LOCUS       NZ_CP084802             3335 bp    DNA     circular CON 26-JAN-2024
DEFINITION  Klebsiella quasipneumoniae subsp. quasipneumoniae strain U41 plasmid
            pKqq_U41_13, complete sequence.
ACCESSION   NZ_CP084802
VERSION     NZ_CP084802.1
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 3335)
  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  JOURNAL   Unpublished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 3335)
  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
            CP084802.1.
            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..3335
                     /organism="Klebsiella quasipneumoniae subsp.
                     quasipneumoniae"
                     /mol_type="genomic DNA"
                     /strain="U41"
                     /host="Environment"
                     /sub_species="quasipneumoniae"
                     /db_xref="taxon:1667327"
                     /plasmid="pKqq_U41_13"
                     /geo_loc_name="Germany"
                     /collection_date="1990"
     gene            join(2747..3335,1..146)
                     /locus_tag="LGM24_RS29805"
                     /old_locus_tag="LGM24_29805"
     CDS             join(2747..3335,1..146)
                     /locus_tag="LGM24_RS29805"
                     /old_locus_tag="LGM24_29805"
                     /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_130953829.1"
                     /translation="MALMVTRRYLLGGEYPSEEFVQASLEKYFFRQGFDIDTGSYIDLI
                     CRDKESRDVVWHIEVKGKTSQPGLDFRTCLGQLVQRMTKDNINYAIAVPRIKQYERLIE
                     ETSILAVSKLNLHWIFVGPDGSVTIKEPDSSTMKNGNGNGNGNGREVSLVNGGFKRFIT
                     GDFMPTCSYGKAPVVFKSSRREMWDWLDDFVISNGVIPSIADIKKEAESRSGKWTLSNV
                     KIEYQFWKIYHLYKGHFFYQSE"
                     /name="hypothetical protein"
     gene            complement(<420..500)
                     /locus_tag="LGM24_RS29810"
                     /old_locus_tag="LGM24_29810"
                     /pseudo=""
     CDS             complement(<420..500)
                     /locus_tag="LGM24_RS29810"
                     /old_locus_tag="LGM24_29810"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001333247.1"
                     /note="incomplete; partial in the middle of a contig;
                     missing C-terminus; 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            934..1125
                     /locus_tag="LGM24_RS29815"
                     /old_locus_tag="LGM24_29815"
     CDS             934..1125
                     /locus_tag="LGM24_RS29815"
                     /old_locus_tag="LGM24_29815"
                     /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_049139654.1"
                     /translation="MTKQQKTALNMAKFIQNQSLLLLEKLNELDLDVEADLCEELHDDA
                     EHLFRTLSSRLDALQDGN"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            1125..1526
                     /locus_tag="LGM24_RS29820"
                     /old_locus_tag="LGM24_29820"
     CDS             1125..1526
                     /locus_tag="LGM24_RS29820"
                     /old_locus_tag="LGM24_29820"
                     /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_048270303.1"
                     /translation="MARVSISEAARLTGKSRTTLHRLIKTGDLSTCSGERNAKMVDTSE
                     LLRVFGPFEQPKGEHHSGQVSEQRDTASADQSEQVIRHLKQEIEHLNILLLSKDSHIDS
                     LKQAMLLLENHQAKLTESPAPWWKFWKKS"
                     /name="helix-turn-helix domain-containing protein"
     gene            2377..2547
                     /locus_tag="LGM24_RS29825"
                     /old_locus_tag="LGM24_29825"
     CDS             2377..2547
                     /locus_tag="LGM24_RS29825"
                     /old_locus_tag="LGM24_29825"
                     /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_157771094.1"
                     /translation="MATATNFDAWLDDVDGDYEEVMALYDSVQNVSDMGLYQCVEGGRG
                     DAWVVSSNHHP"
                     /name="hypothetical protein"
     Typing          complement(374..758)
                     /name="rep_cluster_2370"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="92.487"
                     /coverage="89.0"
                     /evalue="2.97e-154"
ORIGIN
        1 atggggtgat cccaagtatt gctgatatta aaaaagaggc tgaatcgcgg agtgggaaat
       61 ggacgctttc taatgttaaa atagagtatc agttttggaa aatatatcac ttgtataagg
      121 ggcatttttt ctatcaatct gagtagctta ctcatttgtt catcaaatgc catgatcttc
      181 ttgagattca ttcgctcaaa gcgtaatctc tttctcggaa aacgaaaaaa ccacctgggg
      241 aggtggtttt tcgaaggttc agtaagttgg ggaacttctg aaccgtggta acagtcttgt
      301 gcgagacatg tcaccaaatc tgtcctttca gtgtagccgc agtcaggcca ccacttcaag
      361 aactctcgat acatctctcg cacatcctgt ctaccagtgg ccgttgtcaa tggcgattag
      421 tcgtgtctta ccgggttgga ctcaagacga tagttaccgg ataaggcgca gcggtcgggc
      481 tgaacggggg gttcgtgcac acagcccagc ttggagcgaa cgacctacac cgaactgaga
      541 taccaacagc gtgagctatg agaaagcgcc acgcttcccg aagggagaaa ggcggacagg
      601 tatctggtaa gcggcagggt cggaacagga gagcgcacga gggagccatc agggggaaac
      661 gcctgatatc tttatagtcc tgtcgggttt cgccaccact gatttgagcg tcagtttctg
      721 tgatgcttgt cagggggggc ggagcctatg gaaaaacggc cgctgtgcgg cctctccttc
      781 tccccatcac gcgatcgctc ggttttctcg agcttttata cgcatgctcc tgccgctcgc
      841 cgcagccgaa cggcaggagc gtagcgactg agtgagcgag gaagcggaaa agagaacatc
      901 cctacattga gcactgacgc tctgaggcct cttatgacga aacaacagaa aacagcgctg
      961 aacatggcta aattcatcca gaatcagtct ctgctcctgc tggagaagct taacgagctt
     1021 gatctcgatg tcgaggccga cctttgtgag gaactccacg atgatgcgga gcatcttttc
     1081 cgtacactgt cctcgagact ggatgcatta caggatggta actgatggcc agagtgtcta
     1141 ttagtgaggc tgcccgactg acgggtaaga gtagaacaac actgcacagg ttaattaaaa
     1201 caggtgacct gtccacctgt agtggtgagc gcaatgcaaa aatggtagat acttcagagc
     1261 ttttacgtgt ctttggtccc tttgagcaac cgaagggtga acaccattct ggacaggtct
     1321 ccgaacagcg tgatacagcc tctgctgacc agagtgaaca ggtgattcgt catctgaaac
     1381 aggagattga acacctgaat atcttacttt tgtccaagga ttcgcacatt gacagcctga
     1441 aacaggccat gctccttctt gaaaatcacc aggcaaaatt aactgaatcc ccggcgccat
     1501 ggtggaaatt ctggaaaaaa tcctgacccc gtcatgcttc cgttttcctc tccggccatc
     1561 ccggggagtt cctgaacctt ccaaaaaatc gccggatttc tgaacgctcc tcaccactaa
     1621 aaatatccac acactacgca aaattaaaat tttgcggatt tgtatttaat atcagtagtt
     1681 taagtctgta aaatttcgtt ttttaaattt gatttatata gatccgactc tatgacgact
     1741 cgtcatagag tccccggcga gtcgtcatag agtcggtaat gactcaggac tataaaaaca
     1801 atgagttaat aacgacccga ctctagaccc gactccccgt ttggttgttt tttaggcgtg
     1861 gcgactctgg gtacgactct agtgaagagt cgccggtgaa tcgtgtggtg agtcgttcgg
     1921 tgacttgcca taacgtgatt gccggccgtc gacgaaccgg attcctgaac gtgctgaaaa
     1981 ccggttttcc ggctgcgccg gcaacgcttc acggccacgc aataaattgc gtccccgttc
     2041 accgttttcg gatgggaagt acgccggaaa caggacttac cctggctgaa tggcgtgaat
     2101 tttcgcgcta tgcacttgcg tgcatactca tgcatgccgt aaaaacagag cctgcgcctt
     2161 tctggcgggt tttcgggtgg tttgttgcct gttttaccgg tttcccgtca gaaacgccct
     2221 gaggccgttt tagcggtgcg tacaatggga cgttatggta aatgcctgtc ttgctcactt
     2281 ttagagcatg aggcaaaaaa ggtaaaaact tatttgctta acagccccta tcactatgta
     2341 aattaactcc tgaaaactaa aaaatggagg attggcatgg cgactgctac taattttgat
     2401 gcgtggttag atgatgttga tggcgattat gaggaggtta tggctcttta tgattccgtt
     2461 cagaatgtaa gtgatatggg gttgtatcag tgtgttgagg gtggtcgggg tgatgcttgg
     2521 gtcgtgagct ctaatcatca tccataagct ctttttctag catcagctgt ggctagggat
     2581 actttcctca aattgattag agaaaggcta tgtggcggcg aagatgttga ttcatggtat
     2641 ggatttcaac gaaatatatc gaatgatcac tcgtaatcgt acagagagtt ccccttgtgg
     2701 gaactcttaa aatatgacgt tatagtaaat aggatgcgta ggggttgtgg ctcttatggt
     2761 gacgagaagg tacttactag gtggtgaata tccctccgag gaatttgttc aagcttcttt
     2821 agaaaaatat ttttttcgac aagggttcga tatagatacg ggttcttata ttgaccttat
     2881 ttgtcgtgat aaagaatcta gggatgttgt gtggcatatt gaagtaaaag gaaaaacatc
     2941 acagccgggg ttggattttc gaacttgtct tggacaatta gtgcagagaa tgacaaaaga
     3001 taatattaat tatgctattg ctgttccaag aataaaacag tatgaaagat taatagaaga
     3061 aacgagcatt cttgctgtta gtaaattgaa tttacactgg atatttgttg ggcctgatgg
     3121 cagtgtgaca attaaggaac ctgatagctc tacgatgaaa aatggtaatg gtaatggtaa
     3181 tggtaatgga agagaagttt ctcttgtgaa tggggggttt aaaagattta ttacggggga
     3241 ttttatgcca acttgctcat atgggaaagc tcctgttgta tttaaatcat ctcggcgaga
     3301 aatgtgggat tggttggacg attttgttat ttcaa
//
