LOCUS       NZ_CP056376             5783 bp    DNA     circular CON 15-MAY-2024
DEFINITION  Klebsiella pneumoniae strain RHBSTW-00636 plasmid pRHBSTW-00636_5,
            complete sequence.
ACCESSION   NZ_CP056376
VERSION     NZ_CP056376.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN15148670
            Assembly: GCF_013734035.1
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 T2-00636
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 68.2714513388374x
            Sequencing Technology :: Hybrid: Illumina and OXFORD_NANOPORE
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_013734035.1-RS_2024_05_15
            Annotation Date                   :: 05/15/2024 03:00:32
            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)                     :: 5,797
            CDSs (total)                      :: 5,674
            Genes (coding)                    :: 5,493
            CDSs (with protein)               :: 5,493
            Genes (RNA)                       :: 123
            rRNAs                             :: 9, 8, 8 (5S, 16S, 23S)
            complete rRNAs                    :: 9, 8, 8 (5S, 16S, 23S)
            tRNAs                             :: 87
            ncRNAs                            :: 11
            Pseudo Genes (total)              :: 181
            CDSs (without protein)            :: 181
            Pseudo Genes (ambiguous residues) :: 0 of 181
            Pseudo Genes (frameshifted)       :: 65 of 181
            Pseudo Genes (incomplete)         :: 122 of 181
            Pseudo Genes (internal stop)      :: 19 of 181
            Pseudo Genes (multiple problems)  :: 23 of 181
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP056376.1.
            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-00636"
                     /isolation_source="Wastewater influent sample"
                     /db_xref="taxon:573"
                     /plasmid="pRHBSTW-00636_5"
                     /geo_loc_name="United Kingdom"
                     /collection_date="2017"
     gene            196..387
                     /locus_tag="HV253_RS28675"
                     /old_locus_tag="HV253_28680"
     CDS             196..387
                     /locus_tag="HV253_RS28675"
                     /old_locus_tag="HV253_28680"
                     /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            387..809
                     /locus_tag="HV253_RS28680"
                     /old_locus_tag="HV253_28685"
     CDS             387..809
                     /locus_tag="HV253_RS28680"
                     /old_locus_tag="HV253_28685"
                     /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            1925..4267
                     /locus_tag="HV253_RS28685"
                     /old_locus_tag="HV253_28690"
     CDS             1925..4267
                     /locus_tag="HV253_RS28685"
                     /old_locus_tag="HV253_28690"
                     /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            4278..4541
                     /locus_tag="HV253_RS28690"
                     /old_locus_tag="HV253_28695"
     CDS             4278..4541
                     /locus_tag="HV253_RS28690"
                     /old_locus_tag="HV253_28695"
                     /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            4723..4980
                     /locus_tag="HV253_RS28695"
                     /old_locus_tag="HV253_28700"
     CDS             4723..4980
                     /locus_tag="HV253_RS28695"
                     /old_locus_tag="HV253_28700"
                     /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            5088..5243
                     /locus_tag="HV253_RS28700"
                     /old_locus_tag="HV253_28705"
     CDS             5088..5243
                     /locus_tag="HV253_RS28700"
                     /old_locus_tag="HV253_28705"
                     /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(5449..5563)
                     /locus_tag="HV253_RS28855"
                     /pseudo=""
     CDS             complement(5449..5563)
                     /locus_tag="HV253_RS28855"
                     /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"
     Typing          complement(5450..5783)
                     /name="ColRNAI_rep_cluster_1987"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="97.313"
                     /coverage="81.0"
                     /evalue="2.79e-159"
ORIGIN
        1 gcggagccta tggaaaaacg gccgctgtgc ggcctctcct tctccccatc acgcgatcgc
       61 tcggttttct cgagctttta tacgcatgct cctgccgctc gccgcagccg aacggcagga
      121 gcgtagcgac tgagtgagcg aggaagcgga aaagagaaca tccctacact gagcactgac
      181 gctctgaggc ctcttatgac gaaacaacag aaaacagcgc tgaacatggc taaattcatc
      241 cagaatcagt ctctgctcct gctggagaag cttaacgagc ttgatctcga tgtcgaggcc
      301 gacctttgtg agaaactcca cgatgatgcg gagcatcttt tccgtacact gtcctcgaga
      361 ctggatgaat tacaggatgg taactgatgg ccagagtgtc tattagtgaa gcggcacggc
      421 ttgttaaggt tagtcgtcct acaatttaca agatgattaa cagtgggaag ttaagttaca
      481 cctctgttgt aaagcacggg aaggctatta aagttattga tacttctgag cttattagag
      541 tgtttggttc tcttgatggt gtaatcgata ctgtaaaata tgatgtaaaa agtgacgcag
      601 aatctacagg tattaacagc gttggtttac atgatttaca acatagaatc gctttacttg
      661 aagctgaaaa cgatggtctt aaaggggctg ttaaggctcg agatgagcat attgattccc
      721 ttcgtcaggc tatgcagctt ctggagcaca agcacgaacc ttcttcacca ccccattccc
      781 cgtggtggaa attctggaaa aaatcctgac cccatcatgc ttcagttttc ctctccggcc
      841 attccgggga gttcctgaac cttccaaaaa atcgccagat ctctgaacgc tcctcaccac
      901 taaaaatacc cacacactac gcaaaattaa aattttgcag attctttatt taaaacaatt
      961 ggttaatgaa aaattaatgt gcagtgatgt gttacaaagt gcagatccaa gtcgtggacg
     1021 actctatggc gaatcgttta cgaattgccc acgattcata tgtgaatcac gctttattat
     1081 catgttgtta tgatgaatcg actcttgatt caattcatca atttgggcgt tttttgttca
     1141 tggtgactct tgattcaatt cacgattcga atcgccggtg aatcgtgtgg tgagtcgtcc
     1201 ggcgacttgc cataacgtga ttgccggccg tcgacgaacc cgattcctga acgtgctgaa
     1261 aaccggtttt ccggctgcgc cggcaacgcc tcacggccac gcaataaatt gcgtccccgt
     1321 tcaccgtttt cggatcagaa gaacgccgga aacaggactt accctggctg aatggcgtga
     1381 atttccgcgc tatgcacttg cgcgcatact catgcatgcc gtaaaaacag agcctgcgcg
     1441 tttctggcgg gttttcgggt ggtttgttgc ctgttttacc ggtttcccgt cagaaacgcc
     1501 ctgaggccgt tttagcggtg cgtacaatta agggattatg gtaaatgggg gcgctcgggt
     1561 ggcggaatac cctctacacc aagacttttt gtacaggtct ctgtccgtca gtcacaccct
     1621 ttttaagagc acatatcgtt aatttttttt ctctgccgag ccgcgtcctg tctgggtttt
     1681 gtcatttcta ttacgcttaa cttaatgaaa attcaaaaga taattgtatc tctccgcgtg
     1741 ttgacagagt tctcatgtca ggagtagtat tcaagtactg tatataaaca catgtattta
     1801 tatacagtac ttggtgtggc agagaactaa taacagcctc cggatacagg ttcgaaggcg
     1861 ataaaccgca caccagattc tgacaagcag gaaaacgata aaaataacaa caaaggagag
     1921 agttatgggt ggtggattta actataacgg ggaaggtgct actggcaccg gattggatcg
     1981 tgatccatat gttcgcgaca gcaatggtaa tgctattggt gttaaatcag gctatcacgc
     2041 ggagtcctat gggacctcaa gtccagcctt agggcctaat ggcgctattc agattactgc
     2101 tggggttatt gctgtgcctg gagataagcc ccgacctgac ggtggtagtg gtggtgggaa
     2161 tactgttaac accggaccgg caggacagct cctggtgatg aataaaggtc agcttggata
     2221 ctgggaaact cgttctacgg gcgcgggtaa caatgagcat aatacgagtg tatttgttgc
     2281 cgtaggtcct tctgaggcag aaaaaactgc ttctgcagag aaggcgttaa aggaaaaaca
     2341 gcaggcagaa gcagcagcaa aagactttgc ggctaaaact gctgccgcat cagccacggc
     2401 ggaaaaagaa cgccagcagg caattgctgc tgcaactgca gcgggtcagc atcagtcagt
     2461 ttctgatgcc cgtaatagcc tgaataacgc gacgtcagat gtgtctcgtc tgaaatcagc
     2521 tgcagacagt gcactgcagg aggcaaaggc aaaacggaag gctgctattg atgctgtacc
     2581 tgttgcaacc caggcggaaa ataaatatca ggagctgcag cagaagatta aaggcctgaa
     2641 gctgaaaaat ggtgagtatg gtacggaaaa atgggaaata attggctcta ataaggagca
     2701 tgatcactgg ggatacaggt tttatccatc cggaattacc aaagctcagg ttgatgtggc
     2761 gcagagcgat gctgtgaata agcgaaatca ggctaccagt cttgccagtc aggcaacagc
     2821 agcagaacag gacagcctga aagctacagc tgcctataat gcggcagaaa cgcgccgtca
     2881 ggctgctcag gcggcgttaa attctgctga acaggctgct gctgctgaac gtaagcggca
     2941 ggaagctgag gcggctgcag cagctgctgc tgagaaaaaa cgtcaggcag acgcagtagc
     3001 aaaagcagca gaggaagcgc gtgcggcagc ggaaaaagcc aggctgatgc aggagcgtca
     3061 ggcagcagca gataagctga aatccacaga tattcagtct gttcgcggga tcccgtctac
     3121 ggcatcgcct gcagcgtcac ccatttcctg ggccgttgca tcacttggtg gtatatcgct
     3181 ggatagtgtt actgcaggga aagcctggac gcagattgct gaggtgatgg ctaaactgcg
     3241 aggtattgcc ggtgcgagtc ttgttggtcc cgtggtggca actgctgtag ggctgttttg
     3301 gtcacgtgat gttggtattg gcagtgatgt ggtgcccgga cgtgacatca gcgggctgat
     3361 gccgggtgat gcactgtcat tacctgatct ggccactttg attaaagctg ctgacagtaa
     3421 aacgggtgtc agtatgccgg ttcgaggccg gattatcgtg cgtgaaggcg attatctgga
     3481 gtctcagttc gttcgaacac ctgttgccgg tagtgttccg gttgttcggg ctactctgga
     3541 taaagctact ggttactggg gatatacgtt gccggcgata cagggcgtgc ccggacagac
     3601 aatactggta agtccgtcag atgcgccggg cgttaatgct cctctgggac ttgctgggcc
     3661 ggttcctttg cctgaaacta ttatacatac cggtgggcaa actacggtcc ctcagggggg
     3721 gactgtgaca gtatctcctg ttattggtga agttgatttt cgagatctta tccttgtttt
     3781 ccctcctgag tcagggttaa agccgttata tgtgatgcca gttagccctt atggagatgc
     3841 aacagaaaaa ggcgagcaca gcggaagacc ttataatccg gataaggcag gtggtcctgt
     3901 acagaatctt aactggcgta gtgcagtcat caacaaggcc gggattgata aggtgaagct
     3961 acataccggt cgctttggtg aatcagcagc aaacaaagta atgatcgacc gtctggagaa
     4021 aatcctgagc ggtcagttac aggtaactga tacggacaag cggttttaca cccatgaact
     4081 cagagagctg gaacgttatc gtgctttagg ggtccctgat aatgtgaagc cagatgataa
     4141 aggtgttacg tggaataaca ctcatacagc aacgctggaa gattataaaa ttaatgaaaa
     4201 aactgatccg ctctatacaa aggatgctga agaggcagag tataaagcag agctaaaaaa
     4261 taaatgaggg ggagagaatg agtaatccga ttgaagacat cattaaaaat gaatcggtaa
     4321 gtgatgtgct tcgctacttt ggtcctggtc gcgacatttc aaaaattgac cgtatgtatg
     4381 tttcatataa gtttgaagtg atctctgaag gcgttctttt atctgaatac aaaaagttat
     4441 tcgacaatgg agaactaaag tatgactcta ataaaaatgt tattaagggg cctaactgga
     4501 aagagcctgc ttttgtaaca caaaaaaaat acggcattta aagtgtgcat atgaagccct
     4561 ttgaaaagag ggctttgatt aaagctcaca tatgaaaagg gtttcttttt tgagtggtcg
     4621 tggtttcgat gatactggca gcatgtcagg tcaacaatat ctggggtaag ctgagtgcat
     4681 taaaacctaa acgccatatt gaaatccata atgggaactg aaatggctaa taaaactttg
     4741 gctgactata cagagcagga atttattgag tttatcgaaa aaattaaaaa agcagacttt
     4801 gctactgagt ctgagcatga tgaggccatt tatgagttca gccagttgac tgaacatcca
     4861 gatggttggg atcttattta tcatcctcaa gcaggagccg ataactctcc tgctggtgtt
     4921 gtaaaaacag taaaagagtg gcgagcagct aacggtaagc caggttttaa aaaatcgtga
     4981 ttgaatgtgc gggttcaagt gatgaatccg cacattttta actctggatt tgaataataa
     5041 ttactaggta tccatttgct tagaataata aaaataaaag gtgatatatg aaaaaattac
     5101 ttttcctggg ggttgttacc gtttctgtgg ttctggcggc atgtcaggtc aataatgttc
     5161 gtgacaccgg aggtggggct gtttcacctt catcgacggt gaccggagtc acgcttgata
     5221 gcggtacgaa cggcaatccg taaaggatct tcttgagatc ccatttggat cgtcgtaatc
     5281 tcttgctctg taaacgaaaa aaccgccttg gcgggcggtt tttcgaaggt tccaagagtt
     5341 ggcgctcttt gaaccgaggt aactggctta tgaggagcac agtaaccaaa acttgttctt
     5401 tcagtttagc cttaaccggc gcataacttc aagactaact cctctaaatc agttaccagt
     5461 ggctgctgcc agtggtgctt ttgcatgtct taccgggttg gactcaagat gatagttacc
     5521 ggatcaaggc gcagcagtcg gactgaacgg ggggttcgtg catacagtcc agcttggagc
     5581 gaactgccta cccggaactg agtgtcaggc gtggaatgag ataaacgcgg ccataacagc
     5641 ggaatgacac cggtaaaccg aatggcagga acaggagagc gcacgaggga gccatcaggg
     5701 ggaaacgcct ggtatcttta tagtcctgtc gggtttcgcc accactgatt tgagcgtcaa
     5761 attctgtgat gcttgtcagg ggg
//
