattctcac aaaccgttca tattttcact ttataatata ccaaaagatg agtgcgtaca
     3661 aaaaactatt taccataacg cgtcattacg cgcaccgctc aaacgcccca gaaacgattc
     3721 tgggccgtaa cccatcaaat cctacatctt accccctgaa aacgcctcaa aatcgcccca
     3781 gggcttttta cgggcatgaa ttgttatgca ccagactgat tggtggcgga tttcagcctg
     3841 aattcacgcc agacaactca aaacccgcac caaaccagac tgcaaacggt gagcggggac
     3901 gcaatttatt gcgtgaccgt gaagcgttgc cggcgcagcc ggaaaaccgg ttttcagcac
     3961 gttcaggaat cgggttcgtc gacggccggc aatcacgtta tggcaagtcg ccggacgact
     4021 caccacacga ttcaccggcg attcgactcg tgacttgact ctagagtcac catggtcaaa
     4081 aagccaccaa cccggcaagt cgactctaga gtcaagtcat cataacgtac tgattatatg
     4141 gcgtgattca catatgaatc gtgggcaagt catcggcgat tcgccataga gtcgtccacg
     4201 actcggattc accttacaaa aaataaaatt gcgtaattta aaatagataa ctgattgaaa
     4261 ataaaggtat atctgcaaaa ttttaatttt gcgtagtgtg tgggtatttt tagtggtgag
     4321 gagcgttcag agatctgacg atttttggga aggttcagga actccccggg atggccggag
     4381 aggaaaactc aagcatggca ggatcaggat tttttccaga atttccacca cggagaatga
     4441 acctgtggag agggttcgtg cttgtgctcc agaagctgca tagcctggcg aagagaatcg
     4501 atatgttcat cacgagcttt aacagcccct ttaagaccat cgttttcagc ttcaagcaaa
     4561 gcaattttat gctgtaaatc atgtaaacca aggatgttaa ccgctgtagc gcctgcgtca
     4621 ccttttacat catgttttac agtgtcgtcc ccaccataca gcgagccaaa aaccctaata
     4681 agctctgatg tatcaataac tttagtatgt ttcccatgct ttacaacaga ggtgtaactt
     4741 agtttcccac tgttaatcat cttgtaaatt gtg
//
