LOCUS       NZ_CP056577             3724 bp    DNA     circular CON 07-APR-2024
DEFINITION  Citrobacter freundii strain RHBSTW-00370 plasmid pRHBSTW-00370_5,
            complete sequence.
ACCESSION   NZ_CP056577
VERSION     NZ_CP056577.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN15148595
            Assembly: GCF_013741395.1
KEYWORDS    RefSeq.
SOURCE      Citrobacter freundii
  ORGANISM  Citrobacter freundii
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Citrobacter; Citrobacter freundii complex.
REFERENCE   1  (bases 1 to 3724)
  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 3724)
  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                     :: WTP4 T2-00370
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 101.654958727184x
            Sequencing Technology :: Hybrid: Illumina and OXFORD_NANOPORE
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_013741395.1-RS_2024_04_07
            Annotation Date                   :: 04/07/2024 07:41:15
            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)                     :: 5,547
            CDSs (total)                      :: 5,424
            Genes (coding)                    :: 5,317
            CDSs (with protein)               :: 5,317
            Genes (RNA)                       :: 123
            rRNAs                             :: 9, 8, 8 (5S, 16S, 23S)
            complete rRNAs                    :: 9, 8, 8 (5S, 16S, 23S)
            tRNAs                             :: 84
            ncRNAs                            :: 14
            Pseudo Genes (total)              :: 107
            CDSs (without protein)            :: 107
            Pseudo Genes (ambiguous residues) :: 0 of 107
            Pseudo Genes (frameshifted)       :: 31 of 107
            Pseudo Genes (incomplete)         :: 70 of 107
            Pseudo Genes (internal stop)      :: 16 of 107
            Pseudo Genes (multiple problems)  :: 11 of 107
            Pseudo Genes (short protein)      :: 1 of 107
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP056577.1.
            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..3724
                     /organism="Citrobacter freundii"
                     /mol_type="genomic DNA"
                     /strain="RHBSTW-00370"
                     /isolation_source="Wastewater influent sample"
                     /db_xref="taxon:546"
                     /plasmid="pRHBSTW-00370_5"
                     /geo_loc_name="United Kingdom"
                     /collection_date="2017"
     gene            join(3142..3724,1..119)
                     /locus_tag="HV178_RS27555"
                     /old_locus_tag="HV178_27575"
     CDS             join(3142..3724,1..119)
                     /locus_tag="HV178_RS27555"
                     /old_locus_tag="HV178_27575"
                     /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_063861804.1"
                     /translation="MTISKKNSELRERFKEYSSNKNIFDLADLRYEILKIYFDFKLKND
                     MNEQERKSQDSRRKAHLTALKKRIKREIVSKIVIDLVKYYNIEKTTFHFFSHICTEILE
                     RNVDNRYILNNFSNMILDEKKELTKLSESRNASNKMSLENSYSELVSMSHIKDKLFRND
                     NFKTAYLKCYGCANEEFSRFKVFAFPDNFETLDFLFEEERIKKEEKEISKIMIEQVEEE
                     PKIQPIKKRRL"
                     /name="hypothetical protein"
     gene            493..1614
                     /locus_tag="HV178_RS27560"
                     /old_locus_tag="HV178_27580"
     CDS             493..1614
                     /locus_tag="HV178_RS27560"
                     /old_locus_tag="HV178_27580"
                     /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_181553786.1"
                     /translation="MEFKIKKMTVKDSREIKKKFEDCIKIAEEKNMQVGSILNIEMQDR
                     LKEINLKVKKETAEQYRNLFNYKLSVNAEDIIQHLLECNTRNSFDKTRSAFRFCIAEKI
                     QELRNEADRARKQKNFDLMKEKTIEAYKLFFFFERDFLSENRVTWNDISYRKIDSKSKK
                     KTMNSVSSIKAIFEDLKQKPELFEKYSMILAISSLTGCRPAEIQKGIGLELSPPLLNIC
                     ISGAKVGEDRGQEKRILKFNINEFAENEQFKLIMSKIKQNNKLEYKCSKQEYDSLRQYL
                     YINHPGFSLYTLRHRAASELKKDGFSEEMIAAFLGHRVTRSLENYGYAKSGKGGPKIAG
                     VEHTNAIKSNTKRYKSKTTPGGGNPSPTRKRAL"
                     /name="hypothetical protein"
     gene            2828..3076
                     /locus_tag="HV178_RS27565"
                     /old_locus_tag="HV178_27585"
     CDS             2828..3076
                     /locus_tag="HV178_RS27565"
                     /old_locus_tag="HV178_27585"
                     /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_063145815.1"
                     /translation="MEIEKLIDRYFLALERKVIREIYDKQTREELEKFIFKCNGEFREF
                     ERRFNTICSTEYYEQQSLIFYINYINAEFEQREKLNY"
                     /name="hypothetical protein"
ORIGIN
        1 tagatttttt atttgaagaa gaaagaataa aaaaagaaga aaaagagata tctaaaataa
       61 tgattgaaca agttgaagaa gaaccaaaaa tacagccaat aaagaaaaga agattataat
      121 ttttttttgc ggcgaatcgt gagaaaaata aaattttaat tttgtttttt gagcgattga
      181 tctgtatgta agttgatgaa aaatctagta aaatctgcga tctatttttt cttttgactt
      241 gccattattg ttatttttgt tataacaata atggggggtt gtcttttact tgaaaaatga
      301 gcgtcagcga aattttgaaa ggaaaagtgt gcgaagagca caaaaccctt ttgctttttt
      361 tcgtaatgac ctttaaattt tttttcatta gagcgaagcg attttgaaaa ataaatttat
      421 tgggaatgaa gaaaaaaggc aaaccagcgg agtgaaatta aaacaataaa actataaaaa
      481 aaagaggtgg ctatggaatt taaaataaag aaaatgactg ttaaagacag cagagaaatt
      541 aaaaaaaaat ttgaagattg cattaagata gcagaagaaa aaaatatgca agtaggttca
      601 attctaaata ttgaaatgca agatagattg aaagaaataa atttaaaagt aaaaaaagaa
      661 acagcagaac aatatagaaa tctgtttaat tataaattgt ctgtgaatgc agaagatatt
      721 attcagcact tgttagaatg caacacaaga aacagttttg ataaaacaag atctgctttt
      781 agattttgca ttgctgaaaa aattcaagag ctaagaaatg aagcagatcg agcaagaaag
      841 caaaagaatt ttgatttaat gaaagaaaaa actattgaag catataaatt atttttcttt
      901 tttgagcgag attttttgag cgaaaaccgg gtaacttgga atgatatttc ttatagaaaa
      961 atagactcta aaagcaaaaa aaagactatg aatagtgttt ccagtattaa agcaattttt
     1021 gaagatttga agcaaaagcc ggagcttttc gaaaaatatt caatgatact ggctatttca
     1081 agtttgaccg gttgccgtcc ggctgagatc caaaaaggaa ttgggctgga actaagccca
     1141 ccactattaa atatatgtat tagcggggcg aaagtgggcg aagatcgagg acaggaaaaa
     1201 agaatattga aattcaatat aaatgaattt gctgaaaatg agcagttcaa attgattatg
     1261 tcaaaaataa agcaaaataa taaattagaa tataaatgct caaagcaaga gtatgattct
     1321 ttgagacaat atttatatat taatcaccca ggtttttctt tgtatacatt aagacatagg
     1381 gcagcaagtg aattaaaaaa agacggattt tcggaagaaa tgatcgctgc tttcctgggg
     1441 cacagggtaa ccagatctct agagaactat ggatacgcaa aatctgggaa aggtggtcca
     1501 aaaatcgcag gtgttgagca cacaaacgcg attaaaagca atacaaagcg atataagagc
     1561 aaaaccaccc ctggaggggg aaacccttcc ccaactcgta aacgagcctt atagtcgatt
     1621 ttagagcgtt acagtgggtc agcaatgctg gccctttata tgtgtgttag cctcgcgcgc
     1681 gcgtcttgcc ggcacagatt tgtggtgact ggttgcatat gtgtattagc agaaccgcag
     1741 gttggtgtgg ttgcttgtgc ggtcggtgta attaactaat caatatatgt attagcaggc
     1801 ggcacgcgtg cgtaatgccc ggaacgggac cccggtaact tttcgttggt ggttttttga
     1861 gcaattaact gtcagtcgtt gacatttgaa gtgtcatttt tgctgttaaa aatgacacaa
     1921 cgagtctcat tgagtgagaa ttttgatttt ttagtcatca aaaaatttga agaactattg
     1981 acagaacaga cagatagatt ataactgagt ccagatacaa caaaaccagc ttttggctgg
     2041 ttttgaggga cttaaagaag tggggacttc tgaaagtctt gtaatcaagt gaaatcagca
     2101 ctcgattacg atatgtaagt gaaaatctaa cttataaaat cgcaattgtc aaacttctct
     2161 tattacaagt ctcttcaaaa atcctcagtt tttcaaatcc ttaagcaacc attgtgccta
     2221 ttgtgtcagg tcgtgatctg tggaatcaag agggtccgga tcaatgttgg ttgtcggcaa
     2281 tagaagggtg cttacgaatt gccaacctgg gaggctgagt tctaaggcta ttttggtgaa
     2341 cagtgtttta tatggtcggc tatgagaaag cccagccaga acctgaaaag gttcaaaaat
     2401 ggggttaact gtcacaagta aaagctatga actgtatcta gagggtgtaa gagggtgcca
     2461 ttagcgagaa attgctaaca aactcaatag tctagaactt tgtggtgaag tctaaaactt
     2521 tgcgatcaca caaatagccc ttactgattt ttttgaaata atccttattt tttatgggat
     2581 taggatcaaa aaatcggtag gggcgacctt tgggtgaagc cccaaaaggg ctgaacccaa
     2641 aggtcgagcg aagccacaga aaaacaatac agatctgtta tagagaaaaa gcaatgctga
     2701 tctgtagaaa atagaaaaac aatactaaag aataaaagaa aaagagttcg gagaaaaaaa
     2761 ttcgaaattt gatttttttt gcgatttgct atttaaattc taaatataaa agaaaaaagg
     2821 aaaaattatg gaaatagaaa aattgataga tagatatttt ttagcattag aaagaaaagt
     2881 gatccgtgaa atttatgata aacagacacg agaagaatta gaaaaattta tttttaagtg
     2941 taatggtgag tttagagagt ttgaaaggcg atttaataca atatgctcta ctgaatatta
     3001 tgaacaacaa agccttatct tttatattaa ttatataaat gcagagtttg agcagaggga
     3061 gaagttaaat tattaaattt gacaacatta aaataatata ttaagcatat atgtattagc
     3121 gaaacacaga gggcttaata tatgacaata tctaagaaaa atagcgaatt gagagagcga
     3181 ttcaaagagt attcaagtaa taaaaacata tttgatcttg ctgatttgag atatgaaata
     3241 ttaaaaatat attttgattt taaattaaaa aacgatatga atgagcaaga aagaaaatct
     3301 caagactcaa gaagaaaagc acatttaaca gcattaaaaa aaagaattaa aagagaaatc
     3361 gtttcgaaaa tagttattga tttagtaaaa tactacaaca tagaaaaaac gacttttcat
     3421 tttttttctc atatatgtac tgagatttta gaaagaaatg tagataacag atacattcta
     3481 aataattttt caaacatgat tttagacgaa aaaaaagagt taacgaaatt aagtgaaagc
     3541 agaaatgctt caaacaaaat gagtttagaa aactcttatt ccgaacttgt ttctatgtca
     3601 catattaaag acaaattatt taggaatgac aatttcaaaa ctgcatattt aaaatgttat
     3661 ggttgtgcaa atgaggaatt ttcaagattt aaagtttttg cttttccaga caattttgag
     3721 acat
//
