LOCUS       NZ_CP056898             4386 bp    DNA     circular CON 17-MAY-2024
DEFINITION  Citrobacter sp. RHBSTW-00021 plasmid pRHBSTW-00021_3, complete
            sequence.
ACCESSION   NZ_CP056898
VERSION     NZ_CP056898.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN15148456
            Assembly: GCF_013797345.1
KEYWORDS    RefSeq.
SOURCE      Citrobacter sp. RHBSTW-00021
  ORGANISM  Citrobacter sp. RHBSTW-00021
            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                     :: WTP4 T1-00021
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 89.6741630612516x
            Sequencing Technology :: Hybrid: Illumina and PACBIO_SMRT
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_013797345.1-RS_2024_05_17
            Annotation Date                   :: 05/17/2024 03:05:27
            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)                     :: 4,974
            CDSs (total)                      :: 4,854
            Genes (coding)                    :: 4,686
            CDSs (with protein)               :: 4,686
            Genes (RNA)                       :: 120
            rRNAs                             :: 9, 8, 8 (5S, 16S, 23S)
            complete rRNAs                    :: 9, 8, 8 (5S, 16S, 23S)
            tRNAs                             :: 84
            ncRNAs                            :: 11
            Pseudo Genes (total)              :: 168
            CDSs (without protein)            :: 168
            Pseudo Genes (ambiguous residues) :: 0 of 168
            Pseudo Genes (frameshifted)       :: 43 of 168
            Pseudo Genes (incomplete)         :: 128 of 168
            Pseudo Genes (internal stop)      :: 34 of 168
            Pseudo Genes (multiple problems)  :: 30 of 168
            CRISPR Arrays                     :: 1
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP056898.1.
            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-00021"
                     /mol_type="genomic DNA"
                     /strain="RHBSTW-00021"
                     /isolation_source="Wastewater effluent sample"
                     /db_xref="taxon:2742630"
                     /plasmid="pRHBSTW-00021_3"
                     /geo_loc_name="United Kingdom"
                     /collection_date="2017"
     gene            complement(join(4066..4386,1..12))
                     /locus_tag="HV039_RS24650"
                     /old_locus_tag="HV039_24655"
     CDS             complement(join(4066..4386,1..12))
                     /locus_tag="HV039_RS24650"
                     /old_locus_tag="HV039_24655"
                     /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            complement(168..413)
                     /locus_tag="HV039_RS24655"
                     /old_locus_tag="HV039_24660"
     CDS             complement(168..413)
                     /locus_tag="HV039_RS24655"
                     /old_locus_tag="HV039_24660"
                     /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_306303658.1"
                     /translation="MSKTMTEMEKQLLSALESLQASYEQQQEAWQDSYSSLQHMFEATS
                     QALTHSDRVCQRLSSQVESLRAQVESLSRNVSRLMR"
                     /name="MbeD family mobilization/exclusion protein"
     gene            complement(462..947)
                     /locus_tag="HV039_RS24660"
                     /old_locus_tag="HV039_24665"
     CDS             complement(462..947)
                     /locus_tag="HV039_RS24660"
                     /old_locus_tag="HV039_24665"
                     /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            complement(<994..1416)
                     /locus_tag="HV039_RS25035"
                     /pseudo=""
     CDS             complement(<994..1416)
                     /locus_tag="HV039_RS25035"
                     /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            1345..1617
                     /locus_tag="HV039_RS25040"
     CDS             1345..1617
                     /locus_tag="HV039_RS25040"
                     /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            complement(1625..1951)
                     /gene="mobC"
                     /locus_tag="HV039_RS24670"
                     /old_locus_tag="HV039_24675"
     CDS             complement(1625..1951)
                     /gene="mobC"
                     /locus_tag="HV039_RS24670"
                     /old_locus_tag="HV039_24675"
                     /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(2196..2696)
                     /locus_tag="HV039_RS24675"
                     /old_locus_tag="HV039_24680"
     CDS             complement(2196..2696)
                     /locus_tag="HV039_RS24675"
                     /old_locus_tag="HV039_24680"
                     /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            complement(2696..3586)
                     /locus_tag="HV039_RS24680"
                     /old_locus_tag="HV039_24685"
     CDS             complement(2696..3586)
                     /locus_tag="HV039_RS24680"
                     /old_locus_tag="HV039_24685"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001517860.1"
                     /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_079967944.1"
                     /translation="MNNAALQLFNERLPHKPYFSDDLHFGVRIAGKERAILAKYIQFNQ
                     PHAMFWLGFDVDRIGAAIDWSDRNAPAPTLTITNPENGHAHLLYALKTSIRTAPDGKMK
                     PLKYAAAVENALRKKLDADTGYSGLICKNPNHGHWKIAVWQPELYTLDWLADSLDLNAA
                     NDKEIVADYGLGRNCTLFDKTRKWAYRAIRQGWPQYEQWLQACYERARAYNLQFSAPLD
                     ENEVSGIAKSIAKWTYKNFSEANFLQYVADTHSSEIQSKRGMKSRGGGRPKIVGSPWLN
                     LGISRSKWYRDFRGL"
                     /name="replication initiation protein"
     gene            complement(3780..4064)
                     /gene="nadS"
                     /locus_tag="HV039_RS24685"
                     /old_locus_tag="HV039_24690"
     CDS             complement(3780..4064)
                     /gene="nadS"
                     /locus_tag="HV039_RS24685"
                     /old_locus_tag="HV039_24690"
                     /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          1626..1818
                     /name="Col(Ye4449)"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="98.969"
                     /coverage="100.0"
                     /evalue="1.72e-93"
     Typing          complement(83..1635)
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="87.838"
                     /coverage="98.0"
                     /evalue="0.0"
ORIGIN
        1 cgtgtgactc acggttgtct cctgtatcta acggagtaca tagtacactt aattctgatt
       61 ccggaaaaga ggtcacatcg aggggccata gtaccgggtc ggctttttct gcggctccgg
      121 ctgttgctcg cgcagctttt ccgcacgggc gcggtcatgc tgcgcaatca gcgcatcaag
      181 cggctgacgt tcctgctcaa gctctcgacc tgcgcgcgca agctctctac ctgactgctc
      241 aagcgctgac acaccctgtc gctgtgcgtc agcgcctgtg aggtagcctc gaacatgtgc
      301 tgcaaactgc tgtagctgtc ctgccacgcc tcctgctgtt gctcgtagct tgcctgtaag
      361 ctctctaagg cgctcagaag ctgtttttcc atctcggtca tggttttgct catcctcggt
      421 gttaaaaccg ctcagacgcg attcagggcg ttctgatgag gttatttcgc cgtgtatttc
      481 accacggtat tcccggcctg cgaggtgtag gtttccacgc cgtgcgcctg cttcggcagc
      541 accgccaggt aggtgttccg gttcttttcg tcgctgtaaa tcgtcacgcc cgcgccgctt
      601 ttcgctttca ggctcgccag cagctgactg tagctgtcca tttcgctcag gcgtgaggtg
      661 atgatcgtgc cttgaaacca aattatcccg cccaggatgc caatcagcag ggcgaagcag
      721 atgaatatcc acgccatcgc cgttgagact gacgttctga gcatgcccgt caacctgccg
      781 ttctgctcgc ggatagcgtt gctgatgctc tgcgagcttg attgcagttc cgcgctgata
      841 gacttctcca gcctcgcgaa ctcgcgcttc acgctctgct cggtatcctg cgcctgctgc
      901 ttcgatttct cctcgaagcc cttcgccaaa tttaaaatct cgctcataaa tcattccttt
      961 cagccggata tttctgccgc cgtccggatc ggcaatgctg atgctgcttt tcgtttcccg
     1021 cgccacggtc aggccgtagc tttccagctg cgtcaccacg tcctgccggc tgcggatcac
     1081 gccctgctgc atcaggttca tcaggccggc ggtgattttc tctgccgcct gctgtttgtc
     1141 gcggggcaga tcactggcct gcgtaagcgg gcggcggtag gtcgggtcat tcgggtcgcg
     1201 tagccccagc cggtcgttgg tcagggtctg ccaggcgttg acgcggggac ggtcggcgcg
     1261 gtcgaaatag ggttgcagac gtttcccgct ctgtaattcg atgttcggga tcacgaagtt
     1321 cagctcgagg cggcctttgt cctgatgctc aacccacaga caggcgtact ggtctttgtc
     1381 gagaccggtc atcagtgtct gttcccattc gtccataaga cgcgcctttt caggctcggc
     1441 aatgtcggct tcctgaaagg acagcacgcc ggaggtgtag gcacgggcaa agtcacagcc
     1501 gtcaatcagt tcgcgggtgc gttcggcgtc tccccgcaac acgcgggcgt cactgcgctg
     1561 gcgatctttg cccagcaggt aatcaacggg gccactgccc gaaccggcac cccgtgagtg
     1621 aattttaacg atcacggtgc tgctccagca gttcaccgag attgcggtcg aggctgttta
     1681 acaccgccag cagggacaca cgctcagtgg gattcagtcc gtcgagctgg ttaagacggc
     1741 gggcgatctg gttcaggttg ttgccaatcc cgctgacctg tcgcagcagt tcgggcgcca
     1801 catcgggcag acggcgcttt ctggcggtgt gttctcccag accgagctga cgcagccatt
     1861 cggccagatg ggttcggtca caccggtcga tcagacgctg atgctctgag tcagtcaggc
     1921 ggattttgat ctctctcgtg cgcttttcca ttcttactcc gctgagaaat attcgcaccc
     1981 aaagtgcgaa agtttcgcag tggatgcccg gggtttcggg gggcggcgag ccccctgaac
     2041 cagtcacaga cggcacctcg tagaggggac gctgtgtgta ctggcttaaa gagtaatgca
     2101 gtatgtcaga ttctgtgctg gctgcaaaaa aaaagccccg cttatacggg gctgttatct
     2161 gatataggtt gttttgtccc aaactacgaa aacagtcagg ctggattata aaatggatat
     2221 atgtcttcac tgagggtttt actgatagtg accgtgcgct cgtggaaaaa tttcagcagt
     2281 gtatctagta cttcgtttga tagaatttgt tgatggatgg gattaacctt caatccgcaa
     2341 aggtccccaa tgacttgatt aagaaaccaa taacccgaca tgttcccttg agaaaaccag
     2401 cgggtgttat cagataatct ttccagcata ctttgatcat ctgttgaatc taggtagtgc
     2461 tttacaaaac caataacttt aactcttaca gcgtctgatt ttctcccatg ttccttaaga
     2521 taagtagcat tgagaaaaag cccagcggct aaaaatacaa caccttcgcc atcaacgatg
     2581 gttacgccat tagcttcaac tatggctaca accttctttg caacacctag aatcttatcg
     2641 ctaacgtata agtcgacttg attgctgcta attttttttc taaaaaaacc aaacattata
     2701 accctctaaa atctctatac catttagaac gactgattcc taaattaagc caagggcttc
     2761 cgacaatctt tggccttccc cctcctcgac ttttcattcc tcttttcgat tgaatttcag
     2821 atgagtgagt atctgcaaca tattgcaaaa aattagcttc agagaagttt ttgtatgtcc
     2881 atttagcaat gctcttagct attccactaa cttcattttc atccagaggg gcagaaaatt
     2941 gcaggttgta agctctggcc cgctcatagc aggcttgcag ccattgctca tactgcggcc
     3001 agccctgacg gatagcgcgg taagcccact tgcgtgtttt atcgaaaaga gtgcagttac
     3061 ggcctaagcc gtaatcggca acgatttctt tatcgttcgc ggcgttcagg tcgagcgagt
     3121 cggccagcca gtccagcgtg tagagttccg gctgccagac ggcaattttc cagtgaccat
     3181 ggttcgggtt cttgcaaatt aaccccgaat atcccgtgtc agcatccagt tttttacgta
     3241 gcgcgttctc tacggcagcg gcgtacttca gcggcttcat ttttccatct ggtgcagtgc
     3301 gtatcgaggt tttcagcgca tagagcaggt gagcatgacc attttcgggg ttggtgatgg
     3361 tcagcgtagg cgcgggcgca ttgcgatcgc tccagtcgat ggcggcaccg atacggtcaa
     3421 cgtcaaaacc gagccagaac atggcgtgag gctggttgaa ctggatgtat ttcgccagaa
     3481 tcgcgcgctc cttaccggca atgcgtacac caaagtgcag atcgtccgaa aagtacggct
     3541 tgtgcggtaa gcgttcgttg aaaagttgga gtgcagcgtt attcaaagcg ccctgcactt
     3601 atggcgggct gttgtctggc acgtttcatg tgctaatatc ctttcaaggt ttcgtacctg
     3661 gccctggtta tcatgcggat ccgccaagat ttgagcatga tgccggggct ttgttttttc
     3721 tgttgccgtt aaattacacg cgaacggcct cgcctgtcga atccttctgt cacaacggct
     3781 tagtgcgccg ccagctcctg gaagaatttc gggttcgcct ggatggttgc cagcaccttc
     3841 gccgccagtc cggtcggatt acggcgtccg gtttcccagc tttttatggt gtcgaggctg
     3901 gttcccagca ctttcgccat ctcactctgt gaaacgttca gttgtgccct gatagccttc
     3961 acgtctgcca gctcgtaacg ggtgacgcgg gcaggctctc tgacgccgtt tttgatttca
     4021 acggcttctt ccagcgatgc tttcagctcg tcaaaaaaac tcatgtcaca cctcgtcttt
     4081 cagttgttgg gtcagcgtct tcagcgcggc tttctccgcg tccgtcaggc tgtctttggt
     4141 gcttttcggg taggccatca ccagataaat cacctcggcg gtggccagaa aataaatcac
     4201 cctcgcgctg ccgctttttc cctggttgcc cgtcgccatt ctgacttttc gcagcccgcc
     4261 ggttttctgg atgagatcgc ctttgtccgg cgactcaatc agcgtctttt gcagctccct
     4321 gagctcttca tccgtggcga tctgttttat ctgacgggta aacatcgggg tctcgataaa
     4381 ttcaat
//
