LOCUS       NZ_CP145185             4183 bp    DNA     circular CON 05-APR-2024
DEFINITION  Raoultella ornithinolytica strain CAV1958 plasmid pCAV1958-4183,
            complete sequence.
ACCESSION   NZ_CP145185
VERSION     NZ_CP145185.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN22875475
            Assembly: GCF_036791365.1
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  JOURNAL   Unpublished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                   :: 205x and 106x
            Sequencing Technology             :: PacBio and Illumina
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_036791365.1-RS_2024_04_05
            Annotation Date                   :: 04/05/2024 15:54:32
            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)                     :: 5,757
            CDSs (total)                      :: 5,633
            Genes (coding)                    :: 5,467
            CDSs (with protein)               :: 5,467
            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)              :: 166
            CDSs (without protein)            :: 166
            Pseudo Genes (ambiguous residues) :: 0 of 166
            Pseudo Genes (frameshifted)       :: 54 of 166
            Pseudo Genes (incomplete)         :: 127 of 166
            Pseudo Genes (internal stop)      :: 25 of 166
            Pseudo Genes (multiple problems)  :: 36 of 166
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP145185.1.
            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="CAV1958"
                     /isolation_source="Hospital waste water"
                     /db_xref="taxon:54291"
                     /plasmid="pCAV1958-4183"
                     /geo_loc_name="USA:Virginia"
                     /lat_lon="38.14 N 78.45 W"
                     /collection_date="2014-03-01"
                     /collected_by="Clinical Microbiology University of Virginia
                     Health System"
     gene            complement(join(3683..4183,1..693))
                     /gene="mobQ"
                     /locus_tag="LMZ25_RS28730"
                     /old_locus_tag="LMZ25_28730"
     CDS             complement(join(3683..4183,1..693))
                     /gene="mobQ"
                     /locus_tag="LMZ25_RS28730"
                     /old_locus_tag="LMZ25_28730"
                     /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            935..1099
                     /locus_tag="LMZ25_RS28735"
                     /old_locus_tag="LMZ25_28735"
     CDS             935..1099
                     /locus_tag="LMZ25_RS28735"
                     /old_locus_tag="LMZ25_28735"
                     /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            1116..1505
                     /locus_tag="LMZ25_RS28740"
                     /old_locus_tag="LMZ25_28740"
     CDS             1116..1505
                     /locus_tag="LMZ25_RS28740"
                     /old_locus_tag="LMZ25_28740"
                     /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            1507..1776
                     /locus_tag="LMZ25_RS28745"
                     /old_locus_tag="LMZ25_28745"
     CDS             1507..1776
                     /locus_tag="LMZ25_RS28745"
                     /old_locus_tag="LMZ25_28745"
                     /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(2022..2291)
                     /locus_tag="LMZ25_RS28750"
                     /old_locus_tag="LMZ25_28750"
     CDS             complement(2022..2291)
                     /locus_tag="LMZ25_RS28750"
                     /old_locus_tag="LMZ25_28750"
                     /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(2288..3145)
                     /locus_tag="LMZ25_RS28755"
                     /old_locus_tag="LMZ25_28755"
     CDS             complement(2288..3145)
                     /locus_tag="LMZ25_RS28755"
                     /old_locus_tag="LMZ25_28755"
                     /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          complement(3867..4183)
                     /name="MOBQ"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="85.0"
                     /evalue="8.92e-49"
ORIGIN
        1 cctgtgtatc ctggtcattg gcgttctgtc cagttcaata gtttttgaaa tccacttggc
       61 tttctctttc ggagttttag caaaaacagc ctttctttct gcctcttctt tttgatcttt
      121 taatgaacgg gaatcaatac gggacttatg accatatttt tttaatctgt catttgctat
      181 tatttcccag ttaactcgcc aggcttcaat attttctcta ttattccatt ctctttgttt
      241 gttcccaaat ccatttgggc taacagttct taaagttagc attacatgag catgagggtt
      301 atgactatca agatcatgaa atgctatgtc tgcaatcatt ccataatcca cgaaattttc
      361 ttggcagtaa tcgaggacga tctgcttctt ctggccgtcg tccagctcct tggggatggc
      421 tatgtccaca tagcgacata attcggcatc ctttcgcttc tcgccagcct ctacggcatt
      481 ccagagggtg cctgagtcct tcaccagttc ggcaggtgtg ccggcagggg agaggatagc
      541 agagccgaaa aatccctctt tttttgaata atcccaggtt gccccggttc gattatcttt
      601 tgtcttttct cggttttgat atgcagataa ataaaccgaa gatttacctt ctgatcttcg
      661 taatttttta aagctgatat gaaatgtcgc catagtctac cccttacttt ttttgtcttt
      721 tgaattttgg tttttagccc cgcagggccc atacgtcgct tgcgacgtgt aagtgggcat
      781 tactaatatt attttttcgg cttcacctca aaataataag taatgaaccc caggcttcgc
      841 ccaatattaa atattattta ttttattcta aaatatattt gactaaagta aataatggag
      901 gtaataaata acaaaataaa ataatggagg ttatatggaa aaagaaacgc tcggccctga
      961 tatacaagtc aattggtgtg atcattgtga aaaaaacact cgccatatat ttagatttac
     1021 tgaggagtat tcaaaagaag agggaccaat tacagaggtt gaatgtacta aatgtggtaa
     1081 tacattcact atcttatagt gtggaggttt ttaatatgca atatagaggt ttagagtttg
     1141 aagaacaaga gtttaacgac tgtttaaaca ttttacataa agaggtagtg tcttttttaa
     1201 ataaaaataa tatggctctg gattttttcc agtatccagt tgaggatata tgtagaataa
     1261 tttttcgaga taaaatagat ctgagaactg ctgttatttt agattttgga attacaacat
     1321 atgatttaag ccctttggga gatcacgatc cttttgtttg gcggttgctt gaatggccat
     1381 tatatgatta tgagaatttc cagtttgtga ttgttcaaaa actggcttct tatgaattag
     1441 ataaattaaa tgaaataatc caagtagaag ataacaaaga taataaagat aaaaggaggt
     1501 tgtaatatga gcaaatcaac agcacagcag atcgcagatc tacaaaataa attacaagca
     1561 ctaagaacaa aaaaagcaag gcaggacaga cgggaagaaa caagacaaaa aataatcctg
     1621 ggtgcagaag tggctaaggt gttagataaa aaaccagagg aaattaacaa ggctttaatt
     1681 cttggcttgt taagtaaaat caatgagtta gacgaagaag agaaaagaga ttttacacga
     1741 atcggaatgg atatattgca acaatggaaa tcgtaaaccg tgaacagtga agaaccagcc
     1801 gctttttggg ctggtttttt gctgtgaagg gttgccagcc aacggctgga ggttttaagg
     1861 ttgccagagg gcctccggtg gctgggtggg tttgttgatt tgttggtacc agagtgtccc
     1921 tcacctatcc agacacaagc ccggatacgg ggaaaggggg aaaaatcccc ccaggggtgg
     1981 agggtttggt taggttaggg ggaaaaactg cttagaagtc gttacaggct gtttttaggc
     2041 atatctaagg caacataacg gcgatacagg gcaacggctc cgtgatacga acagcccatt
     2101 ttgtcggcta cctgttgcca tttcagcccc tggcttcgta gttcgtaagc ctgacgacga
     2161 cgatcagccg ctgtttgttc gtattgttca cgcggttcgg atgtatattt ttttaccgtt
     2221 ttaacagata tattaaatct ttcagccatt tctttttgag ttaaaccttt tcttattgtg
     2281 cttcttctca tttttcacct cctataaaac caagcatttc tttaacatta ctcttcttgg
     2341 gtttgttttt atttttcgca cctcttgaag attgtattag tgaaaatgta tggctatcaa
     2401 aatttttcca ggtccaacgg gctatgcttc ttgctgttgc ctttaactct ttgtattgta
     2461 acggatttag tggattgcaa aaagtattta aaccctgtgc ttttaataat agttcgtttt
     2521 cgaatttctc gaaagtagat atttttttga aatttaaaac cgttctgtaa gcatattgtc
     2581 gtagatcttc aaacaaatta acattgcgac ctaaaccata agcctcgctt tttttctctt
     2641 gtatttgagg tttttctaag tccacaaaat cagctaaata atccaggtcg taaaggtcag
     2701 cacctgacca gaacggcgac cagtgatcat tgagtggatt ttttgtaatc aatccagcaa
     2761 accccagatc tgctttgagt tttttcgcca tagccatttc aacggcagcg gcatacttca
     2821 acggcttcaa ccttgcttgt tgtgtcttac aaacaccggc tttaagcatg tacccgtaat
     2881 ggcaacgacc tgtctttggt gtttttgtaa taaagtgagg tatgggtaag cccaccttct
     2941 caaatgtata gaatgagttt ttcttatcta aatcaaagag taagcaagtt tggattgctg
     3001 gctgatttgc ctgtaaatac agcatttcta aggcttttgc cttgttcctt atgcttaatc
     3061 ccatatcgag gttatttgta caataaggct tgttaggcat ttgattttta aaaaaatcga
     3121 tgttatgttc ttcttgtatt atcatttttt cagtcctttt tatctggccc tactctctgt
     3181 tttctgtcgc caaaacaaaa tcgcagaggg tggggttttt atttttatag gtttttcaat
     3241 cctgtaccag ttctaaccga tcttaaaaat ttgtcaagtg gggagcttaa ccatatcaga
     3301 taacagccca acgaagttgg ggcagttctt tacatacggc agcaaagcat tactatcaga
     3361 tctatggtgc gaagcattac cgaagataga aaaacaataa aaaaagaaaa aagagtattg
     3421 ttcgaagaaa aattggcgat tcgatttttt ttggtgaata tatgaaaaaa aagaaagtgc
     3481 agaaaaaacg gaaaagaaat aagcatagta aattttttaa aatgcttatg aagtcagtta
     3541 atgaagctgt ggcaatacat aaaggggaaa tagaaccggc gaggatcaca actctaaaaa
     3601 tgtagtatat tatagtatag tattaaataa tattaagttg tattaagtga tactactata
     3661 taggaatata taccactata tactacattc caaatttctt cttcctctta ggttgctgat
     3721 cttcgaattc cggcattggt tccggctcag gctcttcaat ttttggttgt ggttggttca
     3781 taggagacat tccagagcct gaacccattt ttccgcctcc attatttcca ccggttccgg
     3841 ttcctgtgcc tgttttaggt tttgtttcta actctgtctt taatatatgt tcgccaaatt
     3901 catttattac ataactacta acgaaatttt gaggatcttc tttttcttct tttttatttt
     3961 tatttacatt aggttttgat ttaaatatat gctgggtctt tttgtataat gcctttaaat
     4021 tatcaatgat tgaccttgca agaggctttt tctctatttt catagtttcc tctggctgag
     4081 gtggtttggt ttgctgtaag tatgttgcat tagctatttt taataataat gctttttctt
     4141 tttgctccat agctcttaat ttttgacctt ttcgccattg gtg
//
