LOCUS       NZ_CP084864             3359 bp    DNA     circular CON 10-JAN-2024
DEFINITION  Klebsiella pneumoniae strain SB1067 plasmid pKp_SB61067_4, complete
            sequence.
ACCESSION   NZ_CP084864
VERSION     NZ_CP084864.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN22024791
            Assembly: GCF_020525845.1
KEYWORDS    RefSeq.
SOURCE      Klebsiella pneumoniae
  ORGANISM  Klebsiella pneumoniae
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Klebsiella/Raoultella group; Klebsiella.
REFERENCE   1  (bases 1 to 3359)
  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  JOURNAL   Unpublished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 3359)
  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 pneumoniae SB1067
            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 04:21:35
            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)                     :: 5,441
            CDSs (total)                      :: 5,314
            Genes (coding)                    :: 5,177
            CDSs (with protein)               :: 5,177
            Genes (RNA)                       :: 127
            rRNAs                             :: 9, 8, 8 (5S, 16S, 23S)
            complete rRNAs                    :: 9, 8, 8 (5S, 16S, 23S)
            tRNAs                             :: 87
            ncRNAs                            :: 15
            Pseudo Genes (total)              :: 137
            CDSs (without protein)            :: 137
            Pseudo Genes (ambiguous residues) :: 0 of 137
            Pseudo Genes (frameshifted)       :: 54 of 137
            Pseudo Genes (incomplete)         :: 90 of 137
            Pseudo Genes (internal stop)      :: 18 of 137
            Pseudo Genes (multiple problems)  :: 22 of 137
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP084864.1.
            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..3359
                     /organism="Klebsiella pneumoniae"
                     /mol_type="genomic DNA"
                     /strain="SB1067"
                     /isolation_source="feces"
                     /host="Homo sapiens"
                     /db_xref="taxon:573"
                     /plasmid="pKp_SB61067_4"
                     /geo_loc_name="Netherlands"
                     /collection_date="2002"
     gene            join(3022..3359,1..85)
                     /locus_tag="LGM10_RS27115"
                     /old_locus_tag="LGM10_27115"
     CDS             join(3022..3359,1..85)
                     /locus_tag="LGM10_RS27115"
                     /old_locus_tag="LGM10_27115"
                     /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_136046361.1"
                     /translation="MARVSISEAARLVKVSCPTIYKMINSGKLSYTSVVKHGKAIKVID
                     TSELIRVFGSLDGVIDTVKYDVKSDAESTSINSVGLHDLQHRIALLEAENDGLKGAVKA
                     RDEHIDSLRQAMQLLEHKREPSSPPHSPWWKFWKKS"
                     /name="helix-turn-helix domain-containing protein"
     gene            complement(833..>1081)
                     /locus_tag="LGM10_RS27120"
                     /old_locus_tag="LGM10_27120"
                     /pseudo=""
     CDS             complement(833..>1081)
                     /locus_tag="LGM10_RS27120"
                     /old_locus_tag="LGM10_27120"
                     /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            <1080..1562
                     /locus_tag="LGM10_RS27125"
                     /old_locus_tag="LGM10_27125"
                     /pseudo=""
     CDS             <1080..1562
                     /locus_tag="LGM10_RS27125"
                     /old_locus_tag="LGM10_27125"
                     /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="S-type pyocin domain-containing protein"
                     /name="S-type pyocin domain-containing protein"
     gene            1564..1821
                     /locus_tag="LGM10_RS27130"
                     /old_locus_tag="LGM10_27130"
     CDS             1564..1821
                     /locus_tag="LGM10_RS27130"
                     /old_locus_tag="LGM10_27130"
                     /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            1929..2084
                     /locus_tag="LGM10_RS27135"
                     /old_locus_tag="LGM10_27135"
     CDS             1929..2084
                     /locus_tag="LGM10_RS27135"
                     /old_locus_tag="LGM10_27135"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_008323621.1"
                     /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_071561715.1"
                     /translation="MKKLLFLGVVTVSVVLAACQVNNVRDTGGGAVSPSSTVTGVTLDS
                     GTNGNP"
                     /name="colicin release lysis protein"
     gene            complement(2332..2415)
                     /locus_tag="LGM10_RS27300"
     CDS             complement(2332..2415)
                     /locus_tag="LGM10_RS27300"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_007772075.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_058655973.1"
                     /translation="MHEPPVQSDRCALSGNYRLESNPERHD"
                     /name="hypothetical protein"
     gene            2831..3022
                     /locus_tag="LGM10_RS27140"
                     /old_locus_tag="LGM10_27140"
     CDS             2831..3022
                     /locus_tag="LGM10_RS27140"
                     /old_locus_tag="LGM10_27140"
                     /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_026056049.1"
                     /translation="MTKQQQTALNMAKFIQNQSLLLLEKLNELDLDVEADLCEKLHDDA
                     EHLFRTLSSRLDELQDGN"
                     /name="Rop family plasmid primer RNA-binding protein"
     Typing          complement(2307..2783)
                     /name="ColRNAI_rep_cluster_1987"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="88.797"
                     /coverage="91.0"
                     /evalue="4.61e-163"
ORIGIN
        1 tcaggctatg cagcttctgg agcacaagcg cgagccttct tcaccacccc attccccgtg
       61 gtggaaattc tggaaaaaat cctgatcctg ccatgcttga gttttcctct ccggccatcc
      121 cagggagttc ctgaaccttc ccaaaaatcg ccagatctct gaacgctcct cacgactaaa
      181 aatacccaca cactacgcaa aattaaaatt ttgcagattc cttatttaaa acaattggtt
      241 aatgaaaaat taatgtgcag tgatgtgtta caaagtgcag atccaagtcg tggacgactc
      301 tatggcgaat cgtttacgaa ttgcccacga ttcatatgtg aatcacgctt tattatcatg
      361 ttgttatgat gaatcgactc ttgattcaat tcatcaattt gggcgttttt tgttcatggt
      421 gactcttgat tcaattcacg attcgaatcg ccggtgaatc gtgtggtgag tcgtccggcg
      481 acttgccata acgtgattgc cggccgtcga cgaacccgat tcctgaacgt gctgaaaacc
      541 ggttttccgg ctgcgccggc aacgcctcac ggccacgcaa taaattgcgt ccccgttcac
      601 cgttttcgga tcagaagaac gccggaaaca ggacttaccc tggctgaatg gcgtgaattt
      661 ccgcgctatg cacttgcgcg catactcatg catgccgtaa aaacagagcc tgcgcgtttc
      721 tggcgggttt tcgggtggtt tgttgcctgt tttaccggtt tcccgtcaga aacgtcctga
      781 ggccgtttta gcggtgcgta caattaaggg attatggtaa atggtgactt ggttaatcat
      841 aaacatcctg ggggatggca tacaccagtt ggatatccgg tgcatcgttg agccatcgac
      901 ctgatttttt cattaagtag ccaccaattt cttcggtagt cagccgggca tgaaacaatg
      961 cttcatcatt gaaccagcag tcagggtgat agatgagatc cagtgggttt gccttgaaat
     1021 taatctccag taactggagt gcatagctgt ggtcagatgc actaccttct gcttttcgta
     1081 tggcggatga cctcgatttt gacgatatta ttctggtgtt tcctccggaa tccggcctaa
     1141 aaccgctgta tgtgatgtac cgtagccctc gtaacatgcc cggtacagtg agcggcaaag
     1201 ggcagaacgt tggcaataac tggatggggg gggccagtac cggggatggt gctcctgttc
     1261 cttcccagat tgcggataaa ttacgcggga agactttcgg tagttttgat tctttccgtc
     1321 gggcgttctg gaaagcggtt gctgacgatt ctgcactgag caagcaattt agtgaagctg
     1381 atattaatca gatgaaagct ggaagggcac ctactgcgga ctttttagaa tcagtaggga
     1441 aacgtgttaa aattgaatta caccacgaaa aagaaatatc tcaaggaggg gctgttatgg
     1501 atgtcgataa cattaaggcg ctaacaccta aaaatcatat tgagacacat aaaggaaaat
     1561 aaaatggctg gtaataaaat ttcagatttt acggaagaag aatttactgc ttttgttagt
     1621 aaaataatcg ctgctgattt tccaactgac aaagagaacg atgatgctat ttattcgttc
     1681 gcccaactaa cagagcatcc tgctggttgg aacctcatct tcaagcctaa ggtaggcgaa
     1741 gattcttcgg cgaaaggaat tgttaaaacc gtaaaggaat ggcgagctgc taacggtaag
     1801 ccaggtttta aaaaagcgtg attgaatttg cgggttcaag ttatgagccc gctcatttgt
     1861 aactctggat ttgaagaata attactagat atccatttgc ctagaataat aaaaataaaa
     1921 ggtgatatat gaaaaaatta cttttcctag gggttgttac cgtttctgtg gttctggcag
     1981 catgtcaggt caataatgtt cgagacaccg gaggtggggc tgtttcacct tcatcgacgg
     2041 tgaccggagt cacgcttgat agcggtacga acggcaatcc gtaaaggatc ttcttgagat
     2101 cccatttgga tcgtcgtaat ctcttgctct gtaaacgaaa aaaccgcctt gcagggcggt
     2161 ttttccgaag gttatttaat cctggcagat tatctaaccg tggtaacagt cttgtgcgag
     2221 acatgtcacc aaatccgtcc ttccagtgta gcctcagtta ggccgccact tcaagaactc
     2281 tcaatacatc tctcgcacat cctgcttacc agtggccgtt gccaatggcg attagtcgtg
     2341 tctttccggg ttggactcaa gacgatagtt accggacaag gcgcagcggt cggactgaac
     2401 ggggggttcg tgcatacagt ccagcttgga gcgaactgcc tacccggaac tgagtgtcag
     2461 gcgtggaatg agataaacgc ggccataaca gcggaatgac accggtaaac cgaaaggcag
     2521 gaacaggaga gcgcacgagg gagccgccta tcagaaatga taggtatctt tatagtcctg
     2581 tcgggtttcg ccaccactga tttgagcgtc cgcttctgtg atgcttgtca ggggggcgga
     2641 gcctatggaa aaacggcaac gccgcgacct tattttgtcc cctccggcta tcagccctgt
     2701 cgtcttatgc tcttatacgt gagttgcgac cgctcgccgc agccgaacgg caggagcgta
     2761 gcgactgagt gagcgaggaa gcggaaagga gacagttttt acattgagca ctgacgctct
     2821 gaggctcttt atgacgaaac aacagcaaac ggcgctaaac atggctaagt tcatccagaa
     2881 tcagtctctg ctcctgctgg agaagcttaa cgagcttgat ctcgatgtag aggccgacct
     2941 ttgtgagaaa ctccacgatg atgcggagca tcttttccgt acactgtcct cgagactgga
     3001 tgaattacag gatggtaatt gatggccaga gtgtctatta gtgaagcggc acggcttgtt
     3061 aaggttagct gtcccacaat ttacaagatg attaacagtg ggaagttaag ttacacctct
     3121 gttgtaaagc acgggaaggc tattaaagtt attgatactt cagagcttat tagagtgttt
     3181 ggttctcttg atggtgtcat cgatactgta aaatatgatg taaaaagtga cgcagaatct
     3241 acaagtatta acagcgttgg tttacatgat ttacaacata gaatcgctct acttgaagct
     3301 gaaaacgatg gtcttaaagg ggctgttaag gctcgagatg agcatattga ttcccttcg
//
