LOCUS       NZ_CP055542             5480 bp    DNA     circular CON 30-APR-2024
DEFINITION  Citrobacter freundii strain RHBSTW-00398 plasmid pRHBSTW-00398_5,
            complete sequence.
ACCESSION   NZ_CP055542
VERSION     NZ_CP055542.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN15148600
            Assembly: GCF_013612875.1
KEYWORDS    RefSeq.
SOURCE      Citrobacter freundii
  ORGANISM  Citrobacter freundii
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Citrobacter; Citrobacter freundii complex.
REFERENCE   1  (bases 1 to 5480)
  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 5480)
  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                     :: WTP4 T2-00398
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 102.020446088887x
            Sequencing Technology :: Hybrid: Illumina and OXFORD_NANOPORE
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_013612875.1-RS_2024_04_30
            Annotation Date                   :: 04/30/2024 03:57:23
            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)                     :: 5,350
            CDSs (total)                      :: 5,235
            Genes (coding)                    :: 5,084
            CDSs (with protein)               :: 5,084
            Genes (RNA)                       :: 115
            rRNAs                             :: 9, 8, 8 (5S, 16S, 23S)
            complete rRNAs                    :: 9, 8, 8 (5S, 16S, 23S)
            tRNAs                             :: 83
            ncRNAs                            :: 7
            Pseudo Genes (total)              :: 151
            CDSs (without protein)            :: 151
            Pseudo Genes (ambiguous residues) :: 0 of 151
            Pseudo Genes (frameshifted)       :: 45 of 151
            Pseudo Genes (incomplete)         :: 109 of 151
            Pseudo Genes (internal stop)      :: 37 of 151
            Pseudo Genes (multiple problems)  :: 31 of 151
            Pseudo Genes (short protein)      :: 1 of 151
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP055542.1.
            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..5480
                     /organism="Citrobacter freundii"
                     /mol_type="genomic DNA"
                     /strain="RHBSTW-00398"
                     /isolation_source="Wastewater effluent sample"
                     /db_xref="taxon:546"
                     /plasmid="pRHBSTW-00398_5"
                     /geo_loc_name="United Kingdom"
                     /collection_date="2017"
     gene            complement(join(5343..5480,1..1434))
                     /locus_tag="HV183_RS26970"
     CDS             complement(join(5343..5480,1..1434))
                     /locus_tag="HV183_RS26970"
                     /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="relaxase/mobilization nuclease domain-containing
                     protein"
                     /protein_id="WP_249414914.1"
                     /translation="MIVKIHSRGAGSGSGPVDYLLGKARDREKAVVLRGEPERVRQLID
                     GCEFARAYTSGVLSFREENLPDDEKVRLMEEFEQTLLPGLDGDQYACLWVEHRDKDRLE
                     LNFVIPNIELQSGKRLQPYYDRADRPRVNAWQTLTNDRLNLDDPHDPARRRTLTPGNDL
                     PGDRQKAAQAITDTLETMMAQGMIRNREDVVRALENGGLTVVRETKSSLSIADPDGGRN
                     IRLKGALYERDFRFSESLRGDLEAAGTAYRGEREERVCEARAIHQRGLTIKREEHQRRY
                     PRAEHPADNPAAALGHDRADMDTGLWCAVDRYVVGDPVVSGSAHRFTAGRDEQLQPAAY
                     RPESEIGGGGGNSHGRHPEKQVLRGAAEEREGRRAIYLEKRQTGSDLHCEIAPSVATEA
                     PYGVLSDKDNQIHDRDRKTVAERVRALTERLRDTTAGMAGQLRQLAEHVHHYFRRADAQ
                     RPGVSALERAGGQLAAAGHELNRSRQPLDAQVARLDSELAQKQERQKTRSFAPGRSRGH
                     DHGMER"
                     /name="relaxase/mobilization nuclease domain-containing
                     protein"
     gene            complement(1415..1750)
                     /gene="mobC"
                     /locus_tag="HV183_RS26610"
                     /old_locus_tag="HV183_26615"
     CDS             complement(1415..1750)
                     /gene="mobC"
                     /locus_tag="HV183_RS26610"
                     /old_locus_tag="HV183_26615"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_006674374.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="plasmid mobilization relaxosome protein MobC"
                     /protein_id="WP_175320710.1"
                     /translation="MDKRTKEIKIRLTESEHERLLARCDRAHLAEWLRSLGLGVHVLRR
                     RRVPDVDPALLRQVTGIGNNLNQIARKLHGLDSLSAHQQVSLLAVLTSLDRQLSELLET
                     QRDRQDS"
                     /name="mobC"
     gene            2015..3100
                     /locus_tag="HV183_RS26615"
                     /old_locus_tag="HV183_26620"
     CDS             2015..3100
                     /locus_tag="HV183_RS26615"
                     /old_locus_tag="HV183_26620"
                     /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="competence protein ComEC"
                     /protein_id="WP_181220000.1"
                     /translation="MVDEYDLDFLAVGDKTSGDAIFIRTKRANQKQIINLVDGGYSGTA
                     ENITQFMRKWYETDVIDNMILTHGDKDHISGLIKILESGEITVKRLWAFLPWDYAEDLI
                     NGEYFQNRNGVKWLQDELKRQYSSLKYLEELAVKNGIAISTPLAGCSIGEFKVLSPTKS
                     FYLDNLASSAKTAQENPNRIYGRELFESTFSAVRDIATSLKEWGFENFKSENTSPENNN
                     SVIQFSTLKNQRVLLTGDAGVEALGMAIGSLDQSNKPMADILQVPHHGSRRNVSSELLD
                     VIVGDKFNTKREAEAAKRLITVISAGKNDSNHPRKAVVRALYHRGAKIFDTKKGGFHKG
                     TSTRDNWKDATLLTYPLDTED"
                     /name="competence protein ComEC"
     gene            complement(3097..3603)
                     /locus_tag="HV183_RS26620"
                     /old_locus_tag="HV183_26625"
     CDS             complement(3097..3603)
                     /locus_tag="HV183_RS26620"
                     /old_locus_tag="HV183_26625"
                     /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_175320708.1"
                     /translation="MESLFEKISAYNIFNNIIPGAVFCYFFNLFFSVNLGGDGTAYNLC
                     LFYFWGVFVSRIGSLLIEMLAIKIKFVKYAPYGDYLMASRNDPDLKMFLEVNNMLRTFS
                     AVFLCLLVVFLLSFLVQHFDIKWFLIEGFSIAGSSASFFLFLIMMFAYRKQTSYIVKRI
                     NNQTA"
                     /name="hypothetical protein"
     gene            complement(3603..4508)
                     /locus_tag="HV183_RS26625"
                     /old_locus_tag="HV183_26630"
     CDS             complement(3603..4508)
                     /locus_tag="HV183_RS26625"
                     /old_locus_tag="HV183_26630"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001697689.1"
                     /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_175320707.1"
                     /translation="MSNQALDLFNERLPRKPYFTDELQFGVRIAGKERAILAKYIQFNQ
                     PHAMFWLGFDVDRPGAAIDWSDRNAPAPTLTIMNPENGHAHLLYALKTAVRTAPDGKMK
                     PLKYAAAVERALCKKLDADTGYSGLICKNPNHDHWQLAVWQPELYTLDWLADSLDLSAA
                     NDKEILPDYGLGRNCTLFDKTRKWAYRAIRQGWPEYDQWLQACYERVSAYNLQFAAPLD
                     ENEVNGIAKSIARWTIKNFDEVSFEKYVLDTHSSEIQAVRGRKGGMKSKGGGRKSLGNP
                     WLDIGVSRASYFRMKKNKGA"
                     /name="replication initiation protein"
     gene            4793..5032
                     /locus_tag="HV183_RS26630"
                     /old_locus_tag="HV183_26635"
     CDS             4793..5032
                     /locus_tag="HV183_RS26630"
                     /old_locus_tag="HV183_26635"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001118105.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="type II toxin-antitoxin system CcdA family
                     antitoxin"
                     /protein_id="WP_012666376.1"
                     /translation="MPVSAMRHKKTVSVTLEPALLRQAREAGINLSATLATALKHQIRE
                     SEAERWKRANRKAIQELNRITDEHGLLSDDHRTF"
                     /name="type II toxin-antitoxin system CcdA family
                     antitoxin"
     gene            5032..5340
                     /locus_tag="HV183_RS26635"
                     /old_locus_tag="HV183_26640"
     CDS             5032..5340
                     /locus_tag="HV183_RS26635"
                     /old_locus_tag="HV183_26640"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001199743.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="CcdB family protein"
                     /protein_id="WP_063448384.1"
                     /translation="MQFMVYRNNGNSRAYPYLLDVQSDIIGELNTRLVIPLFLLDEVSG
                     RPARRLNPVLNVDGEDFLVMTHEMASVRQSQLGEEVVSVREQRQAIKNALDFLLDGF"
                     /name="CcdB family protein"
ORIGIN
        1 ctcatgacct gctgccgcaa gctgtccacc tgcccgctca agtgctgaca cgcctggtcg
       61 ctgcgcatca gcgcggcgga agtagtggtg aacatgctct gcaagttgtc gtaactggcc
      121 tgccatgcct gctgtcgtgt ctcgtaatcg ttctgtaagc gctctaacgc gctcagcaac
      181 agtttttcgg tctcggtcat ggatttgatt gtccttatcg cttaaaacgc cgtatggcgc
      241 ttctgtggca actgacgggg ctatttcgca gtgtaggtca ctacctgttt gtcgtttttc
      301 gaggtatata gctcgacgcc cttcgcgctc ttcggcagca ccacgtaata cttgtttttc
      361 cgggtgtcgt ccgtgagaat ttccaccccc gcccccgatt tcgctttcag gtcggtaagc
      421 tgctggctgt agctgttcat ctcgtccagc cgtgaagcga tgagcgctcc ctgaaaccac
      481 aggatccccg acaacatacc gatcaacagc acaccacaga ccagtatcca tatcagcgcg
      541 atcgtgaccg agcgccgcag cagggttgtc tgccgggtgt tctgctcgtg gatagcgtcg
      601 ctgatgctct tcccgcttga ttgtaaggcc tcgctgatgg attgctcgag cttcacaaac
      661 tcgctcttca cgctctcccc ggtacgctgt gcctgctgct tcgaggtctc ctcgaaggct
      721 ttcgctaaat ctaaaatccc gctcatataa cgctcctttt aaccggatat ttcgtccacc
      781 gtccgggtcg gcaatgctga gactgctttt cgtttcccgt accaccgtca gcccgccatt
      841 ttccagcgcc ctgaccacat cctcacggtt acggatcatc ccctgtgcca tcatcgtttc
      901 cagcgtgtcc gtaatggcct gcgccgcctt ctgacggtcg ccgggaaggt cattgcccgg
      961 tgtcagggtt cgccgtcggg cgggatcatg agggtcatcg aggttcaggc ggtcattggt
     1021 cagagtctgc caggcgttga ccctgggacg gtcagcccgg tcatagtagg gttgcaggcg
     1081 ttttccgctc tgcaattcga tgttcgggat cacaaaattc agctccagcc tgtccttgtc
     1141 ccggtgctcc acccacagac aggcatactg gtcaccgtcc agaccgggaa gcagtgtctg
     1201 ctcaaactcc tccatcagac gcactttctc atcgtcaggg aggttttctt cccggaacga
     1261 caacaccccg gaggtgtagg cgcgggcaaa ctcgcatccg tcaatcagtt gtctgacacg
     1321 ctcaggctca ccccgcagta ccaccgcttt ttcccggtct cgcgcctttc ccagcaggta
     1381 atccaccggg ccactgcctg aacccgcacc ccggctatga atcttgacga tcacgctgtg
     1441 tctccagaag ctcagataac tggcgatcaa gactggtcag taccgccaga agagaaacct
     1501 gctgatgggc cgaaagcgaa tccagaccat gcagcttacg ggctatctga ttgaggttat
     1561 tgccgatgcc ggtcacctga cgaagcagtg ccggatcaac gtcaggcaca cgccggcgac
     1621 gcaatacatg tacacccaga ccgagcgaac gtaaccattc agcgagatga gcacgatcac
     1681 aacgtgccag cagtcgctca tgttcactct cagtcaggcg gatttttatc tctttcgttc
     1741 gcttgtccat gacactccgc tgagaaaact ttcgcaccca gagtgcgaat tttcgcagtg
     1801 gatgccaggg gtttcggggg gcggcgagcc ccctgaacca gtcacagaag gaaccctcgt
     1861 agaggggacg ctgtgtgtac tggcttaaag tataggggag tatgtcagat caataacgtg
     1921 ggaaaaagca aaaagcccta aaagaaggct gttatctgat ataggcttgt ttagtctcac
     1981 ggcgtagaat ggagaaaaaa acaaggagta agtaatggtt gatgaatacg atctggattt
     2041 tttggcagtt ggtgataaga caagtggtga tgctatattc ataagaacga agcgagctaa
     2101 tcaaaaacaa ataataaacc ttgtcgacgg tggctactcg ggaacagcag aaaacatcac
     2161 tcaatttatg cgtaagtggt atgaaactga tgtaattgac aacatgatcc ttactcacgg
     2221 ggataaagac cacatatctg gtttaataaa gattctagaa tcaggtgaga ttaccgttaa
     2281 aagattgtgg gcgtttctcc cttgggatta tgcagaagat ctaattaatg gtgaatattt
     2341 ccaaaatagg aatggggtta aatggcttca ggatgaactc aagagacaat actcatcgct
     2401 gaaatattta gaagaattag cagtaaaaaa tggaatagct ataagcacac cacttgctgg
     2461 atgctcaatt ggtgaattta aagtactatc accaacaaaa tctttttatt tggataacct
     2521 agcttcatca gcaaaaacag ctcaagaaaa tccaaataga atttacggta gagagttatt
     2581 tgaatcaacc ttctctgcgg ttagagatat cgccacatca ttaaaagagt gggggttcga
     2641 gaattttaaa tcagagaata catctccaga aaacaacaat agcgtaattc aattctcaac
     2701 tttaaaaaac caacgggtac tcttaactgg agatgcagga gtagaggctt taggaatggc
     2761 aattggaagt ttagaccaaa gcaataagcc tatggctgac atattacaag taccacatca
     2821 tggctctaga agaaatgttt cctcagaact attagatgtc attgttggtg ataaatttaa
     2881 cacgaaacga gaagctgaag cggcaaaaag actaattact gtaattagtg cagggaagaa
     2941 tgattctaac caccctagaa aagcagtagt tagagctctt taccatcgag gggctaaaat
     3001 atttgataca aaaaagggtg gttttcacaa aggtacttct acaagagaca attggaagga
     3061 tgccacgtta ctaacttatc ctttagatac tgaggactaa gcagtctgat tattaatcct
     3121 ttttactata tatgatgttt gttttctgta agcaaacatc attatcaaaa ataaaaaaaa
     3181 tgatgcacta gaacctgcga tactaaagcc ttcaattaaa aaccacttga tatcaaagtg
     3241 ctgaactaaa aaagacaaca aaaaaacaac cagcaaacac aaaaaaactg cggagaatgt
     3301 tctaagcatg ttattaactt ctaaaaacat ttttagatca gggtcgtttc tacttgccat
     3361 caaataatca ccataaggtg cgtatttaac aaactttatt tttatcgcaa gcatttctat
     3421 gagtagagat ccgattctag atacaaatac cccccaaaaa taaaaaagac ataggttata
     3481 tgcagttcca tcaccaccaa gattaaccga aaaaaataaa ttaaaaaaat aacaaaacac
     3541 agcaccgggt ataatgttgt taaaaatatt atacgcagat atcttttcaa acaatgactc
     3601 cattacgccc ccttgttttt tttcattctg aaatagcttg ctctactaac tccaatatct
     3661 aaccatggat tgcctaaaga ttttcttcca cctcccttac ttttcatccc acctttacga
     3721 cctctaactg cctgtatttc acttgaatga gtgtccaaca catacttttc aaaagaaact
     3781 tcatcgaagt tcttaatagt ccatctagca atacttttag caataccatt aacctcattt
     3841 tcatccagag gtgctgcaaa ttgcagattg taggcactga cacgttcata gcaggcttgc
     3901 aaccactggt catactcagg ccagccctga cggatagcgc ggtatgccca cttacgggtt
     3961 ttatcgaaca gggtgcagtt acggcctaaa ccataatcgg gtaggatttc tttatcgttc
     4021 gccgcactca ggtcgagtga gtcagctaac cagtccagcg tgtagagttc cggctgccac
     4081 acggcaagct gccagtgatc atggttcgga ttcttgcaga tgagcccaga atagcctgtg
     4141 tcagcgtcca gttttttaca cagcgcacgc tcaaccgccg ccgcatactt cagcggcttc
     4201 attttgccgt caggtgcggt gcgtaccgct gttttcagcg cgtacagcaa atgggcgtga
     4261 ccattttcgg gattcatgat ggtcagggtt ggggctgggg cgttccggtc actccagtct
     4321 atcgccgcac cagggcggtc aacgtcaaaa ccgagccaga acatcgcgtg tggctggttg
     4381 aactggatat atttcgcaag aatggcgcgc tctttcccgg caatgcgtac gccgaactgg
     4441 agttcgtcgg taaaataggg tttgcgggga agccgctcgt taaaaaggtc gagtgcctgg
     4501 ttactcaatc tcgcctgcgc ttatggcggg ctgttgtttc gcacggtgca tgtgctagta
     4561 tccttgttag gttttgtgcc tacgccctcg ttaatcatgt ctcttccgcc aagttgaaat
     4621 catgattacg ggggcgttgt cttttctgcc gcttaacgtt acacacccca ccgaactttg
     4681 tcacctgtca ccatcagtta ttgccagagg caacagacca ttaccttcct ggtgaaaaac
     4741 gcgtacactg aaaacacgtg tcagatacac gtgtaaaaat caggagatta tcatgcccgt
     4801 atcagccatg cgccataaaa aaaccgtcag tgtgacgctc gagcctgcgc ttttgcgtca
     4861 ggcccgcgaa gccgggatta atctgtctgc cacgctcgcc accgccctga aacatcagat
     4921 ccgtgagtca gaagcggagc gctggaaacg cgctaaccgt aaggcaatcc aggaactgaa
     4981 ccgtattacg gacgaacacg gcttactctc tgacgatcac aggacgttct gatgcagttc
     5041 atggtgtacc gcaataacgg caacagccgg gcttatccct atctgctcga tgtacagagc
     5101 gatattatcg gcgaactgaa tacccgcctg gtgatcccgc tgtttctgct cgatgaagtg
     5161 agcggacggc ccgcccgccg cctgaacccg gtgctgaatg tggacggtga ggattttctg
     5221 gtcatgacgc atgaaatggc cagcgttcgc cagtcacagc ttggggaaga ggtggtgagc
     5281 gtacgggagc agcggcaggc catcaagaat gcgctggatt ttctgctcga cggtttctga
     5341 gtttaccttt ccatcccgtg atcgtgtccc cggctgcgtc cgggggcaaa tgagcgcgtt
     5401 ttctgtcgtt cctgtttctg cgccagttca ctgtccagtc tggctacctg cgcgtcaagc
     5461 ggctgacggc ttcggttaag
//
