LOCUS       NZ_CP086446             3541 bp    DNA     circular CON 28-MAY-2024
DEFINITION  Klebsiella pneumoniae strain AE-2247421-T5-MAC plasmid
            p2247421-T5-MAC_7, complete sequence.
ACCESSION   NZ_CP086446
VERSION     NZ_CP086446.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN22108732
            Assembly: GCF_022759925.1
KEYWORDS    RefSeq.
SOURCE      Klebsiella pneumoniae
  ORGANISM  Klebsiella pneumoniae
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Klebsiella/Raoultella group; Klebsiella.
REFERENCE   1  (bases 1 to 3541)
  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  JOURNAL   Unpublished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 3541)
  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                   :: 452x
            Sequencing Technology :: Illumina NovaSeq; Oxford Nanopore MiniION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_022759925.1-RS_2024_05_28
            Annotation Date                   :: 05/28/2024 04:43:56
            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)                     :: 5,930
            CDSs (total)                      :: 5,809
            Genes (coding)                    :: 5,641
            CDSs (with protein)               :: 5,641
            Genes (RNA)                       :: 121
            rRNAs                             :: 9, 8, 8 (5S, 16S, 23S)
            complete rRNAs                    :: 9, 8, 8 (5S, 16S, 23S)
            tRNAs                             :: 87
            ncRNAs                            :: 9
            Pseudo Genes (total)              :: 168
            CDSs (without protein)            :: 168
            Pseudo Genes (ambiguous residues) :: 0 of 168
            Pseudo Genes (frameshifted)       :: 64 of 168
            Pseudo Genes (incomplete)         :: 100 of 168
            Pseudo Genes (internal stop)      :: 28 of 168
            Pseudo Genes (multiple problems)  :: 20 of 168
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP086446.1.
            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..3541
                     /organism="Klebsiella pneumoniae"
                     /mol_type="genomic DNA"
                     /strain="AE-2247421-T5-MAC"
                     /isolation_source="stool"
                     /host="Homo sapiens"
                     /db_xref="taxon:573"
                     /plasmid="p2247421-T5-MAC_7"
                     /geo_loc_name="Switzerland"
                     /collection_date="2013"
                     /collected_by="Institute for Infectious Diseases Bern"
     gene            235..1128
                     /locus_tag="LNN53_RS29525"
                     /old_locus_tag="LNN53_29530"
     CDS             235..1128
                     /locus_tag="LNN53_RS29525"
                     /old_locus_tag="LNN53_29530"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000422436.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="endonuclease"
                     /protein_id="WP_032419557.1"
                     /translation="MELNLCWWNIGISPPVKGVKKDKAEAIRLAKHYIKKMSQEKTLDF
                     LGICEISEDEAIDFKPLADKLHLEYLNLSGTVGRIIMDVSIMYEASKLEYIDYKYIIKI
                     QPDDRTLRIAVRVVFKDAVTGNLITFFLSHWPSIRSADEKIREDAAESLRNNVNKILDD
                     HGIESQIICMGDYNTNPYSVAINEKLYATRDYHRIKNKRKLLFNPFWYLLSDKKTNNLG
                     TYHYKSGASNRWFVFDQMLFSSSFIYGGKDCLKLDMNSLDFHRILSDDNQCLDQRFFNT
                     FDHYPIFCRIYHDNQK"
                     /name="endonuclease"
     gene            1112..1549
                     /locus_tag="LNN53_RS29530"
                     /old_locus_tag="LNN53_29535"
     CDS             1112..1549
                     /locus_tag="LNN53_RS29530"
                     /old_locus_tag="LNN53_29535"
                     /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_032419556.1"
                     /translation="MTTKNEEFQERLKASLKKANETLILKEKIESDISSILSMLKGITS
                     DSIDFDIFQNSSKIPKYKDCKKIVRIKKNSSMAYPKGFILFGFSINESTGYPVQVETED
                     EAAECTDVDNLKESIVYIIEKRSIEIMKLISEQQEDDDIPF"
                     /name="hypothetical protein"
     gene            complement(2359..2760)
                     /locus_tag="LNN53_RS29535"
                     /old_locus_tag="LNN53_29540"
     CDS             complement(2359..2760)
                     /locus_tag="LNN53_RS29535"
                     /old_locus_tag="LNN53_29540"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_009310048.1"
                     /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 domain-containing protein"
                     /protein_id="WP_009310048.1"
                     /translation="MARVSISEAARLTGKSRTTLHRLIKAGDLSTCSGERNAKMVDTSE
                     LLRVFGPFEQPKGEHHSGQVSEQRDTASADQSEQVIRHLKQEIEHLNTLLLSKDSHIDS
                     LKQAMLLLENHQAKLTESPAPWWKFWKKS"
                     /name="helix-turn-helix domain-containing protein"
     gene            complement(2760..2951)
                     /locus_tag="LNN53_RS29540"
                     /old_locus_tag="LNN53_29545"
     CDS             complement(2760..2951)
                     /locus_tag="LNN53_RS29540"
                     /old_locus_tag="LNN53_29545"
                     /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_004187666.1"
                     /translation="MTKQQKTALNMAKFIQNQSLLLLEKLNELDLDVEADLCEKLHDDA
                     EHLFRTLSSRLDALQDGN"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            3365..3478
                     /locus_tag="LNN53_RS29545"
                     /old_locus_tag="LNN53_29550"
     CDS             3365..3478
                     /locus_tag="LNN53_RS29545"
                     /old_locus_tag="LNN53_29550"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_005761324.1"
                     /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_072032591.1"
                     /translation="MHEPPVQSDCCALSGNYHLESNPKRHDKAPLAAATGN"
                     /name="replication initiation protein"
     Typing          3073..3478
                     /name="ColRNAI_rep_cluster_1987"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="93.643"
                     /coverage="99.0"
                     /evalue="4.5799999999999997e-172"
ORIGIN
        1 tgactgcgct cctctactag ccagttacct aggttcaaaa gacctgcaag ttatttgaac
       61 ccttgaaaaa accgccctgc aaggcggttt tttcatttcc agccaagaag ataacgcctt
      121 aaaaggggta gcgcaacacc atttatcaac aaacagataa ataaaatgtt taacccccac
      181 atcaaaagca atacaataaa cccaatgaat acaatgcatt aagaaagaaa caccatggaa
      241 ttgaatttat gttggtggaa tattggaata tcaccacctg taaaaggcgt gaagaaagac
      301 aaggctgagg ctattagatt ggccaagcac tatataaaaa aaatgtctca agaaaaaaca
      361 ttggattttt tgggtatctg tgaaatatca gaagatgagg ctatagattt taaacctttg
      421 gctgataaac tacatcttga atacttgaat ttatcaggga ctgttggtcg gataattatg
      481 gatgtatcca taatgtacga agcatcaaaa cttgagtaca tagattataa atatataatt
      541 aaaatacaac cagatgatag aactttgcgt attgctgtca gagttgtttt taaggatgca
      601 gtaacaggaa atctaataac attcttttta tcacactggc catccataag aagcgcagat
      661 gaaaagattc gagaggacgc tgccgagtca ctgcgcaaca atgtgaataa aatactagat
      721 gaccacggca ttgagtccca aataatatgc atgggtgatt acaacacaaa cccttactct
      781 gttgcaataa acgaaaaact ttacgccact agagattacc atcgaataaa gaataaacga
      841 aaacttcttt ttaacccttt ttggtattta ctttcagaca aaaagaccaa taacttagga
      901 acttatcatt ataaatcagg agcatcgaat agatggtttg tttttgatca aatgttgttt
      961 tcatcatcat ttatatacgg aggaaaagat tgtcttaagc tagacatgaa cagccttgat
     1021 tttcatcgta tacttagtga tgataaccaa tgtttagatc aaagattttt taacactttt
     1081 gatcattacc caatattttg taggatttac catgacaacc aaaaatgaag agttccaaga
     1141 aagactaaag gcatcactaa aaaaagccaa tgaaacacta attttaaaag aaaaaataga
     1201 gtcagatatt tcatcaattt tgtcaatgct aaagggtata acatccgact caattgactt
     1261 tgatattttt cagaatagtt cgaaaattcc caaatataaa gattgtaaaa aaattgtcag
     1321 aataaagaaa aactctagca tggcataccc taaaggtttc attttatttg gatttagcat
     1381 aaatgagtct accggatatc ctgtacaggt agaaacggaa gacgaagccg cagagtgtac
     1441 agatgtggat aacttaaaag aatcaattgt ttacataata gaaaaaagat ctatagagat
     1501 aatgaaatta atatccgagc aacaagaaga cgatgacatt cctttttaaa aaggtagcat
     1561 gtaatgccat tatcaacggc actttttcat agaaggtgcc atatatctta gaatcaacta
     1621 atttaacata agaccataat tgtacgcacc gctaaaacgg cctcagggcg tttctgacgg
     1681 gaaaccggta aaacaggcaa caaaccaccc gaaaacccgc cagaaacgcg caggctctgt
     1741 ttttacggca tgcatgagta tgcacgcaag tgcatagcgc gaaaattcac gccattcagc
     1801 cagggtaagt cctgtttccg gcgttcttcc catccgaaaa cggtgaacgg ggacgcaatt
     1861 tattgcgtgg ccgtgaagcg ttgccggcgc agccggaaaa ccggttttca gcacgttcag
     1921 gaatcgggtt cgtcgacggc cggcaatcac gttatggcaa gtcgccggac gactcaccac
     1981 acgattcacc ggcgactctt cactagagtc gtacccagag tcgccgcgtc taaaaaacaa
     2041 ccaaacgggg agtcgtgtcc agagtcgggt cgttattaac tcattgtttt tatagtcctg
     2101 agtcgttacc gactctatga cgactcgccg gggactctat gacgagtcgt catagagtcg
     2161 gatctatgta aataaaattt aaaaaacgaa atttcaggaa agtaaacaac tgatattaaa
     2221 tacaaatctg caaaatttta attttgcgta gtgtgtgggt atttttagtc gtgaggagcg
     2281 ttcagagatc tggcgatttt tgggaaggtt caggaactcc ccgggatggc cggagaggaa
     2341 aactcaagca tggcaggatc aggatttttt ccagaatttc caccatggtg ccggggattc
     2401 cgttaatttt gcctggtgat tttcaagaag gagcatggcc tgtttcaggc tgtcaatgtg
     2461 cgaatccttg gacaaaagta aggtattcag gtgttcaatc tcctgtttca gatgacgaat
     2521 cacctgttca ctctggtcag cagaggctgt atcacgctgt tcagagacct gtccagaatg
     2581 gtgttcaccc ttcggttgtt caaagggacc aaagacacgt aaaagctctg aagtatctac
     2641 catttttgca tttcgttcac cgctacaggt ggacaggtca cctgctttaa ttaacctgtg
     2701 cagtgttgtt ctactcttac ccgtcagtcg ggcagcctca ctaatagaca ctctggccat
     2761 cagttaccat cctgtaatgc atccagtctc gaggacagtg tacggaaaag atgctccgca
     2821 tcatcgtgga gtttctcaca aaggtcggcc tcgacatcaa gatcaagctc gttaagcttc
     2881 tccagcagga gcagagactg attctggatg aatttagcca tgttcagcgc tgttttctgt
     2941 tgtttcgtca taagaagcct cagagcgtca gtgctcagtg taagaacagt ctcttttccg
     3001 cttcctcgct cactcagtcg ctacgctccg gtcgttcggc tgcggcgagc ggcaggagca
     3061 tgcgtataaa agctcgagaa gaccgagcgg tcaaatgggg aagaaggaaa ggccgcaaag
     3121 cggccgtttt tccataggct ccgcccccct gacaagcatc accgaagcgg acgctcaaat
     3181 cagtggtggc gaaacccgac aggactataa agataccagg cgtttccccc tgatggctcc
     3241 ctcgtgcgct ctcctgttcc tgccattcgg tttaccggtg tcattccgct gttatggccg
     3301 cgtttttctc attccacgcc tgacactcag ttccgggtag gcagttcgct ccaagctgga
     3361 ctgtatgcac gaaccccccg ttcagtccga ctgctgcgcc ttatccggta actatcatct
     3421 tgagtccaac ccgaaaagac acgacaaagc gccactggca gcagccactg gtaactgatt
     3481 tagaggagtt agtcttgaag ttatgggtca gttaaggcta cactgaaaga acaagttttg
     3541 g
//
