LOCUS       NZ_CP084863             3629 bp    DNA     circular CON 10-JAN-2024
DEFINITION  Klebsiella pneumoniae strain SB1067 plasmid pKp_SB61067_3, complete
            sequence.
ACCESSION   NZ_CP084863
VERSION     NZ_CP084863.1
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 3629)
  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  JOURNAL   Unpublished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 3629)
  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
            CP084863.1.
            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..3629
                     /organism="Klebsiella pneumoniae"
                     /mol_type="genomic DNA"
                     /strain="SB1067"
                     /isolation_source="feces"
                     /host="Homo sapiens"
                     /db_xref="taxon:573"
                     /plasmid="pKp_SB61067_3"
                     /geo_loc_name="Netherlands"
                     /collection_date="2002"
     gene            complement(join(3378..3629,1..150))
                     /locus_tag="LGM10_RS27090"
                     /old_locus_tag="LGM10_27090"
     CDS             complement(join(3378..3629,1..150))
                     /locus_tag="LGM10_RS27090"
                     /old_locus_tag="LGM10_27090"
                     /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            complement(150..341)
                     /locus_tag="LGM10_RS27095"
                     /old_locus_tag="LGM10_27095"
     CDS             complement(150..341)
                     /locus_tag="LGM10_RS27095"
                     /old_locus_tag="LGM10_27095"
                     /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            756..884
                     /locus_tag="LGM10_RS27100"
                     /old_locus_tag="LGM10_27100"
                     /pseudo=""
     CDS             756..884
                     /locus_tag="LGM10_RS27100"
                     /old_locus_tag="LGM10_27100"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_005761324.1"
                     /note="internal stop; 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            1113..1553
                     /locus_tag="LGM10_RS27105"
                     /old_locus_tag="LGM10_27105"
     CDS             1113..1553
                     /locus_tag="LGM10_RS27105"
                     /old_locus_tag="LGM10_27105"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002642251.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_019704629.1"
                     /translation="MSKYLITFDLDTTKLKTLYHGKNYNNAYYDIRSTLSRRGFENIQG
                     SVYLGQEGISEAHGTIAIQELTAKYSWFYECVSNIKFYRIESDLNAQFIADGVNEARKR
                     FYTQLEDMRKSLLSVGLTVEQVNEIIGQQQFKLESTISPDKM"
                     /name="hypothetical protein"
     gene            1622..1924
                     /locus_tag="LGM10_RS27110"
                     /old_locus_tag="LGM10_27110"
     CDS             1622..1924
                     /locus_tag="LGM10_RS27110"
                     /old_locus_tag="LGM10_27110"
                     /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_128316336.1"
                     /translation="MKIGSTREYGATKSHLLLMITTLPAGVGVFIYPIAEAVWGELPLL
                     KVVGYTALSLMIGGVVGNIVVRGLFSTSLGILFINPLAMISSLTGIAFLIVQYLP"
                     /name="hypothetical protein"
     Typing          463..866
                     /name="ColRNAI_rep_cluster_1987"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="91.912"
                     /coverage="99.0"
                     /evalue="1.01e-158"
ORIGIN
        1 aaagacacgt aaaagctctg aagtatctac catttttgca ttgcgctcac cactacaggt
       61 ggacaggtca cctgttttaa ttaacctgtg cagtgttgtt ctactcttgc ccgtcagtcg
      121 ggcagcctca ctaatagaca ctctggccat cagttaccat cctgtaatgc atccagtctc
      181 gaggacagtg tacggaaaag atgctccgca tcatcgtgga gttcctcaca aaggtcggcc
      241 tcgacatcga gatcaagctc gttaagcttc tccagcagga gcagagactg attctggatg
      301 aatttagcca tgttcagcgc tgttttctgt tgtttcgtca taagaggcct cagagcgtca
      361 gtgctcagtg tagggatgtt ctcttttccg cttcctcgct cactcagtcg ctacgctccg
      421 gtcgttcggc tgcggcgagc ggcaggagca tgcgtataag agctcgagaa aaccgagagg
      481 tcaaggtagg ggaaaacggg aggccgcagc gcggccgttt ttccataggc tccgcccccc
      541 tgacaagcat cacagaattt gacgctcaaa tcagtggtgg cgaaacccga caggactata
      601 aagataccag gcgtttcccc ctgatggctc cctcgtgcgc tctcctgttc ctgccattcg
      661 gtttaccggt gtcattccgc tgttatggcc gcgtttgtct cattccacgc ctgacactca
      721 gttccgggta ggcagttcgc tccaagctgg actgtatgca cgaacccccc gttcagtccg
      781 actgctgcgc ctaatccggt aactatcgtc ttgagtccaa tccggaaaga cgcgacttat
      841 cgccactggc agcagccatt ggtaacagaa ccaggtggat ttagatatta agagtcttga
      901 agtgatggcc ctactgcggc tacactggaa ggacagtatt tggtatctgt gctccaccaa
      961 gccagttacc cggttaagca gttccccaac tgacttaacc tttgaaaaaa ccgcctcccc
     1021 aggcggtttt tttcgtttaa cgtcggtaag atacgcttta gggttccagc tagtcaagct
     1081 ggctactaaa agttaataag cgcaggaaaa atatgagcaa atacctgatt acatttgacc
     1141 ttgatacaac aaagttaaaa accttgtatc acggcaagaa ctacaataat gcttattacg
     1201 atattcgaag cacgttgagc cgacgcggct ttgaaaacat acaaggtagc gtttatttag
     1261 gtcaggaagg tataagtgag gctcacggaa ccattgcaat tcaagagcta acagctaaat
     1321 acagctggtt ctatgaatgc gtatctaaca taaaattcta tcgtatagaa tctgatttaa
     1381 acgcacagtt tatcgctgat ggcgttaacg aagcgagaaa aagattctat acccaacttg
     1441 aagatatgcg caaaagttta ctatccgttg gtttaacagt agaacaagta aacgaaataa
     1501 taggtcagca acaattcaaa ttagaaagca cgataagccc tgataaaatg tgagcataag
     1561 taaaatggtt tttcttctta taatgacgct atggtgggca tcctcattca tcactcatct
     1621 aatgaagatt ggtagcacca gagagtacgg tgcaactaaa tctcatttac ttttgatgat
     1681 caccacactt cccgctggag ttggcgtctt tatctaccca atagcagaag ctgtatgggg
     1741 tgagctaccg ttactgaaag ttgtaggcta taccgcctta tccctcatga taggaggggt
     1801 tgttggcaac atagttgttc gtggattatt ttcaacttcg ctgggtattt tgtttataaa
     1861 ccccctagca atgatctcca gtcttacagg tatagcattc ttaatcgtgc aatacttacc
     1921 ataacattaa ccccaacgcg catgaaaggc ccgcactgcg ggcttttttt tagaagagat
     1981 gtgccttcgt ttcaacttag cttcaataga ggcaccggca acatacaaaa tatccgtatt
     2041 ttaatactag ccaccgagcg gtttcctacg catcgcgatc aaaaatgcac gagcaatctg
     2101 atcgggcata aaatttcagc aacccactaa actcacccaa ggaagagtaa acataatcta
     2161 ttgataaaaa ataattttat atttttagaa aagtactgaa tgttctttcg cggcaaacgg
     2221 ttcaataaaa atgagcatca gagcaagttg gaaggcactt ttgagtactt gataggagac
     2281 tttaaaatga taattacaat tgagttaaaa ggggcattga tggccaaaaa tcactcagag
     2341 tataaggttt tgtttgaggg taaatatctc gcggtaatat ggatactata gattcgtcgg
     2401 cgaacgtcgg cgaacgtcgg cgaacgtcgg cgaacgtcgg cgaacgtcgg aataagatca
     2461 attaaatatt acatcaagat aaaaacaata aaaaattaaa aaataagtac tgaatgttct
     2521 ttcgcggcaa acggttatat aaaaattagc atcagagcaa gttggaaggc acttttgagt
     2581 actaacaaac actcatctca ctccgctgta gggaccagta accccaacca ttcgatgtca
     2641 tttaacataa ggccctgatt gtacgcaccg ctaaaacggc ctcagggcgt ttctgacggg
     2701 aaaccggtaa aacaggcaac aaaccacccg aaaacccgcc agaaacgcgc aggctctgtt
     2761 tttacggcat gcatgagtat gcacgcaagt gcatagcgcg aaaattcacg ccattcagcc
     2821 agggtaagtc ctgtttcggg cgtacttccc atccgaaaac ggtgaacggg gacgcaattt
     2881 attgcgtggc cgtgaagcgt tgccggcgca gccggaaaac cggttttcag cacgttcagg
     2941 aatccggttc gtcgacggcc ggcaatcacg ttatggcaag tcaccgaacg actcaccaca
     3001 cgattcaccg gcaactcttc actagagtcg tacccagagt cgccacgcct aaaaaacaac
     3061 caaacgggga gtcgggtcta gagtcgggtc gttattaact cattgttttt atagtcctga
     3121 gtcgttaccg actctatgac gactcgccgg ggactctatg acgagtcgtc atagagtcgg
     3181 atctatataa atcaaattta aaaaacaaaa ttttacagac ttaaactact gatattaaat
     3241 acaaatccgc aaaattttaa ttttgcgtag tgtgtgggta tttttagtgg tgaggagcgt
     3301 tcagaaatcc ggcgattttt tggaaggttc aggaactccc cgggatggcc ggagaggaaa
     3361 acggaagcat gacggggtca ggattttttc cagaatttcc accatggcgc cggggattca
     3421 gttaattttg cctggtgatt ttcaagaagg agcatggcct gtttcaggct gtcaatgtgc
     3481 gaatccttgg acaaaagtaa gatattcagg tgttcaatct cctgtttcag atgacgaatc
     3541 acctgttcac tctggtcagc agaggctgta tcacgctgtt cagagacctg tccagaatgg
     3601 tgttcaccct tcggttgctc aaagggacc
//
