LOCUS       NZ_CP056368             5631 bp    DNA     circular CON 30-MAR-2024
DEFINITION  Citrobacter freundii strain RHBSTW-00658 plasmid pRHBSTW-00658_4,
            complete sequence.
ACCESSION   NZ_CP056368
VERSION     NZ_CP056368.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN15148674
            Assembly: GCF_013739375.1
KEYWORDS    RefSeq.
SOURCE      Citrobacter freundii
  ORGANISM  Citrobacter freundii
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Citrobacter; Citrobacter freundii complex.
REFERENCE   1  (bases 1 to 5631)
  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 5631)
  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 T2-00658
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 108.849774211442x
            Sequencing Technology :: Hybrid: Illumina and OXFORD_NANOPORE
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_013739375.1-RS_2024_03_30
            Annotation Date                   :: 03/30/2024 05:03:34
            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)                     :: 4,967
            CDSs (total)                      :: 4,846
            Genes (coding)                    :: 4,751
            CDSs (with protein)               :: 4,751
            Genes (RNA)                       :: 121
            rRNAs                             :: 9, 8, 8 (5S, 16S, 23S)
            complete rRNAs                    :: 9, 8, 8 (5S, 16S, 23S)
            tRNAs                             :: 84
            ncRNAs                            :: 12
            Pseudo Genes (total)              :: 95
            CDSs (without protein)            :: 95
            Pseudo Genes (ambiguous residues) :: 0 of 95
            Pseudo Genes (frameshifted)       :: 25 of 95
            Pseudo Genes (incomplete)         :: 63 of 95
            Pseudo Genes (internal stop)      :: 22 of 95
            Pseudo Genes (multiple problems)  :: 14 of 95
            Pseudo Genes (short protein)      :: 1 of 95
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP056368.1.
            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..5631
                     /organism="Citrobacter freundii"
                     /mol_type="genomic DNA"
                     /strain="RHBSTW-00658"
                     /isolation_source="Wastewater effluent sample"
                     /db_xref="taxon:546"
                     /plasmid="pRHBSTW-00658_4"
                     /geo_loc_name="United Kingdom"
                     /collection_date="2017"
     gene            join(5457..5631,1..110)
                     /gene="nadS"
                     /locus_tag="HV257_RS24660"
                     /old_locus_tag="HV257_24655"
     CDS             join(5457..5631,1..110)
                     /gene="nadS"
                     /locus_tag="HV257_RS24660"
                     /old_locus_tag="HV257_24655"
                     /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_003030988.1"
                     /translation="MSFFDELKASLEEAVEIKNGVRAPARVTRYELADVKAIRAQLNVS
                     QSEMAKVLGTSLDTIKSWETGRRNPTGLAAKVLATIQANPKFFQELAAH"
                     /name="nadS"
     gene            302..1204
                     /locus_tag="HV257_RS24665"
                     /old_locus_tag="HV257_24660"
     CDS             302..1204
                     /locus_tag="HV257_RS24665"
                     /old_locus_tag="HV257_24660"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_009652796.1"
                     /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_003030989.1"
                     /translation="MHNAALELFNERLPHKPYFSDDLHFGVRIAGKERAILAKYIQFNQ
                     PHAMFWLGFDVDRAGAAIDWSDRNAPAPTLTITNPDNGHAHLLYALETSIRTAPDGKMK
                     PLRYAAAVENALRKKLEADAGYSGLICKNPNHGHWKIAVWQPELYTLDWLADFLDLNAA
                     NDKEIVADYGLGRNCTLFDKTRKWAYRAIRQGWPEYDQWLQACYERASAYNLQFASPLE
                     DKEVMGIAKSISKWTEKNFTASSFKEYVINSHKSDIQSKRGRLGGLKSKGGGRPTINSP
                     WKDMGISKSTYYRNIHDKR"
                     /name="replication initiation protein"
     gene            1191..2951
                     /locus_tag="HV257_RS24670"
                     /old_locus_tag="HV257_24665"
     CDS             1191..2951
                     /locus_tag="HV257_RS24670"
                     /old_locus_tag="HV257_24665"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_009652795.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="AIPR family protein"
                     /protein_id="WP_003030990.1"
                     /translation="MTRDDFNSDTRTVGLARLANSLEETYGSFINMENTNSKGEARREV
                     LITRCIAAHAVRMYGDELDPEVAAASVCDGSDDGGVDAVYVNPSSKKLILVQSKYIKDG
                     NGSVTIKDFGRFKDACAKVVANDLNSFNDRFLEHKESVTTAITSSSYKCICVFIYSGTQ
                     GLSSEVIGEIDFWEKSQNKALLFRDLESRDEYTILFETPNVTDISTSLSNQSTGAIDIS
                     NVILESYGEITEPYGAIYGTIAARVIHDWWKKYKYALFEKNIRSVLGDSTSVNAGIMST
                     IENSPENFWYYNNGITATYEEVDESIANAGASRKIGIFGFKKLNIINGAQTVSSIGAIF
                     DSIPEEKKDKARVMIRFINAKDPVFLGDVTKYNNTQNRVTGRDFTTQRPEQQKIQREIN
                     FVGGYTYKLLRQEDSGIAASNVIDIDDSLNALICASKKPQLIATLKSNRGRFFDTTEGN
                     LYEQVFNPRNPPSGLSVINAVNLYRVCFDVLKDTITNASNSSEEEYSKIPSLLTHGNYV
                     FISILMGKIQPTNTVNDINTYDKNSVSVDTLELAKSIFEYIQSNYPNSYLARFFQNKEK
                     VEQIITHFSA"
                     /name="AIPR family protein"
     gene            3178..3504
                     /locus_tag="HV257_RS24675"
                     /old_locus_tag="HV257_24670"
     CDS             3178..3504
                     /locus_tag="HV257_RS24675"
                     /old_locus_tag="HV257_24670"
                     /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_003030983.1"
                     /translation="MEKRTKEIKIRLTETEHQRLLDRCDRTHLAEWLRQLGLGEHTSRK
                     RRVPDVAPELLRQVSGIGNNLNQIARRLNQTDSLTPSERASLLIVLTSLDRQLGDLLEQ
                     NRDR"
                     /name="MobC family plasmid mobilization relaxosome protein"
     gene            3713..>4135
                     /locus_tag="HV257_RS24970"
                     /pseudo=""
     CDS             3713..>4135
                     /locus_tag="HV257_RS24970"
                     /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            4182..4667
                     /locus_tag="HV257_RS24975"
     CDS             4182..4667
                     /locus_tag="HV257_RS24975"
                     /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_145981112.1"
                     /translation="MSEILNLAKGFEEKSKQQAQDTEQSVKREFARLETSISAELQSSS
                     QSISNAIREQNGRLTGMIRTSVSTAMMWIFLCFALLIGILGGIIWFQGTIITSRLSEMD
                     SYSQQLASLKAKSGAGVTIYSDDTRRNTYLVVLPKQAHGVETYTSTTDNTVVKYTAK"
                     /name="MbeB family mobilization protein"
     gene            4737..4961
                     /locus_tag="HV257_RS24685"
                     /old_locus_tag="HV257_24680"
     CDS             4737..4961
                     /locus_tag="HV257_RS24685"
                     /old_locus_tag="HV257_24680"
                     /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_029498753.1"
                     /translation="MEKQLLSALESLQTSYEQQQQAWQDSYSSLQHMFEATSQALTHSD
                     RVCQHLSSQVDSLRAQVESLSRNVSRLMR"
                     /name="MbeD family mobilization/exclusion protein"
     gene            5123..5455
                     /locus_tag="HV257_RS24690"
                     /old_locus_tag="HV257_24685"
     CDS             5123..5455
                     /locus_tag="HV257_RS24690"
                     /old_locus_tag="HV257_24685"
                     /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_181548356.1"
                     /translation="MSHAIEFIETPMFTRQIKQIATDEELRELQKTLIESPDKGDLIQK
                     TGGLRKVRMATGNQGKSGSARVIYFLATAEVIYLVMAYPKSTKDSLTGAEKAALKMLTQ
                     QLKDEV"
                     /name="type II toxin-antitoxin system RelE/ParE family
                     toxin"
     Typing          3495..5059
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="93.103"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 ctatcaagag ctgggaaacc ggacgccgca atccgaccgg actggcggca aaggtgctgg
       61 caaccatcca ggcaaacccg aaattcttcc aggagctggc ggcgcactaa gccgttgtga
      121 cagaaggatt cgacaggcga ggccgttcgc gtgtaattta acggcaacag aaaaaacaaa
      181 gccccggcat catgtctaat cttggcggat ccgcatgata accagggcca ggtcgaaacc
      241 ttgaaaggat attagcacat gaaccgtgcc agacaacagc ccgccataag cgcagggcgc
      301 attgcataac gccgcactcg aactcttcaa cgaacgctta ccgcacaagc cgtacttttc
      361 ggacgatctg cactttggtg tacgcattgc cggtaaggaa cgcgccattc tggcgaaata
      421 cattcagttc aatcagcctc acgccatgtt ctggctggga ttcgacgtcg atcgcgccgg
      481 tgccgccatc gactggagcg accgtaacgc ccccgcgccc acgctgacca tcaccaaccc
      541 cgacaacgga cacgcgcacc tgctgtacgc gttggaaacc tcgatacgca ccgcgccgga
      601 cggaaaaatg aagccgctgc gctacgccgc tgccgtggag aacgcgctac gtaaaaaatt
      661 agaggctgac gcggggtatt cggggctaat ctgtaaaaat ccgaaccacg ggcactggaa
      721 aattgccgta tggcagccgg aactctacac actggactgg ttagccgatt ttctcgatct
      781 gaacgcggcg aacgacaaag agattgtcgc cgactacggc ctgggtcgta actgcacgtt
      841 gttcgacaaa actcgcaagt gggcataccg cgccatccgt cagggctggc ctgagtacga
      901 ccagtggttg caagcctgtt acgaaagagc cagcgcttac aacctacaat ttgcttctcc
      961 tttagaggat aaagaagtaa tgggcattgc aaaaagcata tcaaaatgga ctgaaaaaaa
     1021 ctttacggca tcttcattta aagagtacgt cattaactct cataagagtg atattcaatc
     1081 taagagaggc cgcttaggcg gattaaaaag caaaggtggc gggcggccaa caataaactc
     1141 cccgtggaaa gatatgggga ttagtaaatc gacatattat aggaatatcc atgacaagag
     1201 atgattttaa tagcgacact agaaccgttg gacttgcaag gttagctaat agcctagaag
     1261 aaacctatgg ttcttttatt aatatggaaa ataccaactc taaaggtgag gctagaagag
     1321 aggttctgat cacaagatgt attgctgcgc atgcagtgag gatgtatggt gatgaactcg
     1381 accctgaagt tgctgctgca tcagtttgcg atggtagcga tgatggggga gttgatgctg
     1441 tttatgtaaa cccaagctct aaaaaactta ttttggtgca gtcaaagtac ataaaagatg
     1501 ggaatgggtc tgtaacaata aaagattttg gacgctttaa agatgcatgt gcaaaagttg
     1561 tagctaacga tctcaattca tttaatgata ggtttttaga gcacaaagaa tcagtgacta
     1621 ctgctatcac tagtagtagc tataaatgta tatgcgtttt tatttactca gggacccaag
     1681 ggttaagctc agaagttatt ggagagattg atttttggga gaaaagccaa aataaagctc
     1741 tgttgtttag ggatttagaa tctagggatg agtatacaat actatttgaa acgcctaatg
     1801 ttactgacat atctactagc ttgagtaatc aatctaccgg agctatagat ataagtaatg
     1861 taatattaga gtcgtatggt gagatcactg aaccttacgg cgcaatctac ggaacgattg
     1921 ctgcaagggt gatacatgat tggtggaaaa aatacaaata tgcgcttttt gagaaaaaca
     1981 taaggagtgt attgggtgat tcgacatcag taaatgcagg aattatgtct accatcgaaa
     2041 atagcccgga gaatttttgg tattataaca atgggattac tgcgacatat gaagaggtag
     2101 atgagagcat agctaatgct ggagcatctc gtaaaattgg aatattcgga tttaaaaagt
     2161 taaatataat aaatggggcg caaactgtaa gctctattgg agctatattt gatagtatac
     2221 ccgaggaaaa aaaagacaaa gctcgggtaa tgattaggtt tataaatgcg aaagatccag
     2281 tgtttttagg tgacgtaact aagtacaaca atactcagaa tagagttact ggcagagatt
     2341 tcacgacaca aagacctgaa caacaaaaaa tacagagaga aataaatttc gttgggggtt
     2401 atacatataa gctcttgcga caggaagatt cagggatagc tgcttctaat gtgatcgata
     2461 tagatgattc attaaatgca ctaatttgcg catcaaagaa acctcaactg attgcaacgt
     2521 tgaagtctaa tagaggtcgt ttttttgata caacagaagg caatctttac gaacaagttt
     2581 tcaacccaag aaatccgcca tccggtcttt ctgttatcaa tgctgtcaat ttgtacagag
     2641 tgtgcttcga tgttttaaaa gatacaatta ctaacgcatc taactcatca gaagaagagt
     2701 atagtaaaat tccatcattg ctgacgcatg gtaactatgt attcatcagt attttaatgg
     2761 gtaaaataca acccacaaat acagttaatg acataaacac ctatgacaag aatagcgttt
     2821 ctgttgatac tcttgaacta gctaaaagca tatttgaata catccagtct aattatccta
     2881 atagttatct ggctagattt ttccagaaca aagaaaaagt agagcagatc atcactcact
     2941 tttcagcgtg agactaaaca agcctatatc agataacagc cctctctagc ggagggcttt
     3001 tttttgcagc cagcacggaa tctgtcatac tgcactttac tttaagccag tacacacagc
     3061 gtcccctcta tgaggtgccg tctgtgactg gttcaggggg ctcgccgccc cccgaaaccc
     3121 ctggcatcca ctgcgaaaaa ttctcacagt ggtgcgaatt tcttctcagc ggaacctatg
     3181 gaaaagcgaa cgaaagagat caaaatccgg cttaccgaaa ccgagcatca gcgactgctt
     3241 gatcgctgcg accggactca ccttgcggag tggcttcgtc agcttggtct gggtgaacac
     3301 acctcacgca agcgccgtgt tcccgacgtg gcacctgaac tgctgcgaca ggtcagcggg
     3361 attggcaaca acctgaacca gatagcccgc cgcctgaacc agactgattc cctgacgcct
     3421 tctgaacgtg cctcgctgct catcgtactg accagccttg accgtcagct tggcgacctg
     3481 ctggagcaga accgtgatcg ttaaaattca ttcgcggggt gcgggttcgg gcagcgggcc
     3541 ggtggattac ctgctgggaa aagaccggca gcgcgaacat gccagcgttc tgcgcggcaa
     3601 tcctgagtac gtacgcgagc tgatcgacgg ctgcgatttt gcccgcgcct acacctccgg
     3661 cgtgctgtca tttcaggagc cggatattgc agacgccgag aaatcgcgcc tgatggatga
     3721 atgggagcat acgctgctga ccggccttga ccgcgaccag tacacctgcc tgtgggtaga
     3781 gcaccgcgac aaggggcggc ttgagctgaa ttttgtcatc ccgaacatcg aattgcagag
     3841 cggcaaacgc ctgcaacctt actttgaccg cgccgaccgt ccccgcgtca acgcctggca
     3901 gaccctgacc aatgaccggc tggggttgcg cgatccgaac gacccgactt tccgccgccc
     3961 gttgacgcag gccagcgatc ttccccgcga caaacagcag gcggcagaga aaatcactgt
     4021 cggcctgatg aacctgatgc agcagggcgt gatccgcagc cggcaggacg tagtggcgca
     4081 gcttgaaagc tacggcctga ccgtagcgcg ggaaacgaaa agcagcatca gtattgccga
     4141 tccggacggc ggtcgaaata tccggctgaa aggaatgatt tatgagcgag attttaaatt
     4201 tggcgaaggg cttcgaggag aaatcgaagc agcaggcgca ggataccgag cagagcgtga
     4261 agcgcgagtt cgcgaggctg gagacgtcta tcagcgcgga actgcaatca agctcgcaga
     4321 gcatcagcaa cgctatccgc gagcagaacg gcaggctgac gggcatgata agaacctccg
     4381 tctcaacggc gatgatgtgg atatttctct gtttcgccct gctgatcggc atcctgggcg
     4441 ggataatctg gtttcagggc acgatcatca cctcgcgcct gagcgaaatg gacagctaca
     4501 gccagcagct ggcgagcctg aaagcgaaaa gcggcgcggg cgtgacgatt tacagcgacg
     4561 acacgcgtcg gaacacctac ctggtggtgc tgccgaagca ggcgcacggc gtagaaacct
     4621 acacctcgac gaccgacaac accgtggtga aatatacggc gaaataaccc cgtcagagcg
     4681 ccctgaaacg ccacagcacg tttttaacac cgaggacgac caaaaccatg accgagatgg
     4741 aaaaacagct tctgagcgcc ttagagagct tacagacaag ctacgaacaa cagcagcagg
     4801 cgtggcagga cagctacagc agtttgcagc acatgttcga ggctacctca caggcgctga
     4861 cgcacagcga ccgggtgtgt cagcacttga gcagtcaggt ggacagcttg cgcgcgcagg
     4921 tcgagagctt gagcaggaac gtcagccgct tgatgcgctg atcaggcagc atgatcgcgc
     4981 ctacgcggag aagctgcgcg atcagcagcc ggaaccggag ccacagaaaa aaccgacccg
     5041 ctactatggt ccctcgatgt gaccgctttt ccgaaatcag agtttggtgt actatgtacc
     5101 ccattaaaaa caggagacag tcgtgagtca cgcgattgag tttatcgaga ccccgatgtt
     5161 tacccgtcag ataaaacaga tcgccacgga tgaagagctc agggagctgc aaaagacgct
     5221 gattgagtcg ccggacaaag gcgatctcat ccagaaaacc ggcgggctgc gaaaagtcag
     5281 aatggcgacg ggcaaccagg gaaaaagcgg tagcgcgagg gtgatttatt ttctggccac
     5341 cgccgaggtt atttatctgg tgatggccta cccgaaaagc accaaagaca gtctgacggg
     5401 cgcggagaaa gccgcgctga agatgctgac ccaacaactg aaagatgagg tgtgacatga
     5461 gtttttttga cgagctgaaa gcatcgctgg aagaagccgt tgaaatcaaa aacggcgtca
     5521 gagcgcccgc ccgcgtcacc cgttacgagc tggcagacgt gaaggccatc agggcacagc
     5581 tgaacgtttc acagagcgag atggcgaaag tgctgggaac cagcctcgac a
//
