LOCUS       NZ_CP028779             3999 bp    DNA     circular CON 09-JAN-2024
DEFINITION  Klebsiella pneumoniae subsp. pneumoniae strain SCKP020046 plasmid
            p1_020046, complete sequence.
ACCESSION   NZ_CP028779
VERSION     NZ_CP028779.2
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN07609114
            Assembly: GCF_002852945.3
KEYWORDS    RefSeq.
SOURCE      Klebsiella pneumoniae subsp. pneumoniae
  ORGANISM  Klebsiella pneumoniae subsp. pneumoniae
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Klebsiella/Raoultella group; Klebsiella.
REFERENCE   1  (bases 1 to 3999)
  AUTHORS   Liu,L., Long,H., Feng,Y. and Zong,Z.
  TITLE     The complete genome of Klebsiella pneumoniae strain SCKP020046
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 3999)
  AUTHORS   Liu,L., Long,H., Feng,Y. and Zong,Z.
  TITLE     Direct Submission
  JOURNAL   Submitted (16-AUG-2019) Center of Infectious Diseases, West China
            Hospital, Sichuan University, Guoxuexiang 37, Chengdu, Sichuan
            610041, China
  REMARK    Sequence update by submitter
REFERENCE   3  (bases 1 to 3999)
  AUTHORS   Liu,L., Long,H., Feng,Y. and Zong,Z.
  TITLE     Direct Submission
  JOURNAL   Submitted (04-APR-2018) Center of Infectious Diseases, West China
            Hospital, Sichuan University, Guoxuexiang 37, Chengdu, Sichuan
            610041, China
REFERENCE   4  (bases 1 to 3999)
  AUTHORS   Liu,L., Lu,Y., Lin,J., Yang,B., Feng,Y. and Zong,Z.
  TITLE     Direct Submission
  JOURNAL   Submitted (07-SEP-2017) Center of Infectious Diseases, West China
            Hospital, Sichuan University, Guoxuexiang 37, Chengdu, Sichuan
            610041, China
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: Unicycler v. 0.4.4
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 200.0x
            Sequencing Technology             :: Illumina HiSeq; MinION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 01/09/2024 08:51:41
            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)                     :: 5,617
            CDSs (total)                      :: 5,495
            Genes (coding)                    :: 5,362
            CDSs (with protein)               :: 5,362
            Genes (RNA)                       :: 122
            rRNAs                             :: 9, 8, 8 (5S, 16S, 23S)
            complete rRNAs                    :: 9, 8, 8 (5S, 16S, 23S)
            tRNAs                             :: 87
            ncRNAs                            :: 10
            Pseudo Genes (total)              :: 133
            CDSs (without protein)            :: 133
            Pseudo Genes (ambiguous residues) :: 0 of 133
            Pseudo Genes (frameshifted)       :: 49 of 133
            Pseudo Genes (incomplete)         :: 82 of 133
            Pseudo Genes (internal stop)      :: 17 of 133
            Pseudo Genes (multiple problems)  :: 15 of 133
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP028779.2.
            On Aug 18, 2021 this sequence version replaced NZ_CP028779.1.
            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..3999
                     /organism="Klebsiella pneumoniae subsp. pneumoniae"
                     /mol_type="genomic DNA"
                     /strain="SCKP020046"
                     /host="Homo sapiens"
                     /sub_species="pneumoniae"
                     /db_xref="taxon:72407"
                     /plasmid="p1_020046"
                     /geo_loc_name="China: Yibin, Sichuan"
                     /collection_date="2016-11-03"
     gene            complement(367..768)
                     /locus_tag="CLQ69_RS00005"
                     /old_locus_tag="CLQ69_00035"
     CDS             complement(367..768)
                     /locus_tag="CLQ69_RS00005"
                     /old_locus_tag="CLQ69_00035"
                     /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_069346840.1"
                     /translation="MARVSISEAARLTGKSRTTLHRLIKAGDLSTCSGERNAKMVDTSE
                     LLRVFGPFEQPKDELHSGQVSEQRDTASADQSEQVIRHLKQEIEHLNSLLLSKDSHIDS
                     LKQAMLLLENHQAKLTESPAPWWKFWKKS"
                     /name="helix-turn-helix domain-containing protein"
     gene            complement(768..959)
                     /locus_tag="CLQ69_RS00010"
                     /old_locus_tag="CLQ69_00030"
     CDS             complement(768..959)
                     /locus_tag="CLQ69_RS00010"
                     /old_locus_tag="CLQ69_00030"
                     /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_004187666.1"
                     /translation="MTKQQKTALNMAKFIQNQSLLLLEKLNELDLDVEADLCEKLHDDA
                     EHLFRTLSSRLDALQDGN"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            1375..1487
                     /locus_tag="CLQ69_RS28310"
                     /old_locus_tag="CLQ69_00020"
                     /pseudo=""
     CDS             1375..1487
                     /locus_tag="CLQ69_RS28310"
                     /old_locus_tag="CLQ69_00020"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_007772075.1"
                     /note="frameshifted; 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            complement(1773..2381)
                     /locus_tag="CLQ69_RS00015"
                     /old_locus_tag="CLQ69_28910"
     CDS             complement(1773..2381)
                     /locus_tag="CLQ69_RS00015"
                     /old_locus_tag="CLQ69_28910"
                     /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_138069329.1"
                     /translation="MTSVSSPYFGDDEDLVFDFSFDLDVSEKIKLIRQGLSNIDRLWRS
                     VRRKNCASNVSPAAFSLRVKFDGENVIWKEPALSFYEMIIKNDSDLQGEADSFMEFMIN
                     EGPFDVKSDVPVLLCLNGFFSCAEYSHVIYSFIDGISKTSPQKEQHTKAYHWDFEYVKQ
                     QDSLEIRSIMAHHSIAYLNNCLELNKEVMKQRKCKKLAH"
                     /name="hypothetical protein"
     gene            complement(2397..3119)
                     /locus_tag="CLQ69_RS00020"
                     /old_locus_tag="CLQ69_00010"
     CDS             complement(2397..3119)
                     /locus_tag="CLQ69_RS00020"
                     /old_locus_tag="CLQ69_00010"
                     /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_099119321.1"
                     /translation="MKKKSNNNQCELEHSRFNYDGISSGDVKSFFSSYDDEVLLLKNYT
                     SGSELFNNEDYDSRNLKYSDQDVVYKIEYDNACKPDGDIKEWSSWVGEFRKISGRIIDC
                     KIISDVIDVINDFNSLGLVELKLKDAFFGCESLPADIKTKKSLINFLKHYPELRKYSDT
                     ISVDYDLSLNVIAVSLRGDNHDGRYMNIQFESDGVITFFSKDADKDDSAYYISGRMFSA
                     KKVAKSYKIRSLFSILND"
                     /name="hypothetical protein"
     gene            complement(3100..3333)
                     /locus_tag="CLQ69_RS00025"
                     /old_locus_tag="CLQ69_00005"
     CDS             complement(3100..3333)
                     /locus_tag="CLQ69_RS00025"
                     /old_locus_tag="CLQ69_00005"
                     /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_069346841.1"
                     /translation="MSDEKQEMKRKMPHSFPLTIRVGATDEVAFVDFANRNGDDLEAFS
                     SVVLTKRVARNLIKQLSEFAGVEIVGNEEKIK"
                     /name="hypothetical protein"
     Typing          1081..1487
                     /name="ColRNAI_rep_cluster_1987"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="96.088"
                     /coverage="99.0"
                     /evalue="0.0"
ORIGIN
        1 cgactcttca ctagagtcgt acctagagtc gctgcgtcta aaaaacaacc aaacggggag
       61 tcgtgtctag agtcgggtcg ttattaactt attgttttta tagtcctgag tcgttaccga
      121 ctctatgacg actcgccggg gactctatga cgagtcgtca tagagtcgga tctatataaa
      181 taaaatttaa aaaacgaaat ttcagtaaag taaccaactg atattaaata caaatctgca
      241 aaatgttaat tttgcgtggg gtgtgggtat ttttagtggt gaggagcgtt cagagatctg
      301 acgatttttg ggaaggttca ggaactcccc gggatggccg gagaggaaaa cggaagcatg
      361 acggggtcag gattttttcc agaatttcca ccatggcgcc ggggattcag ttaattttgc
      421 ctggtgattt tcaagaagga gcatggcctg tttcaggctg tcaatgtgcg aatccttgga
      481 caaaagtaag gagttcaggt gttcaatctc ctgtttcaga tgacgaatca cctgttcact
      541 ctggtcagca gaggctgtat cacgctgttc agagacctgt ccagaatgga gttcatcctt
      601 cggttgttca aagggaccaa agacacgcaa aagctctgaa gtatctacca tttttgcatt
      661 gcgttcaccg ctacaggtgg acaggtcacc tgctttaatt aacctgtgta gtgttgttct
      721 actcttaccc gtcagtcggg cagcctcact aatagacact ctggccatca gttaccatcc
      781 tgtaatgcat ccagtctcga ggacagtgta cggaaaagat gctccgcatc atcgtggagt
      841 ttctcacaaa ggtcggcctc tacatcaaga tcaagctcat taagcttctc tagcaggagc
      901 agagactgat tctggatgaa tttagccatg ttcagcgctg ttttctgttg tttcgtcata
      961 agaggcctca gagcgtcagt gctcagtgta gggatgttct cttttccgct tcctcgctca
     1021 ctcagtcgct atgctcctgc cgttcggctg cggcgagcgg caggagcatg cgtataaaag
     1081 ctcgagaaaa ccgagcggtc gcgtgacggg aaaaaggaaa ggccgctaag cggccgtttt
     1141 tccataggct ccgcccccct gacaagcatc acagaaactg acgctcaaat cagtggtggc
     1201 gaaacccgac aggactataa agatatcagg cgtttccccc tgatggctcc ctcgtgcgct
     1261 ctcctgttcc tgccattcgg tttaccggtg tcattccgct gttatggccg cgtttatctc
     1321 attccacgcc agacactcag ttccgggaag gcagttcgct ccaagctgga ctgtatgcac
     1381 gaaccccccg ttcagtccga ccgctgcgcc ttaaccggta actatcatct tgagtccaac
     1441 ccggaaagac acgaaaaacg ccactggcag cagccattgg taactgattt agaggagata
     1501 gtcttgaagt catgcgcctg ttaaggctaa actgaaagaa caatttttgg tgactgcgct
     1561 cctccaagcc agtaaccttg gttccaccac ctgcaagtgg ctgaaccttc gaagaaaccg
     1621 ccctgcaagg cggtttcttc gttttcgtcc acagaagatt acaatttgcg ttgaagaagt
     1681 acaaggacaa caaagcaaaa gaggtgattg actaaaaatc accccttgga ttgaaaatga
     1741 aaaaacacca tcacaacaac aatgcaaata catcaatgag ctaatttttt gcatttcctt
     1801 tgtttcatca cttccttatt taattccagg caattattta gatatgctat tgaatggtgt
     1861 gccataatgg accggatctc taaagagtct tgttgtttta catattcaaa atcccagtga
     1921 taagctttgg tgtgctgttc tttttgtggc gatgtcttag atataccatc aataaaagaa
     1981 tatataacat gtgaatactc agcgcaggaa aaaaaaccat ttagacacaa aagcactggc
     2041 acatcagact tcacatcaaa aggcccctca tttatcatga attccataaa agaatcagcc
     2101 tcgccctgca aatcactatc attttttatt atcatttcat aaaaacttaa cgctggctct
     2161 ttccatataa cattttcacc atcaaattta accctcaaag aaaaggctgc gggactaaca
     2221 ttactagcgc aattttttcg tctcacagat cgccagagtc tatctatatt tgatagaccc
     2281 tgtcttatca attttatttt ttcgctgaca tccaagtcaa aagaaaaatc aaaaaccaaa
     2341 tcttcatcat ccccaaaata cggtgaagaa acagaagtca tatgtcgacc accttattaa
     2401 tcattgagaa tagaaaataa acttcttatt ttgtaagact tagccacttt cttagctgaa
     2461 aacatcctcc cagatatata gtaagcagag tcatctttat cagcgtcttt ggagaagaat
     2521 gttatgactc catcactctc aaactgtata ttcatatacc ggccatcgtg attatcacca
     2581 cgcaaactaa cagcaataac atttagagag aggtcgtaat caacagaaat agtatcgcta
     2641 tattttctta gctcaggata gtgtttcaag aagttgatga gtgatttttt tgtctttata
     2701 tctgccggca aactctcaca cccaaaaaag gcatctttaa gctttaactc aacaagccca
     2761 agtgaattaa agtcatttat cacatcaata acatcactta ttattttaca atcaataatg
     2821 cggccagata tttttctaaa ctcaccaacc catgaagacc actccttaat atcgccatca
     2881 ggtttacacg cattatcgta ttctattttg tagacgacat cctggtcgct atactttaga
     2941 ttacgagagt cgtaatcttc attattaaat agttcagagc cagaggtgta atttttcaaa
     3001 agaagcacct catcatcata ggatgaaaaa aaactcttca catcacccga gcttatccca
     3061 tcataattaa aacgcgagtg ttctaattca cattgattat tatttgattt tttcttcatt
     3121 gcctacaatc tccacgccgg caaattcaga taattgtttt atcaagtttc ttgccactct
     3181 tttagtcagg acaacacttg aaaaggcctc caaatcgtca ccattgcggt tagcaaaatc
     3241 aacaaaagca acctcatcag tagccccgac acgaatagtc agagggaatg aatgaggcat
     3301 ttttcttttc atttcttgct tttcatcaga cataaaaatc tccaccatta taaaaaaagt
     3361 tttttacgca catcaattat cgcacataat cacttgatct atagtgcatt tttcaacata
     3421 aaattcaata atttaaaaca acagcctaaa catagcagct cgcaccaacc ccagaatcca
     3481 accctaacat ttattttatt cgcgtctaaa tgatataaat tatccccccc ccaacgaaga
     3541 tggtcacaaa ggaaacagct aaacaggtct acagggggtc agtccgcttc atccataaag
     3601 ccacttcagt ttttgttgcg cctgttattt aacataaagc catgattgta cgcaccgcta
     3661 aaacggcctc agggcgtttc tgacgggaaa ccggtaaaac aggcaacaaa ccacccgaaa
     3721 acccgccaga aacgcgcagg ctctgttttt acggcatgca tgagtatgca cgcaagtgca
     3781 tagcgcgaaa attcacgcca ttcagccaga gtaagtcctg tttccggcgt tctttccatc
     3841 cgaaaacggt gaacggggac gcaatttatt gcgtggccgt gaagcgttgc cggcgcagcc
     3901 ggaaaaccgg ttttcagcac gttcaggaat cgggttcgtc gacggccggc aatcacgtta
     3961 tggcaagtcg ccggacgact caccacacga ctctaggta
//
