LOCUS       NZ_CP125163             5010 bp    DNA     circular CON 05-APR-2024
DEFINITION  Klebsiella pneumoniae strain 165 plasmid unnamed4, complete
            sequence.
ACCESSION   NZ_CP125163
VERSION     NZ_CP125163.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN33790396
            Assembly: GCF_037477855.1
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 (19-APR-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                   :: 54x
            Sequencing Technology             :: Illumina; Oxford Nanopore
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_037477855.1-RS_2024_04_05
            Annotation Date                   :: 04/05/2024 19:45:59
            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)                     :: 5,818
            CDSs (total)                      :: 5,695
            Genes (coding)                    :: 5,548
            CDSs (with protein)               :: 5,548
            Genes (RNA)                       :: 123
            rRNAs                             :: 9, 8, 8 (5S, 16S, 23S)
            complete rRNAs                    :: 9, 8, 8 (5S, 16S, 23S)
            tRNAs                             :: 85
            ncRNAs                            :: 13
            Pseudo Genes (total)              :: 147
            CDSs (without protein)            :: 147
            Pseudo Genes (ambiguous residues) :: 0 of 147
            Pseudo Genes (frameshifted)       :: 56 of 147
            Pseudo Genes (incomplete)         :: 88 of 147
            Pseudo Genes (internal stop)      :: 28 of 147
            Pseudo Genes (multiple problems)  :: 22 of 147
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP125163.1.
            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="165"
                     /db_xref="taxon:573"
                     /plasmid="unnamed4"
                     /geo_loc_name="Russia"
                     /collection_date="2022"
     gene            137..382
                     /locus_tag="P4G12_RS29015"
                     /old_locus_tag="P4G12_28995"
     CDS             137..382
                     /locus_tag="P4G12_RS29015"
                     /old_locus_tag="P4G12_28995"
                     /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            363..638
                     /locus_tag="P4G12_RS29020"
                     /old_locus_tag="P4G12_29000"
     CDS             363..638
                     /locus_tag="P4G12_RS29020"
                     /old_locus_tag="P4G12_29000"
                     /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            886..1791
                     /locus_tag="P4G12_RS29025"
                     /old_locus_tag="P4G12_29005"
     CDS             886..1791
                     /locus_tag="P4G12_RS29025"
                     /old_locus_tag="P4G12_29005"
                     /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            1788..2495
                     /locus_tag="P4G12_RS29030"
                     /old_locus_tag="P4G12_29010"
     CDS             1788..2495
                     /locus_tag="P4G12_RS29030"
                     /old_locus_tag="P4G12_29010"
                     /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(2532..3146)
                     /locus_tag="P4G12_RS29035"
                     /old_locus_tag="P4G12_29015"
     CDS             complement(2532..3146)
                     /locus_tag="P4G12_RS29035"
                     /old_locus_tag="P4G12_29015"
                     /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            3548..3949
                     /locus_tag="P4G12_RS29040"
                     /old_locus_tag="P4G12_29020"
     CDS             3548..3949
                     /locus_tag="P4G12_RS29040"
                     /old_locus_tag="P4G12_29020"
                     /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"
     gene            complement(4749..4910)
                     /locus_tag="P4G12_RS29045"
                     /old_locus_tag="P4G12_29025"
     CDS             complement(4749..4910)
                     /locus_tag="P4G12_RS29045"
                     /old_locus_tag="P4G12_29025"
                     /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"
ORIGIN
        1 gacttgttgt ttttgtggtt attcgattga gttcacattt tgagctgatt tggttgtggg
       61 tttttaggga aatatcttta tgtacttatt tgcgtacatg ttctatgcta agccccaaca
      121 aatgggggtt aacaacatgc atgcaatcaa ttttactgat gcccgtaaac attttgccga
      181 gacgatgaag cgcgtcactg atgatgctga accggtacgt gtcatgcgcc gtgatgcgcc
      241 tgatattgtt atgatcgatg cgggagagta tgaggcgcta atcgaaacgg tctatctgtt
      301 cagcaatccg gcgaacgcag agcatatcaa tgagtcaatg aaacaggcgg agcgcggcga
      361 atttgtcgaa gtggaatatt aagttcacta ggaatggcgc tgatgacctt aactactggc
      421 gtgatactga caaaaagaag tttgagcgta tccggcaact gttgctcagc atcgaggctg
      481 atccgctgac aggtatagga aaacccgaac ggctgcggca ccacaaagat ccggcactct
      541 actcccgcag gattgatcag agccaccgtc tggtctattc aatccagaac ggagaaatca
      601 tcatctacgc agcccgttat cactatggtg acaaatagca aaagtcgata tagcccgctt
      661 gatgcgggct tttcatgcaa ggcgtacaac ggatgttagg gtaagtcgct gtcagatcga
      721 cacaaaggca aagtcggtgt aacgttagcc tcagaaaaaa caaagccccg gaaatcatgt
      781 catatcttgg cggatcgcat gataaccagg gctaggtcga aaccttgaaa ggatattagc
      841 acatgaaccg tgccagacaa cagcccgcca taagcgcagg gcacattgca taacgccgca
      901 ctcgaacttt tcaacgaacg cttaccacac aagccgtact tttcggacga tctgcacttt
      961 ggtgtccgta tcgccggtaa ggaacgcgct attctggcga aatatatcca gttcaatcag
     1021 cctcacgcca tgttctggct gggatttgac gttgaccgcg ccggttcctc catcgactgg
     1081 agcgaccgca acgcgcctgc accgacgctg accataacta accccgaaaa cggacacgcg
     1141 cacctgctgt acgcgctgga aaactcgata cgcaccgcgc cggacggcaa aataaaaccg
     1201 ttacgctacg ccgcctccgt ggagaatgcg ctacgtaaaa aattagaggc tgacgctgga
     1261 tattcggggc tcatctgcaa aaatccgaac cacaaccact ggaaaatcgc cgtgtggcag
     1321 ccgaagctct acactctgga ctggctggcc gactttctcg atctgaacac agggaatgac
     1381 aaggaaatcg ttgccgacta cggcttaggc cgtaactgca cgttgttcga caaaacccgt
     1441 aagtgggcat atcgcgccat ccgtcagggc tggcctgagt atgagcagtg gctgcaagcc
     1501 tgctacgaac gcgcttgcgc atacaacctg caatttgcac ggcctctgga tgaaaatgag
     1561 gtaagaggga tagctaagag cattgctaaa tggacatcaa ataaattttc acctgaagaa
     1621 ttcagtaaat ttgttgatat tactcattcc tctgaaattc aatcaaagag agggaaaaag
     1681 tcaggacagt caaggaggaa aggaagccta gaggaaataa aaccttgggt agctatggga
     1741 ataagcaggc ggaagtattt ttatatcaag aaaaatggtg aaataagatg aaaaccttcg
     1801 taactctttg gactatagtt tttttagcat ttattgccgt gatgtgtact gttgatatat
     1861 ctaattacat tccgtctgtt tacacagttt ttagtaagaa tagacctctt gtaactggcg
     1921 ccctttctat tcttttgata tctgttttta tttggctgat ggtatccctc tacttactta
     1981 aaaagtattc ggttaaggtt gagaaactta gccttggtgg agtgaatata cttttcaatg
     2041 agagtgctac actttacaaa aagagtgtaa aaaatcacct agattcaaaa agagcaattt
     2101 tcaaattaag aaaaaacgtt gatgcctttg atgaggttat ttcatcatat tatcagactt
     2161 accaatttat tcgtgatgaa atgaaaatac taaaccctaa aaaagatcgt gagatttatg
     2221 atttcagcaa tgagatgctc atggtgttaa atagatttct aactaactac cagaacaact
     2281 acaagcgttg gtataagtac atatcagaca aagatgaggt tgttgatagg gttagcggtg
     2341 atgtcatgag atttcatgca accagcataa ataaaataca aatgcagtat tatgattatg
     2401 agcgtatttt aaaaggtttt aaagatgtta accggttctt tgttaatgat gtgaagccta
     2461 agtttggaat caatacagat aagtggaact ggtaaattaa aggagtagcc aaggctactc
     2521 cttggatagt actatgaatt atgcattctc atttctctcg acatatcata cgttgctttt
     2581 tctctatcgt tataagtcat gtctattaat tttctgagtg tttctgggtt gttttctatt
     2641 tgattccagt tgaccactga tatataagac ccgctcttca tgaagttgtc tattattctt
     2701 gctggcatat atgggaacct ttcctcataa gttgagcgct tatcaataga aaaccattca
     2761 gttacggtag gatgaacttc tgatttttca ttagttccat gtgttgaacg aatgtacgta
     2821 gtatttgttg acgggagatt gacgactaaa attcctgatt ttttgttaat ggtactatct
     2881 ctcatgctag agtaaagttc ccaatctacg tgttttctgt tttttgtttc agttccaaca
     2941 agaaggataa gaactgatgt atctctaaga tattcatctc ttattatctc tcttattttt
     3001 tgtggggctt catcttcatc tatatcacct aatgatactg agcgattcac gaatatttca
     3061 tgttcctcat tcattttttc aagtgcgttt ttgtagtact gatcattcgc atggtggtag
     3121 ctaatgaata ccttatgctt tcccattttt attgtccttt ttttgtttgt gtgcactcta
     3181 ttttgcactt gaacctatat cagataacag ctctctttta gagagctctt tttttctcag
     3241 ccagcacaca tagggtccct tcagcaaggt ctcgccatga ctggtttagg gcgggctcgt
     3301 tgcttcccta aacgccttga gaagagagct atcacctcac tttattctta cgtaccgctc
     3361 gccgcagtct tatgaccgaa cgtagtgagc gaatgcgcga ggaagcggaa agtcatttgt
     3421 tgcctgcatt ttgcacggtc actcctgtgt ttcatcgccc ttctgaaaaa cacatcactt
     3481 ctggaccagt atgtcgtaag ctggcccctg tttccttgag actgaatgta ttaaaggatg
     3541 ataactgatg accagagtgt ctattagtga ggctgcacgg ctgacgggta agagccggac
     3601 aacgctgcac aggttaatca aaacaggtga actgtccact tgtagcggtg aacgaaatac
     3661 aaaaatggtc gatatatcag agcttttacg tgttttcgga ccgtttgacc aaccgaagaa
     3721 tgaacacctt actcgacaag tacctgaaca gcgtgataca gcgcctgctg accagagtga
     3781 acatgtcatt cgtcaactga aacagcagat tgaacacctt aacatattga ttttatcgaa
     3841 ggattcgcac attgacagcc tgaaacaggc catgctcctt cttgaaaatc accaggcaaa
     3901 attaactgaa cccccggcgc cgtggtggaa attctggaaa aaatcctgac cccgtcatgc
     3961 ttcagttttc ctctccggcc attccgggga gttcctgaac cttcccgaaa atcgtcagat
     4021 ctctgaacgc tcctcaccac gaaaaatacc cacaccccac gcaaaatttt aattttgcag
     4081 atttgtattt aatatcagca gcttacttta ctgaaatttc gttttttaaa ttttatttat
     4141 atagatccga ctctatgacg agtcgtcata gagtccccgg cgagtcgtca tagagtcggt
     4201 aacgactcag gcctataaaa acaatgagtt aataacgacc cgactctaga tccgactccc
     4261 cgtttggttg ttttttagac gtggcgactc tgggtacgac tctagtgaag agtcgccggg
     4321 gaatcgtgtg gtgagtcgtc cggcgacttg ccataacgtg attgccggcc gtggacgaac
     4381 cgattcctga acgtgctgaa aaccggtttt ccggctgcgc cggcaacgct tcacggccac
     4441 gcaataaatt gcgtccccgt tcaccgtttt cggatgggaa gaacgccgga aacaggactt
     4501 cccctggctg aatggtgtca atttccgcgc tatgcacttg tgcgcatact catgcatgcc
     4561 gtaaaaacag agcctgcgcg tttctggcgg gttttcgggt ggtttgttgc cttgtttacc
     4621 ggtttcccgt cagaaacgcc ctgagggcat ctcaggcggt gctgataacg gatgttatgg
     4681 taaatcaagt gaatggcagg tacaaaaaaa gccccagagg gcttttagtt tagacttctg
     4741 aagatatttt atttttcttg gaagtggtgg ttgtttttgc tcggagggaa cttatcaccc
     4801 ttgctcacat ggcgatcata ttcagaacca gcgtatgagt tgtcggtatc atgatattga
     4861 ccgtaagtac ctgtttttgg acattcttgc ccagaccaat gttttgccat ttacttttcc
     4921 tttgctcgtt ttaggagcta agctcctagc ggtacgaaat tgtgccgcac ttcataaatg
     4981 taattgcttg aaattatgct tcaatgtatt
//
