LOCUS       NZ_CP086457             3991 bp    DNA     circular CON 28-MAY-2024
DEFINITION  Klebsiella pneumoniae strain MCL-2017-2-T20-ESBL plasmid
            pMCL-2017-T20-ESBL_2, complete sequence.
ACCESSION   NZ_CP086457
VERSION     NZ_CP086457.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN22108730
            Assembly: GCF_022759685.1
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  JOURNAL   Unpublished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                   :: 420x
            Sequencing Technology :: Illumina NovaSeq; Oxford Nanopore MiniION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_022759685.1-RS_2024_05_28
            Annotation Date                   :: 05/28/2024 04:34:29
            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)                    :: 5,355
            CDSs (with protein)               :: 5,355
            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)              :: 121
            CDSs (without protein)            :: 121
            Pseudo Genes (ambiguous residues) :: 0 of 121
            Pseudo Genes (frameshifted)       :: 56 of 121
            Pseudo Genes (incomplete)         :: 68 of 121
            Pseudo Genes (internal stop)      :: 19 of 121
            Pseudo Genes (multiple problems)  :: 18 of 121
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP086457.1.
            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-T20-ESBL"
                     /host="Homo sapiens"
                     /db_xref="taxon:573"
                     /plasmid="pMCL-2017-T20-ESBL_2"
                     /geo_loc_name="Switzerland"
                     /collection_date="2017"
                     /collected_by="Institute for Infectious Diseases Bern"
     gene            42..233
                     /locus_tag="LNN48_RS27905"
                     /old_locus_tag="LNN48_27905"
     CDS             42..233
                     /locus_tag="LNN48_RS27905"
                     /old_locus_tag="LNN48_27905"
                     /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            233..655
                     /locus_tag="LNN48_RS27910"
                     /old_locus_tag="LNN48_27910"
     CDS             233..655
                     /locus_tag="LNN48_RS27910"
                     /old_locus_tag="LNN48_27910"
                     /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            1459..1731
                     /locus_tag="LNN48_RS27915"
                     /old_locus_tag="LNN48_27915"
     CDS             1459..1731
                     /locus_tag="LNN48_RS27915"
                     /old_locus_tag="LNN48_27915"
                     /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            2312..3286
                     /locus_tag="LNN48_RS27920"
                     /old_locus_tag="LNN48_27920"
     CDS             2312..3286
                     /locus_tag="LNN48_RS27920"
                     /old_locus_tag="LNN48_27920"
                     /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(3513..3625)
                     /locus_tag="LNN48_RS27925"
                     /old_locus_tag="LNN48_27925"
                     /pseudo=""
     CDS             complement(3513..3625)
                     /locus_tag="LNN48_RS27925"
                     /old_locus_tag="LNN48_27925"
                     /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"
     Typing          complement(3514..3985)
                     /name="ColRNAI_rep_cluster_1987"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="86.777"
                     /coverage="92.0"
                     /evalue="7.8799999999999974e-146"
ORIGIN
        1 agactagttt gacattgagc actgacgctc tgaggcttct tatgacaaaa caacagaaaa
       61 cagcgctgaa catggctaaa ttcatccaga atcagtctct gctcctgctg gataagctta
      121 acgagcttga tctcgatgtc gaggccgacc tttgtgagaa actccatgat gatgcggagc
      181 atcttttccg tacactgtcc tcgagactgg atgaattaca ggatggtaac tgatggccat
      241 agtgtctatt agtgaagcgg cacggcttgt taaggttagt cgccccacaa tttacaagat
      301 gattaacagt gggaagttaa gttacacctc tgtggtaaag cacgggaaag ctattaaagt
      361 tattgatact tcagagctaa ttagagtgtt tggttctctt gatggtgtaa tcgatactgt
      421 aaaatatgat gtaaaaagtg acgcagaatc tacaggtatt aacagcgttg gtttacatga
      481 tttacaacat agaatcgctt tacttgaagc tgaaaacgat ggtcttaaag gggctgttaa
      541 ggctcgagat gagcatattg attcccttcg tcaggctatg cagcttctgg agcacaagca
      601 cgaaccttct tcaccacccc attccccgtg gtggaaattc tggaaaaaat cctgatcccg
      661 ccatgcttcc attttgctct ccggccattc cggggagttc ctgaaccttc ccaaaaatcg
      721 tcagatccct gaacgctcct caccactaaa aatacccaca cactacgcaa aattaaaatt
      781 ttgcagatag acctttattt tcaatcagtt atctatttta aattacgcaa ttttattttt
      841 tgtaaggtga atccgagtcg tggacgactc tatggcgaat cgccgatgac ttgcccacga
      901 ttcatatgtg aatcacgcca tataatcagt acgttatgat gacttgactc tagagtcgac
      961 ttgccgggtt ggtggctttt tgaccatggc gactctagag tcaagtcacg agtcgaatcg
     1021 ccggtgaatc gtgtggtgag tcgtccggcg acttgccata atgtgattgc tggtctcgac
     1081 aaacccgatt cctgaacgtg ctgaaaaccg gttttccggc tgcgccggca acgcttcacg
     1141 gccacgcaat aaattgcgca cccgttcacc gttttcagtc tggtttggtg cgggttttga
     1201 gttgcctggc ctgaattcag gctgaaatcc ccagacagtc agtcaagtgc ataacgattc
     1261 atgcccgtaa aacgccctgg agcgattttg aggcgttttc agggggtaag acgtaggatt
     1321 taatgggtta cgccccagaa tcgttctgag gccgttttag cggtgcgtgt aatgggacgt
     1381 tatggtaaat caacggcgga tgcctgagtc tgtgttagag tcagcggatt gtgataatca
     1441 gtgactcagg gagatgtttt ggctactgac gctcaggtaa aagaaattaa tgcactcatc
     1501 aaaaaatacc cggactcatg ctccatctgt catgaagtct atgatgagga tgatgtgacc
     1561 tacaccgttt ttgggtatga ccggaaaggt aaaatacagg tcaccacggg atgctgtgcc
     1621 ggaatgctga cagagccggt tctgctgggt gtctgtgggt gctttgaccc ggaagaacgt
     1681 gacgagatca tgcagaatca ccccatggca aagcagtttt tcacagagtg attccgtatc
     1741 tgttgagtct gaagcccgcc ttgtgcgggc tttttcatat ctgcgtgaaa tgaggcgtta
     1801 tggtaaatgc acgcattcat tcttttgaaa aatccagaat gacgaataca tggggcatgt
     1861 ttatatgact attgagagga aggatgttat tgtaaaaaaa tcctttaaat tcaatcattt
     1921 aattatggta gccaaagggg cggggcttcg cttattcctt aggaataagc gaagccccgc
     1981 ccctttggct accagtgcat tatacttttt ttttcaccca atgtcaatac atgggttgat
     2041 tttatcattt taagcatttt tgttgttgtg agtgctgggt ttatgcccta tattcagcgc
     2101 taagcaagca tgggcttgca aaggaacaat taatgagagg tgctctatga aaaaaatcaa
     2161 acttcacgat gagcgtccag acttgtaagt gtcaagtcag cagaaaaagg cagccaaggc
     2221 tgcctttttt gttattggtt agtatatgat tgagcttatc ttaacttacc tgaacaaagt
     2281 tttattgttt gctttgcgca aggattctct catggctttt tttaacctat tgtttgttgc
     2341 atctctaatt tgttttggtg gtgttatggg gagctattcc agaggttgcc gagactccca
     2401 aaataaattt tcaaaagata aggatgagaa taataaaaga gctagtgttt atagatttgg
     2461 tatagcatcc gcatttattt gtgttccttt catatcatca tttcttcatg ttgattactc
     2521 aagtataata tttcctgtgg ctgatggtgg tggaactaag ttcatagaac aaatattgct
     2581 tcttatttct gtttcgggga tctctgcgta tcttgggtac gcattactgg atggtcttgc
     2641 caacaaagta ttaaaagagc aagtagacgg tatagataaa aagcaacaag atttggaggc
     2701 tgaacaagat gagtttaaag atgagcttga taggagcaag gagctgatag aacagcttga
     2761 aatggataag aaaacaacaa aattcgagct aggatacttt aaagccattt cagctgtgga
     2821 taaagcagaa tcaatgatgt ccattccgga tgaggctctt tctgttaaga aaaaactaac
     2881 tgaggcatta gatgctgtaa cggaatcatt gtctcttgtt aaaagagagg atgtagctaa
     2941 ggatgactac gacaagctct tagtgcttaa agcttatatt ttgaaaagac ttgatcgtat
     3001 tgatgatgct ctgtcaatta cggatgagtt acttatgagt aatgaggata accctatact
     3061 tatttacaat aaggcttgct atcaatatat tttgcgtcgt tgccaagctg ataactccga
     3121 tattaaggat atgattcgca gggctctgac tattaaagtt acagatcctg aattcattcg
     3181 caggcaagaa aaaataagaa ccaaggtcat aggaaataaa gataatgatc ttgaagggtt
     3241 gtttactgac gctgagctgg aggaattaaa ggtggctatc aaataggcag tggctagctc
     3301 tatgaattcc aaaaagatcc ttgacgatcc tttgaggtgc agcgtactct acccctcaaa
     3361 cgaaaaaacc acccggcaag gtggtttttc gaaggttcag taaccggcaa gtttctgaac
     3421 cgaggtaact ggcttagagg agcgcagtca ccaaaacagt tcgtttagtt tagccttaac
     3481 tggcgcataa cttcaagact aactcctcta aatcaattac cagtggctgc tgccaatggc
     3541 gataagtcgt gtctttccgg gttggactca agagatagtt actggaacgg gcgcagcagt
     3601 cggactgaac ggggggttcg tgcatacagt ccagcttgga gcgaactgcc ttcccggagc
     3661 cgagtatcag gcatggaatg agaaaacgcg gccataacag cggaatgaca ccggtaaacc
     3721 gaaaggcagg aacaggagag cgcacgaggg agccaccagg gggaaacgcc tggtatcttt
     3781 aagtcctgtc gggtttcgcc accactgatt tgagcgtccg tttccgcgat gcttgtcagg
     3841 ggggcggagc ctatggaaaa acagccgttc ggcggccttt gcttttctgc ctcatatctt
     3901 ggttgcctac gtttttatgt acacgctcct gccgctcgcc gcagccgaac ggctggagcg
     3961 tagcgactga gtgagcgagg aagcggaaaa g
//
