LOCUS       NZ_CP071031             4167 bp    DNA     circular CON 10-JUN-2024
DEFINITION  Klebsiella pneumoniae strain KP-1Pi plasmid pKP-1PI_ColE2, complete
            sequence.
ACCESSION   NZ_CP071031
VERSION     NZ_CP071031.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN15437778
            Assembly: GCF_022369925.1
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., Antonelli,A., Noemi,A., Ilaria,B., Giani,T. and
            Rossolini,G.M.
  TITLE     Direct Submission
  JOURNAL   Submitted (23-FEB-2021) Department of Surgical Sciences and
            Integrated Diagnostics (DISC), University of Florence, Largo
            Brambilla 3, Florence, FI 50134, Italy
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: Unicycler v. 0.4.8
            Assembly Name                     :: K. pneumoniae 1PI
            Genome Representation             :: Full
            Expected Final Version            :: No
            Genome Coverage                   :: 90.0x
            Sequencing Technology :: Illumina MiSeq; Oxford Nanopore MiniION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_022369925.1-RS_2024_06_10
            Annotation Date                   :: 06/10/2024 04:29:43
            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)                     :: 5,797
            CDSs (total)                      :: 5,675
            Genes (coding)                    :: 5,532
            CDSs (with protein)               :: 5,532
            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)              :: 143
            CDSs (without protein)            :: 143
            Pseudo Genes (ambiguous residues) :: 0 of 143
            Pseudo Genes (frameshifted)       :: 64 of 143
            Pseudo Genes (incomplete)         :: 87 of 143
            Pseudo Genes (internal stop)      :: 27 of 143
            Pseudo Genes (multiple problems)  :: 30 of 143
            CRISPR Arrays                     :: 1
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP071031.1.
            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-1Pi"
                     /isolation_source="blood"
                     /host="Homo sapiens"
                     /db_xref="taxon:573"
                     /plasmid="pKP-1PI_ColE2"
                     /geo_loc_name="Italy: Pisa"
                     /lat_lon="43.705580 N 10.443560 E"
                     /collection_date="2018-07-19"
                     /collected_by="Diagnostic Microbiology and Virology Unit,
                     Pisa"
     gene            complement(join(3647..4167,1..112))
                     /locus_tag="HZC88_RS28880"
                     /old_locus_tag="HZC88_28765"
     CDS             complement(join(3647..4167,1..112))
                     /locus_tag="HZC88_RS28880"
                     /old_locus_tag="HZC88_28765"
                     /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            complement(112..1227)
                     /locus_tag="HZC88_RS28885"
                     /old_locus_tag="HZC88_28770"
     CDS             complement(112..1227)
                     /locus_tag="HZC88_RS28885"
                     /old_locus_tag="HZC88_28770"
                     /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_012579087.1"
                     /translation="MIKEISLKNFKCFNELYLKQLKTLNIIAGKNNYGKTSILDAIFCF
                     YDVKNPAVLLNIQAFRKEMAEINKNKPFWVSYFHDMDTSQKMSIVIRDERSEVTQTYET
                     ETNQRLESSLSLNVDTVLSNQNIPRQTIGSQATVNSLKINVTETPNAKNRVSNKLFSMQ
                     LKEDGVEIKSEIKNERDGINYKFKTATIITTSRKINKEATITNVSSLLTQKRKKDILEN
                     LKKIDDRIVDIAISAIGNNKEIYLDIGFSELNEISMLGEGISRALSFISSVLVQENSII
                     LIDEIENGIHYSVIKDIIKSLISSAKQNNNQIFATTHSQDVIRAINEIDSKNEDIAYIR
                     LGREKNSLKPTAVQFNMDDFSYSVENDWEVR"
                     /name="ATP-binding protein"
     gene            complement(1572..1685)
                     /locus_tag="HZC88_RS28890"
                     /old_locus_tag="HZC88_28775"
                     /pseudo=""
     CDS             complement(1572..1685)
                     /locus_tag="HZC88_RS28890"
                     /old_locus_tag="HZC88_28775"
                     /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            2101..2292
                     /locus_tag="HZC88_RS28895"
                     /old_locus_tag="HZC88_28780"
     CDS             2101..2292
                     /locus_tag="HZC88_RS28895"
                     /old_locus_tag="HZC88_28780"
                     /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            2292..2693
                     /locus_tag="HZC88_RS28900"
                     /old_locus_tag="HZC88_28785"
     CDS             2292..2693
                     /locus_tag="HZC88_RS28900"
                     /old_locus_tag="HZC88_28785"
                     /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(3039..3281)
                     /locus_tag="HZC88_RS28905"
                     /old_locus_tag="HZC88_28790"
     CDS             complement(3039..3281)
                     /locus_tag="HZC88_RS28905"
                     /old_locus_tag="HZC88_28790"
                     /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"
     Typing          complement(1573..1980)
                     /name="ColRNAI_rep_cluster_1987"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="93.399"
                     /coverage="99.0"
                     /evalue="5.92e-171"
ORIGIN
        1 tttcgacaaa aacatcggta atgccttgta tttcaagtag gttgcataga aaatgaaaat
       61 catcatcacc ctcaacgaaa atgatctttt tgctattatt tatgtctttc attatcttac
      121 ctcccagtcg ttctcaactg agtaggagaa atcatccata ttgaattgta cggctgttgg
      181 ttttagggag ttcttttctc ttcctagtct aatataagcg atatcttcat ttttgctatc
      241 tatttcgttt attgctcgta tcacatcttg actatgagtt gttgcaaata tttgattgtt
      301 gttttgtttt gcagatgaaa ttaatgattt tattatgtct ttaattactg agtaatgtat
      361 tccgttctcg atttcatcaa taagaataat tgagttttcc tgtaccagca ctgagctgat
      421 aaaagataat gctcgactga taccctcgcc aagcattgat atttcattta gctcactaaa
      481 tccaatgtct aaatatattt ccttattgtt acctatcgca gatattgcta tatctacaat
      541 tctgtcatct atttttttta agttttctag tatgtctttt ttcctttttt gtgttagtag
      601 gctagataca tttgtaattg ttgcctcttt gtttatcttt ctggatgttg ttattattgt
      661 tgctgtctta aatttataat taatcccatc cctttcgttt tttatttcgg attttatttc
      721 tacgccatct tctttcaatt gcatagagaa aagcttattg gaaaccctgt ttttcgcatt
      781 gggtgtctcg gtcacattta tttttaaaga gtttactgtg gcctgagaac cgatagtttg
      841 acgaggtatg ttttggttag atagtacggt gtcaacgttt agagacaaac ttgattctaa
      901 tctctgattt gtttctgttt catatgtttg tgttacttca gagcgttcat ctcgaatgac
      961 tatggacatc ttttgtgatg tgtccatatc atgaaagtaa ctaacccaaa atggcttgtt
     1021 tttgtttatt tctgccattt cttttctgaa tgcttgaatg tttaacaaaa cagccgggtt
     1081 ttttacatca taaaaacaaa aaatagcatc cagtatagat gttttcccgt agttgttttt
     1141 cccagctatg atatttaaag tctttaattg ctttagatat agctcattga agcatttgaa
     1201 gttctttaaa cttatttcct ttatcatgat agcctctgtt cgtgtttttg ttatatgcca
     1261 tacgatttgt tagtacctta ataaaatgta cagctttcat tgtgattagc tagactttat
     1321 gtcaaagatt aactttgatt gcttgtgttt taatcgattt tttttacttt cttcttgaga
     1381 ttatctggca gcagccgtaa gcttccggct gtgaacgaaa aaaaccgcct tggcgggcgg
     1441 ttttttcgaa aggttcagta gagttggcgc tctatgaacc gaggtaactg gcttaaaggg
     1501 agcgcagtca ccaaaactgt tcgtttagtt tagctttaac tggcgtataa cttcaagact
     1561 aactccctaa atcagttacc agtggctgct gccagtggcg ctttgtcgtg tctttccggg
     1621 ttggactcaa gacgatagtt accggattag gcgcagcagt cggactgaac ggggggttcg
     1681 tgcatacagt ccagcttgga gcgaactgcc tacccggaac tgagtgtcag gcgtggaatg
     1741 agacaaacgc ggccataaca gcggaatgac accggtaaac cgaaaggcag gaacaggaga
     1801 gcgcacgagg gagccatcag ggggaaacgc ctggtatctt tatagtcctg tcgggtttcg
     1861 ccaccactga tttgagcgtc agattccgtg atgctcgtca ggggggcgga gcctatggaa
     1921 aaacggccgc tgtgcggcct ttccttcttt cctccatgcg attactcggt tttctcgagc
     1981 gtttctacgc atgctcctgc cgctcgccgc agccgaacgg caggagcgta gcgactgagt
     2041 gagcgaggaa gcggaaaaga ggagatccct acactgacca ctgacgctct gaggcctctt
     2101 atgacgaaac aacagaaaac agcgctgaac atggctaaat tcatccagaa tcagtctctg
     2161 ctcctgctgg agaagcttaa cgagcttgat ctcgatgtcg aggccgacct ttgtgagaaa
     2221 ctccacgatg atgcggagca tcttttccgt acactgtcct cgagactgga tgcattacag
     2281 gatggtaact gatggccaga gtgtctatta gtgaggctgc ccgactgacg ggtaagagta
     2341 gaacaacact gcacaggtta attaaagcag gtgacctgtc cacctgtagc ggtgagcgca
     2401 atgcaaaaat ggtagatact tcagagcttt tacgtgtctt tggccccttt gagcaaccga
     2461 agggtgaaca ccattctgga caggtctctg gacagcgtga tacagcctct gctgaccaga
     2521 gtgaacaggt gatccgtcat ctgaaacagg agattgaaca cctgaacacc ttacttttgt
     2581 ccaaggattc gcacattgac agcctgaaac aggccatgct ccttcttgaa aatcaccagg
     2641 caaaattaac tgaatccccg gcgccatggt ggaaattctg gaaaaaatcc tgaccccgtc
     2701 atgcttcagt tttcctctcc ggccatccca gggagttcct gaaccttccc aaaaatcgtc
     2761 agatctctga acgctcctca ccactaaaaa tacccacacc ccacgcaaaa ttaaaatttt
     2821 gcagattcct tatttacaac aatgggttaa tgaaaaataa atgtgcggtg atgtgttaca
     2881 aagtgcagat ccaagtcgtg gacgactcta tggcgaatcg ctgacgaatt gcccacgatt
     2941 catatgtgaa tcacgcttta ttatcatatt gttatgatga atcgactctt gattcaattc
     3001 atcactttgg gtgttttttg ctcatggtga ctcttgattc aattcacgat tcgaatcgcc
     3061 ggtgaatcgt gtggtgagtc gtccggcgac ttgccataac gtgattgccg gccgtcgacg
     3121 aacccgattc ctgaaggtgc tgaaaaccgg ttttccggct gcgccggcaa cgcttcacgg
     3181 ccacgcaata aattgcgtcc ccgttcaccg ttttcggagg agaagaacgc cggaaacagg
     3241 acttcccctg gctgaatggt gtgaatttcc gcgctatgca cttgcgcgca tactcatgca
     3301 tgccgtaaaa acagagcctg cgcgtttctg gcgggttttc gggtggtttg ttgcctgttt
     3361 taccggtttc ccgtcagaaa cgtcctgagt ccgttttagc ggtgcgtaca attatgattt
     3421 tatgttaaat tgttttaagt gaatagagag aatataactt aagggagcat cttgtgctgg
     3481 gtcttttaca ttagatctgc acaatcattg ttttggcatc tggtgatgtc tttaggacgt
     3541 ttgagattgc tgataactaa agtgtatgat gctttctata cgttatccgg cgtttaataa
     3601 caccctggtg ataagccagc ccgtgaaggg ctggcttgat ttggatttat atttttgaaa
     3661 taaaatcttt tatttcatca aagcaattgt ctgctgtgtt tattattcca tttttcatgg
     3721 atattcctat tcttgagtcg gattctctat tgcagctaag atagacttgt accttagctt
     3781 ttttttcgtt tgttggataa gtgtactctt tgtcactcgc tgagatgtca tctttattat
     3841 ttttaatttt ttcgaaaaat tctattatgt attcatataa cgctcgagtg cttgcgtgtt
     3901 caattatcag atcttcaatg gcaccttgct tgtcttttcc tggcattata aagaaagaaa
     3961 tttttgtatt gccattcata gctatctcgt tatgcgagct gggggaggag atttgtagtt
     4021 ctcgcaatgt ggcaattatt gatctttctg tgtcagaaaa tgatgtgtca gcatctaata
     4081 taataaaaat actttctttt tcatcgaaag aatcaatgtt tttgaatgct ctaagtgctt
     4141 gttttaattt tgattttcca tttattt
//
