LOCUS       CP063017                3808 bp    DNA     linear   BCT 29-OCT-2020
DEFINITION  Klebsiella pneumoniae strain CriePir99 plasmid unnamed4, complete
            sequence.
ACCESSION   CP063017
VERSION     CP063017.1
DBLINK      BioProject: PRJNA580263
            BioSample: SAMN13153742
KEYWORDS    .
SOURCE      Klebsiella pneumoniae
  ORGANISM  Klebsiella pneumoniae
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Klebsiella/Raoultella group; Klebsiella.
REFERENCE   1  (bases 1 to 3808)
  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), E261 (2020)
   PUBMED   32429555
  REMARK    Publication Status: Online-Only
REFERENCE   2  (bases 1 to 3808)
  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
REFERENCE   3  (bases 1 to 3808)
  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
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: Unicycler v. v0.4.8-beta
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 105x
            Sequencing Technology             :: Oxford Nanopore MinION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI
            Annotation Date                   :: 10/13/2020 18:40:18
            Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline
            (PGAP)
            Annotation Method :: Best-placed reference protein set; GeneMarkS-2+
            Annotation Software revision      :: 4.13
            Features Annotated :: Gene; CDS; rRNA; tRNA; ncRNA; repeat_region
            Genes (total)                     :: 5,516
            CDSs (total)                      :: 5,392
            Genes (coding)                    :: 5,268
            CDSs (with protein)               :: 5,268
            Genes (RNA)                       :: 124
            rRNAs                             :: 9, 8, 8 (5S, 16S, 23S)
            complete rRNAs                    :: 9, 8, 8 (5S, 16S, 23S)
            tRNAs                             :: 88
            ncRNAs                            :: 11
            Pseudo Genes (total)              :: 124
            CDSs (without protein)            :: 124
            Pseudo Genes (ambiguous residues) :: 0 of 124
            Pseudo Genes (frameshifted)       :: 58 of 124
            Pseudo Genes (incomplete)         :: 68 of 124
            Pseudo Genes (internal stop)      :: 27 of 124
            Pseudo Genes (multiple problems)  :: 25 of 124
            CRISPR Arrays                     :: 1
            ##Genome-Annotation-Data-END##
            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..3808
                     /organism="Klebsiella pneumoniae"
                     /mol_type="genomic DNA"
                     /strain="CriePir99"
                     /isolation_source="urine"
                     /host="Homo sapiens"
                     /db_xref="taxon:573"
                     /plasmid="unnamed4"
                     /geo_loc_name="Russia: Moscow"
                     /lat_lon="55.76 N 37.62 E"
                     /collection_date="2017"
                     /collected_by="Pir Nat Surg Centre"
     gene            250..678
                     /locus_tag="GJJ02_027535"
     CDS             250..678
                     /locus_tag="GJJ02_027535"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000222531.1"
                     /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="QOU65312.1"
                     /translation="MTYSIEEKWKAGGLSLGWTAIPTVLFFIQNEKKLTSVAFNTLLNL
                     IVHWWNLQEWPHPSMESLAIRMGVSVRTVQRAINDLEKANLLDKKPTSKSDSRYGGRNI
                     YDLTKLVDYLDTMGPSVAEQVKKPRHKRPVYTVRKTTT"
                     /name="helix-turn-helix domain-containing protein"
     gene            962..1162
                     /locus_tag="GJJ02_027540"
     CDS             962..1162
                     /locus_tag="GJJ02_027540"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_017802053.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="sigma-70 region 4 domain-containing protein"
                     /protein_id="QOU65313.1"
                     /translation="MFGFGIQGTINKGFFLQMARRDQDAFLQYLYDQGYSAKDISKNFD
                     IPVPSVYNRINAHRGRGPLPN"
                     /name="sigma-70 region 4 domain-containing protein"
     gene            complement(1964..2386)
                     /locus_tag="GJJ02_027545"
     CDS             complement(1964..2386)
                     /locus_tag="GJJ02_027545"
                     /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="QOU65314.1"
                     /translation="MARVSISEAARLVKVSRPTIYKMINSGKLSYTSVVKHGKAIKVID
                     TSELIRVFGSLDGVIDTVKYDVKSDAESTGVNSVGLHDLQHRIALLEAENDGLKGAVKA
                     RDEHIDSLRQAMQLLEYNHEPSSPPHSPWWKFWKKS"
                     /name="helix-turn-helix domain-containing protein"
     gene            complement(2386..2577)
                     /locus_tag="GJJ02_027550"
     CDS             complement(2386..2577)
                     /locus_tag="GJJ02_027550"
                     /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="QOU65315.1"
                     /translation="MTKQQQTALNMAKFIQNQSLLLLEKLNELDLDVEADLCEKLHDDA
                     EHLFRTLSSRLDELQDGN"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            complement(3338..3766)
                     /locus_tag="GJJ02_027555"
     CDS             complement(3338..3766)
                     /locus_tag="GJJ02_027555"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000534558.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="QOU65316.1"
                     /translation="MGSGAGAQNPQLNIVSFSETFNLYYTSRFSAKTLDKIDDFIEHFE
                     KYNLFGDPLKKHPAWIGKVSPSWKVPDHYENKEAIELHARANKLWHAHLGDPVFKDTFH
                     GKYKVSDWVIHFQRLTPNHIKLLELGYHDPMELPQNFE"
                     /name="hypothetical protein"
     Typing          2626..3102
                     /name="ColRNAI_rep_cluster_1987"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="88.797"
                     /coverage="91.0"
                     /evalue="4.61e-163"
ORIGIN
        1 gacttctcat tcgctctgga aatcaacaga gacaaggata cgccaaatac ttcagtatct
       61 ttaataagat catgacgttg ttcggttttc atatcgttaa ctccgtatct aattcagaca
      121 ggaaaaaatc ttttttccgc tttcagagta gtcttttgta gttgcactat aatggcgttg
      181 atgtcaccct attcatatga ataatcatat aatatatact tcaaatattt ttgtttttta
      241 ggaaaatcaa tgacttactc tattgaggaa aaatggaagg ctggcggttt gtctcttggc
      301 tggactgcaa tacctactgt cttgtttttt atacagaacg agaaaaagct aacctccgta
      361 gcctttaaca ctctgcttaa cctgatcgtt cattggtgga atttgcaaga atggccgcat
      421 ccatcaatgg aaagcctagc catacgtatg ggggtttctg taaggacagt tcagagagct
      481 atcaatgatc tggaaaaagc taatctcttg gacaagaaac caacgtcgaa gagtgatagc
      541 cgatatggag gtcgtaatat ttatgatcta acaaagctcg ttgattacct ggatacaatg
      601 ggcccatcag tagctgaaca ggttaagaaa ccccgtcata aaagaccggt atataccgta
      661 agaaaaacaa caacttaaaa aagagcaatt gcactgttcg aaggaaaaac gataactact
      721 ctatggtatt gcttgctgta taggtattgg tggtcctgcg gctggttcat cgcttcacgg
      781 ttaaaatagt cctgtaagct gttaatattt aacataacac tactaccacg aacctacgta
      841 acaatcgcta ccaacacaga agtgacaaat ttataaaaaa acaaaaacca taaaaaaact
      901 tgactttatg ttttttttgg ctaatttctt tatcatttct ttatcaaaaa tagaggtggc
      961 tatgtttggt tttggaattc aaggtactat taataaagga ttttttcttc agatggctcg
     1021 tagagatcag gatgcatttt tgcaatatct ctatgaccaa gggtactcag caaaagatat
     1081 cagcaagaac ttcgatattc cggttcctag cgtctacaac agaatcaacg ctcaccgagg
     1141 ccgtggacct cttcccaatt aatggttctt ctatacaaaa aagtcgcctg gataggcgac
     1201 ttttttaact gaactctgtg tatagattta ccataacgtc tcaattgtac gcaccgctaa
     1261 aacggcctca gggcgtttct gacggaaaac cggcaaaaca ggcaacaaac cacccgaaaa
     1321 cccgccagaa acgcgcaggc tccgttttta cggcatgcat gagtatgcgc acaagtgcat
     1381 agcgcgaaaa ctcacgccat tcagccaggg taagtcctgt ttccggcgtt ctttccatcc
     1441 gaaaacggtg aacggggacg caatttattg cgtggccgtg aagcgttgcc ggcgcagccg
     1501 gaaaaccggt tttcagcacg ttcaggaatc gtgttcgtcg acggccggca atcacgttat
     1561 ggcaagtcgc cggacgactc accacacgat tcaccggcga ctcttcacta gagtcgtacc
     1621 cagagtcgcc gagtctaaaa aacaaccaaa cggggagtcg ggtctagagt cgggtcgtta
     1681 ttaactcatt gtttttatag tcctgagtcg ttaccgactc tatgacgact cgccggggac
     1741 tctatgacga gtcgtcatag agtcggatct atgtaaataa aatttaaaaa acgaaatttc
     1801 acgaaagtaa accactgata ttaaatacaa atctgcaaaa ttttaatttt gcgtagtgtg
     1861 tgggtatttt tagtcgtgag gagcgttcag agatctggcg atttttggga aggttcagga
     1921 actccccggg atggccggag aggaaaactg aagcatgacg gggtcaggat tttttccaga
     1981 atttccacca cggggaatgg ggtggtgaag aaggttcgtg attgtactcc agaagctgca
     2041 tagcctgacg aagggaatca atatgctcat ctcgagcctt aacagcccct ttaagaccat
     2101 cgttttcagc ttctagtaaa gcaattctat gttgtaaatc atgtaaacca acgctgttaa
     2161 cacctgtaga ttctgcgtca ctttttacat catattttac agtatcgatg acaccatcaa
     2221 gagaaccaaa cactctaata agctctgagg tatcaataac tttaatagcc ttcccgtgct
     2281 ttacaacaga ggtgtaactt aacttcccac tgttaatcat cttgtaaatt gtggggcgac
     2341 taaccttaac aagccgtgcc gcttcactaa tagacactct ggccatcagt taccatcctg
     2401 taattcatcc agtctcgagg acagtgtacg gaaaagatgc tccgcatcat cgtggagttt
     2461 ctcacaaagg tcggcctcta catcgagatc aagctcgtta agcttctcca gcaggagcag
     2521 agactgattc tggatgaact tagccatgtt tagcgccgtt tgctgttgtt tcgtcataaa
     2581 gagcctcaga gcgtcagtgc tcaatgtaaa aactgtctcc tttccgcttc ctcgctcact
     2641 cagtcgctac gctcctgccg ttcggctgcg gcgagcggtc gcaactcacg tataagagca
     2701 taagacgaca gggctgatag ccggagggga caaaataagg tcgcggcgtt gccgtttttc
     2761 cataggctcc gcccccctga caagcatcac agaagcggac gctcaaatca gtggtggcga
     2821 aacccgacag gactataaag atacctatca tttctgatag gcggctccct cgtgcgctct
     2881 cctgttcctg cctttcggtt taccggtgtc attccgctgt tatggccgcg tttatctcat
     2941 tccacgcctg acactcagtt ccgggtaggc agttcgctcc aagctggact gtatgcacga
     3001 accccccgtt cagtccgacc gctgcgcctt gtccggtaac tatcgtcttg agtccaaccc
     3061 ggaaagacac gactaatcgc cattggcaac ggccactggt aagcaggatg tgcgagagat
     3121 gtattgagag ttcttgaagt ggcggcctaa ctgaggctac actggaagga cggatttggt
     3181 gacatgtctc gcacaagact gttaccacgg ttagataatc tgccaggatt aaataacctt
     3241 cgaaaaacca cctgccaggg tggttttttc gttttcacaa caggagatta cgacgaggtt
     3301 gaatgaatct caagatttca tttagtctgc tacccgatca ttcaaagttt tggggtagtt
     3361 ccatcgggtc atggtatccc agttctaaaa gctttatatg gttcggtgtc agccgctgga
     3421 aatggataac ccagtcagaa accttgtatt tcccatgaaa cgtatctttg aaaaccggat
     3481 cgcctaaatg agcatgccat aacttgttag ctctagcgtg cagctcaata gcttctttgt
     3541 tttcgtaatg atcaggcact ttccacgacg gcgatacttt accaatccaa gctggatgtt
     3601 tttttaaagg atcgccaaag aggttatatt tttcgaaatg ctcaatgaaa tcatcgattt
     3661 tatcgagtgt ttttgcagaa aatcgggatg tgtaatagag attgaaagtc tcagagaacg
     3721 agacaatatt caactgtgga ttttgcgcac ctgctccgct gcccatgctc ttctctgctc
     3781 cctacttaga ccagatggca ttgtaaca
//
