LOCUS       NZ_AP023458             3991 bp    DNA     circular CON 28-NOV-2023
DEFINITION  Klebsiella pneumoniae strain M941 plasmid pM941-d, complete
            sequence.
ACCESSION   NZ_AP023458
VERSION     NZ_AP023458.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMD00237915
            Sequence Read Archive: DRR238844, DRR238850
            Assembly: GCF_014905815.1
KEYWORDS    RefSeq.
SOURCE      Klebsiella pneumoniae
  ORGANISM  Klebsiella pneumoniae
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Klebsiella/Raoultella group; Klebsiella.
REFERENCE   1
  AUTHORS   Sugawara,Y., Akeda,Y., Hagiya,H., Zin,K.N., Aye,M.M., Takeuchi,D.,
            Matsumoto,Y., Motooka,D., Nishi,I., Tomono,K. and Hamada,S.
  TITLE     Occurrence and characterisation of Klebsiella pneumoniae sequence
            type 11 international high-risk clone harbouring blaNDM-5 in a
            clinical setting in Myanmar
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 3991)
  AUTHORS   Sugawara,Y., Akeda,Y. and Hamada,S.
  TITLE     Direct Submission
  JOURNAL   Submitted (23-SEP-2020) Contact:Yo Sugawara Osaka University,
            Research Institute for Microbial Diseases; 3-1 Yamadaoka, Suita,
            Osaka 565-0871, Japan
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: Flye v. 2.5
            Genome Coverage                   :: 327x
            Sequencing Technology             :: GridION; Illumina MiSeq
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 11/28/2023 10:03:21
            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)                     :: 5,693
            CDSs (total)                      :: 5,569
            Genes (coding)                    :: 5,362
            CDSs (with protein)               :: 5,362
            Genes (RNA)                       :: 124
            rRNAs                             :: 9, 8, 8 (5S, 16S, 23S)
            complete rRNAs                    :: 9, 8, 8 (5S, 16S, 23S)
            tRNAs                             :: 87
            ncRNAs                            :: 12
            Pseudo Genes (total)              :: 207
            CDSs (without protein)            :: 207
            Pseudo Genes (ambiguous residues) :: 0 of 207
            Pseudo Genes (frameshifted)       :: 125 of 207
            Pseudo Genes (incomplete)         :: 82 of 207
            Pseudo Genes (internal stop)      :: 15 of 207
            Pseudo Genes (multiple problems)  :: 15 of 207
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            AP023458.1.
            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..3991
                     /organism="Klebsiella pneumoniae"
                     /mol_type="genomic DNA"
                     /strain="M941"
                     /isolation_source="human sputum"
                     /host="Homo sapiens"
                     /db_xref="taxon:573"
                     /plasmid="pM941-d"
                     /geo_loc_name="Myanmar:Yangon"
                     /lat_lon="16.7788 N 96.1490 E"
                     /collection_date="2018-12"
     gene            complement(join(3570..3991,1))
                     /locus_tag="JLF44_RS28300"
     CDS             complement(join(3570..3991,1))
                     /locus_tag="JLF44_RS28300"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:YP_005229777.1"
                     /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="WP_040214596.1"
                     /translation="MAIVSISEAARLVKVSRPTIYKMINSGKLSYTSVVKHGKAIKVID
                     TSELIRVFGSLDGVIDTVKYDVKSDAESTGINSVGLHDLQHRIALLEAENDGLKGAVKA
                     RDEHIDSLRQAMQLLEHKHEPSSPPHSPWWKFWKKS"
                     /name="helix-turn-helix domain-containing protein"
     gene            complement(1..192)
                     /locus_tag="JLF44_RS28305"
     CDS             complement(1..192)
                     /locus_tag="JLF44_RS28305"
                     /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_040198051.1"
                     /translation="MTKQQKTALNMAKFIQNQSLLLLDKLNELDLDVEADLCEKLHDDA
                     EHLFRTLSSRLDELQDGN"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            600..712
                     /locus_tag="JLF44_RS28625"
                     /pseudo=""
     CDS             600..712
                     /locus_tag="JLF44_RS28625"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_005761324.1"
                     /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            complement(939..1979)
                     /locus_tag="JLF44_RS28310"
     CDS             complement(939..1979)
                     /locus_tag="JLF44_RS28310"
                     /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_040198047.1"
                     /translation="MIELILTYLNKVLLFALRKDSLMAFFNLLFVASLICFGGVMGSYS
                     RGCRDSQNKFSKDKDENNKRASVYRFGIASAFICVPFISSFLHVDYSSIIFPVADGGGT
                     KFIEQILLLISVSGISAYLGYALLDGLANKVLKEQVDGIDKKQQDLEAEQDEFKDELDR
                     SKELIEQLEMDKKTTKFELGYFKAISAVDKAESMMSIPDEALSVKKKLTEALDAVTESL
                     SLVKREDVAKDDYDKLLVLKAYILKRLDRIDDALSITDELLMSNEDNPILIYNKACYQY
                     ILRRCQADNSDIKDMIRRALTIKVTDPEFIRRQEKIRTKVIGNKDNDLEGLFTDAELEE
                     LKVAIK"
                     /name="hypothetical protein"
     gene            complement(2494..2766)
                     /locus_tag="JLF44_RS28315"
     CDS             complement(2494..2766)
                     /locus_tag="JLF44_RS28315"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_004897311.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_019405140.1"
                     /translation="MATDAQVKEINALIKKYPDSCSICHEVYDEDDVTYTVFGYDRKGK
                     IQVTTGCCAGMLTEPVLLGVCGCFDPEERDEIMQNHPMAKQFFTE"
                     /name="hypothetical protein"
     Typing          241..712
                     /name="ColRNAI_rep_cluster_1987"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="86.777"
                     /coverage="92.0"
                     /evalue="7.8799999999999974e-146"
ORIGIN
        1 tcagttacca tcctgtaatt catccagtct cgaggacagt gtacggaaaa gatgctccgc
       61 atcatcatgg agtttctcac aaaggtcggc ctcgacatcg agatcaagct cgttaagctt
      121 atccagcagg agcagagact gattctggat gaatttagcc atgttcagcg ctgttttctg
      181 ttgttttgtc ataagaagcc tcagagcgtc agtgctcaat gtcaaactag tctcttttcc
      241 gcttcctcgc tcactcagtc gctacgctcc agccgttcgg ctgcggcgag cggcaggagc
      301 gtgtacataa aaacgtaggc aaccaagata tgaggcagaa aagcaaaggc cgccgaacgg
      361 ctgtttttcc ataggctccg cccccctgac aagcatcgcg gaaacggacg ctcaaatcag
      421 tggtggcgaa acccgacagg acttaaagat accaggcgtt tccccctggt ggctccctcg
      481 tgcgctctcc tgttcctgcc tttcggttta ccggtgtcat tccgctgtta tggccgcgtt
      541 ttctcattcc atgcctgata ctcggctccg ggaaggcagt tcgctccaag ctggactgta
      601 tgcacgaacc ccccgttcag tccgactgct gcgcccgttc cagtaactat ctcttgagtc
      661 caacccggaa agacacgact tatcgccatt ggcagcagcc actggtaatt gatttagagg
      721 agttagtctt gaagttatgc gccagttaag gctaaactaa acgaactgtt ttggtgactg
      781 cgctcctcta agccagttac ctcggttcag aaacttgccg gttactgaac cttcgaaaaa
      841 ccaccttgcc gggtggtttt ttcgtttgag gggtagagta cgctgcacct caaaggatcg
      901 tcaaggatct ttttggaatt catagagcta gccactgcct atttgatagc cacctttaat
      961 tcctccagct cagcgtcagt aaacaaccct tcaagatcat tatctttatt tcctatgacc
     1021 ttggttctta ttttttcttg cctgcgaatg aattcaggat ctgtaacttt aatagtcaga
     1081 gccctgcgaa tcatatcctt aatatcggag ttatcagctt ggcaacgacg caaaatatat
     1141 tgatagcaag ccttattgta aataagtata gggttatcct cattactcat aagtaactca
     1201 tccgtaattg acagagcatc atcaatacga tcaagtcttt tcaaaatata agctttaagc
     1261 actaagagct tgtcgtagtc atccttagct acatcctctc ttttaacaag agacaatgat
     1321 tccgttacag catctaatgc ctcagttagt tttttcttaa cagaaagagc ctcatccgga
     1381 atggacatca ttgattctgc tttatccaca gctgaaatgg ctttaaagta tcctagctcg
     1441 aattttgttg ttttcttatc catttcaagc tgttctatca gctccttgct cctatcaagc
     1501 tcatctttaa actcatcttg ttcagcctcc aaatcttgtt gctttttatc tataccgtct
     1561 acttgctctt ttaatacttt gttggcaaga ccatccagta atgcgtaccc aagatacgca
     1621 gagatccccg aaacagaaat aagaagcaat atttgttcta tgaacttagt tccaccacca
     1681 tcagccacag gaaatattat acttgagtaa tcaacatgaa gaaatgatga tatgaaagga
     1741 acacaaataa atgcggatgc tataccaaat ctataaacac tagctctttt attattctca
     1801 tccttatctt ttgaaaattt attttgggag tctcggcaac ctctggaata gctccccata
     1861 acaccaccaa aacaaattag agatgcaaca aacaataggt taaaaaaagc catgagagaa
     1921 tccttgcgca aagcaaacaa taaaactttg ttcaggtaag ttaagataag ctcaatcata
     1981 tactaaccaa taacaaaaaa ggcagccttg gctgcctttt tctgctgact tgacacttac
     2041 aagtctggac gctcatcgtg aagtttgatt tttttcatag agcacctctc attaattgtt
     2101 cctttgcaag cccatgcttg cttagcgctg aatatagggc ataaacccag cactcacaac
     2161 aacaaaaatg cttaaaatga taaaatcaac ccatgtattg acattgggtg aaaaaaaaag
     2221 tataatgcac tggtagccaa aggggcgggg cttcgcttat tcctaaggaa taagcgaagc
     2281 cccgcccctt tggctaccat aattaaatga ttgaatttaa aggatttttt tacaataaca
     2341 tccttcctct caatagtcat ataaacatgc cccatgtatt cgtcattctg gatttttcaa
     2401 aagaatgaat gcgtgcattt accataacgc ctcatttcac gcagatatga aaaagcccgc
     2461 acaaggcggg cttcagactc aacagatacg gaatcactct gtgaaaaact gctttgccat
     2521 ggggtgattc tgcatgatct cgtcacgttc ttccgggtca aagcacccac agacacccag
     2581 cagaaccggc tctgtcagca ttccggcaca gcatcccgtg gtgacctgta ttttaccttt
     2641 ccggtcatac ccaaaaacgg tgtaggtcac atcatcctca tcatagactt catgacagat
     2701 ggagcatgag tccgggtatt ttttgatgag tgcattaatt tcttttacct gagcgtcagt
     2761 agccaaaaca tctccctgag tcactgatta tcacaatccg ctgactctaa cacagactca
     2821 ggcatccgcc gttgatttac cataacgtcc cattacacgc accgctaaaa cggcctcaga
     2881 acgattctgg ggcgtaaccc attaaatcct acgtcttacc ccctgaaaac gcctcaaaat
     2941 cgctccaggg cgttttacgg gcatgaatcg ttatgcactt gactgactgt ctggggattt
     3001 cagcctgaat tcaggccagg caactcaaaa cccgcaccaa accagactga aaacggtgaa
     3061 cgggtgcgca atttattgcg tggccgtgaa gcgttgccgg cgcagccgga aaaccggttt
     3121 tcagcacgtt caggaatcgg gtttgtcgag accagcaatc acattatggc aagtcgccgg
     3181 acgactcacc acacgattca ccggcgattc gactcgtgac ttgactctag agtcgccatg
     3241 gtcaaaaagc caccaacccg gcaagtcgac tctagagtca agtcatcata acgtactgat
     3301 tatatggcgt gattcacata tgaatcgtgg gcaagtcatc ggcgattcgc catagagtcg
     3361 tccacgactc ggattcacct tacaaaaaat aaaattgcgt aatttaaaat agataactga
     3421 ttgaaaataa aggtctatct gcaaaatttt aattttgcgt agtgtgtggg tatttttagt
     3481 ggtgaggagc gttcagggat ctgacgattt ttgggaaggt tcaggaactc cccggaatgg
     3541 ccggagagca aaatggaagc atggcgggat caggattttt tccagaattt ccaccacggg
     3601 gaatggggtg gtgaagaagg ttcgtgcttg tgctccagaa gctgcatagc ctgacgaagg
     3661 gaatcaatat gctcatctcg agccttaaca gcccctttaa gaccatcgtt ttcagcttca
     3721 agtaaagcga ttctatgttg taaatcatgt aaaccaacgc tgttaatacc tgtagattct
     3781 gcgtcacttt ttacatcata ttttacagta tcgattacac catcaagaga accaaacact
     3841 ctaattagct ctgaagtatc aataacttta atagctttcc cgtgctttac cacagaggtg
     3901 taacttaact tcccactgtt aatcatcttg taaattgtgg ggcgactaac cttaacaagc
     3961 cgtgccgctt cactaataga cactatggcc a
//
