LOCUS       NZ_CP059308             4936 bp    DNA     circular CON 10-JAN-2024
DEFINITION  Klebsiella pneumoniae strain Kp46596 plasmid pKp46596-4, complete
            sequence.
ACCESSION   NZ_CP059308
VERSION     NZ_CP059308.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN15578212
            Assembly: GCF_013694405.1
KEYWORDS    RefSeq.
SOURCE      Klebsiella pneumoniae
  ORGANISM  Klebsiella pneumoniae
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Klebsiella/Raoultella group; Klebsiella.
REFERENCE   1  (bases 1 to 4936)
  AUTHORS   Chen,L.
  TITLE     Genome sequencing of Kp46564 and Kp46596
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 4936)
  AUTHORS   Chen,L.
  TITLE     Direct Submission
  JOURNAL   Submitted (19-JUL-2020) HMH-CDI, Hackensack-Meridian Health Center
            for Discovery and Innovation, 340 Kingsland Street, Building 102,
            Nutley, NJ 07110, USA
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Date                     :: 01-SEP-2019
            Assembly Method                   :: Unicycler v. v0.4.8
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 100x
            Sequencing Technology             :: Oxford Nanopore MiniION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 01/10/2024 01:29:58
            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)                     :: 5,730
            CDSs (total)                      :: 5,608
            Genes (coding)                    :: 5,473
            CDSs (with protein)               :: 5,473
            Genes (RNA)                       :: 122
            rRNAs                             :: 9, 8, 8 (5S, 16S, 23S)
            complete rRNAs                    :: 9, 8, 8 (5S, 16S, 23S)
            tRNAs                             :: 86
            ncRNAs                            :: 11
            Pseudo Genes (total)              :: 135
            CDSs (without protein)            :: 135
            Pseudo Genes (ambiguous residues) :: 0 of 135
            Pseudo Genes (frameshifted)       :: 57 of 135
            Pseudo Genes (incomplete)         :: 79 of 135
            Pseudo Genes (internal stop)      :: 22 of 135
            Pseudo Genes (multiple problems)  :: 18 of 135
            CRISPR Arrays                     :: 1
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP059308.1.
            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..4936
                     /organism="Klebsiella pneumoniae"
                     /mol_type="genomic DNA"
                     /strain="Kp46596"
                     /host="Homo sapiens"
                     /db_xref="taxon:573"
                     /plasmid="pKp46596-4"
                     /collection_date="2009"
                     /collected_by="CDI"
     gene            join(4562..4936,1..531)
                     /locus_tag="H1D28_RS00085"
                     /old_locus_tag="H1D28_00085"
     CDS             join(4562..4936,1..531)
                     /locus_tag="H1D28_RS00085"
                     /old_locus_tag="H1D28_00085"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001697689.1"
                     /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_019725130.1"
                     /translation="MHNAALELFNERLPHKPYFSDDLHFGVRIAGKERAILAKYIQFNQ
                     PHAMFWLGFDVDRAGSSIDWSDRNAPAPTLTITNPENGHAHLLYALENSIRTAPDGKIK
                     PLRYAASVENALRKKLEADAGYSGLICKNPNHNHWKIAVWQPKLYTLDWLADFLDLNTG
                     NDKEIVADYGLGRNCTLFDKTRKWAYRAIRQGWPEYEQWLQACYERACAYNLQFARPLD
                     ENEVRGIAKSIAKWTSNKFSPEEFSKFVDITHSSEIQSKRGKKSGQSRRKGSLEEIKPW
                     VAMGISRRKYFYIKKNGEIR"
                     /name="replication initiation protein"
     gene            528..1235
                     /locus_tag="H1D28_RS00090"
                     /old_locus_tag="H1D28_00090"
     CDS             528..1235
                     /locus_tag="H1D28_RS00090"
                     /old_locus_tag="H1D28_00090"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001258875.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_004198042.1"
                     /translation="MKTFVTLWTIVFLAFIAVMCTVDISNYIPSVYTVFSKNRPLVTGA
                     LSILLISVFIWLMVSLYLLKKYSVKVEKLSLGGVNILFNESATLYKKSVKNHLDSKRAI
                     FKLRKNVDAFDEVISSYYQTYQFIRDEMKILNPKKDREIYDFSNEMLMVLNRFLTNYQN
                     NYKRWYKYISDKDEVVDRVSGDVMRFHATSINKIQMQYYDYERILKGFKDVNRFFVNDV
                     KPKFGINTDKWNW"
                     /name="hypothetical protein"
     gene            complement(1272..1886)
                     /locus_tag="H1D28_RS00095"
                     /old_locus_tag="H1D28_00095"
     CDS             complement(1272..1886)
                     /locus_tag="H1D28_RS00095"
                     /old_locus_tag="H1D28_00095"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_012822468.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="TIR domain-containing protein"
                     /protein_id="WP_019725132.1"
                     /translation="MGKHKVFISYHHANDQYYKNALEKMNEEHEIFVNRSVSLGDIDED
                     EAPQKIREIIRDEYLRDTSVLILLVGTETKNRKHVDWELYSSMRDSTINKKSGILVVNL
                     PSTNTTYIRSTHGTNEKSEVHPTVTEWFSIDKRSTYEERFPYMPARIIDNFMKSGSYIS
                     VVNWNQIENNPETLRKLIDMTYNDREKATYDMSREMRMHNS"
                     /name="TIR domain-containing protein"
     gene            2212..2613
                     /locus_tag="H1D28_RS00100"
                     /old_locus_tag="H1D28_00100"
     CDS             2212..2613
                     /locus_tag="H1D28_RS00100"
                     /old_locus_tag="H1D28_00100"
                     /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_045328244.1"
                     /translation="MTRVSISEAARLTGKSRTTLHRLIKTGELSTCSGERNKKMVDISE
                     LLRVFGPFDQPKNEHLTRQVPEQRDTAPADQSEHVIRQLKQQIEHLNILILSKDSHIDS
                     LKQAMLLLENHQAKLTEPPAPWWKFWKKS"
                     /name="helix-turn-helix domain-containing protein"
     gene            complement(3415..3576)
                     /locus_tag="H1D28_RS00105"
                     /old_locus_tag="H1D28_00105"
     CDS             complement(3415..3576)
                     /locus_tag="H1D28_RS00105"
                     /old_locus_tag="H1D28_00105"
                     /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_162870772.1"
                     /translation="MAKHWSGQECPKTGTYGQYHDTDNSYAGSEYDRHVSKGDKFPPSK
                     NNHHFQEK"
                     /name="hypothetical protein"
     gene            3813..4058
                     /locus_tag="H1D28_RS00110"
                     /old_locus_tag="H1D28_00110"
     CDS             3813..4058
                     /locus_tag="H1D28_RS00110"
                     /old_locus_tag="H1D28_00110"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_012848468.1"
                     /GO_component="GO:0110001 - toxin-antitoxin complex
                     [Evidence IEA]"
                     /GO_function="GO:0003677 - DNA binding [Evidence IEA];
                     GO:0097351 - toxin sequestering activity [Evidence IEA]"
                     /GO_process="GO:0045927 - positive regulation of growth
                     [Evidence IEA]; GO:0006355 - regulation of DNA-templated
                     transcription [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="type II toxin-antitoxin system Phd/YefM family
                     antitoxin"
                     /protein_id="WP_025987695.1"
                     /translation="MHAINFTDARKHFAETMKRVTDDAEPVRVMRRDAPDIVMIDAGEY
                     EALIETVYLFSNPANAEHINESMKQAERGEFVEVEY"
                     /name="type II toxin-antitoxin system Phd/YefM family
                     antitoxin"
     gene            4039..4314
                     /locus_tag="H1D28_RS00115"
                     /old_locus_tag="H1D28_00115"
     CDS             4039..4314
                     /locus_tag="H1D28_RS00115"
                     /old_locus_tag="H1D28_00115"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_017412855.1"
                     /GO_process="GO:0008219 - cell death [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="Txe/YoeB family addiction module toxin"
                     /protein_id="WP_019725129.1"
                     /translation="MSKWNIKFTRNGADDLNYWRDTDKKKFERIRQLLLSIEADPLTGI
                     GKPERLRHHKDPALYSRRIDQSHRLVYSIQNGEIIIYAARYHYGDK"
                     /name="Txe/YoeB family addiction module toxin"
ORIGIN
        1 tattcggggc tcatctgcaa aaatccgaac cacaaccact ggaaaatcgc cgtgtggcaa
       61 ccgaagctct acactctgga ctggctggcc gactttctcg atctgaacac agggaatgac
      121 aaggaaatcg ttgccgacta cggcttaggt cgtaactgca cgttgttcga caaaacccgt
      181 aagtgggcat atcgcgccat ccgtcagggc tggcctgagt atgagcagtg gctgcaagcc
      241 tgctacgaac gcgcttgcgc atacaacctg caatttgcac ggcctctgga tgaaaatgag
      301 gtaagaggga tagctaagag cattgctaaa tggacatcaa ataaattttc acctgaagaa
      361 ttcagtaaat ttgttgatat tactcattcc tctgaaattc aatcaaagag agggaaaaag
      421 tcagggcagt caaggaggaa aggaagccta gaggaaataa aaccttgggt agctatggga
      481 ataagcaggc ggaagtattt ttatatcaag aaaaatggtg aaataagatg aaaaccttcg
      541 taactctttg gactatagtt tttttagcat ttattgccgt gatgtgtact gttgatatat
      601 ctaattacat tccgtctgtt tacacagttt ttagtaagaa tagacctctt gtaactggcg
      661 ccctttctat tcttttgata tctgttttta tttggctgat ggtatccctc tacttactta
      721 aaaagtattc ggttaaggtt gagaaactta gccttggtgg agtgaatata cttttcaatg
      781 agagtgctac actttacaaa aagagtgtaa aaaatcacct agattcaaaa agagcaattt
      841 tcaaattaag aaaaaacgtt gatgcctttg atgaggttat ttcatcatat tatcagactt
      901 accaatttat tcgtgatgaa atgaaaatac taaaccctaa aaaagatcgt gagatttatg
      961 atttcagcaa tgagatgctc atggtgttaa atagatttct aactaactac cagaacaact
     1021 acaagcgttg gtataagtac atatcagaca aagatgaggt tgttgatagg gttagcggtg
     1081 atgtcatgag atttcatgca accagcataa ataaaataca aatgcagtat tatgattatg
     1141 agcgtatttt aaaaggtttt aaagatgtta accggttctt tgttaatgat gtgaagccta
     1201 agtttggaat caatacagat aagtggaact ggtaaattaa aggagtagcc aaggctactc
     1261 cttggatagt actatgaatt atgcattctc atttctctcg acatatcata cgttgctttt
     1321 tctctatcgt tataagtcat gtctattaat tttctgagtg tttctgggtt gttttctatt
     1381 tgattccagt tgaccactga tatataagac ccgctcttca tgaagttgtc tattattctt
     1441 gctggcatat atgggaacct ttcctcataa gttgagcgct tatcaataga aaaccattca
     1501 gttacggtag gatgaacttc tgatttttca ttagttccat gtgttgaacg aatgtacgta
     1561 gtatttgttg acgggagatt gacgactaaa attcctgatt ttttgttaat ggtactatct
     1621 ctcatgctag agtaaagttc ccaatctacg tgttttctgt tttttgtttc agttccaaca
     1681 agaaggataa gaactgatgt atctctaaga tattcatctc ttattatctc tcttattttt
     1741 tgtggggctt catcttcatc tatatcacct aatgatactg agcgattcac gaatatttca
     1801 tgttcctcat tcattttttc aagtgcgttt ttgtagtact gatcattcgc atggtggtag
     1861 ctaatgaata ccttatgctt tcccattttt attgtccttt ttttgtttgt gtgcactcta
     1921 ttttgcactt gaacctatat cagataacag ctctctttta gagagctctt tttttctcag
     1981 ccagcacaca tagggtccct tcagcaaggt ctcaccatga ctggtttagg gcgggctcgt
     2041 tgaacgtagt gagcgaatgc gcgaggaagc ggaaagtcat ttgttgcctg cattttgcac
     2101 ggtcactcct gtgtttcatc gcccttccga aaaacacatc acttctggac cagtatgtcg
     2161 taagctggcc cctgtttcct tgagactgaa tgtattaaag gatgataact gatgaccaga
     2221 gtgtctatta gtgaggctgc acggctgacg ggtaagagcc ggacaacgct gcacaggtta
     2281 atcaaaacag gtgaactgtc cacttgtagc ggtgaacgaa ataaaaaaat ggtcgatata
     2341 tcagagcttt tacgtgtttt cggaccgttt gaccaaccga agaatgaaca ccttactcga
     2401 caagtacctg aacagcgtga tacagcgcct gctgaccaga gtgaacatgt cattcgtcaa
     2461 ctgaaacagc agattgaaca ccttaacata ttgattttat ccaaggattc gcacattgac
     2521 agcctgaaac aggccatgct ccttcttgaa aatcaccagg caaaattaac tgaacccccg
     2581 gcgccgtggt ggaaattctg gaaaaaatcc tgaccccgtc atgcttcagt tttcctctcc
     2641 ggccattccg gggagttcct gaaccttccc gaaaatcgtc agatctctga acgctcctca
     2701 ccacgaaaaa tacccacacc ccacgcaaaa ttaaaatttt gcagatttgt atttaatatc
     2761 agcagcttac tttactgaaa tttcgttttt taaattttat ttatatagat ccgactctat
     2821 gacgactcgt catagagtcc ccggcgagtc gtcatagagt cggtaacgac tcaggcctat
     2881 aaaaacaatg agttaataac gacccgactc tagatccgac tccccgtttg gttgtttttt
     2941 agacgcggcg actctgggta cgactctagt gaagagtcgc cggtgaatcg tgtggtgagt
     3001 cgtccggcga cttgccataa cgtgattgcc ggccgtcgac gaaccggatt cctgaacgtg
     3061 ctgaaaaccg gttttccggc tgcgccggca acgcttcacg gccacgcaat aaattgcgtc
     3121 cccgttcacc gttttcggat gggaagaacg ccggaaacag gacttcccct ggctgaatgg
     3181 tgtcaatttc cgcgctatgc acttgtgcgc atactcatgc atgccgtaaa aacagagcct
     3241 gcgcgtttct ggcgggtttt cgggtggttt gttgccttgt tttaccggtt tcccgtcaga
     3301 aacgccctga gggcctctca ggcggtgctg ataacggatg ttatggtaaa tcaagtgaat
     3361 ggcaggtaca aaaaaagccc cagagggctt ttagtttaga cttctgaaga tattttattt
     3421 ttcttggaag tggtggttgt ttttgctcgg agggaactta tcacccttgc tcacatggcg
     3481 atcatattca gaaccagcgt atgagttgtc ggtatcatga tattgaccgt aagtacctgt
     3541 ttttggacat tcttgcccag accaatgttt tgccatttac ttttcctttg ctcgttttag
     3601 gagctaagct cctagcggta cgaaattgtg ccgcacttca taaatgtaat tgcttgaaat
     3661 tatgcttcaa tgtattgact tgttgttttt gtggttattc gattgagttc acattttgag
     3721 ctgatttggt tgtgggtttt tagggaaata tctttatgta cttatttgcg tacatgttct
     3781 atgctaagcc ccaacaaatg ggggttaaca acatgcatgc aatcaatttt actgatgccc
     3841 gtaaacattt tgccgagacg atgaagcgcg tcactgatga tgctgaaccg gtacgtgtca
     3901 tgcgccgtga tgcgcctgat attgttatga tcgatgcggg agagtatgag gcgctaatcg
     3961 aaacggtcta tctgttcagc aatccggcga acgcagagca tatcaatgag tcaatgaaac
     4021 aggcggagcg cggcgaattt gtcgaagtgg aatattaagt tcactaggaa tggcgctgat
     4081 gaccttaact actggcgtga tactgacaaa aagaagtttg agcgtatccg gcaactgttg
     4141 ctcagcatcg aggctgatcc gctgacaggt ataggaaaac ccgaacggct gcggcaccac
     4201 aaagatccgg cactctactc ccgcaggatt gatcagagcc accgtctggt ctattcaatc
     4261 cagaacggag aaatcatcat ctacgcagcc cgttatcact atggtgacaa atagcaaaag
     4321 tcgatatagc ccgcttgatg cgagcttttc atgcaaggcg tacaacggat gttagggtaa
     4381 gtcgctgtca gatcgacaca aaggcaaagt cggtgtaacg ttagcctcag aaaaaacaaa
     4441 gccccggaaa tcatgtcata tcttggcgga tcgcatgata accagggcta ggtcgaaacc
     4501 ttgaaaggat attagcacat gaaccgtgcc agacaacagc ccgccataag cgcagggcac
     4561 attgcataac gccgcactcg aacttttcaa cgaacgctta ccacacaagc cgtacttttc
     4621 ggacgatctg cactttggtg tccgtatcgc cggtaaggaa cgcgctattc tggcgaaata
     4681 tatccagttc aatcagcctc acgccatgtt ctggctggga tttgacgttg accgcgccgg
     4741 ttcctccatc gactggagcg accgcaacgc gcctgcaccg acgctgacca taactaaccc
     4801 cgaaaacgga cacgcgcacc tgctgtacgc gctggaaaac tcgatacgca ccgcgccgga
     4861 cggcaaaata aaaccgttac gctacgccgc ctccgtggag aatgcgctac gtaaaaaatt
     4921 agaggctgac gctgga
//
