LOCUS       NZ_CP041952             4507 bp    DNA     circular CON 26-NOV-2023
DEFINITION  Klebsiella pneumoniae strain KP2 plasmid pKP2_6, complete sequence.
ACCESSION   NZ_CP041952
VERSION     NZ_CP041952.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN12307651
            Assembly: GCF_009720445.1
KEYWORDS    RefSeq.
SOURCE      Klebsiella pneumoniae
  ORGANISM  Klebsiella pneumoniae
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Klebsiella/Raoultella group; Klebsiella.
REFERENCE   1  (bases 1 to 4507)
  AUTHORS   Khan,A., Shropshire,W.C., Hanson,B., Dinh,A.Q., Wagner,A.,
            Ostrosky-Zeichner,L., Arias,C.A. and Miller,W.R.
  TITLE     Simultaneous Infection with Enterobacteriaceae and Pseudomonas
            aeruginosa harboring Multiple Carbapenemases in a Returning Traveler
            colonized with Candida auris
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 4507)
  AUTHORS   Khan,A., Shropshire,W.C., Hanson,B., Dinh,A.Q., Wagner,A.,
            Ostrosky-Zeichner,L., Arias,C.A. and Miller,W.R.
  TITLE     Direct Submission
  JOURNAL   Submitted (18-JUL-2019) Epidemiology, Human Genetics and
            Environmental Sciences, The University of Texas Health Science
            Center at Houston, 1200 Pressler Street, Houston, TX 77030, USA
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: Celera Assembler v. 1.8
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 448x
            Sequencing Technology             :: Oxford Nanopore GridION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 11/26/2023 04:10:46
            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)                     :: 5,759
            CDSs (total)                      :: 5,632
            Genes (coding)                    :: 5,471
            CDSs (with protein)               :: 5,471
            Genes (RNA)                       :: 127
            rRNAs                             :: 9, 8, 8 (5S, 16S, 23S)
            complete rRNAs                    :: 9, 8, 8 (5S, 16S, 23S)
            tRNAs                             :: 89
            ncRNAs                            :: 13
            Pseudo Genes (total)              :: 161
            CDSs (without protein)            :: 161
            Pseudo Genes (ambiguous residues) :: 0 of 161
            Pseudo Genes (frameshifted)       :: 84 of 161
            Pseudo Genes (incomplete)         :: 79 of 161
            Pseudo Genes (internal stop)      :: 16 of 161
            Pseudo Genes (multiple problems)  :: 18 of 161
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP041952.1.
            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..4507
                     /organism="Klebsiella pneumoniae"
                     /mol_type="genomic DNA"
                     /strain="KP2"
                     /isolation_source="urine"
                     /host="Homo sapiens"
                     /db_xref="taxon:573"
                     /plasmid="pKP2_6"
                     /geo_loc_name="USA:Houston"
                     /lat_lon="29.712470 N 95.397690 W"
                     /collection_date="2017-09-29"
                     /collected_by="William R. Miller"
                     /genotype="ST16"
     gene            <104..>279
                     /locus_tag="FOZ68_RS29170"
                     /old_locus_tag="FOZ68_28685"
                     /pseudo=""
     CDS             <104..>279
                     /locus_tag="FOZ68_RS29170"
                     /old_locus_tag="FOZ68_28685"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_015167793.1"
                     /note="frameshifted; incomplete; partial in the middle of a
                     contig; missing N-terminus and C-terminus; Derived by
                     automated computational analysis using gene prediction
                     method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="type II restriction endonuclease"
                     /name="type II restriction endonuclease"
     gene            complement(314..1140)
                     /gene="yhdJ"
                     /locus_tag="FOZ68_RS27840"
                     /old_locus_tag="FOZ68_28690"
                     /pseudo=""
     CDS             complement(314..1140)
                     /gene="yhdJ"
                     /locus_tag="FOZ68_RS27840"
                     /old_locus_tag="FOZ68_28690"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_006687795.1"
                     /GO_function="GO:0003677 - DNA binding [Evidence IEA];
                     GO:0008170 - N-methyltransferase activity [Evidence IEA]"
                     /GO_process="GO:0006306 - DNA methylation [Evidence IEA]"
                     /note="frameshifted; internal stop; Derived by automated
                     computational analysis using gene prediction method:
                     Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="adenine-specific DNA-methyltransferase"
                     /name="yhdJ"
     gene            2260..2451
                     /locus_tag="FOZ68_RS27850"
                     /old_locus_tag="FOZ68_28700"
     CDS             2260..2451
                     /locus_tag="FOZ68_RS27850"
                     /old_locus_tag="FOZ68_28700"
                     /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_087812789.1"
                     /translation="MRKEQKTALNMAKFIQNQSLLLLEKLNELDLDVEADLCEKLHDDA
                     EHLFRTLSSRLDELQDGN"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            2451..2908
                     /locus_tag="FOZ68_RS27855"
                     /old_locus_tag="FOZ68_28705"
                     /pseudo=""
     CDS             2451..2908
                     /locus_tag="FOZ68_RS27855"
                     /old_locus_tag="FOZ68_28705"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000135004.1"
                     /note="frameshifted; Derived by automated computational
                     analysis using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="helix-turn-helix domain-containing protein"
                     /name="helix-turn-helix domain-containing protein"
     gene            3832..4041
                     /locus_tag="FOZ68_RS27860"
                     /old_locus_tag="FOZ68_28710"
     CDS             3832..4041
                     /locus_tag="FOZ68_RS27860"
                     /old_locus_tag="FOZ68_28710"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_013321970.1"
                     /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 transcriptional regulator"
                     /protein_id="WP_064168505.1"
                     /translation="MNPEDIKKVFGENLRRIRMEKNISQENLAFLSGMDRTYVSGIERG
                     KRNVSLVNINKIALALNVEIKELF"
                     /name="helix-turn-helix transcriptional regulator"
ORIGIN
        1 ttttaatatt gaaaactcga atgaaaaaga agggatattg aaatttatcc ttttcagtgc
       61 taaaattata cttctctaaa atattgtaat aaatggaaga gaggagttct tccagctgtt
      121 taaaacagga aggactaatg ctaatgatgg tgggatagat tttgttttaa agccagtagg
      181 aaggtttttt caagtgactg aggttttaga cttcaaaaaa tactttttag atttcgataa
      241 gacgaataaa ttcctattag ttttgttgtt aaaacggatc ttgatccaga aggagttatg
      301 aggttaataa aggttaatgc gaaactatgg gcgaagaatt agcgaataga tattttggct
      361 tgtttgaagc tcttgaagaa ctctttttta atttttctaa ttcttttggg gtgtaacttg
      421 aaggtatgtt taaccttctt atgcccattt ttacatactc ttcgtttatt tctataccta
      481 taaatcttct atctagagac ttagatacat ctcccgttgt aaagctacca gaaaaaggat
      541 ctaaaactac atcccctgga tttgatgaag ctaaaacaat tctctttaga agagaaattg
      601 gtttttgcgt tgggtggttt tcatattcct ccataaggaa tcttactcgg ggaaattccc
      661 aaacatttcc aggtactttt tgagtattat aaggttgagg tggattcttc ctgtaatcaa
      721 ttaaagctct tttggaacct gtttttgctt caaccaagat atctttactg ttaaaagtat
      781 attttttggg gtctttaacc atcattaata ttggttcata catagaacca aagtagtttt
      841 tagcttgaac cccagagcta tcataagacc aaactattct actctttata tgaaaggtat
      901 tcctgcattt tatgtcaata tatggcatgt tctcagtact attcattata catagtgcca
      961 ttttaaaact cgatgacatt catcaatgca ctcgaatagc caatgaagaa attcattatc
     1021 atcccaagac tcaataagac catcgaaatc tttaccgata ttatatggcg gatctgcaaa
     1081 ccaaatctac gctttcgatg gtaacttctt taattcagtt aaagcatcac catggataat
     1141 ttatttgttc atctgtgaaa tatctggctt cgaattcaat ttcatcttac ccttagtgtg
     1201 actcatagtc actatgctac cgtcaaattg atgctgtaca accttcatag ctctacttta
     1261 tgattgcctt taaacatata agttgcatat ataatgtatt aaattttaac ttattgattt
     1321 cgtgttaatg cttaaatctt aggtggtgaa gagctctgag gttatcaaag actgccataa
     1381 caatattgat gcttaattgc ttcgtcagtt ttcagtagga tccaaagatc tcttgagatc
     1441 atctatatct gagcgtaatc tcttgctctg taaacgaaaa ccaccggagg tggttttcga
     1501 aggttcccaa tctgtccttc cagtgtagcc tcactcaggc caccacttca agaactcgat
     1561 acttcgcatt ctgtttacca gcggctgccg ccagtgccgt ctgtctttcc gctttatctc
     1621 aagttcgata gttaccggac gcagcgtttc gtcatacgag tagcttcatg aacaaacaac
     1681 ttctggacag gcttaatgag ctggatctgg atcatgaggc tgatttcgcg agaaactcca
     1741 tgaggatgcg gaacgccttt accgaagcct gtcagcgcgc ctgaatgagc agcaggacgg
     1801 tgcgtatggc tcgttctggt attaccggag taataccggc atcgccttaa ttttcattgt
     1861 ctggcgctaa tattattacc ccggtaatac ccagaatccc ttatttttct tttatttatt
     1921 ttcatgaagt tgcgatgaaa atcgcggctg cgttagtgta tgaccattta agggcaaaat
     1981 tatcattctg gccgcgtgat ctgcgcaggt taaggagcat cggcgacgaa aagcgtcctt
     2041 aactgcttcg ttcatgcaag catgaacgga ttattttccg gactacaggt aaactacagg
     2101 aagactacaa aagttgatga cttaatcctg atttttagtg cgatgactac agataaacta
     2161 caaaataact acaggattac ctcagatccg ttctctgaac cattcgtaca tccgacccct
     2221 taccggttga cattgagcac tgacgctctg aggcccttta tgaggaaaga acagaaaaca
     2281 gcgctgaaca tggctaaatt catccagaat cagtctctgc tcttgttgga gaagcttaac
     2341 gagcttgatc tcgatgtcga ggccgacctt tgtgagaaac tccacgatga tgcggagcat
     2401 cttttccgta cactgtcctc gagactggat gaattacagg atggtaactg atggccagag
     2461 tgtctattag tgaagcggca cggcttgtta aggttagtcg ccccacaatt tacaagatga
     2521 ttaacagtgg gaagttaagt tacacctctg ttgtaaagca cgggaaggct attaaagtta
     2581 ttgatacttc agagcttatt agagtgtttg gctctcttga tggtgtcatc gatgatgtaa
     2641 aagtgacgca gaatctacag gtattaacag cgttggttta catgatttac aacatagaat
     2701 cgctttactt gaagctgaaa acgatggtct taaaggggct gttaaggctc gagatgagca
     2761 tattgattcc cttcgtcagg ctatgcagct tctggagcac aagcacgaac cttcttcacc
     2821 accccattcc ccgtggtgga aattctggaa aaatcctgat cccgccatgc ttgagttttc
     2881 ctctccggcc atcccggggc gttcctgaac cttccaaaaa tcgccagatc cgggaacact
     2941 cctcaccacg aaaaataccc acaccacgca aaattaaaat tttgcagata actccttatt
     3001 atcagttggt taggttttat taaattacgc agtattacct tctgtaaggt caatccaagt
     3061 cgtcggtgat tcgtgtacga cttgccgacg actcgtcata gagtcatcga cgactcactc
     3121 cacactatca gtaacttatg acgacttgac tctagagtcg aatcgtcgct ttggcgtttt
     3181 tttgaccgcg gtgactctag agtcaagtca cgagtcgaat cgccggtgag tcgtccggcg
     3241 acttgccata acgtgattgc cggccgtcga cgaacccgat tcctgaacgt gctgaaaacc
     3301 ggttttccgg ctgcgccggc aacgcttcac ggccacgcaa taaattgcgt ccccgttcac
     3361 cgttttcgga tgggaagaac gccggaaaca ggacttcccc tggctgaatg gtgtcaattt
     3421 ccgcgctatg cacttgtgcg catactcatg catgccgtaa aaacagagcc tgcgcgtttc
     3481 tggcgggttt tcgggtggtt tgttgccttg tttaccggtt tcccgtcaga aacgccctga
     3541 gggcatctca ggcggtgctg ataacggatg ttatggtaaa tgcaaatggt tctggtgatg
     3601 tgaaaaagcc gcctgaaagg tggctttttc attttttaga tagagtcgaa cggcatttac
     3661 gacaccagct ttggttagtt gctcctgagg gggggggggc cgttcttaat ccgaatagtg
     3721 ccgatagaga aaactaacca tttgacaata ataaacacgg aatgtgactt aaagtccgtt
     3781 gggttttgag tcaccaaatg caattataaa ttttttttac ggatttaatg tatgaatcca
     3841 gaagatatca aaaaagtttt tggtgaaaac ttaagacgaa tcagaatgga gaaaaatatt
     3901 agccaagaga atcttgcgtt tttatccgga atggacagga cttacgtaag tgggatagag
     3961 cgagggaagc ggaatgtaag tctggttaac ataaataaaa tagcattggc tttgaatgtg
     4021 gaaataaagg agctctttta atggtggatt tcgttaagaa aatagatgag ttagcatcta
     4081 aatataatgt aagtcaaagg tctgtagttt acaaatatat cgaaaaagac tagagcatca
     4141 ggcagagata gcaaagctag gcgttcactt ggcaatttat atgcgctata tgttctttgt
     4201 gaagcatata atgatgggcg acggcgggac ctccttctct gttttaatgc agagaatgag
     4261 agcgcttcct tggttctaaa ctgcaaaatc atcctttgga taatagattg aatgatgagg
     4321 taagaagaag tttttagtgc aggataatat gttacctgtg caaagtgcga cagaaggaac
     4381 agtaaaaaag aataatttct attgattttc ttcagagttt ggcatgatcc cggttcatct
     4441 tcattgttta tcactaaagc aattgattta tatattgacg aaataactga aaaacaaaat
     4501 gaattcc
//
