LOCUS       NZ_CP086463             3989 bp    DNA     circular CON 28-MAY-2024
DEFINITION  Klebsiella pneumoniae strain MCL-2017-2-T5-ESBL plasmid
            pMCL-2017-T5-ESBL_2, complete sequence.
ACCESSION   NZ_CP086463
VERSION     NZ_CP086463.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN22108728
            Assembly: GCF_022759645.1
KEYWORDS    RefSeq.
SOURCE      Klebsiella pneumoniae
  ORGANISM  Klebsiella pneumoniae
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Klebsiella/Raoultella group; Klebsiella.
REFERENCE   1  (bases 1 to 3989)
  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  JOURNAL   Unpublished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 3989)
  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                   :: 247x
            Sequencing Technology :: Illumina NovaSeq; Oxford Nanopore MiniION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_022759645.1-RS_2024_05_28
            Annotation Date                   :: 05/28/2024 04:35:52
            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)                     :: 5,601
            CDSs (total)                      :: 5,476
            Genes (coding)                    :: 5,353
            CDSs (with protein)               :: 5,353
            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)              :: 123
            CDSs (without protein)            :: 123
            Pseudo Genes (ambiguous residues) :: 0 of 123
            Pseudo Genes (frameshifted)       :: 58 of 123
            Pseudo Genes (incomplete)         :: 68 of 123
            Pseudo Genes (internal stop)      :: 19 of 123
            Pseudo Genes (multiple problems)  :: 18 of 123
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP086463.1.
            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..3989
                     /organism="Klebsiella pneumoniae"
                     /mol_type="genomic DNA"
                     /strain="MCL-2017-2-T5-ESBL"
                     /host="Homo sapiens"
                     /db_xref="taxon:573"
                     /plasmid="pMCL-2017-T5-ESBL_2"
                     /geo_loc_name="Switzerland"
                     /collection_date="2017"
                     /collected_by="Institute for Infectious Diseases Bern"
     gene            139..411
                     /locus_tag="LNN56_RS27905"
                     /old_locus_tag="LNN56_27905"
     CDS             139..411
                     /locus_tag="LNN56_RS27905"
                     /old_locus_tag="LNN56_27905"
                     /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"
     gene            990..1964
                     /locus_tag="LNN56_RS27910"
                     /old_locus_tag="LNN56_27910"
     CDS             990..1964
                     /locus_tag="LNN56_RS27910"
                     /old_locus_tag="LNN56_27910"
                     /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(2191..2303)
                     /locus_tag="LNN56_RS27915"
                     /old_locus_tag="LNN56_27915"
                     /pseudo=""
     CDS             complement(2191..2303)
                     /locus_tag="LNN56_RS27915"
                     /old_locus_tag="LNN56_27915"
                     /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            2711..2902
                     /locus_tag="LNN56_RS27920"
                     /old_locus_tag="LNN56_27920"
     CDS             2711..2902
                     /locus_tag="LNN56_RS27920"
                     /old_locus_tag="LNN56_27920"
                     /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            2902..3324
                     /locus_tag="LNN56_RS27925"
                     /old_locus_tag="LNN56_27925"
     CDS             2902..3324
                     /locus_tag="LNN56_RS27925"
                     /old_locus_tag="LNN56_27925"
                     /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"
     Typing          complement(2192..2663)
                     /name="ColRNAI_rep_cluster_1987"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="86.777"
                     /coverage="92.0"
                     /evalue="7.8799999999999974e-146"
ORIGIN
        1 taatgggtta cgccccagaa tcgttctgag gccgttttag cggtgcgtgt aatgggacgt
       61 tatggtaaat caacggcgga tgcctgagtc tgtgttagag tcagcggatt gtgataatca
      121 gtgactcagg gagatgtttt ggctactgac gctcaggtaa aagaaattaa tgcactcatc
      181 aaaaaatacc cggactcatg ctccatctgt catgaagtct atgatgagga tgatgtgacc
      241 tacaccgttt ttgggtatga ccggaaaggt aaaatacagg tcaccacggg atgctgtgcc
      301 ggaatgctga cagagccggt tctgctgggt gtctgtgggt gctttgaccc ggaagaacgt
      361 gacgagatca tgcagaatca ccccatggca aagcagtttt tcacagagtg attccgtatc
      421 tgttgagtct gaagcccgcc ttgtgcgggc tttttcatat ctgcgtgaaa tgaggcgtta
      481 tggtaaatgc acgcattcat tcttttgaaa aatccagaat gacgaataca tggggcatgt
      541 ttatatgact attgagagga aggatgttat tgtaaaaaaa tcctttaaat tcaatcattt
      601 aattatggta gccaaagggc ggggcttcgc ttattcctta ggaataagcg aagccccgcc
      661 cctttggcta ccagtgcatt atactttttt ttcacccaat gtcaatacat gggttgattt
      721 tatcatttta agcatttttg ttgttgtgag tgctgggttt atgccctata ttcagcgcta
      781 agcaagcatg ggcttgcaaa ggaacaatta atgagaggtg ctctatgaaa aaaatcaaac
      841 ttcacgatga gcgtccagac ttgtaagtgt caagtcagca gaaaaaggca gccaaggctg
      901 ccttttttgt tattggttag tatatgattg agcttatctt aacttacctg aacaaagttt
      961 tattgtttgc tttgcgcaag gattctctca tggctttttt taacctattg tttgttgcat
     1021 ctctaatttg ttttggtggt gttatgggga gctattccag aggttgccga gactcccaaa
     1081 ataaattttc aaaagataag gatgagaata ataaaagagc tagtgtttat agatttggta
     1141 tagcatccgc atttatttgt gttcctttca tatcatcatt tcttcatgtt gattactcaa
     1201 gtataatatt tcctgtggct gatggtggtg gaactaagtt catagaacaa atattgcttc
     1261 ttatttctgt ttcggggatc tctgcgtatc ttgggtacgc attactggat ggtcttgcca
     1321 acaaagtatt aaaagagcaa gtagacggta tagataaaaa gcaacaagat ttggaggctg
     1381 aacaagatga gtttaaagat gagcttgata ggagcaagga gctgatagaa cagcttgaaa
     1441 tggataagaa aacaacaaaa ttcgagctag gatactttaa agccatttca gctgtggata
     1501 aagcagaatc aatgatgtcc attccggatg aggctctttc tgttaagaaa aaactaactg
     1561 aggcattaga tgctgtaacg gaatcattgt ctcttgttaa aagagaggat gtagctaagg
     1621 atgactacga caagctctta gtgcttaaag cttatatttt gaaaagactt gatcgtattg
     1681 atgatgctct gtcaattacg gatgagttac ttatgagtaa tgaggataac cctatactta
     1741 tttacaataa ggcttgctat caatatattt tgcgtcgttg ccaagctgat aactccgata
     1801 ttaaggatat gattcgcagg gctctgacta ttaaagttac agatcctgaa ttcattcgca
     1861 ggcaagaaaa aataagaacc aaggtcatag gaaataaaga taatgatctt gaagggttgt
     1921 ttactgacgc tgagctggag gaattaaagg tggctatcaa ataggcagtg gctagctcta
     1981 tgaattccaa aaagatcctt gacgatcctt tgaggtgcag cgtactctac ccctcaaacg
     2041 aaaaaaccac ccggcaaggt ggtttttcga aggttcagta accggcaagt ttctgaaccg
     2101 aggtaactgg cttagaggag cgcagtcacc aaaacagttc gtttagttta gccttaactg
     2161 gcgcataact tcaagactaa ctcctctaaa tcaattacca gtggctgctg ccaatggcga
     2221 taagtcgtgt ctttccgggt tggactcaag agatagttac tggaacgggc gcagcagtcg
     2281 gactgaacgg ggggttcgtg catacagtcc agcttggagc gaactgcctt cccggagccg
     2341 agtatcaggc atggaatgag aaaacgcggc cataacagcg gaatgacacc ggtaaaccga
     2401 aaggcaggaa caggagagcg cacgagggag ccaccagggg gaaacgcctg gtatctttaa
     2461 gtcctgtcgg gtttcgccac cactgatttg agcgtccgtt tccgcgatgc ttgtcagggg
     2521 ggcggagcct atggaaaaac agccgttcgg cggcctttgc ttttctgcct catatcttgg
     2581 ttgcctacgt ttttatgtac acgctcctgc cgctcgccgc agccgaacgg ctggagcgta
     2641 gcgactgagt gagcgaggaa gcggaaaaga gactagtttg acattgagca ctgacgctct
     2701 gaggcttctt atgacaaaac aacagaaaac agcgctgaac atggctaaat tcatccagaa
     2761 tcagtctctg ctcctgctgg ataagcttaa cgagcttgat ctcgatgtcg aggccgacct
     2821 ttgtgagaaa ctccatgatg atgcggagca tcttttccgt acactgtcct cgagactgga
     2881 tgaattacag gatggtaact gatggccata gtgtctatta gtgaagcggc acggcttgtt
     2941 aaggttagtc gccccacaat ttacaagatg attaacagtg ggaagttaag ttacacctct
     3001 gtggtaaagc acgggaaagc tattaaagtt attgatactt cagagctaat tagagtgttt
     3061 ggttctcttg atggtgtaat cgatactgta aaatatgatg taaaaagtga cgcagaatct
     3121 acaggtatta acagcgttgg tttacatgat ttacaacata gaatcgcttt acttgaagct
     3181 gaaaacgatg gtcttaaagg ggctgttaag gctcgagatg agcatattga ttcccttcgt
     3241 caggctatgc agcttctgga gcacaagcac gaaccttctt caccacccca ttccccgtgg
     3301 tggaaattct ggaaaaaatc ctgatcccgc catgcttcca ttttgctctc cggccattcc
     3361 ggggagttcc tgaaccttcc caaaaatcgt cagatccctg aacgctcctc accactaaaa
     3421 atacccacac actacgcaaa attaaaattt tgcagataga cctttatttt caatcagtta
     3481 tctattttaa attacgcaat tttatttttt gtaaggtgaa tccgagtcgt ggacgactct
     3541 atggcgaatc gccgatgact tgcccacgat tcatatgtga atcacgccat ataatcagta
     3601 cgttatgatg acttgactct agagtcgact tgccgggttg gtggcttttt gaccatggcg
     3661 actctagagt caagtcacga gtcgaatcgc cggtgaatcg tgtggtgagt cgtccggcga
     3721 cttgccataa tgtgattgct ggtctcgaca aacccgattc ctgaacgtgc tgaaaaccgg
     3781 ttttccggct gcgccggcaa cgcttcacgg ccacgcaata aattgcgcac ccgttcaccg
     3841 ttttcagtct ggtttggtgc gggttttgag ttgcctggcc tgaattcagg ctgaaatccc
     3901 cagacagtca gtcaagtgca taacgattca tgcccgtaaa acgccctgga gcgattttga
     3961 ggcgttttca gggggtaaga cgtaggatt
//
