LOCUS       NZ_CP056591             3066 bp    DNA     circular CON 18-MAY-2024
DEFINITION  Citrobacter freundii strain RHBSTW-00355 plasmid pRHBSTW-00355_6,
            complete sequence.
ACCESSION   NZ_CP056591
VERSION     NZ_CP056591.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN15148590
            Assembly: GCF_013738135.1
KEYWORDS    RefSeq.
SOURCE      Citrobacter freundii
  ORGANISM  Citrobacter freundii
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Citrobacter; Citrobacter freundii complex.
REFERENCE   1  (bases 1 to 3066)
  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 3066)
  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                     :: WTP2 T1-00355
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 64.3410414469136x
            Sequencing Technology :: Hybrid: Illumina and PACBIO_SMRT
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_013738135.1-RS_2024_05_18
            Annotation Date                   :: 05/18/2024 02:43:40
            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)                     :: 5,492
            CDSs (total)                      :: 5,375
            Genes (coding)                    :: 5,195
            CDSs (with protein)               :: 5,195
            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)              :: 180
            CDSs (without protein)            :: 180
            Pseudo Genes (ambiguous residues) :: 0 of 180
            Pseudo Genes (frameshifted)       :: 54 of 180
            Pseudo Genes (incomplete)         :: 121 of 180
            Pseudo Genes (internal stop)      :: 37 of 180
            Pseudo Genes (multiple problems)  :: 26 of 180
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP056591.1.
            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..3066
                     /organism="Citrobacter freundii"
                     /mol_type="genomic DNA"
                     /strain="RHBSTW-00355"
                     /isolation_source="Freshwater sample from downstream of
                     wastewater treatment plant"
                     /db_xref="taxon:546"
                     /plasmid="pRHBSTW-00355_6"
                     /geo_loc_name="United Kingdom"
                     /collection_date="2017"
     gene            complement(555..830)
                     /locus_tag="HV173_RS27245"
                     /old_locus_tag="HV173_27250"
     CDS             complement(555..830)
                     /locus_tag="HV173_RS27245"
                     /old_locus_tag="HV173_27250"
                     /inference="COORDINATES: protein motif:HMM:NF016875.4"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="type II toxin-antitoxin system RelE/ParE family
                     toxin"
                     /protein_id="WP_094544860.1"
                     /translation="MIKNFKSKKLKQFNSGDTSKVAQAHKKKIEIILNALDTATSINDL
                     DLPGLDLHSYAEYTPTRWSLKVSANYRIFFEWDGANVRNVDYDDPH"
                     /name="type II toxin-antitoxin system RelE/ParE family
                     toxin"
     gene            1100..1441
                     /locus_tag="HV173_RS27250"
                     /old_locus_tag="HV173_27255"
     CDS             1100..1441
                     /locus_tag="HV173_RS27250"
                     /old_locus_tag="HV173_27255"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_011330340.1"
                     /GO_function="GO:0003677 - DNA binding [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="HigA family addiction module antitoxin"
                     /protein_id="WP_049592808.1"
                     /translation="MFTLQKPMHPGEFIREVYLEPLELQIGTFAEKLGVDTSTVSRLVN
                     QKADLSYEMALRLSKALGRSADSWMKMQIAYGLYRAQDKVNLEEVEVVYRPRNLDAPEK
                     QVHEFYENI"
                     /name="HigA family addiction module antitoxin"
     gene            1878..2066
                     /locus_tag="HV173_RS27255"
                     /old_locus_tag="HV173_27260"
     CDS             1878..2066
                     /locus_tag="HV173_RS27255"
                     /old_locus_tag="HV173_27260"
                     /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(2114..2341)
                     /locus_tag="HV173_RS27260"
                     /old_locus_tag="HV173_27265"
     CDS             complement(2114..2341)
                     /locus_tag="HV173_RS27260"
                     /old_locus_tag="HV173_27265"
                     /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_224019247.1"
                     /translation="MFGFSPGELMNLCPDERLLFVRMISAMLRRSGGDAGAVMFEAYRH
                     IVSDTNQARRSYMLDLLESVRHDYVHGGYT"
                     /name="hypothetical protein"
     Typing          2..405
                     /name="rep_cluster_2358"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="85.952"
                     /coverage="91.0"
                     /evalue="1.39e-118"
     Typing          2811..3066
                     /name="rep_cluster_2335"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="84.444"
                     /coverage="98.0"
                     /evalue="4.18e-64"
ORIGIN
        1 cgctctcctg ttcctgcctt tcggtttacc ggtgtcactc cgctgttatg gccgcgttta
       61 tctcattcca cgcctgacac tcagttccgg gtaggcagtt cgctccaagc tggactgtat
      121 gcacgaaccc cccgttcagt ccgaccgctg cgccttttcc ggtaactatc gtcttgagtc
      181 caacccggaa aggcacgact tatcgccact ggcagcggcc actggtaaga gggtgtacaa
      241 gagattacta atgcagagtt cttgaagtat cagcctaact acggctaaac tggaaggacg
      301 tatttggtgg cagcggtctt gtacaccctg ttaccacggt tcagaagttc cccaacttgc
      361 tgaaccttcg aaaaaccacc tccccaggtg gttttttcgt ttcaggatta aagatactct
      421 gcgtcccact caatctcaag aaattatctt taccaagcca ttgacttaat aaaaaaaaac
      481 catataatag cctcatgggc ttgaatcact ttagtgattc aagcccatga cctaagtcgt
      541 tgatttaact gacattaatg tggatcgtcg taatccacat tacggacgtt ggcaccatcc
      601 cactcaaaga aaatacgata gttcgccgac acctttaatg accagcgggt tggggtatat
      661 tcagcatacg aatgaagatc caaaccagga aggtcaagat catttattga agtagcggta
      721 tctaaagcgt ttaagataat ctctattttc tttttatgcg cttgtgctac cttacttgta
      781 tcaccactgt taaattgttt tagttttttg gatttaaaat ttttaatcat tgaacttctc
      841 catatgaaaa tttttatgtt ttagaagttc ttcttgttta gtaaagtttc ttgactgtgt
      901 tctatttata ggtagtattc tacgcctgcg aagctttaga actgccagat agtcactaca
      961 agaacaaaac agaagaacca aactgttaac gttaagaaaa aattaccctt aactaatcca
     1021 ttttatcaca aatggattgc ttatgtcaat aggtttgcgc gttgcgcaag gcacaaaatc
     1081 agagtattta ggaggttgca tgtttacatt gcaaaaacct atgcaccccg gcgagtttat
     1141 ccgcgaagta tatttagagc cgttagagct tcaaatagga acgtttgcag aaaagcttgg
     1201 ggttgataca tcaaccgtta gccggttagt aaaccaaaaa gctgaccttt cttatgaaat
     1261 ggcattacgc ctatcaaaag ccttagggcg ttctgctgac tcttggatga aaatgcaaat
     1321 agcatatggt ttatatcgtg ctcaagataa agtaaatctt gaagaagttg aggtggttta
     1381 ccgcccacgg aacttggatg ctcctgaaaa acaggtccat gaattttatg aaaatatcta
     1441 aaaacgatat ttcatttagg taaagaaaag ctcctaacca taggggcttt ttgtctctac
     1501 acctgtgtat ttatgtgaag acctaacttg cactcgcaga ggcggcagca tcgttattcc
     1561 tgaagatgct taaacagcgg gtgttgagcc tgtatcaacc attgatagtg atctgtatat
     1621 cctcttcact aaccccaaac ttcatagcca gcccccttct atgcttacct agagaattta
     1681 ccataacatc cgttgcgtgc accgcctgag aggctctcag ggcgtttcta cgacctcacc
     1741 tgcaaaagaa cacatcttac cccctgaaaa ccgctcagaa acgcgctgat gatttctgcg
     1801 tacctgcatg gctatgcact caagtgaatg aagtaagatt tcagtctgcg atcaccataa
     1861 aaccgggaaa aagccgtatg acaaaacagg aatcagccgc actgaacatg gcaaaattta
     1921 tccgggcgca gtcgctgctg ctgctcgaaa aactcgacgt gctcgatctt gatgacgagg
     1981 cagccgactg tgagcgaatg cacgaacagg cagaagcgct ttatcagaag ctgagcgcac
     2041 gcttcggtat acaggacggc gaataaagag acgaaaagaa cgctcactta gacgaaaagc
     2101 gtatccaggg caactatgta tatccaccgt gtacatagtc atgcctgacg ctttcgagca
     2161 ggtcgagcat gtaggaacga cgagcttgat tggtatcgga cacaatatgg cgatacgcct
     2221 caaacataac agcacccgca tcaccgcccg aacggcgaag catagcggaa atcatccgca
     2281 caaagagcag acgttcatcg gggcaaaggt tcataagttc tcctggtgaa aaaccaaaca
     2341 tgaaagcacc catctattaa cgtcagctgt gaacgcttca ttagaagaaa ataggtaaac
     2401 ccgggaaaaa gatccaaacg ttaacatcac aggtaaacag aaacgtcggg tcgatcggga
     2461 aattctttcc cggacggcgc ggggttgggc aagccgcagg cgcgtcagtg cttttagcgg
     2521 gtgtcggggc gcagccctga accagtcacg tagcgctagc ggagtgtata ctggctaaac
     2581 ttcagagatg ccaaggaagg gacaggatat gttttgtagc accgccacca cggtggcgat
     2641 actccaaaac gcctggtcag ggcacagccc cgacacccca gagccgactg taggtcactg
     2701 gacgaacgcg gcggaatgat gtcggatgac gtcattttgc ggcgtttgcc ctatcctgca
     2761 tcgtattaaa aaatgcagct atggcgcgta cggtgccaaa gataagcccg gagatattcc
     2821 gcttcctcgc tcactgactc gctacgctcg gtcgttcggc tgcggcgagc ggaaggagaa
     2881 tattcacaaa ggcatatggc gatgaagacg agataaagcg agggaggaaa ggccgcggcg
     2941 ctgccggttt tccataggct ccgcccccct gacaagcatc acagaatctg acgctcaaat
     3001 cagtggtggc gaaacccgac aggactataa agatcccagg cgtttccccc tggtagctcc
     3061 ctcgtg
//
