LOCUS       NZ_CP056183             4863 bp    DNA     circular CON 26-JAN-2024
DEFINITION  Citrobacter freundii strain RHBSTW-01016 plasmid pRHBSTW-01016_3,
            complete sequence.
ACCESSION   NZ_CP056183
VERSION     NZ_CP056183.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN15148768
            Assembly: GCF_013781965.1
KEYWORDS    RefSeq.
SOURCE      Citrobacter freundii
  ORGANISM  Citrobacter freundii
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Citrobacter; Citrobacter freundii complex.
REFERENCE   1  (bases 1 to 4863)
  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 4863)
  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 T3-01016
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 61.6339889191906x
            Sequencing Technology :: Hybrid: Illumina and OXFORD_NANOPORE
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 01/24/2024 14:08:30
            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)                     :: 5,209
            CDSs (total)                      :: 5,084
            Genes (coding)                    :: 4,951
            CDSs (with protein)               :: 4,951
            Genes (RNA)                       :: 125
            rRNAs                             :: 9, 8, 8 (5S, 16S, 23S)
            complete rRNAs                    :: 9, 8, 8 (5S, 16S, 23S)
            tRNAs                             :: 87
            ncRNAs                            :: 13
            Pseudo Genes (total)              :: 133
            CDSs (without protein)            :: 133
            Pseudo Genes (ambiguous residues) :: 0 of 133
            Pseudo Genes (frameshifted)       :: 31 of 133
            Pseudo Genes (incomplete)         :: 97 of 133
            Pseudo Genes (internal stop)      :: 23 of 133
            Pseudo Genes (multiple problems)  :: 16 of 133
            Pseudo Genes (short protein)      :: 1 of 133
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP056183.1.
            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..4863
                     /organism="Citrobacter freundii"
                     /mol_type="genomic DNA"
                     /strain="RHBSTW-01016"
                     /isolation_source="Wastewater effluent sample"
                     /db_xref="taxon:546"
                     /plasmid="pRHBSTW-01016_3"
                     /geo_loc_name="United Kingdom"
                     /collection_date="2017"
     gene            join(3725..4863,1..160)
                     /locus_tag="HV351_RS25860"
                     /old_locus_tag="HV351_25870"
     CDS             join(3725..4863,1..160)
                     /locus_tag="HV351_RS25860"
                     /old_locus_tag="HV351_25870"
                     /inference="COORDINATES: ab initio prediction:GeneMarkS-2+"
                     /GO_function="GO:0005524 - ATP binding [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GeneMarkS-2+."
                     /codon_start=1
                     /transl_table=11
                     /product="ATP-binding protein"
                     /protein_id="WP_097414638.1"
                     /translation="MMVNFSLSNAFSFMDAQNMSMLAVSSAKDDINLANVVSVSDVRIL
                     KSALIFGANASGKSNLMKTISLMKDIVLHSVQAIESSITKNVIPFLLDEDGPNKPSEME
                     MTFISDGVKYRYGLSIFQGKIKEEWLYYTPKSRETILFERDGLSIEVNKAAFSESNLFI
                     KEGIIQKTREDVPFVSVVAGFNGEHSKRVVNWFNNIVFLSGSNEGMFTAITMKLINESE
                     DFKAWLKKILPAFQINDIYLDEVAPDFPFGNIKTDDDNLKNLFSSIQNFAKNQKVFSLR
                     VVKKTASGEISVPIDFESEGTKKIVYLLGPIYNAMINGNLLLVDEFDSKFHTLLSKFLF
                     RIFHAQSEGLSQIIAAVQDVNLMNTDCFRRDQIWFVDKDIKSGSSHLYSLVEYKEKQRT
                     LKSSYGHDYLSGAFDAIPLFDNLDEFEKLMPEG"
                     /name="ATP-binding protein"
     gene            233..601
                     /locus_tag="HV351_RS25865"
                     /old_locus_tag="HV351_25875"
     CDS             233..601
                     /locus_tag="HV351_RS25865"
                     /old_locus_tag="HV351_25875"
                     /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_045626380.1"
                     /translation="MKTTDRFISVSFRYFHNVDDIGQSIDSWRVDGSLPDLIEKLVYLT
                     ANGITKVSSDGIFTNYTRFPDSAVNDFKCPDEISVDENWGVIKNIGGQKRRVAGFLKDN
                     VFYIVFFDKDHRFWKSRK"
                     /name="hypothetical protein"
     gene            complement(838..951)
                     /locus_tag="HV351_RS25870"
                     /old_locus_tag="HV351_25880"
     CDS             complement(838..951)
                     /locus_tag="HV351_RS25870"
                     /old_locus_tag="HV351_25880"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_005761324.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_032634168.1"
                     /translation="MHEPPVQSDCCALSGNYRLESNPERHAKAPLAAATGN"
                     /name="hypothetical protein"
     gene            1367..1558
                     /locus_tag="HV351_RS25875"
                     /old_locus_tag="HV351_25885"
     CDS             1367..1558
                     /locus_tag="HV351_RS25875"
                     /old_locus_tag="HV351_25885"
                     /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_045265536.1"
                     /translation="MTKQQKTALNMAKFIQNQSLLLLEKLNELALDVEADLCEKLHDDA
                     EHLFRTLSSRLDELQDGN"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            1558..1980
                     /locus_tag="HV351_RS25880"
                     /old_locus_tag="HV351_25890"
     CDS             1558..1980
                     /locus_tag="HV351_RS25880"
                     /old_locus_tag="HV351_25890"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:YP_005229777.1"
                     /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_181641389.1"
                     /translation="MARVSISEAARLVKVSRPTIYKMINSGKLSYTSVVKQGKAIKVID
                     TSELIRVFGSLDGVIDTVKYDVKSDAESTGVNSVGLHDLQHRIALLEAENDGLKGAVKA
                     RDEHIDSLRQAMQLLEHKHEPSSPPHSPWWKFWKKS"
                     /name="helix-turn-helix domain-containing protein"
     Typing          complement(839..1246)
                     /name="ColRNAI_rep_cluster_1987"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="91.484"
                     /coverage="99.0"
                     /evalue="1.3e-157"
ORIGIN
        1 aaaatcagga agtagtcatc tctattcttt ggttgagtat aaagagaagc agcgaacttt
       61 aaaatcatcg tatgggcatg attatttatc tggtgcattt gatgctatcc cattgtttga
      121 taatttagat gaatttgaaa aacttatgcc tgagggatga tttatgtcaa agagaggccg
      181 cggtcttcgt agctcttcga ggaaagagga aacaaaatcc tcaaagagca ttatgaaaac
      241 tacagataga tttatttctg ttagttttag atattttcat aacgtcgatg atattggtca
      301 gtctattgat tcttggaggg ttgacggcag tttgccagat ttaattgaaa agcttgttta
      361 tcttacagct aatgggataa caaaagtcag ctctgatggt atttttacta actacactcg
      421 atttccagat tcagcagtta atgattttaa atgccctgat gaaatatcag ttgatgagaa
      481 ctggggtgtt ataaaaaata taggaggcca gaaaagaagg gttgctggtt ttttaaagga
      541 taatgtgttt tatatagttt tttttgataa ggatcatcgg ttttggaaga gcaggaaata
      601 ggcttagtta cgattgtact gtatgttgag gcaagatctt cttgagatca ctgtgttctc
      661 gtcgtaatct ctcgctctgt aaacgaaaaa accgccttgg cgggcggttt tttcgaaggt
      721 tccaagagtt ggcgctctta gaaccaaggt aactggcttg gaggagcgca gtaaccaaaa
      781 cttgttcttt cagtttagcc ttaaccggcg cataacttca agactaactc ctctaaatca
      841 gttaccagtg gctgctgcca gtggcgcttt tgcatgtctt tccgggttgg actcaagacg
      901 atagttaccg gataaggcgc agcagtcgga ctgaacgggg ggttcgtgca tacagtccag
      961 cttggagcga actgcctacc cggaactgag tgtctggcgt ggaatgagat aaacgcggcc
     1021 ataacagcgg aatggcaccg gtaaaccgaa aggcaggaac aggagagcgc acgagggagc
     1081 cgcctatcag aaatgatagg tatctttata gtcctgtcgg gtttcgccac cactgatttg
     1141 agcgtccgtt tctgtgatgc ttgtcagggg ggcggagcct atggaaaaac ggccgctgcg
     1201 cggcctcctc ttttcctcct accttgatcg ctcggttttc tcgagctttt ataagaatgg
     1261 tcttgccgct cgccgcagcc gaacgaccgg agcgtagcga ctgagtgagc gaggaagcgg
     1321 aaaagagact ggttttacac tgagcactga cgctctgagg cttcttatga cgaaacaaca
     1381 gaaaacagcg ctgaacatgg ctaaattcat ccagaatcag tctctgctcc tgctggagaa
     1441 gcttaacgag cttgctctcg atgtcgaggc cgacctttgt gagaaactcc acgatgatgc
     1501 ggagcatctt ttccgtacac tgtcctcgag actggatgaa ttacaggatg gtaactgatg
     1561 gccagagtgt ctattagtga agcggcacgg cttgttaagg ttagtcgccc cacaatttac
     1621 aagatgatta acagtgggaa gttaagttac acctctgttg taaagcaggg taaggctatt
     1681 aaagttattg atacttcaga gcttattaga gtgtttggtt ctcttgatgg tgtcatcgat
     1741 actgtaaaat atgatgtaaa aagtgacgca gaatctacag gtgttaacag cgttggttta
     1801 catgatttac aacatagaat cgctttactt gaagctgaaa acgatggtct taaaggggct
     1861 gttaaggctc gagatgagca tattgattcc cttcgtcagg ctatgcagct tctggagcac
     1921 aagcacgaac cttcttcacc accccattcc ccgtggtgga aattctggaa aaaatcctga
     1981 ccccgtcatg cttccgtttt cctctccggc catcccgggg agttcctgaa ccttcccaaa
     2041 aatcgtcaga tctctgaacg ctcctcacca ctaaaaatac ccacacccca cgcaaaatta
     2101 acattttgca gatttgtatt taatatcagt gggttacttt cctgaaattt cgttttttaa
     2161 attttattta tatagatccg actctatgac gagtcgtcat agagtccccg gcgagtcgtc
     2221 atagagtcgg taacgactca ggactataaa aacaataagt taataacgac ccgactctag
     2281 acacgactcc ccgtttggtt gttttttaga ctcggcgact ctgggtacga ctctagtgaa
     2341 gattcgccgg tgaatcgtgt ggtgagtcgt ccggcgactt gccataacgt gattgccggc
     2401 cgtcgacgaa cccgatttct gaacgtgctg aaaaccggtt ttccggctgc gccggcaacg
     2461 cttcacggcc acgcaataaa ttgcgtcccc gttcaccgtt ttcggatggg aagaacgccg
     2521 gaaacaggac ttaccctggc tgaatggcgt gaattttcgc gctatgcact tgcgtgcata
     2581 ctcatgcatg ccgtaaaaac agagcctgcg cgtttctggc gggttttcgg gtggtttgtt
     2641 gcctgtttta ccggtttccc gtcagaaacg ccctgaggcc gttttagcgg tgcgtacaat
     2701 tagggggtta tgttaaatcc acaccagcta cagacgtaaa aaaagccccg cagggcttta
     2761 tatctatata tctgttctca tccaatccca tgtgtcttgg gtgagccatc ctgcgtattc
     2821 tttggttaca ccaatcacaa gcaaggtgtc attattgtcc agatgcctac gcaaacgatc
     2881 cgacagttgt tgcgctgttt ctccggttga tattagccat gtggaatcta aagggtggca
     2941 ccaccccggc gattttttta actcatcata tagtgcattg tagttttgac ctgcttgatt
     3001 caggtcataa gagacacagt aaactgacat agaaccatcc tctttaatca aatgtggggc
     3061 agcccgttag ggctgcagtc acaacttact tcttcttttc acgattaatt ggaattttga
     3121 acatcccacc gtttggacgg gtgatccgtt tgccctttac tgtgatataa gggcgaaaaa
     3181 tgtatgcctg agactcgtct gtctgcatgg tgcatttcct atttttcgcc acatgagtgt
     3241 tgatttttgc tatcaaaatt gtactgtagc aaccaacaaa tcttgtggct ggctttatca
     3301 agctcttgag gtggtactca agtgccgcat ttgtgtatgg tttgttacgg gttagttctg
     3361 gtggtacagg ctaacccact tacttcaaaa aacgtcgttt ttctcctttc atgcgtcatt
     3421 tcctagatgt ttcttcactg tatcagctcc gctgagcata aatgctacaa agagaaacca
     3481 tccccatcct gaaaccgagt gtaaagctag cactgctgag ctgacaactg cggctaaagg
     3541 aaccatttgg tatagaaaaa atctcataga ccccctgcat ttagcttttt ttaacaagtg
     3601 ttccataacg tgctatctat taaacgcacc tgttgtttta gaacgcttgt atgctatcct
     3661 taagtcctga ttttgtcaat atttactcat tttgttgttt aaggatggcg taaggggtgt
     3721 tcttatgatg gttaatttta gtctttctaa cgcattttcc tttatggatg ctcaaaatat
     3781 gagcatgttg gcggtgtcat ccgcgaaaga cgacataaac ttggctaacg tggtttcagt
     3841 gagtgatgtt cggatactga aatctgctct gatatttggg gctaacgcta gcgggaagtc
     3901 taatctcatg aaaacaattt ctttaatgaa agatattgtt ttgcattccg tgcaagctat
     3961 tgaaagtagc attacaaaga acgtaatacc gtttttgctt gatgaggatg gaccaaataa
     4021 accatctgaa atggaaatga cttttatttc agatggggtt aaatatagat atggattgtc
     4081 tatttttcag gggaaaataa aagaagaatg gttgtactac acaccaaaat caagagaaac
     4141 aattctcttt gaaagagatg gtctttctat tgaggtaaat aaggcggctt ttagtgagtc
     4201 aaaccttttt atcaaagaag ggattattca aaaaacaagg gaggatgttc catttgtttc
     4261 ggttgttgct ggttttaatg gtgagcattc aaaacgagta gttaattggt ttaacaatat
     4321 cgtattcctt tctggttcta atgaagggat gtttacagca attaccatga agttaataaa
     4381 tgagtctgag gattttaagg cttggctaaa aaaaatactt ccagcattcc agattaatga
     4441 tatttacctc gatgaggtcg cacctgattt tccatttgga aatataaaaa cagatgatga
     4501 taatttaaaa aatttattta gttcaataca aaattttgca aaaaaccaga aggttttttc
     4561 tcttagagta gtgaaaaaaa cagctagcgg tgagatttca gtacctattg attttgagtc
     4621 tgagggtact aaaaagatag tttatcttct tggtccaatc tacaatgcca tgataaacgg
     4681 taacttattg ttagttgatg agtttgattc taagtttcac acccttttgt ctaagttttt
     4741 gtttagaata ttccatgcgc aaagcgaggg gcttagccaa ataatagctg ctgttcagga
     4801 tgttaatcta atgaacactg attgttttag acgtgaccag atttggtttg ttgataaaga
     4861 tat
//
