LOCUS       CP057322                4839 bp    DNA     circular BCT 13-MAY-2022
DEFINITION  Citrobacter freundii strain RHB30-C04 plasmid pRHB30-C04_4, complete
            sequence.
ACCESSION   CP057322
VERSION     CP057322.1
DBLINK      BioProject: PRJNA605147
            BioSample: SAMN15148289
KEYWORDS    .
SOURCE      Citrobacter freundii
  ORGANISM  Citrobacter freundii
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Citrobacter; Citrobacter freundii complex.
REFERENCE   1  (bases 1 to 4839)
  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 4839)
  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                     :: RH02 T3-C04
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 132.92226518279x
            Sequencing Technology :: Hybrid: Illumina and OXFORD_NANOPORE
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI
            Annotation Date                   :: 06/19/2020 11:03:05
            Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline
            (PGAP)
            Annotation Method :: Best-placed reference protein set; GeneMarkS-2+
            Annotation Software revision      :: 4.11
            Features Annotated :: Gene; CDS; rRNA; tRNA; ncRNA; repeat_region
            Genes (total)                     :: 4,896
            CDSs (total)                      :: 4,780
            Genes (coding)                    :: 4,717
            CDSs (with protein)               :: 4,717
            Genes (RNA)                       :: 116
            rRNAs                             :: 9, 8, 8 (5S, 16S, 23S)
            complete rRNAs                    :: 9, 8, 8 (5S, 16S, 23S)
            tRNAs                             :: 84
            ncRNAs                            :: 7
            Pseudo Genes (total)              :: 63
            CDSs (without protein)            :: 63
            Pseudo Genes (ambiguous residues) :: 0 of 63
            Pseudo Genes (frameshifted)       :: 21 of 63
            Pseudo Genes (incomplete)         :: 37 of 63
            Pseudo Genes (internal stop)      :: 13 of 63
            Pseudo Genes (multiple problems)  :: 8 of 63
            ##Genome-Annotation-Data-END##
            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/
FEATURES             Location/Qualifiers
     source          1..4839
                     /organism="Citrobacter freundii"
                     /mol_type="genomic DNA"
                     /strain="RHB30-C04"
                     /isolation_source="Pooled pig faecal samples collected from
                     floor of farm"
                     /db_xref="taxon:546"
                     /plasmid="pRHB30-C04_4"
                     /geo_loc_name="United Kingdom"
                     /collection_date="2017"
     gene            complement(join(4723..4839,1..324))
                     /locus_tag="HVY72_24445"
     CDS             complement(join(4723..4839,1..324))
                     /locus_tag="HVY72_24445"
                     /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="QMF90504.1"
                     /translation="MEEKDQKEILETARVDDKDWFLQMLVGMANDGVGIGLSLNVGGLI
                     ISGTLCGGKEYFYEFGKQLGDGMYPEDADSAEEFAAAYKKIGDDVYSESEITPNPSSYI
                     HMKNALFFSPKGDSIPSNAQGALWRGKVSDVDGFSLGRFSKG"
                     /name="hypothetical protein"
     gene            565..735
                     /locus_tag="HVY72_24450"
     CDS             565..735
                     /locus_tag="HVY72_24450"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_005074609.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="QMF90499.1"
                     /translation="MSKAPIGTTASTGQKCPESGVWKVVGTPSTTAPIAKGNVMPPYDG
                     KGVTWKLTQYA"
                     /name="hypothetical protein"
     gene            complement(1268..1483)
                     /gene="mbeD"
                     /locus_tag="HVY72_24455"
     CDS             complement(1268..1483)
                     /gene="mbeD"
                     /locus_tag="HVY72_24455"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000137422.1"
                     /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="QMF90500.1"
                     /translation="MTELEKQLLSALEQLQLDYSQRLDEWESAFAEWRSMCGLMQRENA
                     MLNERVSDLSRQVQSLSEQLRRLSGN"
                     /name="mbeD"
     gene            complement(1490..1981)
                     /locus_tag="HVY72_24460"
     CDS             complement(1490..1981)
                     /locus_tag="HVY72_24460"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_015060400.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="mobilization protein"
                     /protein_id="QMF90501.1"
                     /translation="MNSLLTLAKDLEQKSKAQQQSTGEMLKAVFREHEQSVRAELSASA
                     KRISDAISAHEQSMSEAMEKNRRSVLLTAGRTWLTILMVSALLIGTSGSILWWQGQQIT
                     DNYTHLRQQEYTLAKMTARTWGVRYQESSDGRRFLILPPGMQAEAIPYDGTTWIRLKQE
                     "
                     /name="mobilization protein"
     gene            complement(1956..2669)
                     /locus_tag="HVY72_24465"
                     /pseudo=""
     CDS             complement(1956..2669)
                     /locus_tag="HVY72_24465"
                     /inference="COORDINATES: protein motif:HMM:NF015397.1"
                     /note="incomplete; partial on complete genome; 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            complement(2659..2982)
                     /locus_tag="HVY72_24470"
     CDS             complement(2659..2982)
                     /locus_tag="HVY72_24470"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000957083.1"
                     /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="QMF90505.1"
                     /translation="MLTMWVTEDEHRRLLERCDGRQLAAWMRQTCLDEKPARTGKLPSI
                     SPALLRQLAGMGNNLNQIARRVNAGGGTGHDRVQIVAALMAIDAGLERLRHAVLEKGTD
                     DDR"
                     /name="MobC family plasmid mobilization relaxosome protein"
     gene            4049..4216
                     /locus_tag="HVY72_24475"
     CDS             4049..4216
                     /locus_tag="HVY72_24475"
                     /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="QMF90502.1"
                     /translation="MNNTPKRKRALGTMIKASMSSYEIEMLVSAGKKMVDEEISALQRE
                     EGGSNAAKKH"
                     /name="hypothetical protein"
     gene            4229..4726
                     /locus_tag="HVY72_24480"
     CDS             4229..4726
                     /locus_tag="HVY72_24480"
                     /inference="COORDINATES: protein motif:HMM:NF025323.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="type II toxin-antitoxin system YafO family toxin"
                     /protein_id="QMF90503.1"
                     /translation="MPKIIVEIHQSIAHLPNIQKLKEQFIQYKSMSYEYAKDTGFAVTE
                     FLPTLSVADQEAFPPDHQMFGKDKLFEGPQRAIQEQLFHVHLFRPNQQKTYWHTDEKPV
                     MQWECTSDSALVYSHIPTSTDDSLFLFIRVIDPGAHDAYKQPGLVEKWAKLAQDYRCTV
                     RR"
                     /name="type II toxin-antitoxin system YafO family toxin"
     Typing          3245..3727
                     /name="rep_cluster_2335"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="90.909"
                     /coverage="94.0"
                     /evalue="0.0"
     Typing          complement(1177..2669)
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="90.8"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 atttttcata tggatatatg atgagggatt cggtgttatc tctgactcag agtacacatc
       61 atctccaatt tttttataag cagccgcgaa ttcctctgca ctatcagcat cttctggata
      121 cataccgtcc cctaactgct tgccgaattc ataaaaatac tctttccctc cacagagggt
      181 acccgaaatg attaacccac caacattgag tgaaagacca atacccaccc catcattagc
      241 cattccaacg agcatctgca gaaaccaatc tttgtcgtct acacgagcag tttctagtat
      301 ctctttttga tctttctctt ccatactctt ctcactttca gtattgcggg catacgcttt
      361 ttctgtcgcc acataatctt aaatccaact atcaccgaac caactctgcc aataccacaa
      421 acacatctaa tttcggttaa agcgtgacca taatcactct tgtaaaaaat gaccttactg
      481 acctcttgaa agctgattcc taaaccagac atctgtattg ctacacaaaa ggcaatacag
      541 ataaaactaa aaagaggaat cagaatgtct aaagcaccaa ttggtacaac tgcttctacc
      601 ggacaaaaat gtcctgaaag tggtgtctgg aaagtggtag gaaccccttc cactacagct
      661 ccaatcgcta aaggaaatgt aatgcctccg tacgacggaa aaggcgtaac ttggaaatta
      721 acccaatacg cttaatacgt tagtttggta aaaaaaagtc tctccggagg ctttttttta
      781 cccgcattaa acataacatc cgttgcccgc accgccccgg acaggttcgc cgcgaacggg
      841 gcggcagtca gccaaaacca acaacaaccc acccagtaaa ccaccccgat cgcgacagat
      901 aaattttacc cgactgcata gccatgcagc cagatgcatg gcgtgtaaag tcacactaaa
      961 atcagcgcca acgccttaaa aaaaggtaaa tgcttctcca gccagtccca cagctcggcc
     1021 gccagataca ggcagttaag tacagcttca atgacgttaa gcaatttcat catttccctc
     1081 caggtatagg ccgtgatctt tttgatcacg aacctattta gcgggagaaa taagagcccc
     1141 tcttcgtgcg ggttgtcagc tgcctggatg gtttaaagtg tcggcccgcg gtaggttttc
     1201 tgcggctggc gctccagctc cagtgttttc tgatactgat tatctctctg ccggcgctcg
     1261 atggcattca gttcccggac aagcggcgca gctgctcgct caaactctgc acctgcctgc
     1321 tcaagtccga cacgcgctcg ttcagcatcg cgttctcccg ttgcataagc ccacacatgc
     1381 tccgccattc cgcgaaggcg ctctcccact cgtccagcct ttgcgagtag tccagctgta
     1441 gctgctctaa tgcgctcagc aactgctttt ccagctctgt cattttccgc tactcctgtt
     1501 tcaggcggat ccaggtcgtc ccgtcgtagg ggatggcttc ggcttgcatc cccggcggca
     1561 ggataagaaa cctccggccg tcgctgctct cctgatagcg cactccccac gtccgggcgg
     1621 tcattttcgc cagggtatat tcctgctgac gaagatgtgt gtaattgtcg gttatctgct
     1681 gcccctgcca ccacagaatg ctcccgctcg tgccaatcaa cagcgctgac accatcagga
     1741 tggtgagcca tgtccgcccg gccgtcagca gcacgctccg ccggtttttc tccatcgcct
     1801 cgctcatact ctgttcgtgg gcgctgatgg cgtcgctgat tctcttcgcg cttgcgctca
     1861 gttccgctct gacagactgc tcgtgctctc tgaatacggc tttcagcatc tcgccggtac
     1921 tctgctgctg cgctttcgat ttctgctcta agtccttcgc cagcgttaaa agactgttca
     1981 tagatggctc ccttcagtcg gatgtttcgc cccccgtccg ggtcggcaat gctgatgctg
     2041 cttttcgtgg ttcgcaccac ctcaaaacct gcgctttcca gcgcctcagt gacgtcctga
     2101 cgcgttttca gctccccgga cgaggctaag gccagtaaac cccgcgtaat cgcctgagcg
     2161 gcttccagct tcgtttccgg cagcgcggac ggcgtgacca gcgcccgccg gttctccggc
     2221 gcgttcgggt cgtgcagccc cagccgaccg ttcacgatgg tctgccaggc atcaatacgc
     2281 ggacggtcgg cgcggtcgta gtacggctgg agccgcctgc cggtcagcag ctcggtattg
     2341 gggatcagaa aattcagctc cagacgcccc ttgtccgcgt gctccaccca cagaatgctg
     2401 tactgatctt tatcgagccc gggcatcaga acacgctcga agctggccat cagtttttcc
     2461 cgctggtcgg gaggcagatc tgcctccgca aacgacagta cgccggaggt gtatttcttc
     2521 acgtaaggtg acgcatcaat cagctcccgg acttcttccg gcttgccccg caggacggtg
     2581 gagccttcac gctgccggtc tttacccagc agatagtcca ccggcccggc gccaccaccg
     2641 cgaccgcgtg gatgaaattt aacgatcatc gtccgttcct ttctcaagaa cagcgtgcct
     2701 cagccgctca aggcctgcat cgattgccat cagcgccgcc acaatctgca ccctgtcatg
     2761 gccggtaccg ccgccggcgt taacacggcg ggctatctgg ttcagattgt tgcccatgcc
     2821 ggcaagctgg cgcagcagcg ccggcgagat cgagggaagc tttccggtac gcgcaggctt
     2881 ttcgtccagg caggtctgcc gcatccaagc cgccagctgt ctgccgtcac agcgctcgag
     2941 tagccgccgg tgctcgtcct ctgtcaccca catagtgagc atcttgttac gtttctctga
     3001 caaaccagcc tcctgataac gccgggacgg acgggaaagg ctttcccggt cggcgcgggg
     3061 ttggacaagc cgcaggcgcg tcagggtttt ggcgggtttc ggggcgcagc cctgaaccag
     3121 tcacatagcg ctagcggagt gtatactggc ttaaaatgta acattgcagg aacaccaagc
     3181 atagctgcca cataaagcag gtgaaaaatc agggtccggt gcgtcaggag aaaatgtact
     3241 gcgggagaaa tgccgcttcc tcgctcactg actcgctacg ctcggtcgtt cgtctgcggc
     3301 gagcggtacc ggcttacgga cgaggcagag aggtcctaga agagacttaa cgaagtgggg
     3361 agtagggcgc ggcgaagccg tttttccata ggctccgccc ccctgacgag catcacagaa
     3421 tctgacgctc gaatcagtgg tggcgaaacc cgacaggact ataaagatac caggcgtttc
     3481 cccctggtgg ctccctcgtg cgctctcctg ttcctgcctt tcggtttacc ggtgtcactc
     3541 cgctgttatg gccgcgttta tctcattcca cgcctgacac tcggttccgg gaaggcagtt
     3601 cgctccaagc tggactgtat gcacgaaccc cccgttcagt ccgaccgctg cgccttttcc
     3661 ggtaactatc gacttgagtc caacctggaa agacacgaca aaacgccact ggcagcagcc
     3721 actggtagac agaatgtgcg agagatgtat cgagagttct tgaagtggtg gccagactga
     3781 ggctacactg aaaggacgaa tttggttaca tgtctcgcac aagactgtta ccacggttag
     3841 agaatctgcc aggattaact aaccttcgaa aaaccacctg ccagggtggt tttttcgttt
     3901 ccgaggttac gcttcaaaag cagcttcagt caagagacgt tcttgttcca gtgctacaat
     3961 gaaagtgtta taacaagcac ctggctaact taaaggtcat atcgctcata aaaaaacaga
     4021 tcgttctgtc atgttatgag ggtgaattat gaacaatact ccgaaaagga aaagagctct
     4081 gggcaccatg ataaaagcct ctatgagttc ttatgaaatt gaaatgctgg tttcagctgg
     4141 caaaaagatg gtagacgaag agatctcggc cttacaaaga gaagaaggcg ggtctaatgc
     4201 ggccaaaaag cactgatgct aaagaaaaat gcctaaaatc atcgtagaaa ttcatcaaag
     4261 catcgctcat ttaccaaaca tacaaaagtt aaaagaacag ttcattcagt acaaatctat
     4321 gtcttatgag tatgccaagg acacaggctt tgcagtaact gaattcttgc caactttgtc
     4381 agtcgcagat caggaagcat tccctccaga tcaccagatg tttggaaaag ataaactctt
     4441 cgaaggtccg caaagggcga tacaagagca gctttttcac gtacatctat tcagaccgaa
     4501 tcaacaaaaa acttactggc atactgacga aaaaccagta atgcaatggg aatgcactag
     4561 cgattcagcg cttgtttact cccatatacc aacctcaaca gatgactctt tgttcttgtt
     4621 tatccgtgtt atcgatccgg gagctcatga tgcttacaag caacccggac ttgtagaaaa
     4681 atgggctaaa ctcgcacaag actacaggtg cactgtcagg cgttagcctt tagaaaaacg
     4741 ccctaagcta aatccatcaa catcagagac tttacctctc cacaatgcac cctgtgcatt
     4801 gcttggaata gagtctccct ttggagagaa aaacaacgc
//
