LOCUS       NZ_CP027041             4940 bp    DNA     circular CON 05-JAN-2024
DEFINITION  Klebsiella pneumoniae strain 16_GR_13 plasmid ColRNAI, complete
            sequence.
ACCESSION   NZ_CP027041
VERSION     NZ_CP027041.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN04868736
            Assembly: GCF_001701835.2
KEYWORDS    RefSeq.
SOURCE      Klebsiella pneumoniae
  ORGANISM  Klebsiella pneumoniae
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Klebsiella/Raoultella group; Klebsiella.
REFERENCE   1  (bases 1 to 4940)
  AUTHORS   Pitt,M.E., Nguyen,S.H., Duarte,T.P.S., Blaskovich,M.A.T.,
            Cooper,M.A. and Coin,L.J.M.
  TITLE     Evaluating the Resistome of Extensively Drug-Resistant Klebsiella
            pneumoniae via MinION Direct RNA Sequencing
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 4940)
  AUTHORS   Pitt,M.E., Nguyen,S.H., Duarte,T.P.S., Blaskovich,M.A.T.,
            Cooper,M.A. and Coin,L.J.M.
  TITLE     Direct Submission
  JOURNAL   Submitted (21-FEB-2018) Institute for Molecular Bioscience, The
            University of Queensland, Carmody Road, Brisbane, Queensland 4067,
            Australia
REFERENCE   3  (bases 1 to 4940)
  AUTHORS   Pitt,M.E., Elliotta,A.G., Cao,M.D., Ganesamoorthy,D., Karaiskos,I.,
            Giamarellou,H., Abboud,C.S., Cooper,M.A. and Coin,L.
  TITLE     Direct Submission
  JOURNAL   Submitted (04-MAY-2016) Institute for Molecular Biosience, The
            University of Queensland, 306 Camordy Rd, St Lucia, Brisbane,
            Queensland 4072, Australia
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Date                     :: 11-DEC-2017
            Assembly Method                   :: Unicycler v. 0.3.1
            Genome Representation             :: Full
            Expected Final Version            :: No
            Genome Coverage                   :: 101x
            Sequencing Technology             :: Illumina MiSeq/ ONT MinION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 01/04/2024 22:01:34
            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)                     :: 5,832
            CDSs (total)                      :: 5,707
            Genes (coding)                    :: 5,568
            CDSs (with protein)               :: 5,568
            Genes (RNA)                       :: 125
            rRNAs                             :: 9, 8, 8 (5S, 16S, 23S)
            complete rRNAs                    :: 9, 8, 8 (5S, 16S, 23S)
            tRNAs                             :: 88
            ncRNAs                            :: 12
            Pseudo Genes (total)              :: 139
            CDSs (without protein)            :: 139
            Pseudo Genes (ambiguous residues) :: 0 of 139
            Pseudo Genes (frameshifted)       :: 62 of 139
            Pseudo Genes (incomplete)         :: 76 of 139
            Pseudo Genes (internal stop)      :: 20 of 139
            Pseudo Genes (multiple problems)  :: 18 of 139
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP027041.1.
            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..4940
                     /organism="Klebsiella pneumoniae"
                     /mol_type="genomic DNA"
                     /strain="16_GR_13"
                     /isolation_source="Stool"
                     /host="Homo sapiens"
                     /db_xref="taxon:573"
                     /plasmid="ColRNAI"
                     /geo_loc_name="Greece: Athens"
                     /lat_lon="38.03 N 23.79 E"
                     /collection_date="2013-11-08"
                     /collected_by="Hygeia General Hospital"
                     /genotype="ST11"
     gene            complement(join(4250..4940,1..7))
                     /locus_tag="A6D82_RS29735"
                     /old_locus_tag="A6D82_030000"
     CDS             complement(join(4250..4698,4698..4940,1..7))
                     /locus_tag="A6D82_RS29735"
                     /old_locus_tag="A6D82_030000"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_086558260.1"
                     /ribosomal_slippage=""
                     /GO_function="GO:0004803 - transposase activity [Evidence
                     IEA]"
                     /GO_process="GO:0006313 - DNA transposition [Evidence IEA]"
                     /note="programmed frameshift; Derived by automated
                     computational analysis using gene prediction method:
                     Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="IS1-like element IS1B family transposase"
                     /protein_id="WP_095033700.1"
                     /translation="MASVSISCPSCSATDGVVRNGKSTAGHQRYLCSHCRKTWQLQFTY
                     TASQPGTHQKIIDMAMNGVGCRATARIMGVGLNTIFRHFKKLRPQSVTSRIQPGSDVIV
                     CAEMDEQWGYVGAKSRQRWLFYAYDRLRKTVVAHVFGERTMATLGRLMSLLSPFDVVIW
                     MTDGWPLYESRLKGKLHVISKRYTQRIERHNLNLRQHLARLGRKSLSFSKSVELHDKVI
                     GHYLNIKHYQ"
                     /name="IS1-like element IS1B family transposase"
     gene            66..299
                     /locus_tag="A6D82_RS29740"
                     /old_locus_tag="A6D82_030005"
     CDS             66..299
                     /locus_tag="A6D82_RS29740"
                     /old_locus_tag="A6D82_030005"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_011953229.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="type II toxin-antitoxin system RelE/ParE family
                     toxin"
                     /protein_id="WP_205634400.1"
                     /translation="MKLVAAGIEPELKVEHLKVVAPGVIELKINGSPAYRCVYTIKSPG
                     KVIVLRVFKKTTNGPARKDLEVVKQRLKNLKI"
                     /name="type II toxin-antitoxin system RelE/ParE family
                     toxin"
     gene            complement(319..630)
                     /locus_tag="A6D82_RS29745"
                     /old_locus_tag="A6D82_030010"
     CDS             complement(319..630)
                     /locus_tag="A6D82_RS29745"
                     /old_locus_tag="A6D82_030010"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_017134632.1"
                     /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 transcriptional regulator"
                     /protein_id="WP_039817123.1"
                     /translation="MSNQNIFEILTSDPVSLNMWNLKSNLILAIHKTVRDNGWNQTEAA
                     AHLGISQPRVSNMLKGKLDKFSTDSLLEIMFKLGYKLDMQVHPSSEVILEMGMKKAML"
                     /name="helix-turn-helix transcriptional regulator"
     gene            complement(988..1101)
                     /locus_tag="A6D82_RS31690"
                     /old_locus_tag="A6D82_030015"
     CDS             complement(988..1101)
                     /locus_tag="A6D82_RS31690"
                     /old_locus_tag="A6D82_030015"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_007772075.1"
                     /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_072016307.1"
                     /translation="MHEPPVQSDCCALSGNYHLESNPVRHAKAPLAAAIGN"
                     /name="replication initiation protein"
     gene            1510..1701
                     /locus_tag="A6D82_RS29760"
                     /old_locus_tag="A6D82_030025"
     CDS             1510..1701
                     /locus_tag="A6D82_RS29760"
                     /old_locus_tag="A6D82_030025"
                     /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_000166328.1"
                     /translation="MTKQQKTALNMAKFIQNQSLLLLEKLNELDLDAEADLCEKLHDDA
                     EHLFRTLSSRLDALQDGN"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            1701..2102
                     /locus_tag="A6D82_RS29765"
                     /old_locus_tag="A6D82_030030"
     CDS             1701..2102
                     /locus_tag="A6D82_RS29765"
                     /old_locus_tag="A6D82_030030"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_009310048.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="transcriptional regulator"
                     /protein_id="WP_039817125.1"
                     /translation="MARVSISEASRLTGKSRTTLHRLIKAGDLSTCSGERNAKMVDTSE
                     LLRVFGPFEQPKSEHHSGQVSEQRDTASADQSEQVIRHLKQEIEHLNTLLLSKDSHIDS
                     LKQAMLLLENHQAKLTESPAPWWKFWKKS"
                     /name="transcriptional regulator"
     gene            complement(2999..3298)
                     /locus_tag="A6D82_RS29775"
     CDS             complement(2999..3298)
                     /locus_tag="A6D82_RS29775"
                     /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_125564845.1"
                     /translation="MSNPPFEFVIRYHDLSPEQVRSFIDDAFHRVDLVLEKQLSDRPGF
                     FIPTCKSLTTNPSLSEIAIAVYNTYAVTEMIKDQLLRQSSNITLIKDIREIFVS"
                     /name="hypothetical protein"
     gene            complement(3389..3649)
                     /locus_tag="A6D82_RS31535"
                     /old_locus_tag="A6D82_030040"
                     /pseudo=""
     CDS             complement(3389..3649)
                     /locus_tag="A6D82_RS31535"
                     /old_locus_tag="A6D82_030040"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_010891192.1"
                     /note="internal stop; Derived by automated computational
                     analysis using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="protein L"
                     /name="protein L"
     Typing          complement(989..1462)
                     /name="ColRNAI_rep_cluster_1987"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="89.627"
                     /coverage="92.0"
                     /evalue="9.83e-170"
ORIGIN
        1 aagccactgg agcacctcaa aaacaccatc atacactaaa tcagtaagtt ggcagcatca
       61 ccaacttgaa gttggttgcc gctggaattg aaccagaact gaaagttgaa cacctgaaag
      121 tagttgctcc aggcgtgatt gagttgaaga taaatggtag ccctgcttat cgttgtgtgt
      181 acacgataaa atcacccggc aaggtgatcg tgttacgtgt cttcaagaaa acgactaacg
      241 gacctgcacg caaagactta gaagtcgtga agcaacggct gaaaaatctc aaaatatagt
      301 atccactcaa ggcgatgttc acagcatcgc ctttttcatg cccatctcta aaattacttc
      361 agaggatggg tgtacttgca tgtctaattt gtaacccagc ttgaacatga tttccagtag
      421 tgaatctgta gaaaacttgt ccagcttccc tttcagcatg ttgctaaccc taggttggct
      481 tatgcctaga tgtgcggccg cctctgtttg gttccagccg ttatctctta ccgtcttatg
      541 tatggcgagg atcaggtttg atttcaggtt ccacatgttt agggataccg gatcactcgt
      601 tagtatttcg aatatgtttt gattgctcat aattttcatc tcctatctga atgcgagcat
      661 ttagttgtca caagacaata ggaacgatta ttagcttaca ctaaagtttg cggattatac
      721 aagttacagt atgcatgaca agatgtagat ggggttttat ttgtaaattt aaagcattct
      781 aacaacactt gttgactgga tcttggtcgt cagcgtagtc ttcatttgtt ttaaaaagaa
      841 aaaccgcctg gggaggcggt ttttcaaggt tcatcaaacc ggcaagttta tgaaccgagg
      901 taactggctt agaggagcac agtcaccaaa tctgttttat cagtgtagcc gtatagtacg
      961 tgtcttttca agacttcact cctctaatca gttaccaatg gctgctgcca gtggcgcttt
     1021 tgcatgtctt accgggttgg actcaagatg atagttaccg gataaggcgc agcagtcgga
     1081 ctgaacgggg ggttcgtgca tacagtccag cttggagcga actgcctacc cggaactgag
     1141 tgtcaggcgt ggaatgagat aaacgcggcc ataactgcgg aatgacaccg gtaaaccgaa
     1201 aggcaggaac aggagagcgc acgagggagc catcaggggg aaacgcctgg tatctttaga
     1261 gtcctgtcgg gtttcgccac cactgatttg agcgtctgtt tttgtgatgc ttatcagggg
     1321 ggcggagcct atggaaaaac ggcaacgccg cggccttccg ttgtcctttc cgagctgtct
     1381 gtcctatgcc cttatgtgtg cgttgcgacc gctcgccgca gccgaacggt aggagcgtag
     1441 cgactgagtg agcgaggaag cggaaaagag accggtttta cattgagcac tgacgctctg
     1501 aggcccttta tgacgaaaca acagaaaacg gcgctgaaca tggctaagtt catccagaat
     1561 cagtccctgc tcctgctgga gaagcttaac gagcttgatc tcgatgctga ggctgacctt
     1621 tgtgagaaac tccacgatga tgcggagcat cttttccgta cactgtcctc gagactggat
     1681 gcattacagg atggtaactg atggcccgag tgtctattag tgaggcttcc cgactgacgg
     1741 gtaagagtag aacaacactg cacaggttaa ttaaagcagg tgacctgtcc acctgtagcg
     1801 gtgaacgtaa tgcaaaaatg gtagatactt cagagctttt acgtgtcttt ggtccctttg
     1861 agcaaccgaa gagtgaacac cattctggac aggtctctga acagcgtgat acagcctctg
     1921 ctgaccagag tgaacaggtg attcgtcatc tgaaacagga gattgaacac ctgaacacct
     1981 tacttttgtc caaggattcg cacattgata gcctgaaaca ggccatgctc cttcttgaaa
     2041 atcaccaggc aaaattaact gaatccccgg cgccatggtg gaaattctgg aaaaaatcct
     2101 gaccccgtca tgcttcagtt ttcctctccg gccatcccgg ggagttcctg aaccttccca
     2161 aaaatcgcca gatctctgaa cgctcctcac cactaaaaat atccacaccc cacgcaaaat
     2221 taaaattttg cagatttgta ttttatatca gcagcttacg ttctataaat ttcgtttttt
     2281 taattttatt tatacagatc cgactctatg acgagtcgtc atagagtccc cggcgagtcg
     2341 tcatagagtc ggtaacgact caggactata aaaacaataa gttaacaacg acccgactct
     2401 agacccgact ccccgtttgg ttgtttttta gacgtgacga ctctgggtac gactctagtg
     2461 aagagtcgcc ggtgaatcgt gtggtgagtc gtccggcgac ttgccataac gtgattgccg
     2521 gccgtcgacg aacccgattc ctgaacgtgc tgaaaaccgg ttttccggct gcgccggcaa
     2581 cgcttcacgg ccacgcaata aattgcgtcc ccgttcaccg ttttcggatg ggaagaacgc
     2641 cggaaacagg acttaccctg gctgaatggc gtgaattttc gcgctatgca cttgcgtgca
     2701 tactcatgca tgccgtaaaa acagagcctg cgcgtttctg gcgggttttc gggtggtttg
     2761 ttgcctgttt taccggtttc ccgtcagaaa cgccctgagg ccgttttagc ggtgcgtaca
     2821 atcatacctt tatgttaaat gatagatgta aaaagccccg attggtctga tggatttcct
     2881 gctgaggtgc gaagcggtcc acctcccggc gacctgttcg gaaactccct ctgcgccagt
     2941 cttgtttggc caaataagct gttatgagat aagcacttgt ggtgtggtag agaagatcct
     3001 agctgacaaa gatctctctt atgtctttaa tgagagtgat attggaagat tgtcgaagca
     3061 attggtcctt tatcatttca gtaacggcat atgtgttgta aacagcgata gctatttcag
     3121 ataaagacgg attagtagtt agtgacttac atgtaggaat aaaaaagcct ggacgatcgg
     3181 ataactgttt ttctagaacg agatcaacac gatgaaaagc atcgtcaata aagctccgca
     3241 cttgctctgg agacaggtca tgataacgaa tgacaaattc aaaaggtgga ttagacataa
     3301 gacctcagat cgtggattgt ttggtacgag tgagtaatga gactttctgg taaatcactg
     3361 agggaaagcc ccgaagggct tccgtgtctc agttaccaaa tttatcaccg tttgtgtctg
     3421 tcctcacaat tagctgccat ttaacatttt gtttttgact atgttgatga tggttttgtg
     3481 gggggaaagg atcgttttta ttactagtta tctctttacc gcatacggta cagcgataaa
     3541 tgcctgatac tggaactgta tcgcttggat cgtatgttga tgttcaccaa gtctgtgtgt
     3601 gtgtaactcg ctgtaagaac tgctctgttt tttccgtata tgcagccatt cttttacctt
     3661 tcttatcgtt tattttcttg gttttcctgc gtctgagcgt tttttgcgca ccgttccgtc
     3721 attgtttctg tctctgggct gggttccgcc accaggcttt ggcactacca catctttgtt
     3781 tagcggtctt ctatctgcca tctcttaact ccttctttca gttgtgatgc tttacggaga
     3841 cttttagctt cgatggagga ttactttcgt aaacagctga tagcttattt attgagctaa
     3901 cggcatgcgc aagcgaagcg gcatattgtt agtttataca acttagagta tattgatgca
     3961 atggatattg cctaaagcag tgtcctgaac cactgaaatt aaatgcctct acctggtgaa
     4021 tctcatcagg cgtagaggtt tggtttttta gtgaggtttt tttaatcgga gtatcaaatg
     4081 agaaatttaa ttgttcgacc actaaacccc aacaaaggag gacactatgt ccgcaagcga
     4141 aatgaaagag atttgtctag acgtaactgg tgttgataaa gagctaaagt ctttacctat
     4201 tgataaagct ttagcttttt tgcacaactt gaagggtaat gactccaact tattgatagt
     4261 gttttatgtt cagataatgc ccgatgactt tgtcatgcag ctccaccgat tttgagaacg
     4321 acagcgactt ccgtcccagc cgtgccaggt gctgcctcag attcaggtta tgccgctcaa
     4381 ttcgctgcgt atatcgcttg ctgattacgt gcagctttcc cttcaggcgg gattcataca
     4441 gcggccagcc atccgtcatc catatcacca cgtcaaaggg tgacagcagg ctcataagac
     4501 gccccagcgt cgccatagtg cgttcaccga atacgtgcgc aacaaccgtc ttccggagcc
     4561 tgtcatacgc gtaaaacagc cagcgctggc gcgatttagc cccgacgtat ccccactgtt
     4621 cgtccatttc cgcgcagacg atgacgtcac tgcccggctg tatgcgcgag gttaccgact
     4681 gcggcctgag ttttttaaat ggcggaaaat cgtgttgagg ccaacgccca taatgcgggc
     4741 ggttgcccgg catccaacgc cattcatggc catatcaatg attttctggt gcgtaccggg
     4801 ttgagaagcg gtgtaagtga actgcagttg ccatgtttta cggcagtgag agcagagata
     4861 gcgctgatgt ccggcggtgc ttttgccgtt acgcaccacc ccgtcagtag ctgaacagga
     4921 gggacagctg atagaaacag
//
