LOCUS       NZ_CP056512             5969 bp    DNA     circular CON 26-JAN-2024
DEFINITION  Citrobacter sp. RHBSTW-00446 plasmid pRHBSTW-00446_5, complete
            sequence.
ACCESSION   NZ_CP056512
VERSION     NZ_CP056512.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN15148616
            Assembly: GCF_013737455.1
KEYWORDS    RefSeq.
SOURCE      Citrobacter sp. RHBSTW-00446
  ORGANISM  Citrobacter sp. RHBSTW-00446
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Citrobacter.
REFERENCE   1  (bases 1 to 5969)
  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 5969)
  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                     :: WTP5 T2-00446
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 91.9836083515939x
            Sequencing Technology :: Hybrid: Illumina and OXFORD_NANOPORE
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 01/24/2024 15:00:43
            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)                     :: 5,699
            CDSs (total)                      :: 5,580
            Genes (coding)                    :: 5,395
            CDSs (with protein)               :: 5,395
            Genes (RNA)                       :: 119
            rRNAs                             :: 9, 8, 8 (5S, 16S, 23S)
            complete rRNAs                    :: 9, 8, 8 (5S, 16S, 23S)
            tRNAs                             :: 85
            ncRNAs                            :: 9
            Pseudo Genes (total)              :: 185
            CDSs (without protein)            :: 185
            Pseudo Genes (ambiguous residues) :: 0 of 185
            Pseudo Genes (frameshifted)       :: 39 of 185
            Pseudo Genes (incomplete)         :: 142 of 185
            Pseudo Genes (internal stop)      :: 27 of 185
            Pseudo Genes (multiple problems)  :: 20 of 185
            Pseudo Genes (short protein)      :: 1 of 185
            CRISPR Arrays                     :: 1
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP056512.1.
            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..5969
                     /organism="Citrobacter sp. RHBSTW-00446"
                     /mol_type="genomic DNA"
                     /strain="RHBSTW-00446"
                     /isolation_source="Wastewater influent sample"
                     /db_xref="taxon:2742648"
                     /plasmid="pRHBSTW-00446_5"
                     /geo_loc_name="United Kingdom"
                     /collection_date="2017"
     gene            join(5733..5969,1..645)
                     /locus_tag="HV199_RS28240"
                     /old_locus_tag="HV199_28250"
     CDS             join(5733..5969,1..645)
                     /locus_tag="HV199_RS28240"
                     /old_locus_tag="HV199_28250"
                     /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="nucleotidyl transferase AbiEii/AbiGii toxin
                     family protein"
                     /protein_id="WP_191212352.1"
                     /translation="MEYSIEDWVGEAPRDRVVFRQAVHIVLSAIASSDYLRPKMIMKGG
                     MLLGIRYRSTRFTEDIDFSTKMKLSELDEDEFRRELNEALLISSDSLPYGVFCAIQSLG
                     IQPKKNYENATFPSFNLKIGYARKSVSGEMERLERGQSPNTIKIDYSFNEISFDVDDLV
                     LDDDGVQSYNITDLMAEKIRSIIQQPYRNRNRRQDIYDLNYLFNCVSLDDDERFAVLTS
                     LILKSEGRIPKEDIHCNTLDREDIKEHSAKDYGTLSQEVSGDIPDFEYAYNKVNDFYKS
                     LPWDLLVNKEGE"
                     /name="nucleotidyl transferase AbiEii/AbiGii toxin family
                     protein"
     gene            642..1310
                     /locus_tag="HV199_RS28245"
                     /old_locus_tag="HV199_28255"
     CDS             642..1310
                     /locus_tag="HV199_RS28245"
                     /old_locus_tag="HV199_28255"
                     /inference="COORDINATES: protein motif:HMM:NF025053.4"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="protein phosphatase 2C domain-containing protein"
                     /protein_id="WP_191212351.1"
                     /translation="MMSSYYHFTSQGDRNENLDRFVYLECNGFNVSFIMDGFCNNTLDM
                     HYVDYFVDVVSRGCLMQIDINHACDFVLSVVNAHDGADGKSTLSMVIYDDEVMKYISIG
                     DSRIYFLDNKERTKDDSVAQRLVDSGFSHESSIPRHPYRNRLLKFVSRKSEHQELSFKD
                     RRLNNSEKVVLCTDGFWCHCNDDVIWDMDTESKVSNAFSAVISGMLVPLDNVSVALLSI
                     "
                     /name="protein phosphatase 2C domain-containing protein"
     gene            2077..2268
                     /locus_tag="HV199_RS28250"
                     /old_locus_tag="HV199_28260"
     CDS             2077..2268
                     /locus_tag="HV199_RS28250"
                     /old_locus_tag="HV199_28260"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000166327.1"
                     /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_191212355.1"
                     /translation="MSKQQKTVLNMAKFIQAQSLLLLEKLNEQDLDAEADLCEKLHDDA
                     EQLYRTLAIRLSNLQGDL"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            2268..2696
                     /locus_tag="HV199_RS28255"
                     /old_locus_tag="HV199_28265"
     CDS             2268..2696
                     /locus_tag="HV199_RS28255"
                     /old_locus_tag="HV199_28265"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000135007.1"
                     /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_191212354.1"
                     /translation="MAHVSISEAARLASVSRPTIYKLLKSGELSYTSSVKYGKPVKIID
                     TAELMRVFGALNVVSDSKRDAVKFDDDSTAINSDFLQDLQHQVALLQTENAGLKDAVNA
                     RDEHISSLRLAMQLLEHKQPLSDTPNLTASPWWKFWQK"
                     /name="helix-turn-helix domain-containing protein"
     gene            complement(3243..3542)
                     /locus_tag="HV199_RS28260"
                     /old_locus_tag="HV199_28270"
     CDS             complement(3243..3542)
                     /locus_tag="HV199_RS28260"
                     /old_locus_tag="HV199_28270"
                     /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="antitoxin HicB"
                     /protein_id="WP_191212353.1"
                     /translation="MTITCRFSVGIESPADTDTAWGIYVPAFDGTEYGCVSAADTEEGT
                     EAAAREAILAMTTYILATGGDLRALRDAGTAEYRDHADYRYCDRWLVIDTELPE"
                     /name="antitoxin HicB"
     gene            complement(4026..4241)
                     /locus_tag="HV199_RS28265"
                     /old_locus_tag="HV199_28275"
     CDS             complement(4026..4241)
                     /locus_tag="HV199_RS28265"
                     /old_locus_tag="HV199_28275"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002241003.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_015387220.1"
                     /translation="MGFWETAGKIAKGAANALDEKAHELQATKMRLESKSSEELKRLIK
                     SDGFFGSASNTEKSMAMKILRERGDV"
                     /name="hypothetical protein"
     gene            4827..5723
                     /locus_tag="HV199_RS28270"
                     /old_locus_tag="HV199_28280"
     CDS             4827..5723
                     /locus_tag="HV199_RS28270"
                     /old_locus_tag="HV199_28280"
                     /inference="COORDINATES: protein motif:HMM:NF020962.4"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="type IV toxin-antitoxin system AbiEi family
                     antitoxin"
                     /protein_id="WP_058845346.1"
                     /translation="MKEETISLRESLSKIVMEHHEKPVISAYEINWYLYELYRDKKFNG
                     LKIGKITADEPDYRVVGDATFHLLRKGIISKCVDGVVYYINNKDKPSAQQVVCSINPCS
                     YISYINAMEWHGITDRIPSEVHVTMSTPRYLKEYFSLKIKESFPLIKNKTFLIPQLVSS
                     IPIYDGKKIIFHKKTDFKIKNEQFASGGIRVTNIGETFLDMLKFPEYCGGFNHVVSVFE
                     GFAEKYLPIIVKEFSKNGNSMDKARAGYILEDICGLTHKGIDSWADSVQRGGSRKLIAS
                     EPYSNVFSERWCISINM"
                     /name="type IV toxin-antitoxin system AbiEi family
                     antitoxin"
ORIGIN
        1 gaattaaatg aggcactttt aatatcttct gatagccttc catatggtgt tttttgtgcg
       61 atccaaagcc tcgggattca gcctaaaaaa aattatgaaa atgcaacatt cccatcattt
      121 aatttgaaga taggctatgc cagaaaaagt gtttccggtg agatggagcg actggaaaga
      181 gggcaaagtc caaatactat aaagatagat tatagtttta atgaaattag ctttgatgtg
      241 gatgatttgg ttctcgatga tgatggtgtg caatcgtata acataacaga tctaatggct
      301 gaaaaaatca ggtctataat tcaacagccg tatagaaaca ggaatcgccg ccaagatatt
      361 tatgatttaa attatttatt taattgcgtt agtcttgatg atgatgagcg ctttgctgtt
      421 ctcacttctt taattttaaa atccgagggt aggattccga aggaagatat tcactgtaat
      481 acattagatc gtgaagatat aaaagaacac tcagccaaag attatggaac tttatctcaa
      541 gaggtgtccg gagatattcc tgatttcgag tatgcttaca ataaggttaa tgatttctat
      601 aaatcacttc cttgggattt gctagtaaat aaagaaggtg aatgatgtca tcatattatc
      661 atttcacctc tcaaggtgat aggaatgaaa atttagatag atttgtttat ctcgaatgta
      721 atggttttaa cgtttcattt attatggatg gtttttgcaa taacacccta gatatgcact
      781 atgtcgatta ctttgttgat gtggtttcta gaggttgtct gatgcagata gatataaatc
      841 acgcttgtga ttttgttctt agcgttgtta acgcccatga tggagcggat ggtaaatcta
      901 cgctctcgat ggttatatat gatgatgaag taatgaaata tatatctata ggtgattcga
      961 gaatttattt tttagataat aaggaaagga ccaaagacga ctccgttgct caacgtttgg
     1021 tcgattctgg tttttctcat gaatccagca taccaaggca cccttacaga aatcgacttc
     1081 ttaaatttgt atcgagaaaa tcagagcatc aagaattatc atttaaagat cggcgattaa
     1141 ataattctga gaaagttgtt ttgtgtaccg atggtttttg gtgccattgt aatgatgatg
     1201 tcatatggga tatggatacc gagagcaaag taagtaatgc attctcagct gtcattagtg
     1261 gtatgttggt gcctctagat aatgtatctg tagcattgct ctcgatataa gcgtaaggca
     1321 ataacaacaa cttgcaccga tagctcgaac agttatatgc tctagaaacg aaaaagccac
     1381 ccggcaaggt ggcttttcga aggttcaata aaccggcaag tttttgaacc gtggtaactg
     1441 catcttagcg ggaacagtca ccaaatctgt actttcagtg tagccggaaa catcgcaaca
     1501 cttcaagctc tagtatagcc tattcagtta caactattcc cgctaataca gttaccagtg
     1561 gctaccgcca gtggcgattc gtcgtgtctt ttcgggttgg attcaagtga aaagttaccg
     1621 gaacaggcgt ggtagtcgga ctaaacgggg agttcgtgca tatagtccag cttggagcga
     1681 accacctaaa aggaacccag ttgcgtgggt aggaatgaga aaacgccacc acagtgtaac
     1741 gaaacggcgg actgcaacgg gtaaacctta cggtgggaac aggagagcgc acgagggagc
     1801 catcaggggg aaactcttgg tatctttaag tcctgtcggg tttcgccact tctgatttga
     1861 gtgcctgaaa tcacctgatt tctgtgaaac tcgtcaggag ggcgaagcct atggaaaaac
     1921 gcccttgcgg gcgtggcctt ttgctcttta ttccgcttac atcatttgtt gttagtgttc
     1981 cccatccgct cgccgcagac aagtgaccga gcatagcgag cgaacggtcg aggaagcgga
     2041 aaataactgt aggtaacctg gagcactgac gctgtgatgt ccaaacaaca gaaaacggta
     2101 ctgaatatgg ctaaattcat ccaggcgcaa tccctgcttt tgctggagaa gctcaatgaa
     2161 caggatctcg atgctgaggc cgacctgtgc gaaaaattgc atgatgatgc ggaacagctc
     2221 taccgtactc tggctattcg tctgagtaat ctacaagggg atctgtaatg gctcatgtat
     2281 caattagcga agcggcacgt ctcgccagtg tcagtcgccc aactatttac aagctactta
     2341 aatctggtga actcagttac acctcatctg taaagtatgg taagcccgta aaaatcattg
     2401 atactgctga gcttatgcgg gttttcggcg ctcttaatgt cgtaagtgat agtaaacgtg
     2461 atgctgtaaa gtttgacgac gattctacag cgattaacag tgatttttta caggatttac
     2521 agcatcaggt ggcacttttg cagacggaaa acgccgggct taaagatgcg gtgaatgccc
     2581 gggatgagca tataagttca cttcgtctgg caatgcagct tctggagcat aaacagccgt
     2641 tatctgacac tccgaatctt acggcatcac cctggtggaa gttctggcag aaatgagcgt
     2701 cgtaatgcaa ctcagtgcaa tttgtcatgg tatcgacgat ctttaatgca acttagtgcg
     2761 cattaacgaa atttagtgca atttagtgca atgccgccat tctccataag gcacgttacc
     2821 gactgtatac agtcgcgtgc caaagggtac ccctttgaaa cccgctgcta cctttctcat
     2881 gcttaacttg tctctttctc atacttaatt actaccacgt ggttttaata ctcccgttcc
     2941 gttccgggta ccatgttgtc actggatttt ccctgttttc tcagccctta accctcagaa
     3001 atggtgatac acaatacgca ccctggcggg gtgcgtgact ggctgaattt taatgatttt
     3061 caggagaaag ctgttttgtg gacatcatac gctccttcat actggaaggg gaaaaatacc
     3121 tgtaagttac tgatttttaa ctcatgacgt atcatacgtc gcataccatg tcatggctcg
     3181 ccgccccgac acccggccag cgcctcacga ccccgtaata aatttcgtgc ccgttcaccg
     3241 cttcactccg gtaattcagt gtcaatcacc agccaccggt cacagtaccg gtaatccgca
     3301 tggtcccggt attctgccgt gccggcatca cgcagtgccc gaagatcgcc cccggtggcc
     3361 agaatatatg tggtcatggc aaggatagcc tcgcgtgctg cggcttcggt accttcctct
     3421 gtgtctgctg ccgacacgca gccatactct gtaccgtcga acgcagggac gtagatcccc
     3481 catgcggtgt ctgtatctgc gggggattcg atcccgaccg agaagcggca cgtgatggtc
     3541 atgtttttct ccggtttaat gtctgatggc tttatacgaa aagacaggcg gtgccagtgc
     3601 gttatctggc agtttactgc atgaaatgcc agacagacgg aagatgccgt ctgtaacgcg
     3661 gtgccagtca gtccggtgca taacgattca tgcctgtaaa attcatcagc gcgattctga
     3721 ggcgttttca gggggtaaga cgtgtggttt tgcgtctccg gcggcaaaat cgcgcacagg
     3781 ccgtttcagc ggtgcgcgaa atgggacgtt atggtaaata agtgggcgta aaaaagcccg
     3841 ggttacgggc ttctggacgc tatgacttac cacgacattc tctgcaccaa ctttgattcg
     3901 ttgcaccaga aggaatggtt ctgaatccga atagagtttg caactcacct gcagtatgag
     3961 cggtggttcg cttgcagtta gggcatgtat gaggaagatt caccgtgcct accatttttc
     4021 tatccttaaa cgtctccgcg ttctctgaga attttcattg ccatgctttt ttctgtgtta
     4081 ctggctgagc cgaaaaaacc atcagattta atgaggcgct ttagttcttc actgcttttg
     4141 ctttctaagc gcattttggt tgcctggagt tcatgagctt tttcatccaa agcgttagct
     4201 gcgccttttg caattttacc ggccgtttcc caaaatccca tttaaccact ccttaatgct
     4261 tatccaattg gacttgttgt gatccgacga ctccgacatt tagggcaata atcaggcgtg
     4321 ccataaccag tacgactggt ccactcatgc ttacaatcca aacacttagc ccggtagatt
     4381 gtcggtgcca ttgaatactc cattgatttt aaaaatattt gtatagtgca ctaaaattat
     4441 cggcagtttt tctcggagct tgagaggtag ataaccctaa gctgatatgt tgcctttatg
     4501 atggttttcg tgtgtcaagg ttagctaggt aagggattta ctgtgggaag tgctggttcg
     4561 cgaagtgagg cgttatggta aatcaggacg ataggttaag ttagatttaa ggatgccccg
     4621 aaaataatgt cattaaaaat acatgaaacc ttactaaact aacgtcctta ggacgttagt
     4681 ttagtaagga aacataaaaa agtcaatttt tgaaaaaaaa cctttatatt catatcatta
     4741 gacaaatata aatcgcgatg ttaaatttga cttttgttag tagatgatgt ataagtcctt
     4801 aggacttata catcatctgg tacatcatga aagaagaaac gatctcccta agagaatcct
     4861 taagtaagat tgtcatggaa caccatgaga aacctgtgat cagtgcatat gaaattaact
     4921 ggtatttata cgagctttat agagacaaaa aatttaatgg attaaagatt gggaaaataa
     4981 cggcagacga gcctgattat agggtcgttg gcgatgctac ttttcacttg cttaggaagg
     5041 ggattatatc taagtgtgtt gatggggttg tttattatat aaacaacaaa gataaacctt
     5101 cagctcagca agtagtttgt tctattaatc catgttcata tatatcgtat ataaatgcaa
     5161 tggagtggca tggaatcact gacagaatac caagtgaagt tcatgttact atgtcgacac
     5221 ctcgatactt aaaagagtat ttttctttaa aaataaaaga aagcttccca ttgattaaaa
     5281 ataaaacctt tttaatccct cagttagtaa gttcaatacc tatatatgat gggaaaaaga
     5341 taatttttca taagaaaaca gacttcaaaa tcaagaatga acaattcgct tctggtggca
     5401 ttagagttac aaatataggt gagacattct tagatatgct taagttccca gaatactgtg
     5461 gtggttttaa tcatgttgtt agtgtttttg aaggttttgc tgagaaatat ttgcctataa
     5521 tagtaaagga attctctaag aatggtaact ctatggataa agctagagct gggtatatat
     5581 tagaagatat ttgtggttta actcataaag gcattgattc ttgggctgat agtgtccagc
     5641 gaggtggaag tcgcaagtta attgcatcag agccatattc aaatgttttt tctgaaagat
     5701 ggtgtatatc tataaatatg taagagggtt ttatggagta ttctattgaa gattgggtcg
     5761 gtgaggcgcc gagggatagg gttgtgttta ggcaagcggt acatatagta ctttccgcta
     5821 ttgcaagcag tgattacctt aggccaaaaa tgataatgaa aggagggatg cttctgggta
     5881 ttagatatag gagcacaaga ttcacggagg atattgattt ctctacaaaa atgaagcttt
     5941 ctgagttgga tgaggatgaa ttcagacgt
//
