LOCUS       NZ_CP084796             5752 bp    DNA     circular CON 26-JAN-2024
DEFINITION  Klebsiella quasipneumoniae subsp. quasipneumoniae strain U41 plasmid
            pKqq_U41_7, complete sequence.
ACCESSION   NZ_CP084796
VERSION     NZ_CP084796.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN22024804
            Assembly: GCF_020525725.1
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 5752)
  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  JOURNAL   Unpublished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 5752)
  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
            U41
            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                   :: 01/24/2024 14:21:43
            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)                     :: 5,967
            CDSs (total)                      :: 5,840
            Genes (coding)                    :: 5,633
            CDSs (with protein)               :: 5,633
            Genes (RNA)                       :: 127
            rRNAs                             :: 9, 8, 8 (5S, 16S, 23S)
            complete rRNAs                    :: 9, 8, 8 (5S, 16S, 23S)
            tRNAs                             :: 90
            ncRNAs                            :: 12
            Pseudo Genes (total)              :: 207
            CDSs (without protein)            :: 207
            Pseudo Genes (ambiguous residues) :: 0 of 207
            Pseudo Genes (frameshifted)       :: 73 of 207
            Pseudo Genes (incomplete)         :: 139 of 207
            Pseudo Genes (internal stop)      :: 38 of 207
            Pseudo Genes (multiple problems)  :: 37 of 207
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP084796.1.
            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..5752
                     /organism="Klebsiella quasipneumoniae subsp.
                     quasipneumoniae"
                     /mol_type="genomic DNA"
                     /strain="U41"
                     /host="Environment"
                     /sub_species="quasipneumoniae"
                     /db_xref="taxon:1667327"
                     /plasmid="pKqq_U41_7"
                     /geo_loc_name="Germany"
                     /collection_date="1990"
     gene            complement(join(5752,1..1031))
                     /locus_tag="LGM24_RS29655"
                     /old_locus_tag="LGM24_29655"
     CDS             complement(join(5752,1..1031))
                     /locus_tag="LGM24_RS29655"
                     /old_locus_tag="LGM24_29655"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_011787828.1"
                     /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="IS630-like element ISSpu2 family transposase"
                     /protein_id="WP_136070816.1"
                     /translation="MPIIAPIPRDERRLMQKAIHKTRDKNYARRLTAMLMLHRGERVSH
                     VARTLCCARSSIGRWINWFTLSGAEGLKSLPSGRGRRWPFEHICALLRELVKHSPGDFG
                     YQRSRWSTELLAIKIRDVTGCPLHASTIRRWLPAAGLVWRRAAPTLRIRDPHKEEKMVA
                     IHEALAKCSAENPVFYEDEVDIHLNPKIGAGWQLRGQQKRVVTPGQNEKYYLAGALHRG
                     TGKVSYVGGNSKGSSLFIRLLKHLKATYRRAKTITLIVDNYIIHKSRETLRWLKANQKF
                     RVIYQPVYSPWVNHVERLWQALHETITRNHQCRSMWQLLKKVHHFMDTVSPFPGGKHGL
                     AKV"
                     /name="IS630-like element ISSpu2 family transposase"
     gene            complement(1884..2306)
                     /locus_tag="LGM24_RS29660"
                     /old_locus_tag="LGM24_29660"
     CDS             complement(1884..2306)
                     /locus_tag="LGM24_RS29660"
                     /old_locus_tag="LGM24_29660"
                     /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_136070815.1"
                     /translation="MARVSISEAARLVKVSRPTIYKMINSGKLSYTSVVKLGKGIKVID
                     TSELIRVFGSLDGVIDAVKYDVKSDAESTGINSVGLHDLQHRIALLEAENDGLKGAVKA
                     RDEHIDSLRQAMQLLEHKHEPSSPPHSPWWKFWKKS"
                     /name="helix-turn-helix domain-containing protein"
     gene            complement(2306..2497)
                     /locus_tag="LGM24_RS29665"
                     /old_locus_tag="LGM24_29665"
     CDS             complement(2306..2497)
                     /locus_tag="LGM24_RS29665"
                     /old_locus_tag="LGM24_29665"
                     /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_023302508.1"
                     /translation="MTKQQKTALNMAKFIQNQSLLLLEKLNELDLDVEADLCEKLHDDA
                     EHLFRTLSSRLDELQDGN"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            complement(2977..3126)
                     /locus_tag="LGM24_RS29670"
                     /old_locus_tag="LGM24_29670"
     CDS             complement(2977..3126)
                     /locus_tag="LGM24_RS29670"
                     /old_locus_tag="LGM24_29670"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_017880354.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_017880354.1"
                     /translation="MPSEYDEQLDSTDTQLPGEYDLFDLMAQVTEENLHAPVDSGPPVG
                     REAL"
                     /name="hypothetical protein"
     gene            4133..4806
                     /locus_tag="LGM24_RS29675"
                     /old_locus_tag="LGM24_29675"
     CDS             join(4133..4382,4382..4806)
                     /locus_tag="LGM24_RS29675"
                     /old_locus_tag="LGM24_29675"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_086558267.1"
                     /ribosomal_slippage=""
                     /GO_function="GO:0004803 - transposase activity [Evidence
                     IEA]"
                     /note="programmed frameshift; Derived by automated
                     computational analysis using gene prediction method:
                     Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="IS1 family transposase"
                     /protein_id="WP_226650009.1"
                     /translation="MASVSVCCPSCSATQGVVRNGKSTAGHQRYLCSHCRKTWQLTFTY
                     TASQPGTHQKIIDMAMNGVGCRATARIMGIGLNTIFRHFKKLRPQSVTSRIQPGSDVIV
                     CAEMDEQWGYVGAKSRQRWLFYAYDRIRRTVGAHVFGELLSLLSAFEVVVWMTDGWPLY
                     ESRLKEKLHVISKHYTQRIERHNLNLRQHLARLGRKSLSFSKSVELHDKVIEHYLNIKH
                     YQ"
                     /name="IS1 family transposase"
     gene            complement(4840..5487)
                     /locus_tag="LGM24_RS29680"
                     /old_locus_tag="LGM24_29680"
     CDS             complement(4840..5487)
                     /locus_tag="LGM24_RS29680"
                     /old_locus_tag="LGM24_29680"
                     /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_117074105.1"
                     /translation="MKINKLNALEDKVELERILKFSVEDGKSLTDDEVIEVYKLIEANI
                     EHVRFSHNEFFIYLSDRYLDLSIAMDEKDREKEKSRKSVIRNSLVILVVMAAIYGSAKL
                     VIYITKPSELDIQQSRAYASLRIDAINRKQQALQFLKSAPDVSKEDLSLITSTITNSGI
                     SFGDSFVLQCQEYGEKVAINTLALSPNLSSETIKALQQAVDAQCELYNLDKQ"
                     /name="hypothetical protein"
     Typing          complement(3120..3335)
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="85.845"
                     /coverage="100.0"
                     /evalue="7.43e-58"
     Typing          3486..3848
                     /name="rep_cluster_2373"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="91.892"
                     /coverage="85.0"
                     /evalue="5.04e-142"
ORIGIN
        1 tacactttag ccagcccgtg ttttccaccg gggaatgggc tgacggtatc cataaagtga
       61 tgaacctttt tcaacagttg ccacattgaa cggcactggt gatttcgggt tattgtctca
      121 tgaagcgcct gccacaaccg ttcgacatga ttgacccatg gcgagtaaac cggctgataa
      181 atgaccctga acttctggtt tgctttcagc cagcgcaacg tttcacggct tttgtggata
      241 atgtagttat cgacaatgag cgtaatcgtt tttgcccgcc ggtatgtcgc cttaagatgt
      301 tttaacagtc tgataaataa agatgaacct ttactgtttc cacctacgta gctgactttt
      361 cccgtaccgc ggtgcagcgc accggcaaga tagtactttt cattctggcc cggtgtgaca
      421 acacgttttt gctgcccgcg taactgccag ccagcaccga ttttcgggtt gagatgaata
      481 tccacttcat cttcgtaaaa cacgggattt tccgcactgc atttcgccag tgcttcatgg
      541 atagcaacca ttttttcttc tttgtgtggg tcacggatac gcagtgtcgg cgctgctctg
      601 cgccatacca gcccggctgc aggtaaccat ctccggatgg ttgaggcatg tagcggacaa
      661 ccggtgacat cacggatttt tatcgccagc agttcggtac tccagcggga acgctgataa
      721 ccgaaatcgc cgggagaatg cttcacaagc tcacgcagca atgcgcaaat atgttcgaac
      781 ggccagcgcc tgccacgtcc tgacggtaat gacttcaggc cttcagcacc agacagagtg
      841 aaccagttaa tccagcgacc aatcgatgag cgggcacagc agagtgttct ggccacatga
      901 ctgacgcgct cgccccggtg caacatcagc atggcggtca gtctgcgggc ataattttta
      961 tcacgcgttt tatggatagc tttctgcatc aggcgtcgtt cgtcacgggg aattggtgct
     1021 atgatcggca tcgctcagtc cggttggtga tttgggatat tcagcgattg atcagatcgt
     1081 acaattcggg ctgagtaccc tcaaagtgat ctactattcc gaacagttat ttaggccacc
     1141 aactctattt accataacat ccgttatcag caccgcctga gaggctctca gggcgtttct
     1201 gacggaaaac cggtaaaaca ggcaacaaac cacccgaaaa cccgccagaa acgcgcaggc
     1261 tctgttttta cggcatgcat gagtatgcgc gcaagtgcat agcgcggaaa ttcacgccat
     1321 tcagccgggg taagtcctgt ttccgatgtt cttcttaccc gaaaacggtg aacggggacg
     1381 caatttattg cgtggccgtg aggcgttgcc ggcacagccg gaaaaaccat tttcagcacg
     1441 ttcaggaatc cggttcagcg acagccggca atgacgtgat ggcaagtcac cggacgactt
     1501 agcacacgat tcaccggcga ttcgactcgt gacttgactc tagagtcacc aaggtcagaa
     1561 aaacaccaaa tgaacgactc aactctagag tcaagtcgtc ataagttact gatagtatgg
     1621 agtgagtcgt cgatgactct atgacgagtc gtcggcaagt cgtacgcgaa tcgccgacga
     1681 cttggattta ccttacagaa ggtaatacag cgtaatttaa taaaacctaa ccaactgata
     1741 ataaggagtt atctgcaaaa ttttaatttt gcgtggtgtg tgggtatttt tcgtggtgag
     1801 gagtgttccc ggatctggcg atatctggga aggttcagga actccccgga atggccggag
     1861 aggaaaactc aaccatggca ggatcaggat ttcttccaga atttccacca cggggaatgg
     1921 ggtggtgaag aaggttcgtg cttgtgctcc agaagctgca tagcctgacg aagggaatca
     1981 atatgctcat ctcgagcctt aacagcccct ttaagaccat cgttttcagc ttcaagtaaa
     2041 gcgattctat gttgtaaatc atgtaaacca acgctgttaa tacctgtaga ttctgcgtca
     2101 ctttttacat catattttac agcatcgatt acaccatcaa gagaaccaaa cactctaata
     2161 agctctgatg tatcaataac tttaataccc ttcccgagct ttacaacaga ggtgtaactt
     2221 aacttaccac tgttaatcat cttgtaaata gtagggcgac taaccttaac aagccgtgct
     2281 gcttcactaa tagacactct ggccatcagt taccatcctg taattcatcc agtctcgagg
     2341 acagtgtacg gaaaagatgc tccgcatcat cgtggagttt ctcacaaagg tccgcctcaa
     2401 catcgagatc aagctcgtta agcttctcca gcaggagcag agactgattc tggatgaatt
     2461 tagccatgtt cagcgctgtt ttctgttgtt tcgtcataag ggccctcaga gcatcagtgc
     2521 tcagtgtaaa ccggtaaggg ggtcggatgt acgaatggtt cagagaacgg atctgaggta
     2581 atcctgtagt tattttgtag tttatctgta gtcatcgcac taaaaatcag gattaaatca
     2641 tcaacttttg tagtcttcct gtagtttacc tgtagtctgg aaaaatcatc cgttcatgca
     2701 agcatgaacg aagcagttaa agacgctttt tcgtcgccga tgctccttaa cctgcgctga
     2761 tcacgcagcc agaatgataa ttttttgccc cttaaatggt catacaccta acgcagccgc
     2821 gattttcatc gcaactgcat gaattaaaag gtaaaaaatg aaatctccgt ttatttatgt
     2881 aatacgcaac gtattacagt cacctgtaac tacatgaaaa taaagaaata aaatgtaata
     2941 ccggcgtatt accacgtacg cgggcaagcg aaaaagctat aacgcttccc ggccgacagg
     3001 cggcccggaa tccacagggg cgtgcaggtt ctcttcagta acctgcgcca ttaaatcaaa
     3061 aaggtcatat tcgccgggaa gctgcgtatc agtcgaatcc agttgttcat catattcaga
     3121 tggcatggag tgatatccag tagcggagag gttgttagcg ggcttcaggg cgcagccctg
     3181 aaccagtcac gtagcactag cggagtgtat actggcttaa tatgttacgg cggagtaaca
     3241 cgttatgaaa gtgcttcatg tgacagggga aaatgcagcc gcggggcgtg cgggagagaa
     3301 tggaggtgcc ggtgatatga cgcctcctcg ctcactcggt cgctgacgct ccggccgttc
     3361 ggctgcggcg ggcgttgcct gcgctcacgt aacaaactcc tggtgtatcc acagattcag
     3421 gggataaggc gccacacaac atgtgcgcaa aaaaagaaga gcgaaaaagg ccacgccccg
     3481 ggggcgtttt tccataggct ccgcccccct gacaagcatc acggaatctg acgctcaaat
     3541 cagtggtggc gaaaccccga caggactata aagataccgt gcgcttcctc ggtggctccc
     3601 gtgcgctctc ctgttcctgc ctttcggttt accggtgtca ttcgctgtta tggccgcgtt
     3661 tatctcattc cacgcctgac actcagttcc gggtaggcag ttcgctccaa gctggactgt
     3721 atgcacgaac cccccgttca gtccgactac tgcgcctttc cggtaactgt cttcttgagt
     3781 ccaacccgga aagacacgac aacgcgccat tggcagcagc cattggtaag aggattcacg
     3841 gagcagagta gtagagtatt tctacggagt tcttgaagtg gtggcctaac tacggctaca
     3901 ctgaaaggac agttttggta tctgcgctcc gtgaaagcca gttaccttcg ggagaaagag
     3961 ttggtagctc tcacttccgg caaacaaacc accgttggta gcggtggttt ttttgtttac
     4021 agagcaagag actacgctgc actctcaaaa atctcaagac gatccttaca cattcttggt
     4081 gatgctacca acttactgat gtagtgtatt atggtgtttt tgaggtgctc ctgtggcttc
     4141 cgtctccgtc tgttgtccct cctgttctgc tacccagggc gtggtgcgta acggcaaaag
     4201 tactgccggg catcagcgtt atctctgttc tcactgccgt aaaacatggc agctcacctt
     4261 cacttacacc gcatctcagc ccggaacaca ccagaaaatc attgatatgg ccatgaatgg
     4321 tgtcggttgc cgcgccaccg cacgcattat gggcattggt ctcaacacca ttttccgcca
     4381 tttaaaaaac tcaggccgca gtcagtaacc tcccggatac agccgggcag tgatgtcatt
     4441 gtctgtgcgg agatggacga gcaatggggc tacgtcgggg caaaatcacg tcagcgctgg
     4501 ctgttttacg cgtatgacag gatacgcaga acggtggggg cgcatgtctt tggtgaactt
     4561 ctgagcctgt tgtcggcctt tgaggtggtg gtatggatga cggacggatg gccgctgtat
     4621 gagtcacgcc tgaaggaaaa gctgcacgtt atcagcaagc attacacgca gagaattgaa
     4681 cggcataacc tgaatctgag gcagcatctt gcccggctgg gcaggaaatc gctgtcgttc
     4741 tcaaaatcgg tggagttgca tgacaaagtc atcgagcatt atctgaacat aaaacactat
     4801 cagtaaattg gagtcattac cgtgttaaac atctccacct tactgtttat caagattata
     4861 caactcacat tgtgcatcaa cggcttgctg taatgcttta attgtttcgc tcgataaatt
     4921 cggagataaa gccaatgtat ttattgcaac cttttctcca tactcttggc attgaagaac
     4981 aaaagaatcc ccaaaactaa taccagaatt cgtaatcgta gacgtaatca aagagagatc
     5041 ttctttcgat acatctggcg cactctttaa aaactgcaac gcctgttgtt tgcggttaat
     5101 ggcatcaata cgtaaagaag cataggcccg agactgttgt atatccagtt cactgggttt
     5161 tgttatatag ataactagct tggcactacc ataaattgca gccatcacga ccagaattac
     5221 caaggaattt ctgataacac ttttacgact tttttctttt tccctatcct tttcatccat
     5281 tgcgatcgat agatctaggt agcgatccga aagataaata aaaaactcat tatgtgagaa
     5341 gcgaacatgt tcaatgttag cctcaatcaa tttatatact tcaataactt catcgtctgt
     5401 cagcgatttt ccatcctcaa ccgaaaattt aagaatcctc tccaattcca ctttgtcctc
     5461 caaagcatta agtttattta ttttcaataa acatctgaca gacggttatt gtcagcttat
     5521 agcagaacaa cataaaccat caattactca atatcgtttt acttcaaaat cctcctcact
     5581 tatattacag atctaagtgg aatgaaagag taatacacca acgccacggg atcgatgtcg
     5641 tgtcgtttgg taactcgctg catgacccgg actgctcgtg cctttgatag ccctgaaagc
     5701 atgactgcgg ttctcgatgt tttttatgct aaataactga tcctaatacc gc
//
