LOCUS       NZ_CP118938             4642 bp    DNA     circular CON 03-MAY-2024
DEFINITION  Klebsiella pneumoniae subsp. pneumoniae strain RX.G5M15 plasmid
            pRX.G5M15_2, complete sequence.
ACCESSION   NZ_CP118938
VERSION     NZ_CP118938.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN33453558
            Assembly: GCF_029025805.1
KEYWORDS    RefSeq.
SOURCE      Klebsiella pneumoniae subsp. pneumoniae
  ORGANISM  Klebsiella pneumoniae subsp. pneumoniae
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Klebsiella/Raoultella group; Klebsiella.
REFERENCE   1  (bases 1 to 4642)
  AUTHORS   Xu,D.Y., Leung,K.M., Lai,G.K.K. and Griffin,S.D.J.
  TITLE     Complete genome sequence of Klebsiella pneumoniae subsp. pneumoniae
            strain RX.G5M15, a facultative methylotroph isolated from Hong Kong
            soil
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 4642)
  AUTHORS   Xu,D.Y., Leung,K.M., Lai,G.K.K. and Griffin,S.D.J.
  TITLE     Direct Submission
  JOURNAL   Submitted (27-FEB-2023) Shuyuan Molecular Biology Laboratory, The
            Independent Schools Foundation Academy, 1 Kong Sin Wan Road,
            Pokfulam, Hong Kong HK SAR, Hong Kong
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Date                     :: 17-FEB-2023
            Assembly Method                   :: Unicycler v. 0.4.8-beta
            Assembly Name :: Klebsiella_pneumoniae_pneumoniae_RX.G5M15 _48Flow_3
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 275.0x
            Sequencing Technology :: Illumina NovaSeq; Oxford Nanopore MinION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_029025805.1-RS_2024_05_03
            Annotation Date                   :: 05/03/2024 04:44:04
            Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline
            (PGAP)
            Annotation Method :: Best-placed reference protein set; GeneMarkS-2+
            Annotation Software revision      :: 6.7
            Features Annotated                :: Gene; CDS; rRNA; tRNA; ncRNA
            Genes (total)                     :: 5,238
            CDSs (total)                      :: 5,117
            Genes (coding)                    :: 5,018
            CDSs (with protein)               :: 5,018
            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)              :: 99
            CDSs (without protein)            :: 99
            Pseudo Genes (ambiguous residues) :: 0 of 99
            Pseudo Genes (frameshifted)       :: 48 of 99
            Pseudo Genes (incomplete)         :: 49 of 99
            Pseudo Genes (internal stop)      :: 15 of 99
            Pseudo Genes (multiple problems)  :: 13 of 99
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP118938.1.
            Bacteria and source DNA available from Dr. Simon D. J. Griffin,
            Shuyuan Molecular Biology Laboratory, The ISF Academy, 1 Kong Sin
            Wan Road, Pokfulam, Hong Kong.
            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..4642
                     /organism="Klebsiella pneumoniae subsp. pneumoniae"
                     /mol_type="genomic DNA"
                     /strain="RX.G5M15"
                     /isolation_source="Shoe"
                     /sub_species="pneumoniae"
                     /db_xref="taxon:72407"
                     /plasmid="pRX.G5M15_2"
                     /geo_loc_name="Hong Kong: Telegraph Bay"
                     /lat_lon="22.263738 N 114.129972 E"
                     /collection_date="2021-11-08"
                     /collected_by="Nathan Sibraa"
     gene            complement(761..1162)
                     /locus_tag="PX704_RS26155"
                     /old_locus_tag="PX704_26160"
     CDS             complement(761..1162)
                     /locus_tag="PX704_RS26155"
                     /old_locus_tag="PX704_26160"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_009310048.1"
                     /GO_function="GO:0003677 - DNA binding [Evidence IEA]"
                     /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_009310048.1"
                     /translation="MARVSISEAARLTGKSRTTLHRLIKAGDLSTCSGERNAKMVDTSE
                     LLRVFGPFEQPKGEHHSGQVSEQRDTASADQSEQVIRHLKQEIEHLNTLLLSKDSHIDS
                     LKQAMLLLENHQAKLTESPAPWWKFWKKS"
                     /name="helix-turn-helix domain-containing protein"
     gene            complement(1162..1353)
                     /locus_tag="PX704_RS26160"
                     /old_locus_tag="PX704_26165"
     CDS             complement(1162..1353)
                     /locus_tag="PX704_RS26160"
                     /old_locus_tag="PX704_26165"
                     /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_023302508.1"
                     /translation="MTKQQKTALNMAKFIQNQSLLLLEKLNELDLDVEADLCEKLHDDA
                     EHLFRTLSSRLDELQDGN"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            1769..1882
                     /locus_tag="PX704_RS26205"
     CDS             1769..1882
                     /locus_tag="PX704_RS26205"
                     /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_080882241.1"
                     /translation="MHEPPVQSDCCVLSGNYHLESNPVRHAKAPLAAATGN"
                     /name="replication initiation protein"
     gene            complement(2086..3768)
                     /locus_tag="PX704_RS26165"
                     /old_locus_tag="PX704_26170"
     CDS             complement(2086..3768)
                     /locus_tag="PX704_RS26165"
                     /old_locus_tag="PX704_26170"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001697690.1"
                     /GO_function="GO:0019239 - deaminase activity [Evidence
                     IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="anti-phage dCTP deaminase"
                     /protein_id="WP_223862165.1"
                     /translation="MSLARKLREKRSNPIHSANEDSSGGDSINQITSRQSMDLVIGFCG
                     AVGSGIKSIVDVTEEELDDLGYDVYRIRVSELMQKLFSEWRDDIVTPFDRYHKLQDFGD
                     ALRNKYYPHILSEAVIHEIKIEKGIDTSSKKNKKAFLVDQLKHQDEIELLRMVYQHNFY
                     LLGVIRSEVERKRNLRDEGLSKSEVDIVIHHDRKSESDYGQQTAKAILDSDYFVKNNQG
                     QRAHLKAKVKRFIGLIHGLNGLTPTTYEKGMYAAHSASLQSACLSRQVGAAILDVNGNL
                     ISVGRNDVPKFNGGLYSADDGVNDHRCVYKGGKCYNEVRKLKIKSKISQILMSESACEL
                     GVKLTEDQAEQLADVIYKKTPVSSIIEYSRSIHAEMDAITSLARLGNGGFSDKVLYTTT
                     FPCHNCARHIVAVGITKVVYIEPYEKSLALELHDDAITEVNEHGKVIFESFEGVSPRRY
                     QKFFFSTDERKDSFGNAEKYSTKYKNHIDIQFIDSYLDFENRVVDIFRTNTNIDSGNHV
                     GRTDSTINLSSQPVPPVPPVPPVPPVPPVPPVPPVPPVPPDSK"
                     /name="anti-phage dCTP deaminase"
     gene            complement(3781..3963)
                     /locus_tag="PX704_RS26170"
                     /old_locus_tag="PX704_26175"
     CDS             complement(3781..3963)
                     /locus_tag="PX704_RS26170"
                     /old_locus_tag="PX704_26175"
                     /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_080882243.1"
                     /translation="MGKELSLNKIYDKNSRYINDSRGHELGKEKKVFDFEVEMIKKRRE
                     DAIRKIIEDSKSLKW"
                     /name="hypothetical protein"
     gene            4351..4560
                     /locus_tag="PX704_RS26175"
                     /old_locus_tag="PX704_26180"
     CDS             4351..4560
                     /locus_tag="PX704_RS26175"
                     /old_locus_tag="PX704_26180"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:YP_005227293.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="YdgH/BhsA/McbA-like domain containing protein"
                     /protein_id="WP_085808090.1"
                     /translation="MKSIKTFVAVVALSMMSFGAFAQSVSATASTLDRAEAKIAAQAAE
                     QGASYKITSAQFNNRVHMTAELTK"
                     /name="YdgH/BhsA/McbA-like domain containing protein"
     Typing          1475..1882
                     /name="ColRNAI_rep_cluster_1987"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="95.355"
                     /coverage="99.0"
                     /evalue="0.0"
ORIGIN
        1 cgggggcttt tttgcatctg tcatttaaca taaaggtatg attgtacgca ccgctaaaac
       61 ggtctcaggg cgtttctgac gggaaaccgg taaaacaggc aacaaaccac ccgaaaaccc
      121 gccagaaacg cgcaggctct gtttttacgg catgcatgag tatgcacgca agtgcatagc
      181 gcgaaaattc acgccattca gccagagtaa gtcctgtttc cggcgttctt tccatccgaa
      241 aacggtgaac ggggacgcaa tttattgcgt ggccgtgaag cgttgccggc gcagccggaa
      301 aaccggtttt cagcacgttc aggaatcggg ttcgtcgacg gccggcaatc acgttatggc
      361 aagtcgccgg acgactcacc acacgattca ccggcgactc ttcactagag tcgtacccag
      421 agtcgccgcg tctaaaaaac aaccaaacgg ggagtcgtgt ctagagtcgg gtcgttatta
      481 acttattgtt tttatagtcc tgagtcgtta ccgactctat gacgactcgc cggggactct
      541 atgacgagtc gtcatagagt cggatctatg taaataaatt ttaaaaaccg aaatttcagg
      601 aaagtaagct actgatatta aatacaaatc tgcaaaattt taattttgcg tagtgtgtgg
      661 gtatttttag tcgtgaggag cgttcagaga tctggcgatt tttgggaagg ttcaggaact
      721 ccccgggatg gccggagagg aaaactgaag catgacgggg tcaggatttt ttccagaatt
      781 tccaccatgg cgccggggat tcagttaatt ttgcctggtg attttcaaga aggagcatgg
      841 cctgtttcag gctgtcaatg tgcgaatcct tggacaaaag taaggtgttc aggtgttcaa
      901 tctcctgttt cagatgacga atcacctgtt cactctggtc agcagaggct gtatcacgtt
      961 gttcagagac ctgtccagaa tggtgttcac ccttcggttg ctcaaaggga ccaaagacac
     1021 gtaaaagctc tgaagtatct accatttttg cattgcgttc accgctacag gtggacaggt
     1081 cacctgcttt aatcaacctg tgcagtgttg ttctactctt acccgtcagt cgggcagcct
     1141 cactaataga cactctggcc atcagttacc atcctgtaat tcatccagtc tcgaggacag
     1201 tgtacggaaa agatgctccg catcatcgtg gagtttctca caaaggtcgg cctcaacatc
     1261 gagatcaagc tcgttaagct tctccagcag gagcagagac tgattctgga tgaatttagc
     1321 catgttcagc gctgttttct gttgtttcgt cataagaagc ctcagagcgt cagtgctcag
     1381 tgtaagaaca gtctcttttc cgcttcctcg ctcactcagt cgctacgctc ctgccgttcg
     1441 gctgcggcga gcggcaggag catgcgtgta aaagctcgag aaaaccgagc ggtctcgtga
     1501 tggggaaaag gaaaggccgc acagcggccg tttttccata ggctccgccc ccctgacgag
     1561 catcacggaa tctgacgctc aaatcagtgg cggcgaaacc cgacaggact ataaagatac
     1621 caggcgtttc cccctgatgg ctccctcgtg cgctctcctg ttcctgccat tcggtttacc
     1681 ggtgtcattc cgctgttatg gccgcgtttg tctcattcca cgcctgacac tcagttccgg
     1741 gtaggcagtt cgctccaagc tggactgtat gcacgaaccc cccgttcagt ccgactgctg
     1801 cgtcttatcc ggtaactatc atcttgagtc caacccggta agacatgcaa aagcaccact
     1861 ggcagcagcc accggtaact gatttagagg agttagtctt gaagttatgc gccagttaag
     1921 gctaaactga aagaacaagt tttggtgact gcgctcctcc aagccagtta ccttggttca
     1981 tagagccgca aactctagaa ccttaaaaaa accgccccgc aaaggcggtt tttttctttc
     2041 tcgtctcaag gttaagctct gtataacatc agagtcaaca gatcttcatt tcgagtctgg
     2101 tggtactggc ggtacgggcg gtacgggcgg tacgggcggt acgggcggta cgggcggtac
     2161 gggcggcacg ggcggcacgg gctgggaaga taaattaata gtcgaatcag ttctcccgac
     2221 atgattgcca gaatcaatat ttgtgttagt tctaaaaata tcaacgactc gattttcgaa
     2281 atctaaatag ctatcaataa actgtatatc aatgtgattt ttatatttag tggagtactt
     2341 ttctgcgtta ccgaaactat ctttcctttc atctgtagaa aagaagaatt tttgatacct
     2401 acgaggtgat acaccttcaa aggactcaaa tataaccttc ccatgctcat tcacctcggt
     2461 tatagcatca tcatgcaatt ctaaagcgag gcttttttca tatggctcta tataaacaac
     2521 ttttgttatt ccaacagcaa caatatgtct cgcgcagtta tgacaaggaa atgtggttgt
     2581 atataaaact ttatcagaaa aacctccatt acctagtcta gctaatgatg taatagcatc
     2641 catctctgca tgaattgagc gagagtactc tataatagaa gatactggtg tttttttata
     2701 tattacatca gccagttgct ctgcttgatc ttctgttaat ttaacaccaa gttcacaagc
     2761 gctttccgac ataagtattt gtgaaatttt gcttttaatc tttagctttc taacttcatt
     2821 ataacattta ccacctttgt atacacaacg atgatcattg acaccatcat ccgcactata
     2881 aagcccacca ttgaatttag gtacatcatt acgcccaacg gaaatcagat tcccattaac
     2941 atccaatata gcagcaccaa cttgacgaga aaggcatgca gattgcagag atgctgaatg
     3001 agctgcatac ataccttttt catacgtggt tggagttaaa ccatttagcc catgtatcaa
     3061 gccaataaaa cgcttaacct tagccttaag gtgcgccctt tgtccttgat tattcttaac
     3121 aaaataatca gagtcaagta tagctttcgc agtctgctga ccataatcgc tctctgattt
     3181 tctatcgtga tgaataacta tatcgacttc tgacttactc agcccttcat ctctaagatt
     3241 acgctttctt tctacttcac ttctaattac acctagtaaa taaaaattat gttggtagac
     3301 cattcttaaa agttcaattt catcctgatg cttcaactga tcgaccaaaa aagccttttt
     3361 atttttttta cttgaggtgt caatgccttt ttctattttt atttcatgga ttacagcttc
     3421 agatagtata tgtgggtaat atttatttct taacgcatca ccaaaatctt gcagcttatg
     3481 atatctatca aacggagtaa caatatcatc acgccattct gaaaaaagtt tttgcataag
     3541 ctcgctaact cttatgcgat aaacatcata tcctagatca tctagttctt cttcagtcac
     3601 atcaacaatt gactttattc ctgagccaac agcaccgcaa aatcctataa caagatccat
     3661 agactgtctg gaggttattt ggtttatgct atcccctcca gaggagtcct cgttagcact
     3721 atgaatcgga ttacttcttt tttctcttaa ctttctagcc aggctcataa aagacctcac
     3781 ttaccatttt aatgattttg aatcctcaat tatcttcctt atagcgtcct ctcttctttt
     3841 tttaatcatt tcaacttcaa aatcgaaaac tttcttttcc tttcccagct catgccctct
     3901 agaatcatta atatatctag aattcttatc ataaatttta tttagagata gctctttacc
     3961 catcacaccc tcctgcaaga cgcatggatt ttactgttat ctttataaca ggcaatagcc
     4021 aagaaacgta atcgatagag attttttttt cttatcctaa acattaggaa attcggcaag
     4081 agaaaagcaa gagagatcac gccaaactaa ccattatttt tcaatttgtt aaaataaaat
     4141 catcaatgtt aacatttcta tccaccacct catttggtac ctagaatcca gagataaacc
     4201 tctggtcttg atgcgctcaa ttcttgttct ttttttttga atgatatccg caaattgttt
     4261 cgattttaat cagtccatgg tcgtcctatc atttatcaca tcagggcaac aacgccccat
     4321 acagaacaaa attacttaag gaatacgacc atgaaatcca tcaaaacttt cgttgcagtt
     4381 gtcgcactat ccatgatgtc tttcggtgcc tttgctcaga gcgtcagcgc taccgcctcc
     4441 accctggatc gtgctgaagc aaaaattgcc gcacaggccg ctgaacaagg tgcgtcatac
     4501 aaaatcacca gcgctcagtt caataaccgt gtccacatga cggctgaact gaccaaataa
     4561 gatggtcgca gagggagctg ccgaacaggt cgccgggagg cggcccgttt cgtcccttag
     4621 caggaaaacc ttcaggcccc tt
//
