LOCUS       NZ_CP125198             5010 bp    DNA     circular CON 05-APR-2024
DEFINITION  Klebsiella pneumoniae strain 59 plasmid unnamed5, complete sequence.
ACCESSION   NZ_CP125198
VERSION     NZ_CP125198.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN33790391
            Assembly: GCF_037477815.1
KEYWORDS    RefSeq.
SOURCE      Klebsiella pneumoniae
  ORGANISM  Klebsiella pneumoniae
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Klebsiella/Raoultella group; Klebsiella.
REFERENCE   1  (bases 1 to 5010)
  AUTHORS   Konanov,D.N.
  TITLE     Direct Submission
  JOURNAL   Submitted (17-MAR-2023) Laboratory of Mathematical Biology and
            Bioinformatics, Research Institute for Systems Biology and Medicine,
            Nauchniy Proezd, Moscow 117246, Russia
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: Unicycler v. 0.4.8
            Genome Representation             :: Full
            Expected Final Version            :: No
            Genome Coverage                   :: 61x
            Sequencing Technology             :: Illumina; Oxford Nanopore
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_037477815.1-RS_2024_04_05
            Annotation Date                   :: 04/05/2024 19:35:36
            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)                     :: 5,798
            CDSs (total)                      :: 5,672
            Genes (coding)                    :: 5,526
            CDSs (with protein)               :: 5,526
            Genes (RNA)                       :: 126
            rRNAs                             :: 9, 8, 8 (5S, 16S, 23S)
            complete rRNAs                    :: 9, 8, 8 (5S, 16S, 23S)
            tRNAs                             :: 88
            ncRNAs                            :: 13
            Pseudo Genes (total)              :: 146
            CDSs (without protein)            :: 146
            Pseudo Genes (ambiguous residues) :: 0 of 146
            Pseudo Genes (frameshifted)       :: 53 of 146
            Pseudo Genes (incomplete)         :: 92 of 146
            Pseudo Genes (internal stop)      :: 23 of 146
            Pseudo Genes (multiple problems)  :: 19 of 146
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP125198.1.
            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..5010
                     /organism="Klebsiella pneumoniae"
                     /mol_type="genomic DNA"
                     /strain="59"
                     /db_xref="taxon:573"
                     /plasmid="unnamed5"
                     /geo_loc_name="Russia"
                     /collection_date="2022"
     gene            complement(93..254)
                     /locus_tag="P4G15_RS28910"
                     /old_locus_tag="P4G15_28880"
     CDS             complement(93..254)
                     /locus_tag="P4G15_RS28910"
                     /old_locus_tag="P4G15_28880"
                     /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_162870772.1"
                     /translation="MAKHWSGQECPKTGTYGQYHDTDNSYAGSEYDRHVSKGDKFPPSK
                     NNHHFQEK"
                     /name="hypothetical protein"
     gene            491..736
                     /locus_tag="P4G15_RS28915"
                     /old_locus_tag="P4G15_28885"
     CDS             491..736
                     /locus_tag="P4G15_RS28915"
                     /old_locus_tag="P4G15_28885"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_012848468.1"
                     /GO_component="GO:0110001 - toxin-antitoxin complex
                     [Evidence IEA]"
                     /GO_function="GO:0003677 - DNA binding [Evidence IEA];
                     GO:0097351 - toxin sequestering activity [Evidence IEA]"
                     /GO_process="GO:0045927 - positive regulation of growth
                     [Evidence IEA]; GO:0006355 - regulation of DNA-templated
                     transcription [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 Phd/YefM family
                     antitoxin"
                     /protein_id="WP_025987695.1"
                     /translation="MHAINFTDARKHFAETMKRVTDDAEPVRVMRRDAPDIVMIDAGEY
                     EALIETVYLFSNPANAEHINESMKQAERGEFVEVEY"
                     /name="type II toxin-antitoxin system Phd/YefM family
                     antitoxin"
     gene            717..992
                     /locus_tag="P4G15_RS28920"
                     /old_locus_tag="P4G15_28890"
     CDS             717..992
                     /locus_tag="P4G15_RS28920"
                     /old_locus_tag="P4G15_28890"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_017412855.1"
                     /GO_process="GO:0008219 - cell death [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="Txe/YoeB family addiction module toxin"
                     /protein_id="WP_019725129.1"
                     /translation="MSKWNIKFTRNGADDLNYWRDTDKKKFERIRQLLLSIEADPLTGI
                     GKPERLRHHKDPALYSRRIDQSHRLVYSIQNGEIIIYAARYHYGDK"
                     /name="Txe/YoeB family addiction module toxin"
     gene            1240..2145
                     /locus_tag="P4G15_RS28925"
                     /old_locus_tag="P4G15_28895"
     CDS             1240..2145
                     /locus_tag="P4G15_RS28925"
                     /old_locus_tag="P4G15_28895"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001697689.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="replication initiation protein"
                     /protein_id="WP_019725130.1"
                     /translation="MHNAALELFNERLPHKPYFSDDLHFGVRIAGKERAILAKYIQFNQ
                     PHAMFWLGFDVDRAGSSIDWSDRNAPAPTLTITNPENGHAHLLYALENSIRTAPDGKIK
                     PLRYAASVENALRKKLEADAGYSGLICKNPNHNHWKIAVWQPKLYTLDWLADFLDLNTG
                     NDKEIVADYGLGRNCTLFDKTRKWAYRAIRQGWPEYEQWLQACYERACAYNLQFARPLD
                     ENEVRGIAKSIAKWTSNKFSPEEFSKFVDITHSSEIQSKRGKKSGQSRRKGSLEEIKPW
                     VAMGISRRKYFYIKKNGEIR"
                     /name="replication initiation protein"
     gene            2142..2849
                     /locus_tag="P4G15_RS28930"
                     /old_locus_tag="P4G15_28900"
     CDS             2142..2849
                     /locus_tag="P4G15_RS28930"
                     /old_locus_tag="P4G15_28900"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001258875.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_004198042.1"
                     /translation="MKTFVTLWTIVFLAFIAVMCTVDISNYIPSVYTVFSKNRPLVTGA
                     LSILLISVFIWLMVSLYLLKKYSVKVEKLSLGGVNILFNESATLYKKSVKNHLDSKRAI
                     FKLRKNVDAFDEVISSYYQTYQFIRDEMKILNPKKDREIYDFSNEMLMVLNRFLTNYQN
                     NYKRWYKYISDKDEVVDRVSGDVMRFHATSINKIQMQYYDYERILKGFKDVNRFFVNDV
                     KPKFGINTDKWNW"
                     /name="hypothetical protein"
     gene            complement(2886..3500)
                     /locus_tag="P4G15_RS28935"
                     /old_locus_tag="P4G15_28905"
     CDS             complement(2886..3500)
                     /locus_tag="P4G15_RS28935"
                     /old_locus_tag="P4G15_28905"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_012822468.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="TIR domain-containing protein"
                     /protein_id="WP_019725132.1"
                     /translation="MGKHKVFISYHHANDQYYKNALEKMNEEHEIFVNRSVSLGDIDED
                     EAPQKIREIIRDEYLRDTSVLILLVGTETKNRKHVDWELYSSMRDSTINKKSGILVVNL
                     PSTNTTYIRSTHGTNEKSEVHPTVTEWFSIDKRSTYEERFPYMPARIIDNFMKSGSYIS
                     VVNWNQIENNPETLRKLIDMTYNDREKATYDMSREMRMHNS"
                     /name="TIR domain-containing protein"
     gene            3902..4303
                     /locus_tag="P4G15_RS28940"
                     /old_locus_tag="P4G15_28910"
     CDS             3902..4303
                     /locus_tag="P4G15_RS28940"
                     /old_locus_tag="P4G15_28910"
                     /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_019725133.1"
                     /translation="MTRVSISEAARLTGKSRTTLHRLIKTGELSTCSGERNTKMVDISE
                     LLRVFGPFDQPKNEHLTRQVPEQRDTAPADQSEHVIRQLKQQIEHLNILILSKDSHIDS
                     LKQAMLLLENHQAKLTEPPAPWWKFWKKS"
                     /name="helix-turn-helix domain-containing protein"
ORIGIN
        1 cggtgctgat aacggatgtt atggtaaatc aagtgaatgg caggtacaaa aaaagcccca
       61 gagggctttt agtttagact tctgaagata ttttattttt cttggaagtg gtggttgttt
      121 ttgctcggag ggaacttatc acccttgctc acatggcgat catattcaga accagcgtat
      181 gagttgtcgg tatcatgata ttgaccgtaa gtacctgttt ttggacattc ttgcccagac
      241 caatgttttg ccatttactt ttcctttgct cgttttagga gctaagctcc tagcggtacg
      301 aaattgtgcc gcacttcata aatgtaattg cttgaaatta tgcttcaatg tattgacttg
      361 ttgtttttgt ggttattcga ttgagttcac attttgagct gatttggttg tgggttttta
      421 gggaaatatc tttatgtact tatttgcgta catgttctat gctaagcccc aacaaatggg
      481 ggttaacaac atgcatgcaa tcaattttac tgatgcccgt aaacattttg ccgagacgat
      541 gaagcgcgtc actgatgatg ctgaaccggt acgtgtcatg cgccgtgatg cgcctgatat
      601 tgttatgatc gatgcgggag agtatgaggc gctaatcgaa acggtctatc tgttcagcaa
      661 tccggcgaac gcagagcata tcaatgagtc aatgaaacag gcggagcgcg gcgaatttgt
      721 cgaagtggaa tattaagttc actaggaatg gcgctgatga ccttaactac tggcgtgata
      781 ctgacaaaaa gaagtttgag cgtatccggc aactgttgct cagcatcgag gctgatccgc
      841 tgacaggtat aggaaaaccc gaacggctgc ggcaccacaa agatccggca ctctactccc
      901 gcaggattga tcagagccac cgtctggtct attcaatcca gaacggagaa atcatcatct
      961 acgcagcccg ttatcactat ggtgacaaat agcaaaagtc gatatagccc gcttgatgcg
     1021 ggcttttcat gcaaggcgta caacggatgt tagggtaagt cgctgtcaga tcgacacaaa
     1081 ggcaaagtcg gtgtaacgtt agcctcagaa aaaacaaagc cccggaaatc atgtcatatc
     1141 ttggcggatc gcatgataac cagggctagg tcgaaacctt gaaaggatat tagcacatga
     1201 accgtgccag acaacagccc gccataagcg cagggcacat tgcataacgc cgcactcgaa
     1261 cttttcaacg aacgcttacc acacaagccg tacttttcgg acgatctgca ctttggtgtc
     1321 cgtatcgccg gtaaggaacg cgctattctg gcgaaatata tccagttcaa tcagcctcac
     1381 gccatgttct ggctgggatt tgacgttgac cgcgccggtt cctccatcga ctggagcgac
     1441 cgcaacgcgc ctgcaccgac gctgaccata actaaccccg aaaacggaca cgcgcacctg
     1501 ctgtacgcgc tggaaaactc gatacgcacc gcgccggacg gcaaaataaa accgttacgc
     1561 tacgccgcct ccgtggagaa tgcgctacgt aaaaaattag aggctgacgc tggatattcg
     1621 gggctcatct gcaaaaatcc gaaccacaac cactggaaaa tcgccgtgtg gcagccgaag
     1681 ctctacactc tggactggct ggccgacttt ctcgatctga acacagggaa tgacaaggaa
     1741 atcgttgccg actacggctt aggccgtaac tgcacgttgt tcgacaaaac ccgtaagtgg
     1801 gcatatcgcg ccatccgtca gggctggcct gagtatgagc agtggctgca agcctgctac
     1861 gaacgcgctt gcgcatacaa cctgcaattt gcacggcctc tggatgaaaa tgaggtaaga
     1921 gggatagcta agagcattgc taaatggaca tcaaataaat tttcacctga agaattcagt
     1981 aaatttgttg atattactca ttcctctgaa attcaatcaa agagagggaa aaagtcagga
     2041 cagtcaagga ggaaaggaag cctagaggaa ataaaacctt gggtagctat gggaataagc
     2101 aggcggaagt atttttatat caagaaaaat ggtgaaataa gatgaaaacc ttcgtaactc
     2161 tttggactat agttttttta gcatttattg ccgtgatgtg tactgttgat atatctaatt
     2221 acattccgtc tgtttacaca gtttttagta agaatagacc tcttgtaact ggcgcccttt
     2281 ctattctttt gatatctgtt tttatttggc tgatggtatc cctctactta cttaaaaagt
     2341 attcggttaa ggttgagaaa cttagccttg gtggagtgaa tatacttttc aatgagagtg
     2401 ctacacttta caaaaagagt gtaaaaaatc acctagattc aaaaagagca attttcaaat
     2461 taagaaaaaa cgttgatgcc tttgatgagg ttatttcatc atattatcag acttaccaat
     2521 ttattcgtga tgaaatgaaa atactaaacc ctaaaaaaga tcgtgagatt tatgatttca
     2581 gcaatgagat gctcatggtg ttaaatagat ttctaactaa ctaccagaac aactacaagc
     2641 gttggtataa gtacatatca gacaaagatg aggttgttga tagggttagc ggtgatgtca
     2701 tgagatttca tgcaaccagc ataaataaaa tacaaatgca gtattatgat tatgagcgta
     2761 ttttaaaagg ttttaaagat gttaaccggt tctttgttaa tgatgtgaag cctaagtttg
     2821 gaatcaatac agataagtgg aactggtaaa ttaaaggagt agccaaggct actccttgga
     2881 tagtactatg aattatgcat tctcatttct ctcgacatat catacgttgc tttttctcta
     2941 tcgttataag tcatgtctat taattttctg agtgtttctg ggttgttttc tatttgattc
     3001 cagttgacca ctgatatata agacccgctc ttcatgaagt tgtctattat tcttgctggc
     3061 atatatggga acctttcctc ataagttgag cgcttatcaa tagaaaacca ttcagttacg
     3121 gtaggatgaa cttctgattt ttcattagtt ccatgtgttg aacgaatgta cgtagtattt
     3181 gttgacggga gattgacgac taaaattcct gattttttgt taatggtact atctctcatg
     3241 ctagagtaaa gttcccaatc tacgtgtttt ctgttttttg tttcagttcc aacaagaagg
     3301 ataagaactg atgtatctct aagatattca tctcttatta tctctcttat tttttgtggg
     3361 gcttcatctt catctatatc acctaatgat actgagcgat tcacgaatat ttcatgttcc
     3421 tcattcattt tttcaagtgc gtttttgtag tactgatcat tcgcatggtg gtagctaatg
     3481 aataccttat gctttcccat ttttattgtc ctttttttgt ttgtgtgcac tctattttgc
     3541 acttgaacct atatcagata acagctctct tttagagagc tctttttttc tcagccagca
     3601 cacatagggt cccttcagca aggtctcgcc atgactggtt tagggcgggc tcgttgcttc
     3661 cctaaacgcc ttgagaagag agctatcacc tcactttatt cttacgtacc gctcgccgca
     3721 gtcttatgac cgaacgtagt gagcgaatgc gcgaggaagc ggaaagtcat ttgttgcctg
     3781 cattttgcac ggtcactcct gtgtttcatc gcccttctga aaaacacatc acttctggac
     3841 cagtatgtcg taagctggcc cctgtttcct tgagactgaa tgtattaaag gatgataact
     3901 gatgaccaga gtgtctatta gtgaggctgc acggctgacg ggtaagagcc ggacaacgct
     3961 gcacaggtta atcaaaacag gtgaactgtc cacttgtagc ggtgaacgaa atacaaaaat
     4021 ggtcgatata tcagagcttt tacgtgtttt cggaccgttt gaccaaccga agaatgaaca
     4081 ccttactcga caagtacctg aacagcgtga tacagcgcct gctgaccaga gtgaacatgt
     4141 cattcgtcaa ctgaaacagc agattgaaca ccttaacata ttgattttat cgaaggattc
     4201 gcacattgac agcctgaaac aggccatgct ccttcttgaa aatcaccagg caaaattaac
     4261 tgaacccccg gcgccgtggt ggaaattctg gaaaaaatcc tgaccccgtc atgcttcagt
     4321 tttcctctcc ggccattccg gggagttcct gaaccttccc gaaaatcgtc agatctctga
     4381 acgctcctca ccacgaaaaa tacccacacc ccacgcaaaa ttttaatttt gcagatttgt
     4441 atttaatatc agcagcttac tttactgaaa tttcgttttt taaattttat ttatatagat
     4501 ccgactctat gacgagtcgt catagagtcc ccggcgagtc gtcatagagt cggtaacgac
     4561 tcaggcctat aaaaacaatg agttaataac gacccgactc tagatccgac tccccgtttg
     4621 gttgtttttt agacgtggcg actctgggta cgactctagt gaagagtcgc cggggaatcg
     4681 tgtggtgagt cgtccggcga cttgccataa cgtgattgcc ggccgtggac gaaccgattc
     4741 ctgaacgtgc tgaaaaccgg ttttccggct gcgccggcaa cgcttcacgg ccacgcaata
     4801 aattgcgtcc ccgttcaccg ttttcggatg ggaagaacgc cggaaacagg acttcccctg
     4861 gctgaatggt gtcaatttcc gcgctatgca cttgtgcgca tactcatgca tgccgtaaaa
     4921 acagagcctg cgcgtttctg gcgggttttc gggtggtttg ttgccttgtt taccggtttc
     4981 ccgtcagaaa cgccctgagg gcatctcagg
//
