LOCUS       NZ_CP056363             4386 bp    DNA     circular CON 26-JAN-2024
DEFINITION  Citrobacter sp. RHBSTW-00667 plasmid pRHBSTW-00667_3, complete
            sequence.
ACCESSION   NZ_CP056363
VERSION     NZ_CP056363.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN15148675
            Assembly: GCF_013746155.1
KEYWORDS    RefSeq.
SOURCE      Citrobacter sp. RHBSTW-00667
  ORGANISM  Citrobacter sp. RHBSTW-00667
            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 T2-00667
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 89.4144395815584x
            Sequencing Technology :: Hybrid: Illumina and OXFORD_NANOPORE
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 01/24/2024 14:21:43
            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)                     :: 5,260
            CDSs (total)                      :: 5,142
            Genes (coding)                    :: 4,959
            CDSs (with protein)               :: 4,959
            Genes (RNA)                       :: 118
            rRNAs                             :: 9, 8, 8 (5S, 16S, 23S)
            complete rRNAs                    :: 9, 8, 8 (5S, 16S, 23S)
            tRNAs                             :: 82
            ncRNAs                            :: 11
            Pseudo Genes (total)              :: 183
            CDSs (without protein)            :: 183
            Pseudo Genes (ambiguous residues) :: 0 of 183
            Pseudo Genes (frameshifted)       :: 47 of 183
            Pseudo Genes (incomplete)         :: 139 of 183
            Pseudo Genes (internal stop)      :: 35 of 183
            Pseudo Genes (multiple problems)  :: 32 of 183
            Pseudo Genes (short protein)      :: 1 of 183
            CRISPR Arrays                     :: 1
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP056363.1.
            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-00667"
                     /mol_type="genomic DNA"
                     /strain="RHBSTW-00667"
                     /isolation_source="Wastewater influent sample"
                     /db_xref="taxon:2742659"
                     /plasmid="pRHBSTW-00667_3"
                     /geo_loc_name="United Kingdom"
                     /collection_date="2017"
     gene            join(3892..4386,1..6)
                     /locus_tag="HV258_RS26055"
                     /old_locus_tag="HV258_26065"
     CDS             join(3892..4386,1..6)
                     /locus_tag="HV258_RS26055"
                     /old_locus_tag="HV258_26065"
                     /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            251..577
                     /gene="mobC"
                     /locus_tag="HV258_RS26060"
                     /old_locus_tag="HV258_26070"
     CDS             251..577
                     /gene="mobC"
                     /locus_tag="HV258_RS26060"
                     /old_locus_tag="HV258_26070"
                     /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(585..857)
                     /locus_tag="HV258_RS26530"
     CDS             complement(585..857)
                     /locus_tag="HV258_RS26530"
                     /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            786..>1208
                     /locus_tag="HV258_RS26535"
                     /pseudo=""
     CDS             786..>1208
                     /locus_tag="HV258_RS26535"
                     /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            1255..1740
                     /locus_tag="HV258_RS26070"
                     /old_locus_tag="HV258_26080"
     CDS             1255..1740
                     /locus_tag="HV258_RS26070"
                     /old_locus_tag="HV258_26080"
                     /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            1810..2034
                     /locus_tag="HV258_RS26075"
                     /old_locus_tag="HV258_26085"
     CDS             1810..2034
                     /locus_tag="HV258_RS26075"
                     /old_locus_tag="HV258_26085"
                     /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            2190..2522
                     /locus_tag="HV258_RS26080"
                     /old_locus_tag="HV258_26090"
     CDS             2190..2522
                     /locus_tag="HV258_RS26080"
                     /old_locus_tag="HV258_26090"
                     /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            2524..2808
                     /gene="nadS"
                     /locus_tag="HV258_RS26085"
                     /old_locus_tag="HV258_26095"
     CDS             2524..2808
                     /gene="nadS"
                     /locus_tag="HV258_RS26085"
                     /old_locus_tag="HV258_26095"
                     /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            3002..3892
                     /locus_tag="HV258_RS26090"
                     /old_locus_tag="HV258_26100"
     CDS             3002..3892
                     /locus_tag="HV258_RS26090"
                     /old_locus_tag="HV258_26100"
                     /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(385..577)
                     /name="Col(Ye4449)"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="98.969"
                     /coverage="100.0"
                     /evalue="1.72e-93"
     Typing          568..2120
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="87.838"
                     /coverage="98.0"
                     /evalue="0.0"
ORIGIN
        1 gcctgactgt tttcgtagtt tgggacaaaa caacctatat cagataacag ccccgtataa
       61 gcggggcttt ttttttgcag ccagcacaga atctgacata ctgcattact ctttaagcca
      121 gtacacacag cgtcccctct acgaggtgcc gtctgtgact ggttcagggg gctcgccgcc
      181 ccccgaaacc ccgggcatcc actgcgaaac tttcgcactt tgggtgcgaa tatttctcag
      241 cggagtaaga atggaaaagc gcacgagaga gatcaaaatc cgcctgactg actcagagca
      301 tcagcgtctg atcgaccggt gtgaccgaac ccatctggcc gaatggctgc gtcagctcgg
      361 tctgggagaa cacaccgcca gaaagcgccg tctgcccgat gtggcgcccg aactgctgcg
      421 acaggtcagc gggattggca acaacctgaa ccagatcgcc cgccgtctta accagctcga
      481 cggactgaat cccactgagc gtgtgtccct gctggcggtg ttaaacagcc tcgaccgcaa
      541 tctcggtgaa ctgctggagc agcaccgtga tcgttaaaat tcactcacgg ggtgccggtt
      601 cgggcagtgg ccccgttgat tacctgctgg gcaaagatcg ccagcgcagt gacgcccgcg
      661 tgttgcgggg agacgccgaa cgcacccgcg aactgattga cggctgtgac tttgcccgtg
      721 cctacacctc cggcgtgctg tcctttcagg aagccgacat tgccgagcct gaaaaggcgc
      781 gtcttatgga cgaatgggaa cagacactga tgaccggtct cgacaaagac cagtacgcct
      841 gtctgtgggt tgagcatcag gacaaaggcc gcctcgagct gaacttcgtg atcccgaaca
      901 tcgaattaca gagcgggaaa cgtctgcaac cctatttcga ccgcgccgac cgtccccgcg
      961 tcaacgcctg gcagaccctg accaacgacc ggctggggct acgcgacccg aatgacccga
     1021 cctaccgccg cccgcttacg caggccagtg atctgccccg cgacaaacag caggcggcag
     1081 agaaaatcac cgccggcctg atgaacctga tgcagcaggg cgtgatccgc agccggcagg
     1141 acgtggtgac gcagctggaa agctacggcc tgaccgtggc gcgggaaacg aaaagcagca
     1201 tcagcattgc cgatccggac ggcggcagaa atatccggct gaaaggaatg atttatgagc
     1261 gagattttaa atttggcgaa gggcttcgag gagaaatcga agcagcaggc gcaggatacc
     1321 gagcagagcg tgaagcgcga gttcgcgagg ctggagaagt ctatcagcgc ggaactgcaa
     1381 tcaagctcgc agagcatcag caacgctatc cgcgagcaga acggcaggtt gacgggcatg
     1441 ctcagaacgt cagtctcaac ggcgatggcg tggatattca tctgcttcgc cctgctgatt
     1501 ggcatcctgg gcgggataat ttggtttcaa ggcacgatca tcacctcacg cctgagcgaa
     1561 atggacagct acagtcagct gctggcgagc ctgaaagcga aaagcggcgc gggcgtgacg
     1621 atttacagcg acgaaaagaa ccggaacacc tacctggcgg tgctgccgaa gcaggcgcac
     1681 ggcgtggaaa cctacacctc gcaggccggg aataccgtgg tgaaatacac ggcgaaataa
     1741 cctcatcaga acgccctgaa tcgcgtctga gcggttttaa caccgaggat gagcaaaacc
     1801 atgaccgaga tggaaaaaca gcttctgagc gccttagaga gcttacaggc aagctacgag
     1861 caacagcagg aggcgtggca ggacagctac agcagtttgc agcacatgtt cgaggctacc
     1921 tcacaggcgc tgacgcacag cgacagggtg tgtcagcgct tgagcagtca ggtagagagc
     1981 ttgcgcgcgc aggtcgagag cttgagcagg aacgtcagcc gcttgatgcg ctgattgcgc
     2041 agcatgaccg cgcccgtgcg gaaaagctgc gcgagcaaca gccggagccg cagaaaaagc
     2101 cgacccggta ctatggcccc tcgatgtgac ctcttttccg gaatcagaat taagtgtact
     2161 atgtactccg ttagatacag gagacaaccg tgagtcacac gattgaattt atcgagaccc
     2221 cgatgtttac ccgtcagata aaacagatcg ccacggatga agagctcagg gagctgcaaa
     2281 agacgctgat tgagtcgccg gacaaaggcg atctcatcca gaaaaccggc gggctgcgaa
     2341 aagtcagaat ggcgacgggc aaccagggaa aaagcggcag cgcgagggtg atttattttc
     2401 tggccaccgc cgaggtgatt tatctggtga tggcctaccc gaaaagcacc aaagacagcc
     2461 tgacggacgc ggagaaagcc gcgctgaaga cgctgaccca acaactgaaa gacgaggtgt
     2521 gacatgagtt tttttgacga gctgaaagca tcgctggaag aagccgttga aatcaaaaac
     2581 ggcgtcagag agcctgcccg cgtcacccgt tacgagctgg cagacgtgaa ggctatcagg
     2641 gcacaactga acgtttcaca gagtgagatg gcgaaagtgc tgggaaccag cctcgacacc
     2701 ataaaaagct gggaaaccgg acgccgtaat ccgaccggac tggcggcgaa ggtgctggca
     2761 accatccagg cgaacccgaa attcttccag gagctggcgg cgcactaagc cgttgtgaca
     2821 gaaggattcg acaggcgagg ccgttcgcgt gtaatttaac ggcaacagaa aaaacaaagc
     2881 cccggcatca tgctcaaatc ttggcggatc cgcatgataa ccagggccag gtacgaaacc
     2941 ttgaaaggat attagcacat gaaacgtgcc agacaacagc ccgccataag tgcagggcgc
     3001 tttgaataac gctgcactcc aacttttcaa cgaacgctta ccgcacaagc cgtacttttc
     3061 ggacgatctg cactttggtg tacgcattgc cggtaaggag cgcgcgattc tggcgaaata
     3121 catccagttc aaccagcctc acgccatgtt ctggctcggt tttgacgttg accgtatcgg
     3181 tgccgccatc gactggagcg atcgcaatgc gcccgcgcct acgctgacca tcaccaaccc
     3241 cgaaaatggt catgctcacc tgctctatgc gctgaaaacc tcgatacgca ctgcaccaga
     3301 tggaaaaatg aagccgctga agtacgccgc tgccgtagag aacgcgctac gtaaaaaact
     3361 ggatgctgac acgggatatt cggggttaat ttgcaagaac ccgaaccatg gtcactggaa
     3421 aattgccgtc tggcagccgg aactctacac gctggactgg ctggccgact cgctcgacct
     3481 gaacgccgcg aacgataaag aaatcgttgc cgattacggc ttaggccgta actgcactct
     3541 tttcgataaa acacgcaagt gggcttaccg cgctatccgt cagggctggc cgcagtatga
     3601 gcaatggctg caagcctgct atgagcgggc cagagcttac aacctgcaat tttctgcccc
     3661 tctggatgaa aatgaagtta gtggaatagc taagagcatt gctaaatgga catacaaaaa
     3721 cttctctgaa gctaattttt tgcaatatgt tgcagatact cactcatctg aaattcaatc
     3781 gaaaagagga atgaaaagtc gaggaggggg aaggccaaag attgtcggaa gcccttggct
     3841 taatttagga atcagtcgtt ctaaatggta tagagatttt agagggttat aatgtttggt
     3901 ttttttagaa aaaaaattag cagcaatcaa gtcgacttat acgttagcga taagattcta
     3961 ggtgttgcaa agaaggttgt agccatagtt gaagctaatg gcgtaaccat cgttgatggc
     4021 gaaggtgttg tatttttagc cgctgggctt tttctcaatg ctacttatct taaggaacat
     4081 gggagaaaat cagacgctgt aagagttaaa gttattggtt ttgtaaagca ctacctagat
     4141 tcaacagatg atcaaagtat gctggaaaga ttatctgata acacccgctg gttttctcaa
     4201 gggaacatgt cgggttattg gtttcttaat caagtcattg gggacctttg cggattgaag
     4261 gttaatccca tccatcaaca aattctatca aacgaagtac tagatacact gctgaaattt
     4321 ttccacgagc gcacggtcac tatcagtaaa accctcagtg aagacatata tccattttat
     4381 aatcca
//
