LOCUS       NZ_CP058126             5010 bp    DNA     circular CON 09-APR-2024
DEFINITION  Klebsiella michiganensis strain RHBSTW-00167 plasmid
            pRHBSTW-00167_9, complete sequence.
ACCESSION   NZ_CP058126
VERSION     NZ_CP058126.1
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 5010)
  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 5010)
  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
            CP058126.1.
            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..5010
                     /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_9"
                     /geo_loc_name="United Kingdom"
                     /collection_date="2017"
     gene            join(4588..5010,1..483)
                     /locus_tag="HV105_RS31735"
                     /old_locus_tag="HV105_31730"
     CDS             join(4588..5010,1..483)
                     /locus_tag="HV105_RS31735"
                     /old_locus_tag="HV105_31730"
                     /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="replication initiation protein"
                     /protein_id="WP_019725130.1"
                     /translation="MHNAALELFNERLPHKPYFSDDLHFGVRIAGKERAILAKYIQFNQ
                     PHAMFWLGFDVDRAGSSIDWSDRNAPAPTLTITNPENGHAHLLYALENSIRTAPDGKIK
                     PLRYAASVENALRKKLEADAGYSGLICKNPNHNHWKIAVWQPKLYTLDWLADFLDLNTG
                     NDKEIVADYGLGRNCTLFDKTRKWAYRAIRQGWPEYEQWLQACYERACAYNLQFARPLD
                     ENEVRGIAKSIAKWTSNKFSPEEFSKFVDITHSSEIQSKRGKKSGQSRRKGSLEEIKPW
                     VAMGISRRKYFYIKKNGEIR"
                     /name="replication initiation protein"
     gene            480..1187
                     /locus_tag="HV105_RS31740"
                     /old_locus_tag="HV105_31735"
     CDS             480..1187
                     /locus_tag="HV105_RS31740"
                     /old_locus_tag="HV105_31735"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001258875.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_004198042.1"
                     /translation="MKTFVTLWTIVFLAFIAVMCTVDISNYIPSVYTVFSKNRPLVTGA
                     LSILLISVFIWLMVSLYLLKKYSVKVEKLSLGGVNILFNESATLYKKSVKNHLDSKRAI
                     FKLRKNVDAFDEVISSYYQTYQFIRDEMKILNPKKDREIYDFSNEMLMVLNRFLTNYQN
                     NYKRWYKYISDKDEVVDRVSGDVMRFHATSINKIQMQYYDYERILKGFKDVNRFFVNDV
                     KPKFGINTDKWNW"
                     /name="hypothetical protein"
     gene            complement(1224..1838)
                     /locus_tag="HV105_RS31745"
                     /old_locus_tag="HV105_31740"
     CDS             complement(1224..1838)
                     /locus_tag="HV105_RS31745"
                     /old_locus_tag="HV105_31740"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_012822468.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="TIR domain-containing protein"
                     /protein_id="WP_019725132.1"
                     /translation="MGKHKVFISYHHANDQYYKNALEKMNEEHEIFVNRSVSLGDIDED
                     EAPQKIREIIRDEYLRDTSVLILLVGTETKNRKHVDWELYSSMRDSTINKKSGILVVNL
                     PSTNTTYIRSTHGTNEKSEVHPTVTEWFSIDKRSTYEERFPYMPARIIDNFMKSGSYIS
                     VVNWNQIENNPETLRKLIDMTYNDREKATYDMSREMRMHNS"
                     /name="TIR domain-containing protein"
     gene            2240..2641
                     /locus_tag="HV105_RS31750"
                     /old_locus_tag="HV105_31745"
     CDS             2240..2641
                     /locus_tag="HV105_RS31750"
                     /old_locus_tag="HV105_31745"
                     /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_019725133.1"
                     /translation="MTRVSISEAARLTGKSRTTLHRLIKTGELSTCSGERNTKMVDISE
                     LLRVFGPFDQPKNEHLTRQVPEQRDTAPADQSEHVIRQLKQQIEHLNILILSKDSHIDS
                     LKQAMLLLENHQAKLTEPPAPWWKFWKKS"
                     /name="helix-turn-helix domain-containing protein"
     gene            complement(3441..3602)
                     /locus_tag="HV105_RS31755"
                     /old_locus_tag="HV105_31750"
     CDS             complement(3441..3602)
                     /locus_tag="HV105_RS31755"
                     /old_locus_tag="HV105_31750"
                     /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="hypothetical protein"
                     /protein_id="WP_162870772.1"
                     /translation="MAKHWSGQECPKTGTYGQYHDTDNSYAGSEYDRHVSKGDKFPPSK
                     NNHHFQEK"
                     /name="hypothetical protein"
     gene            3839..4084
                     /locus_tag="HV105_RS31760"
                     /old_locus_tag="HV105_31755"
     CDS             3839..4084
                     /locus_tag="HV105_RS31760"
                     /old_locus_tag="HV105_31755"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_012848468.1"
                     /GO_component="GO:0110001 - toxin-antitoxin complex
                     [Evidence IEA]"
                     /GO_function="GO:0003677 - DNA binding [Evidence IEA];
                     GO:0097351 - toxin sequestering activity [Evidence IEA]"
                     /GO_process="GO:0045927 - positive regulation of growth
                     [Evidence IEA]; GO:0006355 - regulation of DNA-templated
                     transcription [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="type II toxin-antitoxin system Phd/YefM family
                     antitoxin"
                     /protein_id="WP_025987695.1"
                     /translation="MHAINFTDARKHFAETMKRVTDDAEPVRVMRRDAPDIVMIDAGEY
                     EALIETVYLFSNPANAEHINESMKQAERGEFVEVEY"
                     /name="type II toxin-antitoxin system Phd/YefM family
                     antitoxin"
     gene            4065..4340
                     /locus_tag="HV105_RS31765"
                     /old_locus_tag="HV105_31760"
     CDS             4065..4340
                     /locus_tag="HV105_RS31765"
                     /old_locus_tag="HV105_31760"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_017412855.1"
                     /GO_process="GO:0008219 - cell death [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="Txe/YoeB family addiction module toxin"
                     /protein_id="WP_019725129.1"
                     /translation="MSKWNIKFTRNGADDLNYWRDTDKKKFERIRQLLLSIEADPLTGI
                     GKPERLRHHKDPALYSRRIDQSHRLVYSIQNGEIIIYAARYHYGDK"
                     /name="Txe/YoeB family addiction module toxin"
ORIGIN
        1 gccgtgtggc agccgaagct ctacactctg gactggctgg ccgactttct cgatctgaac
       61 acagggaatg acaaggaaat cgttgccgac tacggcttag gccgtaactg cacgttgttc
      121 gacaaaaccc gtaagtgggc atatcgcgcc atccgtcagg gctggcctga gtatgagcag
      181 tggctgcaag cctgctacga acgcgcttgc gcatacaacc tgcaatttgc acggcctctg
      241 gatgaaaatg aggtaagagg gatagctaag agcattgcta aatggacatc aaataaattt
      301 tcacctgaag aattcagtaa atttgttgat attactcatt cctctgaaat tcaatcaaag
      361 agagggaaaa agtcaggaca gtcaaggagg aaaggaagcc tagaggaaat aaaaccttgg
      421 gtagctatgg gaataagcag gcggaagtat ttttatatca agaaaaatgg tgaaataaga
      481 tgaaaacctt cgtaactctt tggactatag tttttttagc atttattgcc gtgatgtgta
      541 ctgttgatat atctaattac attccgtctg tttacacagt ttttagtaag aatagacctc
      601 ttgtaactgg cgccctttct attcttttga tatctgtttt tatttggctg atggtatccc
      661 tctacttact taaaaagtat tcggttaagg ttgagaaact tagccttggt ggagtgaata
      721 tacttttcaa tgagagtgct acactttaca aaaagagtgt aaaaaatcac ctagattcaa
      781 aaagagcaat tttcaaatta agaaaaaacg ttgatgcctt tgatgaggtt atttcatcat
      841 attatcagac ttaccaattt attcgtgatg aaatgaaaat actaaaccct aaaaaagatc
      901 gtgagattta tgatttcagc aatgagatgc tcatggtgtt aaatagattt ctaactaact
      961 accagaacaa ctacaagcgt tggtataagt acatatcaga caaagatgag gttgttgata
     1021 gggttagcgg tgatgtcatg agatttcatg caaccagcat aaataaaata caaatgcagt
     1081 attatgatta tgagcgtatt ttaaaaggtt ttaaagatgt taaccggttc tttgttaatg
     1141 atgtgaagcc taagtttgga atcaatacag ataagtggaa ctggtaaatt aaaggagtag
     1201 ccaaggctac tccttggata gtactatgaa ttatgcattc tcatttctct cgacatatca
     1261 tacgttgctt tttctctatc gttataagtc atgtctatta attttctgag tgtttctggg
     1321 ttgttttcta tttgattcca gttgaccact gatatataag acccgctctt catgaagttg
     1381 tctattattc ttgctggcat atatgggaac ctttcctcat aagttgagcg cttatcaata
     1441 gaaaaccatt cagttacggt aggatgaact tctgattttt cattagttcc atgtgttgaa
     1501 cgaatgtacg tagtatttgt tgacgggaga ttgacgacta aaattcctga ttttttgtta
     1561 atggtactat ctctcatgct agagtaaagt tcccaatcta cgtgttttct gttttttgtt
     1621 tcagttccaa caagaaggat aagaactgat gtatctctaa gatattcatc tcttattatc
     1681 tctcttattt tttgtggggc ttcatcttca tctatatcac ctaatgatac tgagcgattc
     1741 acgaatattt catgttcctc attcattttt tcaagtgcgt ttttgtagta ctgatcattc
     1801 gcatggtggt agctaatgaa taccttatgc tttcccattt ttattgtcct ttttttgttt
     1861 gtgtgcactc tattttgcac ttgaacctat atcagataac agctctcttt tagagagctc
     1921 tttttttctc agccagcaca catagggtcc cttcagcaag gtctcgccat gactggttta
     1981 gggcgggctc gttgcttccc taaacgcctt gagaagagag ctatcacctc actttattct
     2041 tacgtaccgc tcgccgcagt cttatgaccg aacgtagtga gcgaatgcgc gaggaagcgg
     2101 aaagtcattt gttgcctgca ttttgcacgg tcactcctgt gtttcatcgc ccttctgaaa
     2161 aacacatcac ttctggacca gtatgtcgta agctggcccc tgtttccttg agactgaatg
     2221 tattaaagga tgataactga tgaccagagt gtctattagt gaggctgcac ggctgacggg
     2281 taagagccgg acaacgctgc acaggttaat caaaacaggt gaactgtcca cttgtagcgg
     2341 tgaacgaaat acaaaaatgg tcgatatatc agagctttta cgtgttttcg gaccgtttga
     2401 ccaaccgaag aatgaacacc ttactcgaca agtacctgaa cagcgtgata cagcgcctgc
     2461 tgaccagagt gaacatgtca ttcgtcaact gaaacagcag attgaacacc ttaacatatt
     2521 gattttatcg aaggattcgc acattgacag cctgaaacag gccatgctcc ttcttgaaaa
     2581 tcaccaggca aaattaactg aacccccggc gccgtggtgg aaattctgga aaaaatcctg
     2641 accccgtcat gcttcagttt tcctctccgg ccattccggg gagttcctga accttcccga
     2701 aaatcgtcag atctctgaac gctcctcacc acgaaaaata cccacacccc acgcaaaatt
     2761 ttaattttgc agatttgtat ttaatatcag cagcttactt tactgaaatt tcgtttttta
     2821 aattttattt atatagatcc gactctatga cgagtcgtca tagagtcccc ggcgagtcgt
     2881 catagagtcg gtaacgactc aggcctataa aaacaatgag ttaataacga cccgactcta
     2941 gatccgactc cccgtttggt tgttttttag acgtggcgac tctgggtacg actctagtga
     3001 agagtcgccg gggaatcgtg tggtgagtcg tccggcgact tgccataacg tgattgccgg
     3061 ccgtggacga accgattcct gaacgtgctg aaaaccggtt ttccggctgc gccggcaacg
     3121 cttcacggcc acgcaataaa ttgcgtcccc gttcaccgtt ttcggatggg aagaacgccg
     3181 gaaacaggac ttcccctggc tgaatggtgt caatttccgc gctatgcact tgtgcgcata
     3241 ctcatgcatg ccgtaaaaac agagcctgcg cgtttctggc gggttttcgg gtggtttgtt
     3301 gccttgttta ccggtttccc gtcagaaacg ccctgagggc atctcaggcg gtgctgataa
     3361 cggatgttat ggtaaatcaa gtgaatggca ggtacaaaaa aagccccaga gggcttttag
     3421 tttagacttc tgaagatatt ttatttttct tggaagtggt ggttgttttt gctcggaggg
     3481 aacttatcac ccttgctcac atggcgatca tattcagaac cagcgtatga gttgtcggta
     3541 tcatgatatt gaccgtaagt acctgttttt ggacattctt gcccagacca atgttttgcc
     3601 atttactttt cctttgctcg ttttaggagc taagctccta gcggtacgaa attgtgccgc
     3661 acttcataaa tgtaattgct tgaaattatg cttcaatgta ttgacttgtt gtttttgtgg
     3721 ttattcgatt gagttcacat tttgagctga tttggttgtg ggtttttagg gaaatatctt
     3781 tatgtactta tttgcgtaca tgttctatgc taagccccaa caaatggggg ttaacaacat
     3841 gcatgcaatc aattttactg atgcccgtaa acattttgcc gagacgatga agcgcgtcac
     3901 tgatgatgct gaaccggtac gtgtcatgcg ccgtgatgcg cctgatattg ttatgatcga
     3961 tgcgggagag tatgaggcgc taatcgaaac ggtctatctg ttcagcaatc cggcgaacgc
     4021 agagcatatc aatgagtcaa tgaaacaggc ggagcgcggc gaatttgtcg aagtggaata
     4081 ttaagttcac taggaatggc gctgatgacc ttaactactg gcgtgatact gacaaaaaga
     4141 agtttgagcg tatccggcaa ctgttgctca gcatcgaggc tgatccgctg acaggtatag
     4201 gaaaacccga acggctgcgg caccacaaag atccggcact ctactcccgc aggattgatc
     4261 agagccaccg tctggtctat tcaatccaga acggagaaat catcatctac gcagcccgtt
     4321 atcactatgg tgacaaatag caaaagtcga tatagcccgc ttgatgcggg cttttcatgc
     4381 aaggcgtaca acggatgtta gggtaagtcg ctgtcagatc gacacaaagg caaagtcggt
     4441 gtaacgttag cctcagaaaa aacaaagccc cggaaatcat gtcatatctt ggcggatcgc
     4501 atgataacca gggctaggtc gaaaccttga aaggatatta gcacatgaac cgtgccagac
     4561 aacagcccgc cataagcgca gggcacattg cataacgccg cactcgaact tttcaacgaa
     4621 cgcttaccac acaagccgta cttttcggac gatctgcact ttggtgtccg tatcgccggt
     4681 aaggaacgcg ctattctggc gaaatatatc cagttcaatc agcctcacgc catgttctgg
     4741 ctgggatttg acgttgaccg cgccggttcc tccatcgact ggagcgaccg caacgcgcct
     4801 gcaccgacgc tgaccataac taaccccgaa aacggacacg cgcacctgct gtacgcgctg
     4861 gaaaactcga tacgcaccgc gccggacggc aaaataaaac cgttacgcta cgccgcctcc
     4921 gtggagaatg cgctacgtaa aaaattagag gctgacgctg gatattcggg gctcatctgc
     4981 aaaaatccga accacaacca ctggaaaatc
//
