LOCUS       NZ_CP139852             3361 bp    DNA     linear   CON 26-JAN-2024
DEFINITION  Citrobacter freundii strain UKJ86 plasmid pUKJ86_3.
ACCESSION   NZ_CP139852
VERSION     NZ_CP139852.1
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 3361)
  AUTHORS   Braun,S.D.
  TITLE     DRESI Project
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 3361)
  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
            CP139852.1.
            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..3361
                     /organism="Citrobacter freundii"
                     /mol_type="genomic DNA"
                     /strain="UKJ86"
                     /host="Homo sapiens"
                     /db_xref="taxon:546"
                     /plasmid="pUKJ86_3"
                     /geo_loc_name="Germany"
                     /collection_date="2017-05-12"
     gene            complement(4..219)
                     /locus_tag="U0541_RS25425"
                     /old_locus_tag="U0541_25425"
     CDS             complement(4..219)
                     /locus_tag="U0541_RS25425"
                     /old_locus_tag="U0541_25425"
                     /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_045350912.1"
                     /translation="MTELEKQLLGALEQLQQDYSKRLDEWENAFAEWRTMSGLMQRENA
                     ALSERVTVLSRQVQSLSDQLRRLSQG"
                     /name="MbeD family mobilization/exclusion protein"
     gene            complement(223..708)
                     /locus_tag="U0541_RS25430"
                     /old_locus_tag="U0541_25430"
     CDS             complement(223..708)
                     /locus_tag="U0541_RS25430"
                     /old_locus_tag="U0541_25430"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_012565228.1"
                     /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_045350913.1"
                     /translation="MNSLLTLAKDLEQKSKAQQQSTGEMLKAAFSEHEQSVRAELSESE
                     KRISAAILDHDRKLSSAMSQRTKGMLRMVSQTWLTIVLVSALLIASSAAILWWQSQQIL
                     DNYMTIREQKSTQAMLSERNSGVQLSTCGDQRRRCVRVNPEAGRFGEDSSWMILAGK"
                     /name="MbeB family mobilization protein"
     gene            complement(<743..1447)
                     /locus_tag="U0541_RS25435"
                     /old_locus_tag="U0541_25435"
                     /pseudo=""
     CDS             complement(<743..1447)
                     /locus_tag="U0541_RS25435"
                     /old_locus_tag="U0541_25435"
                     /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(1386..1709)
                     /locus_tag="U0541_RS25440"
                     /old_locus_tag="U0541_25440"
     CDS             complement(1386..1709)
                     /locus_tag="U0541_RS25440"
                     /old_locus_tag="U0541_25440"
                     /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_172843362.1"
                     /translation="MLTMWVTEDEHRRLLERCDGKQLAAWMRQTCLDEKPARAGKLPSL
                     SPALLRQLAGMGNNLNQIARQVNGGGGSGHDRVQVVAALMAIDAGLERLRHAVLEKGAD
                     DDR"
                     /name="MobC family plasmid mobilization relaxosome protein"
     gene            2349..2507
                     /locus_tag="U0541_RS25445"
                     /old_locus_tag="U0541_25445"
     CDS             2349..2507
                     /locus_tag="U0541_RS25445"
                     /old_locus_tag="U0541_25445"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_007772075.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="replication initiation protein"
                     /protein_id="WP_069678388.1"
                     /translation="MHEPPVQSDCCALSGNYRLESNPERHEKTLLAAAISNWRYTRGKL
                     RGLEVWA"
                     /name="replication initiation protein"
     gene            2793..3224
                     /locus_tag="U0541_RS25450"
                     /old_locus_tag="U0541_25450"
     CDS             2793..3224
                     /locus_tag="U0541_RS25450"
                     /old_locus_tag="U0541_25450"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_003511628.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="DUF6530 family protein"
                     /protein_id="WP_001025244.1"
                     /translation="MNIPTHLKHKPIIAVENYDRIDGPYADDTDAMGLSVGIAQWNTPG
                     YTELSAKVWRNTGEKWSRQSEELPLHRVIDLATLICIAMDYSKHGRLSSSDDFPVSRSG
                     GNPELSRHIDLMKNELKENHEHLDESLKRLAAELKRLGY"
                     /name="DUF6530 family protein"
     Typing          complement(1811..1997)
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="86.316"
                     /coverage="87.0"
                     /evalue="1.25e-50"
     Typing          1977..2461
                     /name="ColRNAI_rep_cluster_1987"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="90.612"
                     /coverage="93.0"
                     /evalue="0.0"
     Typing          complement(3..1396)
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="92.903"
                     /coverage="99.0"
                     /evalue="0.0"
ORIGIN
        1 cattcagcct tgtgacaacc ggcgcagctg atcgctcaaa ctctgcacct gcctgctcaa
       61 gaccgtgacg cgctcgctca gcgccgcgtt ctcccgttgc ataagaccag acatcgtccg
      121 ccattccgcg aaggcgttct cccactcgtc cagccttttc gagtagtcct gctgtagctg
      181 ctctaatgcg cccagcaact gtttttccag ctccgtcatg tgctatttcc ccgccagtat
      241 catccagctc gaatcctctc cgaaccgtcc cgcttccggg ttcaccctca cgcagcggcg
      301 tctctgatcg ccgcaggtcg agagctgcac gccgctgttc cgctcggaca gcatggcctg
      361 cgtgctcttc tgctcccgga tggtcatgta attgtcgagt atctgctgac tctgccacca
      421 cagaatggcc gcgctcgaag cgatcagcag cgcggagacc aggacgatgg tcagccacgt
      481 ctggctgacc atacgcagca tccctttcgt gcgctggctc atggctgagg acagcttccg
      541 gtcgtggtcg aggatggcgg cgctgattct cttctcgctt tcgctcagtt ccgctctgac
      601 agactgctcg tgctcgctga atgcggcttt cagcatctcg ccggtactct gctgctgcgc
      661 tttcgatttc tgctctaagt ccttcgccag cgttaaaaga ctgttcatag atggctccct
      721 tcagtcggat gtttcgcccc ccgtccgggt cggcaatgct gatactgctt ttcgtggtgc
      781 gcaccacctc aaaacccgcg ctttccagcg cctcagtgac gtcctgacgg gttttcagct
      841 ccccggatga ggcaagggca agcaggccgc gcgtaatagc ctgggcggcc tcctgcttcg
      901 cttccggcag cgcggacggc gtgaccagcg cccgccggtt ttccggcgcg ttcgggtcgt
      961 gcagccccag cctgccgttc actatggtct gccaggcatc gatgcgcgga cgatcggccc
     1021 ggtcgtaata cggctggaga cgcctgccgg tcagcagctc cgtgttagga atcaggaagt
     1081 tcagctccag ccgccccttg tcccggtgct caacccacag cacgctgtac tggtctttat
     1141 cgagtccggg catcagaacc cgctcaaagc tcgccatcag cttttcccgc tggccgggcg
     1201 gtaagtcctt ttcggcaaag gacaggacgc cggatgtgta ctttttggcg tagggcgagg
     1261 cgtcgataag ctcccggact tcctccggct tcccctgcag aacgctggca ccgtcgcgct
     1321 ggcggtcttt gcccagcaaa taatcccccg gaccggcgcc cccgccgcgc ccccgggggt
     1381 gaaacttaac gatcatcgtc tgcccccttt tccagcacgg cgtgccgcag ccgctcgagt
     1441 ccggcatcga tggccatcag cgcggcgacg acctgtacac ggtcgtgccc gctgccgcca
     1501 cctccgttaa cctgccgggc aatctggtta aggttgttcc ccatgccggc aagctgacga
     1561 agcagcgccg gcgagagcga aggaagttta ccggcgcggg ctggcttctc gtccaggcac
     1621 gtctgccgca tccaggctgc gagctgttta ccgtcgcagc gctccagcag acgccggtgc
     1681 tcgtcttccg ttacccacat cgtgagcatt ttgctgcgtt tgtctgccaa tccagcctcc
     1741 tgataacgcc gggacgggcg ggaaatcttt tcccggtcgg cgcggtgttg ggcaagccgc
     1801 aggcgcgaca gtggttttgg cgggtttcgg ggcgcagccc tgaaccagtc acgtagcgct
     1861 agcggagtgt atactggctt aatatgttaa atcgaagtgg aaattcagga aagtgcttca
     1921 tgtggcaggg gaaaaatgcg gctgtgggac gtaagtgcga aatactggag acgatgaaat
     1981 gacgcctcct cgctcactcg gtcgctacgc tcctgccgtg agactgcggc gggcgttacc
     2041 tgctcacgaa tagcgagata aagaggctga gcggaaatcg ggaagggctg gtaaaggatg
     2101 cggcgttgcc gtttttccat aggctccgcc ccctgacaag catcacaaaa tctgacgctc
     2161 aaatcagtgg cggcgaaacc cgacaggact ataaagatcc caggcgtttc cccctggtag
     2221 ctccctcgtg cgctctcctg ttcctgcctt tcggtttacc ggtgtcattc cgctgttatg
     2281 gccgcgtttg tctcattcca cgcctgacac tcagttccgg gaaggcagtt cgctccaagc
     2341 tggactgtat gcacgaaccc cccgttcagt ccgactgctg cgccttgtcc ggtaactatc
     2401 gtcttgagtc caacccggaa agacacgaaa aaacgctact ggcagcagcc attagtaact
     2461 ggagatatac gagaggcaaa ttgagaggtc ttgaagtatg ggcctgagag aggctacact
     2521 gaaagaacag ttttggtttc tgcggtctcg tatacccagt tacctggtta agcagttccc
     2581 caactgacct aaccttcgat caaaccacct ccccaggtgg ttttttcgtt ttcagagcaa
     2641 gagattacgc tcagccataa atgatctcaa gaagatccac tccaacaact ccaaatctgc
     2701 aagacacaaa ttgttacact tactaattag taaattaact tgttttgttg ttttatgaat
     2761 aaataaatca atttcacaca gcagagaaca atatgaacat ccctactcat ttgaaacaca
     2821 aaccgattat tgctgtagaa aactatgatc gaattgacgg cccctacgct gacgacactg
     2881 atgccatggg gctttctgtt ggaattgctc aatggaacac tcccggatat acagagctat
     2941 cagcaaaagt ctggcgcaac actggagaaa agtggtcacg gcaatctgaa gagctgcctc
     3001 ttcaccgtgt catcgatttg gcaacgctta tatgcatagc aatggattac agtaagcatg
     3061 gtcgcttatc ttccagcgac gacttcccag tcagtcgttc aggaggtaat cctgagttat
     3121 ctcgccacat tgatttgatg aagaacgaac taaaagagaa tcacgagcat ttagatgaaa
     3181 gccttaaacg tttagcagca gaactaaaac gtttaggtta ttaagtagca agccgtccat
     3241 ctgggcggct tttcttatta aagcgttggg ccgttataac ttcgctgccg agttgaacgc
     3301 tcaagttcta gcgctttttg gtgccgagcc gcgcgctcct gctcccggtg cgcctcgata
     3361 c
//
