LOCUS       NZ_CP058123             5997 bp    DNA     circular CON 09-APR-2024
DEFINITION  Klebsiella michiganensis strain RHBSTW-00167 plasmid
            pRHBSTW-00167_6, complete sequence.
ACCESSION   NZ_CP058123
VERSION     NZ_CP058123.1
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 5997)
  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 5997)
  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
            CP058123.1.
            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..5997
                     /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_6"
                     /geo_loc_name="United Kingdom"
                     /collection_date="2017"
     gene            54..605
                     /locus_tag="HV105_RS31635"
                     /old_locus_tag="HV105_31635"
     CDS             54..605
                     /locus_tag="HV105_RS31635"
                     /old_locus_tag="HV105_31635"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_008815340.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="DUF4468 domain-containing protein"
                     /protein_id="WP_055312415.1"
                     /translation="MNKVMMKTVLASLVVSSITVLTGCVTSPDMEAAKQPLGSIVSVVN
                     VPGVKKDALYSSSKIWVAKAFTDSNSVIQYADKEEGSIVGKGNVKYPCDGFNDCLANED
                     VRYKFTMKIDTKDDKARITFDDIHIYRPAHVTSGIAFPAIDSPNMTVGGQAKAKKALND
                     IVEQYKREIVTESSSAAKDW"
                     /name="DUF4468 domain-containing protein"
     gene            complement(823..>960)
                     /locus_tag="HV105_RS31640"
                     /old_locus_tag="HV105_31640"
                     /pseudo=""
     CDS             complement(823..>960)
                     /locus_tag="HV105_RS31640"
                     /old_locus_tag="HV105_31640"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_011787828.1"
                     /note="incomplete; partial in the middle of a contig;
                     missing N-terminus; Derived by automated computational
                     analysis using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="IS630 family transposase"
                     /name="IS630 family transposase"
     gene            complement(1001..1633)
                     /locus_tag="HV105_RS31645"
                     /old_locus_tag="HV105_31645"
     CDS             complement(1001..1633)
                     /locus_tag="HV105_RS31645"
                     /old_locus_tag="HV105_31645"
                     /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_181250937.1"
                     /translation="MLALIQDSNALSKIKVMFCVVGFVVLILFVVVVFVFLFNIFLNYN
                     ESRKYRVETTSALIKLESGLKKSIGRRFTIKDSGDESFEVVLSSCHINGDVIECTFSPG
                     FTRFGVHYMGLDLAYGYIVSELSRLKLLSAQLESKSELNTFVCDLLNPEDMKALLYGGK
                     QISYRVPDLDESSRQGSIVYTGYYPVQIRNSCSLDVRTGFSSGVKSL"
                     /name="hypothetical protein"
     gene            complement(2628..3050)
                     /locus_tag="HV105_RS31650"
                     /old_locus_tag="HV105_31650"
     CDS             complement(2628..3050)
                     /locus_tag="HV105_RS31650"
                     /old_locus_tag="HV105_31650"
                     /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_061500298.1"
                     /translation="MARVSISEAARLVKVSRPTIYKMINSGKLSYTSVVKHGKGIKVID
                     TSELIRVFGSLDGVIDTVKYDVKSDAESTGINSVGLHDLQHRIALLEAENDGLKGAVKA
                     RDEHIDSLRQAMQLLEHKHEPSSPPHSPWWKFWKKS"
                     /name="helix-turn-helix domain-containing protein"
     gene            complement(3050..3241)
                     /locus_tag="HV105_RS31655"
                     /old_locus_tag="HV105_31655"
     CDS             complement(3050..3241)
                     /locus_tag="HV105_RS31655"
                     /old_locus_tag="HV105_31655"
                     /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_032421723.1"
                     /translation="MTKQQKTALNMAKFIQNQSLLLLEKLNELDLDAEADLCEKLHDDA
                     EHLFRTLSSRLDELQDGN"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            complement(3712..3903)
                     /locus_tag="HV105_RS31660"
                     /old_locus_tag="HV105_31660"
     CDS             complement(3712..3903)
                     /locus_tag="HV105_RS31660"
                     /old_locus_tag="HV105_31660"
                     /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_021314601.1"
                     /translation="MNKQQKTAVNMAKFIQDQSLLLLDRLNDLDLDHEADFCEKLHEDA
                     ERLYRSLSARLNEQQDGA"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            4322..4434
                     /locus_tag="HV105_RS32205"
                     /pseudo=""
     CDS             4322..4434
                     /locus_tag="HV105_RS32205"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001422066.1"
                     /note="frameshifted; internal stop; 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(<4690..5118)
                     /locus_tag="HV105_RS31665"
                     /old_locus_tag="HV105_31665"
                     /pseudo=""
     CDS             complement(<4690..5118)
                     /locus_tag="HV105_RS31665"
                     /old_locus_tag="HV105_31665"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_011787828.1"
                     /GO_function="GO:0004803 - transposase activity [Evidence
                     IEA]"
                     /GO_process="GO:0006313 - DNA transposition [Evidence IEA]"
                     /note="incomplete; partial in the middle of a contig;
                     missing C-terminus; Derived by automated computational
                     analysis using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="IS630-like element ISSpu2 family transposase"
                     /name="IS630-like element ISSpu2 family transposase"
     gene            5376..5948
                     /locus_tag="HV105_RS31670"
                     /old_locus_tag="HV105_31670"
     CDS             5376..5948
                     /locus_tag="HV105_RS31670"
                     /old_locus_tag="HV105_31670"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001276588.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_064179602.1"
                     /translation="MPVSNYYQAQPDGYVRFDWHGNSIEGEFFSYVECGRDIDPKWGYI
                     RPFDRVTRQQLIDNLQATHGIDLQTFTSQGDLITCDAFVTHKNLQAAHQVVVESFDFVD
                     ESELTTERERIGNCRVDLLRRQYIIGVQLKQPQESLDNLNAEFLKWVTPFYTPLRYERK
                     WLTKHRKGLLRFGALVAVAVMAYIHYG"
                     /name="hypothetical protein"
     Typing          4071..4429
                     /name="rep_cluster_2373"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="92.818"
                     /coverage="84.0"
                     /evalue="6.47e-146"
ORIGIN
        1 ccgcgccatt tttacatact gcacttaata aaaatgcgct aaggaccaat cgaatgaaca
       61 aagtaatgat gaaaactgtt ttagcaagtt tggttgtatc cagtattaca gtgttgacag
      121 gttgtgttac ctcaccagat atggaagcag ctaaacaacc gctgggtagt atagtcagtg
      181 ttgttaacgt tcccggggtt aaaaaggatg cactttacag cagttccaaa atttgggttg
      241 caaaggcctt cactgattct aacagcgtaa ttcaatatgc agataaagaa gaaggttcga
      301 ttgttggtaa agggaatgtt aaatacccat gcgacggttt taatgattgt ctggctaatg
      361 aagatgttcg atataaattc actatgaaaa tcgacacaaa ggatgataaa gctcgcatca
      421 cctttgatga tatccacatt tatcgtccgg ctcatgtaac cagcggaatt gcgttccctg
      481 ccatagattc gccaaatatg actgttggtg gacaagcaaa agccaaaaaa gcgttgaatg
      541 atattgtgga acaatacaaa cgcgagatcg tgactgaaag tagctctgct gcaaaagact
      601 ggtaacagcc atcagctcaa aaacttgccg gataagtttt tgagctttct atagccggga
      661 ttatatgtgg gtgcataatg atagttatga cagcttatca cacggcattt ttattccatt
      721 cgaaagcatc cagtttcact tggctacgct agcaactcta tgagagcgcc gcaaattccg
      781 caccacaatt tcatcccccc taaataactg atcctaatac cgctacactt tagccagccc
      841 gtgttttcca ccggggaatg ggctgacggt atccataaag tgatgaacct ttttcaacag
      901 atgccacatt gaacggcact ggtgatttcg ggttattgtc tcatgaagcg cctgccacac
      961 acaaacacca tatattaaaa aacaaccact gcgaatatat tcacaaactc ttgacaccac
     1021 tcgaaaatcc agttcttaca tctaaagaac atgaattacg tatttgcaca ggataatacc
     1081 ccgtgtaaac aatagaaccc tgtctactag attcgtcgag atcaggcacc cgatatgata
     1141 tctgcttccc cccatacaat agcgccttca tatcttcagg gtttaataaa tcgcaaacaa
     1201 atgtgtttaa ttcggattta gattcaagct gagcagaaag aagttttaat cttgataact
     1261 cactaacaat atacccatat gctaaatcaa gccccatgta atgtacaccg aaccttgtaa
     1321 aacctggaga gaaagtacat tcaataacat caccattaat atggcaactc gatagcacca
     1381 cttcgaaact ttcatcccct gaatctttta tagtgaatct tctccctatg cttttcttaa
     1441 gacccgactc aagcttaatt aatgcagaag tagtttccac tcgatacttg cgagactcat
     1501 tgtaattcaa gaatatatta aataaaaaaa caaaaaccac cacaacaaat aagattaaaa
     1561 caacaaaacc aaccacgcaa aacataacct taattttact taaagcattt gagtcttgaa
     1621 ttaaagccag caattcactc ttttttttta tttaaaagcc acttcctttt agcttttctg
     1681 aggttatatt ccttctccca ctctatttcg ctttcacttt tcttttcgtt tttcatcatt
     1741 tgaccattat gaaaatatca tttgtagcgc attcttccta caacttgtga ctgataccac
     1801 tcatcaaaaa cttccgtagt aacaacaccc aacatcacaa atctctttga agcattaacc
     1861 tcaaaaaagg ttatggccta ttagctataa catcaagagg gtatttacca taacatctgt
     1921 tgcgtgcacc gcctcagagc ctctgaggac gtttctgacg ggaaaccggt aaaacaggca
     1981 acaaaccacc cgaaaacccg ccagaaacgc gcaggctctg tttttacggc atgcatgagt
     2041 atgcgcacaa gtgcatagcg cggaaattca cgccattcag ccggggtaag tcctgtttcc
     2101 ggcgttcttc ccatccgaaa acggtgaacg gggacgcaat ttattgcgtg gccgtgaagc
     2161 gttgccggcg cagccggaaa accggttttc agcacgttca ggaatcgggt tcgtcgacgg
     2221 ccggcaatca cgttatggca agtcgccgga cgactcaccg gcgattcgac tcgtgacttg
     2281 actctagagt caccgcggtc aaaaaaacgc caaagcgacg attcgactct agagtcaagt
     2341 cgtcataagt tactgatagt gtggagtgag tcgtcgatga ctctatgacg agtcgtcggc
     2401 aagtcgtaca cgaatcaccg acgacttgga ttgaccttac agaaggtaat actgcgtaat
     2461 ttaataaaac ctaaccaact gataataagg agttatctgc aaaattttaa ttttgcgtgg
     2521 tgtgtgggta tttttcgtgg tgaggagtgt tcccggatct ggcgattttt gggaaggttc
     2581 aggaacgccc cgggatggcc ggagaggaaa actcaagcat ggcgggatca ggattttttc
     2641 cagaatttcc accacgggga atggggtggt gaagaaggtt cgtgcttgtg ctccagaagc
     2701 tgcatagcct gacgaaggga atcaatatgc tcatctcgag ccttaacagc ccctttaaga
     2761 ccatcgtttt cagcttcaag taaagcgatt ctatgttgta aatcatgtaa accaacgctg
     2821 ttaatacctg tagattctgc gtcacttttt acatcatatt ttacagtatc gatgacacca
     2881 tcaagagaac caaacactct aataagctct gatgtatcaa taactttaat acccttcccg
     2941 tgctttacaa cagaggtgta acttaactta ccactgttaa tcatcttgta aatagtaggg
     3001 cgactaacct taacaagccg tgctgcttca ctaatagaca ctctggccat cagttaccat
     3061 cctgtaattc atccagtctc gaggacagtg tacggaaaag atgctccgca tcatcgtgga
     3121 gtttctcaca aaggtcggcc tcagcatcga gatcaagctc gttaagcttc tccagcagga
     3181 gcagagactg attctggatg aatttagcca tgttcagcgc tgttttctgt tgtttcgtca
     3241 taagggacct cagagcatca gtgctcagtg taaaaccggt aagggggtcg gatgtacgaa
     3301 tggttcagag aacggatctg aggtaatcct gtagttattt tgtagtttat ctgtagtcat
     3361 cgcactaaaa atcaggatta agtcatcagc ttttgtagtc tttctgtagt ttacctgtag
     3421 tccggaaaaa taatccgttc atgcgagcat gaacgaggtc gttaatgacg tttttttgtc
     3481 accgacgccc cttaacctgc gtaaatcacc cgccatggtt gattattttt caacctcaaa
     3541 atggtcatac acctaacgca gccgcgattt tcatcgcaac ttcatgaaaa ataaataaaa
     3601 aagaaaaaat acagggattc tgggtattac cggggtaata atgttaagcg ctaacacaat
     3661 gaaaattaag gcgatgccgg tattactccg gtaataccca gaacggagcc attacgcacc
     3721 gtcctgctgc tcattcaggc gcgctgacag gcttcggtaa aggcgttccg catcctcatg
     3781 gagtttctcg cagaaatcag cctcatgatc cagatccagg tcattaagcc tgtccagaag
     3841 aagcagggac tgatcctgga tgaatttagc catgttaacg gcagtctttt gttgtttgtt
     3901 catgaaagcc ccggcgcgaa agtgcttact gtacgttcgg atggttttcc gcttcctcgc
     3961 tcattcgctc actccgttcg gtcatgagtc tgcggcgagc ggagggagga taagcagata
     4021 acgtaacggt aagcataacg aaagctaagg acaagggcga aaaggccacg ccccggcggg
     4081 gcgtttttcc ataggctccg cccccctgac aagcatcaca gaatctgacg ctcaaatcag
     4141 tggtggcgaa acccgacagg actataaaga taccaggcgt ttccccctgg tcgctccctc
     4201 gtgcgctctc ctgttcctgc ctttcggttt accggtgtca ttccgctgtt atggccgcgt
     4261 ttatctcatt ccacgcctga cactcggttc cgggtaggca gttcgctcca agctggactg
     4321 tatgcacgaa ccccccgttc agtccgacta ccacgccttg taaggtaact atcacttgag
     4381 tccaaccctt acagacacgc aaaaacgcca ctggcggtag ccattggtaa ctaagttaaa
     4441 gtggagcgag ctattaagag ttcttgaagt tgcagcccaa ctgcggctaa actgaaagga
     4501 caaatttggt atctgcgctc cacgaaagcc agttacctta ggttagaaag cctgagaaac
     4561 ttctaacctt cggaaaaacc cgcgcctgag aacgcgggtt ttttcgtttc agagaaagag
     4621 actacgacga cattgaaata atctcaatac cccaccctta ctttctgcaa aaatcaccaa
     4681 tgtgtagatc cataccagcc cggctgcagg taaccatctc cggatggttg aggcatgtag
     4741 cggacaaccg gtgacatcac ggatttttat cgccagcagt tcggtactcc agcgggaacg
     4801 ctgataaccg aaatcgccgg gagaatgctt cacaagctca cgcagcaatg cgcaaatatg
     4861 ttcgaacggc cagcgcctgc cacgtcctga cggtaatgac ttcaggcctt cagcaccaga
     4921 cagagtgaac cagttaatcc agcgaccaat cgatgagcgt gcacagcaga gtgttctggc
     4981 cacatgactg acgcgctcgc cccggtgcaa catcagcatg gcggtcagtc tgcgggcata
     5041 atttttatca cgcgttttat ggatagcttt ctgcatcagg cgtcgttcgt cacggggaat
     5101 tggtgctatg atcggcatcg ctcagtccgg ttggtgattt gggatattca gcgattgatc
     5161 agatcgcaca attcgggctg agttccctca aagtgatcta ctattccgaa cagttattta
     5221 ggtttggaag tccccctctc aggcattgcg tccaaaaact tcggtggtgg caaaatcatc
     5281 cttatacttg cagataaaca ttgttgaaaa attctctccc gcatagttca attaaccact
     5341 taggattttt ctgatctcct ttttcaagga agcttatgcc cgtatccaat tattaccaag
     5401 cccaaccgga tggttatgtg cgctttgatt ggcatggcaa ttccatagaa ggcgagtttt
     5461 tcagctatgt ggagtgtggt cgagatatcg atcccaaatg gggttacatc cgaccatttg
     5521 atagagtcac cagacagcaa ctcattgata atttacaggc aactcacggt atcgacctcc
     5581 agacattcac ctcgcaaggc gacctgatca cctgtgatgc ttttgtcacc cacaaaaatt
     5641 tgcaggcagc acaccaggtt gttgtagagt cgtttgattt cgttgatgag tctgagctta
     5701 caactgaaag agaacgcatc ggtaactgcc gggtcgattt actacgacgc caatacatta
     5761 tcggtgtcca acttaaacag ccccaagagt ctttggacaa cctcaatgca gagtttctta
     5821 aatgggtaac acctttctac acgccgttgc gttacgagcg gaaatggtta accaagcatc
     5881 gtaaagggtt attacgtttt ggcgcactcg ttgctgtcgc agttatggcc tatatccact
     5941 atggctgaca atagaaaagc gagacctttc ctgcggcttt gagaaaccaa cttcatt
//
