LOCUS       NZ_CP041950             5386 bp    DNA     circular CON 26-NOV-2023
DEFINITION  Klebsiella pneumoniae strain KP2 plasmid pKP2_4, complete sequence.
ACCESSION   NZ_CP041950
VERSION     NZ_CP041950.1
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 5386)
  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  JOURNAL   Unpublished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 5386)
  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
            CP041950.1.
            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..5386
                     /organism="Klebsiella pneumoniae"
                     /mol_type="genomic DNA"
                     /strain="KP2"
                     /isolation_source="urine"
                     /host="Homo sapiens"
                     /db_xref="taxon:573"
                     /plasmid="pKP2_4"
                     /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            complement(join(4995..5386,1..532))
                     /gene="yhdJ"
                     /locus_tag="FOZ68_RS27780"
                     /old_locus_tag="FOZ68_28600"
     CDS             complement(join(4995..5386,1..532))
                     /gene="yhdJ"
                     /locus_tag="FOZ68_RS27780"
                     /old_locus_tag="FOZ68_28600"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001399826.1"
                     /GO_function="GO:0003677 - DNA binding [Evidence IEA];
                     GO:0008170 - N-methyltransferase activity [Evidence IEA]"
                     /GO_process="GO:0006306 - DNA methylation [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="adenine-specific DNA-methyltransferase"
                     /protein_id="WP_155367702.1"
                     /translation="MKIEFEARYFTDEQNKIIHGDALTELKKLPSESVDLVFADPPYNI
                     GKDFDGLIESWDDNEFLHWLFECIDECHRVLKKNGTMYIMNSTENMPYIDIKCRNTFHI
                     KSRIVWSYDSSGVQAKNYFGSMYEPILMMVKDPKKYTFNSKDILVEAKTGSKRALIDYR
                     KNPPQPYNTQKVPGNVWEFPRVRFLMEEYENHPTQKPISLLKRIVLASSNPGDVVLDPF
                     SGSFTTGDVSKSLDRRFIGIEINEEYVKMGIRRLNIPSSYTPKELEKLKKRKTKNKSKN
                     VRGDDNDISDLLIDDLPSSQEGHTLI"
                     /name="yhdJ"
     gene            complement(966..1127)
                     /locus_tag="FOZ68_RS29370"
                     /old_locus_tag="FOZ68_28605"
     CDS             complement(966..1127)
                     /locus_tag="FOZ68_RS29370"
                     /old_locus_tag="FOZ68_28605"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_005019281.1"
                     /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_096111359.1"
                     /translation="MHEPPVQSDRCALSGNYRLESNPERHAKAPLAAAAGKQNVREKYR
                     EFLKWWPE"
                     /name="replication initiation protein"
     gene            1546..1737
                     /locus_tag="FOZ68_RS27790"
                     /old_locus_tag="FOZ68_28620"
     CDS             1546..1737
                     /locus_tag="FOZ68_RS27790"
                     /old_locus_tag="FOZ68_28620"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001041614.1"
                     /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_001041614.1"
                     /translation="MNKQQKTAVNMAKFIQDQSLLLLDRLNELDLDHEADFCEKLHEDA
                     ERLYRSLSARLNEQQDGA"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            2208..2399
                     /locus_tag="FOZ68_RS27795"
                     /old_locus_tag="FOZ68_28625"
     CDS             2208..2399
                     /locus_tag="FOZ68_RS27795"
                     /old_locus_tag="FOZ68_28625"
                     /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_032421723.1"
                     /translation="MTKQQKTALNMAKFIQNQSLLLLEKLNELDLDAEADLCEKLHDDA
                     EHLFRTLSSRLDELQDGN"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            2399..2809
                     /locus_tag="FOZ68_RS27800"
                     /old_locus_tag="FOZ68_28630"
     CDS             2399..2809
                     /locus_tag="FOZ68_RS27800"
                     /old_locus_tag="FOZ68_28630"
                     /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_048295909.1"
                     /translation="MARVSISEAARLVKVSRPTIYKMINSGKLSYTSVVKHGKGIKVID
                     TSELIRVFGSLDGVIDDVKSDAESTGINSVGLHDLQHRIALLEAENDGLKGAVKARDEH
                     IDSLRQAMQLLEHKHEPSSPPHSPWWKFWKKS"
                     /name="helix-turn-helix domain-containing protein"
     gene            3783..3992
                     /locus_tag="FOZ68_RS27805"
                     /old_locus_tag="FOZ68_28635"
     CDS             3783..3992
                     /locus_tag="FOZ68_RS27805"
                     /old_locus_tag="FOZ68_28635"
                     /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"
     gene            3992..5023
                     /locus_tag="FOZ68_RS27810"
                     /old_locus_tag="FOZ68_28640"
     CDS             3992..5023
                     /locus_tag="FOZ68_RS27810"
                     /old_locus_tag="FOZ68_28640"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001399825.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="type II restriction endonuclease"
                     /protein_id="WP_155367701.1"
                     /translation="MVDFVKKIDELASKYNVSQRSVVYKYIEKKTRASGRDSKARRSLG
                     NLYALYVLCEAYNDGAKGGTSFSVLMQRMRALPFGSKLQNHPLDNRLNDEVRRSFLVQD
                     NMLPVQSATEGTVKKRIISIDFLSEFGMDPGSSSLFITKAIDLYIDEITEKQNEFLFNI
                     ENSNGKEGILKFIENSFSPNADARLFEVVSFSVLKLYFSKKNIVINGREEFFQLFKTGR
                     TNANDGGIDFVLKPVGRFFQVTEVLDFKKYFLDFDKTNKFPMSFVVKTDLDPEGVMRLI
                     KVNAEKTMGEELANRYFGLFEEVFTLPTLRNIVGVISDSLEDLEELKRVIIENFKLEYG
                     LLD"
                     /name="type II restriction endonuclease"
     Typing          complement(1052..1671)
                     /name="rep_cluster_2327"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="84.929"
                     /coverage="99.0"
                     /evalue="2.55e-171"
ORIGIN
        1 ttccaggtac tttttgagta ttataaggtt gaggtggatt cttcctgtaa tcaattaaag
       61 ctcttttgga acctgttttt gcttcaacca agatatcttt actgttaaaa gtatattttt
      121 tggggtcttt aaccatcatt aatattggtt catacataga accaaagtag tttttagctt
      181 gaaccccaga gctatcataa gaccaaacta ttctactctt tatatgaaag gtattcctgc
      241 attttatgtc aatatatggc atgttctcag tactattcat tatatacata gtgccatttt
      301 tttttaaaac tcgatgacat tcatcaatgc actcgaatag ccaatgaaga aattcattat
      361 catcccaaga ctcaataaga ccatcgaaat ctttaccgat attatatggc ggatctgcaa
      421 aaaccaaatc tacgctttct gatggtaact tctttaattc agttaaagca tcaccatgga
      481 taattttatt ttgttcatct gtgaaatatc tggcttcgaa ttcaattttc atcttttacc
      541 cttagtgtga ctcatagtct actatgctac cgtcaaaatt gatgctgtac aaccttcata
      601 gctctacttt tgtgctttat gattgccttt aaaaacatat ataagttgca tatataatgt
      661 attaaatttt aacttattga ttttcatgtg ttaatgctta aatcttaggt ggtggtgaag
      721 aggctctgag ggttatcaaa gactgccact aacaatattg atgcttaatt gcttcgtcag
      781 ttttcagtag gatctcaaaa gatcctcttg agatcatcta tatctgagcg taatctcttg
      841 ctctgtaaac gaaaaaacca cctggggagg tggtttttcg aaggttcagt aagttgggga
      901 acttctgaac cgtggtaaca gtcttgtgcg agacatgtca cccaatctgt ccttccagtg
      961 tagcctcact caggccacca cttcaagaac tctcgatact tctctcgcac attctgttta
     1021 ccagcggctg ctgccagtgg cgcttttgca tgtctttccg ggttggactc aagtcgatag
     1081 ttaccggaca aggcgcagcg gtcggactga acggggggtt cgtgcataca gtccagcttg
     1141 gagcgaactg cctacccgga actgagtgtc aggcgtggaa tgagataaac gcggccataa
     1201 cagcggaatg acaccggtaa accgaaaggc aggaacagga gagcgcacga gggagccacc
     1261 agggggaaac gcctggtatc tttatagtcc tgtcgggttt cgccaccact gatttgagcg
     1321 tcagatttcg tgatgcttgt caggggggcg gagcctatgg aaaaacgccc cggtggggcg
     1381 tggccttttc gcccttgtcc ttagttttcg ttatgcttac cgttatgtta tctgcttatc
     1441 ttccctccgc tcgccgcaga ctcatgaccg aacggagtga gcgaatgagc gaggaagcgg
     1501 aaaaccatca gaacgtacag taagtacttt cgcgccgggg ccttcatgaa caaacaacaa
     1561 aagacagccg ttaacatggc taaattcatc caggatcagt ccctgcttct tctggacagg
     1621 cttaatgagc tggatctgga tcatgaggct gatttctgcg agaaactcca tgaggatgcg
     1681 gaacgccttt accgaagcct gtcagcgcgc ctgaatgagc agcaggacgg tgcgtaatgg
     1741 ctccgttctg ggtattaccg gagtaatacc ggcatcgcct taattttcat tgtcctggcg
     1801 cttaatatta ttaccccggt aatacccaga atccctttat tttttctttt ttatttattt
     1861 ttcatgaagt tgcgatgaaa atcgcggctg cgttaggtgt atgaccattt aaggggcaaa
     1921 aaattatcat tctggccgcg tgatctgcgc aggttaagga gcatcggcga cgaaaaagcg
     1981 tccttaactg cttcgttcat gcaagcatga acggattatt tttccggact acaggtaaac
     2041 tacaggaaga ctacaaaagt tgatgactta atcctgattt ttagtgcgat gactacagat
     2101 aaactacaaa ataactacag gattacctca gatccgttct ctgaaccatt cgtacatccg
     2161 acccccttac cggttttaca ctgagcactg atgctctgag gtcccttatg acgaaacaac
     2221 agaaaacagc gctgaacatg gctaaattca tccagaatca gtctctgctc ctgctggaga
     2281 agcttaacga gcttgatctc gatgctgagg ccgacctttg tgagaaactc cacgatgatg
     2341 cggagcatct tttccgtaca ctgtcctcga gactggatga attacaggat ggtaactgat
     2401 ggccagagtg tctattagtg aagcagcacg gcttgttaag gttagtcgcc ctactattta
     2461 caagatgatt aacagtggta agttaagtta cacctctgtt gtaaagcacg ggaagggtat
     2521 taaagttatt gatacatcag agcttattag agtgtttggt tctcttgatg gtgtcatcga
     2581 tgatgtaaaa agtgacgcag aatctacagg tattaacagc gttggtttac atgatttaca
     2641 acatagaatc gctttacttg aagctgaaaa cgatggtctt aaaggggctg ttaaggctcg
     2701 agatgagcat attgattccc ttcgtcaggc tatgcagctt ctggagcaca agcacgaacc
     2761 ttcttcacca ccccattccc cgtggtggaa attctggaaa aaatcctgat cccgccatgc
     2821 ttgagttttc ctctccggcc atcccggggc gttcctgaac cttcccaaaa atcgccagat
     2881 ccgggaacac tcctcaccac gaaaaatacc cacacaccac gcaaaattaa aattttgcag
     2941 ataactcctt attatcagtt ggttaggttt tattaaatta cgcagtatta ccttctgtaa
     3001 ggtcaatcca agtcgtcggt gattcgtgta cgacttgccg acgactcgtc atagagtcat
     3061 cgacgactca ctccacacta tcagtaactt atgacgactt gactctagag tcgaatcgtc
     3121 gctttggcgt ttttttgacc gcggtgactc tagagtcaag tcacgagtcg aatcgccggt
     3181 gagtcgtccg gcgacttgcc ataacgtgat tgccggccgt cgacgaaccc gattcctgaa
     3241 cgtgctgaaa accggttttc cggctgcgcc ggcaacgctt cacggccacg caataaattg
     3301 cgtccccgtt caccgttttc ggatgggaag aacgccggaa acaggacttc ccctggctga
     3361 atggtgtcaa tttccgcgct atgcacttgt gcgcatactc atgcatgccg taaaaacaga
     3421 gcctgcgcgt ttctggcggg ttttcgggtg gtttgttgcc ttgtttaccg gtttcccgtc
     3481 agaaacgccc tgagggcatc tcaggcggtg ctgataacgg atgttatggt aaatgcaaat
     3541 ggttctggtg atgtgaaaaa gccgcctgaa aggtggcttt ttcatttttt agatagagtc
     3601 gaacggcatt tacgacacca gctttggtta gttgctcctg aggggggggg ccgttcttaa
     3661 tccgaatagt gccgatagag aaaactaacc atttgacaat aataaacacg gaatgtgact
     3721 taaagtccgt tgggttttga gtcaccaaat gcaattataa atttttttta cggatttaat
     3781 gtatgaatcc agaagatatc aaaaaagttt ttggtgaaaa cttaagacga atcagaatgg
     3841 agaaaaatat tagccaagag aatcttgcgt ttttatccgg aatggacagg acttacgtaa
     3901 gtgggataga gcgagggaag cggaatgtaa gtctggttaa cataaataaa atagcattgg
     3961 ctttgaatgt ggaaataaag gagctctttt aatggtggat ttcgttaaga aaatagatga
     4021 gttagcatct aaatataatg taagtcaaag gtctgtagtt tacaaatata tcgaaaaaaa
     4081 gactagagca tcaggcagag atagcaaagc taggcgttca cttggcaatt tatatgcgct
     4141 atatgttctt tgtgaagcat ataatgatgg ggcgaagggc gggacctcct tctctgtttt
     4201 aatgcagaga atgagagcgc ttccttttgg ttctaaactg caaaatcatc ctttggataa
     4261 tagattgaat gatgaggtaa gaagaagttt tttagtgcag gataatatgt tacctgtgca
     4321 aagtgcgaca gaaggaacag taaaaaaaag aataatttct attgattttc tttcagagtt
     4381 tggcatggat cccggttcat cttcattgtt tatcactaaa gcaattgatt tatatattga
     4441 cgaaataact gaaaaacaaa atgaattcct ttttaatatt gaaaactcga atggaaaaga
     4501 agggatattg aaatttattg aaaattcctt tagcccaaat gcagatgcta ggttgtttga
     4561 ggtcgtatcc ttttcagtgc taaaattata cttctctaaa aaaaatattg taataaatgg
     4621 aagagaggag ttcttccagc tgtttaaaac aggaaggact aatgctaatg atggtgggat
     4681 agattttgtt ttaaagccag taggaaggtt ttttcaagtg actgaggttt tagacttcaa
     4741 aaaatacttt ttagatttcg ataagacgaa taaattccct atgagttttg ttgttaaaac
     4801 ggatcttgat ccagaaggag ttatgaggtt aataaaggtt aatgcagaaa aaactatggg
     4861 cgaagaatta gcgaatagat attttggctt gtttgaagag gtttttactt taccgaccct
     4921 tagaaatatt gtaggagtga tatctgactc tcttgaggat cttgaagaac tcaagagagt
     4981 cattattgaa aactttaaat tagagtatgg ccttcttgac tagagggcag atcatcaatt
     5041 aacaaatcag aaatgtcatt atcatccccc ctgacattct tcgatttgtt ttttgtcttc
     5101 ctttttttta atttttctaa ttcttttggg gtgtaacttg aaggtatgtt taaccttctt
     5161 atgcccattt ttacatactc ttcgtttatt tctataccta taaatcttct atctagagac
     5221 ttagatacat ctcccgttgt aaagctacca gaaaaaggat ctaaaactac atcccctgga
     5281 tttgatgaag ctaaaacaat tctctttaga agagaaattg gtttttgcgt tgggtggttt
     5341 tcatattcct ccataaggaa tcttactcgg ggaaattccc aaacat
//
