LOCUS       NZ_CP056892             5193 bp    DNA     circular CON 26-JAN-2024
DEFINITION  Citrobacter sp. RHBSTW-00053 plasmid pRHBSTW-00053_5, complete
            sequence.
ACCESSION   NZ_CP056892
VERSION     NZ_CP056892.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN15148462
            Assembly: GCF_013796805.1
KEYWORDS    RefSeq.
SOURCE      Citrobacter sp. RHBSTW-00053
  ORGANISM  Citrobacter sp. RHBSTW-00053
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Citrobacter.
REFERENCE   1  (bases 1 to 5193)
  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 5193)
  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 T1-00053
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 85.8393625726566x
            Sequencing Technology :: Hybrid: Illumina and PACBIO_SMRT
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 01/24/2024 14:10:43
            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)                     :: 5,477
            CDSs (total)                      :: 5,361
            Genes (coding)                    :: 5,182
            CDSs (with protein)               :: 5,182
            Genes (RNA)                       :: 116
            rRNAs                             :: 9, 8, 8 (5S, 16S, 23S)
            complete rRNAs                    :: 9, 8, 8 (5S, 16S, 23S)
            tRNAs                             :: 82
            ncRNAs                            :: 9
            Pseudo Genes (total)              :: 179
            CDSs (without protein)            :: 179
            Pseudo Genes (ambiguous residues) :: 0 of 179
            Pseudo Genes (frameshifted)       :: 48 of 179
            Pseudo Genes (incomplete)         :: 138 of 179
            Pseudo Genes (internal stop)      :: 36 of 179
            Pseudo Genes (multiple problems)  :: 35 of 179
            Pseudo Genes (short protein)      :: 1 of 179
            CRISPR Arrays                     :: 1
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP056892.1.
            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..5193
                     /organism="Citrobacter sp. RHBSTW-00053"
                     /mol_type="genomic DNA"
                     /strain="RHBSTW-00053"
                     /isolation_source="Wastewater effluent sample"
                     /db_xref="taxon:2742632"
                     /plasmid="pRHBSTW-00053_5"
                     /geo_loc_name="United Kingdom"
                     /collection_date="2017"
     gene            210..542
                     /locus_tag="HV045_RS27115"
                     /old_locus_tag="HV045_27135"
     CDS             210..542
                     /locus_tag="HV045_RS27115"
                     /old_locus_tag="HV045_27135"
                     /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_077295872.1"
                     /translation="MSHAIEFIETPMFTRQIKQIATDDELKELQKALIESPDKGDLIRQ
                     TGGLRKIRMATGTQGKSGSARVIYFLATEEIIYLVMAYPKSTKDSLTDAEKADLKKLTK
                     LLKDEV"
                     /name="type II toxin-antitoxin system RelE/ParE family
                     toxin"
     gene            544..828
                     /gene="nadS"
                     /locus_tag="HV045_RS27120"
                     /old_locus_tag="HV045_27140"
     CDS             544..828
                     /gene="nadS"
                     /locus_tag="HV045_RS27120"
                     /old_locus_tag="HV045_27140"
                     /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_004088972.1"
                     /translation="MSFFDELKASLEEAVEIKNGVKAPARVTRYELADVKALRAQLNVT
                     QDEMAKVLGTSLDTIKSWETGRRNPTGLAAKVLATIQANPKFFQELASH"
                     /name="nadS"
     gene            1023..1928
                     /locus_tag="HV045_RS27125"
                     /old_locus_tag="HV045_27145"
     CDS             1023..1928
                     /locus_tag="HV045_RS27125"
                     /old_locus_tag="HV045_27145"
                     /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_103767546.1"
                     /translation="MTNLALDLFNERLPHKPYFSDDLHFGVRIAGKERAILAKYIQFNQ
                     PHAMFWLGFDVDRIGAAIDWSDRNAPAPTLTITNPENGHAHLLYALKTSIRTAPDGKMK
                     PLKYAAAVENALRKKLDADVGYSGLICKNPNHGYWKIAVWQPELYTLDWLADSLDLNAA
                     NDKEIVADYGLGRNCTLFDKTRKWAYRAIRQGWPEYDQWLQACYERASAYNIKFETPLD
                     ENEVNGIAKSIAKWTFNNFSDSDFKSYVDRTHTSEIQSIRGKKSKGGGRPVNQDSERQK
                     EPWKAIGVSRRQYYLLKTKN"
                     /name="replication initiation protein"
     gene            complement(1925..2362)
                     /locus_tag="HV045_RS27130"
                     /old_locus_tag="HV045_27150"
     CDS             complement(1925..2362)
                     /locus_tag="HV045_RS27130"
                     /old_locus_tag="HV045_27150"
                     /inference="COORDINATES: protein motif:HMM:NF027298.4"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_103767545.1"
                     /translation="MKIKDFITGLTVIALCNGVGFGALYLSKKYLFHTVTFKDNLGNLG
                     SSLVTYSTAMMALLIAMVVVIFGLDGPRLDNFKKGGYLHTTYFIYMITFLELGVTMCLS
                     LLCLSNIQSIKVASYSLTFSMITFLLIGFLGIQLLNIKKNN"
                     /name="hypothetical protein"
     gene            complement(2374..3183)
                     /locus_tag="HV045_RS27135"
                     /old_locus_tag="HV045_27155"
     CDS             complement(2374..3183)
                     /locus_tag="HV045_RS27135"
                     /old_locus_tag="HV045_27155"
                     /inference="COORDINATES: protein motif:HMM:NF027299.4"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_103791768.1"
                     /translation="MKTNYFTHRLFPSDGSVICEPLKTSFDNMIRNNQNTATMSGEYFV
                     IQHVGGDVYTFIKTNSRDVFRKLDLSNNICVDLSQILTANEKIAFASFFIVKNNLIGFS
                     NTLYSPRIGKLAEIYDLVMLARNNNHNINFEPIANQVTEQEVLNYAHVGRITMKLDKSQ
                     NLIGRLGTLFAGNVSYNDVDSFEIKIIPKRTKDIKDTFSGVMSAMPQEVTSVAVSAKEH
                     IGDVATDLNVIMSNTVCDFVNTSSTTDINTQMENNYTNNSTLRNLGY"
                     /name="hypothetical protein"
     gene            3469..3795
                     /locus_tag="HV045_RS27140"
                     /old_locus_tag="HV045_27160"
     CDS             3469..3795
                     /locus_tag="HV045_RS27140"
                     /old_locus_tag="HV045_27160"
                     /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="MobC family plasmid mobilization relaxosome
                     protein"
                     /protein_id="WP_103767548.1"
                     /translation="MEKRTREIKIRLTDSEHQRLIDRCDRTHLAEWLRQLGLGEHTARK
                     RRLPDVAPELLRQVSGIGNNLNQIARRLNQLDGLTPTDRVSLLAVLNSLDRNLSELLEQ
                     HRDR"
                     /name="MobC family plasmid mobilization relaxosome protein"
     gene            4004..>4426
                     /locus_tag="HV045_RS27675"
                     /pseudo=""
     CDS             4004..>4426
                     /locus_tag="HV045_RS27675"
                     /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            4473..4958
                     /locus_tag="HV045_RS27680"
     CDS             4473..4958
                     /locus_tag="HV045_RS27680"
                     /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_146052617.1"
                     /translation="MSEILNLAKGFEEKSKQQAQDTEQSVKREFERLETSISEDLKSSS
                     QSISNAIHEQNGRLTGMIRATATTALIWIVVCSALLIGILSGIIWLQGQIISSRLSDID
                     GYSQQLASLKAKSGAGVTIYSDDSQKNGYLVVLPVKAHGVETYTSTAGNTVVKYTAK"
                     /name="MbeB family mobilization protein"
     Typing          complement(3603..3795)
                     /name="Col(Ye4449)"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="92.268"
                     /coverage="100.0"
                     /evalue="8.220000000000004e-72"
     Typing          3786..5191
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="97.015"
                     /coverage="99.0"
                     /evalue="0.0"
ORIGIN
        1 acagcttgcg cggtcaggtc gagagcttga gcgacaatct cagccggtta atgcgctcgt
       61 aaaacagcac gaacaccagc tgaaactgga aaagcagcgt acccgctacc acggcccgac
      121 gctttagcac cgctcatacg ggatgcccac gtagacgcaa tattattttg gtgtacaatg
      181 tacatcaata atgcaaaggg aatgacacag tgagccatgc gatagagttt atcgaaacgc
      241 cgatgtttac ccgtcagata aagcaaatcg ccacggacga cgagctcaaa gagctccaga
      301 aagcgctgat tgaatcaccg gacaaaggcg atctcatcag gcaaaccggt gggctgcgaa
      361 aaatcagaat ggcgaccggc acacagggga aaagcggcag tgcgcgggtg atttactttc
      421 tggccaccga ggaaattatc tatctggtga tggcctaccc gaaaagcacc aaagacagcc
      481 tgacggacgc cgaaaaagcc gacctgaaaa agctgaccaa actactgaaa gacgaggtgt
      541 agcatgagtt tttttgacga actgaaagcg tctctggaag aagccgttga gatcaaaaat
      601 ggagttaaag caccagcccg cgtcacacgc tatgaactgg cagacgtgaa ggcacttcgc
      661 gcccagctta acgtgacgca ggatgaaatg gcgaaggtgc tcggcaccag cctcgatact
      721 atcaaaagct gggaaacagg cagacgtaat ccgaccggac tggcggcaaa ggtgctggcg
      781 accatacagg ccaaccctaa attctttcag gaacttgcct cacattaagg ctttatgacg
      841 gaaggattcg acagaagccg ccgttcgcgt gtaactttaa cggcagaaaa aacaaagccc
      901 cgataatcat gatttcaact tggcggaaga gacatgatca atcagggcta ggcataaaac
      961 ctaagaagga tattagcaca tgcacagtgc aagacaacag cccgccataa gctcaggcgt
     1021 gagtgactaa cctagccctc gacctgttca acgagcgttt accacacaaa ccgtactttt
     1081 cggacgatct gcattttggt gtacgcatcg cgggaaaaga gcgcgcgatt ctggcgaaat
     1141 acatccagtt caaccagcct catgccatgt tctggctcgg ttttgacgtt gaccgcatcg
     1201 gtgccgccat cgactggagc gatcgcaatg ccccagcgcc cacgctgacc atcaccaatc
     1261 ccgaaaacgg acacgcacac ctgctctatg cgttgaaaac ctcgatacgt accgcaccag
     1321 acggaaaaat gaagccgctg aagtacgctg ctgctgtcga gaacgcgcta cgtaaaaaac
     1381 tggacgctga cgtggggtat tcggggttaa tttgcaaaaa tccgaaccac gggtactgga
     1441 aaattgccgt ctggcagccg gaactctaca cactggactg gctggccgac tcgctcgacc
     1501 tgaacgcagc gaacgacaaa gaaatcgttg ccgactacgg cttaggccgt aactgcaccc
     1561 tgtttgataa aactcgtaag tgggcttacc gagctatccg gcagggctgg cctgagtatg
     1621 accagtggct gcaagcctgc tatgaacgtg ccagcgccta caatataaaa tttgaaacgc
     1681 cgctggacga aaatgaggtc aatggcatag ctaaaagtat agctaaatgg acttttaata
     1741 acttttctga ttctgatttt aaatcttatg tagataggac tcacactagt gaaattcaat
     1801 caattagagg taaaaagagc aaaggtggag ggcgccctgt aaatcaggat agtgaaaggc
     1861 aaaaagaacc atggaaagct attggtgtta gcagaaggca gtattacctt ctgaaaacaa
     1921 aaaattaatt atttttcttt atattcaaga gttgaatccc aaggaagcct ataagtaaaa
     1981 aagttatcat tgagaaagtt aatgagtatg atgcaacctt aatactttgt atgttagaca
     2041 agcaaagcag ggacaggcac attgtaaccc caagctcaag aaaagttatc atataaataa
     2101 aataagttgt gtgtagataa ccaccttttt taaagttatc caatctcggc ccatccaatc
     2161 caaaaatcac aacaaccata gctataagta atgccatcat tgctgttgag taggtaacca
     2221 gagacgaacc taggttacct aagttgtctt taaaggtaac cgtatggaaa aggtattttt
     2281 ttgacaggta aagcgcacca aatcccactc cattgcagag tgcgatcaca gtgaggcctg
     2341 taataaaatc ctttattttc atatacctac ctcttaataa cccaagtttc ttagagttga
     2401 gttgttagtg tagttgtttt ccatctgtgt gtttatgtct gtagtgctac tcgtatttac
     2461 aaagtcacaa acggtattgg acatgattac attcagatca gtagccacat ccccgatatg
     2521 ttccttagcg gacactgcaa ccgatgttac ttcctgaggc attgcgctca tcactcctga
     2581 gaatgtgtct ttaatgtctt ttgttctttt tggtattatc tttatctcaa aagaatcaac
     2641 atcattgtat gaaacgttac ccgcaaataa tgtgcctagg cgaccaatca gattctgaga
     2701 cttatctaac ttcattgtta ttctaccaac gtgagcatag ttaagtactt cttgttctgt
     2761 tacctgattc gctatcggtt caaaatttat attgtgatta ttgtttcttg ctaacattac
     2821 caggtcataa atttcagcta gcttacctat tcttggtgag tacaaagtat tgctaaaccc
     2881 aattaaattg ttcttaacaa tgaagaatga agcgaaggct atcttttcat ttgcggttaa
     2941 tatctgagat aaatccacac atatattatt actaagatcc agctttctaa atacatctct
     3001 actgttagtc tttatgaacg tatatacgtc accaccaacg tgctgaatta caaaatactc
     3061 accagacatt gtggctgtgt tttgattatt tctaatcata ttatcaaaac tggttttcaa
     3121 tggctcacaa ataacagaac catcagacgg gaaaagtcta tgcgtaaagt aattagtttt
     3181 catgttcaac ttgcctgtca attgttgttc gctattttcg cttatttata tttcgttttt
     3241 tgcaccaaaa caacctatat cagataacag cctcttttcg aggtcttttt ttttgcagcg
     3301 cccacagaat ctgacatact ccactatgct ttaagccagt acacacagcg tcccctctac
     3361 gaggtgccgt ctgtgactgg ttcagggggc tcgccgcccc ccgaaacccc gggcatccgc
     3421 tgcgaaactt tcgcactttg ggtgcgaata tttctcagcg gagtgagaat ggaaaagcgc
     3481 acgagagaga tcaaaatccg tctgaccgac tcagagcatc agcgtctgat agaccggtgt
     3541 gaccgaaccc atctggctga atggctgcgt cagctcggtc tgggagaaca caccgcccga
     3601 aagcgccgtc ttcctgacgt tgcgcccgaa ctgctgcgac aggtcagcgg gataggcaac
     3661 aacctcaacc agatcgcccg acgccttaac cagcttgacg ggcttacccc cactgatcgt
     3721 gtttccctgc ttgcggtgtt aaacagcctc gaccgcaatc tcagtgaact gctggagcag
     3781 caccgtgatc gttaaaattc actcacgtgg tgccggttcg ggcagtggcc ccgttgatta
     3841 cctgctgggc aaagatcgcc agcgcagtga cgcccgcgtg ctgcggggag atgctgaacg
     3901 cacacgcgaa ctgattgatg gctgtgactt tgcccgcgcc tacacatccg gcgtgctgtc
     3961 ctttcaggag gccgacattg ctgagcctga aaaggcgcgt cttatggacg aatgggaaca
     4021 gacactgatg accggtctcg acaaaaacca gtacgcctgt ctgtgggttg agcatcagga
     4081 caaaggccgc cttgagctga acttcgtgat cccgaacatc gaattgcaga gcgggaaacg
     4141 gctgcaaccc tactttgacc gcgccgaccg tcccagggta aacgcctggc agacgctgac
     4201 caacgaccga ctcggactgc gcgaccccaa tgaccccgcc tatcgccgcc cgctgacgca
     4261 ggccagcgac ctgccgcgag acaaacagca ggcagcggaa aagctgaccg ccggcctgat
     4321 gaacctgatg gcacagggcg caatacgcag ccggcaggac gtggtgactc agatcgagag
     4381 cattggtctc accgtggcgc gggaaaccaa aagcagcatc agtattgccg acccgtcagg
     4441 cggcagaaac atccggctga aaggaatgat ttatgagcga gattttaaat ttggcgaagg
     4501 gcttcgagga gaaatcgaag cagcaagcgc aggataccga gcagagcgtg aagcgcgagt
     4561 tcgagaggct ggaaacgtct atcagcgagg atttgaaatc aagctcgcag agcatcagca
     4621 acgctatcca cgaacagaac ggcaggttga cgggcatgat cagagccacg gcgaccaccg
     4681 cgctgatctg gatagtggtc tgctccgcgc tgctgattgg catcctgagt gggataatct
     4741 ggcttcaggg gcagatcatc agctcacgcc tgagcgacat cgatggctac agccagcagt
     4801 tggcgagcct gaaagcgaaa agcggcgcgg gggtgacgat ctacagcgac gacagccaga
     4861 agaacggcta tctggtggtg ctgccggtga aagcgcacgg cgtggaaacc tacacctcga
     4921 cggcgggcaa cacggtggtg aagtacaccg cgaaataacc ccgccagaac gcacagaaac
     4981 gcccctgaac gattttgacc cacaggacac agaaaaccat gaccgaaatg gaaaaacagc
     5041 ttctgagcgc cttagagagc ttacaggcca gctacgagca acagcatcag gcgtggcagg
     5101 aaagctacag cagtttgcag cacatgttcg agactacctc acaggcactg aaccgcagcg
     5161 acagggcgtg tcagcacttg agcaatcagg tga
//
