LOCUS       NZ_CP056142             4773 bp    DNA     circular CON 03-SEP-2023
DEFINITION  Klebsiella michiganensis strain RHBSTW-00909 plasmid
            pRHBSTW-00909_7, complete sequence.
ACCESSION   NZ_CP056142
VERSION     NZ_CP056142.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN15148741
            Assembly: GCF_013732655.1
KEYWORDS    RefSeq.
SOURCE      Klebsiella michiganensis
  ORGANISM  Klebsiella michiganensis
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Klebsiella/Raoultella group; Klebsiella.
REFERENCE   1  (bases 1 to 4773)
  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 4773)
  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 T3-00909
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 120.157574954315x
            Sequencing Technology :: Hybrid: Illumina and OXFORD_NANOPORE
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 09/02/2023 16:20:10
            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)                     :: 6,484
            CDSs (total)                      :: 6,360
            Genes (coding)                    :: 6,136
            CDSs (with protein)               :: 6,136
            Genes (RNA)                       :: 124
            rRNAs                             :: 9, 8, 8 (5S, 16S, 23S)
            complete rRNAs                    :: 9, 8, 8 (5S, 16S, 23S)
            tRNAs                             :: 86
            ncRNAs                            :: 13
            Pseudo Genes (total)              :: 224
            CDSs (without protein)            :: 224
            Pseudo Genes (ambiguous residues) :: 0 of 224
            Pseudo Genes (frameshifted)       :: 83 of 224
            Pseudo Genes (incomplete)         :: 171 of 224
            Pseudo Genes (internal stop)      :: 42 of 224
            Pseudo Genes (multiple problems)  :: 62 of 224
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP056142.1.
            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..4773
                     /organism="Klebsiella michiganensis"
                     /mol_type="genomic DNA"
                     /strain="RHBSTW-00909"
                     /isolation_source="Wastewater influent sample"
                     /db_xref="taxon:1134687"
                     /plasmid="pRHBSTW-00909_7"
                     /geo_loc_name="United Kingdom"
                     /collection_date="2017"
     gene            45..935
                     /locus_tag="HV324_RS32070"
                     /old_locus_tag="HV324_32080"
     CDS             45..935
                     /locus_tag="HV324_RS32070"
                     /old_locus_tag="HV324_32080"
                     /inference="COORDINATES: protein motif:HMM:NF015983.3"
                     /GO_function="GO:0051539 - 4 iron, 4 sulfur cluster binding
                     [Evidence IEA]; GO:0003824 - catalytic activity [Evidence
                     IEA]; GO:1904047 - S-adenosyl-L-methionine binding
                     [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="radical SAM protein"
                     /protein_id="WP_048290309.1"
                     /translation="MFELKSPLLLVIDITNECNLSCNYCFQDFRSDTKNSINLGTITEI
                     LSEAKDMGIFEINICGGEPFKHKDIINIISEVKRVGFNLSIVTNGTLINKKTALLLNEL
                     DVIKNMQISFDSHIDSIHNKLRGGYHQAIRGLDYLLSYDSPPPSIGIVISKENVNHINE
                     TIDFFSRKGIRRFHIMNLLGNKELSCSDAELNEATKRINESFLQSRDGDKKLIISNLDF
                     KEKKDYQYKDVHINCLAGYTTLVLTSSLNIIPCDMVNYIIKKWKKKGDLRDGFELSKKQ
                     WLGLKESWCKGCFKC"
                     /name="radical SAM protein"
     gene            complement(1470..1760)
                     /locus_tag="HV324_RS32075"
                     /old_locus_tag="HV324_32085"
     CDS             complement(1470..1760)
                     /locus_tag="HV324_RS32075"
                     /old_locus_tag="HV324_32085"
                     /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_226554717.1"
                     /translation="MVRLIKDDRLRTLATFDGKTLKDDRLRTLATFDGKTLKDDRLRTL
                     ATFDGKTLKDDRLRTLATFDGKTLKDDRLRTLATVDGSVSIVIIAFAARIF"
                     /name="hypothetical protein"
     gene            complement(1878..2291)
                     /locus_tag="HV324_RS32080"
                     /old_locus_tag="HV324_32090"
     CDS             complement(1878..2291)
                     /locus_tag="HV324_RS32080"
                     /old_locus_tag="HV324_32090"
                     /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_071997596.1"
                     /translation="MTIPKIKSFPEVGSRREEQAHFVWIALTSWCLFNKNKTITYGELA
                     KLIGYPAQAGRTLAEALGTVSLYCLYNDLPPLSCIVVAKNTNHPGWEGMIPSNSSLEKE
                     QNKVWETSWNLYRTPSVGTLRRAREELNWDEFI"
                     /name="hypothetical protein"
     gene            complement(3100..3522)
                     /locus_tag="HV324_RS32085"
                     /old_locus_tag="HV324_32095"
     CDS             complement(3100..3522)
                     /locus_tag="HV324_RS32085"
                     /old_locus_tag="HV324_32095"
                     /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_048290308.1"
                     /translation="MARVSISEAARLVKVSRPTIYKMINSGKLSYTSVVKHGKHTKVID
                     TSELIRVFGSLYGGDDTVKHDVKGDAGATAVNILGLHDLQHKIALLEAENDGLKGAVKA
                     RDEHIDSLRQAMQLLEHKHEPSPQVHSPWWKFWKKS"
                     /name="helix-turn-helix domain-containing protein"
     gene            complement(3522..3713)
                     /locus_tag="HV324_RS32090"
                     /old_locus_tag="HV324_32100"
     CDS             complement(3522..3713)
                     /locus_tag="HV324_RS32090"
                     /old_locus_tag="HV324_32100"
                     /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            4129..4242
                     /locus_tag="HV324_RS32600"
     CDS             4129..4242
                     /locus_tag="HV324_RS32600"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_005761324.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="replication initiation protein"
                     /protein_id="WP_071997595.1"
                     /translation="MHEPPVQSDCCACFGNYRLESNPKRHDKTPLAAATGN"
                     /name="replication initiation protein"
     gene            complement(4457..4681)
                     /locus_tag="HV324_RS32095"
                     /old_locus_tag="HV324_32105"
     CDS             complement(4457..4681)
                     /locus_tag="HV324_RS32095"
                     /old_locus_tag="HV324_32105"
                     /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_197986819.1"
                     /translation="MKIKLLDSVYNVEPKTDIMAWDNHWNYQWSGRTSGITKDAIKWRK
                     ESDGQFIVCDETGAVWLVDQNELDNLLAA"
                     /name="hypothetical protein"
     Typing          3835..4242
                     /name="ColRNAI_rep_cluster_1987"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="91.484"
                     /coverage="99.0"
                     /evalue="1.3e-157"
ORIGIN
        1 taattgaaaa atataataaa aaccaaaaac acagggtaac gattatgttc gaattgaaat
       61 caccattgct attggtcatt gatataacca atgagtgtaa tttatcatgc aattattgct
      121 tccaagattt cagatcggat actaaaaaca gcatcaactt aggtacaatc accgaaatat
      181 tatcagaagc aaaagatatg ggtatttttg agataaacat atgtggcgga gaaccattta
      241 agcacaaaga tattataaat ataatatctg aagtaaagag agttgggttt aatttatcca
      301 ttgtaactaa cggtacattg atcaataaaa aaacagcatt actactcaat gaacttgacg
      361 ttataaaaaa catgcagatt agttttgata gccatataga ttccattcac aacaagttaa
      421 gaggaggtta ccatcaagca attagagggt tagactactt gctttcttat gattcccctc
      481 ccccatcaat aggcatagtt ataagtaaag aaaatgttaa tcatataaat gaaactatag
      541 attttttttc caggaaggga atacgcagat ttcacataat gaacctactg ggtaacaaag
      601 agctatcatg ttcagatgct gaattaaacg aagcaacaaa aagaataaat gaatcatttt
      661 tacaatcaag agatggcgat aaaaaattaa taatatccaa cttagatttt aaagaaaaga
      721 aagactatca atataaagat gtgcacatca actgccttgc cggatacact acgttagtct
      781 tgacatcatc tttaaatata ataccttgcg atatggttaa ttatattata aaaaaatgga
      841 aaaaaaaagg tgatttgcgt gatggctttg aactttcaaa aaaacaatgg cttggattaa
      901 aggaatcatg gtgtaagggt tgttttaaat gctaagtgta ttaacatgta aatgcgagta
      961 aaatagtttt ccactactct atactgaata ctaaaaatct ttttaatggg gtttgatggc
     1021 caaccgtacg aaaacgtacg gtaagaggaa aattatcgtc tgaaaaatcg atttatagac
     1081 aagcctgtcc gttaaatgcc aattttcgat taaaaagaca ccgttttgag ggcgtttttc
     1141 aatgtccatt atgtttcgat atatcagaca cttacttaac taacgtacgt ttccgttcca
     1201 ttggacttca tacccgtggt acggtttctt tggcaaacgc agactgaata gatcaatggc
     1261 atggctagtc aatgtagcat gagcttatgg cgggctgttg tttggcgcat ttcatgcgct
     1321 aatatccttt taggttttgt acctgcgccc tagtaattgg gaatctaccg ccaagttgag
     1381 tccacgattt ctggggcgtt gtttttttta caaaaaaatc atactcattt ataacacctg
     1441 tagatataag tactttttta taaaaaaagt caaaagatgc gggcggcaaa agcgataatt
     1501 acaatactta ccgaaccatc tacagttgct aaggttctta gcctgtcatc cttgagggtc
     1561 ttgccatcaa aggtcgccaa agttcttagc ctgtcatcct tgagggtctt accatcaaag
     1621 gtcgccaaag ttcttaacct gtcatccttg agagtcttgc catcaaaggt cgccaaagtt
     1681 cttaacctgt catccttgag agttttacca tcaaaggtcg ccaaggttct tagtctgtca
     1741 tccttgatga gtcttaccat caaaggtcgc taaagttctt aacctgtcat cttttatagt
     1801 tatagtcata tacatcccct attagaaatt catttttctc aggtttggat taattctgaa
     1861 tattactttt cataaaatta aataaattca tcccaattaa gttcctctct cgctcttctt
     1921 aacgttccaa ccgatggtgt cctatataga ttccacgatg tttcccatac cttattttgt
     1981 tctttttcta atgatgaatt tgaagggatc attccttccc atccgggatg attggtattt
     2041 ttggcaacaa caatgcaact taagggggga agatcgttat ataaacaata cagtgagact
     2101 gtacctaaag cctcagctaa agtgcgtcct gcttgcgcag gatacccaat aagtttcgca
     2161 agttctccat atgtgattgt tttattctta ttgaacaaac accatgacgt caaagcgatc
     2221 cacacaaaat gagcctgctc ttctcttctt gaaccaactt ctggaaatga ttttattttt
     2281 ggaattgtca ttgttaaaat tctcacaaac cgttcatatt ttcactttat aatataccaa
     2341 aagatgagtg cgtacaaaaa actatttacc ataacgcgtc attacgcgca ccgctcaaac
     2401 gccccagaaa cgattctggg ccgtaaccca tcaaatccta catcttaccc cctgaaaacg
     2461 cctcaaaatc gccccagggc tttttacggg catgaattgt tatgcaccag actgattggt
     2521 ggcggatttc agcctgaatt cacgccagac aactcaaaac ccgcaccaaa ccagactgca
     2581 aacggtgagc ggggacgcaa tttattgcgt gaccgtgaag cgttgccggc gcagccggaa
     2641 aaccggtttt cagcacgttc aggaatcggg ttcgtcgacg gccggcaatc acgttatggc
     2701 aagtcgccgg acgactcacc acacgattca ccggcgattc gactcgtgac ttgactctag
     2761 agtcaccatg gtcaaaaagc caccaacccg gcaagtcgac tctagagtca agtcatcata
     2821 acgtactgat tatatggcgt gattcacata tgaatcgtgg gcaagtcatc ggcgattcgc
     2881 catagagtcg tccacgactc ggattcacct tacaaaaaat aaaattgcgt aatttaaaat
     2941 agataactga ttgaaaataa aggtatatct gcaaaatttt aattttgcgt agtgtgtggg
     3001 tatttttagt ggtgaggagc gttcagagat ctgacgattt ttgggaaggt tcaggaactc
     3061 cccgggatgg ccggagagga aaactcaagc atggcaggat caggattttt tccagaattt
     3121 ccaccacgga gaatgaacct gtggagaggg ttcgtgcttg tgctccagaa gctgcatagc
     3181 ctggcgaaga gaatcgatat gttcatcacg agctttaaca gcccctttaa gaccatcgtt
     3241 ttcagcttca agcaaagcaa ttttatgctg taaatcatgt aaaccaagga tgttaaccgc
     3301 tgtagcgcct gcgtcacctt ttacatcatg ttttacagtg tcgtccccac catacagcga
     3361 gccaaaaacc ctaataagct ctgatgtatc aataacttta gtatgtttcc catgctttac
     3421 aacagaggtg taacttagtt tcccactgtt aatcatcttg taaattgtgg ggcgactaac
     3481 cttaacaagc cgtgccgctt cactaataga cactctggcc atcaattacc atcctgtaat
     3541 tcatccagtc tcgaggacag tgtacggaaa agatgctccg catcatcgtg gagtttctca
     3601 caaaggtcgg cctcagcatc aagatcaagc tcgttaagct tctccagcag gagcagagac
     3661 tgattctgga tgaatttagc catgttcagc gctgttttct gttgtttcgt cataagaggc
     3721 ctcacagcgt cagtgctcag tgtagggatg ttctcttttc cgcttcctcg ctcactcagt
     3781 cgctatgctc ctgccgttcg gctgcggcga gcggcaggag catgcgtgta aaagctcgag
     3841 aaaaccgagc ggtcgcgtga cggggaaaag gaaaggccgc taagcggccg tttttccata
     3901 ggctccgccc ccctgacaag catcacgaaa tctgacactc aaatcagtgg tggcgaaacc
     3961 cgacaggact ataaagatac ctatcatttc tgataggcgg ctccctcgtg cgctctcctg
     4021 ttcctgcctt tcggtttacc ggtgtcactc cgctgttatg gccgcgttta tctcattcca
     4081 cgcctgacac tcagttccgg gtaggcagtt cgctccaagc tggactgtat gcacgaaccc
     4141 cccgttcagt ccgactgctg cgcctgtttc ggtaactatc gacttgagtc caacccgaaa
     4201 agacacgaca aaacgccact ggcagcagcc actggtaact gatttagagg agttagtctt
     4261 gaagtcatac gccagttaag gctaaactaa acgaacagtt ttggttactg cgctcctcca
     4321 agccagttac ctcggttcaa agagttgctg ctcagagaac ctttgaaaaa ccgccttgct
     4381 gggcggtttt tctctttcag gggagaagat tacgatggga aggtgaggat ctcaagtaaa
     4441 tactagaaat atggcgttat gcagcgagca agttatccaa ctcattctga tctactagcc
     4501 agacagctcc tgtctcatca caaacaataa actgcccatc agactctttc ctccacttaa
     4561 tggcatcctt cgtaattccc gatgtacggc cactccattg ataattccaa tgattatccc
     4621 acgccatgat atccgtttta ggctctacgt tataaaccga atctaacagc ttgattttca
     4681 ccgcaattac ctctcaagaa aaaatctaga actacagatg agcatataaa atactgaatc
     4741 gaattttatt gactaccgtc aagactaatc aat
//
