LOCUS       NZ_CP070894             4167 bp    DNA     circular CON 10-JUN-2024
DEFINITION  Klebsiella pneumoniae strain KP-135LU plasmid pKP-135LU_ColE2,
            complete sequence.
ACCESSION   NZ_CP070894
VERSION     NZ_CP070894.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN15437788
            Assembly: GCF_022369815.1
KEYWORDS    RefSeq.
SOURCE      Klebsiella pneumoniae
  ORGANISM  Klebsiella pneumoniae
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Klebsiella/Raoultella group; Klebsiella.
REFERENCE   1  (bases 1 to 4167)
  AUTHORS   Di Pilato,V., Henrici De Angelis,L., Aiezza,N., Baccani,I.,
            Niccolai,C., Parisio,E.M., Giordano,C., Camarlinghi,G., Barnini,S.,
            Forni,S., Righi,L., Mechi,M.T., Giani,T., Antonelli,A. and
            Rossolini,G.M.
  TITLE     Resistome and virulome accretion in an NDM-1-producing ST147
            sublineage of Klebsiella pneumoniae associated with an outbreak in
            Tuscany, Italy: a genotypic and phenotypic characterisation
  JOURNAL   Lancet Microbe 3 (3), e224-e234 (2022)
REFERENCE   2  (bases 1 to 4167)
  AUTHORS   Di Pilato,V., Henrici De Angelis,L., Aiezza,N., Baccani,I.,
            Niccolai,C., Giani,T., Antonelli,A. and Rossolini,G.M.
  TITLE     Direct Submission
  JOURNAL   Submitted (21-FEB-2021) Department of Surgical Sciences and
            Integrated Diagnostics (DISC), University of Genoa, V. Benedetto XV,
            6, Genoa, Italy 16132, Italy
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: Unicycler v. 0.4.8
            Assembly Name                     :: KP-135LU
            Genome Representation             :: Full
            Expected Final Version            :: No
            Genome Coverage                   :: 270.0x
            Sequencing Technology :: Illumina MiSeq; Oxford Nanopore MinION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_022369815.1-RS_2024_06_10
            Annotation Date                   :: 06/10/2024 04:24:48
            Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline
            (PGAP)
            Annotation Method :: Best-placed reference protein set; GeneMarkS-2+
            Annotation Software revision      :: 6.7
            Features Annotated                :: Gene; CDS; rRNA; tRNA; ncRNA
            Genes (total)                     :: 5,790
            CDSs (total)                      :: 5,668
            Genes (coding)                    :: 5,528
            CDSs (with protein)               :: 5,528
            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)              :: 140
            CDSs (without protein)            :: 140
            Pseudo Genes (ambiguous residues) :: 0 of 140
            Pseudo Genes (frameshifted)       :: 62 of 140
            Pseudo Genes (incomplete)         :: 86 of 140
            Pseudo Genes (internal stop)      :: 26 of 140
            Pseudo Genes (multiple problems)  :: 29 of 140
            CRISPR Arrays                     :: 1
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP070894.1.
            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="KP-135LU"
                     /isolation_source="blood"
                     /host="Homo sapiens"
                     /db_xref="taxon:573"
                     /plasmid="pKP-135LU_ColE2"
                     /geo_loc_name="Italy: Lucca"
                     /lat_lon="43.843435 N 10.533636 E"
                     /collection_date="2019-07-05"
                     /collected_by="Diagnostic Microbiology and Virology Unit,
                     Lucca"
     gene            join(3694..4167,1..159)
                     /locus_tag="HZC98_RS28850"
                     /old_locus_tag="HZC98_28730"
     CDS             join(3694..4167,1..159)
                     /locus_tag="HZC98_RS28850"
                     /old_locus_tag="HZC98_28730"
                     /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            525..767
                     /locus_tag="HZC98_RS28855"
                     /old_locus_tag="HZC98_28735"
     CDS             525..767
                     /locus_tag="HZC98_RS28855"
                     /old_locus_tag="HZC98_28735"
                     /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(1113..1514)
                     /locus_tag="HZC98_RS28860"
                     /old_locus_tag="HZC98_28740"
     CDS             complement(1113..1514)
                     /locus_tag="HZC98_RS28860"
                     /old_locus_tag="HZC98_28740"
                     /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(1514..1705)
                     /locus_tag="HZC98_RS28865"
                     /old_locus_tag="HZC98_28745"
     CDS             complement(1514..1705)
                     /locus_tag="HZC98_RS28865"
                     /old_locus_tag="HZC98_28745"
                     /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            2121..2234
                     /locus_tag="HZC98_RS28870"
                     /old_locus_tag="HZC98_28750"
                     /pseudo=""
     CDS             2121..2234
                     /locus_tag="HZC98_RS28870"
                     /old_locus_tag="HZC98_28750"
                     /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"
     gene            2579..3694
                     /locus_tag="HZC98_RS28875"
                     /old_locus_tag="HZC98_28755"
     CDS             2579..3694
                     /locus_tag="HZC98_RS28875"
                     /old_locus_tag="HZC98_28755"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_019405083.1"
                     /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: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="ATP-binding protein"
                     /protein_id="WP_239739055.1"
                     /translation="MIKEISLKNFKCFNELYLKQLKTLNIIAGKNNYGKTSILDAIFCF
                     YDVKNPAVLLNIQAFRKEMAEINKNKPFWVSYFHDMDTSQKMSIVIRDERSEVTQTYET
                     ETNQRLESSLSLNVDTVLSNQNIPRQTIGSQATVNSLKINMTETPNAKNRVSNKLFSMQ
                     LKEDGVEIKSEIKNERDGINYKFKTATIITTSRKINKEATITNVSSLLTQKRKKDILEN
                     LKKIDDRIVDIAISAIGNNKEIYLDIGFSELNEISMLGEGISRALSFISSVLVQENSII
                     LIDEIENGIHYSVIKDIIKSLISSAKQNNNQIFATTHSQDVIRAINEIDSKNEDIAYIR
                     LGREKNSLKPTAVQFNMDDFSYSVENDWEVR"
                     /name="ATP-binding protein"
     Typing          1827..2234
                     /name="ColRNAI_rep_cluster_1987"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="93.399"
                     /coverage="99.0"
                     /evalue="5.92e-171"
ORIGIN
        1 tacacttatc caacaaacga aaaaaaagct aaggtacaag tctatcttag ctgcaataga
       61 gaatccgact caagaatagg aatatccatg aaaaatggaa taataaacac agcagacaat
      121 tgctttgatg aaataaaaga ttttatttca aaaatataaa tccaaatcaa gccagccctt
      181 cacgggctgg cttatcacca gggtgttatt aaacgccgga taacgtatag aaagcatcat
      241 acactttagt tatcagcaat ctcaaacgtc ctaaagacat caccagatgc caaaacaatg
      301 attgtgcaga tctaatgtaa aagacccagc acaagatgct cccttaagtt atattctctc
      361 tattcactta aaacaattta acataaaatc ataattgtac gcaccgctaa aacggactca
      421 ggacgtttct gacgggaaac cggtaaaaca ggcaacaaac cacccgaaaa cccgccagaa
      481 acgcgcaggc tctgttttta cggcatgcat gagtatgcgc gcaagtgcat agcgcggaaa
      541 ttcacaccat tcagccaggg gaagtcctgt ttccggcgtt cttctcctcc gaaaacggtg
      601 aacggggacg caatttattg cgtggccgtg aagcgttgcc ggcgcagccg gaaaaccggt
      661 tttcagcacc ttcaggaatc gggttcgtcg acggccggca atcacgttat ggcaagtcgc
      721 cggacgactc accacacgat tcaccggcga ttcgaatcgt gaattgaatc aagagtcacc
      781 atgagcaaaa aacacccaaa gtgatgaatt gaatcaagag tcgattcatc ataacaatat
      841 gataataaag cgtgattcac atatgaatcg tgggcaattc gtcagcgatt cgccatagag
      901 tcgtccacga cttggatctg cactttgtaa cacatcaccg cacatttatt tttcattaac
      961 ccattgttgt aaataaggaa tctgcaaaat tttaattttg cgtggggtgt gggtattttt
     1021 agtggtgagg agcgttcaga gatctgacga tttttgggaa ggttcaggaa ctccctggga
     1081 tggccggaga ggaaaactga agcatgacgg ggtcaggatt ttttccagaa tttccaccat
     1141 ggcgccgggg attcagttaa ttttgcctgg tgattttcaa gaaggagcat ggcctgtttc
     1201 aggctgtcaa tgtgcgaatc cttggacaaa agtaaggtgt tcaggtgttc aatctcctgt
     1261 ttcagatgac ggatcacctg ttcactctgg tcagcagagg ctgtatcacg ctgtccagag
     1321 acctgtccag aatggtgttc acccttcggt tgctcaaagg ggccaaagac acgtaaaagc
     1381 tctgaagtat ctaccatttt tgcattgcgc tcaccgctac aggtggacag gtcacctgct
     1441 ttaattaacc tgtgcagtgt tgttctactc ttacccgtca gtcgggcagc ctcactaata
     1501 gacactctgg ccatcagtta ccatcctgta atgcatccag tctcgaggac agtgtacgga
     1561 aaagatgctc cgcatcatcg tggagtttct cacaaaggtc ggcctcgaca tcgagatcaa
     1621 gctcgttaag cttctccagc aggagcagag actgattctg gatgaattta gccatgttca
     1681 gcgctgtttt ctgttgtttc gtcataagag gcctcagagc gtcagtggtc agtgtaggga
     1741 tctcctcttt tccgcttcct cgctcactca gtcgctacgc tcctgccgtt cggctgcggc
     1801 gagcggcagg agcatgcgta gaaacgctcg agaaaaccga gtaatcgcat ggaggaaaga
     1861 aggaaaggcc gcacagcggc cgtttttcca taggctccgc ccccctgacg agcatcacgg
     1921 aatctgacgc tcaaatcagt ggtggcgaaa cccgacagga ctataaagat accaggcgtt
     1981 tccccctgat ggctccctcg tgcgctctcc tgttcctgcc tttcggttta ccggtgtcat
     2041 tccgctgtta tggccgcgtt tgtctcattc cacgcctgac actcagttcc gggtaggcag
     2101 ttcgctccaa gctggactgt atgcacgaac cccccgttca gtccgactgc tgcgcctaat
     2161 ccggtaacta tcgtcttgag tccaacccgg aaagacacga caaagcgcca ctggcagcag
     2221 ccactggtaa ctgatttagg gagttagtct tgaagttata cgccagttaa agctaaacta
     2281 aacgaacagt tttggtgact gcgctccctt taagccagtt acctcggttc atagagcgcc
     2341 aactctactg aacctttcga aaaaaccgcc cgccaaggcg gtttttttcg ttcacagccg
     2401 gaagcttacg gctgctgcca gataatctca agaagaaagt aaaaaaaatc gattaaaaca
     2461 caagcaatca aagttaatct ttgacataaa gtctagctaa tcacaatgaa agctgtacat
     2521 tttattaagg tactaacaaa tcgtatggca tataacaaaa acacgaacag aggctatcat
     2581 gataaaggaa ataagtttaa agaacttcaa atgcttcaat gagctatatc taaagcaatt
     2641 aaagacttta aatatcatag ctgggaaaaa caactacggg aaaacatcta tactggatgc
     2701 tattttttgt ttttatgatg taaaaaaccc ggctgttttg ttaaacattc aagcattcag
     2761 aaaagaaatg gcagaaataa acaaaaacaa gccattttgg gttagttact ttcatgatat
     2821 ggacacatca caaaagatgt ccatagtcat tcgagatgaa cgctctgaag taacacaaac
     2881 atatgaaaca gaaacaaatc agagattaga atcaagtttg tctctaaacg ttgacaccgt
     2941 actatctaac caaaacatac ctcgtcaaac tatcggttct caggccacag taaactcttt
     3001 aaaaataaat atgaccgaga cacccaatgc gaaaaacagg gtttccaata agcttttctc
     3061 tatgcaattg aaagaagatg gcgtagaaat aaaatccgaa ataaaaaacg aaagggatgg
     3121 gattaattat aaatttaaga cagcaacaat aataacaaca tccagaaaga taaacaaaga
     3181 ggcaacaatt acaaatgtat ctagcctact aacacaaaaa aggaaaaaag acatactaga
     3241 aaacttaaaa aaaatagatg acagaattgt agatatagca atatctgcga taggtaacaa
     3301 taaggaaata tatttagaca ttggatttag tgagctaaat gaaatatcaa tgcttggcga
     3361 gggtatcagt cgagcattat cttttatcag ctcagtgctg gtacaggaaa actcaattat
     3421 tcttattgat gaaatcgaga acggaataca ttactcagta attaaagaca taataaaatc
     3481 attaatttca tctgcaaaac aaaacaacaa tcaaatattt gcaacaactc atagtcaaga
     3541 tgtgatacga gcaataaacg aaatagatag caaaaatgaa gatatcgctt atattagact
     3601 aggaagagaa aagaactccc taaaaccaac agccgtacaa ttcaatatgg atgatttctc
     3661 ctactcagtt gagaacgact gggaggtaag ataatgaaag acataaataa tagcaaaaag
     3721 atcattttcg ttgagggtga tgatgatttt cattttctat gcaacctact tgaaatacaa
     3781 ggcattaccg atgtttttgt cgaaaaaata aatggaaaat caaaattaaa acaagcactt
     3841 agagcattca aaaacattga ttctttcgat gaaaaagaaa gtatttttat tatattagat
     3901 gctgacacat cattttctga cacagaaaga tcaataattg ccacattgcg agaactacaa
     3961 atctcctccc ccagctcgca taacgagata gctatgaatg gcaatacaaa aatttctttc
     4021 tttataatgc caggaaaaga caagcaaggt gccattgaag atctgataat tgaacacgca
     4081 agcactcgag cgttatatga atacataata gaatttttcg aaaaaattaa aaataataaa
     4141 gatgacatct cagcgagtga caaagag
//
