LOCUS       NZ_CP056824             5788 bp    DNA     circular CON 26-JAN-2024
DEFINITION  Citrobacter sp. RHBSTW-00137 plasmid pRHBSTW-00137_3, complete
            sequence.
ACCESSION   NZ_CP056824
VERSION     NZ_CP056824.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN15148508
            Assembly: GCF_013790835.1
KEYWORDS    RefSeq.
SOURCE      Citrobacter sp. RHBSTW-00137
  ORGANISM  Citrobacter sp. RHBSTW-00137
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Citrobacter.
REFERENCE   1  (bases 1 to 5788)
  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 5788)
  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                     :: WTP1 T1-00137
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 89.8124067554789x
            Sequencing Technology :: Hybrid: Illumina and OXFORD_NANOPORE
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 01/24/2024 13:57:48
            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)                     :: 5,379
            CDSs (total)                      :: 5,263
            Genes (coding)                    :: 5,090
            CDSs (with protein)               :: 5,090
            Genes (RNA)                       :: 116
            rRNAs                             :: 9, 8, 8 (5S, 16S, 23S)
            complete rRNAs                    :: 9, 8, 8 (5S, 16S, 23S)
            tRNAs                             :: 80
            ncRNAs                            :: 11
            Pseudo Genes (total)              :: 173
            CDSs (without protein)            :: 173
            Pseudo Genes (ambiguous residues) :: 0 of 173
            Pseudo Genes (frameshifted)       :: 45 of 173
            Pseudo Genes (incomplete)         :: 132 of 173
            Pseudo Genes (internal stop)      :: 36 of 173
            Pseudo Genes (multiple problems)  :: 33 of 173
            Pseudo Genes (short protein)      :: 1 of 173
            CRISPR Arrays                     :: 1
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP056824.1.
            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..5788
                     /organism="Citrobacter sp. RHBSTW-00137"
                     /mol_type="genomic DNA"
                     /strain="RHBSTW-00137"
                     /isolation_source="Wastewater influent sample"
                     /db_xref="taxon:2742638"
                     /plasmid="pRHBSTW-00137_3"
                     /geo_loc_name="United Kingdom"
                     /collection_date="2017"
     gene            complement(35..217)
                     /locus_tag="HV091_RS26645"
                     /old_locus_tag="HV091_26645"
     CDS             complement(35..217)
                     /locus_tag="HV091_RS26645"
                     /old_locus_tag="HV091_26645"
                     /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_191221304.1"
                     /translation="MTTENHAKASRKKARWRSLTSTEKTSPDFLVERPDVIEDQARFIE
                     GIKPSDSGTGHPAKK"
                     /name="hypothetical protein"
     gene            complement(1537..2598)
                     /locus_tag="HV091_RS26655"
                     /old_locus_tag="HV091_26650"
     CDS             complement(1537..2598)
                     /locus_tag="HV091_RS26655"
                     /old_locus_tag="HV091_26650"
                     /EC_number="3.1.21.-"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000034299.1"
                     /GO_function="GO:0003677 - DNA binding [Evidence IEA];
                     GO:0009036 - type II site-specific deoxyribonuclease
                     activity [Evidence IEA]"
                     /GO_process="GO:0009307 - DNA restriction-modification
                     system [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="HindVP family restriction endonuclease"
                     /protein_id="WP_191221306.1"
                     /translation="MDKKESLYGLKNTNRKGGDLWGKNQFNSSFPASLACYMRDNNINP
                     IYLYLDKNLDVKAKEVSFDFIFNTKTKNEDLTFSFESKYEPYQQYAYDDIRGIDLVIKE
                     ENEFLRALEIKLTVVPDNATYNEKESNWGSEIVIRPASTSYCALGIMHSCRNEFNKIRG
                     IFERTCENIQHWGNETEVLSKKSGIIDCLNDFQSSFNDFQSPFLMQPIWKTKGKTPILD
                     KNAFDIFIWSDFALCRTFIDRSSNNNSSASRLMRSSARLTRMLYEIASKNKTHIDRIYT
                     DMNFGYQSDKEFSLNGKITRTYMDHPRRSNPQLPPSILKEIILNGGQNKLSPERRFDQS
                     VYYTAAHIFDEMD"
                     /name="HindVP family restriction endonuclease"
     gene            2688..3854
                     /locus_tag="HV091_RS26660"
                     /old_locus_tag="HV091_26655"
     CDS             2688..3854
                     /locus_tag="HV091_RS26660"
                     /old_locus_tag="HV091_26655"
                     /EC_number="2.1.1.37"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001219937.1"
                     /GO_function="GO:0003886 - DNA
                     (cytosine-5-)-methyltransferase activity [Evidence IEA];
                     GO:0003677 - DNA binding [Evidence IEA]; GO:1904047 -
                     S-adenosyl-L-methionine binding [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="DNA cytosine methyltransferase"
                     /protein_id="WP_191221307.1"
                     /translation="MRIIDLFSGCGGLSLGFQKGGHEVIGAYDFWDPAIECYRDNFNHP
                     ITKLDLGNVDEVVKELASLDFDMIIGGPPCQDFSHAGLRVEGARANLTLSFSEVIKRIK
                     PKWFVMENVDRALKSSTYSVVRKTFKEAGYGLTEVVLDASKCGVPQKRKRLFVIGCIGR
                     EDDFLIEEINNGLSIDSMTVRDYFGDELGIDYYYRHPRNYNRRGVFSIDEPAPTIRGVN
                     RPIPDGYTGHVGDPVKISNNVRPLTTLERAQIQTFPKDFKFKGAKTHLEQMIGNAVPVE
                     LARYVAVAIMNDINKNLNYVAYDKDNFRKWLSLNKKLTRKSLSDVISRFNRAVSFFGDE
                     YVDFHVYKIDEILMRLERIHLFDILSVSLKSQLRRSFKLYYEFCNDRK"
                     /name="DNA cytosine methyltransferase"
     gene            4765..4956
                     /locus_tag="HV091_RS26665"
                     /old_locus_tag="HV091_26660"
     CDS             4765..4956
                     /locus_tag="HV091_RS26665"
                     /old_locus_tag="HV091_26660"
                     /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_191221302.1"
                     /translation="MTKQQKTALNMAKFIQAQSLLLLEKLNELDLDTEADLCEALHEDA
                     EHLFRSLTIRIDGLQEKY"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            4956..5363
                     /locus_tag="HV091_RS26670"
                     /old_locus_tag="HV091_26665"
     CDS             4956..5363
                     /locus_tag="HV091_RS26670"
                     /old_locus_tag="HV091_26665"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_014440114.1"
                     /GO_function="GO:0003677 - DNA binding [Evidence IEA]"
                     /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_191221303.1"
                     /translation="MAQVSISEAARLTGKSRTTLHRLIKAGELSTCHGERNAKMLDTSE
                     LLRVFGALRGLPDKQVVEQVTGQCVTVSLSENEQVVRALKQEVEHLKSLVSAQNSHIDS
                     LKQAMQLLEHKQSASDPQKVPAKPWWQFWKG"
                     /name="helix-turn-helix domain-containing protein"
     Typing          complement(4239..4586)
                     /name="rep_cluster_2373"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="94.286"
                     /coverage="81.0"
                     /evalue="2.99e-149"
ORIGIN
        1 gctttttaag cgtaaattct ggatgtgaac cgggctattt tttcgctgga tgtcctgttc
       61 ccgagtccga aggctttatc ccctcgatga atcgcgcctg atcttctatc acgtcggggc
      121 gctcgaccag gaagtcgggt gatgtttttt ctgtactggt cagcgagcgc caccgggctt
      181 ttttcctgga cgcttttgca tgattttcag tggtcattgt ggaggccata gatgttcgcg
      241 tgaacggtat cgtgggtata cacgttatca aggttgttta ccgcctttcg cggatcaaaa
      301 tccggcgttg cgttccactc tgccgagtat tccgcatcca gagtatccgt gtcgtcatct
      361 atggggtccg cttggaaaag ggaaaataac ctacgctaag actacttttt aaccaatcgg
      421 ctattggata tcactcggtt cgcggggcta cagcgtttct gtgtccgaaa ccgaacgatt
      481 gcgtacacca tgccaataac atgtacgaaa gtaagcaaaa ctgttaacgg acagtcagat
      541 cgttccgtac atcccttacg gtcaggggtt cgcgctcaat ggaacgaaat cactcgttaa
      601 gctcaaaacg cttaacgtag gaaaatttcc gttttccaag cggacccctt atcgcttgcc
      661 agcttctcca ctgtttggct tcggttatct cactgaatgc ttcgtcaaac accgcctgat
      721 gactctttag cgacccgaaa ttcagcagaa agatcgtttt gttcaacgat tcttttgtcg
      781 ttttcagacc gaggctatgt agcgtttccg tgattatctt ttccattttt ttgtttgttt
      841 tttgctccat ctagttcatg tgtacgcaat gttgtacgtc gttttgtagg catatttcgt
      901 ggatgtgtac gttgttttgt acggaaccat tcggttcatg tacgcagatt tgtacgcagg
      961 acaaaaatga atctagaact acaggcacga gggcgatgta tacacgggga aattccccgt
     1021 tacacaatcg acgtgccaaa gggttcccct ttgaaacccg gatgcggttc tacgaacctt
     1081 taaaataact accgcctcgc cttgctcgtt ggtcaacgct tcacgacacc ggattaaaat
     1141 ccgttcccgt tcaccgtttc agcctggggg cgtgcagctc cttcacgcaa aaggcgtgtt
     1201 ttgatgattt gaggggcttt cgtgtctgaa atcggcagcc agtcagtcgg gtgcataacc
     1261 attcacgccc gtaaaactca tcagcgcgat tttcagcggt ttttaggggg gcggcgtagg
     1321 atttcatggg ttagagcgta aaacggcgct aaggccgttt tagcggtgcg cgtaatgacg
     1381 cgttatggta aataagacca aggtacgttg acggtgttca ttatttgttc attttttgca
     1441 ctgtctttca tgtgtgctga acatactagc aatatgaatt gtatggtgat tttttgtaaa
     1501 acgggcggaa ataaaaccgc ccgtttatca catatattaa tccatttcat caaatatatg
     1561 tgctgcagta taataaacgc tttggtcaaa tcgcctttca gggcttaatt tattttgacc
     1621 gccattcagt attatttctt taagtattga tggcggtagt tgtgggtttg atcttcttgg
     1681 gtgatccata tacgttcttg ttattttgcc attcaatgag aattctttat cactttgata
     1741 cccaaagttc atgtcagtat agattctatc tatatgtgtc ttgtttttac ttgctatttc
     1801 ataaagcatt cgggttaatc tagctgatga tctcattaat ctacttgcgg atgaattatt
     1861 gttagatgat ctgtcaataa atgttctgca taaagcaaag tcactccaaa tgaaaatatc
     1921 aaatgcattc ttatctaata ttggtgtttt gccttttgtt ttccatatcg gttgcattag
     1981 gaatggtgat tgaaaatcat tgaagctcga ttgaaaatcg ttcaaacaat ctattatccc
     2041 agatttttta gataaaacct ctgtttcatt accccagtgt tgtatatttt cgcatgtcct
     2101 ttcgaaaata cctcttattt tgttaaattc atttctgcag gaatgcatta tccccaaggc
     2161 acagtatgat gtgctagctg gccttatgac tatttcagaa ccccaattgc tttctttttc
     2221 attatatgtg gcattatctg gaactacagt taactttatc tctagcgctc tcaggaattc
     2281 attttcttct ttaattacta agtctatacc tcgaatgtca tcataggcat actgttgata
     2341 tggttcgtat ttgctttcga atgaaaatgt tagatcttca ttttttgttt ttgtattgaa
     2401 tataaaatca aaagaaacct cttttgcctt tacatccaag tttttatcta agtaaagata
     2461 tattgggtta atgttattat ccctcatata gcatgctaac gaggctggaa atgagctatt
     2521 aaattgattt ttaccccata agtcaccgcc tttcctgtta gtgtttttta agccataaag
     2581 tgattctttt ttatccattt ttttcaccta tcgacgtcta tttgttgacg tcttttgaat
     2641 gcgggcatag tatcaatatg tgtatataat aatgagtttt tcgtgctatg agaattattg
     2701 atctttttag tggttgcggc ggtctctctc tggggtttca gaaggggggg catgaggtta
     2761 ttggtgctta tgatttttgg gatccagcca ttgagtgcta tcgagacaat tttaatcatc
     2821 cgataacaaa actagactta gggaatgtag atgaggtagt aaaagaactt gcgagtttag
     2881 atttcgatat gattattgga gggcctccat gtcaagattt tagtcatgcg ggactgagag
     2941 ttgaaggggc aagagctaac ttaacgttat cattttcaga agttataaaa agaataaaac
     3001 caaaatggtt tgttatggag aacgtggatc gtgcattgaa aagcagcacg tattcagtag
     3061 tcagaaaaac atttaaagaa gcagggtatg gtctaactga agtcgttttg gatgctagta
     3121 aatgtggcgt tccacaaaaa aggaaaagat tatttgtaat tgggtgtatt gggagagagg
     3181 acgattttct tattgaagaa ataaataatg gattatctat cgatagtatg acagtaagag
     3241 actattttgg tgatgaactc gggatagatt actattatag acacccccga aactataata
     3301 gaagaggtgt tttttctata gatgagccag ctccaacaat tagaggtgtt aatagaccaa
     3361 tacctgacgg ttatactgga catgttggtg atccggtaaa aatttcaaat aatgtaaggc
     3421 cattaacaac ccttgaacga gctcagatac aaacgtttcc taaggacttt aaattcaaag
     3481 gggcgaaaac tcatcttgaa cagatgattg gaaatgctgt acccgttgaa ctggctagat
     3541 atgttgcggt ggctataatg aatgatataa ataaaaattt aaattacgtt gcttatgata
     3601 aggataactt tagaaagtgg ttgtctttga ataaaaaact cactagaaaa tccttgagtg
     3661 atgtcatttc tagatttaat cgagctgtat ctttttttgg tgatgaatat gttgattttc
     3721 atgtctataa aattgatgaa attttaatga gattagaaag gattcatttg tttgatattc
     3781 ttagtgttag cctaaaatca caattaagac gatcttttaa attgtattat gagttttgta
     3841 acgataggaa ataatagttt tatagtgtaa ctactgaggc cacataatgt taatgaacga
     3901 aggtgttaca ttaacattgt gtctttgttt attcatattt attttataac aaatatagtc
     3961 ttcggtatgt ggtttattgt gaaaatgtaa ttcaggaata gtattcagta aacattgttt
     4021 cattcctttg aaaggatctt cttgagatcc tttttttcta cgcgtaatct tctagcctga
     4081 aaacgaaaaa accgccttgc agggcggttt tttcaacggt tcaagaactt gcaggttttg
     4141 aaccgaggta actggcttgg aggagcgcag tcaccaaaac ttgttctttc agtttagcct
     4201 taaccggtgc ataacttcaa gaccaactcc tctagaacag ttaccaatgg ctgctgccag
     4261 tggcgctttg tcgtgtcttt ccggattgga ctcaagtcga tagttaccgg aattgacgca
     4321 gcagtcggac tgaacggggg gttcgtgcat acagtccagc ttggagcgaa ctgccttccc
     4381 ggagctgagt gtcaggcgtg gaatgagaaa ccgcggccat aacagcggaa tgacaccggt
     4441 aaaccgaaag gcaggaacag gagagcgcac gagggagccg ctagggggaa acgcctggta
     4501 tctttatagt cctgtcgggt ttcgccacca ctgatttgaa cgtcatattt tgtgatgttt
     4561 gtcagggggg cgaagcctat ggaaaaacgc ccatacgggc gtggcattat tgtccatgtc
     4621 ctgtcctttg gttacgctta ccgtctacgt catttgtcat ttcgaaagac tggtccgctc
     4681 gccgcagaca agtgaccgag cgtagcgagc gaacggtcga ggaagcggaa aagaacgaag
     4741 ataagctgga gcactgacgc actgatgact aaacaacaga aaacggcact gaacatggcg
     4801 aaatttattc aggcgcaatc tctgcttttg cttgagaagc tcaacgaact ggatctcgat
     4861 actgaggccg acttgtgtga agcattacat gaggatgcgg aacacctttt tcgtagcctc
     4921 acgatacgga ttgatggtct tcaggagaag tactaatggc tcaggtatct atcagtgaag
     4981 ccgctcgtct taccgggaaa agtcgtacca cgctgcacag gttgattaaa gcaggtgagt
     5041 tgtccacctg tcacggcgaa cgaaatgcaa aaatgttaga tacatcagag ttattgcgtg
     5101 tgtttggtgc gttgcgtggt cttcctgata aacaggttgt tgaacaggtc actggacagt
     5161 gtgttacagt atcattgtct gagaatgaac aggtggtcag ggcgttgaaa caggaagttg
     5221 aacacctgaa atcgctggtt tctgctcaga attctcatat cgatagtctg aaacaggcga
     5281 tgcagctcct ggagcacaaa cagagcgctt ctgacccgca gaaggttcct gcaaaaccat
     5341 ggtggcagtt ctggaaggga tgatttcccc tgaaattctg ccttttatcc tgtcagggct
     5401 gcaccccgac acccgccagc gcctcaccgc cacgcaataa attgcgttcc agttcaccgc
     5461 ttctgtttcc tgtctgaacg ataagtcttc tggtggctga aaacagccag aaaatcgtgt
     5521 cacacctgac gcactataca gtactgctcc caaagccttg caggacaagg ctttgcggcg
     5581 ctacaccccc actgtctgaa ttgtagcgaa aagcccctaa agacgcagtt atctcattgt
     5641 tttatatgaa ataaaaagtg tagcgctcgc cgctacactt tttatcttaa atttcgcttt
     5701 aattgcatgt tttataatgg ttttatttga gttttagggt gtagcgcgga tacggttttt
     5761 ggggatggta gcctgtttca ggctttcg
//
