LOCUS       NZ_CP025580             4163 bp    DNA     circular CON 26-NOV-2023
DEFINITION  Klebsiella pneumoniae strain 08EU827 plasmid p08EU827_4, complete
            sequence.
ACCESSION   NZ_CP025580
VERSION     NZ_CP025580.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN08222595
            Assembly: GCF_004010995.1
KEYWORDS    RefSeq.
SOURCE      Klebsiella pneumoniae
  ORGANISM  Klebsiella pneumoniae
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Klebsiella/Raoultella group; Klebsiella.
REFERENCE   1  (bases 1 to 4163)
  AUTHORS   Bikkarolla,S.K., Nordberg,V., Kabir,M.H., Muller,V., Fritzsche,J.,
            Ambjornsson,T., Giske,C.G., Naver,L., Sandegren,L. and Westerlund,F.
  TITLE     Combining optical DNA mapping and long-read sequencing for full
            genomic characterization of plasmids in a nosocomial resistance
            outbreak
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 4163)
  AUTHORS   Sandegren,L.
  TITLE     Direct Submission
  JOURNAL   Submitted (21-DEC-2017) Medical Biochemistry and Microbiology,
            Uppsala University, Husargatan 3, Uppsala SE-75123, Sweden
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Date                     :: DEC-2017
            Assembly Method                   :: CLC Genomics Workbench v. 11
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 57.0x
            Sequencing Technology             :: Illumina MiSeq; PacBio
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 11/26/2023 02:51:35
            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)                     :: 5,431
            CDSs (total)                      :: 5,311
            Genes (coding)                    :: 5,175
            CDSs (with protein)               :: 5,175
            Genes (RNA)                       :: 120
            rRNAs                             :: 9, 8, 8 (5S, 16S, 23S)
            complete rRNAs                    :: 9, 8, 8 (5S, 16S, 23S)
            tRNAs                             :: 86
            ncRNAs                            :: 9
            Pseudo Genes (total)              :: 136
            CDSs (without protein)            :: 136
            Pseudo Genes (ambiguous residues) :: 0 of 136
            Pseudo Genes (frameshifted)       :: 60 of 136
            Pseudo Genes (incomplete)         :: 73 of 136
            Pseudo Genes (internal stop)      :: 29 of 136
            Pseudo Genes (multiple problems)  :: 20 of 136
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP025580.1.
            Bacteria and source DNA available from Christian Giske, Klinisk
            Mikrobiologi, Baktlab, Karolinska Universitetssjukhuset, L7:01.
            SE-17176 Stockholm.
            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..4163
                     /organism="Klebsiella pneumoniae"
                     /mol_type="genomic DNA"
                     /strain="08EU827"
                     /host="Homo sapiens"
                     /db_xref="taxon:573"
                     /plasmid="p08EU827_4"
                     /geo_loc_name="Sweden: Stockholm"
                     /collection_date="2008"
     gene            125..238
                     /locus_tag="CY656_RS29270"
                     /old_locus_tag="CY656_27865"
     CDS             125..238
                     /locus_tag="CY656_RS29270"
                     /old_locus_tag="CY656_27865"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_007772075.1"
                     /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_072016307.1"
                     /translation="MHEPPVQSDCCALSGNYHLESNPVRHAKAPLAAAIGN"
                     /name="replication initiation protein"
     gene            596..907
                     /locus_tag="CY656_RS27740"
                     /old_locus_tag="CY656_27870"
     CDS             596..907
                     /locus_tag="CY656_RS27740"
                     /old_locus_tag="CY656_27870"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_017134632.1"
                     /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 transcriptional regulator"
                     /protein_id="WP_039817123.1"
                     /translation="MSNQNIFEILTSDPVSLNMWNLKSNLILAIHKTVRDNGWNQTEAA
                     AHLGISQPRVSNMLKGKLDKFSTDSLLEIMFKLGYKLDMQVHPSSEVILEMGMKKAML"
                     /name="helix-turn-helix transcriptional regulator"
     gene            complement(927..1262)
                     /locus_tag="CY656_RS27745"
                     /old_locus_tag="CY656_27875"
     CDS             complement(927..1262)
                     /locus_tag="CY656_RS27745"
                     /old_locus_tag="CY656_27875"
                     /inference="COORDINATES: protein motif:HMM:NF017757.3"
                     /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_077255464.1"
                     /translation="MSASEMKEICLDVTGVDKELKSLPIDKALAFLHNLKLVAAGIEPE
                     LKVEHLKVVAPGVIELKINGSPAYRCVYTIKSPGKVIVLRVFKKTTNGPARKDLEVVKQ
                     RLKNLKI"
                     /name="type II toxin-antitoxin system RelE/ParE family
                     toxin"
     gene            1740..2000
                     /locus_tag="CY656_RS27750"
                     /old_locus_tag="CY656_27880"
     CDS             1740..2000
                     /locus_tag="CY656_RS27750"
                     /old_locus_tag="CY656_27880"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_010891192.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="protein L"
                     /protein_id="WP_072016306.1"
                     /translation="MAAYTEKTEQFLQRVTHTQTWWTSTYDPSDTVPVSGIYRCTVCGK
                     EITSNKNDPFPPQNHHQHSQKQNVKWQLIVRTDTNGDKFGN"
                     /name="protein L"
     gene            2091..2390
                     /locus_tag="CY656_RS27755"
     CDS             2091..2390
                     /locus_tag="CY656_RS27755"
                     /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_125564845.1"
                     /translation="MSNPPFEFVIRYHDLSPEQVRSFIDDAFHRVDLVLEKQLSDRPGF
                     FIPTCKSLTTNPSLSEIAIAVYNTYAVTEMIKDQLLRQSSNITLIKDIREIFVS"
                     /name="hypothetical protein"
     gene            complement(3287..3688)
                     /locus_tag="CY656_RS27765"
                     /old_locus_tag="CY656_27890"
     CDS             complement(3287..3688)
                     /locus_tag="CY656_RS27765"
                     /old_locus_tag="CY656_27890"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_009310048.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="transcriptional regulator"
                     /protein_id="WP_039817125.1"
                     /translation="MARVSISEASRLTGKSRTTLHRLIKAGDLSTCSGERNAKMVDTSE
                     LLRVFGPFEQPKSEHHSGQVSEQRDTASADQSEQVIRHLKQEIEHLNTLLLSKDSHIDS
                     LKQAMLLLENHQAKLTESPAPWWKFWKKS"
                     /name="transcriptional regulator"
     gene            complement(3688..3879)
                     /locus_tag="CY656_RS27770"
                     /old_locus_tag="CY656_27895"
     CDS             complement(3688..3879)
                     /locus_tag="CY656_RS27770"
                     /old_locus_tag="CY656_27895"
                     /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"
     Typing          2..415
                     /name="rep_cluster_2358"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="84.944"
                     /coverage="95.0"
                     /evalue="1.08e-114"
     Typing          3928..4163
                     /name="ColRNAI_rep_cluster_1987"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="82.377"
                     /coverage="92.0"
                     /evalue="4.19e-49"
ORIGIN
        1 ctcgtgcgct ctcctgttcc tgcctttcgg tttaccggtg tcattccgca gttatggccg
       61 cgtttatctc attccacgcc tgacactcag ttccgggtag gcagttcgct ccaagctgga
      121 ctgtatgcac gaaccccccg ttcagtccga ctgctgcgcc ttatccggta actatcatct
      181 tgagtccaac ccggtaagac atgcaaaagc gccactggca gcagccattg gtaactgatt
      241 agaggagtga agtcttgaaa agacacgtac tatacggcta cactgataaa acagatttgg
      301 tgactgtgct cctctaagcc agttacctcg gttcataaac ttgccggttt gatgaacctt
      361 gaaaaaccgc ctccccaggc ggtttttctt tttaaaacaa atgaagacta cgctgacgac
      421 caagatccag tcaacaagtg ttgttagaat gctttaaatt tacaaataaa accccatcta
      481 catcttgtca tgcatactgt aacttgtata atccgcaaac tttagtgtaa gctaataatc
      541 gttcctattg tcttgtgaca actaaatgct cgcattcaga taggagatga aaattatgag
      601 caatcaaaac atattcgaaa tactaacgag tgatccggta tccctaaaca tgtggaacct
      661 gaaatcaaac ctgatcctcg ccatacataa gacggtaaga gataacggct ggaaccaaac
      721 agaggcggcc gcacatctag gcataagcca acctagggtt agcaacatgc tgaaagggaa
      781 gctggacaag ttttctacag attcactact ggaaatcatg ttcaagctgg gttacaaatt
      841 agacatgcaa gtacacccat cctctgaagt aattttagag atgggcatga aaaaggcgat
      901 gctgtgaaca tcgccttgag tggatactat attttgagat ttttcagccg ttgcttcacg
      961 acttctaagt ctttgcgtgc aggtccgtta gtcgttttct tgaagacacg taacacgatc
     1021 accttgccgg gtgattttat cgtgtacaca caacgataag cagggctacc atttatcttc
     1081 aactcaatca cgcctggagc aactactttc aggtgttcaa ctttcagttc tggttcaatt
     1141 ccagcggcaa ccaacttcaa gttgtgcaaa aaagctaaag ctttatcaat aggtaaagac
     1201 tttagctctt tatcaacacc agttacgtct agacaaatct ctttcatttc gcttgcggac
     1261 atagtgtcct cctttgttgg ggtttagtgg tcgaacaatt aaatttctca tttgatactc
     1321 cgattaaaaa aacctcacta aaaaaccaaa cctctacgcc tgatgagatt caccaggtag
     1381 aggcatttaa tttcagtggt tcaggacact gctttaggca atatccattg catcaatata
     1441 ctctaagttg tataaactaa caatatgccg cttcgcttgc gcatgccgtt agctcaataa
     1501 ataagctatc agctgtttac gaaagtaatc ctccatcgaa gctaaaagtc tccgtaaagc
     1561 atcacaactg aaagaaggag ttaagagatg gcagatagaa gaccgctaaa caaagatgtg
     1621 gtagtgccaa agcctggtgg cggaacccag cccagagaca gaaacaatga cggaacggtg
     1681 cgcaaaaaac gctcagacgc aggaaaacca agaaaataaa cgataagaaa ggtaaaagaa
     1741 tggctgcata tacggaaaaa acagagcagt tcttacagcg agttacacac acacagactt
     1801 ggtggacatc aacatacgat ccaagcgata cagttccagt atcaggcatt tatcgctgta
     1861 ccgtatgcgg taaagagata actagtaata aaaacgatcc tttcccccca caaaaccatc
     1921 atcaacatag tcaaaaacaa aatgttaaat ggcagctaat tgtgaggaca gacacaaacg
     1981 gtgataaatt tggtaactga gacacggaag cccttcgggg ctttccctca gtgatttacc
     2041 agaaagtctc attactcact cgtaccaaac aatccacgat ctgaggtctt atgtctaatc
     2101 caccttttga atttgtcatt cgttatcatg acctgtctcc agagcaagtg cggagcttta
     2161 ttgacgatgc ttttcatcgt gttgatctcg ttctagaaaa acagttatcc gatcgtccag
     2221 gcttttttat tcctacatgt aagtcactaa ctactaatcc gtctttatct gaaatagcta
     2281 tcgctgttta caacacatat gccgttactg aaatgataaa ggaccaattg cttcgacaat
     2341 cttccaatat cactctcatt aaagacataa gagagatctt tgtcagctag gatcttctct
     2401 accacaccac aagtgcttat ctcataacag cttatttggc caaacaagac tggcgcagag
     2461 ggagtttccg aacaggtcgc cgggaggtgg accgcttcgc acctcagcag gaaatccatc
     2521 agaccaatcg gggcttttta catctatcat ttaacataaa ggtatgattg tacgcaccgc
     2581 taaaacggcc tcagggcgtt tctgacggga aaccggtaaa acaggcaaca aaccacccga
     2641 aaacccgcca gaaacgcgca ggctctgttt ttacggcatg catgagtatg cacgcaagtg
     2701 catagcgcga aaattcacgc cattcagcca gggtaagtcc tgtttccggc gttcttccca
     2761 tccgaaaacg gtgaacgggg acgcaattta ttgcgtggcc gtgaagcgtt gccggcgcag
     2821 ccggaaaacc ggttttcagc acgttcagga atcgggttcg tcgacggccg gcaatcacgt
     2881 tatggcaagt cgccggacga ctcaccacac gattcaccgg cgactcttca ctagagtcgt
     2941 acccagagtc gtcacgtcta aaaaacaacc aaacggggag tcgggtctag agtcgggtcg
     3001 ttgttaactt attgttttta tagtcctgag tcgttaccga ctctatgacg actcgccggg
     3061 gactctatga cgactcgtca tagagtcgga tctgtataaa taaaattaaa aaaacgaaat
     3121 ttatagaacg taagctgctg atataaaata caaatctgca aaattttaat tttgcgtggg
     3181 gtgtggatat ttttagtggt gaggagcgtt cagagatctg gcgatttttg ggaaggttca
     3241 ggaactcccc gggatggccg gagaggaaaa ctgaagcatg acggggtcag gattttttcc
     3301 agaatttcca ccatggcgcc ggggattcag ttaattttgc ctggtgattt tcaagaagga
     3361 gcatggcctg tttcaggcta tcaatgtgcg aatccttgga caaaagtaag gtgttcaggt
     3421 gttcaatctc ctgtttcaga tgacgaatca cctgttcact ctggtcagca gaggctgtat
     3481 cacgctgttc agagacctgt ccagaatggt gttcactctt cggttgctca aagggaccaa
     3541 agacacgtaa aagctctgaa gtatctacca tttttgcatt acgttcaccg ctacaggtgg
     3601 acaggtcacc tgctttaatt aacctgtgca gtgttgttct actcttaccc gtcagtcggg
     3661 aagcctcact aatagacact cgggccatca gttaccatcc tgtaatgcat ccagtctcga
     3721 ggacagtgta cggaaaagat gctccgcatc atcgtggagt ttctcacaaa ggtcagcctc
     3781 agcatcgaga tcaagctcgt taagcttctc cagcaggagc agggactgat tctggatgaa
     3841 cttagccatg ttcagcgccg ttttctgttg tttcgtcata aagggcctca gagcgtcagt
     3901 gctcaatgta aaaccggtct cttttccgct tcctcgctca ctcagtcgct acgctcctac
     3961 cgttcggctg cggcgagcgg tcgcaacgca cacataaggg cataggacag acagctcgga
     4021 aaggacaacg gaaggccgcg gcgttgccgt ttttccatag gctccgcccc cctgataagc
     4081 atcacaaaaa cagacgctca aatcagtggt ggcgaaaccc gacaggactc taaagatacc
     4141 aggcgtttcc ccctgatggc tcc
//
