LOCUS       NZ_CP057070             4225 bp    DNA     circular CON 30-APR-2024
DEFINITION  Klebsiella pneumoniae strain RHB39-C09 plasmid pRHB39-C09_2,
            complete sequence.
ACCESSION   NZ_CP057070
VERSION     NZ_CP057070.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN15148398
            Assembly: GCF_013811845.1
KEYWORDS    RefSeq.
SOURCE      Klebsiella pneumoniae
  ORGANISM  Klebsiella pneumoniae
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Klebsiella/Raoultella group; Klebsiella.
REFERENCE   1  (bases 1 to 4225)
  AUTHORS   AbuOun,M., Jones,H., Stubberfield,E., Gilson,D., Shaw,L.P.,
            Hubbard,A.T.M., Chau,K.K., Sebra,R., Peto,T.E.A., Crook,D.W.,
            Read,D.S., Gweon,H.S., Walker,A.S., Stoesser,N., Smith,R.P.,
            Anjum,M.F. and On Behalf Of The Rehab,Consortium.
  TITLE     A genomic epidemiological study shows that prevalence of
            antimicrobial resistance in Enterobacterales is associated with the
            livestock host, as well as antimicrobial usage
  JOURNAL   Microb Genom 7 (10) (2021)
   PUBMED   34609275
REFERENCE   2  (bases 1 to 4225)
  AUTHORS   Shaw,L.P.
  TITLE     Direct Submission
  JOURNAL   Submitted (12-JUN-2020) Nuffield Department of Medicine, University
            of Oxford, John Radcliffe Hospital, Oxford OX3 9DU, United Kingdom
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: Unicycler v. v0.4.7
            Assembly Name                     :: RH09 T3-C09
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 169.937154635236x
            Sequencing Technology :: Hybrid: Illumina and OXFORD_NANOPORE
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_013811845.1-RS_2024_04_30
            Annotation Date                   :: 04/30/2024 03:30:22
            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)                     :: 5,327
            CDSs (total)                      :: 5,201
            Genes (coding)                    :: 5,107
            CDSs (with protein)               :: 5,107
            Genes (RNA)                       :: 126
            rRNAs                             :: 9, 8, 8 (5S, 16S, 23S)
            complete rRNAs                    :: 9, 8, 8 (5S, 16S, 23S)
            tRNAs                             :: 88
            ncRNAs                            :: 13
            Pseudo Genes (total)              :: 94
            CDSs (without protein)            :: 94
            Pseudo Genes (ambiguous residues) :: 0 of 94
            Pseudo Genes (frameshifted)       :: 46 of 94
            Pseudo Genes (incomplete)         :: 45 of 94
            Pseudo Genes (internal stop)      :: 16 of 94
            Pseudo Genes (multiple problems)  :: 11 of 94
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP057070.1.
            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..4225
                     /organism="Klebsiella pneumoniae"
                     /mol_type="genomic DNA"
                     /strain="RHB39-C09"
                     /isolation_source="Pooled cattle faecal samples collected
                     from floor of farm"
                     /db_xref="taxon:573"
                     /plasmid="pRHB39-C09_2"
                     /geo_loc_name="United Kingdom"
                     /collection_date="2017"
     gene            join(4073..4225,1..249)
                     /locus_tag="HVZ81_RS26435"
                     /old_locus_tag="HVZ81_26445"
     CDS             join(4073..4225,1..249)
                     /locus_tag="HVZ81_RS26435"
                     /old_locus_tag="HVZ81_26445"
                     /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_102776604.1"
                     /translation="MARVSISEAARLTGKSRTTLHRLIKTGDLSTCSGERNAKMVDTSE
                     LLRVFGPFEQPKGEHHSGQVSEQRDTASADQSEQVIRHLKQEIEHLNTLLLSKDSHIDS
                     LKQAMLLLENHQAKLTESPAPWWKFWKKS"
                     /name="helix-turn-helix domain-containing protein"
     gene            1065..2315
                     /locus_tag="HVZ81_RS26440"
                     /old_locus_tag="HVZ81_26450"
     CDS             1065..2315
                     /locus_tag="HVZ81_RS26440"
                     /old_locus_tag="HVZ81_26450"
                     /EC_number="2.1.1.37"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_015160339.1"
                     /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: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="DNA cytosine methyltransferase"
                     /protein_id="WP_001584442.1"
                     /translation="MTRPIAVDLFAGAGGLSLGFEQAGFDIMASVEIDPIHCSAHKYNF
                     PMCKTICRSVVDVTGEYVREVSGIGEKEIDVVIGGAPCQGFSLIGKRALDDDRNKLVYH
                     YVRLVLELKPKYFVFENVKGLTVGKHKQFLVEIMDAFKDGGYDVVSDYKVLNAADYGVP
                     QDRRRLFLMGGRKGIALPSYPEPLSIRTTVGDAIGDIPDAEKYPELWGRDWVYAKFGEQ
                     SLYSSYLHGVGKDPSDFSYPRIFNKDKLTCSLLTDHSDISRGRFVETLPDTVEPISRFK
                     KLSMNGLCNTLRAGTASDRGAFTSPRPIHPIYPRVITVREAARLHSYPDWFRFHVTKWH
                     GFRQVGNSVPPMLARSVGLQIMKVLGVTPKKPTKKIKLGDESLVAISMSDAASMFGVSS
                     NVIAKRIKNSNKEVVCE"
                     /name="DNA cytosine methyltransferase"
     gene            2308..3117
                     /locus_tag="HVZ81_RS26445"
                     /old_locus_tag="HVZ81_26455"
     CDS             2308..3117
                     /locus_tag="HVZ81_RS26445"
                     /old_locus_tag="HVZ81_26455"
                     /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_032446875.1"
                     /translation="MSKDKKERSKNRYHQLVEKIFFDKYVDGDLEVLFERLDINSAAKD
                     LGIELPSNVGDVIYSIRFRTPMPESILLTQPEGKEWIIELAGRSKYRFRLVTISRILPN
                     PNMVAIKIPDNTPEIITGYSLDDEQALLAKVRYNRLIDIFLGITTYSLQNHLRTTVKGI
                     GQIEIDELYVGIDKYGCHYIIPVQAKGGTDQISMVQTSQDTAWCEQKYPNVRCRAISAQ
                     FVSSDLIALFELKIDEGQVKLIEERHYKLVPVKELDSSDISNYRMSV"
                     /name="hypothetical protein"
     gene            complement(3337..3468)
                     /locus_tag="HVZ81_RS26755"
     CDS             complement(3337..3468)
                     /locus_tag="HVZ81_RS26755"
                     /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            3882..4073
                     /locus_tag="HVZ81_RS26450"
                     /old_locus_tag="HVZ81_26460"
     CDS             3882..4073
                     /locus_tag="HVZ81_RS26450"
                     /old_locus_tag="HVZ81_26460"
                     /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_032446876.1"
                     /translation="MTKQQKTALNMAKFIQNQSLLLLEKLNEFDLDVEADLCEKLHDDA
                     EHLFRTLSSRLDALQDGN"
                     /name="Rop family plasmid primer RNA-binding protein"
     Typing          complement(3360..3760)
                     /name="ColRNAI_rep_cluster_1987"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="93.812"
                     /coverage="98.0"
                     /evalue="5.92e-171"
ORIGIN
        1 ccctttgagc aaccgaaggg tgaacaccat tctggacagg tctctgaaca gcgtgataca
       61 gcctctgctg accagagtga acaggtgatt cgtcatctga aacaggagat tgaacacctg
      121 aacaccttac ttttgtccaa ggattcgcac attgacagcc tgaaacaggc catgctcctt
      181 cttgaaaatc accaggcaaa attaactgaa tccccggcgc catggtggaa attctggaaa
      241 aaatcctgat cctgccatgc ttgagttttc ctctccggcc atcccgggga gttcctgaac
      301 cttcccaaaa atcgccagat ctctgaacgc tcctcacgac taaaaatacc cacacactac
      361 gcaaaattaa aattttgcag atttgtattt aatatcagtg gtttactttc ctgaaatttc
      421 gttttttaaa ttttatttac atagatccga ctctatgacg actcgtcata gagtccccgg
      481 cgagtcgtca tagagtcggt aacgactcag gactataaaa acaatgagtt aataacgacc
      541 cgactctaga cacgactccc cgtttggttg ttttttagac tcggcgactc tgggtacgac
      601 tctagtgaag agtcgccggg gaatcgtgtg gtgagtcgtc cggcgacttg ccataacgtg
      661 attgccggcc gtcgacgaac acgattcctg aacgtgctga aaaccggttt tccggctgcg
      721 ccggcaacgc ttcacggcca cgcaataaat tgcgtccccg ttcaccgttt tcggatggga
      781 agaacgccgg aaacaggact taccatggct gaatggcgtg aattttcgcg ctacgcactt
      841 gcgtgcatac tcatgcatgc cgtaaaaaca gagcctgcgc gtttctggcg ggttttcggg
      901 tggtttgttg cctgttttac cggtttcccg tcagaaacgc cctgaggccg ttttagcggt
      961 gcgggcaaga gatgttatgt tcaatcgaaa tcagaaaaac gatcggtaaa gcgatcgttt
     1021 ttctgatagc atcatgttga ttttatataa cgtgggtgta aagaatgact agaccgattg
     1081 ctgttgattt atttgctgga gcgggtgggc tgagtctcgg tttcgagcaa gctggctttg
     1141 atataatggc atcagttgaa atagatccaa tacattgctc tgctcacaaa tataactttc
     1201 ctatgtgcaa aacgatatgt agaagtgttg ttgatgttac cggagaatac gttagggaag
     1261 tttcaggtat tggtgagaaa gagattgatg tagtgatcgg aggcgctccc tgccaaggct
     1321 tttcattaat aggaaaacgc gcgcttgatg atgatagaaa caaactggtc tatcactatg
     1381 tacggctggt tcttgagcta aagcctaaat actttgtttt tgaaaatgta aaagggttga
     1441 cggttggtaa gcataagcag tttttagtag agataatgga tgcatttaaa gatggcgggt
     1501 acgacgttgt aagcgattat aaagtgctaa acgcagctga ttatggagtt cctcaagatc
     1561 gccgtcgtct tttcttaatg gggggaagga aaggaattgc tctgccatca taccctgagc
     1621 cattatccat tagaacaacg gttggggacg ctattgggga tattcctgat gcggaaaaat
     1681 atcctgagct atggggtaga gattgggttt atgctaaatt tggtgagcaa tcactatact
     1741 catcctattt gcatggcgta ggaaaagatc ctagtgattt tagctaccca aggattttta
     1801 ataaagacaa attaacgtgt tctttactga cagatcactc tgacatttct agagggcggt
     1861 ttgttgaaac tttgcctgac acggtagaac caatcagcag gtttaaaaag ctctcgatga
     1921 atgggctatg taatacttta agggcaggaa cagcaagtga cagaggtgct tttacatctc
     1981 ctcgtcctat acatccgatc tatcctaggg tcatcacggt cagagaggca gcaagactgc
     2041 attcatatcc tgattggttc agatttcatg tgactaagtg gcatggattt agacaggtcg
     2101 gtaatagtgt tcctcctatg ctagctagaa gtgttggctt gcagattatg aaggttcttg
     2161 gtgttacgcc aaaaaaacca acgaagaaaa tcaaactcgg tgatgaaagt ttggttgcta
     2221 tttctatgtc cgatgctgca tctatgtttg gtgtgtcatc aaatgtaatt gctaagagaa
     2281 taaaaaatag taacaaggag gttgtttgtg agtaaggata aaaaagaaag gtccaaaaat
     2341 agataccatc agttggtaga aaagatattt ttcgataaat atgttgatgg tgacttagag
     2401 gttttgtttg aaaggttaga tataaacagt gctgcaaaag atttaggtat agaactccca
     2461 tctaatgttg gtgatgttat atattcaatc agatttagaa cgcctatgcc agaaagtatt
     2521 ctgttgactc agccagaagg taaggagtgg attattgagc tggctggtag gtcaaagtat
     2581 cgatttagat tagtaactat tagtaggatt ttgccaaatc ctaatatggt ggcaataaaa
     2641 attccagaca ataccccgga gataattaca ggttattctt tagacgacga gcaggcattg
     2701 ctggcgaagg tgagatataa ccggctaata gatatatttc taggtataac cacatattct
     2761 ttacagaatc atttaagaac tacggtgaag ggaattggtc aaatagagat cgatgaactt
     2821 tatgtaggta tagataaata cggttgccat tatataatac cagttcaagc aaaaggtggg
     2881 acagatcaaa tatcaatggt gcaaacatcg caagatacag cgtggtgtga acaaaaatac
     2941 ccaaatgtta gatgtagagc tatttccgct cagtttgttt cgagcgattt gattgcactg
     3001 tttgagctaa agatagacga aggacaagtg aaattgattg aggaaaggca ttacaaactg
     3061 gttccggtaa aagagttaga tagctctgac atctcaaact accgcatgtc tgtataattt
     3121 ctgagaggat cttcttgaga tcctttcgtt ctagccgtaa tctcctaagc cgtaaacaaa
     3181 aaaaccaccg ctaccaacgg tggttcgttt gccggaattt agagctacca actctttctt
     3241 ccgaaggtaa ctggctttca cggagcgcag ataccaaaac tgtcctttca gtgtagccgt
     3301 agtcaggcca ccacttcaag aactctgtag ataactctac tccgctccgt gaatccgatt
     3361 accagtggct gctgccagtg gcgcttttgc atgtcttttc gggttggact caagacgata
     3421 gttaccggac aaggcgcagc agtcggactg aacggggggt tcgtgcatac agtccagctt
     3481 ggagcgaact gcctacccgg aactgagtgt caggcgtgga atgagacaaa cgcggccata
     3541 acagcggaat gacaccggta aaccgaaagg caggaacagg agagcgcacg agggagccac
     3601 cagggggaaa cgcctggtat ctttatagtc ctgtcgggtt tcgccaccac tgatttgagc
     3661 gtcagattcc gtgatgcttg tcaggggggc ggagcctatg aaaaaacggc cgctttgcgg
     3721 cctttccttc ttccccattt gaccgctcgg tcttctcgag tttttatacg catgctcctg
     3781 ccgctcgccg cagccgaacg accggagcgt agcgactgag tgagcgagga agcggaaaag
     3841 agactggttt tacactgagc actgacgctc tgaggccatt tatgacgaaa caacagaaaa
     3901 cagcgctgaa catggctaaa ttcatccaga atcagtctct gctcctgctg gagaagctta
     3961 acgagtttga tctcgatgtc gaggccgacc tttgtgagaa actccacgat gatgcggagc
     4021 atcttttccg tacactgtcc tcgagactgg atgcattaca ggatggtaac tgatggccag
     4081 agtgtctatt agtgaggctg cccgactgac gggtaagagt agaacaacac tgcacaggtt
     4141 aattaaaaca ggtgacctgt ccacctgtag tggtgagcgc aatgcaaaaa tggtagatac
     4201 ttcagagctt ttacgtgtct ttggt
//
