LOCUS       NZ_CP151208             4922 bp    DNA     circular CON 17-APR-2024
DEFINITION  Citrobacter freundii strain CFTMDU plasmid p6_CFTMDU, complete
            sequence.
ACCESSION   NZ_CP151208
VERSION     NZ_CP151208.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN23449392
            Assembly: GCF_038180105.1
KEYWORDS    RefSeq.
SOURCE      Citrobacter freundii
  ORGANISM  Citrobacter freundii
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Citrobacter; Citrobacter freundii complex.
REFERENCE   1  (bases 1 to 4922)
  AUTHORS   Ota,Y.
  TITLE     Emergence of KPC-2-producing Citrobacter freundii from hospital
            sewage
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 4922)
  AUTHORS   Ota,Y.
  TITLE     Direct Submission
  JOURNAL   Submitted (26-NOV-2021) Molecular Microbiology, Tokyo Medical and
            Dental University, 1-5-45, Yushima, Bunkyo-ku 113-8510, Japan
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: Unicycler v. June-2021
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 236.0x
            Sequencing Technology             :: Illumina MiSeq; Oxford Nanopore
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_038180105.1-RS_2024_04_17
            Annotation Date                   :: 04/17/2024 11:53:04
            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)                     :: 5,881
            CDSs (total)                      :: 5,759
            Genes (coding)                    :: 5,582
            CDSs (with protein)               :: 5,582
            Genes (RNA)                       :: 122
            rRNAs                             :: 9, 8, 8 (5S, 16S, 23S)
            complete rRNAs                    :: 9, 8, 8 (5S, 16S, 23S)
            tRNAs                             :: 85
            ncRNAs                            :: 12
            Pseudo Genes (total)              :: 177
            CDSs (without protein)            :: 177
            Pseudo Genes (ambiguous residues) :: 0 of 177
            Pseudo Genes (frameshifted)       :: 46 of 177
            Pseudo Genes (incomplete)         :: 138 of 177
            Pseudo Genes (internal stop)      :: 27 of 177
            Pseudo Genes (multiple problems)  :: 31 of 177
            Pseudo Genes (short protein)      :: 1 of 177
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP151208.1.
            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..4922
                     /organism="Citrobacter freundii"
                     /mol_type="genomic DNA"
                     /strain="CFTMDU"
                     /isolation_source="sewage"
                     /db_xref="taxon:546"
                     /plasmid="p6_CFTMDU"
                     /geo_loc_name="Japan"
                     /lat_lon="35.701 N 139.764 E"
                     /collection_date="2021-06"
                     /collected_by="Tokyo Medical and Dental University"
     gene            205..396
                     /locus_tag="AADQ96_RS29375"
                     /old_locus_tag="AADQ96_29375"
     CDS             205..396
                     /locus_tag="AADQ96_RS29375"
                     /old_locus_tag="AADQ96_29375"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000166328.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="Rop family plasmid primer RNA-binding protein"
                     /protein_id="WP_025714792.1"
                     /translation="MTKQQKTALNMAKFIQNQSLLLLEKLNELDLDAEADLCEKLHDDA
                     EHLFRTLSSRLDELLDGN"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            396..806
                     /locus_tag="AADQ96_RS29380"
                     /old_locus_tag="AADQ96_29380"
     CDS             396..806
                     /locus_tag="AADQ96_RS29380"
                     /old_locus_tag="AADQ96_29380"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:YP_005229777.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="helix-turn-helix domain-containing protein"
                     /protein_id="WP_025714791.1"
                     /translation="MARVSISEAARLVKVSRPTIYKMINSGKLSYTSVVKHGKSIKVID
                     TSELIRVFGSLDGVIDDVKSDAESTGINSVGLHDLQHRIALLEAENDGLKGAVKARDEH
                     IDSLRQAMQLLEHKHEPSSPPHSPWWKFWKKS"
                     /name="helix-turn-helix domain-containing protein"
     gene            1589..1945
                     /locus_tag="AADQ96_RS29385"
                     /old_locus_tag="AADQ96_29385"
     CDS             1589..1945
                     /locus_tag="AADQ96_RS29385"
                     /old_locus_tag="AADQ96_29385"
                     /inference="COORDINATES: ab initio prediction:GeneMarkS-2+"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GeneMarkS-2+."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_025714790.1"
                     /translation="MAGNILDVFESCDLTNEKIDELISNKKTFVINNIPSSFFDQLLLR
                     IEKSIEDKSMKCRVYTEYRSAIFAAMTIPTGVTQIIGIASAIGVGIHNLVTYNPDYELA
                     KNLTSTKLGVIYKK"
                     /name="hypothetical protein"
     gene            complement(2523..>2626)
                     /locus_tag="AADQ96_RS29390"
                     /old_locus_tag="AADQ96_29390"
                     /pseudo=""
     CDS             complement(2523..>2626)
                     /locus_tag="AADQ96_RS29390"
                     /old_locus_tag="AADQ96_29390"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_086558297.1"
                     /GO_process="GO:0015074 - DNA integration [Evidence IEA]"
                     /note="frameshifted; incomplete; partial in the middle of a
                     contig; missing N-terminus; Derived by automated
                     computational analysis using gene prediction method:
                     Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="IS3 family transposase"
                     /name="IS3 family transposase"
     gene            complement(2655..3590)
                     /locus_tag="AADQ96_RS29395"
                     /old_locus_tag="AADQ96_29395"
     CDS             complement(2655..3590)
                     /locus_tag="AADQ96_RS29395"
                     /old_locus_tag="AADQ96_29395"
                     /inference="COORDINATES: ab initio prediction:GeneMarkS-2+"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GeneMarkS-2+."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_087777346.1"
                     /translation="MTAQDLINVLTILKANDSTSFSKIQRALKMSISQLEGIIDGLTAM
                     GIVYKSSFTSYSLTELTSKPVVSDGVRKAFEDIITNRGTYLSEELLQKVSTPFIPLMTH
                     EYKNAPVKVMIVGQETLGMEDAFSTIVSVDDYINESIESFNKFNFGEDLRNSHFWYAFD
                     EVVKYFNLPSRRHAYWTNLHKFQLIENDGDSVSISKLPSKDIMTMIHMQRELFLAEIKD
                     TKPDIIIYFTGGQTWVLDHYLNNGKKLAVKAIDERSHLGIIQTEFLHCPIAICTDHPSR
                     RGYTQAIVDHRANLLKYAADKFHASESARV"
                     /name="hypothetical protein"
     gene            complement(3915..4046)
                     /locus_tag="AADQ96_RS29400"
                     /old_locus_tag="AADQ96_29400"
     CDS             complement(3915..4046)
                     /locus_tag="AADQ96_RS29400"
                     /old_locus_tag="AADQ96_29400"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_005019281.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_047741455.1"
                     /translation="MHEPPVQSDCCALSGNYRLESNPERHAKAPLAAATGKQDVREM"
                     /name="hypothetical protein"
     gene            4465..4656
                     /locus_tag="AADQ96_RS29405"
                     /old_locus_tag="AADQ96_29405"
     CDS             4465..4656
                     /locus_tag="AADQ96_RS29405"
                     /old_locus_tag="AADQ96_29405"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001041614.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="Rop family plasmid primer RNA-binding protein"
                     /protein_id="WP_001041614.1"
                     /translation="MNKQQKTAVNMAKFIQDQSLLLLDRLNELDLDHEADFCEKLHEDA
                     ERLYRSLSARLNEQQDGA"
                     /name="Rop family plasmid primer RNA-binding protein"
     Typing          complement(3971..4590)
                     /name="rep_cluster_2327"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="84.772"
                     /coverage="99.0"
                     /evalue="1.1900000000000001e-169"
ORIGIN
        1 agcatgaacg gattattttt ccggactaca ggtaaactac agaaagacta caaaagctga
       61 tgacttaatc ctgattttta gtgcgatgac tacagataaa ctacaaaata actacaggat
      121 tacctcagat ccgttctctg aaccattcgt acatccgacc cccttaccgg ttttacactg
      181 agcactgatg ctctgaggtc ccttatgacg aaacaacaga aaacagcgct gaacatggct
      241 aaattcatcc agaatcagtc tctgctcctg ctggagaagc ttaacgagct tgatctcgat
      301 gctgaggccg acctttgtga gaaactccac gatgatgcgg agcatctttt ccgtacactg
      361 tcctcgagac tggatgaatt actggatggt aactgatggc cagagtgtct attagtgaag
      421 cagcacggct tgtgaaggtt agtcgcccaa ctatttacaa gatgattaac agtggtaagt
      481 taagttacac ctctgttgta aagcacggga agagtatcaa agttattgat acatcagagc
      541 ttattagggt gtttggttct cttgatggtg tcatcgatga tgtaaaaagt gacgcagaat
      601 ctacaggtat taacagcgtt ggtttacatg atttacaaca tagaatcgct ttacttgaag
      661 ctgaaaacga tggtcttaaa ggggctgtta aggctcgaga tgagcatatt gattcccttc
      721 gtcaggctat gcagcttctg gagcacaagc acgaaccttc ttcaccaccc cattccccgt
      781 ggtggaaatt ctggaaaaaa tcctgatccc gccatgcttg agttttcctc tccggccatc
      841 ccggggcgtt cctgaacctt cccaaaaatc gccagatccg ggaacactcc tcaccacgaa
      901 aaatacccac acaccacgca aaattaaaat tttgcagata actccttatt atcagttggt
      961 taggttttat taaattacgc agtattacct tctgtaaggt caatccaagt cgtcggtgat
     1021 tcgtgtacga cttaccgacg actcgtcata gagtcatcga cgactcactc cacactatca
     1081 gtaacttatg acgacttgac tctagagtcg aatcgtcgct ttggcgtttt tttgaccgtg
     1141 gtgactctag agtcaagtca cgagtcgaat cgccggtgaa tcgtgtggtg agtcgtccgg
     1201 cgacttgcca taacgtgatt gccggccgtc gacgaaccca attcctgaac gtgctgaaaa
     1261 ccggttttcc ggctgcgccg gcaacgcttc acggccacgc aatagattgc gtccccgttc
     1321 accgttttcg gatgggaaga acgccggaaa caggacttac cctggctgaa tggtgtcaat
     1381 tcccgcgcta tgcacttgtg cgcatactca tgcatgccgt aaaaacagag cctgcgcgtt
     1441 tccgggtggt ttgttgcctt tttgttggtt tcccgtcaga aacgccctga gggcctctca
     1501 gggcgtgcac gtaatgcggt attatggtaa ctttttaatt atataaactt tcatggttct
     1561 gatatttaac aaaacaaggg gttgttatat ggcaggtaac attctggatg tttttgaaag
     1621 ttgtgattta actaatgaaa agattgatga gcttattagt aataaaaaaa ccttcgtcat
     1681 aaataacatc ccttcatctt tttttgacca gttattactg cgaatagaaa aatcaattga
     1741 agataagtca atgaaatgtc gcgtatacac agagtataga agtgctattt ttgcggccat
     1801 gacaattccc acaggtgtaa cacagataat tggaatagca tctgcgatag gagttggaat
     1861 acataattta gttacttata atccagatta tgaattggcg aaaaatctaa catcaacaaa
     1921 acttggagtt atttataaaa aataaatgat ttcttttaag atgaatccaa ttcgttgatg
     1981 actctatggt gaatcgctga cgaattgccc acgattcata tgtgaatcac gctttattat
     2041 catattgtta tgatgaattg aatccagatt caattcatca ttctgggtgt tttttgttca
     2101 tagcgactct agagtcaatt cacgattcga atcgccggtg aatcgtgtgg taagtcgtcc
     2161 ggtgactcgc cataacgtga ttgccggctg tcgacgaacc cgattcctga acgtgctgaa
     2221 acggggtttc cggctgtgcc ggcaacgcct cacggccacg caataaattg cgtccccgtt
     2281 caccgttttc gggtaagaag aacatcggaa acaggactta ccccggctga atggcgtgaa
     2341 tttccgcgct atgcacttgc gcgcatactc atgcatgccg taaaaacaga gcctgcgcgt
     2401 ttctggcggg ttttcgggtg gtttgttgcc tgttttgccg gtttcccgtc agaaacgccc
     2461 tgagagcctc tcaggcggtg ctgataacgg atgttatggt aaattgaatc gccacggata
     2521 atctagacac ttccgagccg ttgataatac tggttttcat attctgtcgg tgacatgtgt
     2581 tcgctagaac catgccgacg ttactgttat aaaacatttc gatgtaagcg atcttaaatg
     2641 actctggggg gctgttaaac ccgtgccgat tcacttgcat gaaatttgtc agcagcatat
     2701 ttaagcagat tagctctatg atctacgatg gcttgagtat atccccttct actaggatgg
     2761 tcggtacata tagcgattgg gcaatgcaaa aattctgtct ggataatccc cagatgcgag
     2821 cgttcatcta ttgccttaac tgctaatttt ttaccattgt ttagataatg atctaacacc
     2881 caggtttgcc cacccgtgaa gtagatgatg atatctggct tggtatcttt aatttcagcc
     2941 aagaataatt cacgctgcat atgaatcatt gtcatgatat cttttgaagg tagtttggaa
     3001 atgctgacac tatctccatc attttcaatt aattgaaact tatgaagatt agtccaataa
     3061 gcatgccttc tggatggtag gttaaaatac tttactactt catcaaatgc ataccaaaag
     3121 tggctattcc ttaaatcttc accaaaattg aatttattga aggattcaat gctctcatta
     3181 atgtagtcat cgaccgaaac gatggtactg aaagcatctt ccattcccag agtttcttgc
     3241 cccacgatca tcactttaac tggggcattt ttgtattcgt gcgtcatcag tgggatgaat
     3301 ggtgtactta ccttttgtag tagttcttct gacaggtaag taccgcgatt ggtaatgata
     3361 tcttcgaatg cctttcttac accgtcacta acaacaggtt tagaggttaa ctcagtaagg
     3421 ctgtatgaag tgaatgatga tttatacact attcccattg cagttaaccc atcaatgatg
     3481 ccctccaact gcgaaatact catctttaac gcgcgttgaa tcttgctaaa actggttgag
     3541 tcgttggcct taagaatagt gagaacgttg attaaatctt gtgctgtcat tcctgttttc
     3601 ctcatattga actgcttcaa tgtagatacg cgtttaactc attctgacgg tcgcagtaca
     3661 ctaaatcagt aagttggcag catcaccttt ggagaacgga aatttttgta cgttaaaagg
     3721 atcttcttga gatccgtcat ttgtcgtcgt agtctcttct ccaagaaacg aaaaaaccac
     3781 ctggggaggt ggtttgatcg aaggttaggt cagttgggga actgcttaac caggtaacag
     3841 tcttgtgcga gacatgtcac caaatttgtc ctttcagtgt agccgcactc aggccatcac
     3901 ttcaagaact cttactacat ctctcgcaca tcctgcttac cagtggctgc tgccagtggc
     3961 gcttttgcat gtctttccgg gttggactca agacgatagt taccggataa ggcgcagcag
     4021 tcggactgaa cggggggttc gtgcatacag tccagcttgg agcgaactgc ctacccggaa
     4081 ctgagtgtca ggcgtggaat gagataaacg cggccataac agcggagtga caccggtaaa
     4141 ccgaaaggca ggaacaggag agcgcacgag ggagccatca gggggaaacg cctggtatct
     4201 ttatagtcct gtcgggtttc gccaccactg atttgagcgt cagatttcgt gatgcttgtc
     4261 aggggggcgg agcctatgga aaaacgcccc ggcggggcgt ggccttttcg cccttgtcct
     4321 tagctttcgt tatgcttacc gttacgttat ctgcttatct tccctccgct cgccgcagac
     4381 tcatgaccga acggagtgag cgaatgagcg aggaagcgga aaaccatcag aacgtacagt
     4441 aagcactttc gcgccggggc cttcatgaac aaacaacaaa agactgccgt taacatggct
     4501 aaattcatcc aggatcagtc cctgcttctt ctggacaggc ttaatgagct ggatctggat
     4561 catgaggctg atttctgcga gaaactccat gaggatgcgg aacgccttta ccgaagcctg
     4621 tcagcgcgcc tgaatgagca gcaggacggt gcgtaatggc tccgttgtgg gtattaccgg
     4681 agtaataccg gcatcgcctt aattttcatt gtcttggcgc ttaacattat taccccggta
     4741 atacccacaa tccctgtatt ttttcttttt tatttatttt tcatgaagtt gcgatgaaaa
     4801 tcgcagctgc gttaggtgta tgaccatttt gaggttgaaa aataatcaac catggcgggt
     4861 gatttacgca ggttaagggg cgtcggtgac aaaaaaacgt cattaacgac ctcgttcatg
     4921 cg
//
