LOCUS       NZ_CP145170             3223 bp    DNA     circular CON 05-APR-2024
DEFINITION  Raoultella ornithinolytica strain CAV1921 plasmid pCAV1921-3223,
            complete sequence.
ACCESSION   NZ_CP145170
VERSION     NZ_CP145170.1
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 3223)
  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  JOURNAL   Unpublished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 3223)
  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
            CP145170.1.
            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..3223
                     /organism="Raoultella ornithinolytica"
                     /mol_type="genomic DNA"
                     /strain="CAV1921"
                     /isolation_source="Hospital waste water"
                     /db_xref="taxon:54291"
                     /plasmid="pCAV1921-3223"
                     /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            232..447
                     /locus_tag="LM286_RS28720"
                     /old_locus_tag="LM286_28725"
     CDS             232..447
                     /locus_tag="LM286_RS28720"
                     /old_locus_tag="LM286_28725"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000137421.1"
                     /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_024195375.1"
                     /translation="MTELEKQLLSALEQLQQDYSKRLDEWENAFAEWRTMSGLIQRENA
                     ALNERVTVLSRQVQSLSEQLRRLSKG"
                     /name="MbeD family mobilization/exclusion protein"
     gene            615..947
                     /locus_tag="LM286_RS28725"
                     /old_locus_tag="LM286_28730"
     CDS             615..947
                     /locus_tag="LM286_RS28725"
                     /old_locus_tag="LM286_28730"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_008784643.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="EmrE family multidrug efflux SMR transporter"
                     /protein_id="WP_001099531.1"
                     /translation="MNTYIFLGGAIVAEVIGTTFMKYSEGFTRLWPSVGTAISYCAAFY
                     LLSQTLENIPTGIAYAIWSGAGIVLISLAGWLVSGQKLDWPAIAGMFLICVGVLVINIF
                     SKSSAH"
                     /name="EmrE family multidrug efflux SMR transporter"
     gene            complement(1156..1326)
                     /locus_tag="LM286_RS28730"
                     /old_locus_tag="LM286_28735"
     CDS             complement(1156..1326)
                     /locus_tag="LM286_RS28730"
                     /old_locus_tag="LM286_28735"
                     /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="hypothetical protein"
                     /protein_id="WP_004193911.1"
                     /translation="MHEPPVQSDYHARSGNYQLESNPERHDKSPVAVAIGNWVHGAEIV
                     ENAYRVLEVKA"
                     /name="hypothetical protein"
     gene            1965..2288
                     /locus_tag="LM286_RS28735"
                     /old_locus_tag="LM286_28740"
     CDS             1965..2288
                     /locus_tag="LM286_RS28735"
                     /old_locus_tag="LM286_28740"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000957083.1"
                     /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_004193914.1"
                     /translation="MLTMWVTEDEHRRLLERCEGKQLAAWMRQTCLDEKPARAGKLPSI
                     SPALLRQLAGMGNNLNQIARQVNAGGGSGHDRVQIVAALMAIDAGLERLRHAVLEKGAD
                     DDR"
                     /name="MobC family plasmid mobilization relaxosome protein"
     gene            2497..>2931
                     /locus_tag="LM286_RS28740"
                     /old_locus_tag="LM286_28745"
                     /pseudo=""
     CDS             2497..>2931
                     /locus_tag="LM286_RS28740"
                     /old_locus_tag="LM286_28745"
                     /inference="COORDINATES: protein motif:HMM:NF015397.4"
                     /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"
     ARG             616..947
                     /name="qacG"
                     /gene="qacG"
                     /gene_name="small multidrug resistance (SMR) antibiotic
                     efflux pump"
                     /tool="rgi"
                     /drug_class="disinfecting agents and antiseptics"
                     /identity="41.35"
                     /coverage="102.8"
     Typing          1678..1869
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="92.821"
                     /coverage="89.0"
                     /evalue="7.28e-73"
     Typing          complement(1215..1695)
                     /name="ColRNAI_rep_cluster_1987"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="84.867"
                     /coverage="93.0"
                     /evalue="1.73e-132"
     Typing          4..545
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="85.246"
                     /coverage="99.0"
                     /evalue="3.13e-88"
     Typing          2276..3222
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="95.886"
                     /coverage="99.0"
                     /evalue="0.0"
ORIGIN
        1 ctgctgatag cgtcgagcgc gggcattctg tggtggcagg ggcagcagat actcgagaac
       61 tatacgacca tccgggagca gaagagcacg caggccatgc tgtcagagag gaacagcggc
      121 gtacagctct cgacctgcgg cgagcagaga cgccgctgcg tgagggtgaa cccggaagcg
      181 ggacagttcg gagaggactc gagctggatg atactggcgg ggaaatagca catgacggag
      241 ctggaaaaac agttgctgag cgcattagag cagctacagc aggactactc gaaaaggctg
      301 gacgagtggg agaacgcctt cgcggaatgg cggacgatgt ctggtcttat tcaacgggag
      361 aacgcggcgc tgaacgagcg cgtcacggtc ttgagcaggc aggtgcagag tttgagcgag
      421 cagctgcgcc ggttgtcgaa aggctgaacg cgatagaaac tcaccggcag caggagcggg
      481 cggtgcagca ccagaaagcg ctggagctgg aacgatcgca gtggcagcat catggtcctt
      541 cgctatgata agccgggttc tattaattag ttgttatgta aagatattta aatttttcaa
      601 catgaggtat ttttatgaat acatatattt tcctgggagg ggctattgtg gctgaagtca
      661 taggcaccac ctttatgaaa tattcagaag gatttacacg cctgtggccg tctgtaggaa
      721 ctgcaataag ttattgcgct gccttttatc tgctttccca aacattggaa aatataccta
      781 ccggtattgc ttacgcaatt tggtctggtg cgggaattgt actaataagc ctagctggtt
      841 ggttggttag cggtcaaaaa cttgattggc ccgcaattgc aggaatgttc cttatttgcg
      901 ttggagtttt ggttattaat attttttcaa aatcttctgc gcattaactt tttaccgaag
      961 catattggcc aaagcaaaag gatttccttg agatcctttc tttctgcgcg taatcttttt
     1021 ccctgtaaac aaaaaaacca ccgctaccaa cggtggttcg tttgccggaa ttcagagcta
     1081 ccaactcttt gttccgatgg taactggctt tcacggagcg cagataccta aactgtcctt
     1141 tcagtgtagc cgcactcagg ctttcacttc aagaactctg taggcattct ctacaatctc
     1201 tgctccgtga acccagttac caatggctac cgccactggc gatttgtcgt gtctttccgg
     1261 gttggactca agttgatagt taccggaacg ggcgtggtag tcggactgaa cggggggttc
     1321 gtgcatacag tccatcctgg agcgaactgc ctacccggaa ccgagtttca ggcgtggaat
     1381 gagaaaccgc ggccataaca gcggaatgac accggtaaac cgaaaggcag gaatgcgggg
     1441 gagcacgagg gagccaccag ggggaaacgc ctggtatctt taagccgcat cgggtttcgc
     1501 caccgctgat ttgagcgtca ttttcgtgat actcgtcagg ggggcggagc ctatggaaaa
     1561 acggcaactc cgcatccttt tcttggcctt tcctgcttcg agcggcattt gcttatcccg
     1621 taatctgtga gctggtaacg cccgccgcag tctcacggca ggagcgtagc gaccgagtga
     1681 gcgaggaggc gtcatttcat caccacctgc attttgcact tacgcccggc agccgcattt
     1741 ttcccctgtc acatgaagca ctttcataaa ttaccactcc gtcataacat gtttagccag
     1801 tatacactcc gctagcgcta cgtgactggt tcagggctgc gccccgaaac ccgctaaaac
     1861 cactgccgcg tctgcggctt gtccaacacc gtgccgaccg ggaaaagatt tcccgtccgt
     1921 cccggcgtta tcaggaggcc ggattggcag acaaacgcag caaaatgctc accatgtggg
     1981 tgactgagga cgagcaccgg cgtctgctgg agcgctgcga gggtaagcaa ctcgcggcct
     2041 ggatgcggca gacgtgcctg gacgagaagc ccgcacgcgc cggcaaactt ccgtcgatct
     2101 cgccggcgct gcttcgtcag cttgccggca tggggaacaa ccttaaccag attgcccgcc
     2161 aggttaacgc cggtggtgga agcggacacg accgcgtgca gattgtcgcc gcgctgatgg
     2221 ccatcgatgc cggactcgag cggttgcggc atgccgtact ggaaaagggt gctgatgatg
     2281 atcgttaagt ttcatcctcg ggggcgcggc ggcggcggcg ggccggtcga ttatctgctg
     2341 ggtaaagatc gccagcgcga cggcgccagc gttctgcagg ggaagccgga tgaagtccgg
     2401 gagcttatcg acgcctcgcc ctacgccaaa aagtacactt ccggcgttct gtcttttgcc
     2461 gaacaggatt taccgcccgg ccagcgcgaa aagctgatgg cgagtttcga gcgggttctg
     2521 atgcccggac tcgataaaga ccagtacagc gtgctgtggg ttgagcaccg ggacaagggg
     2581 cggctggagc tgaacttcct gatcccgaac acggagcttc tgaccggcaa gcggctacag
     2641 ccgtattacg accgcgccga ccgtccgcgc atcgatgcct ggcagaccat agtgaacggc
     2701 aggctggggc tgcatgaccc gaacgcgccg gagaaccggc gggtgctggt ctcgccttcc
     2761 gcgctgccgg aagcgaagca ggaagccgcc caggcgatta cgagcggcct gcttgccctt
     2821 gcctcatccg gggagctgaa aacgcgtcag gacgtcactg aggcgctgga aagcgcaggt
     2881 tttgaggtgg tgcgcaccac aaaaagcagc atcagcattg ccgacccgga cggggggcga
     2941 aacatccgac tgaagggagc catctatgaa cagtctttta acgctggcga aggacttaga
     3001 gcagaaatcg aaagcgcagc agcagactac cggcgagatg ctgaaagccg cattcagcga
     3061 gcacgagaag tctgtcagag cggaactgag cgaaagcgag aagagaatca gcgccgccat
     3121 cctcgaccac gaccggaagc tgtcctcagc catgagccag cgcacgaaag ggatgctgcg
     3181 catggtcagc cagacgtggc tgaccatcgt tctggtctcc gcg
//
