LOCUS       NZ_CP056468             4183 bp    DNA     circular CON 15-APR-2024
DEFINITION  Citrobacter freundii strain RHBSTW-00486 plasmid pRHBSTW-00486_3,
            complete sequence.
ACCESSION   NZ_CP056468
VERSION     NZ_CP056468.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN15148631
            Assembly: GCF_013748235.1
KEYWORDS    RefSeq.
SOURCE      Citrobacter freundii
  ORGANISM  Citrobacter freundii
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Citrobacter; Citrobacter freundii complex.
REFERENCE   1  (bases 1 to 4183)
  AUTHORS   AbuOun,M., Jones,H., Stubberfield,E., Gilson,D., Shaw,L.P.,
            Hubbard,A.T.M., Chau,K.K., Sebra,R., Peto,T.E.A., Crook,D.W.,
            Read,D.S., Gweon,H.S., Walker,A.S., Stoesser,N., Smith,R.P.,
            Anjum,M.F. and On Behalf Of The Rehab,Consortium.
  TITLE     A genomic epidemiological study shows that prevalence of
            antimicrobial resistance in Enterobacterales is associated with the
            livestock host, as well as antimicrobial usage
  JOURNAL   Microb Genom 7 (10) (2021)
   PUBMED   34609275
REFERENCE   2  (bases 1 to 4183)
  AUTHORS   Shaw,L.P.
  TITLE     Direct Submission
  JOURNAL   Submitted (12-JUN-2020) Nuffield Department of Medicine, University
            of Oxford, John Radcliffe Hospital, Oxford OX3 9DU, United Kingdom
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: Unicycler v. v0.4.7
            Assembly Name                     :: WTP5 T2-00486
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 117.291758332781x
            Sequencing Technology :: Hybrid: Illumina and OXFORD_NANOPORE
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_013748235.1-RS_2024_04_15
            Annotation Date                   :: 04/15/2024 04:21:23
            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)                     :: 4,943
            CDSs (total)                      :: 4,819
            Genes (coding)                    :: 4,721
            CDSs (with protein)               :: 4,721
            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)              :: 98
            CDSs (without protein)            :: 98
            Pseudo Genes (ambiguous residues) :: 0 of 98
            Pseudo Genes (frameshifted)       :: 28 of 98
            Pseudo Genes (incomplete)         :: 64 of 98
            Pseudo Genes (internal stop)      :: 22 of 98
            Pseudo Genes (multiple problems)  :: 15 of 98
            Pseudo Genes (short protein)      :: 1 of 98
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP056468.1.
            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="Citrobacter freundii"
                     /mol_type="genomic DNA"
                     /strain="RHBSTW-00486"
                     /isolation_source="Freshwater sample from downstream of
                     wastewater treatment plant"
                     /db_xref="taxon:546"
                     /plasmid="pRHBSTW-00486_3"
                     /geo_loc_name="United Kingdom"
                     /collection_date="2017"
     gene            complement(join(3404..4183,1..414))
                     /gene="mobQ"
                     /locus_tag="HV214_RS24585"
                     /old_locus_tag="HV214_24595"
     CDS             complement(join(3404..4183,1..414))
                     /gene="mobQ"
                     /locus_tag="HV214_RS24585"
                     /old_locus_tag="HV214_24595"
                     /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            837..1226
                     /locus_tag="HV214_RS24590"
                     /old_locus_tag="HV214_24600"
     CDS             837..1226
                     /locus_tag="HV214_RS24590"
                     /old_locus_tag="HV214_24600"
                     /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            1228..1497
                     /locus_tag="HV214_RS24595"
                     /old_locus_tag="HV214_24605"
     CDS             1228..1497
                     /locus_tag="HV214_RS24595"
                     /old_locus_tag="HV214_24605"
                     /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(1743..2012)
                     /locus_tag="HV214_RS24600"
                     /old_locus_tag="HV214_24610"
     CDS             complement(1743..2012)
                     /locus_tag="HV214_RS24600"
                     /old_locus_tag="HV214_24610"
                     /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(2009..2866)
                     /locus_tag="HV214_RS24605"
                     /old_locus_tag="HV214_24615"
     CDS             complement(2009..2866)
                     /locus_tag="HV214_RS24605"
                     /old_locus_tag="HV214_24615"
                     /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(2..414)
                     /name="MOBQ"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="99.275"
                     /coverage="85.0"
                     /evalue="8.02e-87"
ORIGIN
        1 cattacatga gcatgagggt tatgactatc aagatcatga aatgctatgt ctgcaatcat
       61 tccataatcc acgaaatttt cttggcagta atcgaggacg atctgcttct tctggccgtc
      121 gtccagctcc ttggggatgg ctatgtccac atagcgacat aattcggcat cctttcgctt
      181 ctcgccagcc tctacggcat tccagagggt gcctgagtcc ttcaccagtt cggcaggtgt
      241 gccggcaggg gagaggatag cagagccgaa aaatccctct ttttttgaat aatcccaggt
      301 tgccccggtt cgattatctt ttgtcttttc tcggttttga tatgcagata aataaaccga
      361 agatttacct tctgatcttc gtaatttttt aaagctgata tgaaatgtcg ccatagtcta
      421 ccccttactt tttttgtctt ttgaattttg gtttttagcc ccgcagggcc catacgtcgc
      481 ttgcgacgtg taagtgggca ttactaatat tattttttcg gcttcacctc aaaataataa
      541 gtaatgaacc ccaggcttcg cccaatatta aatattattt attttattct aaaatatatt
      601 tgactaaagt aaataatgga ggtaataaat aacaaaataa aataatggag gttatatgga
      661 aaaagaaacg ctcggccctg atatacaagt caattggtgt gatcattgtg aaaaaaacac
      721 tcgccatata tttagattta ctgaggagta ttcaaaagaa gagggaccaa ttacagaggt
      781 tgaatgtact aaatgtggta atacattcac tatcttatag tgtggaggtt tttaatatgc
      841 aatatagagg tttagagttt gaagaacaag agtttaacga ctgtttaaac attttacata
      901 aagaggtagt gtctttttta aataaaaata atatggctct ggattttttc cagtatccag
      961 ttgaggatat atgtagaata atttttcgag ataaaataga tctgagaact gctgttattt
     1021 tagattttgg aattacaaca tatgatttaa gccctttggg agatcacgat ccttttgttt
     1081 ggcggttgct tgaatggcca ttatatgatt atgagaattt ccagtttgtg attgttcaaa
     1141 aactggcttc ttatgaatta gataaattaa atgaaataat ccaagtagaa gataacaaag
     1201 ataataaaga taaaaggagg ttgtaatatg agcaaatcaa cagcacagca gatcgcagat
     1261 ctacaaaata aattacaagc actaagaaca aaaaaagcaa ggcaggacag acgggaagaa
     1321 acaagacaaa aaataatcct gggtgcagaa gtggctaagg tgttagataa aaaaccagag
     1381 gaaattaaca aggctttaat tcttggcttg ttaagtaaaa tcaatgagtt agacgaagaa
     1441 gagaaaagag attttacacg aatcggaatg gatatattgc aacaatggaa atcgtaaacc
     1501 gtgaacagtg aagaaccagc cgctttttgg gctggttttt tgctgtgaag ggttgccagc
     1561 caacggctgg aggttttaag gttgccagag ggcctccggt ggctgggtgg gtttgttgat
     1621 ttgttggtac cagagtgtcc ctcacctatc cagacacaag cccggatacg gggaaagggg
     1681 gaaaaatccc cccaggggtg gagggtttgg ttaggttagg gggaaaaact gcttagaagt
     1741 cgttacaggc tgtttttagg catatctaag gcaacataac ggcgatacag ggcaacggct
     1801 ccgtgatacg aacagcccat tttgtcggct acctgttgcc atttcagccc ctggcttcgt
     1861 agttcgtaag cctgacgacg acgatcagcc gctgtttgtt cgtattgttc acgcggttcg
     1921 gatgtatatt tttttaccgt tttaacagat atattaaatc tttcagccat ttctttttga
     1981 gttaaacctt ttcttattgt gcttcttctc atttttcacc tcctataaaa ccaagcattt
     2041 ctttaacatt actcttcttg ggtttgtttt tatttttcgc acctcttgaa gattgtatta
     2101 gtgaaaatgt atggctatca aaatttttcc aggtccaacg ggctatgctt cttgctgttg
     2161 cctttaactc tttgtattgt aacggattta gtggattgca aaaagtattt aaaccctgtg
     2221 cttttaataa tagttcgttt tcgaatttct cgaaagtaga tatttttttg aaatttaaaa
     2281 ccgttctgta agcatattgt cgtagatctt caaacaaatt aacattgcga cctaaaccat
     2341 aagcctcgct ttttttctct tgtatttgag gtttttctaa gtccacaaaa tcagctaaat
     2401 aatccaggtc gtaaaggtca gcacctgacc agaacggcga ccagtgatca ttgagtggat
     2461 tttttgtaat caatccagca aaccccagat ctgctttgag ttttttcgcc atagccattt
     2521 caacggcagc ggcatacttc aacggcttca accttgcttg ttgtgtctta caaacaccgg
     2581 ctttaagcat gtacccgtaa tggcaacgac ctgtctttgg tgtttttgta ataaagtgag
     2641 gtatgggtaa gcccaccttc tcaaatgtat agaatgagtt tttcttatct aaatcaaaga
     2701 gtaagcaagt ttggattgct ggctgatttg cctgtaaata cagcatttct aaggcttttg
     2761 ccttgttcct tatgcttaat cccatatcga ggttatttgt acaataaggc ttgttaggca
     2821 tttgattttt aaaaaaatcg atgttatgtt cttcttgtat tatcattttt tcagtccttt
     2881 ttatctggcc ctactctctg ttttctgtcg ccaaaacaaa atcgcagagg gtggggtttt
     2941 tatttttata ggtttttcaa tcctgtacca gttctaaccg atcttaaaaa tttgtcaagt
     3001 ggggagctta accatatcag ataacagccc aacgaagttg gggcagttct ttacatacgg
     3061 cagcaaagca ttactatcag atctatggtg cgaagcatta ccgaagatag aaaaacaata
     3121 aaaaaagaaa aaagagtatt gttcgaagaa aaattggcga ttcgattttt tttggtgaat
     3181 atatgaaaaa aaagaaagtg cagaaaaaac ggaaaagaaa taagcatagt aaatttttta
     3241 aaatgcttat gaagtcagtt aatgaagctg tggcaataca taaaggggaa atagaaccgg
     3301 cgaggatcac aactctaaaa atgtagtata ttatagtata gtattaaata atattaagtt
     3361 gtattaagtg atactactat ataggaatat ataccactat atactacatt ccaaatttct
     3421 tcttcctctt aggttgctga tcttcgaatt ccggcattgg ttccggctca ggctcttcaa
     3481 tttttggttg tggttggttc ataggagaca ttccagagcc tgaacccatt tttccgcctc
     3541 cattatttcc accggttccg gttcctgtgc ctgttttagg ttttgtttct aactctgtct
     3601 ttaatatatg ttcgccaaat tcatttatta cataactact aacgaaattt tgaggatctt
     3661 ctttttcttc ttttttattt ttatttacat taggttttga tttaaatata tgctgggtct
     3721 ttttgtataa tgcctttaaa ttatcaatga ttgaccttgc aagaggcttt ttctctattt
     3781 tcatagtttc ctctggctga ggtggtttgg tttgctgtaa gtatgttgca ttagctattt
     3841 ttaataataa tgctttttct ttttgctcca tagctcttaa tttttgacct tttcgccatt
     3901 ggtgcctgtg tatcctggtc attggcgttc tgtccagttc aatagttttt gaaatccact
     3961 tggctttctc tttcggagtt ttagcaaaaa cagcctttct ttctgcctct tctttttgat
     4021 cttttaatga acgggaatca atacgggact tatgaccata tttttttaat ctgtcatttg
     4081 ctattatttc ccagttaact cgccaggctt caatattttc tctattattc cattctcttt
     4141 gtttgttccc aaatccattt gggctaacag ttcttaaagt tag
//
