LOCUS       NZ_CP063000             5409 bp    DNA     linear   CON 08-MAY-2024
DEFINITION  Klebsiella pneumoniae strain CriePir197 plasmid unnamed3.
ACCESSION   NZ_CP063000
VERSION     NZ_CP063000.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN13153760
            Assembly: GCF_009661415.2
KEYWORDS    RefSeq.
SOURCE      Klebsiella pneumoniae
  ORGANISM  Klebsiella pneumoniae
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Klebsiella/Raoultella group; Klebsiella.
REFERENCE   1  (bases 1 to 5409)
  AUTHORS   Shelenkov,A., Mikhaylova,Y., Yanushevich,Y., Samoilov,A.,
            Petrova,L., Fomina,V., Gusarov,V., Zamyatin,M., Shagin,D. and
            Akimkin,V.
  TITLE     Molecular Typing, Characterization of Antimicrobial Resistance,
            Virulence Profiling and Analysis of Whole-Genome Sequence of
            Clinical Klebsiella pneumoniae Isolates
  JOURNAL   Antibiotics (Basel) 9 (5), 261 (2020)
   PUBMED   32429555
  REMARK    Publication Status: Online-Only
REFERENCE   2  (bases 1 to 5409)
  AUTHORS   Shelenkov,A., Mikhaylova,Y., Yanushevich,Y., Petrova,L., Fomina,V.,
            Zamyatin,M. and Shagin,D.
  TITLE     Direct Submission
  JOURNAL   Submitted (24-SEP-2020) Department Of Molecular Diagnostics and
            Epidemiology, Central Research Institute of Epidemiology,
            Novogireevskaya str., 3a, Moscow 111123, Russia
REFERENCE   3  (bases 1 to 5409)
  AUTHORS   Shelenkov,A., Mikhaylova,Y., Yanushevich,Y., Samoilov,A.,
            Petrova,L., Fomina,V., Gusarov,V., Zamyatin,M. and Shagin,D.
  TITLE     Direct Submission
  JOURNAL   Submitted (29-OCT-2019) Department Of Molecular Diagnostics and
            Epidemiology, Central Research Institute of Epidemiology,
            Novogireevskaya str., 3a, Moscow 111123, Russia
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: Unicycler v. v0.4.8-beta
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 214x
            Sequencing Technology             :: Oxford Nanopore MinION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_009661415.2-RS_2024_05_08
            Annotation Date                   :: 05/08/2024 05:36:25
            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)                     :: 5,441
            CDSs (total)                      :: 5,324
            Genes (coding)                    :: 5,156
            CDSs (with protein)               :: 5,156
            Genes (RNA)                       :: 117
            rRNAs                             :: 9, 8, 8 (5S, 16S, 23S)
            complete rRNAs                    :: 9, 8, 8 (5S, 16S, 23S)
            tRNAs                             :: 80
            ncRNAs                            :: 12
            Pseudo Genes (total)              :: 168
            CDSs (without protein)            :: 168
            Pseudo Genes (ambiguous residues) :: 0 of 168
            Pseudo Genes (frameshifted)       :: 62 of 168
            Pseudo Genes (incomplete)         :: 110 of 168
            Pseudo Genes (internal stop)      :: 19 of 168
            Pseudo Genes (multiple problems)  :: 20 of 168
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP063000.1.
            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/
FEATURES             Location/Qualifiers
     source          1..5409
                     /organism="Klebsiella pneumoniae"
                     /mol_type="genomic DNA"
                     /strain="CriePir197"
                     /isolation_source="Gall bladder"
                     /host="Homo sapiens"
                     /db_xref="taxon:573"
                     /plasmid="unnamed3"
                     /geo_loc_name="Russia: Moscow"
                     /lat_lon="55.76 N 37.62 E"
                     /collection_date="2018"
                     /collected_by="Pir Nat Surg Centre"
     gene            complement(<1..283)
                     /locus_tag="GJJ12_RS27305"
                     /pseudo=""
     CDS             complement(<1..283)
                     /locus_tag="GJJ12_RS27305"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_006122514.1"
                     /note="incomplete; too short partial abutting assembly gap;
                     missing C-terminus; Derived by automated computational
                     analysis using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /name="hypothetical protein"
     gene            complement(290..>472)
                     /locus_tag="GJJ12_RS27465"
                     /pseudo=""
     CDS             complement(290..>472)
                     /locus_tag="GJJ12_RS27465"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001479923.1"
                     /note="incomplete; partial in the middle of a contig;
                     missing N-terminus; Derived by automated computational
                     analysis using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /name="hypothetical protein"
     gene            complement(1118..2185)
                     /locus_tag="GJJ12_RS27000"
                     /old_locus_tag="GJJ12_027000"
     CDS             complement(1118..2185)
                     /locus_tag="GJJ12_RS27000"
                     /old_locus_tag="GJJ12_027000"
                     /EC_number="3.1.21.-"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001009472.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="CfrBI family restriction endonuclease"
                     /protein_id="WP_101990831.1"
                     /translation="MNFKDKNCFPNELIALAKISKNDVLDKFGPDVFKKVVYDVLTGKN
                     VREFTEILTRTRLLESNLSLFDFFVDKMKEGLTPKQLYLIAKDALSNKAYIKSNQPVLE
                     WMVMMTNKQTQNVLRDDHGDGFDRLALRTQEEILQIKNKYEDKIGEISIGGQKVSLEDF
                     CYILLSLGSQTLTIRGSEKSLHGKYFEKLILGSLFTIMGFEYKEKIEEGLNDKCFTLST
                     RAEDRESDATLVFNGKAIRVDIGFIGRGNTEISLDKVSRFRRIDDIGGVTHNVSTMIIV
                     DVIGDRSRIADMAEEIDGKVVAMSDPYWVAKVSSYVSSKLNVDDLLEDKPQLKYIQPFI
                     SDALDKVDLEKYIKL"
                     /name="CfrBI family restriction endonuclease"
     gene            2262..3392
                     /locus_tag="GJJ12_RS27005"
                     /old_locus_tag="GJJ12_027005"
     CDS             2262..3392
                     /locus_tag="GJJ12_RS27005"
                     /old_locus_tag="GJJ12_027005"
                     /EC_number="2.1.1.-"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000216732.1"
                     /GO_function="GO:0003677 - DNA binding [Evidence IEA];
                     GO:0008170 - N-methyltransferase activity [Evidence IEA]"
                     /GO_process="GO:0009307 - DNA restriction-modification
                     system [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="site-specific DNA-methyltransferase"
                     /protein_id="WP_101990832.1"
                     /translation="MTIKNNYLNRGYLVTSTTQAKKIAKSHLEKLDLVDKFSFGLPEVD
                     DRYHVWRVPLVITGQRIGEIVINSRTSTIDHEKSSKSPFLIKKAMEVSHTPKKVKQGKK
                     IISKSPLNNTLLQGNCAETLKKLPDESVNLVFTSPPYYNAKPEYSEYHTYEEYLSLLRS
                     VIKECHRVLSEGRFFVINVSPVLIRRASRNEASKRIAVPFDLHRLFIEEGYEFVDDIHW
                     VKPEGAGWALGRGRRFAADRNPLQYKPVPVTEYILVYRKKTDKLIDWNIRNHHSKEDVF
                     ESKIGDGYEKTNLWKINPSRYRKHPATFPYELAERVIKYYSFKNDVVLDPFAGSGTTAK
                     AAIDLGRKFVMCEISEQYIDLIIEETMLGGDLEIIN"
                     /name="site-specific DNA-methyltransferase"
     gene            complement(3840..4055)
                     /locus_tag="GJJ12_RS27010"
                     /old_locus_tag="GJJ12_027010"
     CDS             complement(3840..4055)
                     /locus_tag="GJJ12_RS27010"
                     /old_locus_tag="GJJ12_027010"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_015328239.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MbeD family mobilization/exclusion protein"
                     /protein_id="WP_015328239.1"
                     /translation="MTELEKQLLSALEQLQQDYSRRLDEWESAFEEWRKMSGLMQRENA
                     ALSERVSGLSRQVQSLSEQLRRLSTG"
                     /name="MbeD family mobilization/exclusion protein"
     gene            complement(4062..4559)
                     /locus_tag="GJJ12_RS27015"
                     /old_locus_tag="GJJ12_027015"
     CDS             complement(4062..4559)
                     /locus_tag="GJJ12_RS27015"
                     /old_locus_tag="GJJ12_027015"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_020325392.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MbeB family mobilization protein"
                     /protein_id="WP_015328238.1"
                     /translation="MSSLLTASRDFEEKSKAQQQLTEERLKAAFSKHENVVKSELNASA
                     KRINDAISAHEQGMNAAMQSNRLSVLRMVGRTWLTITMVSGLLFASLSGVLWYQGNRIA
                     ANLAEIRQQRDTLSKLHMQTWGVTYLENRNGRFLVLPEGMKAETGRTVDNKTRNAVKLV
                     RE"
                     /name="MbeB family mobilization protein"
     gene            complement(<4600..5298)
                     /locus_tag="GJJ12_RS27470"
                     /old_locus_tag="GJJ12_027020"
                     /pseudo=""
     CDS             complement(<4600..5298)
                     /locus_tag="GJJ12_RS27470"
                     /old_locus_tag="GJJ12_027020"
                     /inference="COORDINATES: protein motif:HMM:NF015397.4"
                     /note="incomplete; partial in the middle of a contig;
                     missing C-terminus; Derived by automated computational
                     analysis using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="relaxase/mobilization nuclease domain-containing
                     protein"
                     /name="relaxase/mobilization nuclease domain-containing
                     protein"
     gene            complement(5237..>5409)
                     /locus_tag="GJJ12_RS27025"
                     /old_locus_tag="GJJ12_027025"
     CDS             complement(5237..>5409)
                     /locus_tag="GJJ12_RS27025"
                     /old_locus_tag="GJJ12_027025"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_015328236.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=3
                     /transl_table=11
                     /product="MobC family plasmid mobilization relaxosome
                     protein"
                     /protein_id="WP_193703693.1"
                     /translation="RQLAGMGNNLNQIARKVNAGGAGHDRVQIVAALMAIDAGLERLRH
                     AVLEKGPDDDC"
                     /name="MobC family plasmid mobilization relaxosome protein"
     Typing          complement(255..427)
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="94.253"
                     /coverage="100.0"
                     /evalue="4.35e-69"
     Typing          352..943
                     /name="rep_cluster_2335"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="90.985"
                     /coverage="98.0"
                     /evalue="0.0"
     Typing          complement(3..148)
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="93.878"
                     /coverage="98.0"
                     /evalue="1.75e-24"
     Typing          complement(3725..5247)
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          complement(5244..5407)
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="91.071"
                     /coverage="98.0"
                     /evalue="4.08e-23"
ORIGIN
        1 gcagcgcggg cgaaatcgag ggaagcctgc cggcgcgtgt cggtttctca tcaaggcagg
       61 tctggcgcat ccacgccgcc agttgttttc cgtcgcaccg ctcaagcaac cgccggtgtt
      121 cgtcttccgt cacccacatc gtgagcatct tgttgcgttt atctgccaga atcgcctcct
      181 gataacgccg tgacggacgg gaaagccttt cccggtcggc gcggggttgg acaagccgca
      241 ggcgcgtcag tggggtttcg gggcgcagcc ctgaaccagt cacgtagcgc tagcggagtg
      301 tatactggct tactatgttg gcacaggtgc gggaatcagt gaagtgcttc atgtggcagg
      361 agaaaaatgc agcagcggag cgtaagcgga atatatgaga caggatatat tccgcttcct
      421 cgctcactga ctcgctacgc tcggtcgttc ggctgcggcg agcggtgcgg gcttacgaat
      481 ggggcggaaa tttcctggta gatgccagga agaaactgaa cagggaaacg ataaggccgc
      541 ggcgaagccg tttttccata ggctccgccc ccctgacaag catcacgaaa tctgacgctc
      601 aaatcagtgg cggcgaaacc cgacaggact taaagatacc aggcgtttcc ccctgatggc
      661 tccctcgtgc gctctcctgt tcctgccttt cggtttaccg gtgtcattcc gctgttatgg
      721 ccgcgtttat ctcattccac gcctgacact cagttccggg taggcagttc gctccaagct
      781 ggactgtatg cacgaacccc ccgttcagtc cgaccgctgc gccttatccg gtaactatcg
      841 tcttgagtcc aacccggata gacgtgcaaa tgcgccattg gcaacggcca ctggtaagca
      901 ggatgtgcga gagatgtatc gagagttctt gaagtggagg ccttagtgag gctacactgg
      961 aaggacggat ttggtgacac gtctcgcaca agactgttac cacggatcag aaacttgcag
     1021 gttcctgatc cttcgaaaaa ccaccgttgg tagcggtggt ttttctttat gtagagatta
     1081 tgcttttaat aagcatgtag tcaaggatta caatatctta taacttaatg tatttttcca
     1141 gatctacttt atctagagca tccgatataa aaggctgtat atatttaagc tgaggtttat
     1201 cctctagaag atcatctaca tttaattttg agctaacata ggaagagacc tttgcaaccc
     1261 aatacgggtc actcatcgca acaactttac catcaatctc ttcagccata tcagctattc
     1321 tacttctatc accaataaca tcaacgataa tcattgtact tacattatgt gttaccccac
     1381 caatgtcatc tattcgtctg aacctagata ctttatctaa acttatttct gtattacctc
     1441 tacctataaa tccaatatca accctaatag ctttcccatt aaaaaccaga gtagcatctg
     1501 actccctatc ctcagctctt gttgaaagag tgaagcattt atcattcaaa ccctcttcaa
     1561 ttttttcttt gtattcaaac cccattattg taaacaaaga tccaagtatt agtttttcaa
     1621 aatatttgcc atgaagagat ttctcagacc ctctaatagt taatgtttgt gagccaagtg
     1681 acaaaagaat atagcaaaaa tcttctaacg ataccttttg cccaccaata gatatctcgc
     1741 caattttatc ttcatactta ttttttattt gaagaatttc ttcttgcgtc cttaaagcaa
     1801 gcctgtcgaa accatctcca tgatcatctc ttaaaacatt ttgcgtctgc ttatttgtca
     1861 tcataaccat ccattcaagg actggttgat tagacttaat ataagccttg ttcgataatg
     1921 catcctttgc aataagataa agctgttttg gcgttaaccc ctctttcatt ttatcaacga
     1981 aaaaatcaaa taaagagaga ttgctttcta acaacctagt ccgagttaat atttcagtaa
     2041 attcacgaac atttttacct gttaaaacat cataaacaac ctttttaaaa acatcaggcc
     2101 caaatttatc taacacatca ttttttgaaa ttttcgctaa cgctatgagt tcattaggga
     2161 aacaattttt atccttgaaa ttcatatcct caccatggac atagtaaaaa agagatgcta
     2221 agatagcagg ttgtatggta acagatcgat agttaggaaa aatgacgatt aaaaacaact
     2281 atttaaacag aggttatttg gtaacttcta cgactcaagc gaaaaaaata gcgaagtcgc
     2341 acttagaaaa attagacttg gttgataaat tttcttttgg gttgcctgaa gtcgatgacc
     2401 gataccacgt atggcgtgta ccattagtaa taacaggtca aagaattggt gaaatagtta
     2461 taaattcaag aacatcaact attgaccatg aaaaaagctc gaaatctcca tttcttatca
     2521 aaaaggcaat ggaggttagt catacaccga aaaaggtaaa gcaagggaaa aaaataatat
     2581 caaagtcccc attaaacaat actttgttac aaggtaactg tgcggagact ttaaagaaat
     2641 tacctgatga atcagtgaat ttagttttca catcaccgcc atattataat gccaaacccg
     2701 agtattcaga atatcataca tatgaggagt acctctcttt gttacgatca gtaataaaag
     2761 agtgccatag ggttttgagt gaaggccgat tttttgttat caatgtctcc cctgttttaa
     2821 taagaagggc gtcacgaaat gaagcatcaa aaagaatagc tgtgcctttt gatttacata
     2881 gattatttat tgaagaaggc tacgaattcg tagatgatat acattgggtc aagccagaag
     2941 gagctggatg ggctttaggt cggggtcgcc gattcgcagc tgaccgcaat ccgttgcaat
     3001 ataaaccagt tccagtaact gagtatattc ttgtttacag aaaaaaaacc gataaattaa
     3061 tagattggaa cataagaaac catcatagca aagaggatgt ttttgaatca aaaatcggcg
     3121 acggttacga aaagaccaat ctgtggaaaa taaacccttc tcgttataga aagcatcctg
     3181 ctacatttcc ttatgagctg gcagaaagag ttataaaata ctattcattc aaaaacgatg
     3241 tcgttttaga tccttttgct ggttcaggaa caacagcaaa agcagcaatt gatttaggta
     3301 gaaaatttgt gatgtgtgaa atatcagagc agtatattga tctaatcata gaagaaacca
     3361 tgctaggtgg tgacctagaa atcataaatt aataaaaaga tggcataaat ttaatttggt
     3421 gaaagccgcc agaaaggcgg cttttttatt cctaccgata gctcgaattt accataatcc
     3481 cttcttaccc gcaccgcgcc ggaggcactc agggcgtttc tgatggctga cgggcaaaag
     3541 gtggtggcaa gtacaccgaa aaccaccaga aacgcacctg atttatttta cgcatatgca
     3601 tcacttattc acatcactgc atagccggtg atttcggtta aaaaagactc tctgtgtgct
     3661 gaaatcgcag aaaatggcca tgatccccgt cacgctcagg ccacctgaga cgggcgttta
     3721 tcagtctcca tactccctgt caccatgaga taatgtgcgt tgccgttccg gtaccagatc
     3781 tgctgtcttc tctggttcct tttccgttgt ttgcccgtat cgctgttgct caatctcatt
     3841 cagcctgtcg ataaccggcg cagctgctcg ctcaaactct gcacctgcct gctcaagccc
     3901 gacacgcgct cgctcagcgc cgcgttctcc cgttgcataa gaccagacat cttccgccat
     3961 tcctcgaagg cgctctccca ctcgtccagc cttctcgagt agtcctgctg tagctgctct
     4021 aacgcgctca gcaattgttt ttccagttcc gtcattctgc tctactcccg taccagcttc
     4081 accgcgttcc gcgtcttgtt gtccaccgtc cggcccgttt cggctttcat cccctccggc
     4141 agcaccagaa accgtccgtt gcggttctcc agataggtca cgccccacgt ctgcatgtgc
     4201 agtttcgaca gcgtatctct ctgctgcctg atttccgcca ggttcgccgc tatccggttc
     4261 ccctggtacc acagcacccc gctcaggctg gcgaacagca gccctgacac catggtgatg
     4321 gtcagccacg tccgcccgac cattcgcagc acgctcagcc ggttcgactg catcgccgcg
     4381 ttcatcccct gttcgtgggc gctgatggcg tcgttgattc tcttcgcgct tgcgttcagt
     4441 tccgatttga caacgttctc gtgcttgctg aatgcggctt tcagcctctc ttcggtaagc
     4501 tgctgctgtg ctttcgattt ctcctcgaag tccctcgagg ccgttaaaag actgctcata
     4561 aatggctccc ctcagtcgga tatttcgccc cccgtccggg tcggcaatgc tgatactgtt
     4621 ttttgtggtt ctgaccacct caaaaccggc cgctgtgagc gcccctgtga cgtcatcacg
     4681 cgttttcagc tctcctgatg aggctaacat cagcaaaccc cgtgtaatcg tctctgcggc
     4741 ttcctgcttc gtttctggca gtcctgaagg cgtgaccagc gcccgccggt tctccgggtc
     4801 gttcggatca tgtagcccca gcctgccgtt gaccactgtc tgccacgcat cgatgcgcgg
     4861 ccggtcggca cgatcgtaat acggctggag gcgtttcccc gtcagtaatt cggtattggg
     4921 gatcagaaaa ttcagctcaa gacgaccctt gtctgcgtgt tccacccaca gaatgctgta
     4981 ctggtcttta tcgagtccgg gcatcagaac ccgctcaaag ctggccatca gtttttcacg
     5041 ctgacccggc ggcaggtccg cctccgcgaa tgacagcacc ccggaggtat attttttcac
     5101 atacggcgac gcatcaatca gctcccggac ttcttccggc ttcccctgca ggacgctggc
     5161 accttcacgc tgccggtctt tacccagaag ataatccaca ggaccggcgc ccccgccgcg
     5221 accccgggga tggaatttaa caatcatcgt ccggcccttt ttccagtacg gcatgccgca
     5281 accgttccag accggcatcg atcgccatca gcgctgccac gatctgcacc cggtcatgac
     5341 cggcaccacc ggcgttcact ttccgggcga tctggttcag gttattgccc atgccggcaa
     5401 gctgacgca
//
