LOCUS       NZ_CP084813             5223 bp    DNA     circular CON 10-JAN-2024
DEFINITION  Klebsiella quasipneumoniae subsp. quasipneumoniae strain SB1124
            plasmid pKqq_SB1124_7, complete sequence.
ACCESSION   NZ_CP084813
VERSION     NZ_CP084813.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN22024802
            Assembly: GCF_020525825.1
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 5223)
  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  JOURNAL   Unpublished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 5223)
  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
            SB1124
            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 04:46:47
            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)                     :: 5,784
            CDSs (total)                      :: 5,657
            Genes (coding)                    :: 5,426
            CDSs (with protein)               :: 5,426
            Genes (RNA)                       :: 127
            rRNAs                             :: 9, 8, 8 (5S, 16S, 23S)
            complete rRNAs                    :: 9, 8, 8 (5S, 16S, 23S)
            tRNAs                             :: 89
            ncRNAs                            :: 13
            Pseudo Genes (total)              :: 231
            CDSs (without protein)            :: 231
            Pseudo Genes (ambiguous residues) :: 0 of 231
            Pseudo Genes (frameshifted)       :: 82 of 231
            Pseudo Genes (incomplete)         :: 153 of 231
            Pseudo Genes (internal stop)      :: 38 of 231
            Pseudo Genes (multiple problems)  :: 36 of 231
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP084813.1.
            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..5223
                     /organism="Klebsiella quasipneumoniae subsp.
                     quasipneumoniae"
                     /mol_type="genomic DNA"
                     /strain="SB1124"
                     /host="Water (environment)"
                     /sub_species="quasipneumoniae"
                     /db_xref="taxon:1667327"
                     /plasmid="pKqq_SB1124_7"
                     /geo_loc_name="Netherlands"
                     /collection_date="2002"
     gene            complement(686..877)
                     /locus_tag="LGM22_RS28740"
                     /old_locus_tag="LGM22_28740"
     CDS             complement(686..877)
                     /locus_tag="LGM22_RS28740"
                     /old_locus_tag="LGM22_28740"
                     /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_049106033.1"
                     /translation="MLKKDDIIFMKSCGNAKTIIFLRGVDEKLMINASFEEIKFAINNN
                     LQELPGVQAVAATLKIAT"
                     /name="hypothetical protein"
     gene            1119..2229
                     /locus_tag="LGM22_RS28745"
                     /old_locus_tag="LGM22_28745"
                     /pseudo=""
     CDS             1119..2229
                     /locus_tag="LGM22_RS28745"
                     /old_locus_tag="LGM22_28745"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_076611476.1"
                     /GO_function="GO:0004803 - transposase activity [Evidence
                     IEA]"
                     /note="frameshifted; internal stop; Derived by automated
                     computational analysis using gene prediction method:
                     Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="IS3 family transposase"
                     /name="IS3 family transposase"
     gene            complement(2599..2712)
                     /locus_tag="LGM22_RS29040"
     CDS             complement(2599..2712)
                     /locus_tag="LGM22_RS29040"
                     /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_071789001.1"
                     /translation="MHEPPVQSDCCALSGNYRLESNPVRHAKAPLAAATGN"
                     /name="replication initiation protein"
     gene            3117..>3191
                     /locus_tag="LGM22_RS28750"
                     /old_locus_tag="LGM22_28750"
                     /pseudo=""
     CDS             3117..>3191
                     /locus_tag="LGM22_RS28750"
                     /old_locus_tag="LGM22_28750"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000165970.1"
                     /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="Rop family plasmid primer RNA-binding protein"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            3269..4186
                     /locus_tag="LGM22_RS28755"
                     /old_locus_tag="LGM22_28755"
     CDS             3269..4186
                     /locus_tag="LGM22_RS28755"
                     /old_locus_tag="LGM22_28755"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000520337.1"
                     /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="IS5-like element ISEc35 family transposase"
                     /protein_id="WP_028016400.1"
                     /translation="MGKSKHKISNWKQYNQALVQRGSLTVWMDEQAIQQWHCQTHHGRR
                     GRGFHYSDSAIETALMLKAVFKLPLRALEGFINSLFKLMKVPLQSPDYSCISKRAKTVE
                     IKYRLPSHGPVAHLVIDATGLKVYGEGEWKIRKHGKEKRRVWRKLHLAVDAATHAIVAA
                     EVSLETVGDNEVLPTLLNPLRRKIEQVSADGAYDTRACYALLQKKGAKATIPPRKNAAF
                     WKTGHPRNEAVAALKAGELEQWKKDSGYHQRSIAETAMYRFKQLIGPKLSLRSYNAQVG
                     EILAGVKVMNKVIGLGMPIRQAVN"
                     /name="IS5-like element ISEc35 family transposase"
     gene            <4243..4368
                     /locus_tag="LGM22_RS28760"
                     /old_locus_tag="LGM22_28760"
                     /pseudo=""
     CDS             <4243..4368
                     /locus_tag="LGM22_RS28760"
                     /old_locus_tag="LGM22_28760"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000166328.1"
                     /note="incomplete; partial in the middle of a contig;
                     missing N-terminus; Derived by automated computational
                     analysis using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="Rop family plasmid primer RNA-binding protein"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            4368..4790
                     /locus_tag="LGM22_RS28765"
                     /old_locus_tag="LGM22_28765"
     CDS             4368..4790
                     /locus_tag="LGM22_RS28765"
                     /old_locus_tag="LGM22_28765"
                     /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_025714834.1"
                     /translation="MARVSISEAARLVKVSRPTIYKMINSGKLSYTSVVKHGKAIKVID
                     TSELIRVFGSLDGVIDTVKYDVKSDAESTSINSVGLHDLQHRIALLEAENDGLKGAVKA
                     RDEHIDSLRQAMQLLEHKREPSSPPHSPWWKFWKKS"
                     /name="helix-turn-helix domain-containing protein"
     Typing          complement(2600..2976)
                     /name="ColRNAI_rep_cluster_1987"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="96.825"
                     /coverage="92.0"
                     /evalue="3.51e-178"
ORIGIN
        1 attcctgaac gtgctgaaaa ccggttttcc ggctgcgccg gcaacgcctc acggccacgc
       61 aataaattgc gtccccgttc accgttttcg gatcagaaga acgccggaaa caggacttac
      121 cctggctgaa tggcgtgaat ttccgcgcta tgcacttgcg cgcatactca tgcatgccgt
      181 aaaaacagag cctgcgcgtt tctggcgggt tttcgggtgg tttgttgcct gttttaccgg
      241 tttcccgtca gaaacgccct gaggccgttt tagcggtgcg cgtaagaaga cgttatggta
      301 aatccaaaaa tgctggcatt cgcaattcag tatatcggta cgcagcataa taatgggggt
      361 taatttccaa cgtatgagcc atcaggtgct aaggttgctt ccgaaccacc aacgtatgag
      421 ccatcaggtg ctaaggttgc ttccgaacca ctaacgtacg atccatcagg tgctaaggtt
      481 acttgggata tcgcggttag tggtaatgct gacatagcca ttaaaacggc accaagagat
      541 aatgctctca tcactattac tcctgttaat atcaaaaata gaattgaatc gttcagcggt
      601 gccgaacgcc ggttccagcc gcgggattcg tgatcgggat gttatagtaa attgatctct
      661 tgattttgag tgcccttact cgaaatcagg ttgctatttt cagtgtcgcg gctactgctt
      721 gtacccccgg aagctcctga agattattat tgatagcaaa ctttatctct tcaaagctcg
      781 cgttaatcat gagcttctca tccacgccac gtaaaaatat tattgttttt gcattaccac
      841 atgatttcat aaagataata tcatcttttt ttagcatgat actgtcgtta cttagtgtag
      901 tgagataaag catagccact gtttttgtgt gtttttgtta aggctgttaa gattattcct
      961 aaccactgat tttgtacata tcatcaaaaa aaataaaaaa actaatgccc ccgtggtggg
     1021 tatataacaa atcacgggga gcggagctga cctgctcccc gttgattaat acaccgcgat
     1081 gttagtaatg tcttcataag ccacatgagg acatcctcat gaagaagcgt ttttccgacg
     1141 aacagatcat cagtattctc cgcgaggccg aagccggggt ttctgcccgt gagctctgcc
     1201 gtaagcacgc catttccgac gccatctttt acacctggcg taagaagtat ggcggtatgg
     1261 aggtgcccga ggttaagcgc cttaagtcgc ttgaggaaga gaacgccaga ctcaagaaac
     1321 tgcttgccga agccatgctg gataagcagg cgcttcaggt ggctctgggg cgaaagtact
     1381 gacgacagac cagaagcagg aagccgttga gtttatgtgt gatgcgaccg gtctgtcgca
     1441 acgtagtgcc tgcaggctta caggtttgcc cctgtcgacc tgccgctatg aggctcagcg
     1501 ttcggcggct gatgcgcatt tatcactgag ctggcactgg agcgcaggcg ttttggctac
     1561 cgacgcatct ggcagttact gcgccgtgaa ggccttcatg ttaatcacaa gcgcgtgtac
     1621 cgtctttacc accttaacgg gctgggtgta aaacgcagac gacgtcgtaa aggtctggca
     1681 acagaacgtc tgccgctgct ccgcccggag gcgcccaacc tgacctggcc gatggatttt
     1741 gtcatggacg cgctggccac cggtcgcagg atcaagtgcc tgacctgcgt ggacgacttc
     1801 acgaaggagt gtctgacaat taccgccgtc ttcgggattt caggcgttca ggtcacgcga
     1861 attctggaca gcattgcact gtttcgcggc tatccggcga cgataagaac tgaccagggg
     1921 ccggagttta cctgcagagc actcgaccag tgggcttatg agcatggggt ggagctacgg
     1981 cttatccagc cgggcaggcc aacacagaac ggatttattg aaagttttaa cggacgattc
     2041 agggatgagt gcctcaatga gcactggttc agcgatatcg ttcacgccag gaaaacgatt
     2101 aatgactggc ggcaggatta gagcgagtgt cgtccacatt catcgctgaa ctaccagact
     2161 ccggctgaat ttgcggcggg ctggcgaaac gggaaatatg aagaaaaacg aaccgacatt
     2221 actaactgaa ggttgtatct aatcctgggg ggcaggtcaa ccgcgttgga tgattgtgga
     2281 tcatgattat atatgttttt ttcttatcag aaacaatggg ttaaatagtt ttattttgat
     2341 ggttggtgtc gcggagtggt gctggtttca cttcaggggt aggcatatgg aacaggatcc
     2401 tcttgagatc ctttctttag catcgtaatc tcttgctcag taaacgaaaa aaccgccctg
     2461 caaggcggtt ttttcgaagg ttctctgagc taccaactct ttgaaccgag gtaactggct
     2521 tggaggagca cagtcaccaa aactgttcgt ttagtttagc cttaaccggc gcataacttc
     2581 aagtccatct cctctaaatc agttaccagt ggctgctgcc agtggcgctt ttgcatgtct
     2641 taccgggttg gactcaagac gatagttacc ggataaggcg cagcagtcgg actgaacggg
     2701 gggttcgtgc atacagtcca gcttggagcg aactgcctac ccggaactga gtgtcaggcg
     2761 tggaatgaga caaacgcggc cataacagcg gaatgacacc ggtaaaccga atggcaggaa
     2821 caggagagcg cacgagggag ccatcagggg gaaacgcctg gtatctttat agtcctgtcg
     2881 ggtttcgcca ccactgattt gagcgtcaaa ttctgtgatg cttgtcaggg gggcggagcc
     2941 tatggaaaaa cggccgctgt gctgccttct ccctctccga gctgtctgct ctatgtcgtt
     3001 atgtgcgcgt tgcgaccgct cgccgcagcc gaacggcagg agcgtagcga ctgagtgagc
     3061 gaggaagcgg aaaagagatc tgtctgacat tgagcactga cgctctgagg ccctttatga
     3121 cgaaacaaca gaaaacagcg ctgaacatgg ctaaattcat ccagcatcag tctctgctcc
     3181 tgctggagaa gggcgttgtt gctcaaatca gggaactatc ccgcagtttg gtgatctgat
     3241 ctcttaggtt caccaccggg agcgccagat gggcaagtcc aagcacaaga tcagcaactg
     3301 gaaacagtac aaccaagcct tggtgcaacg tggttcgttg accgtctgga tggatgagca
     3361 agccatccag cagtggcatt gccaaaccca tcatggccgc cgagggcgag gcttccatta
     3421 cagcgactcc gccattgaaa ccgcgctgat gctcaaggcg gtattcaagc taccgctgcg
     3481 tgccttggaa ggcttcatca actcgctgtt caagctgatg aaggtgccct tacagtcgcc
     3541 ggactacagc tgtatcagca agcgcgccaa gacggtcgaa atcaagtacc gcctaccgag
     3601 ccatggccca gtggctcacc tggtcattga tgccaccgga ctcaaggtct atggcgaagg
     3661 cgaatggaaa attcgcaagc acggcaagga gaaacgccgc gtctggcgca agcttcacct
     3721 ggccgtagat gcggcgaccc atgccatcgt tgcagccgaa gtcagcctgg aaacggtggg
     3781 cgataacgag gtgttgccca cgctgctcaa ccccttgcgc cgcaagatag aacaagtcag
     3841 cgccgatggt gcctatgaca ccagagcctg ttatgcccta ctgcaaaaga agggcgccaa
     3901 ggccaccata ccgccgagaa aaaatgcggc attctggaag acaggccatc cacgcaacga
     3961 ggcggttgcc gcgctcaagg caggagaact ggagcaatgg aaaaaggact ctggctatca
     4021 tcagcgctcg atagctgaga ccgccatgta tcgcttcaag cagctcatcg gtccgaaact
     4081 gagtctgcgg agctacaacg cccaggtggg tgagatcctg gccggggtga aagtcatgaa
     4141 caaggtcata gggcttggta tgcctattcg gcaggctgtc aactaagccc gcccggcggg
     4201 ttggggagcg accatccaac tttggatttg ctcaacaagg ccctggagaa gcttaacgag
     4261 cttgatctcg atgttgaggc cgacctttgt gagaaactcc acgatgatgc ggagcatctt
     4321 ttccgtacac tgtcctcgag actggatgaa ttacaggatg gtaattgatg gccagagtgt
     4381 ctattagtga agcggcacgg cttgttaagg ttagccgtcc cacaatttac aagatgatta
     4441 acagtgggaa gttaagttac acctctgttg taaagcacgg gaaggctatt aaagttattg
     4501 atacttcaga gcttattaga gtttttggtt ctcttgatgg tgtcatcgat actgtaaaat
     4561 atgatgtaaa aagtgacgca gaatctacaa gtattaacag cgttggttta catgatttac
     4621 aacatagaat cgctctactt gaagctgaaa acgatggtct taaaggggct gttaaggctc
     4681 gagatgagca tattgattcc cttcgtcagg ctatgcagct tctggagcac aagcgcgagc
     4741 cttcttcacc accccattcc ccgtggtgga aattctggaa aaaatcctga tcctgccatg
     4801 cttgagtttt cctctccggc catcccaggg agttcctgaa ccttcccaaa aatcgccaga
     4861 tctctgaacg ctcctcacga ctaaaaatac ccacacacta cgcaaaatta aaattttgca
     4921 gattccttat ttaaaacaat tggttaatga aaaattaatg tgcagtgatg tgttacaaag
     4981 tgcagatcca agtcgtggac gactctatgg cgaatcgttt acgaattgcc cacgattcat
     5041 atgtgaatca cgctttatta tcatgttgtt atgatgaatc gactcttgat tcaattcatc
     5101 aatttgggcg ttttttgttc atggtgactc ttgattcaat tcacgattcg aatcgccggt
     5161 gaatcgtgtg gtgagtcgtc cggcgacttg ccataacgtg attgccggcc gtcgacgaac
     5221 ccg
//
