LOCUS       NZ_CP056287             5969 bp    DNA     circular CON 26-JAN-2024
DEFINITION  Citrobacter sp. RHBSTW-00859 plasmid pRHBSTW-00859_4, complete
            sequence.
ACCESSION   NZ_CP056287
VERSION     NZ_CP056287.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN15148719
            Assembly: GCF_013729795.1
KEYWORDS    RefSeq.
SOURCE      Citrobacter sp. RHBSTW-00859
  ORGANISM  Citrobacter sp. RHBSTW-00859
            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 T3-00859
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 181.325365466083x
            Sequencing Technology :: Hybrid: Illumina and OXFORD_NANOPORE
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 01/24/2024 14:10:43
            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)                     :: 5,633
            CDSs (total)                      :: 5,514
            Genes (coding)                    :: 5,341
            CDSs (with protein)               :: 5,341
            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)              :: 173
            CDSs (without protein)            :: 173
            Pseudo Genes (ambiguous residues) :: 0 of 173
            Pseudo Genes (frameshifted)       :: 33 of 173
            Pseudo Genes (incomplete)         :: 134 of 173
            Pseudo Genes (internal stop)      :: 25 of 173
            Pseudo Genes (multiple problems)  :: 16 of 173
            Pseudo Genes (short protein)      :: 1 of 173
            CRISPR Arrays                     :: 1
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP056287.1.
            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-00859"
                     /mol_type="genomic DNA"
                     /strain="RHBSTW-00859"
                     /isolation_source="Wastewater effluent sample"
                     /db_xref="taxon:2742666"
                     /plasmid="pRHBSTW-00859_4"
                     /geo_loc_name="United Kingdom"
                     /collection_date="2017"
     gene            227..442
                     /locus_tag="HV302_RS27940"
                     /old_locus_tag="HV302_27850"
     CDS             227..442
                     /locus_tag="HV302_RS27940"
                     /old_locus_tag="HV302_27850"
                     /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            926..1225
                     /locus_tag="HV302_RS27945"
                     /old_locus_tag="HV302_27855"
     CDS             926..1225
                     /locus_tag="HV302_RS27945"
                     /old_locus_tag="HV302_27855"
                     /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(1772..2200)
                     /locus_tag="HV302_RS27950"
                     /old_locus_tag="HV302_27860"
     CDS             complement(1772..2200)
                     /locus_tag="HV302_RS27950"
                     /old_locus_tag="HV302_27860"
                     /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(2200..2391)
                     /locus_tag="HV302_RS27955"
                     /old_locus_tag="HV302_27865"
     CDS             complement(2200..2391)
                     /locus_tag="HV302_RS27955"
                     /old_locus_tag="HV302_27865"
                     /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            complement(3158..3826)
                     /locus_tag="HV302_RS27960"
                     /old_locus_tag="HV302_27870"
     CDS             complement(3158..3826)
                     /locus_tag="HV302_RS27960"
                     /old_locus_tag="HV302_27870"
                     /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            complement(3823..4704)
                     /locus_tag="HV302_RS27965"
                     /old_locus_tag="HV302_27875"
     CDS             complement(3823..4704)
                     /locus_tag="HV302_RS27965"
                     /old_locus_tag="HV302_27875"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_008110254.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /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            complement(4714..5610)
                     /locus_tag="HV302_RS27970"
                     /old_locus_tag="HV302_27880"
     CDS             complement(4714..5610)
                     /locus_tag="HV302_RS27970"
                     /old_locus_tag="HV302_27880"
                     /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 cctctcaagc tccgagaaaa actgccgata attttagtgc actatacaaa tatttttaaa
       61 atcaatggag tattcaatgg caccgacaat ctaccgggct aagtgtttgg attgtaagca
      121 tgagtggacc agtcgtactg gttatggcac gcctgattat tgccctaaat gtcggagtcg
      181 tcggatcaca acaagtccaa ttggataagc attaaggagt ggttaaatgg gattttggga
      241 aacggccggt aaaattgcaa aaggcgcagc taacgctttg gatgaaaaag ctcatgaact
      301 ccaggcaacc aaaatgcgct tagaaagcaa aagcagtgaa gaactaaagc gcctcattaa
      361 atctgatggt tttttcggct cagccagtaa cacagaaaaa agcatggcaa tgaaaattct
      421 cagagaacgc ggagacgttt aaggatagaa aaatggtagg cacggtgaat cttcctcata
      481 catgccctaa ctgcaagcga accaccgctc atactgcagg tgagttgcaa actctattcg
      541 gattcagaac cattccttct ggtgcaacga atcaaagttg gtgcagagaa tgtcgtggta
      601 agtcatagcg tccagaagcc cgtaacccgg gcttttttac gcccacttat ttaccataac
      661 gtcccatttc gcgcaccgct gaaacggcct gtgcgcgatt ttgccgccgg agacgcaaaa
      721 ccacacgtct taccccctga aaacgcctca gaatcgcgct gatgaatttt acaggcatga
      781 atcgttatgc accggactga ctggcaccgc gttacagacg gcatcttccg tctgtctggc
      841 atttcatgca gtaaactgcc agataacgca ctggcaccgc ctgtcttttc gtataaagcc
      901 atcagacatt aaaccggaga aaaacatgac catcacgtgc cgcttctcgg tcgggatcga
      961 atcccccgca gatacagaca ccgcatgggg gatctacgtc cctgcgttcg acggtacaga
     1021 gtatggctgc gtgtcggcag cagacacaga ggaaggtacc gaagccgcag cacgcgaggc
     1081 tatccttgcc atgaccacat atattctggc caccgggggc gatcttcggg cactgcgtga
     1141 tgccggcacg gcagaatacc gggaccatgc ggattaccgg tactgtgacc ggtggctggt
     1201 gattgacact gaattaccgg agtgaagcgg tgaacgggca cgaaatttat tacggggtcg
     1261 tgaggcgctg gccgggtgtc ggggcggcga gccatgacat ggtatgcgac gtatgatacg
     1321 tcatgagtta aaaatcagta acttacaggt atttttcccc ttccagtatg aaggagcgta
     1381 tgatgtccac aaaacagctt tctcctgaaa atcattaaaa ttcagccagt cacgcacccc
     1441 gccagggtgc gtattgtgta tcaccatttc tgagggttaa gggctgagaa aacagggaaa
     1501 atccagtgac aacatggtac ccggaacgga acgggagtat taaaaccacg tggtagtaat
     1561 taagtatgag aaagagacaa gttaagcatg agaaaggtag cagcgggttt caaaggggta
     1621 ccctttggca cgcgactgta tacagtcggt aacgtgcctt atggagaatg gcggcattgc
     1681 actaaattgc actaaatttc gttaatgcgc actaagttgc attaaagatc gtcgatacca
     1741 tgacaaattg cactgagttg cattacgacg ctcatttctg ccagaacttc caccagggtg
     1801 atgccgtaag attcggagtg tcagataacg gctgtttatg ctccagaagc tgcattgcca
     1861 gacgaagtga acttatatgc tcatcccggg cattcaccgc atctttaagc ccggcgtttt
     1921 ccgtctgcaa aagtgccacc tgatgctgta aatcctgtaa aaaatcactg ttaatcgctg
     1981 tagaatcgtc gtcaaacttt acagcatcac gtttactatc acttacgaca ttaagagcgc
     2041 cgaaaacccg cataagctca gcagtatcaa tgatttttac gggcttacca tactttacag
     2101 atgaggtgta actgagttca ccagatttaa gtagcttgta aatagttggg cgactgacac
     2161 tggcgagacg tgccgcttcg ctaattgata catgagccat tacagatccc cttgtagatt
     2221 actcagacga atagccagag tacggtagag ctgttccgca tcatcatgca atttttcgca
     2281 caggtcggcc tcagcatcga gatcctgttc attgagcttc tccagcaaaa gcagggattg
     2341 cgcctggatg aatttagcca tattcagtac cgttttctgt tgtttggaca tcacagcgtc
     2401 agtgctccag gttacctaca gttattttcc gcttcctcga ccgttcgctc gctatgctcg
     2461 gtcacttgtc tgcggcgagc ggatggggaa cactaacaac aaatgatgta agcggaataa
     2521 agagcaaaag gccacgcccg caagggcgtt tttccatagg cttcgccctc ctgacgagtt
     2581 tcacagaaat caggtgattt caggcactca aatcagaagt ggcgaaaccc gacaggactt
     2641 aaagatacca agagtttccc cctgatggct ccctcgtgcg ctctcctgtt cccaccgtaa
     2701 ggtttacccg ttgcagtccg ccgtttcgtt acactgtggt ggcgttttct cattcctacc
     2761 cacgcaactg ggttcctttt aggtggttcg ctccaagctg gactatatgc acgaactccc
     2821 cgtttagtcc gactaccacg cctgttccgg taacttttca cttgaatcca acccgaaaag
     2881 acacgacgaa tcgccactgg cggtagccac tggtaactgt attagcggga atagttgtaa
     2941 ctgaataggc tatactagag cttgaagtgt tgcgatgttt ccggctacac tgaaagtaca
     3001 gatttggtga ctgttcccgc taagatgcag ttaccacggt tcaaaaactt gccggtttat
     3061 tgaaccttcg aaaagccacc ttgccgggtg gctttttcgt ttctagagca tataactgtt
     3121 cgagctatcg gtgcaagttg ttgttattgc cttacgctta tatcgagagc aatgctacag
     3181 atacattatc tagaggcacc aacataccac taatgacagc tgagaatgca ttacttactt
     3241 tgctctcggt atccatatcc catatgacat catcattaca atggcaccaa aaaccatcgg
     3301 tacacaaaac aactttctca gaattattta atcgccgatc tttaaatgat aattcttgat
     3361 gctctgattt tctcgataca aatttaagaa gtcgatttct gtaagggtgc cttggtatgc
     3421 tggattcatg agaaaaacca gaatcgacca aacgttgagc aacggagtcg tctttggtcc
     3481 tttccttatt atctaaaaaa taaattctcg aatcacctat agatatatat ttcattactt
     3541 catcatcata tataaccatc gagagcgtag atttaccatc cgctccatca tgggcgttaa
     3601 caacgctaag aacaaaatca caagcgtgat ttatatctat ctgcatcaga caacctctag
     3661 aaaccacatc aacaaagtaa tcgacatagt gcatatctag ggtgttattg caaaaaccat
     3721 ccataataaa tgaaacgtta aaaccattac attcgagata aacaaatcta tctaaatttt
     3781 cattcctatc accttgagag gtgaaatgat aatatgatga catcattcac cttctttatt
     3841 tactagcaaa tcccaaggaa gtgatttata gaaatcatta accttattgt aagcatactc
     3901 gaaatcagga atatctccgg acacctcttg agataaagtt ccataatctt tggctgagtg
     3961 ttcttttata tcttcacgat ctaatgtatt acagtgaata tcttccttcg gaatcctacc
     4021 ctcggatttt aaaattaaag aagtgagaac agcaaagcgc tcatcatcat caagactaac
     4081 gcaattaaat aaataattta aatcataaat atcttggcgg cgattcctgt ttctatacgg
     4141 ctgttgaatt atagacctga ttttttcagc cattagatct gttatgttat acgattgcac
     4201 accatcatca tcgagaacca aatcatccac atcaaagcta atttcattaa aactataatc
     4261 tatctttata gtatttggac tttgccctct ttccagtcgc tccatctcac cggaaacact
     4321 ttttctggca tagcctatct tcaaattaaa tgatgggaat gttgcatttt cataattttt
     4381 tttaggctga atcccgaggc tttggatcgc acaaaaaaca ccatatggaa ggctatcaga
     4441 agatattaaa agtgcctcat ttaattcacg tctgaattca tcctcatcca actcagaaag
     4501 cttcattttt gtagagaaat caatatcctc cgtgaatctt gtgctcctat atctaatacc
     4561 cagaagcatc cctcctttca ttatcatttt tggcctaagg taatcactgc ttgcaatagc
     4621 ggaaagtact atatgtaccg cttgcctaaa cacaacccta tccctcggcg cctcaccgac
     4681 ccaatcttca atagaatact ccataaaacc ctcttacata tttatagata tacaccatct
     4741 ttcagaaaaa acatttgaat atggctctga tgcaattaac ttgcgacttc cacctcgctg
     4801 gacactatca gcccaagaat caatgccttt atgagttaaa ccacaaatat cttctaatat
     4861 atacccagct ctagctttat ccatagagtt accattctta gagaattcct ttactattat
     4921 aggcaaatat ttctcagcaa aaccttcaaa aacactaaca acatgattaa aaccaccaca
     4981 gtattctggg aacttaagca tatctaagaa tgtctcacct atatttgtaa ctctaatgcc
     5041 accagaagcg aattgttcat tcttgatttt gaagtctgtt ttcttatgaa aaattatctt
     5101 tttcccatca tatataggta ttgaacttac taactgaggg attaaaaagg ttttattttt
     5161 aatcaatggg aagctttctt ttatttttaa agaaaaatac tcttttaagt atcgaggtgt
     5221 cgacatagta acatgaactt cacttggtat tctgtcagtg attccatgcc actccattgc
     5281 atttatatac gatatatatg aacatggatt aatagaacaa actacttgct gagctgaagg
     5341 tttatctttg ttgtttatat aataaacaac cccatcaaca cacttagata taatcccctt
     5401 cctaagcaag tgaaaagtag catcgccaac gaccctataa tcaggctcgt ctgccgttat
     5461 tttcccaatc tttaatccat taaatttttt gtctctataa agctcgtata aataccagtt
     5521 aatttcatat gcactgatca caggtttctc atggtgttcc atgacaatct tacttaagga
     5581 ttctcttagg gagatcgttt cttctttcat gatgtaccag atgatgtata agtcctaagg
     5641 acttatacat catctactaa caaaagtcaa atttaacatc gcgatttata tttgtctaat
     5701 gatatgaata taaaggtttt ttttcaaaaa ttgacttttt tatgtttcct tactaaacta
     5761 acgtcctaag gacgttagtt tagtaaggtt tcatgtattt ttaatgacat tattttcggg
     5821 gcatccttaa atctaactta acctatcgtc ctgatttacc ataacgcctc acttcgcgaa
     5881 ccagcacttc ccacagtaaa tcccttacct agctaacctt gacacacgaa aaccatcata
     5941 aaggcaacat atcagcttag ggttatcta
//
