LOCUS       NZ_CP084801             3534 bp    DNA     circular CON 26-JAN-2024
DEFINITION  Klebsiella quasipneumoniae subsp. quasipneumoniae strain U41 plasmid
            pKqq_U41_12, complete sequence.
ACCESSION   NZ_CP084801
VERSION     NZ_CP084801.1
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 3534)
  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  JOURNAL   Unpublished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 3534)
  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
            CP084801.1.
            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..3534
                     /organism="Klebsiella quasipneumoniae subsp.
                     quasipneumoniae"
                     /mol_type="genomic DNA"
                     /strain="U41"
                     /host="Environment"
                     /sub_species="quasipneumoniae"
                     /db_xref="taxon:1667327"
                     /plasmid="pKqq_U41_12"
                     /geo_loc_name="Germany"
                     /collection_date="1990"
     gene            complement(241..>582)
                     /locus_tag="LGM24_RS29775"
                     /old_locus_tag="LGM24_29775"
                     /pseudo=""
     CDS             complement(241..>582)
                     /locus_tag="LGM24_RS29775"
                     /old_locus_tag="LGM24_29775"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_004178052.1"
                     /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="hypothetical protein"
                     /name="hypothetical protein"
     gene            <581..1183
                     /locus_tag="LGM24_RS29780"
                     /old_locus_tag="LGM24_29780"
                     /pseudo=""
     CDS             <581..1183
                     /locus_tag="LGM24_RS29780"
                     /old_locus_tag="LGM24_29780"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_004178051.1"
                     /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="klebicin B-related nuclease bacteriocin"
                     /name="klebicin B-related nuclease bacteriocin"
     gene            1185..1442
                     /locus_tag="LGM24_RS29785"
                     /old_locus_tag="LGM24_29785"
     CDS             1185..1442
                     /locus_tag="LGM24_RS29785"
                     /old_locus_tag="LGM24_29785"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_013365855.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="bacteriocin immunity protein"
                     /protein_id="WP_025714833.1"
                     /translation="MAGNKISDFTEEEFTAFVSKIIAADFPTDKENDDAIYSFAQLTEH
                     PAGWNLIFKPKVGEDSSAKGIVKTVKEWRAANGKPGFKKA"
                     /name="bacteriocin immunity protein"
     gene            1550..1663
                     /locus_tag="LGM24_RS29790"
                     /old_locus_tag="LGM24_29790"
     CDS             1550..1663
                     /locus_tag="LGM24_RS29790"
                     /old_locus_tag="LGM24_29790"
                     /inference="COORDINATES: protein motif:HMM:NF014457.4"
                     /GO_component="GO:0019867 - outer membrane [Evidence IEA]"
                     /GO_process="GO:0019835 - cytolysis [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="colicin release lysis protein"
                     /protein_id="WP_327021887.1"
                     /translation="MKKLLFLGVVTVSVVLAACQVNNVRDTGGGTFHLHRR"
                     /name="colicin release lysis protein"
     gene            2414..2605
                     /locus_tag="LGM24_RS29795"
                     /old_locus_tag="LGM24_29795"
     CDS             2414..2605
                     /locus_tag="LGM24_RS29795"
                     /old_locus_tag="LGM24_29795"
                     /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            2605..3027
                     /locus_tag="LGM24_RS29800"
                     /old_locus_tag="LGM24_29800"
     CDS             2605..3027
                     /locus_tag="LGM24_RS29800"
                     /old_locus_tag="LGM24_29800"
                     /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(1909..2366)
                     /name="ColRNAI_rep_cluster_1987"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="82.887"
                     /coverage="92.0"
                     /evalue="2.98e-110"
ORIGIN
        1 ccgttcaccg ttttcggatc agaagaacgc cggaaacagg acttaccctg gctgaatggc
       61 gtgaatttcc gcgctatgca cttgcgcgca tactcatgca tgccgtaaaa acagagcctg
      121 cgcgtttctg gcgggttttc gggtggtttg ttgcctgttt taccggtttc ccgtcagaaa
      181 cgtcctgagg ccgttttagc ggtgcgtaca attaagggat tatggtaaat ggtgacttgg
      241 ttaatcataa acatcctggg ggatggcata caccagttgg atatccggtg catcgttgag
      301 ccatcgacct gattttttca ttaagtagcc accaatttct tcggtagtca gccgggcatg
      361 aaacaatgct tcatcattga accagcagtc agggtgatag atgagatcca gtgggtttgc
      421 cttgaaatta atctccagta actggagtgc atagctgtgg tcagatgcac taccttctgc
      481 tttgcgtatg aagttgataa cgtcgttcag ttctttccat gtaaagtcat cgaggtattt
      541 ttcctgatta agcgccatcc tggtgaaatc tagtgcactt gacgcacctg gtgcaaacgg
      601 accactgacg ctaagcgggc cggtaccact accggagcgt attctgcata ccggtgatca
      661 gatttcggcg ccacaggcta cagataaaac cgtgacgccg gtagcggatg acctcgattt
      721 tgacgatatt attctggtgt ttcctccgga atccggccta aaaccgctgt atgtgatgta
      781 ccgtagccct cgtaacatgc ccggtacagt gagcggcaaa gggcagaacg ttggcaataa
      841 ctggatgggg ggggccagta ccggggatgg tgctcctgtt ccttcccaga ttgcggataa
      901 attacgcggg aagactttcg gtagttttga ttctttccgt cgggcgttct ggaaagcggt
      961 tgctgacgat tctgcactga gcaagcaatt tagtgaagct gatattaatc agatgaaagc
     1021 tggaagggca cctactgcgg actttttaga atcagtaggg aaacgtgtta aaattgaatt
     1081 acaccacgaa aaagaaatat ctcaaggagg ggctgttatg gatgtcgata acattaaggc
     1141 gctaacacct aaaaatcata ttgagacaca taaaggaaaa taaaatggct ggtaataaaa
     1201 tttcagattt tacggaagaa gaatttactg cttttgttag taaaataatc gctgctgatt
     1261 ttccaactga caaagagaac gatgatgcta tttattcgtt cgcccaacta acagagcatc
     1321 ctgctggttg gaacctcatc ttcaagccta aggtaggcga agattcttcg gcgaaaggaa
     1381 ttgttaaaac cgtaaaggaa tggcgagctg ctaacggtaa gccaggtttt aaaaaagcgt
     1441 gattgaattt gcgggttcaa gttatgagcc cgctcatttg taactctgga tttgaagaat
     1501 aattactaga tatccatttg cctagaataa taaaaataaa aggtgatata tgaaaaaatt
     1561 acttttccta ggggttgtta ccgtttctgt ggttctggca gcatgtcagg tcaataatgt
     1621 tcgagacacc ggaggtggaa catttcacct tcatcgacgg tgaccgggtc acgcttgata
     1681 gcggtacaga cggcaatccg taaaggatct tcttgagatc catttggatc gtgtcgtaat
     1741 ccctacccac tctgtaaacg aaaaaaccgc cttgcagggc ggttttccga agtttttgca
     1801 ggtgattgaa ccaaggtaac actggcttag gagcgcagtc accacaaagc ttgttctttc
     1861 agttttagcc ttaacaggcg catgacttca agaccaactc ctctaaatcc gttaccagtg
     1921 gctgctgccc ggtggcgctt tgtcgtgtct ttccgggttg gactcaagat gatagttacc
     1981 ggataagacg cagcagtcgg actgaacggg gggttcgtgc atacgggcca gcttggagca
     2041 ggcactaccc gggactgagt gtcaggcgta gatgaggaca acgtggcctg ctggcggaat
     2101 gacaccggta aaccgaatgg cagaacagga gagcgcgagg gccatcaggg ggaaaacgca
     2161 cggtatcttt atagtcctgt cgggtttcgc caccactgat ttgagcgtca aattctgtga
     2221 tgcttgtcgg ggcggagcct ggaaaagcgg ccgctgtgct gccttctccc tctccgagct
     2281 gtctgctcta tgtcgttatg tgcgcgttgc gaccgctcgc cgcagccgaa cggcaggagc
     2341 gtagcgactg agtgagcgag gaagcggaaa agagatctgt ctgacattga gcactgacgc
     2401 tctgaggccc tttatgacga aacaacagaa aacagcgctg aacatggcta aattcatcca
     2461 gaatcagtct ctgctcctgc tggagaagct taacgagctt gatctcgatg ttgaggccga
     2521 cctttgtgag aaactccacg atgatgcgga gcatcttttc cgtacactgt cctcgagact
     2581 ggatgaatta caggatggca attgatggcc agagtgtcta ttagtgaagc ggcacggctt
     2641 gttaaggtta gccgtcccac aatttacaag atgattaaca gtgggaagtt aagttacacc
     2701 tctgttgtaa agcacgggaa ggctattaaa gttattgata cttcagagct tattagagtt
     2761 tttggttctc ttgatggtgt catcgatact gtaaaatatg atgtaaaaag tgacgcagaa
     2821 tctacaagta ttaacagcgt tggtttacat gatttacaac atagaatcgc tctacttgaa
     2881 gctgaaaacg atggtcttaa aggggctgtt aaggctcgag atgagcatat tgattccctt
     2941 cgtcaggcta tgcagcttct ggagcacaag cgcgagcctt cttcaccacc ccattccccg
     3001 tggtggaaat tctggaaaaa atcctgatcc tgccatgctt gagttttcct ctccggccat
     3061 cccagggagt tcctgaacct tcccaaaaat cgccagatct ctgaacgctc ctcacgacta
     3121 aaaataccca cacactacgc aaaattaaaa ttttgcagat tccttattta aaacaattgg
     3181 ttaatgaaaa attaatgtgc agtgatgtgt tacaaagtgc agatccaagt cgtggacgac
     3241 tctatggcga atcgtttacg aattgcccac gattcatatg tgaatcacgc tttattatca
     3301 tgttgttatg atgaatcgac tcttgattca attcatcaat ttgggcgttt tttgttcatg
     3361 gtgactcttg attcaattca cgattcgaat cgccggtgaa tcgtgtggtg agtcgtccgg
     3421 cgacttgcca taacgtgatt gccggccgtc gacgaacccg attcctgaac gtgctgaaaa
     3481 ccggttttcc ggctgcgccg gcaacgcctc acggccacgc aataaattgc gtcc
//
