LOCUS       NZ_CP056469             2349 bp    DNA     circular CON 15-APR-2024
DEFINITION  Citrobacter freundii strain RHBSTW-00486 plasmid pRHBSTW-00486_4,
            complete sequence.
ACCESSION   NZ_CP056469
VERSION     NZ_CP056469.1
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 2349)
  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 2349)
  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
            CP056469.1.
            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..2349
                     /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_4"
                     /geo_loc_name="United Kingdom"
                     /collection_date="2017"
     gene            65..811
                     /locus_tag="HV214_RS24610"
                     /old_locus_tag="HV214_24620"
     CDS             65..811
                     /locus_tag="HV214_RS24610"
                     /old_locus_tag="HV214_24620"
                     /inference="COORDINATES: protein motif:HMM:NF017542.4"
                     /GO_process="GO:0006260 - DNA replication [Evidence IEA];
                     GO:0006276 - plasmid maintenance [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="replication/maintenance protein RepL"
                     /protein_id="WP_074098254.1"
                     /translation="MDLGNILNESLSIDYEKLDLFLEKYDLTPEQKVAVYEFHAKAYKK
                     NKTLVISETKENKFKSISEGVEYVHLFPKNLKILIKKYGLNTNELLVLTEIMESMLSHG
                     NLLINFSQKALCELTGINKSTMCKTFKTLKQKQCLIEKNGHIYLNSVIFMKGLPHKLFM
                     QFRDHFLNSISYKLDDEEEFEKVFDDNFIKAYEKNLKEIKKKKQQIKEKKISKALDNFE
                     KEISNEWKEKFKDEEENFEFGFESEM"
                     /name="replication/maintenance protein RepL"
     gene            1180..1908
                     /locus_tag="HV214_RS24615"
                     /old_locus_tag="HV214_24625"
     CDS             1180..1908
                     /locus_tag="HV214_RS24615"
                     /old_locus_tag="HV214_24625"
                     /inference="COORDINATES: protein motif:HMM:NF012798.4"
                     /GO_function="GO:0003677 - DNA binding [Evidence IEA]"
                     /GO_process="GO:0015074 - DNA integration [Evidence IEA];
                     GO:0006310 - DNA recombination [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="site-specific integrase"
                     /protein_id="WP_085280960.1"
                     /translation="MGNSKRNIKKLNDNFREDILDYAIAHNLKCANALAILYATGCRPD
                     ELQTGVTVNYDSKKNEIEFRIIGSKLNRRMRRGIGVRKIKVKINNENARFFKSIVDKFI
                     ENPMSYDHKIKIESAKAFSGYITKISKKLWPRKTYHASAYSFRHAKATELKNSDYDKIE
                     IAQIMGHASVRSQQSYGRKSKKSKGGFNDIADVETNVKPRGGDRLLRFKIANKNKAAAK
                     IADTSTPSSPPPAPVRRFKM"
                     /name="site-specific integrase"
     Typing          1970..2153
                     /name="Col(IRGK)"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="97.838"
                     /coverage="100.0"
                     /evalue="1.26e-84"
ORIGIN
        1 attgactagt tttatataaa tgttaaaaca tatatataga aataaataaa aaaaggaggt
       61 ttctatggat ttaggaaata tattaaatga gagtttaagt attgattacg aaaaattaga
      121 tttgtttttg gaaaaatatg atttaacacc agaacaaaaa gttgcagttt atgaatttca
      181 cgcaaaagct tataaaaaaa ataaaacttt agttatttct gaaacaaaag aaaataaatt
      241 taaatctatt tccgaaggtg ttgaatacgt gcatttattc ccaaaaaatt taaaaatttt
      301 aattaaaaaa tatggtttaa atacaaacga attattggtt ttaacggaaa taatggagtc
      361 aatgctttca cacggaaatt tattaattaa tttttcgcaa aaggcacttt gcgaattaac
      421 aggaattaat aaatctacaa tgtgtaaaac atttaaaacc ctcaaacaaa agcagtgttt
      481 aattgagaaa aacggacata tttatttaaa ttctgtgata tttatgaaag ggttacctca
      541 taaattgttt atgcaattta gagatcattt tttaaattct atctcatata aattagatga
      601 tgaagaagaa tttgaaaaag tcttcgacga taatttcatt aaagcatatg aaaaaaatct
      661 caaagaaatt aaaaagaaaa aacaacagat aaaagaaaag aaaatatcaa aagcattaga
      721 taattttgaa aaagaaattt ctaatgaatg gaaagaaaag tttaaagacg aagaggaaaa
      781 tttcgaattt ggttttgaat cggaaatgta aaaccgccct cgccgggcag gcgaatccct
      841 tactgaaata gaataaaatt ctattccact aagggatttt ttttatccat tgattctcca
      901 catttcaaat attgacagca ttttccaccc ggttataaca gtactataag tagttgtttc
      961 aacccgtctt tttgggtgga acaacaaggc attttaggga tagagcaaag cgaaggccat
     1021 aaaattgcca cccccaaccg ggggtcgttg ttcgatttga gcgatagcga aaaattgaac
     1081 ataagggggg agggtttggg ttttacggta tttcaaattt gagcaaagcg aatttttgaa
     1141 atttccggtt cttttaattt gcaatgagga aaaatcaata tgggtaattc aaaaagaaat
     1201 ataaaaaaac taaatgataa ttttagagag gatattttag attatgcgat cgcgcacaat
     1261 ctaaaatgtg ctaacgcact tgctatttta tacgcaacgg gttgccgtcc ggacgaactc
     1321 caaactgggg ttactgtaaa ttatgacagc aaaaaaaatg aaattgaatt tagaataatt
     1381 ggatcaaaac tcaatagaag aatgagaaga ggcattgggg ttagaaaaat aaaagtaaaa
     1441 atcaataatg aaaatgccag gttttttaaa agcattgttg ataaatttat tgaaaaccca
     1501 atgtcatatg atcataaaat caaaattgaa agtgcaaaag cgttttcagg ttacataact
     1561 aaaatatcga aaaaactatg gcccagaaaa acatatcatg cttctgcata ttctttcaga
     1621 catgcaaaag caacggaatt gaaaaattcc gattatgaca aaatcgaaat agcccaaatt
     1681 atgggccatg cctcagtcag atctcagcag agttacggaa gaaagagcaa aaaaagcaaa
     1741 ggtggattta atgacatcgc agatgtcgaa accaatgtta agccccgtgg tggagataga
     1801 ttattgagat ttaaaatagc aaataaaaac aaagcagcgg caaaaattgc cgatacttcc
     1861 acccccagca gtcctccacc ggctcccgtt cgtcgcttca aaatgtgaac cgtgagcagt
     1921 tcaggaggtc ccctcctgga ctgtgaaggg ttggcccgtc cggcaggacg gttttacagc
     1981 aaaatcctcc atagcgaagc agaagcccgg aaccgggtaa ctggatgggt ttcccctgtg
     2041 ggggattgat ctgttacttg aaaaccaatg atcttaaaaa ccatctcaaa agttgaaaat
     2101 ttcaccccct tagtgttctt aaaattctta gatgttctta ggagttaaaa aaccactctc
     2161 taaccattga tattactcac tttttaaaaa tggcagttgt caaattcgtc aactggagtt
     2221 gtcaaattcg tcaactggag ttgtcaaatt cgtcaactgg agttgtcaaa tccgacaact
     2281 ctagccagtt tctgtttgta gaatgcagtt tccaaactgc aactttttct actttttgca
     2341 acttaatct
//
