LOCUS       NZ_CP057071             2475 bp    DNA     circular CON 30-APR-2024
DEFINITION  Klebsiella pneumoniae strain RHB39-C09 plasmid pRHB39-C09_3,
            complete sequence.
ACCESSION   NZ_CP057071
VERSION     NZ_CP057071.1
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 2475)
  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 2475)
  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
            CP057071.1.
            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..2475
                     /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_3"
                     /geo_loc_name="United Kingdom"
                     /collection_date="2017"
     gene            join(2232..2475,1..158)
                     /locus_tag="HVZ81_RS26455"
                     /old_locus_tag="HVZ81_26465"
     CDS             join(2232..2475,1..158)
                     /locus_tag="HVZ81_RS26455"
                     /old_locus_tag="HVZ81_26465"
                     /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_064175096.1"
                     /translation="MARVSISEAARLTGKSRTTLHRLIKTGDLSTCSGERNAKMVDTSE
                     LLRVFGPFEQPKGEHHSGQVSEQRDTASADQSEQVIRHLKQEIEHLNTLLLSKDSHIDS
                     LKQAMLLLENHQAKLTESPTPWWKFWKKS"
                     /name="helix-turn-helix domain-containing protein"
     gene            complement(901..1017)
                     /locus_tag="HVZ81_RS26460"
                     /old_locus_tag="HVZ81_26470"
     CDS             complement(901..1017)
                     /locus_tag="HVZ81_RS26460"
                     /old_locus_tag="HVZ81_26470"
                     /inference="COORDINATES: protein motif:HMM:NF033853.2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="small membrane protein"
                     /protein_id="WP_016947047.1"
                     /translation="MDWISLAIAIALLVVAVYSGISYFREKKTISRTFRRRR"
                     /name="small membrane protein"
     gene            2041..2232
                     /locus_tag="HVZ81_RS26465"
                     /old_locus_tag="HVZ81_26475"
     CDS             2041..2232
                     /locus_tag="HVZ81_RS26465"
                     /old_locus_tag="HVZ81_26475"
                     /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_000166328.1"
                     /translation="MTKQQKTALNMAKFIQNQSLLLLEKLNELDLDAEADLCEKLHDDA
                     EHLFRTLSSRLDALQDGN"
                     /name="Rop family plasmid primer RNA-binding protein"
     Typing          complement(1522..1993)
                     /name="ColRNAI_rep_cluster_1987"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="88.125"
                     /coverage="91.0"
                     /evalue="2.16e-156"
ORIGIN
        1 gtcatctgaa acaggagatt gaacacctga acaccttact tttgtccaag gattcgcaca
       61 ttgacagcct gaaacaggcc atgctccttc ttgaaaatca ccaggcaaaa ttaactgaat
      121 ccccgacgcc atggtggaaa ttctggaaaa aatcctgacc ccgtcatgct tcagttttcc
      181 tctccggcca tcccggggag ttcctgaacc ttcccaaaaa tcgtcagatc tctgaacgct
      241 cctcaccact aaaaataccc acaccccacg caaaattaaa attttgcaga ttccttattt
      301 acaacaatgg gttaatgaaa aataaatgtg cggtgatgtg ttacaaagtg cagatccaag
      361 tcgtggacaa ctctatggcg aatcgctgac gaattgccca cgattcatat gtgaatcacg
      421 ctttattatc atattgttat gatgaatcga ctcttgattc aattcatcac tctgggtgtt
      481 ttttgttcat ggtgactctt gattcaattc acgattcgaa tcgccggtga atcgtgtggt
      541 gagtcgtccg gcgacttgcc ataacgtgat tgccggccgt cgacgaaccc gattcctgaa
      601 cgtgctgaaa accggttttc cggctgcgcc ggcaacgctt cacggccacg caataaattg
      661 cgtccccgtt caccgttttc ggataggaag aacgctggaa acaggactta ccctggctga
      721 atggcgtgaa ttttcgcgct atgcacttgc gtgcatactc atgcatgccg taaaaacaga
      781 gcctgcgcgt ttctggcggg ttttcgggtg gtttgttgcc tgttttaccg gtttcccgtc
      841 agaaacgccc tgaggccgtt ttcgcggtgc gtacaagaag ggattatggt aaatagggcg
      901 ctatcgccta cgcctaaatg tacgactgat tgtttttttt tctctgaagt atgagattcc
      961 tgagtagaca gctacaacaa gtagagcaat ggcgatagca agtgaaatcc agtccataaa
     1021 tgcctgatta atttaataaa aacagcctgt tatgatttca taaagataat atcatctttt
     1081 tttagcatga tactgtcgtt acttattgtg gtgagatgaa acataaccgc tgtttttgta
     1141 tgtgtttgtt aaggtttcta agattattcc taaccactga ttttgtacat atcatcaaaa
     1201 aaaatataaa aaactaatgc cctgtggtgg gtatgtaaca aatcacgggg agcgggtcag
     1261 aactacgcca aaactttgaa tgatcgggtg gcaggctaaa tgaaatcttg agattcattc
     1321 agtctcgtcg taatctcttg ctctgtaaac gaaaaaaccg ccttgcaggg cggtttttcg
     1381 aaggttcagc aagttgggga acttctgaac cgtggtaaca gggtgtacaa gaccgctgcc
     1441 accaaatacg tccttccagt ttagccgtag ttaggcttca acttcaagaa ctctgtacca
     1501 gttatctctt gtacacccct ttaccagtgg ctaccgccaa tggcgatttg tcgtgccttt
     1561 tcgggttgga ctcaagacga tagttaccga aaagagcgtg gtagtcggac tgaacggggg
     1621 gttcgtgcat acagtccagc ttggagcgaa ctgcctaccc ggaactgagt gtcaggcgtg
     1681 gaatgagata aacgcggcca taacagcgga atgacaccgg taaaccgaaa ggcaggaaca
     1741 ggagagcgca cgagggagcc accaggggga aacgcctggt atctttaagt cctgtcgggt
     1801 ttcgccaccg ctgatttgag cgtccgtttc tgtgatgctt gtcagggggg cggagcctat
     1861 ggaaaaacgg caacgccgtg gctttttcca caggctcttc tcttcctggt gatagcgatg
     1921 actcttctgt gtgtcccgtc cgctcgccgc agccgaacgg caggagcgta gcgactgagt
     1981 gagcgaggaa gcggaaaaga gaccggtttt acactgagca ctgacgccct gaggcccctt
     2041 atgacgaaac aacagaaaac tgccctgaac atggctaaat tcatccagaa tcagtccctg
     2101 ctcctgctgg agaagcttaa cgagcttgat ctcgatgcgg aggctgacct ttgtgagaaa
     2161 ctccacgatg atgcggagca tcttttccgt acactgtcct cgagactgga tgcattacag
     2221 gatggtaact gatggccaga gtgtctatta gtgaggctgc ccgactgacg ggtaagagta
     2281 gaacaacact gcacaggtta attaaaacag gtgacctgtc cacctgtagt ggtgagcgca
     2341 atgcaaaaat ggtagatact tcagagcttt tacgtgtctt tggtcccttt gagcaaccga
     2401 agggtgaaca ccattctgga caggtctctg aacagcgtga tacagcctct gctgaccaga
     2461 gtgaacaggt gattc
//
