LOCUS       NZ_CP056353             4386 bp    DNA     circular CON 26-JAN-2024
DEFINITION  Citrobacter sp. RHBSTW-00678 plasmid pRHBSTW-00678_4, complete
            sequence.
ACCESSION   NZ_CP056353
VERSION     NZ_CP056353.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN15148682
            Assembly: GCF_013738915.1
KEYWORDS    RefSeq.
SOURCE      Citrobacter sp. RHBSTW-00678
  ORGANISM  Citrobacter sp. RHBSTW-00678
            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                     :: WTP2 T2-00678
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 97.3983658811909x
            Sequencing Technology :: Hybrid: Illumina and OXFORD_NANOPORE
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 01/24/2024 14:01:46
            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)                     :: 5,445
            CDSs (total)                      :: 5,328
            Genes (coding)                    :: 5,147
            CDSs (with protein)               :: 5,147
            Genes (RNA)                       :: 117
            rRNAs                             :: 9, 8, 8 (5S, 16S, 23S)
            complete rRNAs                    :: 9, 8, 8 (5S, 16S, 23S)
            tRNAs                             :: 83
            ncRNAs                            :: 9
            Pseudo Genes (total)              :: 181
            CDSs (without protein)            :: 181
            Pseudo Genes (ambiguous residues) :: 0 of 181
            Pseudo Genes (frameshifted)       :: 52 of 181
            Pseudo Genes (incomplete)         :: 134 of 181
            Pseudo Genes (internal stop)      :: 33 of 181
            Pseudo Genes (multiple problems)  :: 32 of 181
            Pseudo Genes (short protein)      :: 1 of 181
            CRISPR Arrays                     :: 1
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP056353.1.
            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-00678"
                     /mol_type="genomic DNA"
                     /strain="RHBSTW-00678"
                     /isolation_source="Wastewater influent sample"
                     /db_xref="taxon:2742661"
                     /plasmid="pRHBSTW-00678_4"
                     /geo_loc_name="United Kingdom"
                     /collection_date="2017"
     gene            join(3974..4386,1..88)
                     /locus_tag="HV265_RS26980"
                     /old_locus_tag="HV265_26990"
     CDS             join(3974..4386,1..88)
                     /locus_tag="HV265_RS26980"
                     /old_locus_tag="HV265_26990"
                     /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            333..659
                     /gene="mobC"
                     /locus_tag="HV265_RS26985"
                     /old_locus_tag="HV265_26995"
     CDS             333..659
                     /gene="mobC"
                     /locus_tag="HV265_RS26985"
                     /old_locus_tag="HV265_26995"
                     /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(667..939)
                     /locus_tag="HV265_RS27495"
     CDS             complement(667..939)
                     /locus_tag="HV265_RS27495"
                     /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            868..>1290
                     /locus_tag="HV265_RS27500"
                     /pseudo=""
     CDS             868..>1290
                     /locus_tag="HV265_RS27500"
                     /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            1337..1822
                     /locus_tag="HV265_RS26995"
                     /old_locus_tag="HV265_27005"
     CDS             1337..1822
                     /locus_tag="HV265_RS26995"
                     /old_locus_tag="HV265_27005"
                     /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            1892..2116
                     /locus_tag="HV265_RS27000"
                     /old_locus_tag="HV265_27010"
     CDS             1892..2116
                     /locus_tag="HV265_RS27000"
                     /old_locus_tag="HV265_27010"
                     /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            2272..2604
                     /locus_tag="HV265_RS27005"
                     /old_locus_tag="HV265_27015"
     CDS             2272..2604
                     /locus_tag="HV265_RS27005"
                     /old_locus_tag="HV265_27015"
                     /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            2606..2890
                     /gene="nadS"
                     /locus_tag="HV265_RS27010"
                     /old_locus_tag="HV265_27020"
     CDS             2606..2890
                     /gene="nadS"
                     /locus_tag="HV265_RS27010"
                     /old_locus_tag="HV265_27020"
                     /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"
     gene            3084..3974
                     /locus_tag="HV265_RS27015"
                     /old_locus_tag="HV265_27025"
     CDS             3084..3974
                     /locus_tag="HV265_RS27015"
                     /old_locus_tag="HV265_27025"
                     /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"
     Typing          complement(467..659)
                     /name="Col(Ye4449)"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="98.969"
                     /coverage="100.0"
                     /evalue="1.72e-93"
     Typing          650..2202
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="87.838"
                     /coverage="98.0"
                     /evalue="0.0"
ORIGIN
        1 tacactgctg aaatttttcc acgagcgcac ggtcactatc agtaaaaccc tcagtgaaga
       61 catatatcca ttttataatc cagcctgact gttttcgtag tttgggacaa aacaacctat
      121 atcagataac agccccgtat aagcggggct ttttttttgc agccagcaca gaatctgaca
      181 tactgcatta ctctttaagc cagtacacac agcgtcccct ctacgaggtg ccgtctgtga
      241 ctggttcagg gggctcgccg ccccccgaaa ccccgggcat ccactgcgaa actttcgcac
      301 tttgggtgcg aatatttctc agcggagtaa gaatggaaaa gcgcacgaga gagatcaaaa
      361 tccgcctgac tgactcagag catcagcgtc tgatcgaccg gtgtgaccga acccatctgg
      421 ccgaatggct gcgtcagctc ggtctgggag aacacaccgc cagaaagcgc cgtctgcccg
      481 atgtggcgcc cgaactgctg cgacaggtca gcgggattgg caacaacctg aaccagatcg
      541 cccgccgtct taaccagctc gacggactga atcccactga gcgtgtgtcc ctgctggcgg
      601 tgttaaacag cctcgaccgc aatctcggtg aactgctgga gcagcaccgt gatcgttaaa
      661 attcactcac ggggtgccgg ttcgggcagt ggccccgttg attacctgct gggcaaagat
      721 cgccagcgca gtgacgcccg cgtgttgcgg ggagacgccg aacgcacccg cgaactgatt
      781 gacggctgtg actttgcccg tgcctacacc tccggcgtgc tgtcctttca ggaagccgac
      841 attgccgagc ctgaaaaggc gcgtcttatg gacgaatggg aacagacact gatgaccggt
      901 ctcgacaaag accagtacgc ctgtctgtgg gttgagcatc aggacaaagg ccgcctcgag
      961 ctgaacttcg tgatcccgaa catcgaatta cagagcggga aacgtctgca accctatttc
     1021 gaccgcgccg accgtccccg cgtcaacgcc tggcagaccc tgaccaacga ccggctgggg
     1081 ctacgcgacc cgaatgaccc gacctaccgc cgcccgctta cgcaggccag tgatctgccc
     1141 cgcgacaaac agcaggcggc agagaaaatc accgccggcc tgatgaacct gatgcagcag
     1201 ggcgtgatcc gcagccggca ggacgtggtg acgcagctgg aaagctacgg cctgaccgtg
     1261 gcgcgggaaa cgaaaagcag catcagcatt gccgatccgg acggcggcag aaatatccgg
     1321 ctgaaaggaa tgatttatga gcgagatttt aaatttggcg aagggcttcg aggagaaatc
     1381 gaagcagcag gcgcaggata ccgagcagag cgtgaagcgc gagttcgcga ggctggagaa
     1441 gtctatcagc gcggaactgc aatcaagctc gcagagcatc agcaacgcta tccgcgagca
     1501 gaacggcagg ttgacgggca tgctcagaac gtcagtctca acggcgatgg cgtggatatt
     1561 catctgcttc gccctgctga ttggcatcct gggcgggata atttggtttc aaggcacgat
     1621 catcacctca cgcctgagcg aaatggacag ctacagtcag ctgctggcga gcctgaaagc
     1681 gaaaagcggc gcgggcgtga cgatttacag cgacgaaaag aaccggaaca cctacctggc
     1741 ggtgctgccg aagcaggcgc acggcgtgga aacctacacc tcgcaggccg ggaataccgt
     1801 ggtgaaatac acggcgaaat aacctcatca gaacgccctg aatcgcgtct gagcggtttt
     1861 aacaccgagg atgagcaaaa ccatgaccga gatggaaaaa cagcttctga gcgccttaga
     1921 gagcttacag gcaagctacg agcaacagca ggaggcgtgg caggacagct acagcagttt
     1981 gcagcacatg ttcgaggcta cctcacaggc gctgacgcac agcgacaggg tgtgtcagcg
     2041 cttgagcagt caggtagaga gcttgcgcgc gcaggtcgag agcttgagca ggaacgtcag
     2101 ccgcttgatg cgctgattgc gcagcatgac cgcgcccgtg cggaaaagct gcgcgagcaa
     2161 cagccggagc cgcagaaaaa gccgacccgg tactatggcc cctcgatgtg acctcttttc
     2221 cggaatcaga attaagtgta ctatgtactc cgttagatac aggagacaac cgtgagtcac
     2281 acgattgaat ttatcgagac cccgatgttt acccgtcaga taaaacagat cgccacggat
     2341 gaagagctca gggagctgca aaagacgctg attgagtcgc cggacaaagg cgatctcatc
     2401 cagaaaaccg gcgggctgcg aaaagtcaga atggcgacgg gcaaccaggg aaaaagcggc
     2461 agcgcgaggg tgatttattt tctggccacc gccgaggtga tttatctggt gatggcctac
     2521 ccgaaaagca ccaaagacag cctgacggac gcggagaaag ccgcgctgaa gacgctgacc
     2581 caacaactga aagacgaggt gtgacatgag tttttttgac gagctgaaag catcgctgga
     2641 agaagccgtt gaaatcaaaa acggcgtcag agagcctgcc cgcgtcaccc gttacgagct
     2701 ggcagacgtg aaggctatca gggcacaact gaacgtttca cagagtgaga tggcgaaagt
     2761 gctgggaacc agcctcgaca ccataaaaag ctgggaaacc ggacgccgta atccgaccgg
     2821 actggcggcg aaggtgctgg caaccatcca ggcgaacccg aaattcttcc aggagctggc
     2881 ggcgcactaa gccgttgtga cagaaggatt cgacaggcga ggccgttcgc gtgtaattta
     2941 acggcaacag aaaaaacaaa gccccggcat catgctcaaa tcttggcgga tccgcatgat
     3001 aaccagggcc aggtacgaaa ccttgaaagg atattagcac atgaaacgtg ccagacaaca
     3061 gcccgccata agtgcagggc gctttgaata acgctgcact ccaacttttc aacgaacgct
     3121 taccgcacaa gccgtacttt tcggacgatc tgcactttgg tgtacgcatt gccggtaagg
     3181 agcgcgcgat tctggcgaaa tacatccagt tcaaccagcc tcacgccatg ttctggctcg
     3241 gttttgacgt tgaccgtatc ggtgccgcca tcgactggag cgatcgcaat gcgcccgcgc
     3301 ctacgctgac catcaccaac cccgaaaatg gtcatgctca cctgctctat gcgctgaaaa
     3361 cctcgatacg cactgcacca gatggaaaaa tgaagccgct gaagtacgcc gctgccgtag
     3421 agaacgcgct acgtaaaaaa ctggatgctg acacgggata ttcggggtta atttgcaaga
     3481 acccgaacca tggtcactgg aaaattgccg tctggcagcc ggaactctac acgctggact
     3541 ggctggccga ctcgctcgac ctgaacgccg cgaacgataa agaaatcgtt gccgattacg
     3601 gcttaggccg taactgcact cttttcgata aaacacgcaa gtgggcttac cgcgctatcc
     3661 gtcagggctg gccgcagtat gagcaatggc tgcaagcctg ctatgagcgg gccagagctt
     3721 acaacctgca attttctgcc cctctggatg aaaatgaagt tagtggaata gctaagagca
     3781 ttgctaaatg gacatacaaa aacttctctg aagctaattt tttgcaatat gttgcagata
     3841 ctcactcatc tgaaattcaa tcgaaaagag gaatgaaaag tcgaggaggg ggaaggccaa
     3901 agattgtcgg aagcccttgg cttaatttag gaatcagtcg ttctaaatgg tatagagatt
     3961 ttagagggtt ataatgtttg gtttttttag aaaaaaaatt agcagcaatc aagtcgactt
     4021 atacgttagc gataagattc taggtgttgc aaagaaggtt gtagccatag ttgaagctaa
     4081 tggcgtaacc atcgttgatg gcgaaggtgt tgtattttta gccgctgggc tttttctcaa
     4141 tgctacttat cttaaggaac atgggagaaa atcagacgct gtaagagtta aagttattgg
     4201 ttttgtaaag cactacctag attcaacaga tgatcaaagt atgctggaaa gattatctga
     4261 taacacccgc tggttttctc aagggaacat gtcgggttat tggtttctta atcaagtcat
     4321 tggggacctt tgcggattga aggttaatcc catccatcaa caaattctat caaacgaagt
     4381 actaga
//
