LOCUS       NZ_CP145162             4183 bp    DNA     circular CON 05-APR-2024
DEFINITION  Raoultella ornithinolytica strain CAVp363 plasmid pCAVP363-4183,
            complete sequence.
ACCESSION   NZ_CP145162
VERSION     NZ_CP145162.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN22837213
            Assembly: GCF_036786065.1
KEYWORDS    RefSeq.
SOURCE      Raoultella ornithinolytica
  ORGANISM  Raoultella ornithinolytica
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Klebsiella/Raoultella group; Raoultella.
REFERENCE   1  (bases 1 to 4183)
  AUTHORS   Sheppard,A.E., Barry,K.E., Parikh,H.I., Vegesana,K., Sebra,R.,
            George,S., Sanderson,N.D., Stoesser,N., Eyre,D.W., Crook,D.W.,
            Walker,A.S. and Mathers,A.J.
  TITLE     Tn5403 promotes plasmid rearrangements and degradation of the
            Klebsiella pneumoniae carbapenemase (KPC) transposon Tn4401
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 4183)
  AUTHORS   Sheppard,A.E., Barry,K.E., Parikh,H.I., Vegesana,K., Sebra,R.,
            George,S., Sanderson,N.D., Stoesser,N., Eyre,D.W., Crook,D.W.,
            Walker,A.S. and Mathers,A.J.
  TITLE     Direct Submission
  JOURNAL   Submitted (11-FEB-2024) Biological Sciences, University of Adelaide,
            Victoria Drive, Adelaide 5005, Australia
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: Unicycler v. 0.4.0
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 18x and 84x
            Sequencing Technology             :: Oxford Nanopore and Illumina
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_036786065.1-RS_2024_04_05
            Annotation Date                   :: 04/05/2024 15:59:10
            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)                     :: 5,742
            CDSs (total)                      :: 5,620
            Genes (coding)                    :: 5,447
            CDSs (with protein)               :: 5,447
            Genes (RNA)                       :: 122
            rRNAs                             :: 9, 8, 8 (5S, 16S, 23S)
            complete rRNAs                    :: 9, 8, 8 (5S, 16S, 23S)
            tRNAs                             :: 85
            ncRNAs                            :: 12
            Pseudo Genes (total)              :: 173
            CDSs (without protein)            :: 173
            Pseudo Genes (ambiguous residues) :: 0 of 173
            Pseudo Genes (frameshifted)       :: 55 of 173
            Pseudo Genes (incomplete)         :: 129 of 173
            Pseudo Genes (internal stop)      :: 24 of 173
            Pseudo Genes (multiple problems)  :: 33 of 173
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP145162.1.
            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..4183
                     /organism="Raoultella ornithinolytica"
                     /mol_type="genomic DNA"
                     /strain="CAVp363"
                     /host="Homo sapiens"
                     /db_xref="taxon:54291"
                     /plasmid="pCAVP363-4183"
                     /geo_loc_name="USA:Virginia"
                     /lat_lon="38.14 N 78.45 W"
                     /collection_date="2016-12-01"
                     /collected_by="Clinical Microbiology University of Virginia
                     Health System"
     gene            join(3982..4183,1..992)
                     /gene="mobQ"
                     /locus_tag="LMH34_RS28685"
                     /old_locus_tag="LMH34_28685"
     CDS             join(3982..4183,1..992)
                     /gene="mobQ"
                     /locus_tag="LMH34_RS28685"
                     /old_locus_tag="LMH34_28685"
                     /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="MobQ family relaxase"
                     /protein_id="WP_000190114.1"
                     /translation="MATFHISFKKLRRSEGKSSVYLSAYQNREKTKDNRTGATWDYSKK
                     EGFFGSAILSPAGTPAELVKDSGTLWNAVEAGEKRKDAELCRYVDIAIPKELDDGQKKQ
                     IVLDYCQENFVDYGMIADIAFHDLDSHNPHAHVMLTLRTVSPNGFGNKQREWNNRENIE
                     AWRVNWEIIANDRLKKYGHKSRIDSRSLKDQKEEAERKAVFAKTPKEKAKWISKTIELD
                     RTPMTRIHRHQWRKGQKLRAMEQKEKALLLKIANATYLQQTKPPQPEETMKIEKKPLAR
                     SIIDNLKALYKKTQHIFKSKPNVNKNKKEEKEDPQNFVSSYVINEFGEHILKTELETKP
                     KTGTGTGTGGNNGGGKMGSGSGMSPMNQPQPKIEEPEPEPMPEFEDQQPKRKKKFGM"
                     /name="mobQ"
     gene            1530..2387
                     /locus_tag="LMH34_RS28690"
                     /old_locus_tag="LMH34_28690"
     CDS             1530..2387
                     /locus_tag="LMH34_RS28690"
                     /old_locus_tag="LMH34_28690"
                     /inference="COORDINATES: protein motif:HMM:NF015076.4"
                     /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_000586611.1"
                     /translation="MIIQEEHNIDFFKNQMPNKPYCTNNLDMGLSIRNKAKALEMLYLQ
                     ANQPAIQTCLLFDLDKKNSFYTFEKVGLPIPHFITKTPKTGRCHYGYMLKAGVCKTQQA
                     RLKPLKYAAAVEMAMAKKLKADLGFAGLITKNPLNDHWSPFWSGADLYDLDYLADFVDL
                     EKPQIQEKKSEAYGLGRNVNLFEDLRQYAYRTVLNFKKISTFEKFENELLLKAQGLNTF
                     CNPLNPLQYKELKATARSIARWTWKNFDSHTFSLIQSSRGAKNKNKPKKSNVKEMLGFI
                     GGEK"
                     /name="replication initiation protein"
     gene            2384..2653
                     /locus_tag="LMH34_RS28695"
                     /old_locus_tag="LMH34_28695"
     CDS             2384..2653
                     /locus_tag="LMH34_RS28695"
                     /old_locus_tag="LMH34_28695"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001324694.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="response regulator transcription factor"
                     /protein_id="WP_021197950.1"
                     /translation="MRRSTIRKGLTQKEMAERFNISVKTVKKYTSEPREQYEQTAADRR
                     RQAYELRSQGLKWQQVADKMGCSYHGAVALYRRYVALDMPKNSL"
                     /name="response regulator transcription factor"
     gene            complement(2899..3168)
                     /locus_tag="LMH34_RS28700"
                     /old_locus_tag="LMH34_28700"
     CDS             complement(2899..3168)
                     /locus_tag="LMH34_RS28700"
                     /old_locus_tag="LMH34_28700"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001549726.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="conjugal transfer protein TraD"
                     /protein_id="WP_000047246.1"
                     /translation="MSKSTAQQIADLQNKLQALRTKKARQDRREETRQKIILGAEVAKV
                     LDKKPEEINKALILGLLSKINELDEEEKRDFTRIGMDILQQWKS"
                     /name="conjugal transfer protein TraD"
     gene            complement(3170..3559)
                     /locus_tag="LMH34_RS28705"
                     /old_locus_tag="LMH34_28705"
     CDS             complement(3170..3559)
                     /locus_tag="LMH34_RS28705"
                     /old_locus_tag="LMH34_28705"
                     /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_223168448.1"
                     /translation="MQYRGLEFEEQEFNDCLNILHKEVVSFLNKNNMALDFFQYPVEDI
                     CRIIFRDKIDLRTAVILDFGITTYDLSPLGDHDPFVWRLLEWPLYDYENFQFVIVQKLA
                     SYELDKLNEIIQVEDNKDNKDKRRL"
                     /name="hypothetical protein"
     gene            complement(3576..3740)
                     /locus_tag="LMH34_RS28710"
                     /old_locus_tag="LMH34_28710"
     CDS             complement(3576..3740)
                     /locus_tag="LMH34_RS28710"
                     /old_locus_tag="LMH34_28710"
                     /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_162865999.1"
                     /translation="MEKETLGPDIQVNWCDHCEKNTRHIFRFTEEYSKEEGPITEVECT
                     KCGNTFTIL"
                     /name="hypothetical protein"
     Typing          4..809
                     /name="MOBQ"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="99.628"
                     /coverage="85.0"
                     /evalue="3.2300000000000003e-173"
ORIGIN
        1 gcaccctctg gaatgccgta gaggctggcg agaagcgaaa ggatgccgaa ttatgtcgct
       61 atgtggacat agccatcccc aaggagctgg acgacggcca gaagaagcag atcgtcctcg
      121 attactgcca agaaaatttc gtggattatg gaatgattgc agacatagca tttcatgatc
      181 ttgatagtca taaccctcat gctcatgtaa tgctaacttt aagaactgtt agcccaaatg
      241 gatttgggaa caaacaaaga gaatggaata atagagaaaa tattgaagcc tggcgagtta
      301 actgggaaat aatagcaaat gacagattaa aaaaatatgg tcataagtcc cgtattgatt
      361 cccgttcatt aaaagatcaa aaagaagagg cagaaagaaa ggctgttttt gctaaaactc
      421 cgaaagagaa agccaagtgg atttcaaaaa ctattgaact ggacagaacg ccaatgacca
      481 ggatacacag gcaccaatgg cgaaaaggtc aaaaattaag agctatggag caaaaagaaa
      541 aagcattatt attaaaaata gctaatgcaa catacttaca gcaaaccaaa ccacctcagc
      601 cagaggaaac tatgaaaata gagaaaaagc ctcttgcaag gtcaatcatt gataatttaa
      661 aggcattata caaaaagacc cagcatatat ttaaatcaaa acctaatgta aataaaaata
      721 aaaaagaaga aaaagaagat cctcaaaatt tcgttagtag ttatgtaata aatgaatttg
      781 gcgaacatat attaaagaca gagttagaaa caaaacctaa aacaggcaca ggaaccggaa
      841 ccggtggaaa taatggaggc ggaaaaatgg gttcaggctc tggaatgtct cctatgaacc
      901 aaccacaacc aaaaattgaa gagcctgagc cggaaccaat gccggaattc gaagatcagc
      961 aacctaagag gaagaagaaa tttggaatgt agtatatagt ggtatatatt cctatatagt
     1021 agtatcactt aatacaactt aatattattt aatactatac tataatatac tacattttta
     1081 gagttgtgat cctcgccggt tctatttccc ctttatgtat tgccacagct tcattaactg
     1141 acttcataag cattttaaaa aatttactat gcttatttct tttccgtttt ttctgcactt
     1201 tctttttttt catatattca ccaaaaaaaa tcgaatcgcc aatttttctt cgaacaatac
     1261 tcttttttct ttttttattg tttttctatc ttcggtaatg cttcgcacca tagatctgat
     1321 agtaatgctt tgctgccgta tgtaaagaac tgccccaact tcgttgggct gttatctgat
     1381 atggttaagc tccccacttg acaaattttt aagatcggtt agaactggta caggattgaa
     1441 aaacctataa aaataaaaac cccaccctct gcgattttgt tttggcgaca gaaaacagag
     1501 agtagggcca gataaaaagg actgaaaaaa tgataataca agaagaacat aacatcgatt
     1561 tttttaaaaa tcaaatgcct aacaagcctt attgtacaaa taacctcgat atgggattaa
     1621 gcataaggaa caaggcaaaa gccttagaaa tgctgtattt acaggcaaat cagccagcaa
     1681 tccaaacttg cttactcttt gatttagata agaaaaactc attctataca tttgagaagg
     1741 tgggcttacc catacctcac tttattacaa aaacaccaaa gacaggtcgt tgccattacg
     1801 ggtacatgct taaagccggt gtttgtaaga cacaacaagc aaggttgaag ccgttgaagt
     1861 atgccgctgc cgttgaaatg gctatggcga aaaaactcaa agcagatctg gggtttgctg
     1921 gattgattac aaaaaatcca ctcaatgatc actggtcgcc gttctggtca ggtgctgacc
     1981 tttacgacct ggattattta gctgattttg tggacttaga aaaacctcaa atacaagaga
     2041 aaaaaagcga ggcttatggt ttaggtcgca atgttaattt gtttgaagat ctacgacaat
     2101 atgcttacag aacggtttta aatttcaaaa aaatatctac tttcgagaaa ttcgaaaacg
     2161 aactattatt aaaagcacag ggtttaaata ctttttgcaa tccactaaat ccgttacaat
     2221 acaaagagtt aaaggcaaca gcaagaagca tagcccgttg gacctggaaa aattttgata
     2281 gccatacatt ttcactaata caatcttcaa gaggtgcgaa aaataaaaac aaacccaaga
     2341 agagtaatgt taaagaaatg cttggtttta taggaggtga aaaatgagaa gaagcacaat
     2401 aagaaaaggt ttaactcaaa aagaaatggc tgaaagattt aatatatctg ttaaaacggt
     2461 aaaaaaatat acatccgaac cgcgtgaaca atacgaacaa acagcggctg atcgtcgtcg
     2521 tcaggcttac gaactacgaa gccaggggct gaaatggcaa caggtagccg acaaaatggg
     2581 ctgttcgtat cacggagccg ttgccctgta tcgccgttat gttgccttag atatgcctaa
     2641 aaacagcctg taacgacttc taagcagttt ttccccctaa cctaaccaaa ccctccaccc
     2701 ctggggggat ttttccccct ttccccgtat ccgggcttgt gtctggatag gtgagggaca
     2761 ctctggtacc aacaaatcaa caaacccacc cagccaccgg aggccctctg gcaaccttaa
     2821 aacctccagc cgttggctgg caacccttca cagcaaaaaa ccagcccaaa aagcggctgg
     2881 ttcttcactg ttcacggttt acgatttcca ttgttgcaat atatccattc cgattcgtgt
     2941 aaaatctctt ttctcttctt cgtctaactc attgatttta cttaacaagc caagaattaa
     3001 agccttgtta atttcctctg gttttttatc taacacctta gccacttctg cacccaggat
     3061 tattttttgt cttgtttctt cccgtctgtc ctgccttgct ttttttgttc ttagtgcttg
     3121 taatttattt tgtagatctg cgatctgctg tgctgttgat ttgctcatat tacaacctcc
     3181 ttttatcttt attatctttg ttatcttcta cttggattat ttcatttaat ttatctaatt
     3241 cataagaagc cagtttttga acaatcacaa actggaaatt ctcataatca tataatggcc
     3301 attcaagcaa ccgccaaaca aaaggatcgt gatctcccaa agggcttaaa tcatatgttg
     3361 taattccaaa atctaaaata acagcagttc tcagatctat tttatctcga aaaattattc
     3421 tacatatatc ctcaactgga tactggaaaa aatccagagc catattattt ttatttaaaa
     3481 aagacactac ctctttatgt aaaatgttta aacagtcgtt aaactcttgt tcttcaaact
     3541 ctaaacctct atattgcata ttaaaaacct ccacactata agatagtgaa tgtattacca
     3601 catttagtac attcaacctc tgtaattggt ccctcttctt ttgaatactc ctcagtaaat
     3661 ctaaatatat ggcgagtgtt tttttcacaa tgatcacacc aattgacttg tatatcaggg
     3721 ccgagcgttt ctttttccat ataacctcca ttattttatt ttgttattta ttacctccat
     3781 tatttacttt agtcaaatat attttagaat aaaataaata atatttaata ttgggcgaag
     3841 cctggggttc attacttatt attttgaggt gaagccgaaa aaataatatt agtaatgccc
     3901 acttacacgt cgcaagcgac gtatgggccc tgcggggcta aaaaccaaaa ttcaaaagac
     3961 aaaaaaagta aggggtagac tatggcgaca tttcatatca gctttaaaaa attacgaaga
     4021 tcagaaggta aatcttcggt ttatttatct gcatatcaaa accgagaaaa gacaaaagat
     4081 aatcgaaccg gggcaacctg ggattattca aaaaaagagg gatttttcgg ctctgctatc
     4141 ctctcccctg ccggcacacc tgccgaactg gtgaaggact cag
//
