LOCUS       CP057825                2683 bp    DNA     circular BCT 13-MAY-2022
DEFINITION  Citrobacter freundii strain RHB14-C12 plasmid pRHB14-C12_2, complete
            sequence.
ACCESSION   CP057825
VERSION     CP057825.1
DBLINK      BioProject: PRJNA605147
            BioSample: SAMN15148109
KEYWORDS    .
SOURCE      Citrobacter freundii
  ORGANISM  Citrobacter freundii
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Citrobacter; Citrobacter freundii complex.
REFERENCE   1  (bases 1 to 2683)
  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 2683)
  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                     :: RH04 T1-C12
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 84.5260350343111x
            Sequencing Technology :: Hybrid: Illumina and PACBIO_SMRT
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI
            Annotation Date                   :: 06/19/2020 15:26:05
            Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline
            (PGAP)
            Annotation Method :: Best-placed reference protein set; GeneMarkS-2+
            Annotation Software revision      :: 4.11
            Features Annotated :: Gene; CDS; rRNA; tRNA; ncRNA; repeat_region
            Genes (total)                     :: 5,034
            CDSs (total)                      :: 4,917
            Genes (coding)                    :: 4,861
            CDSs (with protein)               :: 4,861
            Genes (RNA)                       :: 117
            rRNAs                             :: 9, 8, 8 (5S, 16S, 23S)
            complete rRNAs                    :: 9, 8, 8 (5S, 16S, 23S)
            tRNAs                             :: 83
            ncRNAs                            :: 9
            Pseudo Genes (total)              :: 56
            CDSs (without protein)            :: 56
            Pseudo Genes (ambiguous residues) :: 0 of 56
            Pseudo Genes (frameshifted)       :: 18 of 56
            Pseudo Genes (incomplete)         :: 31 of 56
            Pseudo Genes (internal stop)      :: 14 of 56
            Pseudo Genes (multiple problems)  :: 7 of 56
            ##Genome-Annotation-Data-END##
            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/
FEATURES             Location/Qualifiers
     source          1..2683
                     /organism="Citrobacter freundii"
                     /mol_type="genomic DNA"
                     /strain="RHB14-C12"
                     /isolation_source="Pooled pig faecal samples collected from
                     floor of farm"
                     /db_xref="taxon:546"
                     /plasmid="pRHB14-C12_2"
                     /geo_loc_name="United Kingdom"
                     /collection_date="2017"
     gene            309..749
                     /locus_tag="HVW92_25165"
     CDS             309..749
                     /locus_tag="HVW92_25165"
                     /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="QMM97679.1"
                     /translation="MSQLFRLASPEDYEYIEELNLWELSFDKRPVQGVRCEDPVIGAEK
                     YNQGREKFKALASRHKKHWKPNGLTFSELIRWAIECGTPEQCQLVLALYHCTNDDDYQA
                     MGIQLSRSIDNANVSPIIFFTGKNQRLLGDISMLKQLEEKVR"
                     /name="hypothetical protein"
     gene            1710..2354
                     /gene="qnrD"
                     /locus_tag="HVW92_25170"
     ARG             1711..2351
                     /name="qnrD"
                     /gene="qnrD"
                     /gene_name="QnrD family quinolone resistance pentapeptide
                     repeat protein"
                     /tool="amrfinderplus"
                     /drug_class="QUINOLONE"
                     /identity="99.53"
                     /coverage="100.0"
     ARG             1711..2354
                     /name="QnrD1"
                     /gene="QnrD1"
                     /gene_name="quinolone resistance protein (qnr)"
                     /tool="rgi"
                     /drug_class="fluoroquinolone antibiotic"
                     /identity="99.53"
                     /coverage="100.0"
     Typing          1461..1616
                     /name="Col3M"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="98.089"
                     /coverage="100.0"
                     /evalue="2.29e-71"
ORIGIN
        1 tccgagtcaa tcaagtggtg catttgggtt aatgtcgttg gctggtattt aatgagaacg
       61 tgacaagcgc ctctcacgtt gctaagattg gattgcgacg tctaatctga gcaacgaatg
      121 cacaagattt agagtaccag agccctgtga tgctgtcacg gggctttgtt acatctggag
      181 cttggtaaac ctcataaatt caattcgcaa cgctcgccgc aaggcgtgaa cttgtttcac
      241 gtcgaggaag cggaatttct cgaaagcctt atactgtctc cgttcacaca tgatcggagg
      301 gtgtctctat gtctcaatta tttcgtttgg catcgccaga agattacgaa tacatcgaag
      361 aattaaattt atgggaattg tcatttgata agcgaccggt tcaaggggtt cgttgtgaag
      421 atccggtgat cggggcagaa aaatataatc aagggcgtga aaaatttaag gcgttagcgt
      481 cacggcataa aaaacactgg aaaccgaacg gattgacctt ttcggagttg atccgctggg
      541 caatagaatg cggaactcca gaacaatgtc agcttgtttt agcgttatac cattgcacaa
      601 acgatgatga ttatcaggcg atgggaattc agttaagccg aagtattgat aatgcaaatg
      661 tcagtccgat catctttttc acaggtaaaa atcaacggtt attaggtgat atttcgatgc
      721 taaaacagct cgaagaaaag gtgcgctgac gttaggttta cctattattt tatgtattat
      781 cctatctatt attctatctc ttattttatc tatttcgtct gtaataggta gaataataca
      841 tagaataaga tacagaataa tagatagaca caagatgacg ttgtgttatt tcttacccat
      901 taatccacct gttattctac ctattacttt acccgttatt gcacccaatt taggtataac
      961 gggcagaata acgggtgaaa taatgggtag aatcatagtt ttactaactt gcaccccatg
     1021 atactttcag tatcaatgcc actcattttc tggacgaaaa tgaatgacat aaggctccgc
     1081 cctctggcta ttttcttcgg ctggacgcct gcgaaaaaaa ccattcaccc aagcccgtca
     1141 aactcactgc gttcgtctga ccaccccctt ttttcgcccc tgtatttggt cgctcaaaaa
     1201 tgtggtggtc agacgcttcg cttgacgggg ggctttgccc ccaaaacgaa acacgttcac
     1261 tggggttcac ttgccatcgc tggggcgtgt catttcgttt cggctccccc tgtttttccc
     1321 tttcttcgct ggacgctcat caggataaaa acaaaaagcc taccgccctc gttttactcg
     1381 gttggtcaaa tcgcttcttg ccacaaaaca agtttgtgac tttcagcgat ttcgcatcgt
     1441 tttacttgtc agtttgcacg atgttaaaaa cgcactcaga agcccgcaaa accgttctaa
     1501 actttcagcg tagatttggg tgttttatag ggtgatcgtg tcttaaaatc gtttcgaggg
     1561 gctttaatgg ggatgaacgg gaggtttttg ctaactaact cgcccgttta acataaaagg
     1621 gattgtatga atcaatttta gctagagttt aaggttgttc aaattaatgt acaatgattg
     1681 cactgtataa ataaccaggt gtagcatgta tggaaaagca ctttatcaat gaaaagtttt
     1741 cacgagatca atttacgggg aatagagtta aaaatattgc cttttcaaat tgtgattttt
     1801 caggggttga tttaactgat actgaatttg ttgattgtag tttttacgac aggaatagct
     1861 tggaagggtg tgattttaat agagccaaac taaaaaacgc tagctttaaa agctgcgatt
     1921 tatcaatgag taattttaaa aacattagcg ccttaggtct tgaaattagt gagtgtttag
     1981 ctcaaggagc tgattttcga ggggctaatt ttatgaatat gataactaca aggtcatggt
     2041 tttgtagtgc ttatataacc aagacaaatc ttagttacgc taatttttct agagtcatat
     2101 tagaaaagtg cgaactgtgg gaaaatcgct ggaatggcac tgtgataact ggcgccgtgt
     2161 ttcgtggctc cgatctttct tgtggggagt tttcatcgtt tgattggtct ttggctgatt
     2221 ttactggttg tgatttaacg ggtggggcgc ttggcgagct tgatacaagg cgaattaatt
     2281 tagatggagt gaagttggat ggagagcagg cgcttcagct tgttgagagt ttaggtgtta
     2341 ttgttcaccg ataaaatcta ggtaaaaaac gcctaatgcc ccaatgtggt actaatcaaa
     2401 acggagcgaa gcgacatctt catcttgtct ttgcttttct ccatgatcag ttattgggtc
     2461 atggtctctt agctcgttaa tctggctaag tttggttagg ttgggcttct ttcgacactt
     2521 cgcaatccaa gaaatcccta gtccgttgat tggtgctctt atcaggtacg cactgtaatc
     2581 tttcgatacc gcagcgtgat tcggaggtag agccggaatt tcgttttccg gtacgtttta
     2641 ctaccacaat ttgcctgttt atcctttcgg agaccgggct aag
//
