LOCUS       NZ_CP042523             3542 bp    DNA     circular CON 09-JAN-2024
DEFINITION  Klebsiella pneumoniae strain C2 plasmid pC2_003, complete sequence.
ACCESSION   NZ_CP042523
VERSION     NZ_CP042523.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN12289275
            Assembly: GCF_008931565.1
KEYWORDS    RefSeq.
SOURCE      Klebsiella pneumoniae
  ORGANISM  Klebsiella pneumoniae
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Klebsiella/Raoultella group; Klebsiella.
REFERENCE   1  (bases 1 to 3542)
  AUTHORS   Phan,H.T.T., Stoesser,N., Gordon,K.A., Crook,D., Walker,S.A.,
            Mathers,A.J., Peto,T.E.A., George,S. and Lipworth,S.I.
  TITLE     Genomic Dynamics of Species and Mobile Genetic Elements in a
            Prolonged blaIMP-4-associated Carbapenemase Outbreak in an
            Australian Hospital
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 3542)
  AUTHORS   Phan,H.T.T.
  TITLE     Direct Submission
  JOURNAL   Submitted (01-AUG-2019) Nuffield Department of Micriobiology,
            University of Oxford, Headley Way, Oxford, Oxford OX3 7BN, United
            Kingdom
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Date                     :: SEP-2017
            Assembly Method                   :: Unicycler v. SEP-2017
            Assembly Name                     :: C2_oz_imp.uniclycerAssembly.fsa
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Reference-guided Assembly         :: na
            Genome Coverage                   :: 4072x
            Sequencing Technology             :: Oxford Nanopore MiniION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 01/09/2024 02:36:29
            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)                     :: 5,442
            CDSs (total)                      :: 5,319
            Genes (coding)                    :: 5,208
            CDSs (with protein)               :: 5,208
            Genes (RNA)                       :: 123
            rRNAs                             :: 9, 8, 8 (5S, 16S, 23S)
            complete rRNAs                    :: 9, 8, 8 (5S, 16S, 23S)
            tRNAs                             :: 87
            ncRNAs                            :: 11
            Pseudo Genes (total)              :: 111
            CDSs (without protein)            :: 111
            Pseudo Genes (ambiguous residues) :: 0 of 111
            Pseudo Genes (frameshifted)       :: 52 of 111
            Pseudo Genes (incomplete)         :: 60 of 111
            Pseudo Genes (internal stop)      :: 18 of 111
            Pseudo Genes (multiple problems)  :: 16 of 111
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP042523.1.
            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..3542
                     /organism="Klebsiella pneumoniae"
                     /mol_type="genomic DNA"
                     /strain="C2"
                     /isolation_source="clinical sample"
                     /host="Homo sapiens"
                     /db_xref="taxon:573"
                     /plasmid="pC2_003"
                     /geo_loc_name="Australia: Sydney"
                     /collection_date="2007-01-17"
                     /collected_by="Concord Repatriation Hospital Sydney
                     Australia"
     gene            join(3389..3542,1..248)
                     /locus_tag="FR744_RS27380"
                     /old_locus_tag="FR744_27380"
     CDS             join(3389..3542,1..248)
                     /locus_tag="FR744_RS27380"
                     /old_locus_tag="FR744_27380"
                     /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_040198057.1"
                     /translation="MARVSISEAARLTGKSRTTLHRLIKAGDLSTCSGERNTKMVDTSE
                     LLRVFGPFEQPKGEHHSGQVSEQRDTASADQSEQVIRHLKQEIEHLNTLLLSKDSHIDS
                     LKQAMLLLENHQAKLTESPAPWWKFWKKS"
                     /name="helix-turn-helix domain-containing protein"
     gene            complement(1058..1495)
                     /locus_tag="FR744_RS27385"
                     /old_locus_tag="FR744_27385"
     CDS             complement(1058..1495)
                     /locus_tag="FR744_RS27385"
                     /old_locus_tag="FR744_27385"
                     /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_032741756.1"
                     /translation="MTTKNEEFQERLKASLKKANETLILKDKIESDISSILSMLKDITS
                     DSIDFDILQNNSKIIKYIGCKKIVRIKKNSIMAYPKGFILFGFSINESTGYPVQVETED
                     EAAECTDVDNLKESIVYIIEKRSIEIMKLISEQQEDDDIPF"
                     /name="hypothetical protein"
     gene            complement(1479..2372)
                     /locus_tag="FR744_RS27390"
                     /old_locus_tag="FR744_27390"
     CDS             complement(1479..2372)
                     /locus_tag="FR744_RS27390"
                     /old_locus_tag="FR744_27390"
                     /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_040198061.1"
                     /translation="MELNLCWWNIGISPPVKGVKKDKDEAIRLAKHYIKKMSQEKTLDF
                     LGICEISEDEAIDFKPLADKLHLEYLNLSGTVGRIIMDISIMYEASKLEYIDYKYIIKI
                     QPDDRTLRIAVRVVFKDAVTGNLITFFLSHWPSIRSADEKIREDAAESLRNNVTKILDD
                     HGIESQIICMGDYNTNPYSVAINEKLYATRDYHRIKNKRKLLFNPFWYLLSDKKTNNLG
                     TYHYKSGTSNRWFVFDQMLFSSSFIYGGKDCLKLDMNSLDFHRILSDDNQCLDQRFFNT
                     FDHYPIFCRIYHDNQK"
                     /name="endonuclease"
     gene            complement(2670..2782)
                     /locus_tag="FR744_RS28285"
                     /old_locus_tag="FR744_27395"
                     /pseudo=""
     CDS             complement(2670..2782)
                     /locus_tag="FR744_RS28285"
                     /old_locus_tag="FR744_27395"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_007772075.1"
                     /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            3198..3389
                     /locus_tag="FR744_RS27405"
                     /old_locus_tag="FR744_27405"
     CDS             3198..3389
                     /locus_tag="FR744_RS27405"
                     /old_locus_tag="FR744_27405"
                     /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"
     Typing          complement(2671..3077)
                     /name="ColRNAI_rep_cluster_1987"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="94.377"
                     /coverage="99.0"
                     /evalue="4.55e-177"
ORIGIN
        1 cctttgagca accgaagggt gaacaccatt ctggacaggt ctctgaacag cgtgatacag
       61 cctctgctga ccagagtgaa caggtgattc gtcatctaaa acaggagatt gaacacctga
      121 acaccttact tttgtccaag gattcgcaca ttgacagcct gaaacaagcc atgctccttc
      181 ttgaaaatca ccaggcaaaa ttaactgaat ccccggcgcc atggtggaaa ttctggaaaa
      241 aatcctgacc ccgtcatgct tgagttttcc tctccggcca tcccggggag ttcctgaacc
      301 ttcccaaaaa tcgccagatc tctgaacgct cctcaccact aaaaataccc acaccccacg
      361 caaaattaac attttgctga tttgtattta atatcagtag tttaagttgg tgaaatttcg
      421 ttttttaaat ttgatttata tagatccgac tctatgacga gtcgtcatag agtccccggc
      481 gagtcgtcat agagtcggta acgactcagg actataaaaa caatgagtta ataacgaccc
      541 gactctagac ccgactcccc gtttggttgt tttttagacg cggcgactct aggtacgact
      601 ctagtgaaga gtcgccggtg aatcgtgtgg tgagtcgtcc ggcgacttgc cataacgtga
      661 ttgccggccg tcgacgaatc ggattcctga acgtgctgaa aaccggtttt ccggctgcgc
      721 cggcaacgct tcacggccac gcaataaatt gcgtccccgt tcaccgtttt cggatggaaa
      781 gaacgccgga aacaggactt actctggctg agtggcgtga attttcgctc tatgcacttg
      841 cgtgcatact catgcatgcc gtaaaaacag agcctgcgcg tttctggcgg gtttgcgggt
      901 ggtttgttgc ctgttttacc ggtttcctgt cagaaacgcc ctgaggccgt tttagcggtg
      961 cgtacaatta tggtcttatg ttaaattagt tgattctaag atatatggca ccttctatga
     1021 aaaagtgccg ttgataatgg cattacatgc taccttttta aaaaggaatg tcatcgtctt
     1081 cttgttgctc ggatattaat ttcattatct ctatagatct tttttctatt atgtaaacaa
     1141 ttgattcttt taagttatcc acatccgtac actctgcggc ttcgtcttcc gtttctacct
     1201 gcacaggata tccggtagac tcatttatgc taaatccaaa taaaatgaaa cctttagggt
     1261 atgccataat agagtttttc tttattctga caattttttt acaacctata tatttgatta
     1321 ttttcgaatt attctgtaaa atatcaaagt caattgagtc ggatgttata tcctttagca
     1381 ttgacaaaat tgatgaaata tctgactcta ttttgtcttt taaaattagt gtttcattgg
     1441 ctttttttag tgatgccttt agtctttctt ggaactcttc atttttggtt gtcatggtaa
     1501 atcctacaaa atattgggta atgatcaaaa gtgttaaaaa atctttgatc taaacattgg
     1561 ttatcatcac taagtatacg atgaaaatca aggctgttca tgtctagctt aagacaatct
     1621 tttcctccgt atataaatga tgatgaaaac aacatttgat caaaaacaaa ccatctattc
     1681 gatgttcctg atttataatg ataagttcct aagttattgg tctttttgtc tgaaagtaaa
     1741 taccaaaaag ggttaaaaag aagctttcgt ttattcttta ttcgatggta atctctagtg
     1801 gcgtaaagtt tttcgtttat tgcaacagag taagggtttg tgttgtaatc acccatgcat
     1861 attatttggg actcaatgcc gtggtcatct agtattttag ttacattgtt gcgcagtgac
     1921 tcggcagcgt cctctcgaat cttttcatct gcgcttctta tggatggcca gtgtgataaa
     1981 aagaatgtta ttagatttcc tgttactgca tccttaaaaa caactctgac agcaatacgc
     2041 aaagttctat catctggttg tattttaatt atatatttat aatctatgta ctcaagtttt
     2101 gatgcttcgt acattatgga tatatccata attatccgac caacagtccc tgataaattc
     2161 aagtattcaa gatgtagttt atcagccaaa ggtttaaaat ctatagcctc atcttctgat
     2221 atttcacaga tacccaaaaa atccaatgtt ttttcttgag acattttttt tatatagtgc
     2281 ttggccaatc taatagcctc atccttgtct ttcttcacgc cttttacagg tggtgatatt
     2341 ccaatattcc accaacataa attcaattcc atggtgttta tttcttaatg cattgtattc
     2401 attgggttta ttgtattgct tttgatgggg ggtttaaaca ttttatttat ctgtttgttg
     2461 ataaatggtg ttgcgctacc ccttttaagg cgttatcttc ttggctggaa atgaaaaaac
     2521 cgccttgcag ggcggttttt tcaagggttc aaataacttg caggtctttt gaacctaggt
     2581 aactggctag tagaggagcg cagtcaccaa aacttgttct ttcagtgtag ccttaactga
     2641 cccataactt caagactaac tcctctaaat cagttaccaa tggctgctgc cagtggtgct
     2701 tttgcatgtc ttaccgggtt ggactcaaga tgatagttac cggataggcg cagcagtcgg
     2761 actgaacggg gggttcgtgc atacagtcca gcttggagcg aactgcctac ccggaactga
     2821 gtgtcaggcg tggaatgaga caaacgcggc cataacagcg gaatgacacc ggtaaaccga
     2881 aaggcaggaa caggagagcg cacgagggag ccatcagggg gaaacgcctg gtatctttat
     2941 agtcctgtcg ggtttcgcca cctctgattt gagtgtcagt ttctgtgatg cttgtcaggg
     3001 gggcgaagcc tatggaaaaa cggccgccgt gcggcctttc cttttctccg tcacgcgacc
     3061 gctcggtttt ctcgagctat tatacgcatg ctcctgccgc tcgccgcagc cgaacggcag
     3121 gagcgtagcg actgagtgag cgaggaagcg gaaaagagaa catccctaca ctgagcactg
     3181 acgctctgag gcttcttatg acgaaacaac agaaaacagc gctgaacatg gctaaattca
     3241 tccagaatca gtctctgctc ctgctggaga agcttaacga gcttgatctc gatgttgagg
     3301 ccgacctttg tgagaaactc cacgatgatg cggagcatct tttccgtaca ctgtcctcga
     3361 gactggatgc attacaggat ggtaactgat ggccagagtg tctattagtg aggctgcccg
     3421 actgacgggt aagagtagaa caacactgca caggttaatt aaagcaggtg acctgtccac
     3481 ctgtagcggt gaacgaaata caaaaatggt agatacttca gagcttttac gtgtctttgg
     3541 tc
//
