LOCUS       NZ_CP084798             4381 bp    DNA     circular CON 26-JAN-2024
DEFINITION  Klebsiella quasipneumoniae subsp. quasipneumoniae strain U41 plasmid
            pKqq_U41_9, complete sequence.
ACCESSION   NZ_CP084798
VERSION     NZ_CP084798.1
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 4381)
  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  JOURNAL   Unpublished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 4381)
  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
            CP084798.1.
            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..4381
                     /organism="Klebsiella quasipneumoniae subsp.
                     quasipneumoniae"
                     /mol_type="genomic DNA"
                     /strain="U41"
                     /host="Environment"
                     /sub_species="quasipneumoniae"
                     /db_xref="taxon:1667327"
                     /plasmid="pKqq_U41_9"
                     /geo_loc_name="Germany"
                     /collection_date="1990"
     gene            complement(join(3964..4381,1..323))
                     /locus_tag="LGM24_RS29715"
                     /old_locus_tag="LGM24_29715"
     CDS             complement(join(3964..4381,1..323))
                     /locus_tag="LGM24_RS29715"
                     /old_locus_tag="LGM24_29715"
                     /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_086893474.1"
                     /translation="MSREHELLKLWRQLNETQQDNFLKWMKAYEIEKIYVNHNKGYFNQ
                     KFIDNFGDRLITHYFNSNRPLTKTLFEHAFNDSLNESGMQSQLAESRTNPGYDITIQNI
                     KASLKTEAARNISQKNIHVSKWMELGKGKWVLEELLARFLAHLNNYDKIFTLRYIKPTY
                     LTFKYQLIEIPKTLLLESKNAHLVVMENSTQDPKPGYGYVFDQNGEKKFSLYFDGGSER
                     KLQIKHLNVSLCIIHAEWCYTLPS"
                     /name="hypothetical protein"
     gene            complement(316..558)
                     /locus_tag="LGM24_RS29720"
                     /old_locus_tag="LGM24_29720"
     CDS             complement(316..558)
                     /locus_tag="LGM24_RS29720"
                     /old_locus_tag="LGM24_29720"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_012575772.1"
                     /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 transcriptional regulator"
                     /protein_id="WP_086893475.1"
                     /translation="MQPFDDDFSNIKTVLSENIKRYRNKNNLSQEDLAELSGLHRTYIG
                     SVERKERNVTLSTLIFIASALKTSVPDLLRKKEDE"
                     /name="helix-turn-helix transcriptional regulator"
     gene            1626..1826
                     /locus_tag="LGM24_RS29725"
                     /old_locus_tag="LGM24_29725"
     CDS             1626..1826
                     /locus_tag="LGM24_RS29725"
                     /old_locus_tag="LGM24_29725"
                     /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_225368679.1"
                     /translation="MFRCSRNPKTALNMAKFIQNQSLLLLEKLNELDLDVEADLCEKLH
                     DDAEHLFRTLTSRLDALQDGN"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            1826..2227
                     /locus_tag="LGM24_RS29730"
                     /old_locus_tag="LGM24_29730"
     CDS             1826..2227
                     /locus_tag="LGM24_RS29730"
                     /old_locus_tag="LGM24_29730"
                     /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_086893472.1"
                     /translation="MARVSISEAARLTGKSRTTLHRLIKAGDLSICSGERNAKMVDTSE
                     LLRVFGPFEQPKGEHHSGQVSGQRDTASADQSEQVIRHLKQEIEHLNTLLLSKDSHIDS
                     LKQAMLLLENHQAKLTESPAPWWKFWKKS"
                     /name="helix-turn-helix domain-containing protein"
     gene            3127..3975
                     /locus_tag="LGM24_RS29735"
                     /old_locus_tag="LGM24_29735"
     CDS             3127..3975
                     /locus_tag="LGM24_RS29735"
                     /old_locus_tag="LGM24_29735"
                     /EC_number="2.1.1.-"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_011346608.1"
                     /GO_function="GO:0003677 - DNA binding [Evidence IEA];
                     GO:0008170 - N-methyltransferase activity [Evidence IEA]"
                     /GO_process="GO:0006306 - DNA methylation [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="site-specific DNA-methyltransferase"
                     /protein_id="WP_225368678.1"
                     /translation="MFGEDLNFSKANNNCEIVIGDSREVIKTLGDKVFDCIVTSPPYWG
                     LRDYGVGNQIGAEINIDDYIFDLVSLFKEAKRTLKDDGTLWVNIGDSYTSGGRTWRDKD
                     DKNKGRAMSYRPPTPEGLKPKDLIGVPWKLAFALQQDGWYLRSDIIWNKPNCQPESVKD
                     RPTRSHEYIFLFSKNKKYHYDSDAIKEPSMDKKQGKKNRRTVWNINTEPYPGSHFAVYP
                     REMARLCVLAGSRPGGLVLDPFFGSGTTGVVCNSLGRKCVGIELNEDYAKLAKERILSG
                     R"
                     /name="site-specific DNA-methyltransferase"
     Typing          complement(850..1257)
                     /name="ColRNAI_rep_cluster_1987"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="95.355"
                     /coverage="99.0"
                     /evalue="0.0"
ORIGIN
        1 aaactagctt taatgttttg tatcgttata tcgtaccccg gattagttcg actttcagct
       61 agttgagatt gcatcccaga ttcgtttaaa gaatcattga aagcatgctc gaataatgtc
      121 ttggttaatg gtctgttgct gttgaaataa tgagttatta gcctgtcgcc aaaattatca
      181 ataaattttt gattgaaata acctttattg tggttaacat atattttttc gatttcatac
      241 gctttcatcc attttaagaa attatcttgc tgcgtttcat ttagctgtct ccatagctta
      301 agtaattcat gctctctact catcttcttt tttccttaat aaatccggta ccgatgtttt
      361 aagcgcgcta gcaataaaaa ttaaagtgct gagggttaca tttctttcct ttctttcaac
      421 tgaaccaata tatgtacggt ggagtccaga aagctccgct aaatcttctt gtgataaatt
      481 atttttattt ctatatcttt tgatattttc agaaagtact gtttttatat ttgaaaaatc
      541 atcatcaaag ggttgcattt cttatttgcc tgtaaataaa ttaatttata aatgcatgat
      601 gattatgagt cgacagacta taagtagctt ttgttcttta acgagcttga ggatgaaaag
      661 aaaatgaggt atgttctgct tgttttaaaa cgaaaaaacc gcctggggag gcggtttttt
      721 cgagggatca gtaagttggg gaactgactg atccgaggta actggctagt agaggagcac
      781 agtcaccaaa tctcgttctc tcagtgtagc cttaacaggt acataagttc aagactcaac
      841 tcctctaatc agttaccagt ggctgctgcc agtggcgctt ttgcatgtct taccgggttg
      901 gactcaagat gatagttacc ggataaggcg cagcagtcgg actgaacggg gggttcgtgc
      961 atacagtcca gcttggagcg aactgccttc ccggaactga gtgtcaggcg tggaatgaga
     1021 taaacgcggc cataacagcg gaatgacacc ggtaaaccga aaggcaggaa caggagagcg
     1081 cacgagggag ccatcagggg gaaacgcctg gtatctttaa agtcctgtcg ggtttcgcca
     1141 ccactgattt gagcgtcaaa ttctgtgatg cttgtcaggg gggcggagcc tatggaaaaa
     1201 ccgccgcggt gcggcctttc cttttcccca tcacgcgatt gctcggcttt cccgagcttt
     1261 tatacgcatg ctcctgccgc tcgccgcagc cgaacggcag gagcgtagcg actgagtgag
     1321 cgaggaagcg gaaaagagaa catccccaca ctgagcactg acgctctgag gcctcttatg
     1381 acgaaacaac agaaaacggg gtttggggag tagtggaacc caaaagacag ttaagcggtt
     1441 caattgaatg gtcaataaca ggtaaatcaa tctcttgagt tcaactgcgt aagttgctct
     1501 gcaaacggcc aagatgagta gagccaattt ggctaccgca aacgagatag ccaaaagagt
     1561 aaattcacga tgtaaattgg ccggttgatt tttggccatt taaaataacc gcttaagggc
     1621 gtttactgtt ccgttgctcc cgaaacccca aaacagcgct gaacatggct aaattcatcc
     1681 agaatcagtc tctgctcctg ctggagaagc ttaacgagct tgatctcgat gtcgaggccg
     1741 acctttgtga gaaactccac gatgatgcag agcatctttt ccgtacactg acctcgagac
     1801 tggatgcatt acaggatggt aactgatggc cagagtgtct attagtgagg ctgcccgact
     1861 gacgggtaag agtagaacaa cactgcacag gttaattaaa gcaggtgacc tgtccatctg
     1921 tagcggtgag cgtaatgcaa aaatggtaga tacttcagag cttttacgtg tctttggtcc
     1981 ctttgagcaa ccgaagggtg aacaccattc tggacaggtc tctggacagc gtgatacagc
     2041 ctctgctgac cagagtgaac aggtgattcg tcatctgaaa caggagattg aacacctgaa
     2101 caccttactt ttgtccaagg attcgcacat tgacagcctg aaacaggcca tgctccttct
     2161 tgaaaatcac caggcaaaat taacggaatc cccggcgcca tggtggaaat tctggaaaaa
     2221 atcctgaccc cgtcatgctt cagttttcct ctccggccat cccggggagt tcctgaacct
     2281 tcccaaaaat cgtcagatct ctgaacgctc ctcacgacta aaaataccca cacactacgc
     2341 aaaattaaaa ttttgcagat ttgtatttaa tatcagtagc ttactttcct gaaatttcgg
     2401 tttttaaatt ttatttacat ggatccgact ctatgacgag tcgtcataga gtccccggcg
     2461 agtcgtcata gagtcggtaa cgactcaggg ctataaaaac aatgagttaa taacgacccg
     2521 actctagacc cgactccccg tttggttgtt ttttagactc ggcgactcta ggtacgactc
     2581 tagtgaagag tcgccggtga atcgtgtggt gagtcgtccg gcgacttgcc ataacgtgat
     2641 tgccggccgt cgacgaaccc gattcctgaa cgtgctgaaa accggttttc cggctgcgcc
     2701 ggcaacgctt cacggccacg caataaattg cgtccccgtt caccgttttc ggatgggaag
     2761 aacgccggaa acaggactta ccctggctga atggggtgaa tttccgcgct atgtacttgc
     2821 gcgcatactc atgcatgccg taaaaacaga gcctgcgcgt ttctggcggg ttttcgggtg
     2881 gtttgttgcc tgttttaccg gtttcccgtc agaaacgccc tgagggcctc tcaggcggtg
     2941 ctgataacgg atgttatggt aaataagtca aagtatgagg ttgctactac tgttctgatg
     3001 ctcttgatga atagatacgt tgcttaagtc agcttgttgt ctttttatgt ttttttgaat
     3061 actataagta gcatcagtca ttaaataaat agtgtgtata tgtacaaaaa ctgcacagag
     3121 ttagatttgt ttggagaaga tttaaacttt tctaaagcta ataataattg cgaaatagtt
     3181 attggtgatt caagagaagt aataaaaaca ctaggtgata aggtgtttga ttgcatcgta
     3241 acttcacctc catactgggg cttgcgagat tatggtgttg gaaatcaaat aggtgctgag
     3301 ataaatattg atgattatat atttgatctt gtctctcttt ttaaagaagc aaaaagaaca
     3361 ttaaaagacg atggtactct ttgggttaac attggtgata gttatacatc tggaggaaga
     3421 acctggagag ataaggatga taaaaataaa ggtagggcta tgtcatatag gcctcctaca
     3481 cctgaagggc taaagccgaa ggatttaatt ggcgttcctt ggaagcttgc atttgcttta
     3541 cagcaagatg gatggtacct acgatctgat attatatgga ataaaccaaa ttgccagcct
     3601 gaaagtgtaa aagataggcc tacaaggtct catgagtata tatttctctt ttctaaaaac
     3661 aaaaaatacc attatgattc cgatgccata aaagaaccat ccatggacaa aaaacaagga
     3721 aaaaaaaatc ggaggacagt ttggaatata aatacagagc cttacccagg tagtcatttt
     3781 gcagtttatc caagagaaat ggcaaggtta tgtgttttag ctggatcaag acctggaggt
     3841 ttggttcttg atcctttctt tggttctggt actacaggtg ttgtgtgtaa ttccttgggt
     3901 agaaaatgcg ttgggattga gctaaatgaa gattacgcta agcttgccaa agagcgtatc
     3961 ctatcaggaa ggtagtgtgt aacaccattc agcgtgaatt atgcacaaac ttacatttag
     4021 atgttttatt tgaagttttc tctctgagcc cccatcaaag tagagagaaa actttttttc
     4081 accattttga tcaaaaacgt aaccatatcc tggttttggg tcttgagtac tattttccat
     4141 tacaactaga tgtgcatttt ttgactccaa aagtagtgtt tttggtatct caataagctg
     4201 atatttaaat gtaagatagg ttggtttaat ataccggagt gtgaatattt tatcgtagtt
     4261 atttaaatgc gctaagaatc tcgctagtaa ttcttctaaa acccactttc ctttaccaag
     4321 ttccatccat ttgcttacat gaatgttttt ttgacttata ttcctggctg cctctgtttt
     4381 t
//
