LOCUS       NZ_CP139851             3198 bp    DNA     linear   CON 26-JAN-2024
DEFINITION  Citrobacter freundii strain UKJ86 plasmid pUKJ86_2.
ACCESSION   NZ_CP139851
VERSION     NZ_CP139851.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN38610813
            Assembly: GCF_034422555.1
KEYWORDS    RefSeq.
SOURCE      Citrobacter freundii
  ORGANISM  Citrobacter freundii
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Citrobacter; Citrobacter freundii complex.
REFERENCE   1  (bases 1 to 3198)
  AUTHORS   Braun,S.D.
  TITLE     DRESI Project
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 3198)
  AUTHORS   Braun,S.D.
  TITLE     Direct Submission
  JOURNAL   Submitted (04-DEC-2023) Optical Molecular Diagnostics and System
            Technology, Leibniz Institute of Photonic Technology, Albert
            Einstein Strasse 9, Jena 07745, Germany
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Date                     :: 02-OCT-2020
            Assembly Method                   :: Flye v. 2.8.1-b1684
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 187.0x
            Sequencing Technology             :: Oxford Nanopore MinION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 01/24/2024 12:07:42
            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)                     :: 5,090
            CDSs (total)                      :: 4,969
            Genes (coding)                    :: 4,815
            CDSs (with protein)               :: 4,815
            Genes (RNA)                       :: 121
            rRNAs                             :: 9, 8, 8 (5S, 16S, 23S)
            complete rRNAs                    :: 9, 8, 8 (5S, 16S, 23S)
            tRNAs                             :: 83
            ncRNAs                            :: 13
            Pseudo Genes (total)              :: 154
            CDSs (without protein)            :: 154
            Pseudo Genes (ambiguous residues) :: 0 of 154
            Pseudo Genes (frameshifted)       :: 97 of 154
            Pseudo Genes (incomplete)         :: 57 of 154
            Pseudo Genes (internal stop)      :: 16 of 154
            Pseudo Genes (multiple problems)  :: 15 of 154
            Pseudo Genes (short protein)      :: 1 of 154
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP139851.1.
            Bacteria and source DNA available from Leibniz-IPHT Jena.
            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..3198
                     /organism="Citrobacter freundii"
                     /mol_type="genomic DNA"
                     /strain="UKJ86"
                     /host="Homo sapiens"
                     /db_xref="taxon:546"
                     /plasmid="pUKJ86_2"
                     /geo_loc_name="Germany"
                     /collection_date="2017-05-12"
     gene            complement(31..246)
                     /locus_tag="U0541_RS25395"
                     /old_locus_tag="U0541_25395"
     CDS             complement(31..246)
                     /locus_tag="U0541_RS25395"
                     /old_locus_tag="U0541_25395"
                     /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(250..735)
                     /locus_tag="U0541_RS25400"
                     /old_locus_tag="U0541_25400"
     CDS             complement(250..735)
                     /locus_tag="U0541_RS25400"
                     /old_locus_tag="U0541_25400"
                     /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(<770..1474)
                     /locus_tag="U0541_RS25405"
                     /old_locus_tag="U0541_25405"
                     /pseudo=""
     CDS             complement(<770..1474)
                     /locus_tag="U0541_RS25405"
                     /old_locus_tag="U0541_25405"
                     /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(1413..1736)
                     /locus_tag="U0541_RS25410"
                     /old_locus_tag="U0541_25410"
     CDS             complement(1413..1736)
                     /locus_tag="U0541_RS25410"
                     /old_locus_tag="U0541_25410"
                     /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            2376..2546
                     /locus_tag="U0541_RS25415"
                     /old_locus_tag="U0541_25415"
     CDS             2376..2546
                     /locus_tag="U0541_RS25415"
                     /old_locus_tag="U0541_25415"
                     /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(2755..3087)
                     /locus_tag="U0541_RS25420"
                     /old_locus_tag="U0541_25420"
     CDS             complement(2755..3087)
                     /locus_tag="U0541_RS25420"
                     /old_locus_tag="U0541_25420"
                     /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_016807542.1"
                     /translation="MNTYIFLGGAIVAEVIGTIFMKYSEGFTRLWPSVGTAISYCAAFY
                     LLSQTLENIPTGIAYAIWSGAGIVLISLAGWLVSGQKLDWPAIAGMFLICVGVLVINIF
                     SKSSAH"
                     /name="EmrE family multidrug efflux SMR transporter"
     ARG             complement(2756..3087)
                     /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(1833..2025)
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="92.821"
                     /coverage="89.0"
                     /evalue="2.02e-73"
     Typing          2005..2488
                     /name="ColRNAI_rep_cluster_1987"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="84.756"
                     /coverage="93.0"
                     /evalue="1.73e-132"
     Typing          complement(3..1423)
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="92.616"
                     /coverage="95.0"
                     /evalue="0.0"
ORIGIN
        1 gctcctgctg ccggtgagtt tctatcgcgt tcagcctttc gacaaccggc gcagctgctc
       61 gctcaaactc tgcacctgcc tgctcaagac cgtgacgcgc tcgttcagcg ccgcgttctc
      121 ccgttgaata agaccagaca tcgtccgcca ttccgcgaag gcgttctccc actcgtccag
      181 ccttttcgag tagtcctgct gtagctgctc taatgcgctc agcaactgtt tttccagctc
      241 cgtcatgtgc tatttccccg ccagtatcat ccagctcgag tcctctccga actgtcccgc
      301 ttccgggttc accctcacgc agcggcgtct ctgctcgccg caggtcgaga gctgtacgcc
      361 gctgttcctc tctgacagca tggcctgcgt gctcttctgc tcccggatgg tcgtatagtt
      421 ctcgagtatc tgctgcccct gccaccacag aatgcccgcg ctcgacgcta tcagcagcgc
      481 ggagaccaga acgatggtca gccacgtctg gctgaccatg cgcagcatcc ctttcgtgcg
      541 ctggctcatg gctgaggaca gcttccggtc gtggtcgagg atggcggcgc tgattctctt
      601 ctcgctttcg ctcagttccg ctctgacaga cttctcgtgc tcgctgaatg cggctttcag
      661 catctcgccg gtagtctgct gctgcgcttt cgatttctgc tctaagtcct tcgccagcgt
      721 taaaagactg ttcatagatg gctcccttca gtcggatgtt tcgccccccg tccgggtcgg
      781 caatgctgat gctgcttttt gtggtgcgca ccacctcaaa acctgcgctt tccagcgcct
      841 cagtgacgtc ctgacgcgtt ttcagctccc cggatgaggc aagggcaagc aggccgctcg
      901 taatcgcctg ggcggcttcc tgcttcgctt ccggcagcgc ggaaggcgag accagcaccc
      961 gccggttctc cggcgcgttc gggtcatgca gccccagcct gccgttcact atggtctgcc
     1021 aggcatcgat gcgcggacgg tcggcgcggt cgtaatacgg ctgtagccgc ttgccggtca
     1081 gaagctccgt gttcgggatc aggaagttca gctccagccg ccccttgtcc cggtgctcaa
     1141 cccacagcac gctgtactgg tctttatcga gtccgggcat cagaacccgc tcgaaactcg
     1201 ccatcagctt ttcgcgctgg ccgggcggta aatcctgttc ggcaaaagac agaacgccgg
     1261 aagtgtactt tttggcgtag ggcgaggcgt cgataagctc ccggacttca tccggcttcc
     1321 cctgcagaac gctggcgccg tcgcgctggc gatctttacc cagcagataa tcgaccggcc
     1381 cgccgccgcc gccgcgcccc cgaggatgaa acttaacgat catcatcagc acccttttcc
     1441 agtacggcat gccgcaaccg ctcgagtccg gcatcgatgg ccatcagcgc ggcgacaatc
     1501 tgcacgcggt cgtgtccgct tccaccaccg gcgttaacct ggcgggcaat ctggttaagg
     1561 ttgttcccca tgccggcaag ctgacgaagc agcgccggcg agatcgacgg aagtttgccg
     1621 gcgcgtgcgg gcttctcgtc caggcacgtc tgccgcatcc aggccgcgag ttgcttaccc
     1681 tcgcagcgct ccagcagacg ccggtgctcg tcctcagtca cccacatggt gagcattttg
     1741 ctgcgtttgt ctgccaatcc ggcctcctga taacgccggg acggacggga aatcttttcc
     1801 cggtcggcac ggtgttggac aagccgcaga cgcggcagtg gttttagcgg gtttcggggc
     1861 gcagccctga accagtcacg tagcgctagc ggagtgtata ctggctaaac atgttatgac
     1921 ggagtggtaa tttatgaaag tgcttcatgt gacaggggga aaaatgcggc tgccgggcgt
     1981 aagtgcaaaa tgcaggtggt gatgaaatga cgcctcctcg ctcactcggt cgctacgctc
     2041 ctgccgtgag actgcggcgg gcgttaccag ctcacagatt acgggataag caaatgccgc
     2101 tcgaagcagg aaaggccaag aaaaggatgc ggagttgccg tttttccata ggctccgccc
     2161 ccctgacgag tatcacgaaa atgacgctca aatcagcggt ggcgaaaccc gatgcggctt
     2221 aaagatacca ggcgtttccc cctggtggct ccctcgtgct cccccgcatt cctgcctttc
     2281 ggtttaccgg tgtcattccg ctgttatggc cgcggtttct cattccacgc ctgaaactcg
     2341 gttccgggta ggcagttcgc tccaggatgg actgtatgca cgaacccccc gttcagtccg
     2401 actaccacgc ccgttccggt aactatcaac ttgagtccaa cccggaaaga cacgacaaat
     2461 cgccagtggc ggtagccatt ggtaactggg ttcacggagc agagattgta gagaatgcct
     2521 acagagttct tgaagtgaaa gcctgagtgc ggctacactg aaaggacagt ttaggtatct
     2581 gcgctccgtg aaagccagtt accatcggaa caaagagttg gtagctctga attccggcaa
     2641 acgaaccacc gttggtagcg gtggtttttt tgtttacagg gaaaaagatt acgcgcagaa
     2701 agaaaggatc tcaaggaaat ccttttgctt tggccaatat gcttcggtaa aaagttaatg
     2761 cgcagaagat tttgaaaaaa tattaataac caaaactcca acgcaaataa ggaacattcc
     2821 tgcaattgcg ggccaatcaa gtttttgacc gctaaccaac caaccagcta ggcttattag
     2881 tacaattccc gcaccagacc aaattgcgta agcaataccg gtaggtatat tttccaatgt
     2941 ttgggaaagc agataaaagg cagcgcaata acttattgca gttcctacag acggccacag
     3001 gcgtgtaaat ccttctgaat atttcataaa gatggtgcct atgacttcag ccacaatagc
     3061 ccctcccagg aaaatatatg tattcataaa aatacctcat gttgaaaaat ttaaatatct
     3121 ttacataaca actaattaat agaacccggc ttatcatagc gaaggaccat gatgctgcca
     3181 ctgcgatcgt tccagctc
//
