LOCUS       NZ_CP042529             3223 bp    DNA     circular CON 26-JAN-2024
DEFINITION  Citrobacter freundii strain E11 plasmid pE11_005, complete sequence.
ACCESSION   NZ_CP042529
VERSION     NZ_CP042529.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN12289395
            Assembly: GCF_008931625.1
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  JOURNAL   Unpublished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 :: E11_oz_imp.uniclycerAssembly.fsa
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Reference-guided Assembly         :: na
            Genome Coverage                   :: 2355x
            Sequencing Technology             :: Oxford Nanopore MiniION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 01/24/2024 13:57:49
            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)                     :: 5,367
            CDSs (total)                      :: 5,244
            Genes (coding)                    :: 5,140
            CDSs (with protein)               :: 5,140
            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)              :: 104
            CDSs (without protein)            :: 104
            Pseudo Genes (ambiguous residues) :: 0 of 104
            Pseudo Genes (frameshifted)       :: 37 of 104
            Pseudo Genes (incomplete)         :: 64 of 104
            Pseudo Genes (internal stop)      :: 26 of 104
            Pseudo Genes (multiple problems)  :: 19 of 104
            Pseudo Genes (short protein)      :: 1 of 104
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP042529.1.
            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="E11"
                     /isolation_source="Shower 3"
                     /db_xref="taxon:546"
                     /plasmid="pE11_005"
                     /geo_loc_name="Australia: Sydney"
                     /collection_date="2012-07-03"
                     /collected_by="Concord Repatriation Hospital Sydney
                     Australia"
     gene            complement(107..439)
                     /locus_tag="FR864_RS26655"
                     /old_locus_tag="FR864_27090"
     CDS             complement(107..439)
                     /locus_tag="FR864_RS26655"
                     /old_locus_tag="FR864_27090"
                     /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(607..822)
                     /locus_tag="FR864_RS26660"
                     /old_locus_tag="FR864_27095"
     CDS             complement(607..822)
                     /locus_tag="FR864_RS26660"
                     /old_locus_tag="FR864_27095"
                     /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            complement(826..1311)
                     /locus_tag="FR864_RS26665"
                     /old_locus_tag="FR864_27100"
     CDS             complement(826..1311)
                     /locus_tag="FR864_RS26665"
                     /old_locus_tag="FR864_27100"
                     /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"
     gene            complement(<1346..2050)
                     /locus_tag="FR864_RS27165"
                     /old_locus_tag="FR864_27105"
                     /pseudo=""
     CDS             complement(<1346..2050)
                     /locus_tag="FR864_RS27165"
                     /old_locus_tag="FR864_27105"
                     /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            complement(1989..2312)
                     /locus_tag="FR864_RS26675"
                     /old_locus_tag="FR864_27110"
     CDS             complement(1989..2312)
                     /locus_tag="FR864_RS26675"
                     /old_locus_tag="FR864_27110"
                     /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            2951..3121
                     /locus_tag="FR864_RS26680"
                     /old_locus_tag="FR864_27120"
     CDS             2951..3121
                     /locus_tag="FR864_RS26680"
                     /old_locus_tag="FR864_27120"
                     /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"
     ARG             complement(108..439)
                     /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          complement(2409..2600)
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="92.821"
                     /coverage="89.0"
                     /evalue="7.28e-73"
     Typing          2580..3063
                     /name="ColRNAI_rep_cluster_1987"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="84.756"
                     /coverage="93.0"
                     /evalue="1.73e-132"
     Typing          complement(510..1999)
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="91.784"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 ccgttggtag cggtggtttt tttgtttaca gggaaaaaga ttacgcgcag aaagaaagga
       61 tctcaaggaa atccttttgc tttggccaat atgcttcggt aaaaagttaa tgcgcagaag
      121 attttgaaaa aatattaata accaaaactc caacgcaaat aaggaacatt cctgcaattg
      181 cgggccaatc aagtttttga ccgctaacca accaaccagc taggcttatt agtacaattc
      241 ccgcaccaga ccaaattgcg taagcaatac cggtaggtat attttccaat gtttgggaaa
      301 gcagataaaa ggcagcgcaa taacttattg cagttcctac agacggccac aggcgtgtaa
      361 atccttctga atatttcata aaggtggtgc ctatgacttc agccacaata gcccctccca
      421 ggaaaatata tgtattcata aaaatacctc atgttgaaaa atttaaatat ctttacataa
      481 caactaatta atagaacccg gcttatcata gcgaaggacc atgatgctgc cactgcgatc
      541 gttccagctc cagcgctttc tggtgctgca ccgcccgctc ctgctgccgg tgagtttcta
      601 tcgcgttcag cctttcgaca accggcgcag ctgctcgctc aaactctgca cctgcctgct
      661 caagaccgtg acgcgctcgt tcagcgccgc gttctcccgt tgaataagac cagacatcgt
      721 ccgccattcc gcgaaggcgt tctcccactc gtccagcctt ttcgagtagt cctgctgtag
      781 ctgctctaat gcgctcagca actgtttttc cagctccgtc atgtgctatt tccccgccag
      841 tatcatccag ctcgagtcct ctccgaactg tcccgcttcc gggttcaccc tcacgcagcg
      901 gcgtctctgc tcgccgcagg tcgagagctg tacgccgctg ttcctctctg acagcatggc
      961 ctgcgtgctc ttctgctccc ggatggtcgt atagttctcg agtatctgct gcccctgcca
     1021 ccacagaatg cccgcgctcg acgctatcag cagcgcggag accagaacga tggtcagcca
     1081 cgtctggctg accatgcgca gcatcccttt cgtgcgctgg ctcatggctg aggacagctt
     1141 ccggtcgtgg tcgaggatgg cggcgctgat tctcttctcg ctttcgctca gttccgctct
     1201 gacagacttc tcgtgctcgc tgaatgcggc tttcagcatc tcgccggtag tctgctgctg
     1261 cgctttcgat ttctgctcta agtccttcgc cagcgttaaa agactgttca tagatggctc
     1321 ccttcagtcg gatgtttcgc cccccgtccg ggtcggcaat gctgatgctg ctttttgtgg
     1381 tgcgcaccac ctcaaaacct gcgctttcca gcgcctcagt gacgtcctga cgcgttttca
     1441 gctccccgga tgaggcaagg gcaagcaggc cgttcgtaat cgcctgggcg gcttcctgct
     1501 tcgcttccgg cagcgcggaa ggcgagacca gcacccgccg gttctccggc gcgttcgggt
     1561 catgcagccc cagcctgccg ttcactatgg tctgccaggc atcgatgcgc ggacggtcgg
     1621 cgcggtcgta atacggctgt agccgcttgc cggtcagaag ctccgtgttc gggatcagga
     1681 agttcagctc cagccgcccc ttgtcccggt gctcaaccca cagcacgctg tactggtctt
     1741 tatcgagtcc gggcatcaga acccgctcga aactcgccat cagcttttcg cgctggccgg
     1801 gcggtaaatc ctgttcggca aaagacagaa cgccggaagt gtactttttg gcgtagggcg
     1861 aggcgtcgat aagctcccgg acttcatccg gcttcccctg cagaacgctg gcgccgtcgc
     1921 gctggcgatc tttacccagc agataatcga ccggcccgcc gccgccgccg cgcccccgag
     1981 gatgaaactt aacgatcatc atcagcaccc ttttccagta cggcatgccg caaccgctcg
     2041 agtccggcat cgatggccat cagcgcggcg acaatctgca cgcggtcgtg tccgcttcca
     2101 ccaccggcgt taacctggcg ggcaatctgg ttaaggttgt tccccatgcc ggcaagctga
     2161 cgaagcagcg ccggcgagat cgacggaagt ttgccggcgc gtgcgggctt ctcgtccagg
     2221 cacgtctgcc gcatccaggc cgcgagttgc ttaccctcgc agcgctccag cagacgccgg
     2281 tgctcgtcct cagtcaccca catggtgagc attttgctgc gtttgtctgc caatccggcc
     2341 tcctgataac gccgggacgg acgggaaatc ttttcccggt cggcacggtg ttggacaagc
     2401 cgcagacgcg gcagtggttt tagcgggttt cggggcgcag ccctgaacca gtcacgtagc
     2461 gctagcggag tgtatactgg ctaaacatgt tatgacggag tggtaattta tgaaagtgct
     2521 tcatgtgaca ggggaaaaat gcggctgccg ggcgtaagtg caaaatgcag gtggtgatga
     2581 aatgacgcct cctcgctcac tcggtcgcta cgctcctgcc gtgagactgc ggcgggcgtt
     2641 accagctcac agattacggg ataagcaaat gccgctcgaa gcaggaaagg ccaagaaaag
     2701 gatgcggagt tgccgttttt ccataggctc cgcccccctg acgagtatca cgaaaatgac
     2761 gctcaaatca gcggtggcga aacccgatgc ggcttaaaga taccaggcgt ttccccctgg
     2821 tggctccctc gtgctccccc gcattcctgc ctttcggttt accggtgtca ttccgctgtt
     2881 atggccgcgg tttctcattc cacgcctgaa actcggttcc gggtaggcag ttcgctccag
     2941 gatggactgt atgcacgaac cccccgttca gtccgactac cacgcccgtt ccggtaacta
     3001 tcaacttgag tccaacccgg aaagacacga caaatcgcca gtggcggtag ccattggtaa
     3061 ctgggttcac ggagcagaga ttgtagagaa tgcctacaga gttcttgaag tgaaagcctg
     3121 agtgcggcta cactgaaagg acagtttagg tatctgcgct ccgtgaaagc cagttaccat
     3181 cggaacaaag agttggtagc tctgaattcc ggcaaacgaa cca
//
