LOCUS       NZ_CP145169             4183 bp    DNA     circular CON 05-APR-2024
DEFINITION  Raoultella ornithinolytica strain CAV1921 plasmid pCAV1921-4183,
            complete sequence.
ACCESSION   NZ_CP145169
VERSION     NZ_CP145169.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN22875523
            Assembly: GCF_036786095.1
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  JOURNAL   Unpublished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                   :: 193x and 91x
            Sequencing Technology             :: PacBio and Illumina
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_036786095.1-RS_2024_04_05
            Annotation Date                   :: 04/05/2024 16:27:51
            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)                     :: 5,748
            CDSs (total)                      :: 5,624
            Genes (coding)                    :: 5,461
            CDSs (with protein)               :: 5,461
            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)              :: 163
            CDSs (without protein)            :: 163
            Pseudo Genes (ambiguous residues) :: 0 of 163
            Pseudo Genes (frameshifted)       :: 54 of 163
            Pseudo Genes (incomplete)         :: 124 of 163
            Pseudo Genes (internal stop)      :: 25 of 163
            Pseudo Genes (multiple problems)  :: 36 of 163
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP145169.1.
            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="CAV1921"
                     /isolation_source="Hospital waste water"
                     /db_xref="taxon:54291"
                     /plasmid="pCAV1921-4183"
                     /geo_loc_name="USA:Virginia"
                     /lat_lon="38.14 N 78.45 W"
                     /collection_date="2014-01-01"
                     /collected_by="Clinical Microbiology University of Virginia
                     Health System"
     gene            join(3935..4183,1..21)
                     /locus_tag="LM286_RS28690"
                     /old_locus_tag="LM286_28695"
     CDS             join(3935..4183,1..21)
                     /locus_tag="LM286_RS28690"
                     /old_locus_tag="LM286_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(267..536)
                     /locus_tag="LM286_RS28695"
                     /old_locus_tag="LM286_28700"
     CDS             complement(267..536)
                     /locus_tag="LM286_RS28695"
                     /old_locus_tag="LM286_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(538..927)
                     /locus_tag="LM286_RS28700"
                     /old_locus_tag="LM286_28705"
     CDS             complement(538..927)
                     /locus_tag="LM286_RS28700"
                     /old_locus_tag="LM286_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(944..1108)
                     /locus_tag="LM286_RS28705"
                     /old_locus_tag="LM286_28710"
     CDS             complement(944..1108)
                     /locus_tag="LM286_RS28705"
                     /old_locus_tag="LM286_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"
     gene            1350..2543
                     /gene="mobQ"
                     /locus_tag="LM286_RS28710"
                     /old_locus_tag="LM286_28715"
     CDS             1350..2543
                     /gene="mobQ"
                     /locus_tag="LM286_RS28710"
                     /old_locus_tag="LM286_28715"
                     /inference="COORDINATES: protein motif:HMM:NF041496.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /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            3081..3938
                     /locus_tag="LM286_RS28715"
                     /old_locus_tag="LM286_28720"
     CDS             3081..3938
                     /locus_tag="LM286_RS28715"
                     /old_locus_tag="LM286_28720"
                     /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"
     Typing          1351..2360
                     /name="MOBQ"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="99.703"
                     /coverage="85.0"
                     /evalue="0.0"
ORIGIN
        1 atgcctaaaa acagcctgta acgacttcta agcagttttt ccccctaacc taaccaaacc
       61 ctccacccct ggggggattt ttcccccttt ccccgtatcc gggcttgtgt ctggataggt
      121 gagggacact ctggtaccaa caaatcaaca aacccaccca gccaccggag gccctctggc
      181 aaccttaaaa cctccagccg ttggctggca acccttcaca gcaaaaaacc agcccaaaaa
      241 gcggctggtt cttcactgtt cacggtttac gatttccatt gttgcaatat atccattccg
      301 attcgtgtaa aatctctttt ctcttcttcg tctaactcat tgattttact taacaagcca
      361 agaattaaag ccttgttaat ttcctctggt tttttatcta acaccttagc cacttctgca
      421 cccaggatta ttttttgtct tgtttcttcc cgtctgtcct gccttgcttt ttttgttctt
      481 agtgcttgta atttattttg tagatctgcg atctgctgtg ctgttgattt gctcatatta
      541 caacctcctt ttatctttat tatctttgtt atcttctact tggattattt catttaattt
      601 atctaattca taagaagcca gtttttgaac aatcacaaac tggaaattct cataatcata
      661 taatggccat tcaagcaacc gccaaacaaa aggatcgtga tctcccaaag ggcttaaatc
      721 atatgttgta attccaaaat ctaaaataac agcagttctc agatctattt tatctcgaaa
      781 aattattcta catatatcct caactggata ctggaaaaaa tccagagcca tattattttt
      841 atttaaaaaa gacactacct ctttatgtaa aatgtttaaa cagtcgttaa actcttgttc
      901 ttcaaactct aaacctctat attgcatatt aaaaacctcc acactataag atagtgaatg
      961 tattaccaca tttagtacat tcaacctctg taattggtcc ctcttctttt gaatactcct
     1021 cagtaaatct aaatatatgg cgagtgtttt tttcacaatg atcacaccaa ttgacttgta
     1081 tatcagggcc gagcgtttct ttttccatat aacctccatt attttatttt gttatttatt
     1141 acctccatta tttactttag tcaaatatat tttagaataa aataaataat atttaatatt
     1201 gggcgaagcc tggggttcat tacttattat tttgaggtga agccgaaaaa ataatattag
     1261 taatgcccac ttacacgtcg caagcgacgt atgggccctg cggggctaaa aaccaaaatt
     1321 caaaagacaa aaaaagtaag gggtagacta tggcgacatt tcatatcagc tttaaaaaat
     1381 tacgaagatc agaaggtaaa tcttcggttt atttatctgc atatcaaaac cgagaaaaga
     1441 caaaagataa tcgaaccggg gcaacctggg attattcaaa aaaagaggga tttttcggct
     1501 ctgctatcct ctcccctgcc ggcacacctg ccgaactggt gaaggactca ggcaccctct
     1561 ggaatgccgt agaggctggc gagaagcgaa aggatgccga attatgtcgc tatgtggaca
     1621 tagccatccc caaggagctg gacgacggcc agaagaagca gatcgtcctc gattactgcc
     1681 aagaaaattt cgtggattat ggaatgattg cagacatagc atttcatgat cttgatagtc
     1741 ataaccctca tgctcatgta atgctaactt taagaactgt tagcccaaat ggatttggga
     1801 acaaacaaag agaatggaat aatagagaaa atattgaagc ctggcgagtt aactgggaaa
     1861 taatagcaaa tgacagatta aaaaaatatg gtcataagtc ccgtattgat tcccgttcat
     1921 taaaagatca aaaagaagag gcagaaagaa aggctgtttt tgctaaaact ccgaaagaga
     1981 aagccaagtg gatttcaaaa actattgaac tggacagaac gccaatgacc aggatacaca
     2041 ggcaccaatg gcgaaaaggt caaaaattaa gagctatgga gcaaaaagaa aaagcattat
     2101 tattaaaaat agctaatgca acatacttac agcaaaccaa accacctcag ccagaggaaa
     2161 ctatgaaaat agagaaaaag cctcttgcaa ggtcaatcat tgataattta aaggcattat
     2221 acaaaaagac ccagcatata tttaaatcaa aacctaatgt aaataaaaat aaaaaagaag
     2281 aaaaagaaga tcctcaaaat ttcgttagta gttatgtaat aaatgaattt ggcgaacata
     2341 tattaaagac agagttagaa acaaaaccta aaacaggcac aggaaccgga accggtggaa
     2401 ataatggagg cggaaaaatg ggttcaggct ctggaatgtc tcctatgaac caaccacaac
     2461 caaaaattga agagcctgag ccggaaccaa tgccggaatt cgaagatcag caacctaaga
     2521 ggaagaagaa atttggaatg tagtatatag tggtatatat tcctatatag tagtatcact
     2581 taatacaact taatattatt taatactata ctataatata ctacattttt agagttgtga
     2641 tcctcgccgg ttctatttcc cctttatgta ttgccacagc ttcattaact gacttcataa
     2701 gcattttaaa aaatttacta tgcttatttc ttttccgttt tttctgcact ttcttttttt
     2761 tcatatattc accaaaaaaa atcgaatcgc caatttttct tcgaacaata ctcttttttc
     2821 tttttttatt gtttttctat cttcggtaat gcttcgcacc atagatctga tagtaatgct
     2881 ttgctgccgt atgtaaagaa ctgccccaac ttcgttgggc tgttatctga tatggttaag
     2941 ctccccactt gacaaatttt taagatcggt tagaactggt acaggattga aaaacctata
     3001 aaaataaaaa ccccaccctc tgcgattttg ttttggcgac agaaaacaga gagtagggcc
     3061 agataaaaag gactgaaaaa atgataatac aagaagaaca taacatcgat ttttttaaaa
     3121 atcaaatgcc taacaagcct tattgtacaa ataacctcga tatgggatta agcataagga
     3181 acaaggcaaa agccttagaa atgctgtatt tacaggcaaa tcagccagca atccaaactt
     3241 gcttactctt tgatttagat aagaaaaact cattctatac atttgagaag gtgggcttac
     3301 ccatacctca ctttattaca aaaacaccaa agacaggtcg ttgccattac gggtacatgc
     3361 ttaaagccgg tgtttgtaag acacaacaag caaggttgaa gccgttgaag tatgccgctg
     3421 ccgttgaaat ggctatggcg aaaaaactca aagcagatct ggggtttgct ggattgatta
     3481 caaaaaatcc actcaatgat cactggtcgc cgttctggtc aggtgctgac ctttacgacc
     3541 tggattattt agctgatttt gtggacttag aaaaacctca aatacaagag aaaaaaagcg
     3601 aggcttatgg tttaggtcgc aatgttaatt tgtttgaaga tctacgacaa tatgcttaca
     3661 gaacggtttt aaatttcaaa aaaatatcta ctttcgagaa attcgaaaac gaactattat
     3721 taaaagcaca gggtttaaat actttttgca atccactaaa tccgttacaa tacaaagagt
     3781 taaaggcaac agcaagaagc atagcccgtt ggacctggaa aaattttgat agccatacat
     3841 tttcactaat acaatcttca agaggtgcga aaaataaaaa caaacccaag aagagtaatg
     3901 ttaaagaaat gcttggtttt ataggaggtg aaaaatgaga agaagcacaa taagaaaagg
     3961 tttaactcaa aaagaaatgg ctgaaagatt taatatatct gttaaaacgg taaaaaaata
     4021 tacatccgaa ccgcgtgaac aatacgaaca aacagcggct gatcgtcgtc gtcaggctta
     4081 cgaactacga agccaggggc tgaaatggca acaggtagcc gacaaaatgg gctgttcgta
     4141 tcacggagcc gttgccctgt atcgccgtta tgttgcctta gat
//
