LOCUS       NZ_CP046651             5897 bp    DNA     circular CON 23-DEC-2023
DEFINITION  Klebsiella pneumoniae strain EGKP3 plasmid pEGKP3.7, complete
            sequence.
ACCESSION   NZ_CP046651
VERSION     NZ_CP046651.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN13497075
            Assembly: GCF_017161135.1
KEYWORDS    RefSeq.
SOURCE      Klebsiella pneumoniae
  ORGANISM  Klebsiella pneumoniae
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Klebsiella/Raoultella group; Klebsiella.
REFERENCE   1  (bases 1 to 5897)
  AUTHORS   Hamza,E., Dona,V., Elhariri,M., Elhelw,R., Hamza,D. and Perreten,V.
  TITLE     WGS of K. pneumoniae producing carbapenamese from Egypt
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 5897)
  AUTHORS   Hamza,E., Dona,V. and Perreten,V.
  TITLE     Direct Submission
  JOURNAL   Submitted (06-DEC-2019) Institute of Veterinary Bacteriology,
            University of Bern, Laenggassstrasse 122, Bern 3012, Switzerland
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Date                     :: DEC-2019
            Assembly Method                   :: Unicycler v. 0.4.4
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 100x
            Sequencing Technology :: Oxford Nanopore MiniION and Illumina
            NovaSeq 6000
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 12/23/2023 20:08:43
            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)                     :: 5,683
            CDSs (total)                      :: 5,562
            Genes (coding)                    :: 5,414
            CDSs (with protein)               :: 5,414
            Genes (RNA)                       :: 121
            rRNAs                             :: 9, 8, 8 (5S, 16S, 23S)
            complete rRNAs                    :: 9, 8, 8 (5S, 16S, 23S)
            tRNAs                             :: 87
            ncRNAs                            :: 9
            Pseudo Genes (total)              :: 148
            CDSs (without protein)            :: 148
            Pseudo Genes (ambiguous residues) :: 0 of 148
            Pseudo Genes (frameshifted)       :: 64 of 148
            Pseudo Genes (incomplete)         :: 86 of 148
            Pseudo Genes (internal stop)      :: 24 of 148
            Pseudo Genes (multiple problems)  :: 22 of 148
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP046651.1.
            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..5897
                     /organism="Klebsiella pneumoniae"
                     /mol_type="genomic DNA"
                     /strain="EGKP3"
                     /isolation_source="fecal isolate from poultry farm worker"
                     /host="Homo sapiens"
                     /db_xref="taxon:573"
                     /plasmid="pEGKP3.7"
                     /geo_loc_name="Egypt"
                     /lat_lon="30.0131 N 31.2089 E"
                     /collection_date="2015"
                     /collected_by="Veterinarian"
     gene            join(5722..5897,1..91)
                     /locus_tag="GPU01_RS28330"
                     /old_locus_tag="GPU01_27900"
     CDS             join(5722..5897,1..91)
                     /locus_tag="GPU01_RS28330"
                     /old_locus_tag="GPU01_27900"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000262326.1"
                     /GO_function="GO:0008657 - DNA topoisomerase type II
                     (double strand cut, ATP-hydrolyzing) inhibitor activity
                     [Evidence IEA]; GO:0042803 - protein homodimerization
                     activity [Evidence IEA]"
                     /GO_process="GO:0030541 - plasmid partitioning [Evidence
                     IEA]; GO:0051290 - protein heterotetramerization [Evidence
                     IEA]"
                     /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_064169725.1"
                     /translation="MVWTINYSDRALKSLRKMDKQNARRIVDFMDLRIAVAADPRHSGK
                     PLKGELGEFWRYRVGDYRILCEIRDDELIILAATIGHRREVYD"
                     /name="type II toxin-antitoxin system RelE/ParE family
                     toxin"
     gene            198..1619
                     /locus_tag="GPU01_RS28335"
                     /old_locus_tag="GPU01_27905"
     CDS             198..1619
                     /locus_tag="GPU01_RS28335"
                     /old_locus_tag="GPU01_27905"
                     /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_064169724.1"
                     /translation="MKYFSTGFFLKGNVEVKDIINECLSWVSTSPFTSFVPASLDMKRG
                     LDEFDIEVGDERIELINFSDDSIMMSCFRYSKISGAHKWVTDVAVNYYFSEGKTWVQVE
                     SSVVTQQAVHKAPVTKTPLIVLRLLDKFSGGRDDVFKVGIEPVLLDGSEHSLGFACDII
                     NGRHKNRLPVVYVSSKYFFKEHPHNVIPGRLARKLSGLAHVVVEPEGHLFSNKLKHEVN
                     NKNSYGGSVGIYWPGGQSISIHKRGSLSAAEFEKEIFKEIITAMTSLAPLRKNGWSEIV
                     SSKNRKAIQVLKDNGSQSSELASLYEEENESLQDEVKELNQKIASYEARIRVLMERTSM
                     QGGVFLKIGNEYELFEGEVLEIIMSSIRKVLPTNYEGGRYHDVLSSISSANPCSTNLLE
                     RDKKLKQALVGYTKMTPKVRGVLNDVGFSISEEGKHYKITYHGDPRYTYILPKTGSDYR
                     GALNAYSDISKKVFS"
                     /name="hypothetical protein"
     gene            3825..4016
                     /locus_tag="GPU01_RS28340"
                     /old_locus_tag="GPU01_27910"
     CDS             3825..4016
                     /locus_tag="GPU01_RS28340"
                     /old_locus_tag="GPU01_27910"
                     /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            4016..4438
                     /locus_tag="GPU01_RS28345"
                     /old_locus_tag="GPU01_27915"
     CDS             4016..4438
                     /locus_tag="GPU01_RS28345"
                     /old_locus_tag="GPU01_27915"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:YP_005229777.1"
                     /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_032451468.1"
                     /translation="MARVSISEAARLVKVSRPTIYKMINSGKLSYTSVVKHGKGIKVID
                     TSELIRVFGPLDGVIDAVKYDVKSDAESTGINSVGLHDLQHRIALLEAENDGLKGAVKA
                     RDEHIDSLRQAMQLLEHKHEPSSPPHSPWWKFWKKS"
                     /name="helix-turn-helix domain-containing protein"
     gene            complement(5224..5352)
                     /locus_tag="GPU01_RS28350"
     CDS             complement(5224..5352)
                     /locus_tag="GPU01_RS28350"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000523570.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_256557297.1"
                     /translation="MALKPGPKRIAESTGQPDQRQRDNKKTPGNTDKLKPSKSSGK"
                     /name="hypothetical protein"
     gene            5514..5738
                     /locus_tag="GPU01_RS28355"
                     /old_locus_tag="GPU01_27920"
     CDS             5514..5738
                     /locus_tag="GPU01_RS28355"
                     /old_locus_tag="GPU01_27920"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000879771.1"
                     /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="TraY domain-containing protein"
                     /protein_id="WP_064169727.1"
                     /translation="MLAIRLSDEIESRLNLLAKQTGRTKTFYAREAILTHLDDLEDYYL
                     SAETVARVRRGDEVVHSSEDVRKSLGLDD"
                     /name="TraY domain-containing protein"
     Typing          2306..2482
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="86.264"
                     /coverage="82.0"
                     /evalue="3.5099999999999995e-46"
     Typing          complement(1847..2356)
                     /name="ColRNAI_rep_cluster_1987"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="93.75"
                     /coverage="98.0"
                     /evalue="0.0"
ORIGIN
        1 tggcgattat cgcatcctat gcgagatcag ggacgacgag ctgattattc tggctgctac
       61 cattggccac cgacgtgaag tctacgactg aagcccgctt tgcgggtttt ttttatgtga
      121 ggcgtgaaaa atatgtcgtt aacaaaatgg ctttttaatt ttaaaaaata ttttactcta
      181 aatcataagg ggtgtttatg aaatattttt ccacgggctt ctttttgaaa ggaaatgttg
      241 aggtaaaaga tataatcaat gagtgtttgt catgggtgtc aacatcacca tttacttcat
      301 ttgttcccgc tagcttagat atgaaaagag ggttggatga gtttgatatt gaggtgggtg
      361 atgaaagaat tgaactgata aatttttcag atgattcgat tatgatgtct tgttttcgtt
      421 actctaaaat atcaggggca cataaatggg tcaccgatgt tgctgttaat tattattttt
      481 cagaagggaa aacctgggtt caagttgaat ctagtgttgt tactcagcaa gctgttcata
      541 aggcacctgt aactaaaaca ccactcattg tattgcgtct gctagataaa ttctctggtg
      601 ggcgtgatga tgtttttaaa gtaggaattg aacctgtttt actggatggt tcagaacatt
      661 ctcttggctt tgcttgtgat ataattaatg gaaggcacaa aaacaggctt cctgtggttt
      721 atgtgagctc taaatatttt ttcaaagaac atccgcataa tgtgatacct ggcaggttgg
      781 ctaggaagct atcagggttg gcccatgtgg ttgtagaacc tgaaggccac ttgttttcta
      841 ataaactcaa gcatgaagtt aataataaaa attcttatgg tggaagcgtt ggtatttact
      901 ggccgggagg gcaaagtatt agtattcata aaagaggtag tcttagtgct gctgaatttg
      961 agaaagagat atttaaagag attataactg ctatgacttc actggccccc ttaaggaaaa
     1021 atgggtggtc tgagatagtc agtagtaaaa acagaaaagc cattcaagtt ttaaaagata
     1081 atggaagtca aagtagtgaa ctcgcttctc tatatgaaga agagaatgaa tccctgcaag
     1141 atgaagtaaa ggagctaaat caaaagatag cttcttatga agcaaggata agagtattga
     1201 tggaaagaac atctatgcag ggtggggttt ttttgaagat tggcaatgag tatgagttgt
     1261 ttgaaggtga ggtattagaa ataataatgt cttcaattag gaaggttctt ccgacaaatt
     1321 atgagggagg tagatatcat gatgttctat cttcaatatc ttccgctaac ccatgcagta
     1381 caaacctctt ggaaagagat aaaaagttga agcaagcgct agtaggctat acaaaaatga
     1441 cgccaaaagt gagaggtgtt ttgaatgatg tcggtttttc aataagcgaa gagggtaagc
     1501 actataaaat aacttaccat ggggatcccc ggtacacata tattttacct aaaacgggga
     1561 gtgactatcg aggggcgtta aatgcttact ccgacatatc aaaaaaggtg ttttcataaa
     1621 ccagtaagac atggtgcttg agttcatctc ttgctggatg tatcttagtt ttgaaacgaa
     1681 aaaaccaccc tggcaggtgg tttttcgaag gttagttaat cctggcagat tctctaaccg
     1741 tggtaacagt cttgtgcgag acatgtcacc aaatctgtcc ttccagtgta gcctcagtaa
     1801 ggccaccact tcaagaactc tcgatacatc tctcgcacat tctgtttacc agtggccgtt
     1861 gccagtggcg ttaagtcgtg tcttttcggg ttggactcaa gatgatagtt accggataag
     1921 gcgcagcggt cggactgaac ggggggttcg tgcatacagt ccagcttgga gcgaactgcc
     1981 ttcccggaac tgagtgtcag gcgtggaatg agataaacgc ggccataaca gcggaatgac
     2041 accggtaaac cgaaaggcag gaacaggaga gcgcacgagg gagctaccag ggggaaacgc
     2101 ctgggatctt tatagtcctg tcgggtttcg ccgccactga tttgagcgtc agatttcgtg
     2161 atgcttgtca ggggggcgga gcctatggaa aaacggcagc gccgtatcct ttttttgccc
     2221 agcttgtcat gccgtatgcc tttgctctta tccgtgtgca ggtaacgccc gccgcagccg
     2281 aacggcagga gcggcagcga ccgagtgagc gaggaggcgt catatcaccg taactcccat
     2341 tttcttcctt acgccctgta gctgcatttt cccctgtcac atgaagcact tttattaagt
     2401 gttactccgc cgtaacatat tgagccagta tacactccgc tagcgcttcg tgactggttc
     2461 agggctgcgc cccgaaaccc gcgaaggacc gtctttttgt ttttttactg ctaaactgtc
     2521 aatattttct ttcggctgcc gttaactgag gtttccttgt ttgatttttc ctctggtatc
     2581 ctgatgaata tgagtgatgc tgaacggcag ctggctgtgt cagtgatttc tgactgctta
     2641 cgccagtctg ggggagactc cggcaaaatg atgctggatg cttactatct ggtcttatct
     2701 gagacagatc cccgggtcag ggagtgcatg ttggcgttcc ttgaatctgt tcgtattaaa
     2761 tatgtcaccg tctgagtttt ttttctgatt tttgaaccat actgtgtgtc aggcggccgt
     2821 catggatgat ggtcgttgtg acatgtccta tgtcacggaa gattgttcca atctaacttg
     2881 acttaccttc cgggctagcc gcccggtttt tttccgttct tctgactgta ctccagagca
     2941 ggttttgcct tttttctact gcgctttcgg agtaggggtc agtttggaga tcggaaattt
     3001 ttgtacgtta agcgcattat ttaaccaatc ttggttcgta aggggttgat tttgcgtcag
     3061 tggctatcgc ttttaagttg tcgctcttgc agtatcgcat ttaggttatc cgattaaggt
     3121 caaacctctg aaaatgccgt atagcgcggg agtacaccct attgctatag gtaagtctgt
     3181 tcaaaaaaca ggcttaccgt acaataattc tctatatcca aactgacccc tgatacgcag
     3241 cttcccggcg aatatgacct ttttgattta atggcgcagg ttactgaaga gaacctgcat
     3301 gcccctgtgg attccgggcc gcctgtcggc cgggaagcgt tatagctttt cgcttgcccg
     3361 cgtacgtggt aatacgccgg tattacattt tatttcttta ttttcatgcg attacaggtg
     3421 attgtaatac gttgcgtatt acataaataa acggagattt cagtttttac cttttaattc
     3481 atgcagttgc gatgaaaatc gcagctgcgt taggtgtatg accatttaag ggccaaaaaa
     3541 ttatcattct ggccgggtga tctgcggagg ttaaggggcg tcggtgacaa aaaaacgtca
     3601 ttaacgacct cgttcatgct cgcatgaacg gattattttt ccggactaca ggtaaactac
     3661 agaaagacta caaaagctga tgacttaatc ctgattttta gtgcgatgac tacagataaa
     3721 ctacaaaata actacaggat tacctcagat ccgttctctg aaccattcgt acatccgacc
     3781 cccttaccgg ttttacactg agcactgatg ctctgaggtc ccttatgacg aaacaacaga
     3841 aaacagcgct gaacatggct aaattcatcc agaatcagtc tctgctcctg ctggagaagc
     3901 ttaacgagct tgatctcgat gctgaggccg acctttgtga gaaactccac gatgatgcgg
     3961 agcatctttt ccgtacactg tcctcgagac tggatgcatt acaggatggt aactgatggc
     4021 cagagtgtct attagtgaag cagcacggct tgttaaggtt agtcgcccta ctatttacaa
     4081 gatgattaac agtggtaagt taagttacac ctctgttgta aagcacggga agggtattaa
     4141 agttattgat acatcagagc ttattagagt atttggtcct cttgatggtg taatcgatgc
     4201 tgtaaaatat gatgtaaaaa gtgacgcaga atctacaggt attaacagcg ttggtttaca
     4261 tgatttacaa catagaatcg ctttacttga agctgaaaac gatggtctta aaggggctgt
     4321 taaggctcga gatgagcata ttgattccct tcgtcaggct atgcagcttc tggagcacaa
     4381 gcacgaacct tcttcaccac cccattcccc gtggtggaaa ttctggaaaa aatcctgatc
     4441 ccgccatgct tgagttttcc tctccggcca tgccggggcg ttcgtgaacc ttcccaaaaa
     4501 tcgccagatc tctgaacgct cctcacacta aaaatatcca caccccacgc aaaattaaat
     4561 ttttgcagat aactcattaa tatcagtcag ttggttgtta ttaaattacg cagtattacc
     4621 ttctgtaagg tcaatccaag tcgtcggtga ttcgtgtacg acttgccgac gattcgtcat
     4681 agagtcatcg acgactcact ccacactatc agtaacttat gacgacttga ctctagagtc
     4741 gaatcgtcgc tttggcgttt ttttgaccgc ggtgactcta gagtcaagtc acgagtcgaa
     4801 tcgccggtga atcgtgtggt gagtcgtccg gcgacttgcc ataacgtgat tgccggccgt
     4861 cgacgaaccc gattcctgat cgtgctgata cggggtttcc ggctgtgccg gcaacgtctc
     4921 acggccacgc aataaattgc gtccccgttc accgttttcg ggtaagaaga acatcggaaa
     4981 caggacttac cccggctgaa tggcgtgaat ttccgcgcta tgcacttgcg cgcatactca
     5041 tgcatgccgt aaaaacagag cctgcgcgtt tctggcgggt tttcgggtgg tttgttgcct
     5101 gttttaccgg tttcccgtca gaaacgccct gagagcctct caggcggtgc acgcaacgga
     5161 tgttatgttt aatccgtctg accgacaagt acaaaaaaaa gcccctaagg gctttgctaa
     5221 caactacttt cctgaagatt tacttggttt taacttgtca gtatttccgg gagttttttt
     5281 attgtcgcgt tggcgctggt caggctgccc tgttgattct gcaattcgtt ttggtccagg
     5341 tttaagagcc ataatggata tccttcatcg tgttaagagg aaactctata actgcatata
     5401 tcgacagttg taggtagtca agatgaatgg aaagattgtt ttttgttctt tgatttttaa
     5461 tgttgtataa ttttgttata catgtatatc aatttggatt cagagaggtc tttatgttgg
     5521 ctatcagatt gtctgacgag attgagtccc gtctaaactt gcttgcgaag caaacaggta
     5581 ggactaaaac gttctatgcg cgtgaagcga tcctgacgca tctggatgat cttgaagatt
     5641 attatctttc agcagaaact gtggcacgtg ttcgccgtgg ggatgaagtt gtacattcgt
     5701 ctgaagacgt gaggaagtcg cttggtctgg acgattaact attccgaccg agcgctcaag
     5761 tcgttacgta agatggacaa gcagaacgca cgacggattg tggattttat ggatttacgt
     5821 attgccgttg ccgcagatcc acgccactca ggtaagccgc ttaaaggtga gcttggagaa
     5881 ttctggcgct atcgagt
//
