LOCUS       NZ_CP147607             2780 bp    DNA     circular CON 05-APR-2024
DEFINITION  Klebsiella pneumoniae strain GN04077 plasmid unnamed2, complete
            sequence.
ACCESSION   NZ_CP147607
VERSION     NZ_CP147607.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN40123774
            Assembly: GCF_037282145.1
KEYWORDS    RefSeq.
SOURCE      Klebsiella pneumoniae
  ORGANISM  Klebsiella pneumoniae
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Klebsiella/Raoultella group; Klebsiella.
REFERENCE   1  (bases 1 to 2780)
  AUTHORS   Parsons,J.B., Sidders,A.E., Velez,A.Z., Hanson,B.M.,
            Angeles-Solano,M., Ruffin,F., Rowe,S.E., Arias,C.A., Fowler,V.G.
            Jr., Thaden,J.T. and Conlon,B.P.
  TITLE     In-patient evolution of a high-persister Escherichia coli strain
            with reduced in vivo antibiotic susceptibility
  JOURNAL   Proc Natl Acad Sci U S A 121 (3), e2314514121 (2024)
   PUBMED   38190524
REFERENCE   2  (bases 1 to 2780)
  AUTHORS   Hanson,B.M., Parsons,J.B. and Conlon,B.P.
  TITLE     Direct Submission
  JOURNAL   Submitted (26-FEB-2024) Center for Antimicrobial Resistance and
            Microbial Genomics, The University of Texas Health Sciences Center,
            1200 Pressler St, Houston, TX 77030, USA
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Date                     :: NOV-2021
            Assembly Method                   :: Flye v. v2.8.3
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 100x
            Sequencing Technology :: Illumina NextSeq and Oxford Nanopore
            GridION X5
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_037282145.1-RS_2024_04_05
            Annotation Date                   :: 04/05/2024 19:08:29
            Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline
            (PGAP)
            Annotation Method :: Best-placed reference protein set; GeneMarkS-2+
            Annotation Software revision      :: 6.7
            Features Annotated                :: Gene; CDS; rRNA; tRNA; ncRNA
            Genes (total)                     :: 5,252
            CDSs (total)                      :: 5,131
            Genes (coding)                    :: 5,000
            CDSs (with protein)               :: 5,000
            Genes (RNA)                       :: 121
            rRNAs                             :: 9, 8, 8 (5S, 16S, 23S)
            complete rRNAs                    :: 9, 8, 8 (5S, 16S, 23S)
            tRNAs                             :: 86
            ncRNAs                            :: 10
            Pseudo Genes (total)              :: 131
            CDSs (without protein)            :: 131
            Pseudo Genes (ambiguous residues) :: 0 of 131
            Pseudo Genes (frameshifted)       :: 61 of 131
            Pseudo Genes (incomplete)         :: 69 of 131
            Pseudo Genes (internal stop)      :: 24 of 131
            Pseudo Genes (multiple problems)  :: 22 of 131
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP147607.1.
            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..2780
                     /organism="Klebsiella pneumoniae"
                     /mol_type="genomic DNA"
                     /strain="GN04077"
                     /isolation_source="bloodstream"
                     /host="Homo sapiens"
                     /db_xref="taxon:573"
                     /plasmid="unnamed2"
                     /geo_loc_name="USA: Durham"
                     /lat_lon="36.0070 N 78.9371 W"
                     /collected_by="Duke Bloodstream Infection Biorepository"
     gene            1..192
                     /locus_tag="WCU02_RS26245"
                     /old_locus_tag="WCU02_26245"
     CDS             1..192
                     /locus_tag="WCU02_RS26245"
                     /old_locus_tag="WCU02_26245"
                     /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_032489493.1"
                     /translation="MTKQQKTALNMAKFIQHQSLLLLEKLNELDLDVEADLCEKLHDDA
                     EHLFRTLSSRLDALQDGN"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            192..593
                     /locus_tag="WCU02_RS26250"
                     /old_locus_tag="WCU02_26250"
     CDS             192..593
                     /locus_tag="WCU02_RS26250"
                     /old_locus_tag="WCU02_26250"
                     /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_050886242.1"
                     /translation="MARVSISEAARLTGKSRTTLHRLIKAGDLSTCSGERNAKMVDTSE
                     LLRVFGPFEQPKGEHHYGQVSGQRDTASADQSEQVIRHLKQEIEHLNTLLSSKDSHIDS
                     LKQGMLLLENHQAKLTESPAPWWKFWKKS"
                     /name="helix-turn-helix domain-containing protein"
     gene            1355..2035
                     /locus_tag="WCU02_RS26255"
                     /old_locus_tag="WCU02_26255"
     CDS             1355..2035
                     /locus_tag="WCU02_RS26255"
                     /old_locus_tag="WCU02_26255"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001572662.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_072042463.1"
                     /translation="MGRKSREKKERHIKDRASPLKVYRFFKEKSHAEALCNGDVWLSTI
                     ETCRRYEDPLQGDPNEAIQTYSSGFISGGSDDSRFVSAAAHAGIHIGPGCSGITIQNCR
                     SFNKMPDAFVLCTTLEFQPENLNDTFGNYCVEISNVEEFFGLITKKLKGLLPIKLGAMG
                     EVRYGSHSFYGYQPPPGPIGFVKNRDKYSSQKEFRFLWVPETFDIQPRLVKCPELSYCC
                     RMIS"
                     /name="hypothetical protein"
     gene            complement(2284..2367)
                     /locus_tag="WCU02_RS26260"
                     /old_locus_tag="WCU02_26260"
     CDS             complement(2284..2367)
                     /locus_tag="WCU02_RS26260"
                     /old_locus_tag="WCU02_26260"
                     /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="replication initiation protein"
                     /protein_id="WP_072042462.1"
                     /translation="MHEPPVQSDCCASSGNYRLESNPERHD"
                     /name="replication initiation protein"
     Typing          complement(2255..2659)
                     /name="ColRNAI_rep_cluster_1987"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="92.157"
                     /coverage="99.0"
                     /evalue="1.6700000000000002e-161"
ORIGIN
        1 atgacgaaac aacagaaaac agcgctgaac atggctaaat tcatccagca tcagtctctg
       61 ctcctgctgg agaagcttaa cgagcttgat ctcgatgtcg aggccgacct ttgtgagaaa
      121 ctccacgatg atgcggagca tcttttccgt acactgtcct cgagactgga tgcattacag
      181 gatggtaact gatggccaga gtgtctatta gtgaggctgc ccgactgacg ggtaagagta
      241 gaacaacact gcacaggtta attaaagcag gtgacctgtc cacctgtagc ggtgagcgca
      301 atgcaaaaat ggtagatact tcagagcttt tacgtgtctt tggtcccttt gagcaaccga
      361 agggtgaaca ccattatgga caggtctctg gacagcgtga tacagcctct gctgaccaga
      421 gtgaacaggt gattcgtcat ctgaaacagg agattgaaca tctgaacacc ttactttcgt
      481 ccaaggattc gcacattgac agcctgaaac agggcatgct ccttcttgaa aatcaccagg
      541 caaaattaac tgaatccccg gcgccatggt ggaaattctg gaaaaaatcc tgatcctgcc
      601 atgcttgagt tttcctctcc ggccatcccg gggagttcct gaaccttccc aaaaatcgcc
      661 agatctctga acgctcctca cgactaaaaa tacccacaca ctacgcaaaa ttaaaatttt
      721 gcagatttgt atttaatatc agtggtttac tttcctgaaa tttcgttttt taaattttat
      781 ttacatagat ccgactctat gacgactcgt catagagtcc ccggcgagtc gtcatagagt
      841 cggtaacgac tcaggactat aaaaacaatg agttaataac gacccgactc tagacacgac
      901 tccccgtttg gttgcttttt agactcggcg actctgggta cgactctagt gaagagtcgc
      961 cggggaatcg tgtggtgagt cgtccggcga cttgccataa cgtgattgcc ggccgtcgac
     1021 gaacacgatt cctgaacgtg ctgaaaaccg gttttccggc tgcgccggca acgcttcacg
     1081 gccacgcaat aaattgcgtc cccgttcacc gttttcggat gggaagaacg ccggaaacag
     1141 gacttaccat ggctgaatgg cgtgaatttt cgcgctacgc acttgcgtgc atactcatgc
     1201 atgccgtaaa aacagagcct gcgcgtttct ggcgggtttt cgggtggttt gttgcctgtt
     1261 ttaccggttt cccgtcagaa acgccctgag gccgttttag cggtgcgggc aagagatgtt
     1321 atggtaaatg aaaatttaaa aaggatattt ttcaatgggt aggaaaagta gagagaaaaa
     1381 agaaaggcat attaaagata gagccagccc ccttaaagta tataggtttt ttaaagagaa
     1441 gagtcatgct gaggcattgt gcaatggcga tgtttggctg agcactattg aaacgtgtag
     1501 acgatacgaa gaccccctac agggagatcc gaatgaagca attcaaacct atagctcggg
     1561 ttttatctca gggggcagtg atgacagccg ttttgtctct gctgcagctc atgccggaat
     1621 ccatattgga cctggctgta gtggaataac gatacaaaat tgtcgctctt ttaataagat
     1681 gcccgacgcc tttgttttat gtacgacact ggaatttcag ccagaaaact tgaacgatac
     1741 ctttggaaat tactgtgtgg aaatatcaaa tgttgaagag ttttttggtc ttattactaa
     1801 aaagttaaag gggttattac ctataaaatt aggtgctatg ggggaggtca gatatgggag
     1861 tcattctttt tatggttacc agcctccacc gggaccgatt gggtttgtaa aaaatcgaga
     1921 taaatattct tcgcagaaag aattcagatt tctttgggtg ccagaaacat ttgatattca
     1981 acccaggtta gtcaaatgcc ctgagctttc atattgttgc cgaatgatat cttagatgac
     2041 attttccata gtgtaattct tgactgagat tacgttacca gcgtaatctc ctttggaaac
     2101 aaaaagaccg cccagcaagg cggtcctttt gaaggttctt agagcagcaa ctctttgaac
     2161 cgcggtaact ggcttggagg agcgcagtaa ccaaaacttg tcctttcagt ttagccttaa
     2221 ccggcgcata acttcaagac taactcctct aaatcaatta ccagtggctg ctgccaatgg
     2281 cgattagtcg tgtctttccg ggttggactc aagacgatag ttaccggacg aggcgcagca
     2341 gtcggactga acggggggtt cgtgcataca gtccagcttg gagcgaactg cctacccgga
     2401 actgagtgtc aggcgtggaa tgagacaaac gcggccataa cagcggaatg acaccggtaa
     2461 accgaaaggc aggaacagga gagcgcacga gggagccacc agggggaaac gcctggtatc
     2521 tttatagtcc tgtcgggttt cgccaccact gatttgagcg tcagattccg tgatgcttgt
     2581 caggggggcg gagcctatga aaaaacggcc gctttgcggc ctttccttct tccccatttg
     2641 accgctcggt cttctcgagt ttttatacgc atgctcctgc cgctcgccgc agccgaacga
     2701 ccggagcgta gcgactgagt gagcgaggaa gcggaaaaga gactggtttt acactgagca
     2761 ctgacgctct gaggccattt
//
