LOCUS       NZ_CP058124             5499 bp    DNA     circular CON 09-APR-2024
DEFINITION  Klebsiella michiganensis strain RHBSTW-00167 plasmid
            pRHBSTW-00167_7, complete sequence.
ACCESSION   NZ_CP058124
VERSION     NZ_CP058124.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN15148522
            Assembly: GCF_013624375.1
KEYWORDS    RefSeq.
SOURCE      Klebsiella michiganensis
  ORGANISM  Klebsiella michiganensis
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Klebsiella/Raoultella group; Klebsiella.
REFERENCE   1  (bases 1 to 5499)
  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 5499)
  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 T1-00167
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 69.9496584429644x
            Sequencing Technology :: Hybrid: Illumina and PACBIO_SMRT
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_013624375.1-RS_2024_04_08
            Annotation Date                   :: 04/08/2024 10:24:09
            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)                     :: 6,406
            CDSs (total)                      :: 6,284
            Genes (coding)                    :: 6,107
            CDSs (with protein)               :: 6,107
            Genes (RNA)                       :: 122
            rRNAs                             :: 9, 8, 8 (5S, 16S, 23S)
            complete rRNAs                    :: 9, 8, 8 (5S, 16S, 23S)
            tRNAs                             :: 86
            ncRNAs                            :: 11
            Pseudo Genes (total)              :: 177
            CDSs (without protein)            :: 177
            Pseudo Genes (ambiguous residues) :: 0 of 177
            Pseudo Genes (frameshifted)       :: 57 of 177
            Pseudo Genes (incomplete)         :: 135 of 177
            Pseudo Genes (internal stop)      :: 31 of 177
            Pseudo Genes (multiple problems)  :: 42 of 177
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP058124.1.
            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..5499
                     /organism="Klebsiella michiganensis"
                     /mol_type="genomic DNA"
                     /strain="RHBSTW-00167"
                     /isolation_source="Freshwater sample from upstream of
                     wastewater treatment plant"
                     /db_xref="taxon:1134687"
                     /plasmid="pRHBSTW-00167_7"
                     /geo_loc_name="United Kingdom"
                     /collection_date="2017"
     gene            join(5289..5499,1..41)
                     /locus_tag="HV105_RS31675"
                     /old_locus_tag="HV105_31675"
     CDS             join(5289..5499,1..41)
                     /locus_tag="HV105_RS31675"
                     /old_locus_tag="HV105_31675"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001676877.1"
                     /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 transcriptional regulator"
                     /protein_id="WP_214680577.1"
                     /translation="MNKINREKFGQIIGNRLRITRCQHGLSQTDLQNITGIDRATLSRI
                     ENGQQQISLFQLLQVLKALQVKPELFLKGIEVNNEDYD"
                     /name="helix-turn-helix transcriptional regulator"
     gene            25..906
                     /locus_tag="HV105_RS31680"
     CDS             25..906
                     /locus_tag="HV105_RS31680"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_015836029.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_080816743.1"
                     /translation="MKTTIELDDGFFPGDISNKIRSTICSSLEGITTDGKKFVINDKIF
                     FRKQKDGNIKPCVMNSASYISKLFQKNLSGYNGCQGETKLLDQSFDGLMRINYSGLSYK
                     LKEEKDVIDVAKEYIELQGLHKSAIYNLFPMFYGMYIDRGCFSIPTLPKTQHLFKSSNV
                     DHIYTIGVEFETGNVSSSFRAINKLNNLFQQGAIDGGCFITSIDKANSATRIWPASNRN
                     GSFQELKQRFYKNQIALPLVGIGFAPDDFSQEVGFLSNTGSIYFLERKKLNDQKTGLAV
                     YQDDEGREFFSV"
                     /name="hypothetical protein"
     gene            complement(1713..2196)
                     /locus_tag="HV105_RS31685"
                     /old_locus_tag="HV105_31680"
                     /pseudo=""
     CDS             complement(1713..2196)
                     /locus_tag="HV105_RS31685"
                     /old_locus_tag="HV105_31680"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000135004.1"
                     /note="frameshifted; Derived by automated computational
                     analysis using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="helix-turn-helix domain-containing protein"
                     /name="helix-turn-helix domain-containing protein"
     gene            complement(2177..2405)
                     /locus_tag="HV105_RS31690"
                     /old_locus_tag="HV105_31685"
                     /pseudo=""
     CDS             complement(2177..2405)
                     /locus_tag="HV105_RS31690"
                     /old_locus_tag="HV105_31685"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000166328.1"
                     /note="frameshifted; Derived by automated computational
                     analysis using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="Rop family plasmid primer RNA-binding protein"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            complement(2845..3039)
                     /locus_tag="HV105_RS32210"
     CDS             complement(2845..3039)
                     /locus_tag="HV105_RS32210"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001041614.1"
                     /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_228761940.1"
                     /translation="MAKFIRDQSLLPVDRLNELDLDHEADFWTQDDALPDKTQQSDHER
                     GFVQVDPVQLGANCLTRLN"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            complement(3909..5162)
                     /locus_tag="HV105_RS31700"
                     /old_locus_tag="HV105_31695"
     CDS             complement(3909..5162)
                     /locus_tag="HV105_RS31700"
                     /old_locus_tag="HV105_31695"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001676879.1"
                     /GO_function="GO:0003677 - DNA binding [Evidence IEA];
                     GO:0008170 - N-methyltransferase activity [Evidence IEA]"
                     /GO_process="GO:0006306 - DNA methylation [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="DNA methyltransferase"
                     /protein_id="WP_128306716.1"
                     /translation="MSYSDQFLRALGELGEAGRAYRSISKKTGIPVDRLKYYNKKNIIP
                     SGKDLQALHDAYNISELYFQIAMGHLDMNALEVIQQNADEVFSLLSSLKKDSHVSTSKT
                     KLDSVLKTKHGTLYQGDCIDVARNITSDSVDMIFADPPFNLDKLYPSKMDDNLKEEEYL
                     KWTQSWLSECIRILKPGGSLFLWNLPVWNSKISSFLHGRLNFRHWIATDIKYSLPIQGR
                     LYPSHYSLMYFVKGEKPNYFSPDRLPAQVCPKCYSDLKDYGGYKNKMNPLGVSLTDVWF
                     DIPPVRHKKYKKRDGSNELSIKLLDRIIEMSTKEGDLVFDPFGGSGTTYAVSEIKKRNW
                     IGSEIDSCEIIKERFINIDMERDYLNEIRSKINSLFPDFIKKQRESRGLWTDETFSKQE
                     VKLEKKASEQFGFFDEEK"
                     /name="DNA methyltransferase"
     Typing          3377..3841
                     /name="rep_cluster_2358"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="82.365"
                     /coverage="89.0"
                     /evalue="2.36e-106"
ORIGIN
        1 ttttaaaagg aattgaagtc aacaatgaag actacgattg aactcgatga cggttttttc
       61 cctggagata tatcaaacaa aatacgcagc actatatgct cttctctcga aggaataact
      121 acagatggga aaaaattcgt aataaatgac aaaatatttt tccgaaagca gaaagacggc
      181 aacataaaac catgcgtaat gaattcagca agttatatat ctaagctttt ccagaaaaac
      241 ttatctggct ataacggatg ccaaggtgag acaaaactcc ttgatcagag ttttgatggg
      301 ttaatgagaa ttaattattc tggattatct tataaattaa aagaagaaaa agatgtaatt
      361 gatgtagcaa aagaatatat agagttacag ggcttgcata aaagtgccat ttacaattta
      421 tttcctatgt tttatgggat gtatatagat agaggttgct ttagtatccc tacgctacct
      481 aaaactcaac atcttttcaa atcgagcaat gtagatcata tatacacaat tggtgttgaa
      541 ttcgaaactg gtaacgtttc aagctctttc agggcaataa ataaacttaa caacctattc
      601 cagcaagggg caatagatgg cgggtgcttt ataactagca ttgacaaagc aaactctgcc
      661 accaggatat ggccagccag caatagaaat ggttcgttcc aagaattaaa gcaaagattt
      721 tataaaaatc aaatcgccct tcctctagta ggcataggtt ttgcaccaga cgacttctct
      781 caagaagtag gatttttatc taacactgga agtatatatt ttttggagag aaaaaaatta
      841 aatgaccaga aaaccggctt ggccgtttac caagatgatg aaggacgtga atttttttca
      901 gtctaaatta ttttttttta gatattaaat aaacctagcc aatgatttca taggttaacc
      961 attggctggg atgaaaactg aaaaaaaaca aaccttcttc aacctcccgg atttaccata
     1021 acatccgttg cgtgcaccgc ctcagacgct ctcagcgcgt ttctgacggg aaaccggtaa
     1081 aacaggcaac aaaccacccg aaaacccgcc agaaacgcgc aggctctgtt tttacggcat
     1141 gcatgagtat gcacgcaagt gcatagcgcg aaaattcacg ccattcagcc ggggtaagtc
     1201 ctgtttccga tgttcttctt acccgaaaac ggtgaacggg gacgcaattt attgcgtggc
     1261 cgtgaagcgt tgccggcgca gccggaaaac ccgctgtcag cacgttcagg aatcgggttc
     1321 gtcgacggcc ggcaatcacg ttatggcaag tcgccggacg actcaccaca cgattcaccg
     1381 gcgattcgac tcgtgacttg actctagagt caccacggtc atacaaaaac gcccaaagcg
     1441 acgattcgag tcagagtcaa gtcaagttac tgataataaa tgataagtgt cgtcgtgagt
     1501 cgtatgatga atctatggca agtcgtcggc aagtcgtaca cgaatcaccg acgacttgga
     1561 ttgacttaca gaaggtaata ctgcgtaatt taataaaaaa attaaccaat tgttttaaat
     1621 aaggttatct gcaaaatttt aattttgcgt ggtgtgtgtg ggtatttttc gtggtgagga
     1681 gtgttcccgg atctggcgat ttttgggaag gttcaggaac cccgggatgg ccggagagga
     1741 aaactcaagc atggcgggat caggattttt tttttccaga atttccacca cggggaatgg
     1801 gggaatgggg tggtgaagaa ggttcgtgct tgtgctccag aagctgcata gcctgacgaa
     1861 gggaatcaat atgctcatct cgagccttaa cagccccttt aagaccatcg ttttcagctt
     1921 caagtaaagc gattctatgt tgtaaatcat gtaaaccaac gctgttaata cctgtagatt
     1981 ctgcgtcact ttttttacat catattttac agtatcgatg acaccatcaa gagaaccaaa
     2041 cactctaata agctctgatg tatcaataac tttaataccc ttcccgtgct ttacaacaga
     2101 ggtgtaactt aacttaccac tgttaatcat cttgtaaata gtagggcgac taaccttaac
     2161 aagccgtgct gcttcactaa tagacactct ggccatcacc attaccatcc tgtaattcat
     2221 ccagtctcga ggacagtgta cggaaaagat gctccgcatc atcgtggagt ttctcacaaa
     2281 ggtcggcctc agcatcgatc aagatcaagc ttctcagtta actgattctg gatctccagc
     2341 aggagcagag actgattctg gatgaattta gccatgttca gcgctgtttt ctgttgtttc
     2401 gtcataaagg gacctcagag catcagtgct cagtgtaaaa ccggtctctt ttcggatgtc
     2461 gaatggttca gagaacggat ctgaggtaat cctgtttatt ttgtagttta tctgtagtca
     2521 tcgcactaaa aatcaggaca gtcatttttt tgtagtcttt ctgtagttta cctgtagtcc
     2581 ggaaaaataa tccgttcatg cgagcatgaa cggccgttaa ttttttgtca ccgacgcccc
     2641 ctaacctgcg taaatcaccc gccatggttg attatttttc aacctcaaaa tggtggcgaa
     2701 acccgacagg actataatca acttaaaaaa aaataaaaaa aaaaaaaata cgtgggattc
     2761 tgggtattac cgggccattc ggtttaacca atgaaaatta aggccgccgt tatggccgcg
     2821 tttgtctcat tccacgcctg acactcagtt caggcgggtg aggcagttcg ctccaagctg
     2881 gactggatca acttgcacga acccccgttc atgatccgac tgctgcgtct tatccggtaa
     2941 cgcatcatct tgagtccaga aatcagcctc atgatccaga tccagctcat taagcctgtc
     3001 cactggaagc agggactgat cacggatgaa tttagccatg ttaacggcag tctttttgtt
     3061 gtttgttcat gaaggccccg gcgcgaaagt gctttactgt acgttctgat ggttttccgc
     3121 ttcctcgctc attcctggtt cgttcacctc aagtgacctt cggtcaaggc gcgggcgttt
     3181 ataagagcaa tagattacga cgatccaaat gggactcaag aagaataacc tttaacgttc
     3241 gacaagggct atcaagcgtg actccggccg gggaaacagt ttttccggtg tctcgcccct
     3301 gacaggctga catgcccaaa atcacagaaa catcacgaaa atctgacgct caaaccccgg
     3361 tgaggactat ttaaaaaacc cgacaggact ataaagatcc cgggcgtttc ccggcggcgt
     3421 tcctgcaaag ctccctcgtg cgctctcctg ttcctgcctt tgggttttac cggtgtcatt
     3481 ccgctcgcat gttccgcgtt tatctcattc cacgcctgac actcagttcc gggtaggcag
     3541 ttcgctccaa gctggactgt atgcacgaac cccccgttca gtccgactac cacgcccgtt
     3601 ccggtaacta tcaacttgag tccaacccgg aaagacacga caaatcgcca gtggcggtag
     3661 ccattggtag acagaatgtg cgagagatgt atcgagagtt cttgaagtgg tgccctaact
     3721 gaggctacac tggaaggacg aatttggtga cacgtctcgc acaagactgt taccacggtt
     3781 cagaagttcc ccaacttact gaaccttcga aaaaccacct ccccaggtgg ttttttcgtt
     3841 tctgaagata ctcgtttcaa atattatcgt caatgctcgg gttgatgctt accatttcct
     3901 acaaggattt acttctcttc atcaaaaaaa ccaaactgct cgctagcctt tttctctaac
     3961 ttaacctctt gtttagaaaa ggtttcatca gtccacaacc cgcgagactc tcgttgcttt
     4021 ttgataaaat ccgggaacaa agaatttatt tttgatctta tctcatttaa ataatccctt
     4081 tccatgtcaa tattaataaa tctttctttt attatttcac aactatcaat ttctgaccca
     4141 atccagttcc tttttttaat ttcagaaaca gcatatgtag ttcctgaccc accaaaagga
     4201 tcgaaaacaa ggtcaccttc cttagtcgac atctcaataa tcctatctaa aagcttaata
     4261 cttaattcat ttgatccatc ccgtttttta tattttttat gtctcactgg aggtatatca
     4321 aaccaaacat ccgtcaagct gacccctaag ggattcattt tatttttata ccctccataa
     4381 tctttaagat cagaatagca cttaggacaa acttgagcag gaagccgatc tggagaaaaa
     4441 taattaggct tctcaccctt tacaaaatac atcaatgaat agtgagaagg atatagcctt
     4501 ccttgaatag ggaggctata ttttatatca gtagcaatcc aatgcctaaa gttcaatcta
     4561 ccatgtaaga aactagatat tttactattc cacacaggaa gattccataa aaacaaactg
     4621 cctccaggct tgagaatcct tatgcactca cttagccaag attgagtcca ttttaaatat
     4681 tcctcttcct ttaaattatc gtccatttta gaagggtaaa gtttgtccag attaaatggt
     4741 ggatcggcaa aaatcatatc tacactgtcg cttgttatat ttctagcgac gtcaatacaa
     4801 tccccttgat aaagggttcc atgtttcgtt tttagcacgc tatccaattt ggttttgcta
     4861 gttgaaacat gagaatcctt cttcaatgag cttaataaac tgaatacttc atcagcattc
     4921 tgctgaatta cctccagagc attcatatct aaatgcccca tggctatctg aaaatatagc
     4981 tcacttatat tataagcatc gtggagagcc tgaagatctt ttccgctagg tattatgttt
     5041 tttttattat aatactttag cctatcgaca ggaatacctg tttttttact tatcgacctg
     5101 taagctcttc ctgcctcacc taactcgccc aacgctctta aaaactgatc tgaatagctc
     5161 ataaatttct ctgcacattt atcaataaag catacccata ggatctcata tccgtgaaga
     5221 tctgtcactc cctatcaatc cctagattgg tagcattcag cggtccatag gctccaggag
     5281 ctattagatt gaacaaaatc aacagggaaa aatttggcca gatcataggt aatcgcttac
     5341 gcattaccag atgtcaacac ggattaagcc agacagacct tcaaaatata acaggcatag
     5401 atagagccac cttgtctcgc atagagaatg gccaacaaca gatttcgtta tttcaacttc
     5461 ttcaagtttt aaaagctttg caagttaaac ctgaattat
//
