LOCUS       NZ_CP083772             5214 bp    DNA     circular CON 18-JUN-2023
DEFINITION  Klebsiella pneumoniae strain KSB1_9E isolate KSB1_9E plasmid
            pKSB1_9E_4, complete sequence.
ACCESSION   NZ_CP083772
VERSION     NZ_CP083772.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMEA3357330
            Assembly: GCF_020149895.1
KEYWORDS    RefSeq.
SOURCE      Klebsiella pneumoniae
  ORGANISM  Klebsiella pneumoniae
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Klebsiella/Raoultella group; Klebsiella.
REFERENCE   1  (bases 1 to 5214)
  AUTHORS   Hawkey,J., Cottingham,H., Tokolyi,A., Wick,R., Judd,L.M.,
            Cerdeira,L., de Oliveira Garcia,D., Wyres,K.L. and Holt,K.E.
  TITLE     Linear plasmids in Klebsiella and other Enterobacteriaceae
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 5214)
  AUTHORS   Hawkey,J., Wyres,K.L., Judd,L.M., Jenney,A. and Holt,K.E.
  TITLE     Direct Submission
  JOURNAL   Submitted (17-SEP-2021) Department of Infectious Diseases, Monash
            University, Level 2, The Burnet Institute, Melbourne, VIC 3004,
            Australia
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: Unicycler v. v4.7
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 135x
            Sequencing Technology :: Illumina; Oxford Nanopore MinION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 06/18/2023 15:43:58
            Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline
            (PGAP)
            Annotation Method :: Best-placed reference protein set; GeneMarkS-2+
            Annotation Software revision      :: 6.5
            Features Annotated                :: Gene; CDS; rRNA; tRNA; ncRNA
            Genes (total)                     :: 5,490
            CDSs (total)                      :: 5,365
            Genes (coding)                    :: 5,219
            CDSs (with protein)               :: 5,219
            Genes (RNA)                       :: 125
            rRNAs                             :: 9, 8, 8 (5S, 16S, 23S)
            complete rRNAs                    :: 9, 8, 8 (5S, 16S, 23S)
            tRNAs                             :: 87
            ncRNAs                            :: 13
            Pseudo Genes (total)              :: 146
            CDSs (without protein)            :: 146
            Pseudo Genes (ambiguous residues) :: 0 of 146
            Pseudo Genes (frameshifted)       :: 55 of 146
            Pseudo Genes (incomplete)         :: 86 of 146
            Pseudo Genes (internal stop)      :: 27 of 146
            Pseudo Genes (multiple problems)  :: 19 of 146
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP083772.1.
            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..5214
                     /organism="Klebsiella pneumoniae"
                     /mol_type="genomic DNA"
                     /strain="KSB1_9E"
                     /isolate="KSB1_9E"
                     /isolation_source="throat swab"
                     /host="Homo sapiens"
                     /db_xref="taxon:573"
                     /plasmid="pKSB1_9E_4"
                     /geo_loc_name="Australia"
                     /collection_date="2013-09"
     gene            join(4718..5214,1..754)
                     /locus_tag="LB480_RS27420"
                     /old_locus_tag="LB480_27420"
     CDS             join(4718..5214,1..754)
                     /locus_tag="LB480_RS27420"
                     /old_locus_tag="LB480_27420"
                     /EC_number="2.1.1.37"
                     /inference="COORDINATES: ab initio prediction:GeneMarkS-2+"
                     /GO_function="GO:0003886 - DNA
                     (cytosine-5-)-methyltransferase activity [Evidence IEA];
                     GO:0008168 - methyltransferase activity [Evidence IEA];
                     GO:1904047 - S-adenosyl-L-methionine binding [Evidence
                     IEA]"
                     /GO_process="GO:0006304 - DNA modification [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GeneMarkS-2+."
                     /codon_start=1
                     /transl_table=11
                     /product="DNA cytosine methyltransferase"
                     /protein_id="WP_138846454.1"
                     /translation="MTRPIAVDLFAGAGGLSLGFEQAGFDIMASVEIDPIHCSAHKYNF
                     PMCKTICRSVVDVTGEYVREVSGIGEKEIDVVIGGAPCQGFSLIGKRALDDDRNKLVYH
                     YVRLVLELKPKYFIFENVKGLTVGKHKQFLVEIMDAFKDGGYDVVSDYKVLNAADYGVP
                     QDRRRLFLMGGRKGIALPSYPEPLSIRTTVGDAIGDIPDAEKYPELWGRDWVYAKFGEQ
                     SLYSSYLHGVRKDPSDFSYPRIFNKDKLTCSLLTDHSDISRGRFVETLPDTVEPISRFK
                     KLSMNGLCNTLRAGTASDRGAFTSPRPIHPIYPRVITVREAARLHSYPDWFRFHVTKWH
                     GFRQVGNSVPPMLARSVGLQIMKVLGVTPKKPTKKIKLGDESLVAISMSDAASMFGVSS
                     NVIAKRIKNSNKEVVCE"
                     /name="DNA cytosine methyltransferase"
     gene            747..1556
                     /locus_tag="LB480_RS27425"
                     /old_locus_tag="LB480_27425"
     CDS             747..1556
                     /locus_tag="LB480_RS27425"
                     /old_locus_tag="LB480_27425"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_010222407.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_044525163.1"
                     /translation="MSKDKKERSKNRYHQLVEKIFFDKYVDGDLEVLFERLEINSAAKD
                     LGIELPSNVGDVIYSIRFRTPMPESILLTQPEGKEWIIELAGRSKYRFRLVTISRILPN
                     PNMVAIKIPDNTPEIITGYSLDDEQALLAKVRYNRLIDIFLGITTYSLQNHLRTTVKGI
                     GQIEIDELYVGIDKYGCHYIIPVQAKGGTDQISMVQTSQDTAWCEQKYPNVRCRAISAQ
                     FVSSDLIALFELKIDEGQVKLIEERHYKLVPAKELDSSDISNYRMSV"
                     /name="hypothetical protein"
     gene            complement(1776..1907)
                     /locus_tag="LB480_RS27430"
                     /old_locus_tag="LB480_27430"
     CDS             complement(1776..1907)
                     /locus_tag="LB480_RS27430"
                     /old_locus_tag="LB480_27430"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_005761324.1"
                     /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_072007956.1"
                     /translation="MHEPPVQSDCCALSGNYRLESNPKRHAKAPLAAATGNRIHGAE"
                     /name="replication initiation protein"
     gene            2528..2869
                     /locus_tag="LB480_RS27435"
                     /old_locus_tag="LB480_27435"
     CDS             2528..2869
                     /locus_tag="LB480_RS27435"
                     /old_locus_tag="LB480_27435"
                     /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="WP_071599364.1"
                     /translation="MADKRNKMLTMWVTEDEHRRLLERCDGKQLAAWMRQTCLDEKPTR
                     AGRLPSISPALLRQLAGMGNNLNQIARKVNAGGAGHDRVQIVAALMAIDAGLERLRHAV
                     LEKGPDDDC"
                     /name="MobC family plasmid mobilization relaxosome protein"
     gene            3078..>3506
                     /locus_tag="LB480_RS27540"
                     /pseudo=""
     CDS             3078..>3506
                     /locus_tag="LB480_RS27540"
                     /inference="COORDINATES: protein motif:HMM:NF015397.2"
                     /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="relaxase/mobilization nuclease domain-containing
                     protein"
                     /name="relaxase/mobilization nuclease domain-containing
                     protein"
     gene            3547..4044
                     /locus_tag="LB480_RS27445"
                     /old_locus_tag="LB480_27445"
     CDS             3547..4044
                     /locus_tag="LB480_RS27445"
                     /old_locus_tag="LB480_27445"
                     /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="MbeB family mobilization protein"
                     /protein_id="WP_015328238.1"
                     /translation="MSSLLTASRDFEEKSKAQQQLTEERLKAAFSKHENVVKSELNASA
                     KRINDAISAHEQGMNAAMQSNRLSVLRMVGRTWLTITMVSGLLFASLSGVLWYQGNRIA
                     ANLAEIRQQRDTLSKLHMQTWGVTYLENRNGRFLVLPEGMKAETGRTVDNKTRNAVKLV
                     RE"
                     /name="MbeB family mobilization protein"
     gene            4051..4266
                     /locus_tag="LB480_RS27450"
                     /old_locus_tag="LB480_27450"
     CDS             4051..4266
                     /locus_tag="LB480_RS27450"
                     /old_locus_tag="LB480_27450"
                     /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="WP_015328239.1"
                     /translation="MTELEKQLLSALEQLQQDYSRRLDEWESAFEEWRKMSGLMQRENA
                     ALSERVSGLSRQVQSLSEQLRRLSTG"
                     /name="MbeD family mobilization/exclusion protein"
     Typing          2270..2443
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="93.785"
                     /coverage="100.0"
                     /evalue="5.6599999999999995e-68"
     Typing          complement(1799..2284)
                     /name="rep_cluster_2335"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="93.238"
                     /coverage="80.0"
                     /evalue="0.0"
     Typing          2860..4382
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 ccgtcgtctt ttcttaatgg ggggaaggaa aggaattgct ctgccatcat accctgagcc
       61 attatccatt agaacaacgg ttggggacgc tattggggat attcctgatg cggaaaaata
      121 tcctgagcta tggggtagag attgggttta tgctaaattt ggtgagcaat cactatactc
      181 atcctatttg catggcgtaa gaaaagatcc tagtgatttt agctacccaa ggatttttaa
      241 taaagacaaa ttaacgtgtt ctttactgac agatcactct gacatttcta gagggcggtt
      301 tgttgaaact ttgcctgaca cggtagaacc aatcagcagg tttaaaaagc tctcgatgaa
      361 tgggctatgt aatactttaa gggcaggaac agcaagtgac agaggtgctt ttacatctcc
      421 tcgtcctata catccgatct atcctagggt catcacggtc agagaggcag caagactgca
      481 ttcatatcct gattggttca gatttcatgt gactaagtgg catggattta gacaggtcgg
      541 taatagtgtt cctcctatgc tagctagaag tgttggcttg cagattatga aggttcttgg
      601 tgttacgcca aaaaaaccaa cgaagaaaat caaactcggt gatgaaagtt tggttgctat
      661 ttctatgtcc gatgctgcat ctatgtttgg tgtgtcatca aatgtaattg ctaagagaat
      721 aaaaaatagt aacaaggagg ttgtttgtga gtaaggataa aaaagaaagg tccaaaaata
      781 gataccatca gttggtagaa aagatatttt tcgataaata tgttgatggt gacttagagg
      841 ttttgtttga aaggttagag ataaacagtg ctgcaaaaga tttaggtata gaactcccat
      901 ctaatgttgg tgatgttata tattcaatca gatttagaac gcctatgcca gaaagtattc
      961 tgttgactca gccagaaggt aaggagtgga ttattgagct ggctggtagg tcaaagtatc
     1021 gatttagatt agtaactatt agtaggattt tgccaaatcc taatatggtg gcaataaaaa
     1081 ttccagacaa taccccggag ataattacag gttattcttt agacgacgag caggcattgc
     1141 tggcgaaggt gagatataac cggctaatag atatatttct aggtataacc acatattctt
     1201 tacagaatca tttaagaact acggtgaagg gaattggtca aatagagatc gatgaacttt
     1261 atgtaggtat agataaatac ggttgccatt atataatacc agttcaagca aaaggtggga
     1321 cagaccaaat atcaatggtg caaacatcgc aagatacagc gtggtgtgaa caaaaatacc
     1381 caaatgttag atgtagagct atttccgctc agtttgtttc gagcgatttg attgcactgt
     1441 ttgagctaaa gatagacgaa ggacaagtga aattgattga ggaaaggcat tacaaactgg
     1501 ttccggcaaa agagttagat agctctgaca tctcaaacta ccgcatgtct gtataatttc
     1561 tgagaggatc ttcttgagat cctttcgttc tagccgtaat ctcctaagcc gtaaacaaaa
     1621 aaaccaccgc taccaacggt ggttcgtttg ccggaattta gagctaccaa ctctttcttc
     1681 cgaaggtaac tggctttcac ggagcgcaga taccaaaact gtcctttcag tgtagccgta
     1741 gtcaggccac cacttcaaga actctgtaga taactctact ccgctccgtg aatccgatta
     1801 ccagtggctg ctgccagtgg cgcttttgca tgtcttttcg ggttggactc aagacgatag
     1861 ttaccggaca aggcgcagca gtcggactga acggggggtt cgtgcataca gtccagcttg
     1921 gagcgaactg cctacccgga actgagtgtc aggcgtggaa tgagacaaac gcggccataa
     1981 cagcggaatg acaccggtaa accgaaaggc aggaacagga gagcgcacga gggagctacc
     2041 agggggaaac ccttgggatc tttatagtcc tgtcgggttt cgccgccact gatttgagcg
     2101 tcagatttcg tgatgcttgt caggggggcg gagcctatgg aaaaacggct tcgccgcagc
     2161 ctcatcgttt ccctgttaag ttccttcctg gcatccacca ggaaatttcc acctcacccg
     2221 taagccggta ccgctcgccg cagccgaacg accgagcgca gcgagtcagt gagcgaggaa
     2281 gcggcacatc tcccgttact acatgttctg ctgacgcgcc ggtgccgcct ttttctcctg
     2341 ctacatgaag cacttccccg aatctccatc tcgccgtaac atactaagcc agtatacact
     2401 ccgctagcgc tacgtgactg gttcagggct gcgccccgaa accccactga cgcgcctgcg
     2461 gcttgtccaa ccccgcgccg accgggaaag gctttcccgt ccgtcacggc gttatcagga
     2521 ggcgattctg gcagataaac gcaacaagat gctcacgatg tgggtgacgg aagacgaaca
     2581 ccggcggttg cttgagcggt gcgacggaaa acaactggcg gcgtggatgc gccagacctg
     2641 ccttgatgag aaaccgacac gcgccggcag gcttccctcg atttcgcccg cgctgctgcg
     2701 tcagcttgcc ggcatgggca ataacctgaa ccagatcgcc cggaaagtga acgccggtgg
     2761 tgccggtcat gaccgggtgc agatcgtggc agcgctgatg gcgatcgatg ccggtctgga
     2821 acggttgcgg catgccgtac tggaaaaagg gccggacgat gattgttaaa ttccatcccc
     2881 ggggtcgcgg cgggggcgcc ggtcctgtgg attatcttct gggtaaagac cggcagcgtg
     2941 aaggtgccag cgtcctgcag gggaagccgg aagaagtccg ggagctgatt gatgcgtcgc
     3001 cgtatgtgaa aaaatatacc tccggggtgc tgtcattcgc ggaggcggac ctgccgccgg
     3061 gtcagcgtga aaaactgatg gccagctttg agcgggttct gatgcccgga ctcgataaag
     3121 accagtacag cattctgtgg gtggaacacg cagacaaggg tcgtcttgag ctgaattttc
     3181 tgatccccaa taccgaatta ctgacgggga aacgcctcca gccgtattac gatcgtgccg
     3241 accggccgcg catcgatgcg tggcagacag tggtcaacgg caggctgggg ctacatgatc
     3301 cgaacgaccc ggagaaccgg cgggcgctgg tcacgccttc aggactgcca gaaacgaagc
     3361 aggaagccgc agagacgatt acacggggtt tgctgatgtt agcctcatca ggagagctga
     3421 aaacgcgtga tgacgtcaca ggggcgctca cagcggccgg ttttgaggtg gtcagaacca
     3481 caaaaaacag tatcagcatt gccgacccgg acggggggcg aaatatccga ctgaggggag
     3541 ccatttatga gcagtctttt aacggcctcg agggacttcg aggagaaatc gaaagcacag
     3601 cagcagctta ccgaagagag gctgaaagcc gcattcagca agcacgagaa cgttgtcaaa
     3661 tcggaactga acgcaagcgc gaagagaatc aacgacgcca tcagcgccca cgaacagggg
     3721 atgaacgcgg cgatgcagtc gaaccggctg agcgtgctgc gaatggtcgg gcggacgtgg
     3781 ctgaccatca ccatggtgtc agggctgctg ttcgccagcc tgagcggggt gctgtggtac
     3841 caggggaacc ggatagcggc gaacctggcg gaaatcaggc agcagagaga tacgctgtcg
     3901 aaactgcaca tgcagacgtg gggcgtgacc tatctggaga accgcaacgg acggtttctg
     3961 gtgctgccgg aggggatgaa agccgaaacg ggccggacgg tggacaacaa gacgcggaac
     4021 gcggtgaagc tggtacggga gtagagcaga atgacggaac tggaaaaaca attgctgagc
     4081 gcgttagagc agctacagca ggactactcg agaaggctgg acgagtggga gagcgccttc
     4141 gaggaatggc ggaagatgtc tggtcttatg caacgggaga acgcggcgct gagcgagcgc
     4201 gtgtcgggct tgagcaggca ggtgcagagt ttgagcgagc agctgcgccg gttatcgaca
     4261 ggctgaatga gattgagcaa cagcgatacg ggcaaacaac ggaaaaggaa ccagagaaga
     4321 cagcagatct ggtaccggaa cggcaacgca cattatctca tggtgacagg gagtatggag
     4381 actgataaac gcccgtctca ggtggcctga gcgtgacggg gatcatggcc attttctgcg
     4441 atttcagcac acagagagtc ttttttaacc gaaatcaccg gctatgcagt gatgtgaata
     4501 agtgatgcat atgcgtaaaa taaatcaggt gcgtttctgg tggttttcgg tgtacttgcc
     4561 accacctttt gcccgtcagc catcagaaac gccctgagtg cctccggcgc ggtgcgggta
     4621 agagatgtta tgttcaatcg aaatcagaaa aacgatcggt aaagcgatcg tttttctgat
     4681 agcatcatgt tgattttata taacgtgggt gtaaagaatg actagaccga ttgctgttga
     4741 tttatttgct ggagcgggtg ggctgagtct cggtttcgag caagctggct ttgatataat
     4801 ggcatcagtt gagatagatc caatacattg ctctgctcac aaatataact ttcctatgtg
     4861 caaaacgata tgtagaagtg ttgttgatgt taccggagaa tacgttaggg aagtttcagg
     4921 tattggtgag aaagagattg atgtagtgat cggaggcgct ccctgccaag gcttttcatt
     4981 aataggaaaa cgcgcgcttg atgatgatag aaacaaactg gtctatcact atgtacggct
     5041 ggttcttgag ctaaagccta aatactttat ttttgaaaat gtaaaagggt tgacggttgg
     5101 taagcataag cagtttttag tagagataat ggatgcattt aaagatggtg ggtacgacgt
     5161 tgtaagcgat tataaagtgc taaacgcagc tgattatgga gttcctcaag atcg
//
