LOCUS       NZ_CP056369             3576 bp    DNA     circular CON 30-MAR-2024
DEFINITION  Citrobacter freundii strain RHBSTW-00658 plasmid pRHBSTW-00658_5,
            complete sequence.
ACCESSION   NZ_CP056369
VERSION     NZ_CP056369.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN15148674
            Assembly: GCF_013739375.1
KEYWORDS    RefSeq.
SOURCE      Citrobacter freundii
  ORGANISM  Citrobacter freundii
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Citrobacter; Citrobacter freundii complex.
REFERENCE   1  (bases 1 to 3576)
  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 3576)
  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 T2-00658
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 108.849774211442x
            Sequencing Technology :: Hybrid: Illumina and OXFORD_NANOPORE
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_013739375.1-RS_2024_03_30
            Annotation Date                   :: 03/30/2024 05:03:34
            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)                     :: 4,967
            CDSs (total)                      :: 4,846
            Genes (coding)                    :: 4,751
            CDSs (with protein)               :: 4,751
            Genes (RNA)                       :: 121
            rRNAs                             :: 9, 8, 8 (5S, 16S, 23S)
            complete rRNAs                    :: 9, 8, 8 (5S, 16S, 23S)
            tRNAs                             :: 84
            ncRNAs                            :: 12
            Pseudo Genes (total)              :: 95
            CDSs (without protein)            :: 95
            Pseudo Genes (ambiguous residues) :: 0 of 95
            Pseudo Genes (frameshifted)       :: 25 of 95
            Pseudo Genes (incomplete)         :: 63 of 95
            Pseudo Genes (internal stop)      :: 22 of 95
            Pseudo Genes (multiple problems)  :: 14 of 95
            Pseudo Genes (short protein)      :: 1 of 95
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP056369.1.
            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..3576
                     /organism="Citrobacter freundii"
                     /mol_type="genomic DNA"
                     /strain="RHBSTW-00658"
                     /isolation_source="Wastewater effluent sample"
                     /db_xref="taxon:546"
                     /plasmid="pRHBSTW-00658_5"
                     /geo_loc_name="United Kingdom"
                     /collection_date="2017"
     gene            complement(791..1222)
                     /locus_tag="HV257_RS24695"
                     /old_locus_tag="HV257_24690"
     CDS             complement(791..1222)
                     /locus_tag="HV257_RS24695"
                     /old_locus_tag="HV257_24690"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000135004.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="helix-turn-helix domain-containing protein"
                     /protein_id="WP_044703046.1"
                     /translation="MARVSISEAARLVSVSRPTIYKLLKSGELSYTSVVKHGKPVKTID
                     TAELIRLFGALDVVSGDKSDTVKFDGVTTSVNSDFLHSLQHQVALLQAENTGLKDAVNA
                     RDEHISSLRQAMQLLEHKQSTSDPQNVPAKSWWQFWKSH"
                     /name="helix-turn-helix domain-containing protein"
     gene            complement(1225..1413)
                     /locus_tag="HV257_RS24700"
                     /old_locus_tag="HV257_24695"
     CDS             complement(1225..1413)
                     /locus_tag="HV257_RS24700"
                     /old_locus_tag="HV257_24695"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000166328.1"
                     /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_044703047.1"
                     /translation="MTKQQKTALNMAKFIQAQSLFLLGNLNEQDLDTEAGLCEKLHEDA
                     ELLFRTLDIRLDDFQED"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            1831..1962
                     /locus_tag="HV257_RS24705"
     CDS             1831..1962
                     /locus_tag="HV257_RS24705"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001422066.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="replication initiation protein"
                     /protein_id="WP_072052181.1"
                     /translation="MHEPPVQSNRCALSGNYRLESNPKRHDKTPLAAATGNGMYKIN"
                     /name="replication initiation protein"
     gene            complement(2272..3210)
                     /locus_tag="HV257_RS24710"
                     /old_locus_tag="HV257_24700"
     CDS             complement(2272..3210)
                     /locus_tag="HV257_RS24710"
                     /old_locus_tag="HV257_24700"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_013185833.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_200002678.1"
                     /translation="MSVLDFLSSGGMASIGGDLSEEEQKHTNEIVKLFAKKLREYARTL
                     QIPASNIKINKCSFLFVAKDDFSYHFVFADKPGGGNNLVYRNLSEYRQLELQSIVHQVR
                     IDVGDVVWAFSCPVSLSGEELDTYINKLSIEYIQSEIQSSKDNNDGRISEEAMNVPEIA
                     SGLEKFRKDYPKGKKTAFIIMQFGSTAAHVKLVDAIKKELSKHNIIALRADDKEYMDDL
                     FSNIKTYMYGCDFGIAIFERITEDNFNPNVSLEVGYMMGMGKQVLLLKDKTLSSLHTDL
                     AGKLYKPFDVFDIESSLSTHIGKWLSDKGFL"
                     /name="hypothetical protein"
     Typing          1592..1939
                     /name="rep_cluster_2373"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="94.269"
                     /coverage="81.0"
                     /evalue="2.99e-149"
ORIGIN
        1 tttgttccgt cccataccat agggggtcag tttcccgtcc ctgatttgca aagcgccccg
       61 tgctaacttc ccggccacgg aagaacggtg catctcatca tgtctccgtc ggttctcctg
      121 agccgtcatc ggcctgatct ccagatccga aaactctctc ttaaactccg cccccagaaa
      181 tttcaggtca tcgataaggg tcgcaaacca ttctttcacc tttttacctc cacactagta
      241 agccattcag ataacagtct ggcacagact ggctaaagaa agcggtgaac gggcacgcaa
      301 tttattgcgg ggtcgtgagg cgctggcagg gtgtcggggc gcatccatga caggtctttt
      361 atctataaca ccgcgcaggg agagatactg atatcgcacc acacaaacag aaaaagggta
      421 taccaagtgc aatcccttat cctgtgtggc actgaagccc tcagagcagc ttttcaggta
      481 taccaagcca gttaccacct ggtatacccc ctacaggtct tgccagaact ggctttaacc
      541 gcataaaaac agatgcgggt ataccatttc atacaagggg tggtataccc ccggaagcct
      601 tgtcagcaaa ggcttccggc attagccgtg tatactgcgt ggggtgtgac acgatttttt
      661 ggcctttatc agccatcaga aatcaaacat gcgggtaaag cggtcagatg agaaagtata
      721 aacatccata tccggtgata gcctggtggc tggccgaacg ctatgaccgg aatgcatgat
      781 tgataatgac tcaatgggat ttccagaact gccaccagga ctttgcagga acattctgcg
      841 ggtcagaagt actctgttta tgctccagaa gttgcatggc ctgacgaagt gaacttatat
      901 gctcatcccg tgcattcact gcatctttaa gcccggtatt ctccgcctgt aaaagcgcca
      961 cttgatgctg taaagaatgt aaaaaatcac tgttaaccga cgtagtgaca ccgtcaaatt
     1021 ttacagtgtc acttttatca ccactgacaa catcaagagc accaaaaaga cgaataagct
     1081 cagctgtatc aatggtttta acgggttttc catgctttac aacggaggtg tagctaagct
     1141 caccagattt aagcagcttg taaatagtcg ggcgactgac actgacaaga cgtgcagctt
     1201 cactaatgga tacgcgagcc attactaatc ctcttgaaaa tcatccagac gaatatccag
     1261 agtacgaaaa agcagttccg catcctcatg caatttttcg cacaagccgg cttcagtatc
     1321 gagatcctgt tcattgagat tacccagcaa gaacagggat tgcgcctgaa tgaatttcgc
     1381 catattcagt gccgttttct gttgtttcgt catcacagtg tcagtgctcc aaatgatatc
     1441 cggttctttt ccgcttcctc gaccgttcgc tcgctacgct cggtcactta tctgcggcga
     1501 gcggacgcat cttcctaaga gacaaataac gtagacggta agcgtaacga aaagccagaa
     1561 caagaacgat aaagccatgc ccgaccaggg cgtttttcca taggcttcgc ccccctgaca
     1621 agcatcacaa aatttgacgc tcaaatcagt ggtggcgaaa cccgacagga ctttaaagat
     1681 accaggcgtt tccccctggt ggctccctcg tgcgctctcc tgttcctgcc tttcggttta
     1741 ccggtgtcat tccgctgtta tggccgcggt tctctcattc cacgcctgac actcagttcc
     1801 gggtaggcag ttcgctccaa gctggactgt atgcacgaac cccccgttca gtccaaccgc
     1861 tgcgccttat ccggtaacta tcgtcttgag tccaacccga aaagacacga caaaacgcca
     1921 ctggcagcgg ccactggtaa tgggatgtac aagattaact gaatgagagt tcttgaagtc
     1981 cgagctaaac tacggctaaa ctgaaaggac agattacggt ttcagcggtc ttgtacaccc
     2041 tgttaccacg gttcagaagt tccccaactt gctgaaccct cgaaaaaacc gactccccag
     2101 tcggtttttt cgtttctgga acaagagact acgacgagag acgaaggatc tcaagaagat
     2161 ctcatcaatc aaacgcgtca agtctcaaat ttgaccatga ttttcgcata accccattcg
     2221 ataactaacg atgtcaaaca agtaccgcac atacggtact tgttccggaa actataaaaa
     2281 tcccttgtct gatagccatt tcccaatatg agtgctgagg gatgactcaa tatcgaaaac
     2341 atcaaatggc ttataaagtt tacctgctaa gtctgtatgt aatgaactta gagtcttatc
     2401 ctttaaaagt aagacctgct tccccattcc catcatatat ccaacttcca atgaaacatt
     2461 agggttaaaa ttatcttctg taatcctctc aaaaatagca ataccgaaat cgcacccata
     2521 catatatgtt ttgatatttg aaaagagatc atccatatac tctttatcat cagcccttaa
     2581 agctattatg ttgtgtttag acaactcttt ctttattgca tcaacaagct ttacgtgcgc
     2641 tgccgtgcta ccaaactgca tgatgataaa tgctgttttt ttcccttttg gatagtcttt
     2701 tctgaatttt tcaaggccag aagctatttc agggacattc atagcctctt ctgaaattct
     2761 accatcattg ttatctttac tactttgaat ttcagactga atatattcaa tagagagttt
     2821 attaatatat gtatcaagtt cttccccgga gagagagact gggcaagaga acgcccaaac
     2881 aacatcacca acatcaatcc gaacctgatg gacgatactt tgaagttcaa gctgtctata
     2941 ttcagataag tttctatata ctaaattatt accgccacca ggtttatcag caaacacgaa
     3001 atgataagaa aaatcgtctt ttgcgacaaa caaaaatgaa catttattta ttttgatatt
     3061 ggatgctgga atttgtaatg tcctagcata ctctctcaat tttttggcaa ataatttaac
     3121 tatttcatta gtatgttttt gttcttcttc agacagatct ccaccaatac tagccatccc
     3181 accggaagat aaaaaatcca aaacagacat agttaatttc ctttttccaa ttctaaagaa
     3241 cgcttggccc ggacatccca aaacctaacc actacttaat ggtaacatca cctattcact
     3301 tgataatgat acaacccacc ttgagtctac tgccatctat ttaacataag cactcattac
     3361 gcgcatcgct cagacgcact ctgagcgctt ttggggtgag tgcgtcgttt tgtacagttt
     3421 acccggggga aaacgctcag aacgccacag atgaatcctg agagggtgaa taactatgct
     3481 cccggctgca tggtgcgtga tttgacggaa aacagccgct aaaagggaga tttttcccgg
     3541 tttactagcc cgggaatccg ggattgatga agccta
//
