LOCUS       NZ_CP056429             5783 bp    DNA     circular CON 25-FEB-2024
DEFINITION  Klebsiella pneumoniae strain RHBSTW-00515 plasmid pRHBSTW-00515_5,
            complete sequence.
ACCESSION   NZ_CP056429
VERSION     NZ_CP056429.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN15148644
            Assembly: GCF_013735895.1
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                     :: WTP1 T2-00515
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 92.2829444239567x
            Sequencing Technology :: Hybrid: Illumina and OXFORD_NANOPORE
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 02/25/2024 08:16:29
            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)                     :: 5,893
            CDSs (total)                      :: 5,768
            Genes (coding)                    :: 5,598
            CDSs (with protein)               :: 5,598
            Genes (RNA)                       :: 125
            rRNAs                             :: 9, 8, 8 (5S, 16S, 23S)
            complete rRNAs                    :: 9, 8, 8 (5S, 16S, 23S)
            tRNAs                             :: 90
            ncRNAs                            :: 10
            Pseudo Genes (total)              :: 170
            CDSs (without protein)            :: 170
            Pseudo Genes (ambiguous residues) :: 0 of 170
            Pseudo Genes (frameshifted)       :: 71 of 170
            Pseudo Genes (incomplete)         :: 106 of 170
            Pseudo Genes (internal stop)      :: 28 of 170
            Pseudo Genes (multiple problems)  :: 31 of 170
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP056429.1.
            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-00515"
                     /isolation_source="Wastewater influent sample"
                     /db_xref="taxon:573"
                     /plasmid="pRHBSTW-00515_5"
                     /geo_loc_name="United Kingdom"
                     /collection_date="2017"
     gene            join(3824..5783,1..383)
                     /locus_tag="HV227_RS29190"
                     /old_locus_tag="HV227_29220"
     CDS             join(3824..5783,1..383)
                     /locus_tag="HV227_RS29190"
                     /old_locus_tag="HV227_29220"
                     /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="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            394..657
                     /locus_tag="HV227_RS29195"
                     /old_locus_tag="HV227_29195"
     CDS             394..657
                     /locus_tag="HV227_RS29195"
                     /old_locus_tag="HV227_29195"
                     /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"
     gene            839..1096
                     /locus_tag="HV227_RS29200"
                     /old_locus_tag="HV227_29200"
     CDS             839..1096
                     /locus_tag="HV227_RS29200"
                     /old_locus_tag="HV227_29200"
                     /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            1204..1359
                     /locus_tag="HV227_RS29205"
                     /old_locus_tag="HV227_29205"
     CDS             1204..1359
                     /locus_tag="HV227_RS29205"
                     /old_locus_tag="HV227_29205"
                     /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(1565..1679)
                     /locus_tag="HV227_RS29315"
                     /pseudo=""
     CDS             complement(1565..1679)
                     /locus_tag="HV227_RS29315"
                     /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            2095..2286
                     /locus_tag="HV227_RS29210"
                     /old_locus_tag="HV227_29210"
     CDS             2095..2286
                     /locus_tag="HV227_RS29210"
                     /old_locus_tag="HV227_29210"
                     /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            2286..2708
                     /locus_tag="HV227_RS29215"
                     /old_locus_tag="HV227_29215"
     CDS             2286..2708
                     /locus_tag="HV227_RS29215"
                     /old_locus_tag="HV227_29215"
                     /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"
     Typing          complement(1566..1974)
                     /name="ColRNAI_rep_cluster_1987"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="96.341"
                     /coverage="99.0"
                     /evalue="0.0"
ORIGIN
        1 aggcaggtgg tcctgtacag aatcttaact ggcgtagtgc agtcatcaac aaggccggga
       61 ttgataaggt gaagctacat accggtcgct ttggtgaatc agcagcaaac aaagtaatga
      121 tcgaccgtct ggagaaaatc ctgagcggtc agttacaggt aactgatacg gacaagcggt
      181 tttacaccca tgaactcaga gagctggaac gttatcgtgc tttaggggtc cctgataatg
      241 tgaagccaga tgataaaggt gttacgtgga ataacactca tacagcaacg ctggaagatt
      301 ataaaattaa tgaaaaaact gatccgctct atacaaagga tgctgaagag gcagagtata
      361 aagcagagct aaaaaataaa tgagggggag agaatgagta atccgattga agacatcatt
      421 aaaaatgaat cggtaagtga tgtgcttcgc tactttggtc ctggtcgcga catttcaaaa
      481 attgaccgta tgtatgtttc atataagttt gaagtgatct ctgaaggcgt tcttttatct
      541 gaatacaaaa agttattcga caatggagaa ctaaagtatg actctaataa aaatgttatt
      601 aaggggccta actggaaaga gcctgctttt gtaacacaaa aaaaatacgg catttaaagt
      661 gtgcatatga agccctttga aaagagggct ttgattaaag ctcacatatg aaaagggttt
      721 cttttttgag tggtcgtggt ttcgatgata ctggcagcat gtcaggtcaa caatatctgg
      781 ggtaagctga gtgcattaaa acctaaacgc catattgaaa tccataatgg gaactgaaat
      841 ggctaataaa actttggctg actatacaga gcaggaattt attgagttta tcgaaaaaat
      901 taaaaaagca gactttgcta ctgagtctga gcatgatgag gccatttatg agttcagcca
      961 gttgactgaa catccagatg gttgggatct tatttatcat cctcaagcag gagccgataa
     1021 ctctcctgct ggtgttgtaa aaacagtaaa agagtggcga gcagctaacg gtaagccagg
     1081 ttttaaaaaa tcgtgattga atgtgcgggt tcaagtgatg aatccgcaca tttttaactc
     1141 tggatttgaa taataattac taggtatcca tttgcttaga ataataaaaa taaaaggtga
     1201 tatatgaaaa aattactttt cctgggggtt gttaccgttt ctgtggttct ggcggcatgt
     1261 caggtcaata atgttcgtga caccggaggt ggggctgttt caccttcatc gacggtgacc
     1321 ggagtcacgc ttgatagcgg tacgaacggc aatccgtaaa ggatcttctt gagatcccat
     1381 ttggatcgtc gtaatctctt gctctgtaaa cgaaaaaacc gccttggcgg gcggtttttc
     1441 gaaggttcca agagttggcg ctctttgaac cgaggtaact ggcttatgag gagcacagta
     1501 accaaaactt gttctttcag tttagcctta accggcgcat aacttcaaga ctaactcctc
     1561 taaatcagtt accagtggct gctgccagtg gtgcttttgc atgtcttacc gggttggact
     1621 caagatgata gttaccggat caaggcgcag cagtcggact gaacgggggg ttcgtgcata
     1681 cagtccagct tggagcgaac tgcctacccg gaactgagtg tcaggcgtgg aatgagataa
     1741 acgcggccat aacagcggaa tgacaccggt aaaccgaatg gcaggaacag gagagcgcac
     1801 gagggagcca tcagggggaa acgcctggta tctttatagt cctgtcgggt ttcgccacca
     1861 ctgatttgag cgtcaaattc tgtgatgctt gtcagggggg cggagcctat ggaaaaacgg
     1921 ccgctgtgcg gcctctcctt ctccccatca cgcgatcgct cggttttctc gagcttttat
     1981 acgcatgctc ctgccgctcg ccgcagccga acggcaggag cgtagcgact gagtgagcga
     2041 ggaagcggaa aagagaacat ccctacactg agcactgacg ctctgaggcc tcttatgacg
     2101 aaacaacaga aaacagcgct gaacatggct aaattcatcc agaatcagtc tctgctcctg
     2161 ctggagaagc ttaacgagct tgatctcgat gtcgaggccg acctttgtga gaaactccac
     2221 gatgatgcgg agcatctttt ccgtacactg tcctcgagac tggatgaatt acaggatggt
     2281 aactgatggc cagagtgtct attagtgaag cggcacggct tgttaaggtt agtcgtccta
     2341 caatttacaa gatgattaac agtgggaagt taagttacac ctctgttgta aagcacggga
     2401 aggctattaa agttattgat acttctgagc ttattagagt gtttggttct cttgatggtg
     2461 taatcgatac tgtaaaatat gatgtaaaaa gtgacgcaga atctacaggt attaacagcg
     2521 ttggtttaca tgatttacaa catagaatcg ctttacttga agctgaaaac gatggtctta
     2581 aaggggctgt taaggctcga gatgagcata ttgattccct tcgtcaggct atgcagcttc
     2641 tggagcacaa gcacgaacct tcttcaccac cccattcccc gtggtggaaa ttctggaaaa
     2701 aatcctgacc ccatcatgct tcagttttcc tctccggcca ttccggggag ttcctgaacc
     2761 ttccaaaaaa tcgccagatc tctgaacgct cctcaccact aaaaataccc acacactacg
     2821 caaaattaaa attttgcaga ttctttattt aaaacaattg gttaatgaaa aattaatgtg
     2881 cagtgatgtg ttacaaagtg cagatccaag tcgtggacga ctctatggcg aatcgtttac
     2941 gaattgccca cgattcatat gtgaatcacg ctttattatc atgttgttat gatgaatcga
     3001 ctcttgattc aattcatcaa tttgggcgtt ttttgttcat ggtgactctt gattcaattc
     3061 acgattcgaa tcgccggtga atcgtgtggt gagtcgtccg gcgacttgcc ataacgtgat
     3121 tgccggccgt cgacgaaccc gattcctgaa cgtgctgaaa accggttttc cggctgcgcc
     3181 ggcaacgcct cacggccacg caataaattg cgtccccgtt caccgttttc ggatcagaag
     3241 aacgccggaa acaggactta ccctggctga atggcgtgaa tttccgcgct atgcacttgc
     3301 gcgcatactc atgcatgccg taaaaacaga gcctgcgcgt ttctggcggg ttttcgggtg
     3361 gtttgttgcc tgttttaccg gtttcccgtc agaaacgccc tgaggccgtt ttagcggtgc
     3421 gtacaattaa gggattatgg taaatggggg cgctcgggtg gcggaatacc ctctacacca
     3481 agactttttg tacaggtctc tgtccgtcag tcacaccctt tttaagagca catatcgtta
     3541 attttttttc tctgccgagc cgcgtcctgt ctgggttttg tcatttctat tacgcttaac
     3601 ttaatgaaaa ttcaaaagat aattgtatct ctccgcgtgt tgacagagtt ctcatgtcag
     3661 gagtagtatt caagtactgt atataaacac atgtatttat atacagtact tggtgtggca
     3721 gagaactaat aacagcctcc ggatacaggt tcgaaggcga taaaccgcac accagattct
     3781 gacaagcagg aaaacgataa aaataacaac aaaggagaga gttatgggtg gtggatttaa
     3841 ctataacggg gaaggtgcta ctggcaccgg attggatcgt gatccatatg ttcgcgacag
     3901 caatggtaat gctattggtg ttaaatcagg ctatcacgcg gagtcctatg ggacctcaag
     3961 tccagcctta gggcctaatg gcgctattca gattactgct ggggttattg ctgtgcctgg
     4021 agataagccc cgacctgacg gtggtagtgg tggtgggaat actgttaaca ccggaccggc
     4081 aggacagctc ctggtgatga ataaaggtca gcttggatac tgggaaactc gttctacggg
     4141 cgcgggtaac aatgagcata atacgagtgt atttgttgcc gtaggtcctt ctgaggcaga
     4201 aaaaactgct tctgcagaga aggcgttaaa ggaaaaacag caggcagaag cagcagcaaa
     4261 agactttgcg gctaaaactg ctgccgcatc agccacggcg gaaaaagaac gccagcaggc
     4321 aattgctgct gcaactgcag cgggtcagca tcagtcagtt tctgatgccc gtaatagcct
     4381 gaataacgcg acgtcagatg tgtctcgtct gaaatcagct gcagacagtg cactgcagga
     4441 ggcaaaggca aaacggaagg ctgctattga tgctgtacct gttgcaaccc aggcggaaaa
     4501 taaatatcag gagctgcagc agaagattaa aggcctgaag ctgaaaaatg gtgagtatgg
     4561 tacggaaaaa tgggaaataa ttggctctaa taaggagcat gatcactggg gatacaggtt
     4621 ttatccatcc ggaattacca aagctcaggt tgatgtggcg cagagcgatg ctgtgaataa
     4681 gcgaaatcag gctaccagtc ttgccagtca ggcaacagca gcagaacagg acagcctgaa
     4741 agctacagct gcctataatg cggcagaaac gcgccgtcag gctgctcagg cggcgttaaa
     4801 ttctgctgaa caggctgctg ctgctgaacg taagcggcag gaagctgagg cggctgcagc
     4861 agctgctgct gagaaaaaac gtcaggcaga cgcagtagca aaagcagcag aggaagcgcg
     4921 tgcggcagcg gaaaaagcca ggctgatgca ggagcgtcag gcagcagcag ataagctgaa
     4981 atccacagat attcagtctg ttcgcgggat cccgtctacg gcatcgcctg cagcgtcacc
     5041 catttcctgg gccgttgcat cacttggtgg tatatcgctg gatagtgtta ctgcagggaa
     5101 agcctggacg cagattgctg aggtgatggc taaactgcga ggtattgccg gtgcgagtct
     5161 tgttggtccc gtggtggcaa ctgctgtagg gctgttttgg tcacgtgatg ttggtattgg
     5221 cagtgatgtg gtgcccggac gtgacatcag cgggctgatg ccgggtgatg cactgtcatt
     5281 acctgatctg gccactttga ttaaagctgc tgacagtaaa acgggtgtca gtatgccggt
     5341 tcgaggccgg attatcgtgc gtgaaggcga ttatctggag tctcagttcg ttcgaacacc
     5401 tgttgccggt agtgttccgg ttgttcgggc tactctggat aaagctactg gttactgggg
     5461 atatacgttg ccggcgatac agggcgtgcc cggacagaca atactggtaa gtccgtcaga
     5521 tgcgccgggc gttaatgctc ctctgggact tgctgggccg gttcctttgc ctgaaactat
     5581 tatacatacc ggtgggcaaa ctacggtccc tcaggggggg actgtgacag tatctcctgt
     5641 tattggtgaa gttgattttc gagatcttat ccttgttttc cctcctgagt cagggttaaa
     5701 gccgttatat gtgatgccag ttagccctta tggagatgca acagaaaaag gcgagcacag
     5761 cggaagacct tataatccgg ata
//
