LOCUS       CP044379                4653 bp    DNA     circular BCT 11-DEC-2019
DEFINITION  Klebsiella pneumoniae strain 2018S06-082 plasmid p2018S06-082-3,
            complete sequence.
ACCESSION   CP044379
VERSION     CP044379.1
DBLINK      BioProject: PRJNA574008
            BioSample: SAMN12838238
KEYWORDS    .
SOURCE      Klebsiella pneumoniae
  ORGANISM  Klebsiella pneumoniae
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Klebsiella/Raoultella group; Klebsiella.
REFERENCE   1  (bases 1 to 4653)
  AUTHORS   Chen,F.-J., Liao,Y.-C., Wu,H.-C., Huang,W.-C., Kuo,S.-C. and
            Lauderdale,T.-L.
  TITLE     Emergence of mcr-like genes in human Klebsiella pneumoniae in Taiwan
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 4653)
  AUTHORS   Chen,F.-J., Liao,Y.-C., Wu,H.-C., Huang,W.-C., Kuo,S.-C. and
            Lauderdale,T.-L.
  TITLE     Direct Submission
  JOURNAL   Submitted (25-SEP-2019) National Institute of Infectious Diseases
            and Vaccinology, National Health Research Institutes, 35 Keyan Road,
            Zhunan, Miaoli 35053, Taiwan
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Date                     :: 2019
            Assembly Method                   :: CCBGpipe v. 1
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 80x
            Sequencing Technology             :: Oxford Nanopore MiniION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI
            Annotation Date                   :: 09/26/2019 14:46:38
            Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline
            (PGAP)
            Annotation Method :: Best-placed reference protein set; GeneMarkS-2+
            Annotation Software revision      :: 4.9
            Features Annotated :: Gene; CDS; rRNA; tRNA; ncRNA; repeat_region
            Genes (total)                     :: 5,774
            CDSs (total)                      :: 5,649
            Genes (coding)                    :: 3,065
            CDSs (with protein)               :: 3,065
            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)              :: 2,584
            CDSs (without protein)            :: 2,584
            Pseudo Genes (ambiguous residues) :: 0 of 2,584
            Pseudo Genes (frameshifted)       :: 2,456 of 2,584
            Pseudo Genes (incomplete)         :: 158 of 2,584
            Pseudo Genes (internal stop)      :: 48 of 2,584
            Pseudo Genes (multiple problems)  :: 72 of 2,584
            ##Genome-Annotation-Data-END##
            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/
            NCBI analysis of this genome has determined that >30% of the
            predicted CDS features contain frameshifts, which is well above the
            usually observed value of <10%.
FEATURES             Location/Qualifiers
     source          1..4653
                     /organism="Klebsiella pneumoniae"
                     /mol_type="genomic DNA"
                     /strain="2018S06-082"
                     /host="Homo sapiens"
                     /db_xref="taxon:573"
                     /plasmid="p2018S06-082-3"
                     /geo_loc_name="Taiwan"
                     /collection_date="2018"
                     /collected_by="NHRI"
     gene            complement(64..459)
                     /locus_tag="F7P07_28825"
     CDS             complement(64..459)
                     /locus_tag="F7P07_28825"
                     /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="QGV92537.1"
                     /translation="MNANEVKDILEHSNHDDWIVDDETGSFTYKNDLNLHIKRADYDNY
                     NSFSEPRAVSHPNPNACSVQYTVNYGSSFVDRKTLVSVDGHRATLPMPASANDLTVTSA
                     DVNFAKIVDTGERVDEYILRSGLKVQP"
                     /name="hypothetical protein"
     gene            849..1091
                     /locus_tag="F7P07_28830"
     CDS             849..1091
                     /locus_tag="F7P07_28830"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_017446859.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="QGV92538.1"
                     /translation="MSKESELEFRTKELERQMKGVQRRIEVVNAKYDSQTKKQERRIRD
                     LEIKTAVQSGVTQREVANIYELSPGRVNQIIKKVG"
                     /name="hypothetical protein"
     gene            1272..1347
                     /locus_tag="F7P07_28835"
     tRNA            1272..1347
                     /locus_tag="F7P07_28835"
                     /product="tRNA-Arg"
                     /inference="COORDINATES: profile:tRNAscan-SE:2.0.3"
                     /note="Derived by automated computational analysis using
                     gene prediction method: tRNAscan-SE."
                     /anticodon=(pos:1305..1307,aa:Arg,seq:tct)
                     /name="tRNA-Arg"
     gene            complement(1433..1750)
                     /locus_tag="F7P07_28840"
     CDS             complement(1433..1750)
                     /locus_tag="F7P07_28840"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_014526571.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="QGV92539.1"
                     /translation="MVSRPSTCHNVIAGRRRTRFLIVLKTGFPAAPATLHGHAINCVPV
                     HRFRMGRTPETGLTLAEWREFSRYALACILMHAVKTEPARFWRVFGWFVACFTGFPSET
                     P"
                     /name="hypothetical protein"
     gene            complement(2129..2530)
                     /locus_tag="F7P07_28845"
     CDS             complement(2129..2530)
                     /locus_tag="F7P07_28845"
                     /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="helix-turn-helix domain-containing protein"
                     /protein_id="QGV92540.1"
                     /translation="MARVSISEAARLTGKSRTTLHRLIKAGDLSTCSGERNAKMVDTSE
                     LLRVFGPFEQPKGEHHSGQVSGQRDTASADQSEQVIRHLKQEIEHLNTLLLSKDSHIDS
                     LKQAMLLLENHQAKLTESPAPWWKFWKKS"
                     /name="helix-turn-helix domain-containing protein"
     gene            complement(2530..2721)
                     /locus_tag="F7P07_28850"
     CDS             complement(2530..2721)
                     /locus_tag="F7P07_28850"
                     /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="QGV92541.1"
                     /translation="MSKQQKTALNMAKFIQNQSLLLLEKLNELDLDVEADLCEKLHDDA
                     EHLFRTLSSRLDALQDGN"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            2678..3112
                     /locus_tag="F7P07_28855"
                     /pseudo=""
     CDS             2678..3112
                     /locus_tag="F7P07_28855"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_014343523.1"
                     /note="internal stop; Derived by automated computational
                     analysis using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="plasmid replication initiation protein"
                     /name="plasmid replication initiation protein"
     gene            3137..3250
                     /locus_tag="F7P07_28860"
     CDS             3137..3250
                     /locus_tag="F7P07_28860"
                     /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="QGV92542.1"
                     /translation="MHEPPVQSDCCALSGNYHLESNPVRHAKAPLAAATGN"
                     /name="replication initiation protein"
     gene            3676..4083
                     /locus_tag="F7P07_28865"
     CDS             3676..4083
                     /locus_tag="F7P07_28865"
                     /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="QGV92543.1"
                     /translation="MIKQSRKKISINEESLGDYEIDSLILTINSSKIKFEPVGTMLIGS
                     KGRVDVTGPFGKEKFILIRKGVKSPSDLIKVRVNVVGAYKPEKDKTDEDVKKPSIDDWE
                     WKTMPSDSRWVKFDDVNSETITNIIMRMING"
                     /name="hypothetical protein"
     gene            4076..4627
                     /locus_tag="F7P07_28870"
     CDS             4076..4627
                     /locus_tag="F7P07_28870"
                     /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="QGV92544.1"
                     /translation="MARVHAIKRSGLHIDIDYVVHKKIALDRAVILRYSTKNPDYHADF
                     VGLSEPEIEREKDLILKENDTTHCLLLLTAIEAIFRLDADQKYCNKKRDPLSRKIKEIY
                     DKTKGEKIKLDDDLINTRMNEDDARLKKDYNDLKTCFKFRHWLAHGRYWHPKRIKNFYF
                     DSILIVIDSILNSTKYNFEV"
                     /name="hypothetical protein"
     Typing          2843..3250
                     /name="ColRNAI_rep_cluster_1987"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="95.11"
                     /coverage="99.0"
                     /evalue="0.0"
ORIGIN
        1 taacgtccct taagcacagc acattatgag ccagcaattt tagattgctg gctcacattt
       61 aaatcatggt tgaactttaa gaccagagcg gagaatgtat tcatcaacac gctccccagt
      121 atctacaatt ttggcaaagt tcacgtcagc tgatgtcacg gttaaatcat ttgcggatgc
      181 aggcataggc aaggttgcgc ggtgaccatc gacagaaacc aaagtctttc tatcaacaaa
      241 tgatgaacca tagtttacgg tgtactgtac tgaacaggca ttcggattcg gatgactaac
      301 agcccggggt tcactaaagg agttgtagtt gtcatagtcc gctctcttaa tgtgcaaatt
      361 taagtcgttt ttatatgtaa acgacccagt ctcatcatcc acaatccaat catcatgatt
      421 agaatgttca agaatgtctt ttacttcatt agcattcatg cataccccca tataaatcaa
      481 tggttagaat gtaaagatcg attgagttct acaccacact gctccgaaaa gttctctatg
      541 tgcaatcaaa ttttccagta aagaatcaaa taataaatac taaacatcga tttgtttttt
      601 cacttaaaaa tcatatacat aaaataggtg tgtttagcct ttttaatatc agaattaaac
      661 caatcgcaac ttattgtttt tattggaaaa taaaaacaaa gaaaaataag gggaaacact
      721 gattatagaa gttgctgtga tcgtaaaaaa aggctattgt tgatttgtca aacataggtt
      781 aagaccttcc ggcaagaaga aaccttcgaa tgacacccaa caataacctt acttagcgag
      841 tatatcatat gagtaaagaa tcagaactag agttcagaac aaaagaactc gaacgtcaaa
      901 tgaaaggtgt ccagcgacgt attgaggtgg ttaacgccaa atacgacagc caaaccaaga
      961 agcaagaacg tcgcattcgt gatttggaaa tcaaaacagc agtccagtca ggcgttacgc
     1021 aacgtgaggt tgcaaacatt tacgaactgt cgccgggtcg cgttaatcag atcattaaaa
     1081 aagtcggcta atctctagag aaaaaaccgc caaaaggcgg ttttttctcg caatacaaac
     1141 tgacgtgctt tttaccataa ggtctcatta cataccctgt tctgatgcga ccggtaaaca
     1201 cataaaaaac ttcacaaaaa gcatgcagtg atgttaaatc aaagacggtc ccgactttgt
     1261 tgggtccaga tggggatata gcttcaacgg tagagcagcg gacttctaat ctgatggttg
     1321 tgggttcaaa tcccattgtc tccaccaaaa gcctccccct aaaaggggga ggcaactatt
     1381 ctggccacag catttaccat aacgtcgcat tacgcgcacc gctaaaacgg cctcagggcg
     1441 tttctgacgg gaaaccggta aaacaggcaa caaaccaccc gaaaacccgc cagaaacgcg
     1501 caggctctgt ttttacggca tgcatgagta tgcacgcaag tgcatagcgc gaaaattcac
     1561 gccattcagc cagggtaagt cctgtttccg gcgttcttcc catccgaaaa cggtgaacgg
     1621 ggacgcaatt tattgcgtgg ccgtgaagcg ttgccggcgc agccggaaaa ccggttttca
     1681 gcacgatcag gaatcgggtt cgtcgacggc cggcaatcac gttatggcaa gtcgacggac
     1741 gactcaccac acgattcacc ggcgattcga ctcgtgactt gactctagag tcgtcaaggt
     1801 caaaaaaaca ccaaaatgac gattcgactc tagagtcaag tcgtcataag ttactgatag
     1861 tcttatgtga gtcgtcgatg actctatgac gagtcgtcgg caagtcgtac acgaatcgcc
     1921 gacgacttgg attcacctta cagaaagtaa tactgcgtaa tttaataacc cacaactaac
     1981 tgatattaat gagttatctt caaaatttta attttgcgtg gggtgtgggt atttttagtg
     2041 gtgaggagcg ttcagagatc tgacgatttt tgggaaggtt caggaactcc ccgggatggc
     2101 cggagaggaa aactgaagca tgacggggtc aggatttttt ccagaatttc caccatggcg
     2161 ccggtgattc agttaatttt gcctggtgat tttcaagaag gagcatggcc tgtttcaggc
     2221 tgtcaatgtg cgaatccttg gacaaaagta aggtgttcag gtgttcaatc tcctgtttca
     2281 gatgacgaat cacctgttca ctctggtcag cagaggctgt atcacgctgt ccagagacct
     2341 gtccagaatg gtgttcaccc ttcggttgct caaagggacc aaagacacgt aaaagctctg
     2401 aagtatctac catttttgca ttacgctcac cgctacaggt ggacaggtca cctgctttaa
     2461 ttaacctgtg cagtgttgtt ctactcttac ccgtcagtcg ggcagcctca ctaatagaca
     2521 ctctggccat cagttaccat cctgtaatgc atccagtctc gaggacagtg tacggaaaag
     2581 atgctccgca tcatcgtgga gtttctcaca aaggtcggct tcgacatcga gatcaagctc
     2641 gttaagtttc tccagcagga gcagagactg attctggatg aatttagcca tgttcagcgc
     2701 tgttttctgt tgtttagaca taagaggcct cagagcgtca gtgctcagtg taggtatgtt
     2761 ctcttttccg cttcctcgct cactcagtcg ctacgctcct gccgttcggc tgcggcgagc
     2821 ggcaggagta tgcgtacaag agctcgagaa aaccgagcgg tagcgtgacg gggaaaagga
     2881 aatgccgcac ggcggccgtt tttccatagg ctccgccccc ctgacaagca tcacagaatt
     2941 tgacgctcaa atcagtggtg gcgaaacccg acaggactat aaagataccg ggcgtttccc
     3001 cctgatggct ccctcgtgcg ctctcctgtt cctgcctttc ggtttaccag tgtcaatccg
     3061 ctgttatggc cgcgtttatc tcattccacg cctgacactc agttccgggt aggcagttcg
     3121 ctccaagctg gactgtatgc acgaaccccc cgttcagtcc gactgctgcg ccttatccgg
     3181 taactatcat cttgagtcca acccggtaag acatgcaaaa gcgccactgg cagcagccac
     3241 tggtaactga tttagaggag tttgtcttga agttatgcgc cagttaaggc taaactgaaa
     3301 gaacaagttt tggtgactgc gctcctccaa gccagttacc tcggttcaac gagcgccaac
     3361 tctatgaacc ttcgaaaaaa ccgcccgcca aggcggtttt ttcgtttcag aagcgacaat
     3421 acctccgagc aagttaagcg tcaagaacaa cacattgctc gacaccaaag caaaggctag
     3481 aatcgtaaaa taattccgat ctagaggtta caaaaaatga acatgaaaac gctgaaagat
     3541 ataattgaaa aacaaaaaaa agaagaagaa gaacaaaaat tcgacccagc tgaacaaata
     3601 gaagaataca taagccttgt tgaaaaatta tatactatta cattagaatc tattgacgaa
     3661 ctaatcaaag atggattgat aaaacaatca agaaaaaaaa tatcaataaa tgaagagtct
     3721 ctaggtgatt atgaaatcga ctctctaata ctcactataa actcaagtaa aataaaattt
     3781 gagccagtag gaaccatgct aataggttca aaaggaaggg ttgacgtcac agggccattt
     3841 ggaaaagaaa aattcattct gatcagaaaa ggagtcaaaa gccccagcga tttaataaaa
     3901 gtaagagtta acgtagtcgg ggcatataaa ccagaaaaag ataagaccga tgaagatgtg
     3961 aaaaagccgt caattgatga ttgggaatgg aaaacaatgc ctagcgatag tcgatgggtt
     4021 aaatttgatg atgtgaattc cgagaccatt acgaatatta ttatgagaat gataaatggc
     4081 tagggttcat gcaattaaaa gatctggtct acacatagac attgactatg tcgtacataa
     4141 aaagatagca ctcgatcgtg ctgtaattct gcggtattca acaaagaacc cagattacca
     4201 tgccgatttc gtcggcttaa gtgagccgga gattgaaaga gaaaaagact taatactaaa
     4261 agaaaatgac acaacacatt gccttttatt gttaacagct attgaagcaa tatttcgatt
     4321 agatgcagat cagaagtact gcaataaaaa aagagaccca ttatcaagaa aaataaaaga
     4381 gatatatgat aaaacaaaag gagaaaaaat aaaattagat gatgatttaa taaataccag
     4441 aatgaatgaa gatgatgcta gattaaaaaa agactacaac gatctaaaaa catgttttaa
     4501 attcaggcat tggcttgctc atggaagata ctggcatcca aagagaataa agaattttta
     4561 tttcgactct atactaatag tgatagattc cattttaaac tcaaccaaat acaattttga
     4621 agtttaggtc agtgacatta aaaaaagtca cca
//
