LOCUS       NZ_CP099219             2833 bp    DNA     circular CON 15-APR-2024
DEFINITION  Citrobacter freundii strain RHB16-SO-C03 plasmid unnamed2, complete
            sequence.
ACCESSION   NZ_CP099219
VERSION     NZ_CP099219.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN15488551
            Assembly: GCF_029716005.1
KEYWORDS    RefSeq.
SOURCE      Citrobacter freundii
  ORGANISM  Citrobacter freundii
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Citrobacter; Citrobacter freundii complex.
REFERENCE   1  (bases 1 to 2833)
  AUTHORS   Matlock,W.
  TITLE     Plasmid overlap and evolution between Enterobacterales isolates from
            bloodstream infections and non-human compartments
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 2833)
  AUTHORS   Matlock,W.
  TITLE     Direct Submission
  JOURNAL   Submitted (13-JUN-2022) Nuffield Department of Medicine, University
            of Oxford, John Radcliffe Hospital, Oxford OX3 9DU, United Kingdom
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: Unicycler v. v0.4.4
            Assembly Name                     :: RHB16-SO-C03
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 101x
            Sequencing Technology             :: Illumina/Nanopore
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_029716005.1-RS_2024_04_14
            Annotation Date                   :: 04/14/2024 22:18:46
            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)                     :: 5,278
            CDSs (total)                      :: 5,159
            Genes (coding)                    :: 5,035
            CDSs (with protein)               :: 5,035
            Genes (RNA)                       :: 119
            rRNAs                             :: 9, 8, 8 (5S, 16S, 23S)
            complete rRNAs                    :: 9, 8, 8 (5S, 16S, 23S)
            tRNAs                             :: 83
            ncRNAs                            :: 11
            Pseudo Genes (total)              :: 124
            CDSs (without protein)            :: 124
            Pseudo Genes (ambiguous residues) :: 0 of 124
            Pseudo Genes (frameshifted)       :: 42 of 124
            Pseudo Genes (incomplete)         :: 81 of 124
            Pseudo Genes (internal stop)      :: 26 of 124
            Pseudo Genes (multiple problems)  :: 20 of 124
            Pseudo Genes (short protein)      :: 1 of 124
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP099219.1.
            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..2833
                     /organism="Citrobacter freundii"
                     /mol_type="genomic DNA"
                     /strain="RHB16-SO-C03"
                     /isolation_source="Pooled soil sample collected from floor
                     of pig farm"
                     /db_xref="taxon:546"
                     /plasmid="unnamed2"
                     /geo_loc_name="United Kingdom"
                     /collection_date="2017"
     gene            join(2317..2833,1..83)
                     /locus_tag="NFJ87_RS26350"
                     /old_locus_tag="NFJ87_26335"
     CDS             join(2317..2833,1..83)
                     /locus_tag="NFJ87_RS26350"
                     /old_locus_tag="NFJ87_26335"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_019704520.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="Crp/Fnr family transcriptional regulator"
                     /protein_id="WP_063842281.1"
                     /translation="MAKAKVLIDDTEEAIIKNALDVDDMNEVNINVTRKKKTGFLGTYS
                     IVFHESVKTLSKMNLKPNAYKIVMYLFGIIEMGNILVNFSQKKIADDLGLQPSNVSRAF
                     NELFKKGVLIKDSEDGHVYLNSNLCTMGVPKNFDQKRMKSLQKSNIETEDFKNQINLFT
                     PTNTTKIKTNDKKVIKKKEKENVLEFPMQNDWVDIE"
                     /name="Crp/Fnr family transcriptional regulator"
     gene            353..1630
                     /locus_tag="NFJ87_RS26355"
                     /old_locus_tag="NFJ87_26340"
     CDS             353..1630
                     /locus_tag="NFJ87_RS26355"
                     /old_locus_tag="NFJ87_26340"
                     /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="plasmid recombination protein"
                     /protein_id="WP_240500736.1"
                     /translation="MKSQFMHVELYSREEPAKKTINKSKNINHKSDVRTTNVDGVLSEM
                     KRDVGFTSHLEAIAAPEVLYGSINALERSIERYEAEYKTTDKNGKEKKLRKDACILLAG
                     VVSLDRADEEIWEEYKTKSIEYLKNKYGENLKCVVEHTDETNPHFHFYVVGNQQQDLNL
                     LHDGKLAVSKLAKEDKKKLHQTAYTEAMIKFQDDFYTQVSNKFGLSRTGEEPRERYKSR
                     PEYLRFKKRQETALNILSDIEEFEADIKEKARKTGYSKGAKQFQNKSWVIKLGEGIKLL
                     GKEHKAELDQKEKELEKIKKEKIEIETELNLKKEELSNAYIQRNEASRKNSVYIDKANA
                     LKKENKLLLPYKDQFDLKLQQEKEPLQAEVNNLTSENNNLKNENSELKKENIGFKEFID
                     GVKNHYGSKFEEWCKETFRTKTKHKY"
                     /name="plasmid recombination protein"
ORIGIN
        1 atgataagaa agttatcaag aaaaaagaaa aagaaaacgt tttagagttt cctatgcaaa
       61 atgattgggt tgatattgaa tagtaaaact accgcgcgtc gcttgctgaa taccagaaca
      121 tcgcaaatat aaaatttgca atgctctggt attttctttt ggttttgact taaaccccgt
      181 agggccgcat ctatgaagcc atattcgaag aatatgatag cgtaatagat atagtcggtt
      241 cctataacta ttgacagaaa aaccaaatat gttatttaaa atataagcaa aacaaaaaag
      301 gctttcttcc tgttatgaag gaaaaatatt atatgtgaaa aaggaataaa atatgaaatc
      361 acaattcatg catgtagaac tctacagccg agaagaaccg gcaaagaaga ctataaataa
      421 aagtaaaaat ataaatcata aatctgatgt ccgtacaact aatgttgatg gcgttttatc
      481 ggagatgaaa cgagatgtag gctttacatc tcatttagaa gccatagctg caccggaggt
      541 gctttatggg tctataaatg ccttagaacg ctctatagag cgttatgagg ccgaatataa
      601 gactactgat aaaaacggca aggagaagaa gctacgcaaa gatgcatgca tcttgctagc
      661 tggtgtagtt tctctagatc gagctgatga agaaatttgg gaagaatata agacaaaatc
      721 aattgaatat ttgaaaaata aatatggtga aaatttaaaa tgtgttgttg agcatacaga
      781 cgaaacaaac ccacattttc atttttatgt cgtaggaaat cagcaacaag atttaaattt
      841 gctgcatgat ggaaagctag cagtatctaa attagcaaaa gaagataaga aaaaattaca
      901 tcaaacagct tacacagaag ctatgattaa gtttcaagat gatttttata cacaagtatc
      961 aaataaattt ggattgagca gaacgggcga ggagccacga gaacgctata aatcccgccc
     1021 tgaatatttg aggtttaaaa aaagacaaga aacagcatta aatatattat ctgatataga
     1081 agaatttgaa gctgatatta aagaaaaagc aaggaaaacc ggatatagca aaggtgcaaa
     1141 gcaatttcaa aataaaagct gggtaattaa gttaggtgaa ggaattaaat tacttggaaa
     1201 agagcataaa gcagaattag accaaaaaga aaaagagtta gaaaaaataa aaaaagaaaa
     1261 aatagaaatt gaaactgagc ttaatttgaa aaaagaagaa ttatccaatg catatatcca
     1321 aaggaatgaa gcgtcgagga aaaatagtgt ttatattgac aaagcaaacg ctctaaaaaa
     1381 agaaaataaa ttattattac catataaaga tcaatttgat ttgaaattac agcaagaaaa
     1441 ggagccatta caagcagaag tcaacaattt gacttctgaa aataacaatt tgaaaaatga
     1501 gaattcagaa ctaaaaaaag aaaatatagg tttcaaagaa tttatagatg gcgtgaaaaa
     1561 tcattatgga tctaaatttg aagaatggtg taaagaaaca ttcagaacaa agacaaaaca
     1621 caaatactaa tctgaaaata ttttcatatt tgccgcctat gtggtgtatg agacaccact
     1681 aaaagcggcc tgacagcgtt tagctgtcat agctgggatt tatcccaaaa aaatggtttt
     1741 gtacgcagtt attaaccttt taatatcagt tacttaaata cataaaatgc aggttgggaa
     1801 aatgtggtca gggagctgac cgcatggggt ggggggaccc tgaacaagag tcacttgttc
     1861 aggtgggggg aacggggcgg ggttccccct ttggtatgta actacatata aaacaaaaga
     1921 aatactgtta aactttgaac cgtgagaact gcagaacctc tggttctgtg gtttgagcgg
     1981 ttgtccaacg acccggaggg gaggcggtaa ggcagttaaa gttacggttt cttctttctt
     2041 attttcttac ttcttaagca ccctttaaac ccttatatat caacacttta ccaaaaaaaa
     2101 aattatgaaa atcataattt tcaattatga aaatcataat gcaaaattat gaaaatcata
     2161 atcggactta tgaaaatcat aattttgcat acaggttcat tgatatgatt tgatgtagaa
     2221 acgataactt tcttatcgtt ttgatattga cattgcattc agatcggtta taaatgcaac
     2281 ataggttatt atttttacta caaaaaggaa tataaaatgg caaaagcaaa agttttaata
     2341 gacgatacag aagaagcaat aataaaaaat gcattagatg ttgatgatat gaatgaagta
     2401 aacattaacg tcacgagaaa aaagaaaacc ggttttctag gaacttattc tatagttttt
     2461 catgagtcag taaaaacact gtctaaaatg aacttaaaac ccaatgctta taagattgta
     2521 atgtatctat ttggcataat agaaatgggt aatattttag ttaacttctc acagaaaaag
     2581 atagctgatg atttaggctt gcagccgtct aacgtctcac gagcattcaa tgagctgttt
     2641 aaaaaaggag ttttaataaa agatagcgag gacggacacg tctacttaaa ttcaaatcta
     2701 tgcacgatgg gtgttccgaa aaactttgat caaaagagaa tgaaaagttt acaaaaatca
     2761 aatattgaaa ctgaagattt taaaaatcag atcaatttat tcactcctac aaatacaaca
     2821 aaaataaaaa cca
//
