LOCUS       NZ_CP086469             3991 bp    DNA     circular CON 28-MAY-2024
DEFINITION  Klebsiella pneumoniae strain MCL-2017-2-T0 plasmid pMCL-2017-T0_2,
            complete sequence.
ACCESSION   NZ_CP086469
VERSION     NZ_CP086469.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN22108726
            Assembly: GCF_022759705.1
KEYWORDS    RefSeq.
SOURCE      Klebsiella pneumoniae
  ORGANISM  Klebsiella pneumoniae
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Klebsiella/Raoultella group; Klebsiella.
REFERENCE   1  (bases 1 to 3991)
  AUTHORS   Moser,A.I., Endimiani,A., Campos-Madueno,E.I. and Vallone,A.
  TITLE     Genome plasticity in E. coli and K. pneumoniae: SNV accumulation
            over time
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 3991)
  AUTHORS   Moser,A.I., Endimiani,A., Campos-Madueno,E.I. and Vallone,A.
  TITLE     Direct Submission
  JOURNAL   Submitted (04-NOV-2021) Institute for Infectious Diseases,
            University of Bern, Friedbuehlstrasse 51, Bern 3001, Switzerland
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: Unicycler v. 0.4.8
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 278x
            Sequencing Technology :: Illumina NovaSeq; Oxford Nanopore MiniION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_022759705.1-RS_2024_05_28
            Annotation Date                   :: 05/28/2024 04:36:02
            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)                     :: 5,600
            CDSs (total)                      :: 5,475
            Genes (coding)                    :: 5,350
            CDSs (with protein)               :: 5,350
            Genes (RNA)                       :: 125
            rRNAs                             :: 9, 8, 8 (5S, 16S, 23S)
            complete rRNAs                    :: 9, 8, 8 (5S, 16S, 23S)
            tRNAs                             :: 87
            ncRNAs                            :: 13
            Pseudo Genes (total)              :: 125
            CDSs (without protein)            :: 125
            Pseudo Genes (ambiguous residues) :: 0 of 125
            Pseudo Genes (frameshifted)       :: 60 of 125
            Pseudo Genes (incomplete)         :: 68 of 125
            Pseudo Genes (internal stop)      :: 19 of 125
            Pseudo Genes (multiple problems)  :: 18 of 125
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP086469.1.
            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..3991
                     /organism="Klebsiella pneumoniae"
                     /mol_type="genomic DNA"
                     /strain="MCL-2017-2-T0"
                     /host="Homo sapiens"
                     /db_xref="taxon:573"
                     /plasmid="pMCL-2017-T0_2"
                     /geo_loc_name="Switzerland"
                     /collection_date="2017"
                     /collected_by="Institute for Infectious Diseases Bern"
     gene            join(3810..3991,1..793)
                     /locus_tag="LNN43_RS27900"
                     /old_locus_tag="LNN43_27900"
     CDS             join(3810..3991,1..793)
                     /locus_tag="LNN43_RS27900"
                     /old_locus_tag="LNN43_27900"
                     /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_114269875.1"
                     /translation="MAFFNLLFVASLICFGGVMGSYSRGCRDSQNKFSKDKDENNKRAS
                     VYRFGIASAFICVPFISSFLHVDYSSIIFPVADGGGTKFIEQILLLISVSGISAYLGYA
                     LLDGLANKVLKEQVDGIDKKQQDLEAEQDEFKDELDRSKELIEQLEMDKKTTKFELGYF
                     KAISAVDKAESMMSIPDEALSVKKKLTEALDAVTESLSLVKREDVAKDDYDKLLVLKAY
                     ILKRLDRIDDALSITDELLMSNEDNPILIYNKACYQYILRRCQADNSDIKDMIRRALTI
                     KVTDPEFIRRQEKIRTKVIGNKDNDLEGLFTDAELEELKVAIK"
                     /name="hypothetical protein"
     gene            complement(1020..1132)
                     /locus_tag="LNN43_RS27905"
                     /old_locus_tag="LNN43_27905"
                     /pseudo=""
     CDS             complement(1020..1132)
                     /locus_tag="LNN43_RS27905"
                     /old_locus_tag="LNN43_27905"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_005761324.1"
                     /note="frameshifted; Derived by automated computational
                     analysis using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="replication initiation protein"
                     /name="replication initiation protein"
     gene            1540..1731
                     /locus_tag="LNN43_RS27910"
                     /old_locus_tag="LNN43_27910"
     CDS             1540..1731
                     /locus_tag="LNN43_RS27910"
                     /old_locus_tag="LNN43_27910"
                     /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_040198051.1"
                     /translation="MTKQQKTALNMAKFIQNQSLLLLDKLNELDLDVEADLCEKLHDDA
                     EHLFRTLSSRLDELQDGN"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            1731..2153
                     /locus_tag="LNN43_RS27915"
                     /old_locus_tag="LNN43_27915"
     CDS             1731..2153
                     /locus_tag="LNN43_RS27915"
                     /old_locus_tag="LNN43_27915"
                     /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="WP_040214596.1"
                     /translation="MAIVSISEAARLVKVSRPTIYKMINSGKLSYTSVVKHGKAIKVID
                     TSELIRVFGSLDGVIDTVKYDVKSDAESTGINSVGLHDLQHRIALLEAENDGLKGAVKA
                     RDEHIDSLRQAMQLLEHKHEPSSPPHSPWWKFWKKS"
                     /name="helix-turn-helix domain-containing protein"
     gene            2957..3229
                     /locus_tag="LNN43_RS27920"
                     /old_locus_tag="LNN43_27920"
     CDS             2957..3229
                     /locus_tag="LNN43_RS27920"
                     /old_locus_tag="LNN43_27920"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_004897311.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_019405140.1"
                     /translation="MATDAQVKEINALIKKYPDSCSICHEVYDEDDVTYTVFGYDRKGK
                     IQVTTGCCAGMLTEPVLLGVCGCFDPEERDEIMQNHPMAKQFFTE"
                     /name="hypothetical protein"
     Typing          complement(1021..1492)
                     /name="ColRNAI_rep_cluster_1987"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="86.777"
                     /coverage="92.0"
                     /evalue="7.8799999999999974e-146"
ORIGIN
        1 atcatcattt cttcatgttg attactcaag tataatattt cctgtggctg atggtggtgg
       61 aactaagttc atagaacaaa tattgcttct tatttctgtt tcggggatct ctgcgtatct
      121 tgggtacgca ttactggatg gtcttgccaa caaagtatta aaagagcaag tagacggtat
      181 agataaaaag caacaagatt tggaggctga acaagatgag tttaaagatg agcttgatag
      241 gagcaaggag ctgatagaac agcttgaaat ggataagaaa acaacaaaat tcgagctagg
      301 atactttaaa gccatttcag ctgtggataa agcagaatca atgatgtcca ttccggatga
      361 ggctctttct gttaagaaaa aactaactga ggcattagat gctgtaacgg aatcattgtc
      421 tcttgttaaa agagaggatg tagctaagga tgactacgac aagctcttag tgcttaaagc
      481 ttatattttg aaaagacttg atcgtattga tgatgctctg tcaattacgg atgagttact
      541 tatgagtaat gaggataacc ctatacttat ttacaataag gcttgctatc aatatatttt
      601 gcgtcgttgc caagctgata actccgatat taaggatatg attcgcaggg ctctgactat
      661 taaagttaca gatcctgaat tcattcgcag gcaagaaaaa ataagaacca aggtcatagg
      721 aaataaagat aatgatcttg aagggttgtt tactgacgct gagctggagg aattaaaggt
      781 ggctatcaaa taggcagtgg ctagctctat gaattccaaa aagatccttg acgatccttt
      841 gaggtgcagc gtactctacc cctcaaacga aaaaaccacc cggcaaggtg gtttttcgaa
      901 ggttcagtaa ccggcaagtt tctgaaccga ggtaactggc ttagaggagc gcagtcacca
      961 aaacagttcg tttagtttag ccttaactgg cgcataactt caagactaac tcctctaaat
     1021 caattaccag tggctgctgc caatggcgat aagtcgtgtc tttccgggtt ggactcaaga
     1081 gatagttact ggaacgggcg cagcagtcgg actgaacggg gggttcgtgc atacagtcca
     1141 gcttggagcg aactgccttc ccggagccga gtatcaggca tggaatgaga aaacgcggcc
     1201 ataacagcgg aatgacaccg gtaaaccgaa aggcaggaac aggagagcgc acgagggagc
     1261 caccaggggg aaacgcctgg tatctttaag tcctgtcggg tttcgccacc actgatttga
     1321 gcgtccgttt ccgcgatgct tgtcaggggg gcggagccta tggaaaaaca gccgttcggc
     1381 ggcctttgct tttctgcctc atatcttggt tgcctacgtt tttatgtaca cgctcctgcc
     1441 gctcgccgca gccgaacggc tggagcgtag cgactgagtg agcgaggaag cggaaaagag
     1501 actagtttga cattgagcac tgacgctctg aggcttctta tgacaaaaca acagaaaaca
     1561 gcgctgaaca tggctaaatt catccagaat cagtctctgc tcctgctgga taagcttaac
     1621 gagcttgatc tcgatgtcga ggccgacctt tgtgagaaac tccatgatga tgcggagcat
     1681 cttttccgta cactgtcctc gagactggat gaattacagg atggtaactg atggccatag
     1741 tgtctattag tgaagcggca cggcttgtta aggttagtcg ccccacaatt tacaagatga
     1801 ttaacagtgg gaagttaagt tacacctctg tggtaaagca cgggaaagct attaaagtta
     1861 ttgatacttc agagctaatt agagtgtttg gttctcttga tggtgtaatc gatactgtaa
     1921 aatatgatgt aaaaagtgac gcagaatcta caggtattaa cagcgttggt ttacatgatt
     1981 tacaacatag aatcgcttta cttgaagctg aaaacgatgg tcttaaaggg gctgttaagg
     2041 ctcgagatga gcatattgat tcccttcgtc aggctatgca gcttctggag cacaagcacg
     2101 aaccttcttc accaccccat tccccgtggt ggaaattctg gaaaaaatcc tgatcccgcc
     2161 atgcttccat tttgctctcc ggccattccg gggagttcct gaaccttccc aaaaatcgtc
     2221 agatccctga acgctcctca ccactaaaaa tacccacaca ctacgcaaaa ttaaaatttt
     2281 gcagatagac ctttattttc aatcagttat ctattttaaa ttacgcaatt ttattttttg
     2341 taaggtgaat ccgagtcgtg gacgactcta tggcgaatcg ccgatgactt gcccacgatt
     2401 catatgtgaa tcacgccata taatcagtac gttatgatga cttgactcta gagtcgactt
     2461 gccgggttgg tggctttttg accatggcga ctctagagtc aagtcacgag tcgaatcgcc
     2521 ggtgaatcgt gtggtgagtc gtccggcgac ttgccataat gtgattgctg gtctcgacaa
     2581 acccgattcc tgaacgtgct gaaaaccggt tttccggctg cgccggcaac gcttcacggc
     2641 cacgcaataa attgcgcacc cgttcaccgt tttcagtctg gtttggtgcg ggttttgagt
     2701 tgcctggcct gaattcaggc tgaaatcccc agacagtcag tcaagtgcat aacgattcat
     2761 gcccgtaaaa cgccctggag cgattttgag gcgttttcag ggggtaagac gtaggattta
     2821 atgggttacg ccccagaatc gttctgaggc cgttttagcg gtgcgtgtaa tgggacgtta
     2881 tggtaaatca acggcggatg cctgagtctg tgttagagtc agcggattgt gataatcagt
     2941 gactcaggga gatgttttgg ctactgacgc tcaggtaaaa gaaattaatg cactcatcaa
     3001 aaaatacccg gactcatgct ccatctgtca tgaagtctat gatgaggatg atgtgaccta
     3061 caccgttttt gggtatgacc ggaaaggtaa aatacaggtc accacgggat gctgtgccgg
     3121 aatgctgaca gagccggttc tgctgggtgt ctgtgggtgc tttgacccgg aagaacgtga
     3181 cgagatcatg cagaatcacc ccatggcaaa gcagtttttc acagagtgat tccgtatctg
     3241 ttgagtctga agcccgcctt gtgcgggctt tttcatatct gcgtgaaatg aggcgttatg
     3301 gtaaatgcac gcattcattc ttttgaaaaa tccagaatga cgaatacatg gggcatgttt
     3361 atatgactat tgagaggaag gatgttattg taaaaaaatc ctttaaattc aatcatttaa
     3421 ttatggtagc caaaggggcg gggcttcgct tattcctaag gaataagcga agccccgccc
     3481 ctttggctac cagtgcatta tacttttttt ttcacccaat gtcaatacat gggttgattt
     3541 tatcatttta agcatttttg ttgttgtgag tgctgggttt atgccctata ttcagcgcta
     3601 agcaagcatg ggcttgcaaa ggaacaatta atgagaggtg ctctatgaaa aaaatcaaac
     3661 ttcacgatga gcgtccagac ttgtaagtgt caagtcagca gaaaaaggca gccaaggctg
     3721 ccttttttgt tattggttag tatatgattg agcttatctt aacttacctg aacaaagttt
     3781 tattgtttgc tttgcgcaag gattctctca tggctttttt taacctattg tttgttgcat
     3841 ctctaatttg ttttggtggt gttatgggga gctattccag aggttgccga gactcccaaa
     3901 ataaattttc aaaagataag gatgagaata ataaaagagc tagtgtttat agatttggta
     3961 tagcatccgc atttatttgt gttcctttca t
//
