LOCUS       NZ_CP059306             4163 bp    DNA     circular CON 10-JAN-2024
DEFINITION  Klebsiella pneumoniae strain Kp46596 plasmid pKp46596-6, complete
            sequence.
ACCESSION   NZ_CP059306
VERSION     NZ_CP059306.1
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 4163)
  AUTHORS   Chen,L.
  TITLE     Genome sequencing of Kp46564 and Kp46596
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 4163)
  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
            CP059306.1.
            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..4163
                     /organism="Klebsiella pneumoniae"
                     /mol_type="genomic DNA"
                     /strain="Kp46596"
                     /host="Homo sapiens"
                     /db_xref="taxon:573"
                     /plasmid="pKp46596-6"
                     /collection_date="2009"
                     /collected_by="CDI"
     gene            join(4034..4163,1..182)
                     /locus_tag="H1D28_RS00030"
                     /old_locus_tag="H1D28_00030"
     CDS             join(4034..4163,1..182)
                     /locus_tag="H1D28_RS00030"
                     /old_locus_tag="H1D28_00030"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_017134632.1"
                     /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_039817123.1"
                     /translation="MSNQNIFEILTSDPVSLNMWNLKSNLILAIHKTVRDNGWNQTEAA
                     AHLGISQPRVSNMLKGKLDKFSTDSLLEIMFKLGYKLDMQVHPSSEVILEMGMKKAML"
                     /name="helix-turn-helix transcriptional regulator"
     gene            complement(202..537)
                     /locus_tag="H1D28_RS00035"
                     /old_locus_tag="H1D28_00035"
     CDS             complement(202..537)
                     /locus_tag="H1D28_RS00035"
                     /old_locus_tag="H1D28_00035"
                     /inference="COORDINATES: protein motif:HMM:NF017757.4"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="type II toxin-antitoxin system RelE/ParE family
                     toxin"
                     /protein_id="WP_077255464.1"
                     /translation="MSASEMKEICLDVTGVDKELKSLPIDKALAFLHNLKLVAAGIEPE
                     LKVEHLKVVAPGVIELKINGSPAYRCVYTIKSPGKVIVLRVFKKTTNGPARKDLEVVKQ
                     RLKNLKI"
                     /name="type II toxin-antitoxin system RelE/ParE family
                     toxin"
     gene            1015..1275
                     /locus_tag="H1D28_RS00040"
                     /old_locus_tag="H1D28_00040"
     CDS             1015..1275
                     /locus_tag="H1D28_RS00040"
                     /old_locus_tag="H1D28_00040"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_010891192.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="protein L"
                     /protein_id="WP_072016306.1"
                     /translation="MAAYTEKTEQFLQRVTHTQTWWTSTYDPSDTVPVSGIYRCTVCGK
                     EITSNKNDPFPPQNHHQHSQKQNVKWQLIVRTDTNGDKFGN"
                     /name="protein L"
     gene            1366..1665
                     /locus_tag="H1D28_RS00045"
                     /old_locus_tag="H1D28_00045"
     CDS             1366..1665
                     /locus_tag="H1D28_RS00045"
                     /old_locus_tag="H1D28_00045"
                     /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_125564845.1"
                     /translation="MSNPPFEFVIRYHDLSPEQVRSFIDDAFHRVDLVLEKQLSDRPGF
                     FIPTCKSLTTNPSLSEIAIAVYNTYAVTEMIKDQLLRQSSNITLIKDIREIFVS"
                     /name="hypothetical protein"
     gene            complement(2562..2963)
                     /locus_tag="H1D28_RS00050"
                     /old_locus_tag="H1D28_00050"
     CDS             complement(2562..2963)
                     /locus_tag="H1D28_RS00050"
                     /old_locus_tag="H1D28_00050"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_009310048.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="transcriptional regulator"
                     /protein_id="WP_039817125.1"
                     /translation="MARVSISEASRLTGKSRTTLHRLIKAGDLSTCSGERNAKMVDTSE
                     LLRVFGPFEQPKSEHHSGQVSEQRDTASADQSEQVIRHLKQEIEHLNTLLLSKDSHIDS
                     LKQAMLLLENHQAKLTESPAPWWKFWKKS"
                     /name="transcriptional regulator"
     gene            complement(2963..3154)
                     /locus_tag="H1D28_RS00055"
                     /old_locus_tag="H1D28_00055"
     CDS             complement(2963..3154)
                     /locus_tag="H1D28_RS00055"
                     /old_locus_tag="H1D28_00055"
                     /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_000166328.1"
                     /translation="MTKQQKTALNMAKFIQNQSLLLLEKLNELDLDAEADLCEKLHDDA
                     EHLFRTLSSRLDALQDGN"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            3563..3676
                     /locus_tag="H1D28_RS28835"
     CDS             3563..3676
                     /locus_tag="H1D28_RS28835"
                     /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_072016307.1"
                     /translation="MHEPPVQSDCCALSGNYHLESNPVRHAKAPLAAAIGN"
                     /name="replication initiation protein"
     Typing          3203..3676
                     /name="ColRNAI_rep_cluster_1987"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="89.627"
                     /coverage="92.0"
                     /evalue="9.83e-170"
ORIGIN
        1 cggccgcaca tctaggcata agccaaccta gggttagcaa catgctgaaa gggaagctgg
       61 acaagttttc tacagattca ctactggaaa tcatgttcaa gctgggttac aaattagaca
      121 tgcaagtaca cccatcctct gaagtaattt tagagatggg catgaaaaag gcgatgctgt
      181 gaacatcgcc ttgagtggat actatatttt gagatttttc agccgttgct tcacgacttc
      241 taagtctttg cgtgcaggtc cgttagtcgt tttcttgaag acacgtaaca cgatcacctt
      301 gccgggtgat tttatcgtgt acacacaacg ataagcaggg ctaccattta tcttcaactc
      361 aatcacgcct ggagcaacta ctttcaggtg ttcaactttc agttctggtt caattccagc
      421 ggcaaccaac ttcaagttgt gcaaaaaagc taaagcttta tcaataggta aagactttag
      481 ctctttatca acaccagtta cgtctagaca aatctctttc atttcgcttg cggacatagt
      541 gtcctccttt gttggggttt agtggtcgaa caattaaatt tctcatttga tactccgatt
      601 aaaaaaacct cactaaaaaa ccaaacctct acgcctgatg agattcacca ggtagaggca
      661 tttaatttca gtggttcagg acactgcttt aggcaatatc cattgcatca atatactcta
      721 agttgtataa actaacaata tgccgcttcg cttgcgcatg ccgttagctc aataaataag
      781 ctatcagctg tttacgaaag taatcctcca tcgaagctaa aagtctccgt aaagcatcac
      841 aactgaaaga aggagttaag agatggcaga tagaagaccg ctaaacaaag atgtggtagt
      901 gccaaagcct ggtggcggaa cccagcccag agacagaaac aatgacggaa cggtgcgcaa
      961 aaaacgctca gacgcaggaa aaccaagaaa ataaacgata agaaaggtaa aagaatggct
     1021 gcatatacgg aaaaaacaga gcagttctta cagcgagtta cacacacaca gacttggtgg
     1081 acatcaacat acgatccaag cgatacagtt ccagtatcag gcatttatcg ctgtaccgta
     1141 tgcggtaaag agataactag taataaaaac gatcctttcc ccccacaaaa ccatcatcaa
     1201 catagtcaaa aacaaaatgt taaatggcag ctaattgtga ggacagacac aaacggtgat
     1261 aaatttggta actgagacac ggaagccctt cggggctttc cctcagtgat ttaccagaaa
     1321 gtctcattac tcactcgtac caaacaatcc acgatctgag gtcttatgtc taatccacct
     1381 tttgaatttg tcattcgtta tcatgacctg tctccagagc aagtgcggag ctttattgac
     1441 gatgcttttc atcgtgttga tctcgttcta gaaaaacagt tatccgatcg tccaggcttt
     1501 tttattccta catgtaagtc actaactact aatccgtctt tatctgaaat agctatcgct
     1561 gtttacaaca catatgccgt tactgaaatg ataaaggacc aattgcttcg acaatcttcc
     1621 aatatcactc tcattaaaga cataagagag atctttgtca gctaggatct tctctaccac
     1681 accacaagtg cttatctcat aacagcttat ttggccaaac aagactggcg cagagggagt
     1741 ttccgaacag gtcgccggga ggtggaccgc ttcgcacctc agcaggaaat ccatcagacc
     1801 aatcggggct ttttacatct atcatttaac ataaaggtat gattgtacgc accgctaaaa
     1861 cggcctcagg gcgtttctga cgggaaaccg gtaaaacagg caacaaacca cccgaaaacc
     1921 cgccagaaac gcgcaggctc tgtttttacg gcatgcatga gtatgcacgc aagtgcatag
     1981 cgcgaaaatt cacgccattc agccagggta agtcctgttt ccggcgttct tcccatccga
     2041 aaacggtgaa cggggacgca atttattgcg tggccgtgaa gcgttgccgg cgcagccgga
     2101 aaaccggttt tcagcacgtt caggaatcgg gttcgtcgac ggccggcaat cacgttatgg
     2161 caagtcgccg gacgactcac cacacgattc accggcgact cttcactaga gtcgtaccca
     2221 gagtcgtcac gtctaaaaaa caaccaaacg gggagtcggg tctagagtcg ggtcgttgtt
     2281 aacttattgt ttttatagtc ctgagtcgtt accgactcta tgacgactcg ccggggactc
     2341 tatgacgact cgtcatagag tcggatctgt ataaataaaa ttaaaaaaac gaaatttata
     2401 gaacgtaagc tgctgatata aaatacaaat ctgcaaaatt ttaattttgc gtggggtgtg
     2461 gatattttta gtggtgagga gcgttcagag atctggcgat ttttgggaag gttcaggaac
     2521 tccccgggat ggccggagag gaaaactgaa gcatgacggg gtcaggattt tttccagaat
     2581 ttccaccatg gcgccgggga ttcagttaat tttgcctggt gattttcaag aaggagcatg
     2641 gcctgtttca ggctatcaat gtgcgaatcc ttggacaaaa gtaaggtgtt caggtgttca
     2701 atctcctgtt tcagatgacg aatcacctgt tcactctggt cagcagaggc tgtatcacgc
     2761 tgttcagaga cctgtccaga atggtgttca ctcttcggtt gctcaaaggg accaaagaca
     2821 cgtaaaagct ctgaagtatc taccattttt gcattacgtt caccgctaca ggtggacagg
     2881 tcacctgctt taattaacct gtgcagtgtt gttctactct tacccgtcag tcgggaagcc
     2941 tcactaatag acactcgggc catcagttac catcctgtaa tgcatccagt ctcgaggaca
     3001 gtgtacggaa aagatgctcc gcatcatcgt ggagtttctc acaaaggtca gcctcagcat
     3061 cgagatcaag ctcgttaagc ttctccagca ggagcaggga ctgattctgg atgaacttag
     3121 ccatgttcag cgccgttttc tgttgtttcg tcataaaggg cctcagagcg tcagtgctca
     3181 atgtaaaacc ggtctctttt ccgcttcctc gctcactcag tcgctacgct cctaccgttc
     3241 ggctgcggcg agcggtcgca acgcacacat aagggcatag gacagacagc tcggaaagga
     3301 caacggaagg ccgcggcgtt gccgtttttc cataggctcc gcccccctga taagcatcac
     3361 aaaaacagac gctcaaatca gtggtggcga aacccgacag gactctaaag ataccaggcg
     3421 tttccccctg atggctccct cgtgcgctct cctgttcctg cctttcggtt taccggtgtc
     3481 attccgcagt tatggccgcg tttatctcat tccacgcctg acactcagtt ccgggtaggc
     3541 agttcgctcc aagctggact gtatgcacga accccccgtt cagtccgact gctgcgcctt
     3601 atccggtaac tatcatcttg agtccaaccc ggtaagacat gcaaaagcgc cactggcagc
     3661 agccattggt aactgattag aggagtgaag tcttgaaaag acacgtacta tacggctaca
     3721 ctgataaaac agatttggtg actgtgctcc tctaagccag ttacctcggt tcataaactt
     3781 gccggtttga tgaaccttga aaaaccgcct ccccaggcgg tttttctttt taaaacaaat
     3841 gaagactacg ctgacgacca agatccagtc aacaagtgtt gttagaatgc tttaaattta
     3901 caaataaaac cccatctaca tcttgtcatg catactgtaa cttgtataat ccgcaaactt
     3961 tagtgtaagc taataatcgt tcctattgtc ttgtgacaac taaatgctcg cattcagata
     4021 ggagatgaaa attatgagca atcaaaacat attcgaaata ctaacgagtg atccggtatc
     4081 cctaaacatg tggaacctga aatcaaacct gatcctcgcc atacataaga cggtaagaga
     4141 taacggctgg aaccaaacag agg
//
