LOCUS       NZ_CP056196             5783 bp    DNA     circular CON 25-FEB-2024
DEFINITION  Klebsiella pneumoniae strain RHBSTW-00995 plasmid pRHBSTW-00995_6,
            complete sequence.
ACCESSION   NZ_CP056196
VERSION     NZ_CP056196.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN15148764
            Assembly: GCF_013782105.1
KEYWORDS    RefSeq.
SOURCE      Klebsiella pneumoniae
  ORGANISM  Klebsiella pneumoniae
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Klebsiella/Raoultella group; Klebsiella.
REFERENCE   1  (bases 1 to 5783)
  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 5783)
  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                     :: WTP3 T3-00995
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 139.174696581201x
            Sequencing Technology :: Hybrid: Illumina and OXFORD_NANOPORE
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 02/25/2024 08:27:12
            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)                     :: 5,523
            CDSs (total)                      :: 5,399
            Genes (coding)                    :: 5,245
            CDSs (with protein)               :: 5,245
            Genes (RNA)                       :: 124
            rRNAs                             :: 9, 8, 8 (5S, 16S, 23S)
            complete rRNAs                    :: 9, 8, 8 (5S, 16S, 23S)
            tRNAs                             :: 86
            ncRNAs                            :: 13
            Pseudo Genes (total)              :: 154
            CDSs (without protein)            :: 154
            Pseudo Genes (ambiguous residues) :: 0 of 154
            Pseudo Genes (frameshifted)       :: 83 of 154
            Pseudo Genes (incomplete)         :: 83 of 154
            Pseudo Genes (internal stop)      :: 23 of 154
            Pseudo Genes (multiple problems)  :: 28 of 154
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP056196.1.
            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..5783
                     /organism="Klebsiella pneumoniae"
                     /mol_type="genomic DNA"
                     /strain="RHBSTW-00995"
                     /isolation_source="Freshwater sample from downstream of
                     wastewater treatment plant"
                     /db_xref="taxon:573"
                     /plasmid="pRHBSTW-00995_6"
                     /geo_loc_name="United Kingdom"
                     /collection_date="2017"
     gene            complement(join(4166..5783,1..725))
                     /locus_tag="HV347_RS27405"
                     /old_locus_tag="HV347_27415"
     CDS             complement(join(4166..5783,1..725))
                     /locus_tag="HV347_RS27405"
                     /old_locus_tag="HV347_27415"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_010904246.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="S-type pyocin domain-containing protein"
                     /protein_id="WP_181486822.1"
                     /translation="MGGGFNYNGEGATGTGLDRDPYVRDSNGNAIGVKSGYHAESYGTS
                     SPALGPNGAIQITAGVIAVPGDKPRPDGGSGGGNTVNTGPAGQLLVMNKGQLGYWETRS
                     TGAGNNEHNTSVFVAVGPSEAEKTASAEKALKEKQQAEAAAKDFAAKTAAASATAEKER
                     QQAIAAATAAGQHQSVSDARNSLNNATSDVSRLKSAADSALQEAKAKRKAAIDAVPVAT
                     QAENKYQELQQKIKGLKLKNGEYGTEKWEIIGSNKEHDHWGYRFYPSGITKAQVDVAQS
                     DAVNKRNQATSLASQATAAEQDSLKATAAYNAAETRRQAAQAALNSAEQAAAAERKRQE
                     AEAAAAAAAEKKRQADAVAKAAEEARAAAEKARLMQERQAAADKLKSTDIQSVRGIPST
                     ASPAASPISWAVASLGGISLDSVTAGKAWTQIAEVMAKLRGIAGASLVGPVVATAVGLF
                     WSRDVGIGSDVVPGRDISGLMPGDALSLPDLATLIKAADSKTGVSMPVRGRIIVREGDY
                     LESQFVRTPVAGSVPVVRATLDKATGYWGYTLPAIQGVPGQTILVSPSDAPGVNAPLGL
                     AGPVPLPETIIHTGGQTTVPQGGTVTVSPVIGEVDFRDLILVFPPESGLKPLYVMPVSP
                     YGDATEKGEHSGRPYNPDKAGGPVQNLNWRSAVINKAGIDKVKLHTGRFGESAANKVMI
                     DRLEKILSGQLQVTDTDKRFYTHELRELERYRALGVPDNVKPDDKGVTWNNTHTATLED
                     YKINEKTDPLYTKDAEEAEYKAELKNK"
                     /name="S-type pyocin domain-containing protein"
     gene            complement(1841..2263)
                     /locus_tag="HV347_RS27410"
                     /old_locus_tag="HV347_27420"
     CDS             complement(1841..2263)
                     /locus_tag="HV347_RS27410"
                     /old_locus_tag="HV347_27420"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:YP_005229777.1"
                     /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_064148699.1"
                     /translation="MARVSISEAARLVKVSRPTIYKMINSGKLSYTSVVKHGKAIKVID
                     TSELIRVFGSLDGVIDTVKYDVKSDAESTGINSVGLHDLQHRIALLEAENDGLKGAVKA
                     RDEHIDSLRQAMQLLEHKHEPSSPPHSPWWKFWKKS"
                     /name="helix-turn-helix domain-containing protein"
     gene            complement(2263..2454)
                     /locus_tag="HV347_RS27415"
                     /old_locus_tag="HV347_27425"
     CDS             complement(2263..2454)
                     /locus_tag="HV347_RS27415"
                     /old_locus_tag="HV347_27425"
                     /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            2870..2984
                     /locus_tag="HV347_RS27505"
                     /pseudo=""
     CDS             2870..2984
                     /locus_tag="HV347_RS27505"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_005761324.1"
                     /note="frameshifted; Derived by automated computational
                     analysis using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="replication initiation protein"
                     /name="replication initiation protein"
     gene            complement(3190..3345)
                     /locus_tag="HV347_RS27420"
                     /old_locus_tag="HV347_27430"
     CDS             complement(3190..3345)
                     /locus_tag="HV347_RS27420"
                     /old_locus_tag="HV347_27430"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_008323621.1"
                     /GO_component="GO:0019867 - outer membrane [Evidence IEA]"
                     /GO_process="GO:0019835 - cytolysis [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="colicin release lysis protein"
                     /protein_id="WP_071561715.1"
                     /translation="MKKLLFLGVVTVSVVLAACQVNNVRDTGGGAVSPSSTVTGVTLDS
                     GTNGNP"
                     /name="colicin release lysis protein"
     gene            complement(3453..3710)
                     /locus_tag="HV347_RS27425"
                     /old_locus_tag="HV347_27435"
     CDS             complement(3453..3710)
                     /locus_tag="HV347_RS27425"
                     /old_locus_tag="HV347_27435"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_015366249.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="bacteriocin immunity protein"
                     /protein_id="WP_010904244.1"
                     /translation="MANKTLADYTEQEFIEFIEKIKKADFATESEHDEAIYEFSQLTEH
                     PDGWDLIYHPQAGADNSPAGVVKTVKEWRAANGKPGFKKS"
                     /name="bacteriocin immunity protein"
     gene            complement(3892..4155)
                     /locus_tag="HV347_RS27430"
                     /old_locus_tag="HV347_27440"
     CDS             complement(3892..4155)
                     /locus_tag="HV347_RS27430"
                     /old_locus_tag="HV347_27440"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_015377593.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_064148700.1"
                     /translation="MSNPIEDIIKNESVSDVLRYFGPGRDISKIDRMYVSYKFEVISEG
                     VLLSEYKKLFDNGELKYDSNKNVIKGPNWKEPAFVTQKKYGI"
                     /name="hypothetical protein"
     Typing          2576..2984
                     /name="ColRNAI_rep_cluster_1987"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="96.341"
                     /coverage="99.0"
                     /evalue="0.0"
ORIGIN
        1 tttttcagct tcaggccttt aatcttctgc tgcagctcct gatatttatt ttccgcctgg
       61 gttgcaacag gtacagcatc aatagcagcc ttccgttttg cctttgcctc ctgcagtgca
      121 ctgtctgcag ctgatttcag acgagacaca tctgacgtcg cgttattcag gctattacgg
      181 gcatcagaaa ctgactgatg ctgacccgct gcagttgcag cagcaattgc ctgctggcgt
      241 tctttttccg ccgtggctga tgcggcagca gttttagccg caaagtcttt tgctgctgct
      301 tctgcctgct gtttttcctt taacgccttc tctgcagaag cagttttttc tgcctcagaa
      361 ggacctacgg caacaaatac actcgtatta tgctcattgt tacccgcgcc cgtagaacga
      421 gtttcccagt atccaagctg acctttattc atcaccagga gctgtcctgc cggtccggtg
      481 ttaacagtat tcccaccacc actaccaccg tcaggtcggg gcttatctcc aggcacagca
      541 ataaccccag cagtaatctg aatagcgcca ttaggcccta aggctggact tgaggtccca
      601 taggactccg cgtgatagcc tgatttaaca ccaatagcat taccattgct gtcgcgaaca
      661 tatggatcac gatccaatcc ggtgccagta gcaccttccc cgttatagtt aaatccacca
      721 cccataactc tctcctttgt tgttattttt atcgttttcc tgcttgtcag aatctggtgt
      781 gcggtttatc gccttcgaac ctgtatccgg aggctgttat tagttctctg ccacaccaag
      841 tactgtatat aaatacatgt gtttatatac agtacttgaa tactactcct gacatgagaa
      901 ctctgtcaac acgcggagag atacaattat cttttgaatt ttcattaagt taagcgtaat
      961 agaaatgaca aaacccagac aggacgcggc tcggcagaga aaaaaaatta acgatatgtg
     1021 ctcttaaaaa gggtgtgact gacggacaga gacctgtaca aaaagtcttg gtgtagaggg
     1081 tattccgcca cccgagcgcc cccatttacc ataatccctt aattgtacgc accgctaaaa
     1141 cggcctcagg gcgtttctga cgggaaaccg gtaaaacagg caacaaacca cccgaaaacc
     1201 cgccagaaac gcgcaggctc tgtttttacg gcatgcatga gtatgcgcgc aagtgcatag
     1261 cgcggaaatt cacgccattc agccagggta agtcctgttt ccggcgttct tctgatccga
     1321 aaacggtgaa cggggacgca atttattgcg tggccgtgag gcgttgccgg cgcagccgga
     1381 aaaccggttt tcagcacgtt caggaatcgg gttcgtcgac ggccggcaat cacgttatgg
     1441 caagtcgccg gacgactcac cacacgattc accggcgatt cgaatcgtga attgaatcaa
     1501 gagtcaccat gaacaaaaaa cgcccaaatt gatgaattga atcaagagtc gattcatcat
     1561 aacaacatga taataaagcg tgattcacat atgaatcgtg ggcaattcgt aaacgattcg
     1621 ccatagagtc gtccacgact tggatctgca ctttgtaaca catcactgca cattaatttt
     1681 tcattaacca attgttttaa ataaagaatc tgcaaaattt taattttgcg tagtgtgtgg
     1741 gtatttttag tggtgaggag cgttcagaga tctggcgatt ttttggaagg ttcaggaact
     1801 ccccggaatg gccggagagg aaaactgaag catgatgggg tcaggatttt ttccagaatt
     1861 tccaccacgg ggaatggggt ggtgaagaag gttcgtgctt gtgctccaga agctgcatag
     1921 cctgacgaag ggaatcaata tgctcatctc gagccttaac agccccttta agaccatcgt
     1981 tttcagcttc aagtaaagcg attctatgtt gtaaatcatg taaaccaacg ctgttaatac
     2041 ctgtagattc tgcgtcactt tttacatcat attttacagt atcgattaca ccatcaagag
     2101 aaccaaacac tctaataagc tcagaagtat caataacttt aatagccttc ccgtgcttta
     2161 caacagaggt gtaacttaac ttcccactgt taatcatctt gtaaattgta ggacgactaa
     2221 ccttaacaag ccgtgccgct tcactaatag acactctggc catcagttac catcctgtaa
     2281 ttcatccagt ctcgaggaca gtgtacggaa aagatgctcc gcatcatcgt ggagtttctc
     2341 acaaaggtcg gcctcgacat cgagatcaag ctcgttaagc ttctccagca ggagcagaga
     2401 ctgattctgg atgaatttag ccatgttcag cgctgttttc tgttgtttcg tcataagagg
     2461 cctcagagcg tcagtgctca gtgtagggat gttctctttt ccgcttcctc gctcactcag
     2521 tcgctacgct cctgccgttc ggctgcggcg agcggcagga gcatgcgtat aaaagctcga
     2581 gaaaaccgag cgatcgcgtg atggggagaa ggagaggccg cacagcggcc gtttttccat
     2641 aggctccgcc cccctgacaa gcatcacaga atttgacgct caaatcagtg gtggcgaaac
     2701 ccgacaggac tataaagata ccaggcgttt ccccctgatg gctccctcgt gcgctctcct
     2761 gttcctgcca ttcggtttac cggtgtcatt ccgctgttat ggccgcgttt atctcattcc
     2821 acgcctgaca ctcagttccg ggtaggcagt tcgctccaag ctggactgta tgcacgaacc
     2881 ccccgttcag tccgactgct gcgccttgat ccggtaacta tcatcttgag tccaacccgg
     2941 taagacatgc aaaagcacca ctggcagcag ccactggtaa ctgatttaga ggagttagtc
     3001 ttgaagttat gcgccggtta aggctaaact gaaagaacaa gttttggtta ctgtgctcct
     3061 cataagccag ttacctcggt tcaaagagcg ccaactcttg gaaccttcga aaaaccgccc
     3121 gccaaggcgg ttttttcgtt tacagagcaa gagattacga cgatccaaat gggatctcaa
     3181 gaagatcctt tacggattgc cgttcgtacc gctatcaagc gtgactccgg tcaccgtcga
     3241 tgaaggtgaa acagccccac ctccggtgtc acgaacatta ttgacctgac atgccgccag
     3301 aaccacagaa acggtaacaa cccccaggaa aagtaatttt ttcatatatc accttttatt
     3361 tttattattc taagcaaatg gatacctagt aattattatt caaatccaga gttaaaaatg
     3421 tgcggattca tcacttgaac ccgcacattc aatcacgatt ttttaaaacc tggcttaccg
     3481 ttagctgctc gccactcttt tactgttttt acaacaccag caggagagtt atcggctcct
     3541 gcttgaggat gataaataag atcccaacca tctggatgtt cagtcaactg gctgaactca
     3601 taaatggcct catcatgctc agactcagta gcaaagtctg cttttttaat tttttcgata
     3661 aactcaataa attcctgctc tgtatagtca gccaaagttt tattagccat ttcagttccc
     3721 attatggatt tcaatatggc gtttaggttt taatgcactc agcttacccc agatattgtt
     3781 gacctgacat gctgccagta tcatcgaaac cacgaccact caaaaaagaa acccttttca
     3841 tatgtgagct ttaatcaaag ccctcttttc aaagggcttc atatgcacac tttaaatgcc
     3901 gtattttttt tgtgttacaa aagcaggctc tttccagtta ggccccttaa taacattttt
     3961 attagagtca tactttagtt ctccattgtc gaataacttt ttgtattcag ataaaagaac
     4021 gccttcagag atcacttcaa acttatatga aacatacata cggtcaattt ttgaaatgtc
     4081 gcgaccagga ccaaagtagc gaagcacatc acttaccgat tcatttttaa tgatgtcttc
     4141 aatcggatta ctcattctct ccccctcatt tattttttag ctctgcttta tactctgcct
     4201 cttcagcatc ctttgtatag agcggatcag ttttttcatt aattttataa tcttccagcg
     4261 ttgctgtatg agtgttattc cacgtaacac ctttatcatc tggcttcaca ttatcaggga
     4321 cccctaaagc acgataacgt tccagctctc tgagttcatg ggtgtaaaac cgcttgtccg
     4381 tatcagttac ctgtaactga ccgctcagga ttttctccag acggtcgatc attactttgt
     4441 ttgctgctga ttcaccaaag cgaccggtat gtagcttcac cttatcaatc ccggccttgt
     4501 tgatgactgc actacgccag ttaagattct gtacaggacc acctgcctta tccggattat
     4561 aaggtcttcc gctgtgctcg cctttttctg ttgcatctcc ataagggcta actggcatca
     4621 catataacgg ctttaaccct gactcaggag ggaaaacaag gataagatct cgaaaatcaa
     4681 cttcaccaat aacaggagat actgtcacag tccccccctg agggaccgta gtttgcccac
     4741 cggtatgtat aatagtttca ggcaaaggaa ccggcccagc aagtcccaga ggagcattaa
     4801 cgcccggcgc atctgacgga cttaccagta ttgtctgtcc gggcacgccc tgtatcgccg
     4861 gcaacgtata tccccagtaa ccagtagctt tatccagagt agcccgaaca accggaacac
     4921 taccggcaac aggtgttcga acgaactgag actccagata atcgccttca cgcacgataa
     4981 tccggcctcg aaccggcata ctgacacccg ttttactgtc agcagcttta atcaaagtgg
     5041 ccagatcagg taatgacagt gcatcacccg gcatcagccc gctgatgtca cgtccgggca
     5101 ccacatcact gccaatacca acatcacgtg accaaaacag ccctacagca gttgccacca
     5161 cgggaccaac aagactcgca ccggcaatac ctcgcagttt agccatcacc tcagcaatct
     5221 gcgtccaggc tttccctgca gtaacactat ccagcgatat accaccaagt gatgcaacgg
     5281 cccaggaaat gggtgacgct gcaggcgatg ccgtagacgg gatcccgcga acagactgaa
     5341 tatctgtgga tttcagctta tctgctgctg cctgacgctc ctgcatcagc ctggcttttt
     5401 ccgctgccgc acgcgcttcc tctgctgctt ttgctactgc gtctgcctga cgttttttct
     5461 cagcagcagc tgctgcagcc gcctcagctt cctgccgctt acgttcagca gcagcagcct
     5521 gttcagcaga atttaacgcc gcctgagcag cctgacggcg cgtttctgcc gcattatagg
     5581 cagctgtagc tttcaggctg tcctgttctg ctgctgttgc ctgactggca agactggtag
     5641 cctgatttcg cttattcaca gcatcgctct gcgccacatc aacctgagct ttggtaattc
     5701 cggatggata aaacctgtat ccccagtgat catgctcctt attagagcca attatttccc
     5761 atttttccgt accatactca cca
//
