LOCUS       NZ_CP137190             3428 bp    DNA     circular CON 31-JAN-2024
DEFINITION  Citrobacter freundii strain F1917 plasmid pF1917-9, complete
            sequence.
ACCESSION   NZ_CP137190
VERSION     NZ_CP137190.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN37933681
            Assembly: GCF_036289145.1
KEYWORDS    RefSeq.
SOURCE      Citrobacter freundii
  ORGANISM  Citrobacter freundii
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Citrobacter; Citrobacter freundii complex.
REFERENCE   1  (bases 1 to 3428)
  AUTHORS   Li,X.
  TITLE     Citrobacter freundii F1917 Genome sequencing and assembly
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 3428)
  AUTHORS   Li,X.
  TITLE     Direct Submission
  JOURNAL   Submitted (23-OCT-2023) Laboratory Medicine Center, Department of
            Clinical Laboratory, Zhejiang Provincial People's Hospital
            (Affiliated People's Hospital, Hangzhou Medical College), Shangtang
            road, Hangzhou 310014, China
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: unicycler v. v0.4.8
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 200.0x
            Sequencing Technology             :: Oxford Nanopore
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 01/31/2024 02:12:19
            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)                     :: 5,708
            CDSs (total)                      :: 5,588
            Genes (coding)                    :: 5,456
            CDSs (with protein)               :: 5,456
            Genes (RNA)                       :: 120
            rRNAs                             :: 9, 8, 8 (5S, 16S, 23S)
            complete rRNAs                    :: 9, 8, 8 (5S, 16S, 23S)
            tRNAs                             :: 83
            ncRNAs                            :: 12
            Pseudo Genes (total)              :: 132
            CDSs (without protein)            :: 132
            Pseudo Genes (ambiguous residues) :: 0 of 132
            Pseudo Genes (frameshifted)       :: 31 of 132
            Pseudo Genes (incomplete)         :: 94 of 132
            Pseudo Genes (internal stop)      :: 25 of 132
            Pseudo Genes (multiple problems)  :: 17 of 132
            Pseudo Genes (short protein)      :: 1 of 132
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP137190.1.
            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..3428
                     /organism="Citrobacter freundii"
                     /mol_type="genomic DNA"
                     /strain="F1917"
                     /isolation_source="urine"
                     /host="Homo sapiens"
                     /db_xref="taxon:546"
                     /plasmid="pF1917-9"
                     /geo_loc_name="China: Hangzhou"
                     /lat_lon="29.86 N 121.56 E"
                     /collection_date="2017-11-22"
                     /collected_by="Jiayao Yao"
     gene            complement(join(3278..3428,1..113))
                     /locus_tag="R4T16_RS26500"
                     /old_locus_tag="R4T16_26480"
     CDS             complement(join(3278..3428,1..113))
                     /locus_tag="R4T16_RS26500"
                     /old_locus_tag="R4T16_26480"
                     /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_138627904.1"
                     /translation="MPLEQAAFLFSGVGGMLLTEMEISNTRNITLIARRLAWINAKRTH
                     IDIPSFAELLFSGQKALFFEQYNYFHSRRYTTAGTSKPPDLP"
                     /name="hypothetical protein"
     gene            complement(652..1349)
                     /locus_tag="R4T16_RS26505"
                     /old_locus_tag="R4T16_26485"
     CDS             complement(join(652..1100,1100..1349))
                     /locus_tag="R4T16_RS26505"
                     /old_locus_tag="R4T16_26485"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_086558153.1"
                     /ribosomal_slippage=""
                     /GO_function="GO:0004803 - transposase activity [Evidence
                     IEA]"
                     /note="programmed frameshift; Derived by automated
                     computational analysis using gene prediction method:
                     Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="IS1 family transposase"
                     /protein_id="WP_094106546.1"
                     /translation="MASISIRCPSCSATEGVVRNGKSTAGHQRYLCSHCRKTWQLQFTY
                     TASQPGTHQKIIDMAMNGVGCRASARIMGVGLNTVLRHFKKLRPQSVTSRIQPGSDVIV
                     CAEMDEQWGYVGAKSRQRWLFYAYDRIRRTVVAHVFGERTLATLERLLSLLSAFEVVVW
                     MTDGWPLYESRLKGKLHVISKRYTQRIERHNLNLRQHLARLGRKSLSFSKSVELHDKVI
                     GHYLNIKHYQ"
                     /name="IS1 family transposase"
     gene            2238..>2333
                     /locus_tag="R4T16_RS26510"
                     /old_locus_tag="R4T16_26490"
                     /pseudo=""
     CDS             2238..>2333
                     /locus_tag="R4T16_RS26510"
                     /old_locus_tag="R4T16_26490"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000957083.1"
                     /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="plasmid mobilization relaxosome protein MobC"
                     /name="plasmid mobilization relaxosome protein MobC"
     gene            complement(2898..3086)
                     /locus_tag="R4T16_RS26515"
                     /old_locus_tag="R4T16_26495"
     CDS             complement(2898..3086)
                     /locus_tag="R4T16_RS26515"
                     /old_locus_tag="R4T16_26495"
                     /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_024157493.1"
                     /translation="MNRQESAVLNIAKFIRAQTLLLLERIDLLDFDDEATDCEQLHEQA
                     EALYRKLSARLESDITA"
                     /name="Rop family plasmid primer RNA-binding protein"
     Typing          2048..2132
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="91.954"
                     /coverage="100.0"
                     /evalue="1.43e-25"
ORIGIN
        1 caggcaagac gccgggcaat aagcgtaata ttccgggtgt tacttatttc catttctgtc
       61 aacagcatcc cccccacgcc ggagaataaa aaagccgcct gttccagcgg caagccctac
      121 atcaagggaa actacgtctt acgattcgtt ttgaaccggg acgctttgtt gctgcgaatc
      181 actaaccaga taatccacgt tttgtgagtg ggtttaggtt aaggcttcaa tagaacaata
      241 ataacgttaa gtgattaggg caacctgtga ttgctaaaat gatgaagtct tcacatcatt
      301 tcggtgaagg cgatatgtgt tacaccacgt attgagagac ctgcatgccc tttacaggtg
      361 aacgggaacg ggaatagagc ggcgatttag ccagagatgg gtttcataac actgtaattc
      421 atatcacaat tattataact ggcggtattt ttttaacctt tgcaattcgt tttatctgat
      481 gtttatgata attttcaaaa agttggcccc ctgacatcac cgggagccaa aaaaaataca
      541 ccagttatta ttgtggctat attatttcat gagtaaacaa atatgtcagg cgtatatttg
      601 tttactcaaa ttgcttgttt tttagtcatc gtgatgggta atgactccaa cttactgata
      661 gtgttttatg ttcagataat gcccgatgac cttgtcatgc agctccaccg attttgagaa
      721 cgacagtgac ttccgtccca gccttgccag atgttgtctc agattcaggt tatgtcgctc
      781 aatgcgctgc gtatatcgct tgctgataac gtgcagcttt cccttcaggc gtgattcata
      841 cagcggccag ccatccgtca tccataccac gacctcaaag gccgacagca ggctcagaag
      901 acgctccagt gtggccagag tgcgttcacc gaagacgtgc gccacaaccg tcctccgtat
      961 cctgtcatac gcgtaaaaca gccagcgctg acgtgattta gcaccgacgt agccccactg
     1021 ttcgtccatt tcagcgcaga caatcacatc actgcccggt tgtatgcgcg aggttaccga
     1081 ctgcggcctg agttttttaa gtgacgtaaa accgtgttga ggccaacgcc cataatgcgt
     1141 gcactggcgc gacatccgac gccattcatg gccatatcaa tgattttctg gtgcgtaccg
     1201 ggctgagagg cggtgtaagt gaactgtagt tgccatgttt tacggcaatg agagcagaga
     1261 tagcgctgat gtccggcagt gcttttgccg ttacgcacca cgccttcagt agcggagcag
     1321 gaaggacatc tgatggaaat ggaagccacg caagcacctt aaaatcacca tcatacacta
     1381 aatcagtaag ttggcagcat tacccggatt tgagagtcgc aaacccatat tagggcaaag
     1441 aaagcctaat gcccccgtgg tgggtacacc agaaaacggg gagcgaagcg accagcatca
     1501 ggccgttcgt atgctgcttc gattttgtgg gtgttgcgcc agaccttggc aatcacgctt
     1561 caccgcaacc gctgccttca ctctcacttt atcaggtacg ttattggtta acgtgagacc
     1621 gggtagagcc agcttctttc ccgagctggt caggttccca ccgcttgcct gtttatcctg
     1681 ccggagtccg gggcgtagac ctgagagtca aggtgcagat atgggtttaa tgtcgttgaa
     1741 tggtattaag ctggtagtga cattcctagc cagccctgct aggatttgat tgcggtctga
     1801 tccgagcagg tatctgcacg aattagagta ctcaagccct gtgattctgt cacggggctt
     1861 ttgtacatct agagccagaa aaatcattat cactcagtca gatcaccgca acgcccgcca
     1921 cagcttcatg accgaacgta gtgagcgaat gagcgaggag gcgtcatttt caccgtccgc
     1981 ccatcattct gcttatgctt cgaagccgca ttttcctctg ccacatagcc cgatttctgt
     2041 caatttccgc acagtgttaa aatagataag ccagtataca ctccgctagc gctatgtgac
     2101 tggttcaggg ctgcgccccg aaacccgcca aaagcctgac gcgcctgcgg cttgtccaac
     2161 cccgcgccga ccgggaaagg gtttcccgcc cgtcacggcg ttatcaggag actggtttgt
     2221 ccgagaaacg gaacaagata ctcaccatgt gggtgacgga ggatgagtac cggctactgc
     2281 tggaacgctg cgggggtaca cagctttctg catgggtgcg cccgtctgct atgtctgttc
     2341 ctcctagttt tggtgggtgc ttatatctct gctcaatggc ataacatgtc actattaacc
     2401 gcgatgctaa agcgggctgt ttttcacagt attaccggct cccgtgccgg ttttttttct
     2461 taccggaagg gacttcgtgt ttattgatgt tctgattttc ggagggtgta ctgatcgcct
     2521 tgcaagggac acgatgagga ttgtagcccg cgaggaagga aagacttacg acgaggtact
     2581 ttctgacatc agggaaggtg gggcagatga gctgacccag atacatttct ggcgtgtcgt
     2641 tagtgcatta tatcccgggg catttaaccg tattgattac ctctctgagt ctcggaaata
     2701 ccgtctctgg ttatcctgat ttttaatctc gtcactgctt gcttacagtt ccagtctgta
     2761 ttgtctgcat ttttctttca tactgagtgc ctcacgaccc gtaataaatt ccgtgtccgt
     2821 tcatccttga gcgacgactg gaggatgaag atctctcaaa agatgatgtg gatgccatga
     2881 tgcaggcgac ggaaaggcta agccgttatg tctgattcca gtcgggcgct gagcttccgg
     2941 taaagcgctt cggcctgctc atgcagctgt tcgcagtctg tcgcttcgtc atcgaagtcg
     3001 agcaggtcaa ttctttccag caggaggagt gtctgggcgc ggataaattt agctatgttg
     3061 agaacggcgg attcctggcg gttcatgtgt gttttcctgt gtcttgtgat gattttgatg
     3121 tgaaaacagg atgccgtcat tctggtgcat agtcatgcat ggcgttaaaa tttacctggc
     3181 acgtttctgg cggcttttcg ggtggtttgt tacctgtttt accgtaccgc cgtcagaaac
     3241 gccctgaggg cgcctgaggc ggtgcgggca acggatgtta tggtaaatcc ggtggctttg
     3301 acgtgcctgc cgttgtgtac cgtcgtgagt gaaaataatt atattgttcg aagaacagcg
     3361 ctttttggcc ggagaaaagc agttctgcaa acgatggtat atcgatatga gttcttttgg
     3421 cattaatc
//
