LOCUS       NZ_CP083040             3541 bp    DNA     circular CON 10-FEB-2024
DEFINITION  Klebsiella pneumoniae strain 4906.28 plasmid p4-4906.28, complete
            sequence.
ACCESSION   NZ_CP083040
VERSION     NZ_CP083040.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN21016535
            Assembly: GCF_021137855.1
KEYWORDS    RefSeq.
SOURCE      Klebsiella pneumoniae
  ORGANISM  Klebsiella pneumoniae
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Klebsiella/Raoultella group; Klebsiella.
REFERENCE   1  (bases 1 to 3541)
  AUTHORS   Campos-Madueno,E.I. and Endimiani,A.
  TITLE     A collection of hybrid assemblies of carbapenemase-producing
            Klebsiella pneumoniae clinical isolates from Switzerland
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 3541)
  AUTHORS   Campos-Madueno,E.I. and Endimiani,A.
  TITLE     Direct Submission
  JOURNAL   Submitted (02-SEP-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                   :: 359.2643x
            Sequencing Technology :: Illumina NovaSeq and Oxford Nanopore MinION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 02/10/2024 03:10:51
            Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline
            (PGAP)
            Annotation Method :: Best-placed reference protein set; GeneMarkS-2+
            Annotation Software revision      :: 6.6
            Features Annotated                :: Gene; CDS; rRNA; tRNA; ncRNA
            Genes (total)                     :: 5,759
            CDSs (total)                      :: 5,635
            Genes (coding)                    :: 5,500
            CDSs (with protein)               :: 5,500
            Genes (RNA)                       :: 124
            rRNAs                             :: 9, 8, 8 (5S, 16S, 23S)
            complete rRNAs                    :: 9, 8, 8 (5S, 16S, 23S)
            tRNAs                             :: 90
            ncRNAs                            :: 9
            Pseudo Genes (total)              :: 135
            CDSs (without protein)            :: 135
            Pseudo Genes (ambiguous residues) :: 0 of 135
            Pseudo Genes (frameshifted)       :: 54 of 135
            Pseudo Genes (incomplete)         :: 82 of 135
            Pseudo Genes (internal stop)      :: 17 of 135
            Pseudo Genes (multiple problems)  :: 14 of 135
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP083040.1.
            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="4906.28"
                     /isolation_source="Tracheobronchial"
                     /host="Homo sapiens"
                     /db_xref="taxon:573"
                     /plasmid="p4-4906.28"
                     /geo_loc_name="Switzerland"
                     /lat_lon="46.947928 N 7.422277 E"
                     /collection_date="2013"
                     /collected_by="Institute for Infectious Diseases (IFIK),
                     University of Bern, Friedbuehlstrasse 51, 3001 Bern,
                     Switzerland"
     gene            join(3156..3541,1..52)
                     /locus_tag="K9F35_RS28660"
                     /old_locus_tag="K9F35_28615"
     CDS             join(3156..3541,1..52)
                     /locus_tag="K9F35_RS28660"
                     /old_locus_tag="K9F35_28615"
                     /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(862..1263)
                     /locus_tag="K9F35_RS28665"
                     /old_locus_tag="K9F35_28620"
     CDS             complement(862..1263)
                     /locus_tag="K9F35_RS28665"
                     /old_locus_tag="K9F35_28620"
                     /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(1263..1454)
                     /locus_tag="K9F35_RS28670"
                     /old_locus_tag="K9F35_28625"
     CDS             complement(1263..1454)
                     /locus_tag="K9F35_RS28670"
                     /old_locus_tag="K9F35_28625"
                     /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            1868..1981
                     /locus_tag="K9F35_RS28675"
     CDS             1868..1981
                     /locus_tag="K9F35_RS28675"
                     /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"
     gene            2279..3172
                     /locus_tag="K9F35_RS28680"
                     /old_locus_tag="K9F35_28630"
     CDS             2279..3172
                     /locus_tag="K9F35_RS28680"
                     /old_locus_tag="K9F35_28630"
                     /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"
     Typing          1576..1981
                     /name="ColRNAI_rep_cluster_1987"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="93.643"
                     /coverage="99.0"
                     /evalue="4.5799999999999997e-172"
ORIGIN
        1 gataatgaaa ttaatatccg agcaacaaga agacgatgac attccttttt aaaaaggtag
       61 catgtaatgc cattatcaac ggcacttttt catagaaggt gccatatatc ttagaatcaa
      121 ctaatttaac ataagaccat aattgtacgc accgctaaaa cggcctcagg gcgtttctga
      181 cgggaaaccg gtaaaacagg caacaaacca cccgaaaacc cgccagaaac gcgcaggctc
      241 tgtttttacg gcatgcatga gtatgcacgc aagtgcatag cgcgaaaatt cacgccattc
      301 agccagggta agtcctgttt ccggcgttct tcccatccga aaacggtgaa cggggacgca
      361 atttattgcg tggccgtgaa gcgttgccgg cgcagccgga aaaccggttt tcagcacgtt
      421 caggaatcgg gttcgtcgac ggccggcaat cacgttatgg caagtcgccg gacgactcac
      481 cacacgattc accggcgact cttcactaga gtcgtaccca gagtcgccgc gtctaaaaaa
      541 caaccaaacg gggagtcgtg tccagagtcg ggtcgttatt aactcattgt ttttatagtc
      601 ctgagtcgtt accgactcta tgacgactcg ccggggactc tatgacgagt cgtcatagag
      661 tcggatctat gtaaataaaa tttaaaaaac gaaatttcag gaaagtaaac aactgatatt
      721 aaatacaaat ctgcaaaatt ttaattttgc gtagtgtgtg ggtattttta gtcgtgagga
      781 gcgttcagag atctggcgat ttttgggaag gttcaggaac tccccgggat ggccggagag
      841 gaaaactcaa gcatggcagg atcaggattt tttccagaat ttccaccatg gtgccgggga
      901 ttccgttaat tttgcctggt gattttcaag aaggagcatg gcctgtttca ggctgtcaat
      961 gtgcgaatcc ttggacaaaa gtaaggtatt caggtgttca atctcctgtt tcagatgacg
     1021 aatcacctgt tcactctggt cagcagaggc tgtatcacgc tgttcagaga cctgtccaga
     1081 atggtgttca cccttcggtt gttcaaaggg accaaagaca cgtaaaagct ctgaagtatc
     1141 taccattttt gcatttcgtt caccgctaca ggtggacagg tcacctgctt taattaacct
     1201 gtgcagtgtt gttctactct tacccgtcag tcgggcagcc tcactaatag acactctggc
     1261 catcagttac catcctgtaa tgcatccagt ctcgaggaca gtgtacggaa aagatgctcc
     1321 gcatcatcgt ggagtttctc acaaaggtcg gcctcgacat caagatcaag ctcgttaagc
     1381 ttctccagca ggagcagaga ctgattctgg atgaatttag ccatgttcag cgctgttttc
     1441 tgttgtttcg tcataagaag cctcagagcg tcagtgctca gtgtaagaac agtctctttt
     1501 ccgcttcctc gctcactcag tcgctacgct ccggtcgttc ggctgcggcg agcggcagga
     1561 gcatgcgtat aaaagctcga gaagaccgag cggtcaaatg gggaagaagg aaaggccgca
     1621 aagcggccgt ttttccatag gctccgcccc cctgacaagc atcaccgaag cggacgctca
     1681 aatcagtggt ggcgaaaccc gacaggacta taaagatacc aggcgtttcc ccctgatggc
     1741 tccctcgtgc gctctcctgt tcctgccatt cggtttaccg gtgtcattcc gctgttatgg
     1801 ccgcgttttt ctcattccac gcctgacact cagttccggg taggcagttc gctccaagct
     1861 ggactgtatg cacgaacccc ccgttcagtc cgactgctgc gccttatccg gtaactatca
     1921 tcttgagtcc aacccgaaaa gacacgacaa agcgccactg gcagcagcca ctggtaactg
     1981 atttagagga gttagtcttg aagttatggg tcagttaagg ctacactgaa agaacaagtt
     2041 ttggtgactg cgctcctcta ctagccagtt acctaggttc aaaagacctg caagttattt
     2101 gaacccttga aaaaaccgcc ctgcaaggcg gttttttcat ttccagccaa gaagataacg
     2161 ccttaaaagg ggtagcgcaa caccatttat caacaaacag ataaataaaa tgtttaaccc
     2221 ccacatcaaa agcaatacaa taaacccaat gaatacaatg cattaagaaa gaaacaccat
     2281 ggaattgaat ttatgttggt ggaatattgg aatatcacca cctgtaaaag gcgtgaagaa
     2341 agacaaggct gaggctatta gattggccaa gcactatata aaaaaaatgt ctcaagaaaa
     2401 aacattggat tttttgggta tctgtgaaat atcagaagat gaggctatag attttaaacc
     2461 tttggctgat aaactacatc ttgaatactt gaatttatca gggactgttg gtcggataat
     2521 tatggatgta tccataatgt acgaagcatc aaaacttgag tacatagatt ataaatatat
     2581 aattaaaata caaccagatg atagaacttt gcgtattgct gtcagagttg tttttaagga
     2641 tgcagtaaca ggaaatctaa taacattctt tttatcacac tggccatcca taagaagcgc
     2701 agatgaaaag attcgagagg acgctgccga gtcactgcgc aacaatgtga ataaaatact
     2761 agatgaccac ggcattgagt cccaaataat atgcatgggt gattacaaca caaaccctta
     2821 ctctgttgca ataaacgaaa aactttacgc cactagagat taccatcgaa taaagaataa
     2881 acgaaaactt ctttttaacc ctttttggta tttactttca gacaaaaaga ccaataactt
     2941 aggaacttat cattataaat caggagcatc gaatagatgg tttgtttttg atcaaatgtt
     3001 gttttcatca tcatttatat acggaggaaa agattgtctt aagctagaca tgaacagcct
     3061 tgattttcat cgtatactta gtgatgataa ccaatgttta gatcaaagat tttttaacac
     3121 ttttgatcat tacccaatat tttgtaggat ttaccatgac aaccaaaaat gaagagttcc
     3181 aagaaagact aaaggcatca ctaaaaaaag ccaatgaaac actaatttta aaagaaaaaa
     3241 tagagtcaga tatttcatca attttgtcaa tgctaaaggg tataacatcc gactcaattg
     3301 actttgatat ttttcagaat agttcgaaaa ttcccaaata taaagattgt aaaaaaattg
     3361 tcagaataaa gaaaaactct agcatggcat accctaaagg tttcatttta tttggattta
     3421 gcataaatga gtctaccgga tatcctgtac aggtagaaac ggaagacgaa gccgcagagt
     3481 gtacagatgt ggataactta aaagaatcaa ttgtttacat aatagaaaaa agatctatag
     3541 a
//
