LOCUS       NZ_CP071268             3223 bp    DNA     circular CON 04-JUN-2024
DEFINITION  Citrobacter freundii strain MEI002 plasmid p3, complete sequence.
ACCESSION   NZ_CP071268
VERSION     NZ_CP071268.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN18062620
            Assembly: GCF_023612475.1
KEYWORDS    RefSeq.
SOURCE      Citrobacter freundii
  ORGANISM  Citrobacter freundii
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Citrobacter; Citrobacter freundii complex.
REFERENCE   1  (bases 1 to 3223)
  AUTHORS   Brilhante,M., Rohrbach,H., Endimiani,A., Schuller,S. and Perreten,V.
  TITLE     Promiscuous carbapenemase-containing plasmid spreads in three
            different Enterobacteriaceae species in the outdoor areas of a
            veterinary clinic
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 3223)
  AUTHORS   Brilhante,M. and Perreten,V.
  TITLE     Direct Submission
  JOURNAL   Submitted (26-FEB-2021) Institute of Veterinary Bacteriology,
            University of Bern, Langgassstrasse 122, Bern, Bern 3012,
            Switzerland
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: Unicycler v. 0.4.8
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 100x
            Sequencing Technology :: Oxford Nanopore MinION; Illumina NovaSeq
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_023612475.1-RS_2024_06_04
            Annotation Date                   :: 06/04/2024 06:22:37
            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)                     :: 4,826
            CDSs (total)                      :: 4,706
            Genes (coding)                    :: 4,639
            CDSs (with protein)               :: 4,639
            Genes (RNA)                       :: 120
            rRNAs                             :: 9, 8, 8 (5S, 16S, 23S)
            complete rRNAs                    :: 9, 8, 8 (5S, 16S, 23S)
            tRNAs                             :: 84
            ncRNAs                            :: 11
            Pseudo Genes (total)              :: 67
            CDSs (without protein)            :: 67
            Pseudo Genes (ambiguous residues) :: 0 of 67
            Pseudo Genes (frameshifted)       :: 21 of 67
            Pseudo Genes (incomplete)         :: 42 of 67
            Pseudo Genes (internal stop)      :: 13 of 67
            Pseudo Genes (multiple problems)  :: 8 of 67
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP071268.1.
            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="MEI002"
                     /isolation_source="Outdoors environment of a veterinary
                     clinic"
                     /db_xref="taxon:546"
                     /plasmid="p3"
                     /geo_loc_name="Switzerland:Bern"
                     /collection_date="2019-08"
                     /genotype="ST22"
     gene            630..800
                     /locus_tag="J0G25_RS24060"
                     /old_locus_tag="J0G25_23985"
     CDS             630..800
                     /locus_tag="J0G25_RS24060"
                     /old_locus_tag="J0G25_23985"
                     /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            complement(1009..1341)
                     /locus_tag="J0G25_RS24065"
                     /old_locus_tag="J0G25_23990"
     CDS             complement(1009..1341)
                     /locus_tag="J0G25_RS24065"
                     /old_locus_tag="J0G25_23990"
                     /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(1509..1724)
                     /locus_tag="J0G25_RS24070"
                     /old_locus_tag="J0G25_23995"
     CDS             complement(1509..1724)
                     /locus_tag="J0G25_RS24070"
                     /old_locus_tag="J0G25_23995"
                     /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(1728..2213)
                     /locus_tag="J0G25_RS24075"
                     /old_locus_tag="J0G25_24000"
     CDS             complement(1728..2213)
                     /locus_tag="J0G25_RS24075"
                     /old_locus_tag="J0G25_24000"
                     /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(<2248..2952)
                     /locus_tag="J0G25_RS24200"
                     /old_locus_tag="J0G25_24005"
                     /pseudo=""
     CDS             complement(<2248..2952)
                     /locus_tag="J0G25_RS24200"
                     /old_locus_tag="J0G25_24005"
                     /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(2891..3214)
                     /locus_tag="J0G25_RS24085"
                     /old_locus_tag="J0G25_24010"
     CDS             complement(2891..3214)
                     /locus_tag="J0G25_RS24085"
                     /old_locus_tag="J0G25_24010"
                     /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"
     ARG             complement(1010..1341)
                     /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(88..279)
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="92.821"
                     /coverage="89.0"
                     /evalue="7.28e-73"
     Typing          259..742
                     /name="ColRNAI_rep_cluster_1987"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="84.756"
                     /coverage="93.0"
                     /evalue="1.73e-132"
     Typing          complement(1412..2901)
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="91.784"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 tttgtctgcc aatccggcct cctgataacg ccgggacgga cgggaaatct tttcccggtc
       61 ggcacggtgt tggacaagcc gcaggcgcgg cagtggtttt agcgggtttc ggggcgcagc
      121 cctgaaccag tcacgtagcg ctagcggagt gtatactggc taaacatgtt atgacggagt
      181 ggtaatttat gaaagtgctt catgtgacag gggaaaaatg cggctgccgg gcgtaagtgc
      241 aaaatgcagg tggtgatgaa atgacgcctc ctcgctcact cggtcgctac gctcctgccg
      301 tgagactgcg gcgggcgtta ccagctcaca gattacggga taagcaaatg ccgctcgaag
      361 caggaaaggc caagaaaagg atgcggagtt gccgtttttc cataggctcc gcccccctga
      421 cgagtatcac gaaaatgacg ctcaaatcag cggtggcgaa acccgatgcg gcttaaagat
      481 accaggcgtt tccccctggt ggctccctcg tgctcccccg cattcctgcc tttcggttta
      541 ccggtgtcat tccgctgtta tggccgcggt ttctcattcc acgcctgaaa ctcggttccg
      601 ggtaggcagt tcgctccagg atggactgta tgcacgaacc ccccgttcag tccgactacc
      661 acgcccgttc cggtaactat caacttgagt ccaacccgga aagacacgac aaatcgccag
      721 tggcggtagc cattggtaac tgggttcacg gagcagagat tgtagagaat gcctacagag
      781 ttcttgaagt gaaagcctga gtgcggctac actgaaagga cagtttaggt atctgcgctc
      841 cgtgaaagcc agttaccatc ggaacaaaga gttggtagct ctgaattccg gcaaacgaac
      901 caccgttggt agcggtggtt tttttgttta cagggaaaaa gattacgcgc agaaagaaag
      961 gatctcaagg aaatcctttt gctttggcca atatgcttcg gtaaaaagtt aatgcgcaga
     1021 agattttgaa aaaatattaa taaccaaaac tccaacgcaa ataaggaaca ttcctgcaat
     1081 tgcgggccaa tcaagttttt gaccgctaac caaccaacca gctaggctta ttagtacaat
     1141 tcccgcacca gaccaaattg cgtaagcaat accggtaggt atattttcca atgtttggga
     1201 aagcagataa aaggcagcgc aataacttat tgcagttcct acagacggcc acaggcgtgt
     1261 aaatccttct gaatatttca taaaggtggt gcctatgact tcagccacaa tagcccctcc
     1321 caggaaaata tatgtattca taaaaatacc tcatgttgaa aaatttaaat atctttacat
     1381 aacaactaat taatagaacc cggcttatca tagcgaagga ccatgatgct gccactgcga
     1441 tcgttccagc tccagcgctt tctggtgctg caccgcccgc tcctgctgcc ggtgagtttc
     1501 tatcgcgttc agcctttcga caaccggcgc agctgctcgc tcaaactctg cacctgcctg
     1561 ctcaagaccg tgacgcgctc gttcagcgcc gcgttctccc gttgaataag accagacatc
     1621 gtccgccatt ccgcgaaggc gttctcccac tcgtccagcc ttttcgagta gtcctgctgt
     1681 agctgctcta atgcgctcag caactgtttt tccagctccg tcatgtgcta tttccccgcc
     1741 agtatcatcc agctcgagtc ctctccgaac tgtcccgctt ccgggttcac cctcacgcag
     1801 cggcgtctct gctcgccgca ggtcgagagc tgtacgccgc tgttcctctc tgacagcatg
     1861 gcctgcgtgc tcttctgctc ccggatggtc gtatagttct cgagtatctg ctgcccctgc
     1921 caccacagaa tgcccgcgct cgacgctatc agcagcgcgg agaccagaac gatggtcagc
     1981 cacgtctggc tgaccatgcg cagcatccct ttcgtgcgct ggctcatggc tgaggacagc
     2041 ttccggtcgt ggtcgaggat ggcggcgctg attctcttct cgctttcgct cagttccgct
     2101 ctgacagact tctcgtgctc gctgaatgcg gctttcagca tctcgccggt agtctgctgc
     2161 tgcgctttcg atttctgctc taagtccttc gccagcgtta aaagactgtt catagatggc
     2221 tcccttcagt cggatgtttc gccccccgtc cgggtcggca atgctgatgc tgctttttgt
     2281 ggtgcgcacc acctcaaaac ctgcgctttc cagcgcctca gtgacgtcct gacgcgtttt
     2341 cagctccccg gatgaggcaa gggcaagcag gccgctcgta atcgcctggg cggcttcctg
     2401 cttcgcttcc ggcagcgcgg aaggcgagac cagcacccgc cggttctccg gcgcgttcgg
     2461 gtcatgcagc cccagcctgc cgttcactat ggtctgccag gcatcgatgc gcggacggtc
     2521 ggcgcggtcg taatacggct gtagccgctt gccggtcaga agctccgtgt tcgggatcag
     2581 gaagttcagc tccagccgcc ccttgtcccg gtgctcaacc cacagcacgc tgtactggtc
     2641 tttatcgagt ccgggcatca gaacccgctc gaaactcgcc atcagctttt cgcgctggcc
     2701 gggcggtaaa tcctgttcgg caaaagacag aacgccggaa gtgtactttt tggcgtaggg
     2761 cgaggcgtcg ataagctccc ggacttcatc cggcttcccc tgcagaacgc tggcgccgtc
     2821 gcgctggcga tctttaccca gcagataatc gaccggcccg ccgccgccgc cgcgcccccg
     2881 aggatgaaac ttaacgatca tcatcagcac ccttttccag tacggcatgc cgcaaccgct
     2941 cgagtccggc atcgatggcc atcagcgcgg cgacaatctg cacgcggtcg tgtccgcttc
     3001 caccaccggc gttaacctgg cgggcaatct ggttaaggtt gttccccatg ccggcaagct
     3061 gacgaagcag cgccggcgag atcgacggaa gtttgccggc gcgtgcgggc ttctcgtcca
     3121 ggcacgtctg ccgcatccag gccgcgagtt gcttaccctc gcagcgctcc agcagacgcc
     3181 ggtgctcgtc ctcagtcacc cacatggtga gcattttgct gcg
//
