LOCUS       CP044392                3850 bp    DNA     circular BCT 11-DEC-2019
DEFINITION  Klebsiella pneumoniae strain 2018N17-066 plasmid p2018N17-066-3,
            complete sequence.
ACCESSION   CP044392
VERSION     CP044392.1
DBLINK      BioProject: PRJNA574008
            BioSample: SAMN12838239
KEYWORDS    .
SOURCE      Klebsiella pneumoniae
  ORGANISM  Klebsiella pneumoniae
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Klebsiella/Raoultella group; Klebsiella.
REFERENCE   1  (bases 1 to 3850)
  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  JOURNAL   Unpublished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 3850)
  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 12:28:42
            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)                     :: 5,546
            CDSs (total)                      :: 5,424
            Genes (coding)                    :: 3,719
            CDSs (with protein)               :: 3,719
            Genes (RNA)                       :: 122
            rRNAs                             :: 9, 8, 8 (5S, 16S, 23S)
            complete rRNAs                    :: 9, 8, 8 (5S, 16S, 23S)
            tRNAs                             :: 87
            ncRNAs                            :: 10
            Pseudo Genes (total)              :: 1,705
            CDSs (without protein)            :: 1,705
            Pseudo Genes (ambiguous residues) :: 0 of 1,705
            Pseudo Genes (frameshifted)       :: 1,599 of 1,705
            Pseudo Genes (incomplete)         :: 113 of 1,705
            Pseudo Genes (internal stop)      :: 48 of 1,705
            Pseudo Genes (multiple problems)  :: 49 of 1,705
            ##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..3850
                     /organism="Klebsiella pneumoniae"
                     /mol_type="genomic DNA"
                     /strain="2018N17-066"
                     /host="Homo sapiens"
                     /db_xref="taxon:573"
                     /plasmid="p2018N17-066-3"
                     /geo_loc_name="Taiwan"
                     /collection_date="2018"
                     /collected_by="NHRI"
     gene            complement(join(3748..3850,1..239))
                     /locus_tag="F7P08_27685"
     CDS             complement(join(3748..3850,1..239))
                     /locus_tag="F7P08_27685"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_006122514.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MobC family plasmid mobilization relaxosome
                     protein"
                     /protein_id="QGV89478.1"
                     /translation="MADKRNKMLTMWVTEDEHRRLLERCDGKQLAAWMRQTCLDEKPTR
                     AGRLPSISPALLRQLAGMGNNLNQIARKVNAGGAGHDRVQIVAALMAIDAGLERLRHAV
                     LEKGPDDDC"
                     /name="MobC family plasmid mobilization relaxosome protein"
     gene            complement(448..655)
                     /locus_tag="F7P08_27690"
                     /pseudo=""
     CDS             complement(448..655)
                     /locus_tag="F7P08_27690"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001347451.1"
                     /note="frameshifted; Derived by automated computational
                     analysis using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /name="hypothetical protein"
     gene            612..836
                     /locus_tag="F7P08_27695"
                     /pseudo=""
     CDS             612..836
                     /locus_tag="F7P08_27695"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001326445.1"
                     /note="incomplete; partial on complete genome; missing
                     N-terminus; Derived by automated computational analysis
                     using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /name="hypothetical protein"
     gene            861..995
                     /locus_tag="F7P08_27700"
     CDS             861..995
                     /locus_tag="F7P08_27700"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_005019281.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="replication initiation protein"
                     /protein_id="QGV89474.1"
                     /translation="MHEPPVQSDRCALSGNYHLDSNPDGHEKTPLAAATGNKGVQDGI"
                     /name="replication initiation protein"
     gene            1012..1193
                     /locus_tag="F7P08_27705"
                     /pseudo=""
     CDS             1012..1193
                     /locus_tag="F7P08_27705"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_004228313.1"
                     /note="frameshifted; incomplete; partial on complete
                     genome; missing C-terminus; Derived by automated
                     computational analysis using gene prediction method:
                     Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /name="hypothetical protein"
     gene            1534..1686
                     /locus_tag="F7P08_27710"
     CDS             1534..1686
                     /locus_tag="F7P08_27710"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_009090372.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="YgdI/YgdR family lipoprotein"
                     /protein_id="QGV89479.1"
                     /translation="MKTTDGRTIVADGKPQIDSDTGLVSYKDAQTGKTEHINRDKITNM
                     SELDN"
                     /name="YgdI/YgdR family lipoprotein"
     gene            1700..1927
                     /locus_tag="F7P08_27715"
     CDS             1700..1927
                     /locus_tag="F7P08_27715"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_010615788.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="YgdI/YgdR family lipoprotein"
                     /protein_id="QGV89475.1"
                     /translation="MTKVIYSALAAIIALSALTGCTRTSYAIHTNDGRTIVSDGKPKES
                     DAGLIGYTDANGVKQQINKQEVKEVSEIPN"
                     /name="YgdI/YgdR family lipoprotein"
     gene            complement(2351..2566)
                     /gene="mbeD"
                     /locus_tag="F7P08_27720"
     CDS             complement(2351..2566)
                     /gene="mbeD"
                     /locus_tag="F7P08_27720"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_015328239.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MbeD family mobilization/exclusion protein"
                     /protein_id="QGV89476.1"
                     /translation="MTELEKQLLSALEQLQQDYSRRLDEWESAFEEWRKMSGLMQRENA
                     ALSERVSGLSRQVQSLSEQLRRLSTG"
                     /name="mbeD"
     gene            complement(2573..3070)
                     /locus_tag="F7P08_27725"
     CDS             complement(2573..3070)
                     /locus_tag="F7P08_27725"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_020325392.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="mobilization protein"
                     /protein_id="QGV89477.1"
                     /translation="MSSLLTASRDFEEKSKAQQQLTEERLKAAFSKHENVVKSELNASA
                     KRINDAISAHEQGMNAAMQSNRLSVLRMVGRTWLTITMVSGLLFASLSGVLWYQGNRIA
                     ANLAEIRQQRDTLSKLQMQTWGVTYLENRNGRFLVLPEGMKAETGRKVDNKTRNAVKLV
                     RE"
                     /name="mobilization protein"
     gene            complement(3051..3809)
                     /locus_tag="F7P08_27730"
                     /pseudo=""
     CDS             complement(3051..3809)
                     /locus_tag="F7P08_27730"
                     /inference="COORDINATES: protein motif:HMM:PF03432.12"
                     /note="incomplete; partial on complete genome; missing
                     C-terminus; Derived by automated computational analysis
                     using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="relaxase/mobilisation nuclease domain-containing
                     protein"
                     /name="relaxase/mobilisation nuclease domain-containing
                     protein"
     Typing          complement(320..507)
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="87.368"
                     /coverage="87.0"
                     /evalue="5.789999999999997e-54"
     Typing          487..971
                     /name="ColRNAI_rep_cluster_1987"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="90.389"
                     /coverage="93.0"
                     /evalue="3.49e-179"
     Typing          complement(4..218)
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="93.056"
                     /coverage="97.0"
                     /evalue="8.11e-39"
     Typing          complement(2236..3758)
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="99.213"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 ccggcaccac cggcgttcac tttccgggcg atctggttca ggttattgcc catgccggca
       61 agctgacgca gcagcgccgg cgaaatcgag ggaagcctgc cggcgcgtgt cggtttctca
      121 tcaaggcagg tctggcgcat ccacgccgcc agttgttttc cgtcgcaccg ctcaagcaac
      181 cgccgatgtt cgtcttccgt cacccacatc gtgagcatct tgttgcgttt atctgccaga
      241 atcgcctcct gataacgccg tggcggacgg gaaagccttt cccggtcggc gcggggttgg
      301 acaagccgca ggcgcgtcag tggtttttag cgggtttcgg ggcgcagccc tgaaccagtc
      361 acgtagcgct agcggagtgt atactggctt aatatgataa atcgaagtgg taattcggga
      421 aagtgcttca tgtggcaggg gaaaaattca gctgcggggc gtaagtgcaa aatgcaggtg
      481 gtgatgacat gacgcctcct cgctcactcg gtcgctgcgc tcctgccgtg agacggcggc
      541 gggcgttacc tgctcacgaa tgacaagata gagagactgc gctgaaatca ggaagggctg
      601 gagaaaggat gcggcgttgc cgtttttcca taggctccgc ccccctgaca agcatcacaa
      661 aatctgacgc tcaaatcagt ggcggcgaaa cccgacagga ctataaagat cccgggcgtt
      721 tccccctggt agctccctcg tgcgctctcc tgttcctgcc tttcggttta ccggtgtcat
      781 tccgctgtta tggccgcgtt tgtctcattc cacgcctgac actcagttcc gggtaggcag
      841 ttcgctccaa gctggactgt atgcacgaac cccccgttca gtccgaccgc tgcgccttat
      901 ccggtaacta tcatcttgat tccaacccgg acggacacga aaaaacgcca ctggcagcag
      961 ccactggtaa caagggtgta caagatggta tttaaagagg tcttgaagtg gatgcctgac
     1021 tgcggctaca ctgaaagaac agttttggta attgcggtct tgtacaccca gttacctcgg
     1081 ttagagaatc tgccgggatc ctctatccat cgaaaaagcc accggaaggt ggttttttcg
     1141 ttttcagagc aagagattac gcgcagaaaa aaatgatctc aagaagatcc tttcttcgca
     1201 ggatcgatat ccatgggatt tatgatgttc cttgtaatga atccatcact ggaatgcatt
     1261 tatcggcgga agaaatcccc ctgcgttaca aaatgattat gattagcaac tagccgttta
     1321 acacagcatt ctgccacctg atttaacata agatttcttt ttttacattt tatctcccct
     1381 tccgatgcag aagccaaaac aatgcctatt attagtaagt tagatactaa cttcgccagt
     1441 actagggata tgggatatct aaaaaagcat tggtttctct taataacttc agttttaacc
     1501 ttctcagtaa ccggcacctc ctaaaatcag gccattaaaa ctaccgacgg acggactatc
     1561 gtcgcagacg gtaagcctca gattgatagt gacaccgggc tggtttctta caaggatgca
     1621 cagacaggaa aaacagaaca tatcaaccgc gacaaaatta ccaacatgag tgaactagat
     1681 aactgataag gaacgttcta tgacgaaagt aatttattca gcgctagctg cgatcattgc
     1741 actttcagct ctgacaggat gcacaaggac aagctatgca attcatacga atgatggccg
     1801 taccattgtg agcgatggca aacccaaaga atcggatgct gggttgattg gctataccga
     1861 tgctaacggc gtgaagcagc aaattaataa acaggaagtc aaagaagtct cagagattcc
     1921 taactgatca taaaaaaccg cctagtggcg gtttttttta catgctagta accgtccaat
     1981 taaacataac atcccttact cgcaccgcgc cggaggcact cagggcgttt ctgatggctg
     2041 acgggcaaaa ggtggtggca agtacaccga aaaccaccag aaacgcacct gatttatttt
     2101 acgcatatgc atcacttatt cacatcactg catagccggt gatttcggtt aaaaaagact
     2161 ctctgtgtgc tgaaatcgca gaaaatggcc atgatccccg tcacgctcag gccacctgag
     2221 acgggcgttt atcagtctcc atactccctg tcaccatgag ataatgtgcg ttgccgttcc
     2281 ggtaccagat ctgctgtctt ctctggttcc ttttccgttg tttgcccgta tcgctgttgc
     2341 tcaatctcat tcagcctgtc gataaccggc gcagctgctc gctcaaactc tgcacctgcc
     2401 tgctcaagcc cgacacgcgc tcgctcagcg ccgcgttctc ccgttgcata agaccagaca
     2461 tcttccgcca ttcctcgaag gcgctctccc actcgtccag ccttctcgag tagtcctgct
     2521 gtagctgctc taacgcgctc agcaattgtt tttccagttc cgtcattctg ctctactccc
     2581 gtaccagctt caccgcgttc cgcgtcttgt tgtccacctt ccggcccgtt tcggctttca
     2641 tcccctccgg cagcaccaga aaccgtccgt tgcggttttc cagataggtc acgccccacg
     2701 tctgcatctg cagtttcgac agcgtatctc tctgctgcct gatttccgcc aggttcgccg
     2761 ctatccggtt cccctggtac cacagcaccc cgctcaggct ggcgaacagc agccctgaca
     2821 ccatggtgat ggtcagccac gtccgcccga ccattcgcag cacgctcagc cggttcgact
     2881 gcatcgccgc gttcatcccc tgttcgtggg cgctgatggc gtcgttgatt ctcttcgcgc
     2941 ttgcgttcag ttccgatttg acaacgttct cgtgcttgct gaatgcggct ttcagcctct
     3001 cttcggtaag ctgctgctgt gctttcgatt tctcctcgaa gtccctcgag gccgttaaaa
     3061 gactgctcat aaatggctcc cctcagtcgg atatttcgcc ccccgtccgg gtcggcaatg
     3121 ctgatactgt tttttgtggt tctgaccacc tcaaaaccgg ccgctgtgag cgcccctgtg
     3181 acgtcatcac gcgttttcag ctctcctgat gaggctaaca tcagcaaacc ccgtgtaatc
     3241 gtctctgcgg cttcctgctt cgtttctggc agtcctgacg gcgtgaccag cgcccgccgg
     3301 ttctccgggt cgttcggatc atgtagcccc agcctgccgt tgaccactgt ctgccacgca
     3361 tcgatgcgcg gccggtcggc acgatcgtaa tacggctgga ggcgtttccc cgtcagtaat
     3421 tcggtattgg ggatcagaaa attcagctca agacgaccct tgtctgcgtg ttccacccac
     3481 agaatgctgt actgatcttt atcgagtccg ggcatcagaa cccgctcaaa gctggccatc
     3541 agtttttcac gctgacccgg cggcagatcc gcctccgcga atgacagcac cccggaggta
     3601 tattttttca catacggcga cgcatcaatc agctcccgga tttcttccgg cttcccctgc
     3661 aggacgctgg caccttcacg ctgccggtct ttacccagaa gatagtccac cggaccggcg
     3721 cccccgccgc gaccccgtgg atggaattta acaatcatca tccggccctt tttccagtac
     3781 ggcatgccgc aaccgttcca gaccggcatc gatcgccatc agcgctgcca cgatctgcac
     3841 ccggtcatga
//
