LOCUS       NZ_CP056184             3728 bp    DNA     circular CON 26-JAN-2024
DEFINITION  Citrobacter freundii strain RHBSTW-01016 plasmid pRHBSTW-01016_4,
            complete sequence.
ACCESSION   NZ_CP056184
VERSION     NZ_CP056184.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN15148768
            Assembly: GCF_013781965.1
KEYWORDS    RefSeq.
SOURCE      Citrobacter freundii
  ORGANISM  Citrobacter freundii
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Citrobacter; Citrobacter freundii complex.
REFERENCE   1  (bases 1 to 3728)
  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 3728)
  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                     :: WTP3 T3-01016
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 61.6339889191906x
            Sequencing Technology :: Hybrid: Illumina and OXFORD_NANOPORE
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 01/24/2024 14:08:30
            Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline
            (PGAP)
            Annotation Method :: Best-placed reference protein set; GeneMarkS-2+
            Annotation Software revision      :: 6.6
            Features Annotated                :: Gene; CDS; rRNA; tRNA; ncRNA
            Genes (total)                     :: 5,209
            CDSs (total)                      :: 5,084
            Genes (coding)                    :: 4,951
            CDSs (with protein)               :: 4,951
            Genes (RNA)                       :: 125
            rRNAs                             :: 9, 8, 8 (5S, 16S, 23S)
            complete rRNAs                    :: 9, 8, 8 (5S, 16S, 23S)
            tRNAs                             :: 87
            ncRNAs                            :: 13
            Pseudo Genes (total)              :: 133
            CDSs (without protein)            :: 133
            Pseudo Genes (ambiguous residues) :: 0 of 133
            Pseudo Genes (frameshifted)       :: 31 of 133
            Pseudo Genes (incomplete)         :: 97 of 133
            Pseudo Genes (internal stop)      :: 23 of 133
            Pseudo Genes (multiple problems)  :: 16 of 133
            Pseudo Genes (short protein)      :: 1 of 133
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP056184.1.
            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..3728
                     /organism="Citrobacter freundii"
                     /mol_type="genomic DNA"
                     /strain="RHBSTW-01016"
                     /isolation_source="Wastewater effluent sample"
                     /db_xref="taxon:546"
                     /plasmid="pRHBSTW-01016_4"
                     /geo_loc_name="United Kingdom"
                     /collection_date="2017"
     gene            join(3099..3728,1..495)
                     /locus_tag="HV351_RS25885"
                     /old_locus_tag="HV351_25895"
     CDS             join(3099..3728,1..495)
                     /locus_tag="HV351_RS25885"
                     /old_locus_tag="HV351_25895"
                     /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_181641390.1"
                     /translation="MDFKIKKMTVKDSREIKNEIELLAKKANAESQNLGVILDRQIKEG
                     LKEINLNVKKETAEQYRKLFGHKLSLNNNDIVSHLLECNTRNSFDKTRSAFRFCIAEKI
                     QELRKESEQARRERNFDLMQKKTIEAYQMFFFFQRDFLSENRVTWNDISYRKIDSKSKK
                     KTMNSVSSIKAIFEDLKQKPDLFDKYSMILAISSLTGCRPAEIQKGISLEVSHQLLNIC
                     ISGAKVGEDRGQEKRILKFNIKEFAQNEQFNLIMSKIKQNNKFEYKCSKQEYDSLRQYL
                     YINHPGFSLYTLRHRAASELKKDGFSEEMIAAFLGHRVTRSLENYGYARSGKGGPKVAG
                     VEHSNAIKSNTRRYKSKTTPGGGNPSPTRKRALK"
                     /name="hypothetical protein"
     gene            1717..1977
                     /locus_tag="HV351_RS25890"
                     /old_locus_tag="HV351_25900"
     CDS             1717..1977
                     /locus_tag="HV351_RS25890"
                     /old_locus_tag="HV351_25900"
                     /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_122652922.1"
                     /translation="MEIEKLIDRYFLALEKKIIAEIYNKQTRKELEKFIFKCDQELMGF
                     EQRFNIICCTEYYEKQKLIFSINYISAEFEQREKLNLTILK"
                     /name="hypothetical protein"
     gene            2023..2724
                     /locus_tag="HV351_RS25895"
                     /old_locus_tag="HV351_25905"
     CDS             2023..2724
                     /locus_tag="HV351_RS25895"
                     /old_locus_tag="HV351_25905"
                     /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_148830253.1"
                     /translation="MTISKKNSELRERFKEYASNKNIFDLADLRYEILKIYCDFKLKSD
                     MNEKERKSQDSRRKAHLTALKKRIKREIVSKIVIDLVKYYNIEKTTFHFFSHICTEILE
                     RNVDNRYILNNFSNMILDEKKELRKLSESRNASNKMSLENSYSELVSMSHIKDKLFRND
                     NFKTAYLKCYGCANEEFSRFKVFAFPDNFETLDFLFEEERIKKEEKEISKIMIEQVEEE
                     QKIQPIKKRRL"
                     /name="hypothetical protein"
ORIGIN
        1 agcctggaag taagccacca actattaaat atatgtatta gcggggcgaa agtgggcgaa
       61 gatcgagggc aagaaaaaag aatattaaaa tttaatataa aggaatttgc acaaaatgag
      121 cagttcaatc taattatgtc aaaaataaaa caaaataata agtttgaata taaatgttcc
      181 aagcaggagt acgattcact gagacagtat ttatatatta accatcctgg attttctctc
      241 tatacattaa gacatagagc agccagtgaa ttaaaaaaag acggcttttc agaagaaatg
      301 atcgcagctt ttttaggtca tagagtaacc agatctctag agaactatgg atacgcaaga
      361 tctgggaaag gtggtccaaa agtggcaggt gttgagcatt caaacgccat aaaaagcaat
      421 acaaggcgat ataagagcaa aacaacccca ggagggggaa acccttcccc aactcgtaaa
      481 cgagccttaa aatgagtttt agagcgtttt acaggagtca gcaaaagctg actcttttta
      541 tttgatatgt gtgttagcct cgcgcgcgcg tcttgccggc agagatctgt gccggctggt
      601 tgcatatgtg tattagcaga accacagatc ggtgtggttg cttgtgtggt cggtgtaatt
      661 aactaatcaa tatatgtatt agcaggcggc acgcgtgcgt aatgcccgga acgggacccc
      721 ggtaactttt cgttggtggt tttttgagca attaactttc agccgttggc atttgaagtg
      781 tcattttttg cctcaaaact gacacaacga gtctcattga gtgagaattt tgattttaaa
      841 gtaatcaaaa attttgaaga agtattgaca gaacaaggag atcggttata acagatccag
      901 atacaacaaa accagcctaa gctggttttg agggacaaga aaagtttggc gacttttcga
      961 gtcttgtaat caagtgagtt cagcactgga ttacgatttg taagtagaaa tctaactcac
     1021 aattcgcaaa aagtcaaatc tctcttcatt gcaatactca gaaaaaaccc atctttttca
     1081 agtctttaag caaccaaatt tgcatattgt gtcgtgcctg gaactgtgga atcaagaggg
     1141 tccggtttcg gttggttgtt ggcaatagaa ggggatctca caaattgccg aacctggagg
     1201 ctgagttcta aggttgtttt ggtgagcagt gttgtattgg taggctatga gaaagcccag
     1261 ccataacagt tataaagctg tttaaaatgg ggtgaactgt cgcaaaaaat gattatgaac
     1321 tgtatctaga gggtgtgagg gggtgccgtg tgttggaaac gatacacagc tcgacagtct
     1381 agaactttgt ggtgaagtcc aaaactttgc aatcacacaa atcgccctta gtgaaaattt
     1441 tctaattacc tgatttttag ggtagatcca gaaaattttc actaggggag acctttgggt
     1501 gaagccctgt aaagggctga acacaaaggt cttagcgaag ccacagcaaa acaataccta
     1561 tctgttatag agaaaaagca atgcttcttt gtagaaagat agaaaaccaa tactaaagaa
     1621 taaaaaaata gagttcgaag aaaaaaattg gcgatttgat ttttttttgc aatttgctat
     1681 ttaaattcta aatataatta aaaaaaagga aaatttatgg aaatagaaaa attgatagat
     1741 agatattttt tagcattaga aaagaaaata attgctgaga tttataataa acaaacaaga
     1801 aaagaattag aaaagtttat atttaagtgc gatcaagagc taatggggtt tgaacagcga
     1861 tttaatataa tatgctgtac tgaatattat gagaaacaga aacttatatt ttctataaat
     1921 tatatttcag cagaatttga gcaaagagaa aaattaaatt tgacaatatt aaaataatat
     1981 attaagcata tatgtattag caaaataaag agggcttaat atatgacaat atcaaaaaaa
     2041 aatagtgaat tgagagagcg atttaaagaa tacgccagta ataaaaacat atttgatctt
     2101 gctgatttga gatatgaaat attaaaaata tattgtgatt tcaaattaaa aagcgatatg
     2161 aatgagaaag aaagaaaatc tcaagactcc agaagaaaag cacatttaac agcattaaaa
     2221 aaaagaatta aaagagaaat tgtttcgaaa atagttattg atttagtgaa gtattacaat
     2281 atagaaaaaa cgacttttca ttttttttct catatatgta ctgagatttt agaaagaaat
     2341 gtagataaca gatacattct aaataatttt tcaaacatga ttttagacga aaaaaaagag
     2401 ttgaggaaat taagtgaaag cagaaatgct tcaaacaaaa tgagtttaga aaactcttat
     2461 tccgaacttg tttctatgtc acatattaaa gacaaattat ttaggaatga caatttcaaa
     2521 actgcatatt taaaatgtta tggttgtgca aatgaggaat tttcaagatt taaagttttt
     2581 gcttttccag acaattttga gacattagat tttttatttg aagaagaaag aataaaaaaa
     2641 gaagaaaaag agatatctaa aataatgatt gaacaagttg aagaagaaca aaaaatacag
     2701 ccaataaaga aaagaagatt ataatttttt ttgcagcgaa tcgtgagaaa aataaaattt
     2761 taattttgtt ttttgagcga ttgatctgtg tgtaagttga tgaaaaacct agtaaaatct
     2821 gcgatctatt ttttcttttg acttgccatt attgttattt ttgttataac aataatgggg
     2881 ggttgtcttt tacttgaaaa atgagcgtca gcgaaatttg aaaggaaaag ttcgcgggag
     2941 cgaaaaaccc tttgtgtttt tttcggaatg acttttaaat tttttttcat tagagcgaag
     3001 cgattttgaa aaataaattt attaggaatg gagaaaaaaa tacaacctac tcaacaaaaa
     3061 gaggaataca aaaaacataa aaaaaaagag gtgatagtat ggattttaaa ataaaaaaaa
     3121 tgacggtgaa agattccaga gaaataaaaa atgagattga actgttagca aaaaaagcaa
     3181 atgctgaaag ccagaacctg ggagtgatac ttgatcgcca gatcaaagaa gggttgaaag
     3241 aaattaattt aaatgtgaaa aaagaaacag cagaacaata tagaaaactg tttggtcaca
     3301 agttaagttt aaacaacaat gacattgttt cacatttatt agaatgcaac acaagaaaca
     3361 gttttgacaa aacaagatct gcttttaggt tttgcattgc tgaaaaaata caagaattga
     3421 ggaaagagtc tgaacaagca agaagagaaa gaaattttga tttaatgcag aaaaaaacca
     3481 ttgaagcata tcaaatgttt tttttcttcc aacgcgattt tttgagtgaa aaccgggtta
     3541 cttggaatga tatttcttat cggaaaatag actcgaaaag caaaaaaaag acaatgaata
     3601 gtgtttccag tattaaagca atttttgaag atttgaagca aaagccagat cttttcgata
     3661 aatattcaat gattttagca atttcaagtt taacaggttg tagacctgct gagatccaga
     3721 aagggatt
//
