LOCUS       NZ_CP042539             3223 bp    DNA     circular CON 26-JAN-2024
DEFINITION  Citrobacter freundii strain E51 plasmid pE51_005, complete sequence.
ACCESSION   NZ_CP042539
VERSION     NZ_CP042539.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN12289332
            Assembly: GCF_008931685.1
KEYWORDS    RefSeq.
SOURCE      Citrobacter freundii
  ORGANISM  Citrobacter freundii
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Citrobacter; Citrobacter freundii complex.
REFERENCE   1  (bases 1 to 3223)
  AUTHORS   Phan,H.T.T., Stoesser,N., Gordon,K.A., Crook,D., Walker,S.A.,
            Mathers,A.J., Peto,T.E.A., George,S. and Lipworth,S.I.
  TITLE     Genomic Dynamics of Species and Mobile Genetic Elements in a
            Prolonged blaIMP-4-associated Carbapenemase Outbreak in an
            Australian Hospital
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 3223)
  AUTHORS   Phan,H.T.T.
  TITLE     Direct Submission
  JOURNAL   Submitted (01-AUG-2019) Nuffield Department of Micriobiology,
            University of Oxford, Headley Way, Oxford, Oxford OX3 7BN, United
            Kingdom
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Date                     :: SEP-2017
            Assembly Method                   :: Unicycler v. SEP-2017
            Assembly Name :: E51_oz_imp.uniclycerAssembly.fsa
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Reference-guided Assembly         :: na
            Genome Coverage                   :: 2513x
            Sequencing Technology             :: Oxford Nanopore MiniION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 01/24/2024 13:51:31
            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)                     :: 5,506
            CDSs (total)                      :: 5,383
            Genes (coding)                    :: 5,273
            CDSs (with protein)               :: 5,273
            Genes (RNA)                       :: 123
            rRNAs                             :: 9, 8, 8 (5S, 16S, 23S)
            complete rRNAs                    :: 9, 8, 8 (5S, 16S, 23S)
            tRNAs                             :: 85
            ncRNAs                            :: 13
            Pseudo Genes (total)              :: 110
            CDSs (without protein)            :: 110
            Pseudo Genes (ambiguous residues) :: 0 of 110
            Pseudo Genes (frameshifted)       :: 35 of 110
            Pseudo Genes (incomplete)         :: 75 of 110
            Pseudo Genes (internal stop)      :: 23 of 110
            Pseudo Genes (multiple problems)  :: 21 of 110
            Pseudo Genes (short protein)      :: 1 of 110
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP042539.1.
            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..3223
                     /organism="Citrobacter freundii"
                     /mol_type="genomic DNA"
                     /strain="E51"
                     /isolation_source="Shower 3"
                     /db_xref="taxon:546"
                     /plasmid="pE51_005"
                     /geo_loc_name="Australia: Sydney"
                     /collection_date="2013-04-09"
                     /collected_by="Concord Repatriation Hospital Sydney
                     Australia"
     gene            join(3124..3223,1..116)
                     /locus_tag="FR801_RS28290"
     CDS             join(3124..3223,1..116)
                     /locus_tag="FR801_RS28290"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000137421.1"
                     /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="WP_024195375.1"
                     /translation="MTELEKQLLSALEQLQQDYSKRLDEWENAFAEWRTMSGLIQRENA
                     ALNERVTVLSRQVQSLSEQLRRLSKG"
                     /name="MbeD family mobilization/exclusion protein"
     gene            284..616
                     /locus_tag="FR801_RS27750"
                     /old_locus_tag="FR801_27750"
     CDS             284..616
                     /locus_tag="FR801_RS27750"
                     /old_locus_tag="FR801_27750"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_008784643.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="EmrE family multidrug efflux SMR transporter"
                     /protein_id="WP_001099531.1"
                     /translation="MNTYIFLGGAIVAEVIGTTFMKYSEGFTRLWPSVGTAISYCAAFY
                     LLSQTLENIPTGIAYAIWSGAGIVLISLAGWLVSGQKLDWPAIAGMFLICVGVLVINIF
                     SKSSAH"
                     /name="EmrE family multidrug efflux SMR transporter"
     gene            complement(825..995)
                     /locus_tag="FR801_RS27760"
                     /old_locus_tag="FR801_27760"
     CDS             complement(825..995)
                     /locus_tag="FR801_RS27760"
                     /old_locus_tag="FR801_27760"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_005761324.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_004193911.1"
                     /translation="MHEPPVQSDYHARSGNYQLESNPERHDKSPVAVAIGNWVHGAEIV
                     ENAYRVLEVKA"
                     /name="hypothetical protein"
     gene            1634..1957
                     /locus_tag="FR801_RS27770"
                     /old_locus_tag="FR801_27770"
     CDS             1634..1957
                     /locus_tag="FR801_RS27770"
                     /old_locus_tag="FR801_27770"
                     /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="WP_004193914.1"
                     /translation="MLTMWVTEDEHRRLLERCEGKQLAAWMRQTCLDEKPARAGKLPSI
                     SPALLRQLAGMGNNLNQIARQVNAGGGSGHDRVQIVAALMAIDAGLERLRHAVLEKGAD
                     DDR"
                     /name="MobC family plasmid mobilization relaxosome protein"
     gene            2166..>2600
                     /locus_tag="FR801_RS28415"
                     /pseudo=""
     CDS             2166..>2600
                     /locus_tag="FR801_RS28415"
                     /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            2635..3120
                     /locus_tag="FR801_RS28300"
     CDS             2635..3120
                     /locus_tag="FR801_RS28300"
                     /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_025367738.1"
                     /translation="MNSLLTLAKDLEQKSKAQQQTTGEMLKAAFSEHEKSVRAELSESE
                     KRISAAILDHDRKLSSAMSQRTKGMLRMVSQTWLTIVLVSALLIASSAGILWWQGQQIL
                     ENYTTIREQKSTQAMLSERNSGVQLSTCGEQRRRCVRVNPEAGQFGEDSSWMILAGK"
                     /name="MbeB family mobilization protein"
     ARG             285..616
                     /name="qacG"
                     /gene="qacG"
                     /gene_name="small multidrug resistance (SMR) antibiotic
                     efflux pump"
                     /tool="rgi"
                     /drug_class="disinfecting agents and antiseptics"
                     /identity="41.35"
                     /coverage="102.8"
     Typing          1347..1538
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="92.821"
                     /coverage="89.0"
                     /evalue="7.28e-73"
     Typing          complement(884..1364)
                     /name="ColRNAI_rep_cluster_1987"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="84.867"
                     /coverage="93.0"
                     /evalue="1.73e-132"
     Typing          1948..3221
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="93.647"
                     /coverage="99.0"
                     /evalue="0.0"
ORIGIN
        1 ggacgatgtc tggtcttatt caacgggaga acgcggcgct gaacgagcgc gtcacggtct
       61 tgagcaggca ggtgcagagt ttgagcgagc agctgcgccg gttgtcgaaa ggctgaacgc
      121 gatagaaact caccggcagc aggagcgggc ggtgcagcac cagaaagcgc tggagctgga
      181 acgatcgcag tggcagcatc atggtccttc gctatgataa gccgggttct attaattagt
      241 tgttatgtaa agatatttaa atttttcaac atgaggtatt tttatgaata catatatttt
      301 cctgggaggg gctattgtgg ctgaagtcat aggcaccacc tttatgaaat attcagaagg
      361 atttacacgc ctgtggccgt ctgtaggaac tgcaataagt tattgcgctg ccttttatct
      421 gctttcccaa acattggaaa atatacctac cggtattgct tacgcaattt ggtctggtgc
      481 gggaattgta ctaataagcc tagctggttg gttggttagc ggtcaaaaac ttgattggcc
      541 cgcaattgca ggaatgttcc ttatttgcgt tggagttttg gttattaata ttttttcaaa
      601 atcttctgcg cattaacttt ttaccgaagc atattggcca aagcaaaagg atttccttga
      661 gatcctttct ttctgcgcgt aatctttttc cctgtaaaca aaaaaaccac cgctaccaac
      721 ggtggttcgt ttgccggaat tcagagctac caactctttg ttccgatggt aactggcttt
      781 cacggagcgc agatacctaa actgtccttt cagtgtagcc gcactcaggc tttcacttca
      841 agaactctgt aggcattctc tacaatctct gctccgtgaa cccagttacc aatggctacc
      901 gccactggcg atttgtcgtg tctttccggg ttggactcaa gttgatagtt accggaacgg
      961 gcgtggtagt cggactgaac ggggggttcg tgcatacagt ccatcctgga gcgaactgcc
     1021 tacccggaac cgagtttcag gcgtggaatg agaaaccgcg gccataacag cggaatgaca
     1081 ccggtaaacc gaaaggcagg aatgcggggg agcacgaggg agccaccagg gggaaacgcc
     1141 tggtatcttt aagccgcatc gggtttcgcc accgctgatt tgagcgtcat tttcgtgata
     1201 ctcgtcaggg gggcggagcc tatggaaaaa cggcaactcc gcatcctttt cttggccttt
     1261 cctgcttcga gcggcatttg cttatcccgt aatctgtgag ctggtaacgc ccgccgcagt
     1321 ctcacggcag gagcgtagcg accgagtgag cgaggaggcg tcatttcatc accacctgca
     1381 ttttgcactt acgcccggca gccgcatttt tcccctgtca catgaagcac tttcataaat
     1441 taccactccg tcataacatg tttagccagt atacactccg ctagcgctac gtgactggtt
     1501 cagggctgcg ccccgaaacc cgctaaaacc actgccgcgt ctgcggcttg tccaacaccg
     1561 tgccgaccgg gaaaagattt cccgtccgtc ccggcgttat caggaggccg gattggcaga
     1621 caaacgcagc aaaatgctca ccatgtgggt gactgaggac gagcaccggc gtctgctgga
     1681 gcgctgcgag ggtaagcaac tcgcggcctg gatgcggcag acgtgcctgg acgagaagcc
     1741 cgcacgcgcc ggcaaacttc cgtcgatctc gccggcgctg cttcgtcagc ttgccggcat
     1801 ggggaacaac cttaaccaga ttgcccgcca ggttaacgcc ggtggtggaa gcggacacga
     1861 ccgcgtgcag attgtcgccg cgctgatggc catcgatgcc ggactcgagc ggttgcggca
     1921 tgccgtactg gaaaagggtg ctgatgatga tcgttaagtt tcatcctcgg gggcgcggcg
     1981 gcggcggcgg gccggtcgat tatctgctgg gtaaagatcg ccagcgcgac ggcgccagcg
     2041 ttctgcaggg gaagccggat gaagtccggg agcttatcga cgcctcgccc tacgccaaaa
     2101 agtacacttc cggcgttctg tcttttgccg aacaggattt accgcccggc cagcgcgaaa
     2161 agctgatggc gagtttcgag cgggttctga tgcccggact cgataaagac cagtacagcg
     2221 tgctgtgggt tgagcaccgg gacaaggggc ggctggagct gaacttcctg atcccgaaca
     2281 cggagcttct gaccggcaag cggctacagc cgtattacga ccgcgccgac cgtccgcgca
     2341 tcgatgcctg gcagaccata gtgaacggca ggctggggct gcatgacccg aacgcgccgg
     2401 agaaccggcg ggtgctggtc tcgccttccg cgctgccgga agcgaagcag gaagccgccc
     2461 aggcgattac gagcggcctg cttgcccttg cctcatccgg ggagctgaaa acgcgtcagg
     2521 acgtcactga ggcgctggaa agcgcaggtt ttgaggtggt gcgcaccaca aaaagcagca
     2581 tcagcattgc cgacccggac ggggggcgaa acatccgact gaagggagcc atctatgaac
     2641 agtcttttaa cgctggcgaa ggacttagag cagaaatcga aagcgcagca gcagactacc
     2701 ggcgagatgc tgaaagccgc attcagcgag cacgagaagt ctgtcagagc ggaactgagc
     2761 gaaagcgaga agagaatcag cgccgccatc ctcgaccacg accggaagct gtcctcagcc
     2821 atgagccagc gcacgaaagg gatgctgcgc atggtcagcc agacgtggct gaccatcgtt
     2881 ctggtctccg cgctgctgat agcgtcgagc gcgggcattc tgtggtggca ggggcagcag
     2941 atactcgaga actatacgac catccgggag cagaagagca cgcaggccat gctgtcagag
     3001 aggaacagcg gcgtacagct ctcgacctgc ggcgagcaga gacgccgctg cgtgagggtg
     3061 aacccggaag cgggacagtt cggagaggac tcgagctgga tgatactggc ggggaaatag
     3121 cacatgacgg agctggaaaa acagttgctg agcgcattag agcagctaca gcaggactac
     3181 tcgaaaaggc tggacgagtg ggagaacgcc ttcgcggaat ggc
//
