LOCUS       NZ_CP040837             6135 bp    DNA     circular CON 10-JAN-2024
DEFINITION  Klebsiella pneumoniae strain SH12 plasmid pSH12_4, complete
            sequence.
ACCESSION   NZ_CP040837
VERSION     NZ_CP040837.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN11963759
            Assembly: GCF_019444635.1
KEYWORDS    RefSeq.
SOURCE      Klebsiella pneumoniae
  ORGANISM  Klebsiella pneumoniae
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Klebsiella/Raoultella group; Klebsiella.
REFERENCE   1  (bases 1 to 6135)
  AUTHORS   Yang,X.
  TITLE     complete sequence of Klebsiella pneumoniae strain SH12
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 6135)
  AUTHORS   Yang,X.
  TITLE     Direct Submission
  JOURNAL   Submitted (05-JUN-2019) The Department of Applied Biology and
            Chemical Technology, The Hong Kong Polytechnic University, Hung Hom,
            Kowloon, Hong Kong 999999, Hong Kong
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: SPAdes v. 3.13.0
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 100.0x
            Sequencing Technology :: Illumina NextSeq; Oxford Nanopore MiniION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 01/10/2024 03:49:39
            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)                     :: 5,944
            CDSs (total)                      :: 5,823
            Genes (coding)                    :: 5,667
            CDSs (with protein)               :: 5,667
            Genes (RNA)                       :: 121
            rRNAs                             :: 9, 8, 8 (5S, 16S, 23S)
            complete rRNAs                    :: 9, 8, 8 (5S, 16S, 23S)
            tRNAs                             :: 86
            ncRNAs                            :: 10
            Pseudo Genes (total)              :: 156
            CDSs (without protein)            :: 156
            Pseudo Genes (ambiguous residues) :: 0 of 156
            Pseudo Genes (frameshifted)       :: 67 of 156
            Pseudo Genes (incomplete)         :: 96 of 156
            Pseudo Genes (internal stop)      :: 20 of 156
            Pseudo Genes (multiple problems)  :: 26 of 156
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP040837.1.
            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..6135
                     /organism="Klebsiella pneumoniae"
                     /mol_type="genomic DNA"
                     /strain="SH12"
                     /isolation_source="sputum"
                     /db_xref="taxon:573"
                     /plasmid="pSH12_4"
                     /geo_loc_name="China"
                     /collection_date="2016"
     gene            join(6091..6135,1..243)
                     /locus_tag="FHY43_RS29420"
                     /old_locus_tag="FHY43_30020"
     CDS             join(6091..6135,1..243)
                     /locus_tag="FHY43_RS29420"
                     /old_locus_tag="FHY43_30020"
                     /function="putative role in conjugative DNA replication"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001517562.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_010895875.1"
                     /translation="MSKAAERLAKLEEQRARINAEIQRVRAREQQQKRKEDTRRKVLVG
                     AWILGKVESGEWPEQRLLDGLDSYLERDHDRALFGLPPKGSFAGEGEILR"
                     /name="hypothetical protein"
     gene            complement(433..1167)
                     /gene="erm"
                     /locus_tag="FHY43_RS29425"
                     /old_locus_tag="FHY43_30025"
     CDS             complement(433..1167)
                     /gene="erm"
                     /locus_tag="FHY43_RS29425"
                     /old_locus_tag="FHY43_30025"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_011282421.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="23S ribosomal RNA methyltransferase Erm"
                     /protein_id="WP_072650419.1"
                     /translation="MNKKNIKDSQNFITSKHHINEILRNVHLNTNDNIIEIGSGKGHFT
                     FELAKRCNYVTAIEIDPKLCRITKNKLIEYENFQVINKDILQFKFPKNKSYKIFGNIPY
                     NISTDIIRKIVFESTATESYLIVEYGFAKRLLNTNRSLALFLMTEVDISILSKIPREYF
                     HPKPRVNSSLIVLKRHPSKISLKDRKQYENFVMKWVNKEYIKLFSKNQFYQALKYARID
                     DLNNISFEQFLSLFNSYKLFNR"
                     /name="erm"
     gene            complement(1858..2700)
                     /gene="repC"
                     /locus_tag="FHY43_RS29430"
                     /old_locus_tag="FHY43_30035"
                     /pseudo=""
     CDS             complement(1858..2700)
                     /gene="repC"
                     /locus_tag="FHY43_RS29430"
                     /old_locus_tag="FHY43_30035"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000240539.1"
                     /note="frameshifted; Derived by automated computational
                     analysis using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="replication protein C, IncQ-type"
                     /name="repC"
     gene            complement(<3034..3390)
                     /locus_tag="FHY43_RS29900"
                     /pseudo=""
     CDS             complement(<3034..3390)
                     /locus_tag="FHY43_RS29900"
                     /inference="COORDINATES: protein motif:HMM:NF024872.4"
                     /note="internal stop; incomplete; partial in the middle of
                     a contig; missing C-terminus; Derived by automated
                     computational analysis using gene prediction method:
                     Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="AAA family ATPase"
                     /name="AAA family ATPase"
     gene            complement(3812..3955)
                     /locus_tag="FHY43_RS29790"
     CDS             complement(3812..3955)
                     /locus_tag="FHY43_RS29790"
                     /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_228750711.1"
                     /translation="MERKTGHEADYIKRTVQKVMELPQVQEARAELAKQAEKQQYRGPT
                     LG"
                     /name="hypothetical protein"
     gene            complement(4023..4649)
                     /locus_tag="FHY43_RS29795"
     CDS             complement(4023..4649)
                     /locus_tag="FHY43_RS29795"
                     /inference="COORDINATES: protein motif:HMM:NF028103.4"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="DNA-primase RepB domain-containing protein"
                     /protein_id="WP_228750712.1"
                     /translation="MVSRRSAPEHAMAQADECRGNDVYIRPAEQERHGLVLVDDLSEFD
                     LDDMKAEGREPALIVETSPKNYQAWVKVAQDAPAGHRGVIARKLAREYDADPASADSRH
                     YGRLAGFTNRKDKHTTRTGYQPWVLLRESKGKTATAGPELMQQAGQVLDSIKRQQERTA
                     RLAEITARGVCAGIAAAPWTTTAAKWPGWSNASVTTSASATSLRP"
                     /name="DNA-primase RepB domain-containing protein"
     gene            complement(4867..4977)
                     /locus_tag="FHY43_RS29910"
     CDS             complement(4867..4977)
                     /locus_tag="FHY43_RS29910"
                     /inference="COORDINATES: protein motif:HMM:NF036929.4"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_267461067.1"
                     /translation="MELAKELREVAAEVSSAAQSAGAPPVAGHGSCGPGS"
                     /name="hypothetical protein"
     gene            complement(5007..5147)
                     /locus_tag="FHY43_RS29915"
     CDS             complement(5007..5147)
                     /locus_tag="FHY43_RS29915"
                     /inference="COORDINATES: protein motif:HMM:NF036929.4"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="IncQ-type mobilization protein MobB"
                     /protein_id="WP_267461065.1"
                     /translation="MKKSRGINELAEQIEPLAQSMATLADEARQVMSQTQQASEAQAAG
                     G"
                     /name="IncQ-type mobilization protein MobB"
     gene            complement(<5320..5544)
                     /locus_tag="FHY43_RS29920"
                     /pseudo=""
     CDS             complement(<5320..5544)
                     /locus_tag="FHY43_RS29920"
                     /inference="COORDINATES: protein motif:HMM:NF015354.4"
                     /note="incomplete; partial in the middle of a contig;
                     missing C-terminus; Derived by automated computational
                     analysis using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="MobA/MobL family protein"
                     /name="MobA/MobL family protein"
     gene            complement(5544..5798)
                     /locus_tag="FHY43_RS29925"
     CDS             complement(5544..5798)
                     /locus_tag="FHY43_RS29925"
                     /inference="COORDINATES: protein motif:HMM:NF015354.4"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MobA/MobL family protein"
                     /protein_id="WP_267461066.1"
                     /translation="MLHTQSGHLPEWAERPADYWDAADLYERANGRLFKEVEFALPVEL
                     TLDQQRELVDEFARHLTEGERLPYTLAIHAGKGENPIAT"
                     /name="MobA/MobL family protein"
     ARG             complement(437..1167)
                     /name="erm(T)"
                     /gene="erm(T)"
                     /gene_name="23S rRNA (adenine(2058)-N(6))-methyltransferase
                     Erm(T)"
                     /tool="amrfinderplus"
                     /drug_class="LINCOSAMIDE/MACROLIDE/STREPTOGRAMIN"
                     /identity="99.59"
                     /coverage="100.0"
     ARG             complement(434..1167)
                     /name="ErmT"
                     /gene="ErmT"
                     /gene_name="Erm 23S ribosomal RNA methyltransferase"
                     /tool="rgi"
                     /drug_class="macrolide antibiotic; lincosamide antibiotic;
                     streptogramin antibiotic; streptogramin A antibiotic;
                     streptogramin B antibiotic"
                     /identity="99.59"
                     /coverage="100.0"
     Typing          complement(5972..6059)
                     /name="MOBQ"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="98.889"
                     /coverage="100.0"
                     /evalue="3.2400000000000003e-37"
     Typing          complement(2688..3521)
                     /name="IncQ1"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="99.286"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          complement(5015..5607)
                     /name="MOBQ"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="93.434"
                     /coverage="93.0"
                     /evalue="0.0"
ORIGIN
        1 gcacgaatca acgccgagat acagcgagtc agggcacggg agcagcagca aaagcgcaag
       61 gaggacaccc ggcgcaaggt gctggtaggc gcgtggatac tcggcaaggt tgaaagcggc
      121 gagtggccag aacagcgcct gctcgatggg ttggatagct acctagagcg cgaccatgat
      181 cgggcgctgt tcggactgcc acccaagggg tcgtttgcgg gagagggcga aatcctacgc
      241 taaggctttg gccaacgata ttctccggta agattgatgt gttcccaggg gataggagaa
      301 gtctagtgaa aatgcctcac atttgtgcca cctaaaaagg agcgatttac atatgagtta
      361 tgcagtttac gggccaagat tgtttaagca aaataagata agttaaggga tgcagtttat
      421 gcacccctta acttatctat taaataattt atagctattg aaaagagaca agaattgttc
      481 aaagctaata ttgtttaaat cgtcaattct tgcatatttt aaggcttgat aaaattggtt
      541 tttggaaaat agttttatgt attctttgtt aacccatttc ataacaaaat tttcatattg
      601 ttttctatct ttgagtgata tttttgaagg gtgtcttttt aatacaatta acgagctatt
      661 aactctaggt tttggatgaa agtattctct agggatttta cttaatatgg atatatcaac
      721 ttctgtcatt aaaaatagtg ctagtgaacg atttgtattt agcaaccttt tagcaaatcc
      781 atattccact attaaataac tttctgtagc tgtgctttca aaaacaattt ttcgaattat
      841 atctgtactt atattgtagg gtatatttcc aaatatctta tatgacttat ttttaggaaa
      901 cttaaattgt aaaatatctt tattgataac ctggaagttc tcatattcaa taagtttgtt
      961 tttagttatc ctacataatt taggatctat ttcaatggcg gttacataat tacacctttt
     1021 agctaattca aacgtgaaat gacctttccc tgaaccaatc tcaataatat tatcatttgt
     1081 atttaaatgt acatttctca aaatttcatt tatatgatgc tttgaagtaa taaagttttg
     1141 actatctttt atattttttt tgttcattat aacccactcc tatggtaatc cccccatttt
     1201 taggacacat ctaaagtaga ggaatttaaa accgttttgt aacaaggtgg cagaccacca
     1261 tttgccatgt ttggcctttc atgattatac agccaaaacc actttgtggc atgatcttgg
     1321 acctcttcaa ttcaaagccc ttttcggcaa gcctgattac tcccatatcg taagggacac
     1381 cacggccact atcagcatca cagccgctga aatggccgct aaatggcccc ttcggggctg
     1441 cacaccgccc ccacccttcg ggtagggaaa aggccgctaa agcggctaaa atcgctccag
     1501 cggattactg cgggtttggt gtggggttta gcgggctttg cccgcctttc cccctgccgc
     1561 gcagcggtgg gggcgggcgt gtagcctagc gcagcggata gatcagttat ccggcctctg
     1621 gccgggcatt ttgggcaagg gcaaacagcg ccccactagg gcgctgttaa ccgcgcctag
     1681 tggattattc ttagataatc atggatggat tttttcagca ctcgccagcc ccgcccctgc
     1741 tgggtttgca ggtttggggc gtgacagtta acgggggttc gtgacagtta acgggggggc
     1801 gtgacagtta acggggggcg tgacagttaa cggggggcgt gacagttatt gcaggggtca
     1861 gcctgccgcc ttgggccgtg cgatgtcgta cttacccgcc gcatactcgt tcaccgtcca
     1921 gcccagcgcg atcagctccg gcagcgcctc gcgcacccgc tggcgtctct tgcgcatggc
     1981 ggccccactg gcctctgacg gccagacgta gccgcacagg gtatctatgg ccgccttgcc
     2041 ggtcttgccg gggtcgatcc agccacacag ccgctggtgc agcaggcggg cggtttcgct
     2101 gtccagcgcc cgcacctcgt ccatgctgat gcgcacatgc tggccgccac ccatgacggc
     2161 ctgcgcgatc aagggttcag ggccacatac aggcgcccgt ctgcctcgtc gctggcgtac
     2221 tcggcaagca gccggaagcc ctgccgcttg cggccattct gggcgatgat ggacaccttc
     2281 caaagccgtt caatgcagtc cctgatgggc tttgagtcct cgatattggc atagcctatt
     2341 tcacgagcca gcgcccgata gctacccttg accaccatgg cgtcagcggt aacggcttcc
     2401 catttgggtt ccgtgaacag ccggagctgc tgcccgccgg ggtctccggt tctggctcta
     2461 gcaccagacc actaggcccg gccatggcca ccagcccctg caggatgcgc aaatcatcag
     2521 cgcccagcgg ctccgggccg ctgaactcga tccgcttgcc gtcgccgtag tcatacgtca
     2581 cgtccagctt gccgcgcttg cgctcgcccc gcttgagggc acggaacagg ccggggccag
     2641 acagtgcgcc gggtcgtgcc ggacgtggct gaggctgtgt ttgttcttag gctttgccac
     2701 gaggcacccc ttgctcttgt gctgcttttc cagcacggcg ggcttgagta ccccgccgtc
     2761 atgccgcctg aaccagcggt ctttgaacgg tgccccatag ttggccttgc tgactccaaa
     2821 gcggacgaaa tagggccgct gcgtgtcgtc tacgccccat tcctcggcct caccggtggt
     2881 catgccggac aggtacgatt gccagcggat gttatccacc agcacggacg atccccggct
     2941 ggcctgctgc tggtcgcctg cgcccatcat ggccgcgccc ttgctggcat ggtgcaggaa
     3001 cacgatagag cacccggtat cggcggcgat ggcctccatg cggccaatca cttgcgccat
     3061 ggggccgctg gcgttctctt cctcgatgtg gaaccggcgc aaggtatcca gcaccatcaa
     3121 gcggcgtccc tcagcggctc gcttgaggcc gtcgaaccac ccggggccat gatgttgggt
     3181 aggctgccga tcagcggtgg attagcagac cgtcagccac ggcttgccgt tgctcgtcgg
     3241 tcaggtgttc cccaatgcgt gcaggcggtg atgtatggcg gtgggcgggt cttcggcggg
     3301 caggtagatc accgggccgg tgcgcaactc gcccacgtcc agcaggtcgg ggccgcctgc
     3361 gatctgtgcg gccagttgca gggccagcat ggacttgccg gccccaccgg ggacaccagc
     3421 gcccccacgg tgccggccac catgttgggc agtacgtagt caatcggtgg cggtagctct
     3481 gtgaagctcg ccagaatgtc gataggctta tgggtagcca ttgatttgcc tcctgtgtag
     3541 gcggttggtg gttaggcgct ggcggggtca ctaccccgcc ctgcgccgcc ctgagttctt
     3601 ccagatacag ccgcagcgcc tcggcctctg cgtctgtggc ccatatcttc cgggccttgc
     3661 ggcccatggc tcgctgctgc tcggcaaagc gggcctgtcg tatagcgttg gggtggccag
     3721 caggttgccg gtacgcttgt cgtgttggtc tttcatattt ctccgcatta gagctaacac
     3781 cataacaggc attagctcta atgcaagtgt tttatcctaa tgtcggccct cggtactgct
     3841 gtttctcggc ctgcttcgcc agctcggcgc gggcctcctg cacctgcggc agctccatca
     3901 ccttctgcac cgtacgcttg atgtaatcgg cctcatggcc cgtcttgcgc tccatgatgg
     3961 cgggctggcc tcggccatgg ccttgccgat ctcgtccggc tcccggccct tgctggccag
     4021 cttcatggcc gcaatgaagt cgcacttgct gaggtcgtca ccgaagcgtt tgaccaaccc
     4081 ggccatttcg ctgcggtagt cgtccacggc gctgcggcga taccggcgca cactccgcgg
     4141 gcggtgatct cggccagtcg tgccgtccgt tcctgttggc gcttaatgct gtccagcacc
     4201 tgcccggcct gctgcatcag ctccggccct gcggtggcgg tcttgccctt tgattcacgc
     4261 agcagcaccc acggctgata accggtgcgg gtggtgtgct tgtccttgcg gttggtgaag
     4321 cccgccaagc gaccatagtg gcggctgtcg gcgctggccg ggtcggcgtc gtactcgcgg
     4381 gccagcttcc gggcgattac gcccctgtga cctgctgggg cgtcctgagc cacttttacc
     4441 catgcctgat agttcttggg gctggtctcc acgatcagcg ccggctcccg gccctcggct
     4501 ttcatgtcat ccaagtcgaa ctcactgaga tcgtccacca gcaccaaacc atgccgctcc
     4561 tgctcggcgg gcctgatata cacgtcattg ccccggcatt catccgcttg agccatggcg
     4621 tgttctggag cacttcggcg gctgaccatt cccggttcat catcttgccg ctggcggcat
     4681 cccgtatgcc ggtgtcgtac cggtcgcagc ccatggcctt gagctgccgg gcgatggctt
     4741 gcgcggtgcg gtcacccttt acttgagctt gaaaccagcc atataccccc tgttgttcga
     4801 tgatttgcgg ctccagccaa agccatgatg cgatcagcag cgccagaata ggcgtcacgg
     4861 aagcgatcaa gaccccggcc cacaacttcc atgtccagcc acgggcggcg ctccggcgct
     4921 ctgcgcggcg ctgctcacct cggcggctac ctcccgcaac tccttggcca gctccaccca
     4981 tgccgcccct gtctggcgtt gggctttcag ccacccgctg cctgcgcctc gctggcctgc
     5041 tgagtctggc tcatgacctg ccgggcctcg tcggccagtg tcgccatgct ctgggccagc
     5101 ggttcgatct gctccgctaa ctcgttgatg cctctggact tcttcactct gtctatcgcg
     5161 ctcatgctcg ataacctccc ggtattcttg taagtcgatg atctggccgt tggccgtgtc
     5221 gatggctagg gcggtgtcgg cccgctcggt gtggatgccc cggccctcca tctccaccac
     5281 gttggggcca agatggatgc ccggcaggcg ctcgatgccc tgcgcctcaa gtgttctatg
     5341 gtcaatgcgg gcgtcgtgac cagcccgctc taatgcccgg ttggcatggt cggcccatgc
     5401 ctcgcgggtc tgctcaagcc atcccttggg cttcaggctc tcggacttct gcgccccgcc
     5461 ccgctctggc tgtttggcgt tgtaccgctt gaaccactgg tcagccgggc gctcgatacc
     5521 gtcgttcttc cgctcagaga tcatcaagtg gcaatggggt tctcaccttt accggcatga
     5581 atggccagcg tatacggcag gcgctcgccc tcggtcagat gccgggcgaa ttcgtccacc
     5641 agctcccgct gctgatctag ggtcagttcg accggcaggg caaactcaac ctctttgaac
     5701 agccgcccat tggcgcgttc atacaggtcg gcagcatccc agtagtcggc ggggcgctcg
     5761 gcccactcgg gcaggtggcc ggactgagtg tgcagcactc gtcacggtcg cgggagtaac
     5821 ggccctcccg ctggatgtaa tcggctttcg cctttgccga ctggccgccg ttccggctgc
     5881 cggtcttggc cgtaaggtga tagatggcca tagggtttag ctccatgcaa tggtcctcgg
     5941 agagcgcaca gccccaaagg gtgcctgcag ggcagtttct cgaagagaaa ccggaagtgc
     6001 gccctcccgt cagaatgacg gtcggggttt gcggcgtatg tgctccgatg atagcataat
     6061 ggcaagcaca taaccaagag gattgtcaac atgtcaaaag cagcggaacg actcgcaaag
     6121 ctagaagagc aacgg
//
