LOCUS       NZ_CP086460             3987 bp    DNA     circular CON 28-MAY-2024
DEFINITION  Klebsiella pneumoniae strain MCL-2017-2-T20-MAC plasmid
            pMCL-2017-T20-MAC_2, complete sequence.
ACCESSION   NZ_CP086460
VERSION     NZ_CP086460.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN22108729
            Assembly: GCF_022759665.1
KEYWORDS    RefSeq.
SOURCE      Klebsiella pneumoniae
  ORGANISM  Klebsiella pneumoniae
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Klebsiella/Raoultella group; Klebsiella.
REFERENCE   1  (bases 1 to 3987)
  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  JOURNAL   Unpublished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 3987)
  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                   :: 431x
            Sequencing Technology :: Illumina NovaSeq; Oxford Nanopore MiniION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_022759665.1-RS_2024_05_28
            Annotation Date                   :: 05/28/2024 04:44:52
            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)                     :: 5,602
            CDSs (total)                      :: 5,477
            Genes (coding)                    :: 5,354
            CDSs (with protein)               :: 5,354
            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
            CP086460.1.
            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..3987
                     /organism="Klebsiella pneumoniae"
                     /mol_type="genomic DNA"
                     /strain="MCL-2017-2-T20-MAC"
                     /host="Homo sapiens"
                     /db_xref="taxon:573"
                     /plasmid="pMCL-2017-T20-MAC_2"
                     /geo_loc_name="Switzerland"
                     /collection_date="2017"
                     /collected_by="Institute for Infectious Diseases Bern"
     gene            144..416
                     /locus_tag="LNN57_RS27910"
                     /old_locus_tag="LNN57_27910"
     CDS             144..416
                     /locus_tag="LNN57_RS27910"
                     /old_locus_tag="LNN57_27910"
                     /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            993..1967
                     /locus_tag="LNN57_RS27915"
                     /old_locus_tag="LNN57_27915"
     CDS             993..1967
                     /locus_tag="LNN57_RS27915"
                     /old_locus_tag="LNN57_27915"
                     /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(2194..2306)
                     /locus_tag="LNN57_RS27920"
                     /old_locus_tag="LNN57_27920"
                     /pseudo=""
     CDS             complement(2194..2306)
                     /locus_tag="LNN57_RS27920"
                     /old_locus_tag="LNN57_27920"
                     /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            2714..2905
                     /locus_tag="LNN57_RS27925"
                     /old_locus_tag="LNN57_27925"
     CDS             2714..2905
                     /locus_tag="LNN57_RS27925"
                     /old_locus_tag="LNN57_27925"
                     /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            2905..3327
                     /locus_tag="LNN57_RS27930"
                     /old_locus_tag="LNN57_27930"
     CDS             2905..3327
                     /locus_tag="LNN57_RS27930"
                     /old_locus_tag="LNN57_27930"
                     /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(2195..2666)
                     /name="ColRNAI_rep_cluster_1987"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="86.777"
                     /coverage="92.0"
                     /evalue="7.8799999999999974e-146"
ORIGIN
        1 ggatttaatg ggttacgccc cagaatcgtt ctgaggccgt tttagcggtg cgtgtaatgg
       61 gacgttatgg taaatcaacg gcggatgcct gagtctgtgt tagagtcagc ggattgtgat
      121 aatcagtgac tcagggagat gttttggcta ctgacgctca ggtaaaagaa attaatgcac
      181 tcatcaaaaa atacccggac tcatgctcca tctgtcatga agtctatgat gaggatgatg
      241 tgacctacac cgtttttggg tatgaccgga aaggtaaaat acaggtcacc acgggatgct
      301 gtgccggaat gctgacagag ccggttctgc tgggtgtctg tgggtgcttt gacccggaag
      361 aacgtgacga gatcatgcag aatcacccca tggcaaagca gtttttcaca gagtgattcc
      421 gtatctgttg agtctgaagc ccgccttgtg cgggcttttt catatctgcg tgaaatgagg
      481 cgttatggta aatgcacgca ttcattcttt tgaaaaatcc agaatgacga atacatgggg
      541 catgtttata tgactattga gaggaaggat gttattgtaa aaaaatcctt taaattcaat
      601 catttaatta tggtagttgg ggcggggctt cgcttattcc taaggaataa gcgaagcccc
      661 gccccttggc taccagtgca ttatactttt tttttcaccc aatgtcaata catgggttga
      721 ttttatcatt ttaagcattt ttgttgttgt gagtgctggg tttatgccct atattcagcg
      781 ctaagcaagc atgggcttgc aaaggaacaa ttaatgagag gtgctctatg aaaaaaatca
      841 aacttcacga tgagcgtcca gacttgtaag tgtcaagtca gcagaaaaag gcagccaagg
      901 ctgccttttt tgttattggt tagtatatga ttgagcttat cttaacttac ctgaacaaag
      961 ttttattgtt tgctttgcgc aaggattctc tcatggcttt ttttaaccta ttgtttgttg
     1021 catctctaat ttgttttggt ggtgttatgg ggagctattc cagaggttgc cgagactccc
     1081 aaaataaatt ttcaaaagat aaggatgaga ataataaaag agctagtgtt tatagatttg
     1141 gtatagcatc cgcatttatt tgtgttcctt tcatatcatc atttcttcat gttgattact
     1201 caagtataat atttcctgtg gctgatggtg gtggaactaa gttcatagaa caaatattgc
     1261 ttcttatttc tgtttcgggg atctctgcgt atcttgggta cgcattactg gatggtcttg
     1321 ccaacaaagt attaaaagag caagtagacg gtatagataa aaagcaacaa gatttggagg
     1381 ctgaacaaga tgagtttaaa gatgagcttg ataggagcaa ggagctgata gaacagcttg
     1441 aaatggataa gaaaacaaca aaattcgagc taggatactt taaagccatt tcagctgtgg
     1501 ataaagcaga atcaatgatg tccattccgg atgaggctct ttctgttaag aaaaaactaa
     1561 ctgaggcatt agatgctgta acggaatcat tgtctcttgt taaaagagag gatgtagcta
     1621 aggatgacta cgacaagctc ttagtgctta aagcttatat tttgaaaaga cttgatcgta
     1681 ttgatgatgc tctgtcaatt acggatgagt tacttatgag taatgaggat aaccctatac
     1741 ttatttacaa taaggcttgc tatcaatata ttttgcgtcg ttgccaagct gataactccg
     1801 atattaagga tatgattcgc agggctctga ctattaaagt tacagatcct gaattcattc
     1861 gcaggcaaga aaaaataaga accaaggtca taggaaataa agataatgat cttgaagggt
     1921 tgtttactga cgctgagctg gaggaattaa aggtggctat caaataggca gtggctagct
     1981 ctatgaattc caaaaagatc cttgacgatc ctttgaggtg cagcgtactc tacccctcaa
     2041 acgaaaaaac cacccggcaa ggtggttttt cgaaggttca gtaaccggca agtttctgaa
     2101 ccgaggtaac tggcttagag gagcgcagtc accaaaacag ttcgtttagt ttagccttaa
     2161 ctggcgcata acttcaagac taactcctct aaatcaatta ccagtggctg ctgccaatgg
     2221 cgataagtcg tgtctttccg ggttggactc aagagatagt tactggaacg ggcgcagcag
     2281 tcggactgaa cggggggttc gtgcatacag tccagcttgg agcgaactgc cttcccggag
     2341 ccgagtatca ggcatggaat gagaaaacgc ggccataaca gcggaatgac accggtaaac
     2401 cgaaaggcag gaacaggaga gcgcacgagg gagccaccag ggggaaacgc ctggtatctt
     2461 taagtcctgt cgggtttcgc caccactgat ttgagcgtcc gtttccgcga tgcttgtcag
     2521 gggggcggag cctatggaaa aacagccgtt cggcggcctt tgcttttctg cctcatatct
     2581 tggttgccta cgtttttatg tacacgctcc tgccgctcgc cgcagccgaa cggctggagc
     2641 gtagcgactg agtgagcgag gaagcggaaa agagactagt ttgacattga gcactgacgc
     2701 tctgaggctt cttatgacaa aacaacagaa aacagcgctg aacatggcta aattcatcca
     2761 gaatcagtct ctgctcctgc tggataagct taacgagctt gatctcgatg tcgaggccga
     2821 cctttgtgag aaactccatg atgatgcgga gcatcttttc cgtacactgt cctcgagact
     2881 ggatgaatta caggatggta actgatggcc atagtgtcta ttagtgaagc ggcacggctt
     2941 gttaaggtta gtcgccccac aatttacaag atgattaaca gtgggaagtt aagttacacc
     3001 tctgtggtaa agcacgggaa agctattaaa gttattgata cttcagagct aattagagtg
     3061 tttggttctc ttgatggtgt aatcgatact gtaaaatatg atgtaaaaag tgacgcagaa
     3121 tctacaggta ttaacagcgt tggtttacat gatttacaac atagaatcgc tttacttgaa
     3181 gctgaaaacg atggtcttaa aggggctgtt aaggctcgag atgagcatat tgattccctt
     3241 cgtcaggcta tgcagcttct ggagcacaag cacgaacctt cttcaccacc ccattccccg
     3301 tggtggaaat tctggaaaaa atcctgatcc cgccatgctt ccattttgct ctccggccat
     3361 tccggggagt tcctgaacct tcccaaaaat cgtcagatcc ctgaacgctc ctcaccacta
     3421 aaaataccca cacactacgc aaaattaaaa ttttgcagat agacctttat tttcaatcag
     3481 ttatctattt taaattacgc aattttattt tttgtaaggt gaatccgagt cgtggacgac
     3541 tctatggcga atcgccgatg acttgcccac gattcatatg tgaatcacgc catataatca
     3601 gtacgttatg atgacttgac tctagagtcg acttgccggg ttggtggctt tttgaccatg
     3661 gcgactctag agtcaagtca cgagtcgaat cgccggtgaa tcgtgtggtg agtcgtccgg
     3721 cgacttgcca taatgtgatt gctggtctcg acaaacccga ttcctgaacg tgctgaaaac
     3781 cggttttccg gctgcgccgg caacgcttca cggccacgca ataaattgcg cacccgttca
     3841 ccgttttcag tctggtttgg tgcgggtttt gagttgcctg gcctgaattc aggctgaaat
     3901 ccccagacag tcagtcaagt gcataacgat tcatgcccgt aaaacgccct ggagcgattt
     3961 tgaggcgttt tcagggggta agacgta
//
