LOCUS       NZ_CP056221             4386 bp    DNA     circular CON 26-JAN-2024
DEFINITION  Citrobacter sp. RHBSTW-00976 plasmid pRHBSTW-00976_3, complete
            sequence.
ACCESSION   NZ_CP056221
VERSION     NZ_CP056221.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN15148758
            Assembly: GCF_013724425.1
KEYWORDS    RefSeq.
SOURCE      Citrobacter sp. RHBSTW-00976
  ORGANISM  Citrobacter sp. RHBSTW-00976
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Citrobacter.
REFERENCE   1  (bases 1 to 4386)
  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 4386)
  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 T3-00976
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 147.527028671662x
            Sequencing Technology :: Hybrid: Illumina and OXFORD_NANOPORE
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 01/24/2024 13:50:24
            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)                     :: 5,298
            CDSs (total)                      :: 5,179
            Genes (coding)                    :: 5,011
            CDSs (with protein)               :: 5,011
            Genes (RNA)                       :: 119
            rRNAs                             :: 9, 8, 8 (5S, 16S, 23S)
            complete rRNAs                    :: 9, 8, 8 (5S, 16S, 23S)
            tRNAs                             :: 83
            ncRNAs                            :: 11
            Pseudo Genes (total)              :: 168
            CDSs (without protein)            :: 168
            Pseudo Genes (ambiguous residues) :: 0 of 168
            Pseudo Genes (frameshifted)       :: 39 of 168
            Pseudo Genes (incomplete)         :: 128 of 168
            Pseudo Genes (internal stop)      :: 33 of 168
            Pseudo Genes (multiple problems)  :: 28 of 168
            Pseudo Genes (short protein)      :: 1 of 168
            CRISPR Arrays                     :: 1
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP056221.1.
            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..4386
                     /organism="Citrobacter sp. RHBSTW-00976"
                     /mol_type="genomic DNA"
                     /strain="RHBSTW-00976"
                     /isolation_source="Wastewater influent sample"
                     /db_xref="taxon:2742674"
                     /plasmid="pRHBSTW-00976_3"
                     /geo_loc_name="United Kingdom"
                     /collection_date="2017"
     gene            join(3511..4386,1..15)
                     /locus_tag="HV341_RS26285"
                     /old_locus_tag="HV341_26295"
     CDS             join(3511..4386,1..15)
                     /locus_tag="HV341_RS26285"
                     /old_locus_tag="HV341_26295"
                     /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="replication initiation protein"
                     /protein_id="WP_079967944.1"
                     /translation="MNNAALQLFNERLPHKPYFSDDLHFGVRIAGKERAILAKYIQFNQ
                     PHAMFWLGFDVDRIGAAIDWSDRNAPAPTLTITNPENGHAHLLYALKTSIRTAPDGKMK
                     PLKYAAAVENALRKKLDADTGYSGLICKNPNHGHWKIAVWQPELYTLDWLADSLDLNAA
                     NDKEIVADYGLGRNCTLFDKTRKWAYRAIRQGWPQYEQWLQACYERARAYNLQFSAPLD
                     ENEVSGIAKSIAKWTYKNFSEANFLQYVADTHSSEIQSKRGMKSRGGGRPKIVGSPWLN
                     LGISRSKWYRDFRGL"
                     /name="replication initiation protein"
     gene            15..515
                     /locus_tag="HV341_RS26290"
                     /old_locus_tag="HV341_26300"
     CDS             15..515
                     /locus_tag="HV341_RS26290"
                     /old_locus_tag="HV341_26300"
                     /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_001715146.1"
                     /translation="MFGFFRKKISSNQVDLYVSDKILGVAKKVVAIVEANGVTIVDGEG
                     VVFLAAGLFLNATYLKEHGRKSDAVRVKVIGFVKHYLDSTDDQSMLERLSDNTRWFSQG
                     NMSGYWFLNQVIGDLCGLKVNPIHQQILSNEVLDTLLKFFHERTVTISKTLSEDIYPFY
                     NPA"
                     /name="hypothetical protein"
     gene            760..1086
                     /gene="mobC"
                     /locus_tag="HV341_RS26295"
                     /old_locus_tag="HV341_26305"
     CDS             760..1086
                     /gene="mobC"
                     /locus_tag="HV341_RS26295"
                     /old_locus_tag="HV341_26305"
                     /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_001715145.1"
                     /translation="MEKRTREIKIRLTDSEHQRLIDRCDRTHLAEWLRQLGLGEHTARK
                     RRLPDVAPELLRQVSGIGNNLNQIARRLNQLDGLNPTERVSLLAVLNSLDRNLGELLEQ
                     HRDR"
                     /name="mobC"
     gene            complement(1094..1366)
                     /locus_tag="HV341_RS26740"
     CDS             complement(1094..1366)
                     /locus_tag="HV341_RS26740"
                     /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_220132918.1"
                     /translation="MLNPQTGVLVFVETGHQCLFPFVHKTRLFRLGNVGFLKGQHAGGV
                     GTGKVTAVNQFAGAFGVSPQHAGVTALAIFAQQVINGATARTGTP"
                     /name="hypothetical protein"
     gene            1295..>1717
                     /locus_tag="HV341_RS26745"
                     /pseudo=""
     CDS             1295..>1717
                     /locus_tag="HV341_RS26745"
                     /inference="COORDINATES: protein motif:HMM:NF015397.4"
                     /note="incomplete; partial in the middle of a contig;
                     missing C-terminus; Derived by automated computational
                     analysis using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="relaxase/mobilization nuclease domain-containing
                     protein"
                     /name="relaxase/mobilization nuclease domain-containing
                     protein"
     gene            1764..2249
                     /locus_tag="HV341_RS26305"
                     /old_locus_tag="HV341_26315"
     CDS             1764..2249
                     /locus_tag="HV341_RS26305"
                     /old_locus_tag="HV341_26315"
                     /inference="COORDINATES: protein motif:HMM:NF016710.4"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MbeB family mobilization protein"
                     /protein_id="WP_139764470.1"
                     /translation="MSEILNLAKGFEEKSKQQAQDTEQSVKREFARLEKSISAELQSSS
                     QSISNAIREQNGRLTGMLRTSVSTAMAWIFICFALLIGILGGIIWFQGTIITSRLSEMD
                     SYSQLLASLKAKSGAGVTIYSDEKNRNTYLAVLPKQAHGVETYTSQAGNTVVKYTAK"
                     /name="MbeB family mobilization protein"
     gene            2319..2543
                     /locus_tag="HV341_RS26310"
                     /old_locus_tag="HV341_26320"
     CDS             2319..2543
                     /locus_tag="HV341_RS26310"
                     /old_locus_tag="HV341_26320"
                     /inference="COORDINATES: protein motif:HMM:NF016769.4"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MbeD family mobilization/exclusion protein"
                     /protein_id="WP_228286434.1"
                     /translation="MEKQLLSALESLQASYEQQQEAWQDSYSSLQHMFEATSQALTHSD
                     RVCQRLSSQVESLRAQVESLSRNVSRLMR"
                     /name="MbeD family mobilization/exclusion protein"
     gene            2699..3031
                     /locus_tag="HV341_RS26315"
                     /old_locus_tag="HV341_26325"
     CDS             2699..3031
                     /locus_tag="HV341_RS26315"
                     /old_locus_tag="HV341_26325"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_015873600.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="type II toxin-antitoxin system RelE/ParE family
                     toxin"
                     /protein_id="WP_001715142.1"
                     /translation="MSHTIEFIETPMFTRQIKQIATDEELRELQKTLIESPDKGDLIQK
                     TGGLRKVRMATGNQGKSGSARVIYFLATAEVIYLVMAYPKSTKDSLTDAEKAALKTLTQ
                     QLKDEV"
                     /name="type II toxin-antitoxin system RelE/ParE family
                     toxin"
     gene            3033..3317
                     /gene="nadS"
                     /locus_tag="HV341_RS26320"
                     /old_locus_tag="HV341_26330"
     CDS             3033..3317
                     /gene="nadS"
                     /locus_tag="HV341_RS26320"
                     /old_locus_tag="HV341_26330"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000007431.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="NadS family protein"
                     /protein_id="WP_001697687.1"
                     /translation="MSFFDELKASLEEAVEIKNGVREPARVTRYELADVKAIRAQLNVS
                     QSEMAKVLGTSLDTIKSWETGRRNPTGLAAKVLATIQANPKFFQELAAH"
                     /name="nadS"
     Typing          complement(894..1086)
                     /name="Col(Ye4449)"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="98.969"
                     /coverage="100.0"
                     /evalue="1.72e-93"
     Typing          1077..2629
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="87.838"
                     /coverage="98.0"
                     /evalue="0.0"
ORIGIN
        1 tttagagggt tataatgttt ggttttttta gaaaaaaaat tagcagcaat caagtcgact
       61 tatacgttag cgataagatt ctaggtgttg caaagaaggt tgtagccata gttgaagcta
      121 atggcgtaac catcgttgat ggcgaaggtg ttgtattttt agccgctggg ctttttctca
      181 atgctactta tcttaaggaa catgggagaa aatcagacgc tgtaagagtt aaagttattg
      241 gttttgtaaa gcactaccta gattcaacag atgatcaaag tatgctggaa agattatctg
      301 ataacacccg ctggttttct caagggaaca tgtcgggtta ttggtttctt aatcaagtca
      361 ttggggacct ttgcggattg aaggttaatc ccatccatca acaaattcta tcaaacgaag
      421 tactagatac actgctgaaa tttttccacg agcgcacggt cactatcagt aaaaccctca
      481 gtgaagacat atatccattt tataatccag cctgactgtt ttcgtagttt gggacaaaac
      541 aacctatatc agataacagc cccgtataag cggggctttt tttttgcagc cagcacagaa
      601 tctgacatac tgcattactc tttaagccag tacacacagc gtcccctcta cgaggtgccg
      661 tctgtgactg gttcaggggg ctcgccgccc cccgaaaccc cgggcatcca ctgcgaaact
      721 ttcgcacttt gggtgcgaat atttctcagc ggagtaagaa tggaaaagcg cacgagagag
      781 atcaaaatcc gcctgactga ctcagagcat cagcgtctga tcgaccggtg tgaccgaacc
      841 catctggccg aatggctgcg tcagctcggt ctgggagaac acaccgccag aaagcgccgt
      901 ctgcccgatg tggcgcccga actgctgcga caggtcagcg ggattggcaa caacctgaac
      961 cagatcgccc gccgtcttaa ccagctcgac ggactgaatc ccactgagcg tgtgtccctg
     1021 ctggcggtgt taaacagcct cgaccgcaat ctcggtgaac tgctggagca gcaccgtgat
     1081 cgttaaaatt cactcacggg gtgccggttc gggcagtggc cccgttgatt acctgctggg
     1141 caaagatcgc cagcgcagtg acgcccgcgt gttgcgggga gacgccgaac gcacccgcga
     1201 actgattgac ggctgtgact ttgcccgtgc ctacacctcc ggcgtgctgt cctttcagga
     1261 agccgacatt gccgagcctg aaaaggcgcg tcttatggac gaatgggaac agacactgat
     1321 gaccggtctc gacaaagacc agtacgcctg tctgtgggtt gagcatcagg acaaaggccg
     1381 cctcgagctg aacttcgtga tcccgaacat cgaattacag agcgggaaac gtctgcaacc
     1441 ctatttcgac cgcgccgacc gtccccgcgt caacgcctgg cagaccctga ccaacgaccg
     1501 gctggggcta cgcgacccga atgacccgac ctaccgccgc ccgcttacgc aggccagtga
     1561 tctgccccgc gacaaacagc aggcggcaga gaaaatcacc gccggcctga tgaacctgat
     1621 gcagcagggc gtgatccgca gccggcagga cgtggtgacg cagctggaaa gctacggcct
     1681 gaccgtggcg cgggaaacga aaagcagcat cagcattgcc gatccggacg gcggcagaaa
     1741 tatccggctg aaaggaatga tttatgagcg agattttaaa tttggcgaag ggcttcgagg
     1801 agaaatcgaa gcagcaggcg caggataccg agcagagcgt gaagcgcgag ttcgcgaggc
     1861 tggagaagtc tatcagcgcg gaactgcaat caagctcgca gagcatcagc aacgctatcc
     1921 gcgagcagaa cggcaggttg acgggcatgc tcagaacgtc agtctcaacg gcgatggcgt
     1981 ggatattcat ctgcttcgcc ctgctgattg gcatcctggg cgggataatt tggtttcaag
     2041 gcacgatcat cacctcacgc ctgagcgaaa tggacagcta cagtcagctg ctggcgagcc
     2101 tgaaagcgaa aagcggcgcg ggcgtgacga tttacagcga cgaaaagaac cggaacacct
     2161 acctggcggt gctgccgaag caggcgcacg gcgtggaaac ctacacctcg caggccggga
     2221 ataccgtggt gaaatacacg gcgaaataac ctcatcagaa cgccctgaat cgcgtctgag
     2281 cggttttaac accgaggatg agcaaaacca tgaccgagat ggaaaaacag cttctgagcg
     2341 ccttagagag cttacaggca agctacgagc aacagcagga ggcgtggcag gacagctaca
     2401 gcagtttgca gcacatgttc gaggctacct cacaggcgct gacgcacagc gacagggtgt
     2461 gtcagcgctt gagcagtcag gtagagagct tgcgcgcgca ggtcgagagc ttgagcagga
     2521 acgtcagccg cttgatgcgc tgattgcgca gcatgaccgc gcccgtgcgg aaaagctgcg
     2581 cgagcaacag ccggagccgc agaaaaagcc gacccggtac tatggcccct cgatgtgacc
     2641 tcttttccgg aatcagaatt aagtgtacta tgtactccgt tagatacagg agacaaccgt
     2701 gagtcacacg attgaattta tcgagacccc gatgtttacc cgtcagataa aacagatcgc
     2761 cacggatgaa gagctcaggg agctgcaaaa gacgctgatt gagtcgccgg acaaaggcga
     2821 tctcatccag aaaaccggcg ggctgcgaaa agtcagaatg gcgacgggca accagggaaa
     2881 aagcggcagc gcgagggtga tttattttct ggccaccgcc gaggtgattt atctggtgat
     2941 ggcctacccg aaaagcacca aagacagcct gacggacgcg gagaaagccg cgctgaagac
     3001 gctgacccaa caactgaaag acgaggtgtg acatgagttt ttttgacgag ctgaaagcat
     3061 cgctggaaga agccgttgaa atcaaaaacg gcgtcagaga gcctgcccgc gtcacccgtt
     3121 acgagctggc agacgtgaag gctatcaggg cacaactgaa cgtttcacag agtgagatgg
     3181 cgaaagtgct gggaaccagc ctcgacacca taaaaagctg ggaaaccgga cgccgtaatc
     3241 cgaccggact ggcggcgaag gtgctggcaa ccatccaggc gaacccgaaa ttcttccagg
     3301 agctggcggc gcactaagcc gttgtgacag aaggattcga caggcgaggc cgttcgcgtg
     3361 taatttaacg gcaacagaaa aaacaaagcc ccggcatcat gctcaaatct tggcggatcc
     3421 gcatgataac cagggccagg tacgaaacct tgaaaggata ttagcacatg aaacgtgcca
     3481 gacaacagcc cgccataagt gcagggcgct ttgaataacg ctgcactcca acttttcaac
     3541 gaacgcttac cgcacaagcc gtacttttcg gacgatctgc actttggtgt acgcattgcc
     3601 ggtaaggagc gcgcgattct ggcgaaatac atccagttca accagcctca cgccatgttc
     3661 tggctcggtt ttgacgttga ccgtatcggt gccgccatcg actggagcga tcgcaatgcg
     3721 cccgcgccta cgctgaccat caccaacccc gaaaatggtc atgctcacct gctctatgcg
     3781 ctgaaaacct cgatacgcac tgcaccagat ggaaaaatga agccgctgaa gtacgccgct
     3841 gccgtagaga acgcgctacg taaaaaactg gatgctgaca cgggatattc ggggttaatt
     3901 tgcaagaacc cgaaccatgg tcactggaaa attgccgtct ggcagccgga actctacacg
     3961 ctggactggc tggccgactc gctcgacctg aacgccgcga acgataaaga aatcgttgcc
     4021 gattacggct taggccgtaa ctgcactctt ttcgataaaa cacgcaagtg ggcttaccgc
     4081 gctatccgtc agggctggcc gcagtatgag caatggctgc aagcctgcta tgagcgggcc
     4141 agagcttaca acctgcaatt ttctgcccct ctggatgaaa atgaagttag tggaatagct
     4201 aagagcattg ctaaatggac atacaaaaac ttctctgaag ctaatttttt gcaatatgtt
     4261 gcagatactc actcatctga aattcaatcg aaaagaggaa tgaaaagtcg aggaggggga
     4321 aggccaaaga ttgtcggaag cccttggctt aatttaggaa tcagtcgttc taaatggtat
     4381 agagat
//
