LOCUS       NZ_CP059313             4167 bp    DNA     circular CON 10-JAN-2024
DEFINITION  Klebsiella pneumoniae strain Kp46564 plasmid pKp46564-4, complete
            sequence.
ACCESSION   NZ_CP059313
VERSION     NZ_CP059313.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN15578211
            Assembly: GCF_013694425.1
KEYWORDS    RefSeq.
SOURCE      Klebsiella pneumoniae
  ORGANISM  Klebsiella pneumoniae
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Klebsiella/Raoultella group; Klebsiella.
REFERENCE   1  (bases 1 to 4167)
  AUTHORS   Chen,L.
  TITLE     Genome sequencing of Kp46564 and Kp46596
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 4167)
  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 01:22:03
            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)                     :: 5,535
            CDSs (total)                      :: 5,411
            Genes (coding)                    :: 5,303
            CDSs (with protein)               :: 5,303
            Genes (RNA)                       :: 124
            rRNAs                             :: 9, 8, 8 (5S, 16S, 23S)
            complete rRNAs                    :: 9, 8, 8 (5S, 16S, 23S)
            tRNAs                             :: 88
            ncRNAs                            :: 11
            Pseudo Genes (total)              :: 108
            CDSs (without protein)            :: 108
            Pseudo Genes (ambiguous residues) :: 0 of 108
            Pseudo Genes (frameshifted)       :: 50 of 108
            Pseudo Genes (incomplete)         :: 52 of 108
            Pseudo Genes (internal stop)      :: 22 of 108
            Pseudo Genes (multiple problems)  :: 14 of 108
            CRISPR Arrays                     :: 1
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP059313.1.
            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..4167
                     /organism="Klebsiella pneumoniae"
                     /mol_type="genomic DNA"
                     /strain="Kp46564"
                     /host="Homo sapiens"
                     /db_xref="taxon:573"
                     /plasmid="pKp46564-4"
                     /collection_date="2010"
                     /collected_by="CDI"
     gene            join(3937..4167,1..885)
                     /locus_tag="H1D29_RS00005"
                     /old_locus_tag="H1D29_00005"
     CDS             join(3937..4167,1..885)
                     /locus_tag="H1D29_RS00005"
                     /old_locus_tag="H1D29_00005"
                     /inference="COORDINATES: ab initio prediction:GeneMarkS-2+"
                     /GO_function="GO:0005524 - ATP binding [Evidence IEA];
                     GO:0016887 - ATP hydrolysis activity [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GeneMarkS-2+."
                     /codon_start=1
                     /transl_table=11
                     /product="ATP-binding protein"
                     /protein_id="WP_012579087.1"
                     /translation="MIKEISLKNFKCFNELYLKQLKTLNIIAGKNNYGKTSILDAIFCF
                     YDVKNPAVLLNIQAFRKEMAEINKNKPFWVSYFHDMDTSQKMSIVIRDERSEVTQTYET
                     ETNQRLESSLSLNVDTVLSNQNIPRQTIGSQATVNSLKINVTETPNAKNRVSNKLFSMQ
                     LKEDGVEIKSEIKNERDGINYKFKTATIITTSRKINKEATITNVSSLLTQKRKKDILEN
                     LKKIDDRIVDIAISAIGNNKEIYLDIGFSELNEISMLGEGISRALSFISSVLVQENSII
                     LIDEIENGIHYSVIKDIIKSLISSAKQNNNQIFATTHSQDVIRAINEIDSKNEDIAYIR
                     LGREKNSLKPTAVQFNMDDFSYSVENDWEVR"
                     /name="ATP-binding protein"
     gene            885..1517
                     /locus_tag="H1D29_RS00010"
                     /old_locus_tag="H1D29_00010"
     CDS             885..1517
                     /locus_tag="H1D29_RS00010"
                     /old_locus_tag="H1D29_00010"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000804504.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="DUF3226 domain-containing protein"
                     /protein_id="WP_012579086.1"
                     /translation="MKDINNSKKIIFVEGDDDFHFLCNLLEIQGITDVFVEKINGKSKL
                     KQALRAFKNIDSFDEKESIFIILDADTSFSDTERSIIATLRELQISSPSSHNEIAMNGN
                     TKISFFIMPGKDKQGAIEDLIIEHASTRALYEYIIEFFEKIKNNKDDISASDKEYTYPT
                     NEKKAKVQVYLSCNRESDSRIGISMKNGIINTADNCFDEIKDFISKI"
                     /name="DUF3226 domain-containing protein"
     gene            1883..2125
                     /locus_tag="H1D29_RS00015"
                     /old_locus_tag="H1D29_00015"
     CDS             1883..2125
                     /locus_tag="H1D29_RS00015"
                     /old_locus_tag="H1D29_00015"
                     /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_098963735.1"
                     /translation="MHSAEIHTIQPGEVLFPAFFSSENGERGRNLLRGREALPAQPENR
                     FSAPSGIGFVDGRQSRYGKSPDDSPHDSPAIRIVN"
                     /name="hypothetical protein"
     gene            complement(2471..2872)
                     /locus_tag="H1D29_RS00020"
                     /old_locus_tag="H1D29_00020"
     CDS             complement(2471..2872)
                     /locus_tag="H1D29_RS00020"
                     /old_locus_tag="H1D29_00020"
                     /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_012579088.1"
                     /translation="MARVSISEAARLTGKSRTTLHRLIKAGDLSTCSGERNAKMVDTSE
                     LLRVFGPFEQPKGEHHSGQVSGQRDTASADQSEQVIRHLKQEIEHLNTLLLSKDSHIDS
                     LKQAMLLLENHQAKLTESPAPWWKFWKKS"
                     /name="helix-turn-helix domain-containing protein"
     gene            complement(2872..3063)
                     /locus_tag="H1D29_RS00025"
                     /old_locus_tag="H1D29_00025"
     CDS             complement(2872..3063)
                     /locus_tag="H1D29_RS00025"
                     /old_locus_tag="H1D29_00025"
                     /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_004187666.1"
                     /translation="MTKQQKTALNMAKFIQNQSLLLLEKLNELDLDVEADLCEKLHDDA
                     EHLFRTLSSRLDALQDGN"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            3479..3592
                     /locus_tag="H1D29_RS27515"
                     /pseudo=""
     CDS             3479..3592
                     /locus_tag="H1D29_RS27515"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_007772075.1"
                     /note="internal stop; Derived by automated computational
                     analysis using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="replication initiation protein"
                     /name="replication initiation protein"
     Typing          3185..3592
                     /name="ColRNAI_rep_cluster_1987"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="93.399"
                     /coverage="99.0"
                     /evalue="5.92e-171"
ORIGIN
        1 tttcatgata tggacacatc acaaaagatg tccatagtca ttcgagatga acgctctgaa
       61 gtaacacaaa catatgaaac agaaacaaat cagagattag aatcaagttt gtctctaaac
      121 gttgacaccg tactatctaa ccaaaacata cctcgtcaaa ctatcggttc tcaggccaca
      181 gtaaactctt taaaaataaa tgtgaccgag acacccaatg cgaaaaacag ggtttccaat
      241 aagcttttct ctatgcaatt gaaagaagat ggcgtagaaa taaaatccga aataaaaaac
      301 gaaagggatg ggattaatta taaatttaag acagcaacaa taataacaac atccagaaag
      361 ataaacaaag aggcaacaat tacaaatgta tctagcctac taacacaaaa aaggaaaaaa
      421 gacatactag aaaacttaaa aaaaatagat gacagaattg tagatatagc aatatctgcg
      481 ataggtaaca ataaggaaat atatttagac attggattta gtgagctaaa tgaaatatca
      541 atgcttggcg agggtatcag tcgagcatta tcttttatca gctcagtgct ggtacaggaa
      601 aactcaatta ttcttattga tgaaatcgag aacggaatac attactcagt aattaaagac
      661 ataataaaat cattaatttc atctgcaaaa caaaacaaca atcaaatatt tgcaacaact
      721 catagtcaag atgtgatacg agcaataaac gaaatagata gcaaaaatga agatatcgct
      781 tatattagac taggaagaga aaagaactcc ctaaaaccaa cagccgtaca attcaatatg
      841 gatgatttct cctactcagt tgagaacgac tgggaggtaa gataatgaaa gacataaata
      901 atagcaaaaa gatcattttc gttgagggtg atgatgattt tcattttcta tgcaacctac
      961 ttgaaataca aggcattacc gatgtttttg tcgaaaaaat aaatggaaaa tcaaaattaa
     1021 aacaagcact tagagcattc aaaaacattg attctttcga tgaaaaagaa agtattttta
     1081 ttatattaga tgctgacaca tcattttctg acacagaaag atcaataatt gccacattgc
     1141 gagaactaca aatctcctcc cccagctcgc ataacgagat agctatgaat ggcaatacaa
     1201 aaatttcttt ctttataatg ccaggaaaag acaagcaagg tgccattgaa gatctgataa
     1261 ttgaacacgc aagcactcga gcgttatatg aatacataat agaatttttc gaaaaaatta
     1321 aaaataataa agatgacatc tcagcgagtg acaaagagta cacttatcca acaaacgaaa
     1381 aaaaagctaa ggtacaagtc tatcttagct gcaatagaga atccgactca agaataggaa
     1441 tatccatgaa aaatggaata ataaacacag cagacaattg ctttgatgaa ataaaagatt
     1501 ttatttcaaa aatataaatc caaatcaagc cagcccttca cgggctggct tatcaccagg
     1561 gtgttattaa acgccggata acgtatagaa agcatcatac actttagtta tcagcaatct
     1621 caaacgtcct aaagacatca ccagatgcca aaacaatgat tgtgcagatc taatgtaaaa
     1681 gacccagcac aagatgctcc cttaagttat attctctcta ttcacttaaa acaatttaac
     1741 ataaaatcat aattgtacgc accgctaaaa cggactcagg acgtttctga cgggaaaccg
     1801 gtaaaacagg caacaaacca cccgaaaacc cgccagaaac gcgcaggctc tgtttttacg
     1861 gcatgcatga gtatgcgcgc aagtgcatag cgcggaaatt cacaccattc agccagggga
     1921 agtcctgttt ccggcgttct tctcctccga aaacggtgaa cggggacgca atttattgcg
     1981 tggccgtgaa gcgttgccgg cgcagccgga aaaccggttt tcagcacctt caggaatcgg
     2041 gttcgtcgac ggccggcaat cacgttatgg caagtcgccg gacgactcac cacacgattc
     2101 accggcgatt cgaatcgtga attgaatcaa gagtcaccat gagcaaaaaa cacccaaagt
     2161 gatgaattga atcaagagtc gattcatcat aacaatatga taataaagcg tgattcacat
     2221 atgaatcgtg ggcaattcgt cagcgattcg ccatagagtc gtccacgact tggatctgca
     2281 ctttgtaaca catcaccgca catttatttt tcattaaccc attgttgtaa ataaggaatc
     2341 tgcaaaattt taattttgcg tggggtgtgg gtatttttag tggtgaggag cgttcagaga
     2401 tctgacgatt tttgggaagg ttcaggaact ccctgggatg gccggagagg aaaactgaag
     2461 catgacgggg tcaggatttt ttccagaatt tccaccatgg cgccggggat tcagttaatt
     2521 ttgcctggtg attttcaaga aggagcatgg cctgtttcag gctgtcaatg tgcgaatcct
     2581 tggacaaaag taaggtgttc aggtgttcaa tctcctgttt cagatgacgg atcacctgtt
     2641 cactctggtc agcagaggct gtatcacgct gtccagagac ctgtccagaa tggtgttcac
     2701 ccttcggttg ctcaaagggg ccaaagacac gtaaaagctc tgaagtatct accatttttg
     2761 cattgcgctc accgctacag gtggacaggt cacctgcttt aattaacctg tgcagtgttg
     2821 ttctactctt acccgtcagt cgggcagcct cactaataga cactctggcc atcagttacc
     2881 atcctgtaat gcatccagtc tcgaggacag tgtacggaaa agatgctccg catcatcgtg
     2941 gagtttctca caaaggtcgg cctcgacatc gagatcaagc tcgttaagct tctccagcag
     3001 gagcagagac tgattctgga tgaatttagc catgttcagc gctgttttct gttgtttcgt
     3061 cataagaggc ctcagagcgt cagtggtcag tgtagggatc tcctcttttc cgcttcctcg
     3121 ctcactcagt cgctacgctc ctgccgttcg gctgcggcga gcggcaggag catgcgtaga
     3181 aacgctcgag aaaaccgagt aatcgcatgg aggaaagaag gaaaggccgc acagcggccg
     3241 tttttccata ggctccgccc ccctgacgag catcacggaa tctgacgctc aaatcagtgg
     3301 tggcgaaacc cgacaggact ataaagatac caggcgtttc cccctgatgg ctccctcgtg
     3361 cgctctcctg ttcctgcctt tcggtttacc ggtgtcattc cgctgttatg gccgcgtttg
     3421 tctcattcca cgcctgacac tcagttccgg gtaggcagtt cgctccaagc tggactgtat
     3481 gcacgaaccc cccgttcagt ccgactgctg cgcctaatcc ggtaactatc gtcttgagtc
     3541 caacccggaa agacacgaca aagcgccact ggcagcagcc actggtaact gatttaggga
     3601 gttagtcttg aagttatacg ccagttaaag ctaaactaaa cgaacagttt tggtgactgc
     3661 gctcccttta agccagttac ctcggttcat agagcgccaa ctctactgaa cctttcgaaa
     3721 aaaccgcccg ccaaggcggt ttttttcgtt cacagccgga agcttacggc tgctgccaga
     3781 taatctcaag aagaaagtaa aaaaaatcga ttaaaacaca agcaatcaaa gttaatcttt
     3841 gacataaagt ctagctaatc acaatgaaag ctgtacattt tattaaggta ctaacaaatc
     3901 gtatggcata taacaaaaac acgaacagag gctatcatga taaaggaaat aagtttaaag
     3961 aacttcaaat gcttcaatga gctatatcta aagcaattaa agactttaaa tatcatagct
     4021 gggaaaaaca actacgggaa aacatctata ctggatgcta ttttttgttt ttatgatgta
     4081 aaaaacccgg ctgttttgtt aaacattcaa gcattcagaa aagaaatggc agaaataaac
     4141 aaaaacaagc cattttgggt tagttac
//
