LOCUS       NZ_CP056529             2746 bp    DNA     circular CON 26-JAN-2024
DEFINITION  Citrobacter freundii strain RHBSTW-00435 plasmid pRHBSTW-00435_3,
            complete sequence.
ACCESSION   NZ_CP056529
VERSION     NZ_CP056529.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN15148611
            Assembly: GCF_013749535.1
KEYWORDS    RefSeq.
SOURCE      Citrobacter freundii
  ORGANISM  Citrobacter freundii
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Citrobacter; Citrobacter freundii complex.
REFERENCE   1  (bases 1 to 2746)
  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 2746)
  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 T2-00435
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 94.901112982724x
            Sequencing Technology :: Hybrid: Illumina and OXFORD_NANOPORE
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 01/24/2024 13:51:31
            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)                     :: 5,190
            CDSs (total)                      :: 5,072
            Genes (coding)                    :: 4,928
            CDSs (with protein)               :: 4,928
            Genes (RNA)                       :: 118
            rRNAs                             :: 9, 8, 8 (5S, 16S, 23S)
            complete rRNAs                    :: 9, 8, 8 (5S, 16S, 23S)
            tRNAs                             :: 85
            ncRNAs                            :: 8
            Pseudo Genes (total)              :: 144
            CDSs (without protein)            :: 144
            Pseudo Genes (ambiguous residues) :: 0 of 144
            Pseudo Genes (frameshifted)       :: 38 of 144
            Pseudo Genes (incomplete)         :: 115 of 144
            Pseudo Genes (internal stop)      :: 23 of 144
            Pseudo Genes (multiple problems)  :: 28 of 144
            Pseudo Genes (short protein)      :: 1 of 144
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP056529.1.
            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..2746
                     /organism="Citrobacter freundii"
                     /mol_type="genomic DNA"
                     /strain="RHBSTW-00435"
                     /isolation_source="Freshwater sample from downstream of
                     wastewater treatment plant"
                     /db_xref="taxon:546"
                     /plasmid="pRHBSTW-00435_3"
                     /geo_loc_name="United Kingdom"
                     /collection_date="2017"
     gene            complement(join(2465..2746,1..93))
                     /locus_tag="HV194_RS25750"
     CDS             complement(join(2465..2746,1..93))
                     /locus_tag="HV194_RS25750"
                     /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_061335866.1"
                     /translation="MNGMSDVRLKKSTIESLKEYVNDFGMTVDDVVLNLIEENNSLKSL
                     LGQGFSLPGGDKDTHSFKDYVIHKLPKGKILVTKDGLKVSNMKKVLIEAGSAVGMDDKE
                     LNPDFTTYEIGRFLFKHLQG"
                     /name="hypothetical protein"
     gene            422..610
                     /locus_tag="HV194_RS25755"
     CDS             422..610
                     /locus_tag="HV194_RS25755"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000165998.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="Rop family plasmid primer RNA-binding protein"
                     /protein_id="WP_000165998.1"
                     /translation="MTKQESAALNMAKFIRAQSLLLLEKLDVLDLDDEAADCERMHEQA
                     EALYQKLSARFGIQDGE"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            complement(658..885)
                     /locus_tag="HV194_RS25760"
     CDS             complement(658..885)
                     /locus_tag="HV194_RS25760"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001046776.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_223229632.1"
                     /translation="MFGFSPGELMNLCPDERLLFVRMISAMLRRSGGDAGAVMFEAYRH
                     IVSDTNQARRSYMLDLLESVRHDYVHDGYT"
                     /name="hypothetical protein"
     gene            <2175..2276
                     /locus_tag="HV194_RS25765"
                     /pseudo=""
     CDS             <2175..2276
                     /locus_tag="HV194_RS25765"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_011847251.1"
                     /note="incomplete; partial in the middle of a contig;
                     missing N-terminus; Derived by automated computational
                     analysis using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="IS30 family transposase"
                     /name="IS30 family transposase"
     Typing          1359..1854
                     /name="rep_cluster_2335"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="95.171"
                     /coverage="82.0"
                     /evalue="0.0"
ORIGIN
        1 aacatcatca accgtcatgc caaagtcatt cacgtactct tttaggctct caatagttga
       61 tttctttagt cttacgtcag acataccatt catattatta ttaccccacc gctctaattt
      121 gaagaaataa tacaacaaaa tacaaattat acaaataaat attgttctga atacaacaag
      181 cggtctgtag gtgcgatgat aactatgctg caccgccaga ttgaacataa catccgttgc
      241 gtgcaccgcc tgagaggctc tcagggcgtt tctacgacct cacctgcaaa agaacacatc
      301 ttaccccctg aaaaccgctc agaaacgcgc tgatgatttc tgcgtacctg catggctatg
      361 cactcaagtg aatgaagtaa gatttcagtc tgcgatcacc ataaaaccgg gaaaaagccg
      421 tatgacaaaa caggaatcag ccgcactgaa catggcaaaa tttatccggg cgcagtcgct
      481 gctgctgctc gaaaaactcg acgtgctcga tcttgatgac gaggcagccg actgtgagcg
      541 aatgcacgaa caggcagaag cgctttatca gaagctgagc gcacgcttcg gtatacagga
      601 cggcgaataa agagacgaaa agaacgctca cttagacgaa aagcgtatcc agggcaacta
      661 tgtatatcca tcgtgtacat agtcatgcct gacgctttcg agcaggtcga gcatgtagga
      721 acgacgagct tgattggtat cggacacaat atggcgatac gcctcaaaca taacagcacc
      781 cgcatcaccg cccgaacggc gaagcatagc ggaaatcatc cgcacaaaga gcagacgttc
      841 atcggggcaa aggttcataa gttctcctgg tgaaaaacca aacatgaaag cacccatcta
      901 ttaacgtcag ctgtgaacgc ttcattagaa gaaaataggt aaacccggga aaaagatcca
      961 aacgttaaca tcacaggtaa acagaaacgt cgggtcgatc gggaaattct ttcccggacg
     1021 gcgcggggtt gggcaagccg caggcgcgtc agtgctttta gcgggtgtcg gggcgcagcc
     1081 ctgaaccagt cacgtagcgc tagcggagtg tatactggct aaacttcaga gatgccaagg
     1141 aagggacagg atatgttttg tagcaccgcc accacggtgg cgatactcca aaacgcctgg
     1201 tcagggcaca gccccgacac cccagagccg actgtaggtc actggacgaa cgcggcggaa
     1261 tgatgtcgga tgacgtcatt ttgcggcgtt tgccctatcc tgcatcgtat taaaaaatgc
     1321 agctatggcg cgtacggtgc caaagataag cccggagata ttccgcttcc tcgctcactg
     1381 actcgctccg ctcggtcgtt cggctgcggc gagcggtacc ggcttactgg cggggcggaa
     1441 atttcctggc atcttccagg aagaagctta acagggaagc aagaaggcca cggcgaagcc
     1501 gtttttccat aggctccgcc cccctgacaa gcatcacgaa atctgacgct caaatcagtg
     1561 gtggcgaaac ccgacaggac ttaaagatac caggcgtttc cccctggtgg ctccctcgtg
     1621 cgctctcctg ttcctgcctt tcggtttacc ggtgtcattc cgctgttatg gccgcgttta
     1681 tctcattcca cgcctgacac tcagttccgg gtaggcagtt cgctccaagc tggactgtat
     1741 gcacgaaccc cccgttcagt ccgaccgctg cgccttgtcc ggtaactatc gtcttgagtc
     1801 caacccggaa agacacgact taacgccatt ggcagcagcc attggtaaga ggattcacgg
     1861 agcagggtag tagagtgctt ctacagagtt cttgaagtgg cggcctgact gcggctacac
     1921 tggaaggaca gttttggtat ctgcgctccg tgaaagccag ttaccttcgg aagaaagagt
     1981 tggtagctct tgattccggc aaacgaacca ccgttggtag cggtggtttt tttgtttaca
     2041 ggacatgaga ttacgacgag agtaaaagga tcacaagaag atccggctgt ttaccagtga
     2101 tttggcttca gtattggttt ccgcctagcg gggccttata cgtaaaaatt ccacacctga
     2161 cttatcacac aggggagctc cgcaagtacc agagagcact gaatagcagg ccacggaaat
     2221 gtcttggatt ccggcaacct tcagtggtct ttgctgagct aagacaggcg gcttagcgtt
     2281 gcacttcgaa cttgaatccg cccagaagca ttcagcagaa gtcgctaacg gtttgcttgc
     2341 aaatgctatc aataatgctt tgcctaaagc aggaataaaa aagccaccta cacggtggct
     2401 ttttttctgt ccgggaacta gctgaattga acctaaaatc ccggccacga actggtagac
     2461 acctttatcc ctgaagatgt ttgaagagaa aacggcctat ttcataggtc gtaaagtcag
     2521 ggtttagctc tttatcatcc atccctacag cgctccctgc ctcgatcaat accttcttca
     2581 tgttgctaac tttaagcccg tctttggtaa ccaagatctt tccttttgga agcttatgaa
     2641 tcacgtaatc cttgaaggaa tgtgtgtcct tatctccacc aggcaaagaa aagccctgac
     2701 ctaataacga ttttaatgaa ttattctctt caattaagtt caggac
//
