LOCUS       NZ_CP053040             4167 bp    DNA     circular CON 10-JAN-2024
DEFINITION  Klebsiella pneumoniae strain P35 plasmid pP35E, complete sequence.
ACCESSION   NZ_CP053040
VERSION     NZ_CP053040.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN14770898
            Assembly: GCF_014524525.1
KEYWORDS    RefSeq.
SOURCE      Klebsiella pneumoniae
  ORGANISM  Klebsiella pneumoniae
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Klebsiella/Raoultella group; Klebsiella.
REFERENCE   1  (bases 1 to 4167)
  AUTHORS   Martins,W.M.B.S., Nicolas,M.F., Yu,Y., Li,M., Dantas,P., Sands,K.,
            Portal,E., Almeida,L.G.P., Vasconcelos,A.T.R.L., Medeiros,E.A.,
            Toleman,M.A., Walsh,T.R., Gales,A.C. and Andrey,D.O.
  TITLE     When KPC- 2, carried by an IncQ1 ubiquitary, wide-host range and
            high copy plasmid, meets the international ST15 Klebsiella
            pneumoniae clone: clinical and molecular description
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 4167)
  AUTHORS   Martins,W.M.B.S., Nicolas,M.F., Yu,Y., Li,M., Dantas,P., Sands,K.,
            Portal,E., Almeida,L.G.P., Vasconcelos,A.T.R.L., Medeiros,E.A.,
            Toleman,M.A., Walsh,T.R., Gales,A.C. and Andrey,D.O.
  TITLE     Direct Submission
  JOURNAL   Submitted (29-APR-2020) Medicine, Universidade Federal de Sao Paulo,
            Pedro de Toledo Street, 781, Sao Paulo, SP 04039-032, Brazil
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Date                     :: 30-MAY-2019
            Assembly Method                   :: Unicycler v. v0.4.0
            Assembly Name                     :: P35
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 120.0x
            Sequencing Technology :: Illumina MiSeq; Oxford Nanopore MiniION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 01/10/2024 01:36:38
            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)                     :: 5,561
            CDSs (total)                      :: 5,437
            Genes (coding)                    :: 5,238
            CDSs (with protein)               :: 5,238
            Genes (RNA)                       :: 124
            rRNAs                             :: 9, 8, 8 (5S, 16S, 23S)
            complete rRNAs                    :: 9, 8, 8 (5S, 16S, 23S)
            tRNAs                             :: 87
            ncRNAs                            :: 12
            Pseudo Genes (total)              :: 199
            CDSs (without protein)            :: 199
            Pseudo Genes (ambiguous residues) :: 0 of 199
            Pseudo Genes (frameshifted)       :: 96 of 199
            Pseudo Genes (incomplete)         :: 109 of 199
            Pseudo Genes (internal stop)      :: 27 of 199
            Pseudo Genes (multiple problems)  :: 30 of 199
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP053040.1.
            Bacteria and source DNA available from Laboratorio Alerta,
            Universidade Federal de Sao Paulo; Pedro de Toledo Street, 781, zip
            code: 04039-032, Brazil.
            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="P35"
                     /isolation_source="blood"
                     /host="Homo sapiens"
                     /db_xref="taxon:573"
                     /plasmid="pP35E"
                     /geo_loc_name="Brazil: Sao Paulo"
                     /lat_lon="23.597500 S 46.643600 W"
                     /collection_date="2015-05"
                     /collected_by="Laboratorio Alerta"
     gene            join(3749..4167,1..697)
                     /locus_tag="HKJ75_RS27555"
                     /old_locus_tag="HKJ75_28150"
     CDS             join(3749..4167,1..697)
                     /locus_tag="HKJ75_RS27555"
                     /old_locus_tag="HKJ75_28150"
                     /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            697..1329
                     /locus_tag="HKJ75_RS27560"
                     /old_locus_tag="HKJ75_28155"
     CDS             697..1329
                     /locus_tag="HKJ75_RS27560"
                     /old_locus_tag="HKJ75_28155"
                     /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            1695..1937
                     /locus_tag="HKJ75_RS27565"
                     /old_locus_tag="HKJ75_28160"
     CDS             1695..1937
                     /locus_tag="HKJ75_RS27565"
                     /old_locus_tag="HKJ75_28160"
                     /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(2283..2684)
                     /locus_tag="HKJ75_RS27570"
                     /old_locus_tag="HKJ75_28165"
     CDS             complement(2283..2684)
                     /locus_tag="HKJ75_RS27570"
                     /old_locus_tag="HKJ75_28165"
                     /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(2684..2875)
                     /locus_tag="HKJ75_RS27575"
                     /old_locus_tag="HKJ75_28170"
     CDS             complement(2684..2875)
                     /locus_tag="HKJ75_RS27575"
                     /old_locus_tag="HKJ75_28170"
                     /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            3291..3404
                     /locus_tag="HKJ75_RS27645"
                     /old_locus_tag="HKJ75_28180"
                     /pseudo=""
     CDS             3291..3404
                     /locus_tag="HKJ75_RS27645"
                     /old_locus_tag="HKJ75_28180"
                     /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          2997..3404
                     /name="ColRNAI_rep_cluster_1987"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="93.399"
                     /coverage="99.0"
                     /evalue="5.92e-171"
ORIGIN
        1 tttaaaaata aatgtgaccg agacacccaa tgcgaaaaac agggtttcca ataagctttt
       61 ctctatgcaa ttgaaagaag atggcgtaga aataaaatcc gaaataaaaa acgaaaggga
      121 tgggattaat tataaattta agacagcaac aataataaca acatccagaa agataaacaa
      181 agaggcaaca attacaaatg tatctagcct actaacacaa aaaaggaaaa aagacatact
      241 agaaaactta aaaaaaatag atgacagaat tgtagatata gcaatatctg cgataggtaa
      301 caataaggaa atatatttag acattggatt tagtgagcta aatgaaatat caatgcttgg
      361 cgagggtatc agtcgagcat tatcttttat cagctcagtg ctggtacagg aaaactcaat
      421 tattcttatt gatgaaatcg agaacggaat acattactca gtaattaaag acataataaa
      481 atcattaatt tcatctgcaa aacaaaacaa caatcaaata tttgcaacaa ctcatagtca
      541 agatgtgata cgagcaataa acgaaataga tagcaaaaat gaagatatcg cttatattag
      601 actaggaaga gaaaagaact ccctaaaacc aacagccgta caattcaata tggatgattt
      661 ctcctactca gttgagaacg actgggaggt aagataatga aagacataaa taatagcaaa
      721 aagatcattt tcgttgaggg tgatgatgat tttcattttc tatgcaacct acttgaaata
      781 caaggcatta ccgatgtttt tgtcgaaaaa ataaatggaa aatcaaaatt aaaacaagca
      841 cttagagcat tcaaaaacat tgattctttc gatgaaaaag aaagtatttt tattatatta
      901 gatgctgaca catcattttc tgacacagaa agatcaataa ttgccacatt gcgagaacta
      961 caaatctcct cccccagctc gcataacgag atagctatga atggcaatac aaaaatttct
     1021 ttctttataa tgccaggaaa agacaagcaa ggtgccattg aagatctgat aattgaacac
     1081 gcaagcactc gagcgttata tgaatacata atagaatttt tcgaaaaaat taaaaataat
     1141 aaagatgaca tctcagcgag tgacaaagag tacacttatc caacaaacga aaaaaaagct
     1201 aaggtacaag tctatcttag ctgcaataga gaatccgact caagaatagg aatatccatg
     1261 aaaaatggaa taataaacac agcagacaat tgctttgatg aaataaaaga ttttatttca
     1321 aaaatataaa tccaaatcaa gccagccctt cacgggctgg cttatcacca gggtgttatt
     1381 aaacgccgga taacgtatag aaagcatcat acactttagt tatcagcaat ctcaaacgtc
     1441 ctaaagacat caccagatgc caaaacaatg attgtgcaga tctaatgtaa aagacccagc
     1501 acaagatgct cccttaagtt atattctctc tattcactta aaacaattta acataaaatc
     1561 ataattgtac gcaccgctaa aacggactca ggacgtttct gacgggaaac cggtaaaaca
     1621 ggcaacaaac cacccgaaaa cccgccagaa acgcgcaggc tctgttttta cggcatgcat
     1681 gagtatgcgc gcaagtgcat agcgcggaaa ttcacaccat tcagccaggg gaagtcctgt
     1741 ttccggcgtt cttctcctcc gaaaacggtg aacggggacg caatttattg cgtggccgtg
     1801 aagcgttgcc ggcgcagccg gaaaaccggt tttcagcacc ttcaggaatc gggttcgtcg
     1861 acggccggca atcacgttat ggcaagtcgc cggacgactc accacacgat tcaccggcga
     1921 ttcgaatcgt gaattgaatc aagagtcacc atgagcaaaa aacacccaaa gtgatgaatt
     1981 gaatcaagag tcgattcatc ataacaatat gataataaag cgtgattcac atatgaatcg
     2041 tgggcaattc gtcagcgatt cgccatagag tcgtccacga cttggatctg cactttgtaa
     2101 cacatcaccg cacatttatt tttcattaac ccattgttgt aaataaggaa tctgcaaaat
     2161 tttaattttg cgtggggtgt gggtattttt agtggtgagg agcgttcaga gatctgacga
     2221 tttttgggaa ggttcaggaa ctccctggga tggccggaga ggaaaactga agcatgacgg
     2281 ggtcaggatt ttttccagaa tttccaccat ggcgccgggg attcagttaa ttttgcctgg
     2341 tgattttcaa gaaggagcat ggcctgtttc aggctgtcaa tgtgcgaatc cttggacaaa
     2401 agtaaggtgt tcaggtgttc aatctcctgt ttcagatgac ggatcacctg ttcactctgg
     2461 tcagcagagg ctgtatcacg ctgtccagag acctgtccag aatggtgttc acccttcggt
     2521 tgctcaaagg ggccaaagac acgtaaaagc tctgaagtat ctaccatttt tgcattgcgc
     2581 tcaccgctac aggtggacag gtcacctgct ttaattaacc tgtgcagtgt tgttctactc
     2641 ttacccgtca gtcgggcagc ctcactaata gacactctgg ccatcagtta ccatcctgta
     2701 atgcatccag tctcgaggac agtgtacgga aaagatgctc cgcatcatcg tggagtttct
     2761 cacaaaggtc ggcctcgaca tcgagatcaa gctcgttaag cttctccagc aggagcagag
     2821 actgattctg gatgaattta gccatgttca gcgctgtttt ctgttgtttc gtcataagag
     2881 gcctcagagc gtcagtggtc agtgtaggga tctcctcttt tccgcttcct cgctcactca
     2941 gtcgctacgc tcctgccgtt cggctgcggc gagcggcagg agcatgcgta gaaacgctcg
     3001 agaaaaccga gtaatcgcat ggaggaaaga aggaaaggcc gcacagcggc cgtttttcca
     3061 taggctccgc ccccctgacg agcatcacgg aatctgacgc tcaaatcagt ggtggcgaaa
     3121 cccgacagga ctataaagat accaggcgtt tccccctgat ggctccctcg tgcgctctcc
     3181 tgttcctgcc tttcggttta ccggtgtcat tccgctgtta tggccgcgtt tgtctcattc
     3241 cacgcctgac actcagttcc gggtaggcag ttcgctccaa gctggactgt atgcacgaac
     3301 cccccgttca gtccgactgc tgcgcctaat ccggtaacta tcgtcttgag tccaacccgg
     3361 aaagacacga caaagcgcca ctggcagcag ccactggtaa ctgatttagg gagttagtct
     3421 tgaagttata cgccagttaa agctaaacta aacgaacagt tttggtgact gcgctccctt
     3481 taagccagtt acctcggttc atagagcgcc aactctactg aacctttcga aaaaaccgcc
     3541 cgccaaggcg gtttttttcg ttcacagccg gaagcttacg gctgctgcca gataatctca
     3601 agaagaaagt aaaaaaaatc gattaaaaca caagcaatca aagttaatct ttgacataaa
     3661 gtctagctaa tcacaatgaa agctgtacat tttattaagg tactaacaaa tcgtatggca
     3721 tataacaaaa acacgaacag aggctatcat gataaaggaa ataagtttaa agaacttcaa
     3781 atgcttcaat gagctatatc taaagcaatt aaagacttta aatatcatag ctgggaaaaa
     3841 caactacggg aaaacatcta tactggatgc tattttttgt ttttatgatg taaaaaaccc
     3901 ggctgttttg ttaaacattc aagcattcag aaaagaaatg gcagaaataa acaaaaacaa
     3961 gccattttgg gttagttact ttcatgatat ggacacatca caaaagatgt ccatagtcat
     4021 tcgagatgaa cgctctgaag taacacaaac atatgaaaca gaaacaaatc agagattaga
     4081 atcaagtttg tctctaaacg ttgacaccgt actatctaac caaaacatac ctcgtcaaac
     4141 tatcggttct caggccacag taaactc
//
