LOCUS       NZ_CP137131             3481 bp    DNA     circular CON 02-NOV-2023
DEFINITION  Citrobacter freundii strain F3121 plasmid pF3121-4, complete
            sequence.
ACCESSION   NZ_CP137131
VERSION     NZ_CP137131.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN37878049
            Assembly: GCF_033162755.1
KEYWORDS    RefSeq.
SOURCE      Citrobacter freundii
  ORGANISM  Citrobacter freundii
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Citrobacter; Citrobacter freundii complex.
REFERENCE   1  (bases 1 to 3481)
  AUTHORS   Li,X.
  TITLE     Citrobacter freundii F3121 Genome sequencing and assembly
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 3481)
  AUTHORS   Li,X.
  TITLE     Direct Submission
  JOURNAL   Submitted (18-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                   :: 11/02/2023 06:50:12
            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)                     :: 5,312
            CDSs (total)                      :: 5,191
            Genes (coding)                    :: 5,046
            CDSs (with protein)               :: 5,046
            Genes (RNA)                       :: 121
            rRNAs                             :: 9, 8, 8 (5S, 16S, 23S)
            complete rRNAs                    :: 9, 8, 8 (5S, 16S, 23S)
            tRNAs                             :: 85
            ncRNAs                            :: 11
            Pseudo Genes (total)              :: 145
            CDSs (without protein)            :: 145
            Pseudo Genes (ambiguous residues) :: 0 of 145
            Pseudo Genes (frameshifted)       :: 47 of 145
            Pseudo Genes (incomplete)         :: 99 of 145
            Pseudo Genes (internal stop)      :: 30 of 145
            Pseudo Genes (multiple problems)  :: 29 of 145
            Pseudo Genes (short protein)      :: 1 of 145
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP137131.1.
            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..3481
                     /organism="Citrobacter freundii"
                     /mol_type="genomic DNA"
                     /strain="F3121"
                     /isolation_source="urine"
                     /host="Homo sapiens"
                     /db_xref="taxon:546"
                     /plasmid="pF3121-4"
                     /geo_loc_name="China: Hangzhou"
                     /lat_lon="29.86 N 121.56 E"
                     /collection_date="2021-12-09"
                     /collected_by="Jiayao Yao"
     gene            complement(799..1227)
                     /locus_tag="R2X29_RS26550"
                     /old_locus_tag="R2X29_26550"
     CDS             complement(799..1227)
                     /locus_tag="R2X29_RS26550"
                     /old_locus_tag="R2X29_26550"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000222531.1"
                     /GO_function="GO:0003677 - DNA binding [Evidence IEA]"
                     /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_025760401.1"
                     /translation="MTYSIDKKWKAGGLSLGWTAVPTVLFFIQNEKKLTSVAFNTLLNL
                     IVHWWSLQEWPHPSMESLAIRMGVSVRTVQRAINDLEKANLLDKKPTSKSDSRYGGRNI
                     YDLTKLVDYLDTMGPSVAEQVKKPRHKKPIYTVRKTTI"
                     /name="helix-turn-helix domain-containing protein"
     gene            1516..1947
                     /locus_tag="R2X29_RS26555"
                     /old_locus_tag="R2X29_26555"
     CDS             1516..1947
                     /locus_tag="R2X29_RS26555"
                     /old_locus_tag="R2X29_26555"
                     /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_025760402.1"
                     /translation="MGDKNGTQSSIVTYAQYTVDFSDSFSTFYASLVEMPTRLNILDCI
                     DEFIDHFEKNGLWGWKGKIAPSSRLPVNIPEPKRSDLIAHAEANKLWHAHIGDPSFRDT
                     GHGYSVSDGVLHFQKLSSYSIKLLEVGYHRPMELPVDVD"
                     /name="hypothetical protein"
     gene            2749..3183
                     /locus_tag="R2X29_RS26560"
                     /old_locus_tag="R2X29_26560"
     CDS             2749..3183
                     /locus_tag="R2X29_RS26560"
                     /old_locus_tag="R2X29_26560"
                     /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_125183090.1"
                     /translation="MSRLYRAALPEDYVHNPETGLWELSFDQRPVAGTRAASPEEGAAQ
                     YNAAREKFKSAVSAVRQRPEPVFSFTEMTEWVVEHGTPEQCQAVRLMFDARDKNEFDIA
                     VREGLKVLPRHLDFAYFFGRFSDRMRVSVPLRERLSLRLS"
                     /name="hypothetical protein"
     Typing          2238..2334
                     /name="ColRNAI_rep_cluster_1857"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="87.755"
                     /coverage="89.0"
                     /evalue="3.35e-23"
ORIGIN
        1 gtaactcgta agctttaaga gggtggtcag gcgcctgcgg caccgacggg ggggcgtagc
       61 ccccgctgcg caaatcgtcc gtgggcggac tcggaacgct ggggcgttcc gttgcttgcg
      121 gctcccccga aagcacgatc ccctggacgg gtatcgcaaa gccttaaccc gcacccgtat
      181 gttcttccgg ctctcttttt ttgatgcgat gcaggatagg gctgacgccg caaagtgacg
      241 tcatctgacg ttctcttgtt gagttatcag gacaggaaat gttttgtggc caccgccact
      301 gcgccgacac cacaaaacag cgggacaaga tgtgtctttg gagtaccgcc ggcacaccaa
      361 atcctcctgg tcaggccccg cccgacaccc tgaaaaattt cgacacgtcg aaatttctgc
      421 gttctggtta tccacgttaa atcgcccccc ttacgaaatc tctgccgcgc ctggcggctt
      481 ggccaacgcc tcacggccgc acagtaaact gcgcccccgt tcaccgttat cggtggggtt
      541 cagcgagcct tttgacccgt tcgcaggatt ttagcggcta aaatcgcagt catgcacctg
      601 cgtgcatagc catgcagtcg cgccaaaatc gtcaggggcg tttttcaggg ttatgggcgg
      661 ggaaaggtgc cggaaatccg caggaggccg cagaaacgcg ctgagggcgt ctcagggggt
      721 gcggccaaga ggtgttatgg taaatcagag taattggcag gctcgcttaa ccatgaaaag
      781 ttgaactcgg cggaaatttc aaattgtagt ttttcttacg gtatatatgg gttttttatg
      841 gcgtggtttt tttacctgtt ctgctactga tggacccatt gtgtctaggt agtcaacaag
      901 ctttgttagg tcataaatgt tacgacctcc atatcggctg tcactttttg atgttggttt
      961 cttgtccaag agattggctt tttccagatc attgatagct ctctgaactg tccttacaga
     1021 aacgcccatt cgtattgcta ggctctccat cgacgggtgc ggccattctt gtagactcca
     1081 ccaatgaact atgaggttaa gcagagtgtt gaaggccaca gaagttagtt ttttttcgtt
     1141 ttgtataaaa aacaacacgg taggcactgc tgtccagcca agagacaaac cgccagcttt
     1201 ccatttttta tcaatggagt aagtcattga ttaccttata taaaaaatta tttggtgtat
     1261 atattatatg attattcata tgaatagggt gacactagcg ccattattgt gcaaccacaa
     1321 aaagctaacc tgaagataga aaaaaaattt ttctgcctcg aataaatacg gagttaacga
     1381 tatgaaaacc gaacaacgtc atgatctttt tgaagatact gaggtatttg gcgtatcctt
     1441 gtctctgttg atttccagag cgaatgagaa gtctgttaca atgccctctg gtctgactag
     1501 ggagcagaga agggaatggg cgataaaaac ggcacgcaaa gttcaatcgt aacatatgcg
     1561 caatataccg tagatttttc tgattcattt tcaacgtttt acgcttccct tgtggagatg
     1621 cctacacgcc tcaatatcct tgattgtatc gatgaattta tcgatcattt tgaaaaaaat
     1681 ggattatggg gttggaaagg taaaatagct ccgtcaagcc gcctgcctgt aaacattcct
     1741 gaaccgaaga gaagcgatct aatcgctcat gcagaagcta ataagctttg gcatgctcat
     1801 atcggcgatc cctctttcag agatacagga catggttact cagtttctga tggcgttttg
     1861 cattttcaaa agctgtcgtc ctacagtatc aaactacttg aggtaggtta ccatcgccca
     1921 atggagctgc cggttgatgt tgattaacat ggtcttcctg ataactaatt acccttgacg
     1981 gtttccggcg acagtagtag tttcccagaa aagaaaaaac cgccctgcaa ggcggttttt
     2041 tcgaaggttc agaaagttgg ggaactaact gaaccgcggt gactggcttt aacggagcgc
     2101 agtaacctaa tctgtccttc cagtgtagcc gtagtctggc acccacttca agaactcttg
     2161 ttaagttagc ttaacatctc gctccgtaaa taagtcacca gtggctaccg ccagtggcga
     2221 ttcgtcgtgt ctgtcagggt tggaatcaag agaacagtta tctgataaag gcgcggtagt
     2281 cgggttgaac ggggagttcg tgcatacagc ccagcttgga gcgaaccacc tacaaggaac
     2341 ccagttgcac gggtaggaat gagaaaacgc caccttacgg cggtctgcaa cgggtaaacc
     2401 tcacggtggg aacaggagag cgcacgaggg agcgacccat cggaaacggt ggggatcttt
     2461 aagtcctgtc gggtttcgcc ccttctgatt tgagcaccgg aaatcgcctg atttctgtga
     2521 agctcgtcag gagggcgaag cctatggaaa accggggaac ccggaggcct ggctcggggg
     2581 ggaaaggggg gtgtgccgtt gatgttagcc agagaagcga tcatctcttt tcccgttagc
     2641 tggtaacgct cgccgcagcg tttaactagc gaagtctgtt aaaccgagga agcggaatat
     2701 cactgatgct aaggttttcg cttacacact gatgttgagg agtttccctt gtcccgtctc
     2761 taccgtgctg cacttcctga agattacgtc cataaccctg aaacaggtct ttgggaactt
     2821 tcattcgatc agcgccccgt agcaggaacg cgcgcagctt ctcctgaaga aggcgctgct
     2881 cagtacaatg ctgcccgcga aaagtttaag tcggctgtgt ctgccgtccg tcagcgtccg
     2941 gaaccggtat tttcttttac cgaaatgacg gagtgggttg tggaacatgg cacgccggag
     3001 caatgtcagg ccgtccgtct tatgtttgat gcacgtgata aaaatgagtt tgatattgcg
     3061 gtgcgtgaag gtctgaaagt gctgccccgg catctcgatt ttgcctactt ctttggtcgc
     3121 ttttccgatc ggatgcgtgt gtctgttccg ctgcgggaac gactcagtct gcgtctgtcc
     3181 tgacgtttac tcagcgtaaa ctctgcgttc tctgcttcct gttttactcc ctattttgac
     3241 ccctattttt atctattgtg atgcataggg agcaaaatag aggtcaaaat aggggggctg
     3301 gcgcattgca tgcgccagaa agggacatga ttttctgaac gaaaatcacg ccccaggggt
     3361 tgcgccgtgc ggcttcaccc tctctgactt ctccgcggct ggacgccact ccgtcgccag
     3421 attcacccgg ccccgtccga cgtctccgac gcctgaccac ccccttaaga cgcttactcg
     3481 t
//
