LOCUS       NZ_CP069817             5665 bp    DNA     circular CON 03-DEC-2023
DEFINITION  Raoultella planticola strain HH15 plasmid pHH15_2, complete
            sequence.
ACCESSION   NZ_CP069817
VERSION     NZ_CP069817.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN14258342
            Assembly: GCF_011290675.2
KEYWORDS    RefSeq.
SOURCE      Raoultella planticola
  ORGANISM  Raoultella planticola
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Klebsiella/Raoultella group; Raoultella.
REFERENCE   1  (bases 1 to 5665)
  AUTHORS   Kang,M., Chmara,J., Naushad,S. and Huang,H.
  TITLE     Complete Genome Sequences of a Canadian Raoultella planticola
            strain, Obtained using Oxford Nanopore and Illumina Sequencing
            Technologies
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 5665)
  AUTHORS   Huang,H.
  TITLE     Direct Submission
  JOURNAL   Submitted (04-FEB-2021) Research and Development, Science Branch,
            Canadian Food Inspection Agency, 960 Carling Ave Bldg. 22, Ottawa,
            Ontario K1A 0Y9, Canada
REFERENCE   3  (bases 1 to 5665)
  AUTHORS   Huang,H., Chmara,J.T. and Duceppe,M.-O.
  TITLE     Direct Submission
  JOURNAL   Submitted (09-MAR-2020) Research and Development, Science Branch,
            Canadian Food Inspection Agency, 960 Carling Ave Bldg. 22, Ottawa,
            Ontario K1A 0Y9, Canada
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Date                     :: 08-JAN-2021
            Assembly Method                   :: Unicycler v. v0.4.9b
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 121.6x
            Sequencing Technology :: Oxford Nanopore MinION; Illumina MiSeq
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 12/03/2023 04:01:00
            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)                     :: 5,675
            CDSs (total)                      :: 5,551
            Genes (coding)                    :: 5,438
            CDSs (with protein)               :: 5,438
            Genes (RNA)                       :: 124
            rRNAs                             :: 9, 8, 8 (5S, 16S, 23S)
            complete rRNAs                    :: 9, 8, 8 (5S, 16S, 23S)
            tRNAs                             :: 85
            ncRNAs                            :: 14
            Pseudo Genes (total)              :: 113
            CDSs (without protein)            :: 113
            Pseudo Genes (ambiguous residues) :: 0 of 113
            Pseudo Genes (frameshifted)       :: 52 of 113
            Pseudo Genes (incomplete)         :: 80 of 113
            Pseudo Genes (internal stop)      :: 37 of 113
            Pseudo Genes (multiple problems)  :: 49 of 113
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP069817.1.
            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..5665
                     /organism="Raoultella planticola"
                     /mol_type="genomic DNA"
                     /strain="HH15"
                     /db_xref="taxon:575"
                     /plasmid="pHH15_2"
                     /collection_date="2010"
                     /collected_by="Canadian Food Inspection Agency"
     gene            join(4939..5665,1..32)
                     /locus_tag="G9395_RS28150"
                     /old_locus_tag="G9395_028150"
     CDS             join(4939..5665,1..32)
                     /locus_tag="G9395_RS28150"
                     /old_locus_tag="G9395_028150"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_013558434.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="PmeII family type II restriction endonuclease"
                     /protein_id="WP_065782962.1"
                     /translation="MIESRIISDFIESCIDEEFHQKKQEKIRAIKLSDITKRKNPYLFK
                     AKGLTSASDLIKSIMDATVSSGEETVFGNFMEKIAIFTCSQAFGGRKSSAVGIDLEFET
                     ESTKYLISIKSGPNWGNSSQKKKMQDNFIKAKKVLGTSGGINSKSITCIEGCCYGYDAR
                     PEKGTHIKLCGQDFWTFISNGNNELYSDIIEPIGKLADEKNKELIELTNAKLNLFTAEF
                     ISEYCNSDGSINWALFVARNSGSKSDYHSN"
                     /name="PmeII family type II restriction endonuclease"
     gene            complement(442..813)
                     /locus_tag="G9395_RS28155"
                     /old_locus_tag="G9395_028155"
     CDS             complement(442..813)
                     /locus_tag="G9395_RS28155"
                     /old_locus_tag="G9395_028155"
                     /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_021314598.1"
                     /translation="MSKKNDLNLSESTLESLREYVDDFGMTVDDVVLKLINENKSLKES
                     LGQDFVLSGEKEAHHFKDYVIHKLPKGKILVTHNGLKASNMKKILIEAGRELGMDENEL
                     NPDFTTYEIGRFLFKHLHA"
                     /name="hypothetical protein"
     gene            complement(1319..1534)
                     /locus_tag="G9395_RS28160"
                     /old_locus_tag="G9395_028160"
     CDS             complement(1319..1534)
                     /locus_tag="G9395_RS28160"
                     /old_locus_tag="G9395_028160"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_015328239.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MbeD family mobilization/exclusion protein"
                     /protein_id="WP_015328239.1"
                     /translation="MTELEKQLLSALEQLQQDYSRRLDEWESAFEEWRKMSGLMQRENA
                     ALSERVSGLSRQVQSLSEQLRRLSTG"
                     /name="MbeD family mobilization/exclusion protein"
     gene            complement(1541..2038)
                     /locus_tag="G9395_RS28165"
                     /old_locus_tag="G9395_028165"
     CDS             complement(1541..2038)
                     /locus_tag="G9395_RS28165"
                     /old_locus_tag="G9395_028165"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_020325392.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MbeB family mobilization protein"
                     /protein_id="WP_015328238.1"
                     /translation="MSSLLTASRDFEEKSKAQQQLTEERLKAAFSKHENVVKSELNASA
                     KRINDAISAHEQGMNAAMQSNRLSVLRMVGRTWLTITMVSGLLFASLSGVLWYQGNRIA
                     ANLAEIRQQRDTLSKLHMQTWGVTYLENRNGRFLVLPEGMKAETGRTVDNKTRNAVKLV
                     RE"
                     /name="MbeB family mobilization protein"
     gene            complement(<2079..2777)
                     /locus_tag="G9395_RS28695"
                     /old_locus_tag="G9395_028170"
                     /pseudo=""
     CDS             complement(<2079..2777)
                     /locus_tag="G9395_RS28695"
                     /old_locus_tag="G9395_028170"
                     /inference="COORDINATES: protein motif:HMM:NF015397.3"
                     /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="relaxase/mobilization nuclease domain-containing
                     protein"
                     /name="relaxase/mobilization nuclease domain-containing
                     protein"
     gene            complement(2716..3057)
                     /locus_tag="G9395_RS28175"
                     /old_locus_tag="G9395_028175"
     CDS             complement(2716..3057)
                     /locus_tag="G9395_RS28175"
                     /old_locus_tag="G9395_028175"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_006122514.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MobC family plasmid mobilization relaxosome
                     protein"
                     /protein_id="WP_071599364.1"
                     /translation="MADKRNKMLTMWVTEDEHRRLLERCDGKQLAAWMRQTCLDEKPTR
                     AGRLPSISPALLRQLAGMGNNLNQIARKVNAGGAGHDRVQIVAALMAIDAGLERLRHAV
                     LEKGPDDDC"
                     /name="MobC family plasmid mobilization relaxosome protein"
     gene            3672..3800
                     /locus_tag="G9395_RS28700"
     CDS             3672..3800
                     /locus_tag="G9395_RS28700"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001505258.1"
                     /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_074440740.1"
                     /translation="MHEPPVQSDRCALSGNYRLESNPERHDKTPLAAANSKRVYKR"
                     /name="replication initiation protein"
     gene            4152..4946
                     /locus_tag="G9395_RS28180"
                     /old_locus_tag="G9395_028180"
     CDS             4152..4946
                     /locus_tag="G9395_RS28180"
                     /old_locus_tag="G9395_028180"
                     /EC_number="2.1.1.-"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_015164793.1"
                     /GO_function="GO:0003677 - DNA binding [Evidence IEA];
                     GO:0008170 - N-methyltransferase activity [Evidence IEA]"
                     /GO_process="GO:0009307 - DNA restriction-modification
                     system [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="site-specific DNA-methyltransferase"
                     /protein_id="WP_227818858.1"
                     /translation="MLQSDSIDLIVTSPPYADQRKKTYGGVSADKYVEWFTPIAKELLR
                     VTKSSGSFVLNIKERAINGERHTYVIELILMMRKLGWLWTEEYIWHKKNSYPGKWPNRF
                     RDSWERCIHFTKSKKFNMYQEEVMVPMGDWKNSRLKNMSDTDKKRDESKVGSGFGKKIE
                     NWVTRDLAYPTNVLHMATECGNRSHSAAFPESLPEWFIKLFTTEGDTVLDPFSGSGTTL
                     KVAKAMKRNAVGIEILDEYCEITANRVGLKKSSQKKYRYTND"
                     /name="site-specific DNA-methyltransferase"
     Typing          complement(3143..3318)
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="81.667"
                     /coverage="100.0"
                     /evalue="2.75e-31"
     Typing          3267..3774
                     /name="ColRNAI_rep_cluster_1987"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="90.411"
                     /coverage="97.0"
                     /evalue="0.0"
     Typing          complement(1204..2726)
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          complement(2723..3036)
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="92.453"
                     /coverage="99.0"
                     /evalue="1.04e-58"
ORIGIN
        1 caggttcaaa atcagactat catagcaact aacagaagag tataaatggg gaaatgcctc
       61 aacaaaaaca aggacactcc atgccagcat gcatagtaaa tggttgccag aatcatgcat
      121 ctaacaactt tggtgtaaga ctccgtagag aggataccag tgcaatctgg gcacccaata
      181 ctgaagccta catctgtgat gttcatgcaa gttcaggctt tgatatcttc gtacagctac
      241 acactcgaac cgacaacaac atagtcacac atgtgagtgc taatggtggg gctgtcgcac
      301 aaagactgac accaataacc aacacacctt agcaaaaagc cgccttttag gcggtttttt
      361 ttgcatcaga ttaaatactc atatttacca taacatccgg gcagcgaagt tcgatgcctg
      421 cccttcaggc ctgcaggatt gttacgcatg taggtgctta aacaaaaaac gccctatctc
      481 ataggttgtg aaatctggat tgagttcatt ttcatccatg cctagctccc tccccgcctc
      541 aatcaatatc ttcttcatgt tgctggcctt aagcccatta tgggtaacca gaatttttcc
      601 tttgggcagt ttatgaatca cataatcttt aaagtggtgc gcttcctttt cgccagataa
      661 cacaaagtct tgtccaagtg attccttcaa tgacttattc tcattaatta acttcagaac
      721 aacatcatca acagtcatac cgaagtcatc gacatactcc ctgaggcttt ctaacgttga
      781 ttcactaagg tttaaatcgt tttttttact catgtagtca ccaccatgct agttgtcaga
      841 aaagaaaaaa cacaacataa gtggtatagt acaccgcttt ttagtattga acaaataaca
      901 tagaagtcac tgatcgctgg ttcaaaaaga acagctacac cgctggattt accataacat
      961 ctcttacccg caccgcgccg gaggcactca gggcgtttct gatggctgac gggcaaaagg
     1021 tggtggcaag tacaccgaaa accaccagaa acgcacctga tttattttac gcatatgcat
     1081 cacttattca catcactgca tagccggtga tttcggttaa aaaagactct ctgtgtgctg
     1141 aaatcgcaga aaatggccat gatccccgtc acgctcaggc cacctgagac gggcgtttat
     1201 cagtctccat actccctgtc accatgagat aatgtgcgtt gccgttccgg taccagatct
     1261 gctgtcttct ctggttcctt ttccgttgtt tgcccgtatc gctgttgctc aatctcattc
     1321 agcctgtcga taaccggcgc agctgctcgc tcaaactctg cacctgcctg ctcaagcccg
     1381 acacgcgctc gctcagcgcc gcgttctccc gttgcataag accagacatc ttccgccatt
     1441 cctcgaaggc gctctcccac tcgtccagcc ttctcgagta gtcctgctgt agctgctcta
     1501 acgcgctcag caattgtttt tccagttccg tcattctgct ctactcccgt accagcttca
     1561 ccgcgttccg cgtcttgttg tccaccgtcc ggcccgtttc ggctttcatc ccctccggca
     1621 gcaccagaaa ccgtccgttg cggttctcca gataggtcac gccccacgtc tgcatgtgca
     1681 gtttcgacag cgtatctctc tgctgcctga tttccgccag gttcgccgct atccggttcc
     1741 cctggtacca cagcaccccg ctcaggctgg cgaacagcag ccctgacacc atggtgatgg
     1801 tcagccacgt ccgcccgacc attcgcagca cgctcagccg gttcgactgc atcgccgcgt
     1861 tcatcccctg ttcgtgggcg ctgatggcgt cgttgattct cttcgcgctt gcgttcagtt
     1921 ccgatttgac aacgttctcg tgcttgctga atgcggcttt cagcctctct tcggtaagct
     1981 gctgctgtgc tttcgatttc tcctcgaagt ccctcgaggc cgttaaaaga ctgctcataa
     2041 atggctcccc tcagtcggat atttcgcccc ccgtccgggt cggcaatgct gatactgttt
     2101 tttgtggttc tgaccacctc aaaaccggcc gctgtgagcg cccctgtgac gtcatcacgc
     2161 gttttcagct ctcctgatga ggctaacatc agcaaacccc gtgtaatcgt ctctgcggct
     2221 tcctgcttcg tttctggcag tcctgaaggc gtgaccagcg cccgccggtt ctccgggtcg
     2281 ttcggatcat gtagccccag cctgccgttg accactgtct gccacgcatc gatgcgcggc
     2341 cggtcggcac gatcgtaata cggctggagg cgtttccccg tcagtaattc ggtattgggg
     2401 atcagaaaat tcagctcaag acgacccttg tctgcgtgtt ccacccacag aatgctgtac
     2461 tggtctttat cgagtccggg catcagaacc cgctcaaagc tggccatcag tttttcacgc
     2521 tgacccggcg gcaggtccgc ctccgcgaat gacagcaccc cggaggtata ttttttcaca
     2581 tacggcgacg catcaatcag ctcccggact tcttccggct tcccctgcag gacgctggca
     2641 ccttcacgct gccggtcttt acccagaaga taatccacag gaccggcgcc cccgccgcga
     2701 ccccggggat ggaatttaac aatcatcgtc cggccctttt tccagtacgg catgccgcaa
     2761 ccgttccaga ccggcatcga tcgccatcag cgctgccacg atctgcaccc ggtcatgacc
     2821 ggcaccaccg gcgttcactt tccgggcgat ctggttcagg ttattgccca tgccggcaag
     2881 ctgacgcagc agcgcgggcg aaatcgaggg aagcctgccg gcgcgtgtcg gtttctcatc
     2941 aaggcaggtc tggcgcatcc acgccgccag ttgttttccg tcgcaccgct caagcaaccg
     3001 ccggtgttcg tcttccgtca cccacatcgt gagcatcttg ttgcgtttat ctgccagaat
     3061 cgcctcctga taacgccgtg acggacggga aagcctttcc cggtcggcgc ggggttggac
     3121 aagccgcagg cgcgtcagtg gggtttcggg gcgcagccct gaaccagtca cgtagcgcta
     3181 gcggagtgta tactggctta ctatggtggc atcggtatgg gtatcagcga aagtgctata
     3241 tatggcaggg atgacatgca gcgaaggtgc gtaaggcaga taatggtagt gccggggata
     3301 tgacgcctcc tcgctcactc ggtcgctgac gctcctgccg tgaggctgcg gcgggcgtta
     3361 cctgctcacg agtgacgaga taaagagatg gagctagagt cagaaaaggg cacgaaaagg
     3421 atgcggcgtt gccgtttttc cataggctcc gcccccctga cgagcatcac agaatctgac
     3481 gctcaaatca gtggtggcga aacccgacag gactataaag ataccaggcg tttccccctg
     3541 atggctccct cgtgcgctct cctgttcctg cctttcggtt taccggtgtc attccgctgt
     3601 tatggccgcg gtttctcatt ccacgcctga cactcagttc cgggtaggca gttcgctcca
     3661 agctggactg tatgcacgaa ccccccgttc agtccgaccg ctgcgcctta tccggtaact
     3721 atcgtcttga gtccaacccg gaaagacacg acaaaacgcc actggcagca gccaacagta
     3781 agagggtgta caagagataa ctgatgcaga gttcttgaag tctcagccca actacggcta
     3841 aactgaaagg acagaatttg gtttcagcgg tcttgtacac cctgttacca cggttcagaa
     3901 gttccccaac ttactgaacc ctcgaaaaaa ccgcctcccc aggcggtttt ttcgtttcag
     3961 acgaggatat tacgtcgcat cttatactta ggtcaacaac catcagcaag actggacctc
     4021 caaaacaaaa ggaggtaata tcctgataat gaacacagaa tgcgacaaaa gaaatgctaa
     4081 tgaaacaaga agttaaagaa aaaaaacaga cgatagaact aatcaatgat gattgtttaa
     4141 tcgctttaaa gatgcttcaa agcgattcaa tagatctgat cgttacatca ccaccttacg
     4201 cagaccaaag gaaaaaaacc tatggcggag taagtgcaga caaatatgtt gagtggttca
     4261 ccccgatagc caaagaacta ctgagagtga caaaatcatc aggctcattt gttctaaaca
     4321 taaaggaaag ggcgattaat ggcgagcgcc atacgtatgt aatagagcta attttaatga
     4381 tgcgaaaatt aggctggtta tggacagagg aatacatatg gcataaaaaa aatagttacc
     4441 ctgggaaatg gccaaatcgc tttagagact cttgggaaag atgcatccac tttacgaaaa
     4501 gtaaaaaatt caacatgtac caagaggaag taatggtgcc tatgggggat tggaaaaact
     4561 cacgacttaa aaacatgagt gatacagata agaaaagaga tgaatcgaaa gtagggagtg
     4621 gtttcggtaa aaaaatagaa aactgggtca ccagggatct agcataccca accaacgtgc
     4681 tacacatggc tacagagtgt ggaaaccgca gtcacagcgc agcttttcct gaaagcctac
     4741 ctgaatggtt catcaaactt ttcaccacag aaggtgacac cgttctggat ccattttccg
     4801 gttctggaac cacattaaaa gttgcgaaag caatgaaaag gaacgctgta ggtattgaaa
     4861 tattagatga atattgcgag ataacggcaa atagagtagg tttgaaaaaa tcgtctcaaa
     4921 aaaaataccg gtatacaaat gattgaatca cggattattt cagattttat agaatcttgc
     4981 attgatgaag agttccatca aaaaaaacaa gaaaaaataa gggcgataaa attatcagat
     5041 ataacaaaaa gaaaaaaccc atatttattt aaggcgaagg ggctaacatc agcaagtgac
     5101 ttaataaagt caataatgga tgcaacggta tcctctggag aggagaccgt ttttggcaat
     5161 ttcatggaaa agattgcaat cttcacatgt tcccaagcat ttggtggaag aaaatccagt
     5221 gcggtaggaa tagatcttga gttcgaaact gaaagcacaa aatatctaat aagcatcaaa
     5281 tccggcccaa actggggtaa ctcatcacaa aaaaagaaaa tgcaagacaa cttcattaaa
     5341 gccaaaaaag tcctaggcac atccggtgga attaattcaa aatcaataac ttgcatcgag
     5401 gggtgttgtt atggttatga cgccagacct gaaaagggaa cccacataaa actatgcggc
     5461 caagacttct ggacatttat atctaacgga aacaacgaat tatatagtga tataattgag
     5521 cctattggta agcttgcaga cgaaaaaaac aaggaactga tagaactaac aaatgccaaa
     5581 ctaaatcttt ttacggctga gtttatttca gaatattgta atagtgatgg ttcaataaat
     5641 tgggctttat ttgtagcaag aaact
//
