LOCUS       NZ_CP137121             3481 bp    DNA     circular CON 02-NOV-2023
DEFINITION  Citrobacter freundii strain F3021 plasmid pF3021-5, complete
            sequence.
ACCESSION   NZ_CP137121
VERSION     NZ_CP137121.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN37878029
            Assembly: GCF_033160275.1
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 F3021 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  JOURNAL   Unpublished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 06:23:09
            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)                     :: 5,321
            CDSs (total)                      :: 5,200
            Genes (coding)                    :: 5,055
            CDSs (with protein)               :: 5,055
            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)         :: 100 of 145
            Pseudo Genes (internal stop)      :: 29 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
            CP137121.1.
            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="F3021"
                     /isolation_source="stool"
                     /host="Homo sapiens"
                     /db_xref="taxon:546"
                     /plasmid="pF3021-5"
                     /geo_loc_name="China: Hangzhou"
                     /lat_lon="29.86 N 121.56 E"
                     /collection_date="2021-11-17"
                     /collected_by="Jiayao Yao"
     gene            complement(join(3261..3481,1..208))
                     /locus_tag="R2X28_RS00005"
                     /old_locus_tag="R2X28_00005"
     CDS             complement(join(3261..3481,1..208))
                     /locus_tag="R2X28_RS00005"
                     /old_locus_tag="R2X28_00005"
                     /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            497..928
                     /locus_tag="R2X28_RS00010"
                     /old_locus_tag="R2X28_00010"
     CDS             497..928
                     /locus_tag="R2X28_RS00010"
                     /old_locus_tag="R2X28_00010"
                     /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            1730..2164
                     /locus_tag="R2X28_RS00015"
                     /old_locus_tag="R2X28_00015"
     CDS             1730..2164
                     /locus_tag="R2X28_RS00015"
                     /old_locus_tag="R2X28_00015"
                     /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          1219..1315
                     /name="ColRNAI_rep_cluster_1857"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="87.755"
                     /coverage="89.0"
                     /evalue="3.35e-23"
ORIGIN
        1 aaacgcccat tcgtattgct aggctctcca tcgacgggtg cggccattct tgtagactcc
       61 accaatgaac tatgaggtta agcagagtgt tgaaggccac agaagttagt tttttttcgt
      121 tttgtataaa aaacaacacg gtaggcactg ctgtccagcc aagagacaaa ccgccagctt
      181 tccatttttt atcaatggag taagtcattg attaccttat ataaaaaatt atttggtgta
      241 tatattatat gattattcat atgaataggg tgacactagc gccattattg tgcaaccaca
      301 aaaagctaac ctgaagatag aaaaaaaatt tttctgcctc gaataaatac ggagttaacg
      361 atatgaaaac cgaacaacgt catgatcttt ttgaagatac tgaggtattt ggcgtatcct
      421 tgtctctgtt gatttccaga gcgaatgaga agtctgttac aatgccctct ggtctgacta
      481 gggagcagag aagggaatgg gcgataaaaa cggcacgcaa agttcaatcg taacatatgc
      541 gcaatatacc gtagattttt ctgattcatt ttcaacgttt tacgcttccc ttgtggagat
      601 gcctacacgc ctcaatatcc ttgattgtat cgatgaattt atcgatcatt ttgaaaaaaa
      661 tggattatgg ggttggaaag gtaaaatagc tccgtcaagc cgcctgcctg taaacattcc
      721 tgaaccgaag agaagcgatc taatcgctca tgcagaagct aataagcttt ggcatgctca
      781 tatcggcgat ccctctttca gagatacagg acatggttac tcagtttctg atggcgtttt
      841 gcattttcaa aagctgtcgt cctacagtat caaactactt gaggtaggtt accatcgccc
      901 aatggagctg ccggttgatg ttgattaaca tggtcttcct gataactaat tacccttgac
      961 ggtttccggc gacagtagta gtttcccaga aaagaaaaaa ccgccctgca aggcggtttt
     1021 ttcgaaggtt cagaaagttg gggaactaac tgaaccgcgg tgactggctt taacggagcg
     1081 cagtaaccta atctgtcctt ccagtgtagc cgtagtctgg cacccacttc aagaactctt
     1141 gttaagttag cttaacatct cgctccgtaa ataagtcacc agtggctacc gccagtggcg
     1201 attcgtcgtg tctgtcaggg ttggaatcaa gagaacagtt atctgataaa ggcgcggtag
     1261 tcgggttgaa cggggagttc gtgcatacag cccagcttgg agcgaaccac ctacaaggaa
     1321 cccagttgca cgggtaggaa tgagaaaacg ccaccttacg gcggtctgca acgggtaaac
     1381 ctcacggtgg gaacaggaga gcgcacgagg gagcgaccca tcggaaacgg tggggatctt
     1441 taagtcctgt cgggtttcgc cccttctgat ttgagcaccg gaaatcgcct gatttctgtg
     1501 aagctcgtca ggagggcgaa gcctatggaa aaccggggaa cccggaggcc tggctcgggg
     1561 gggaaagggg ggtgtgccgt tgatgttagc cagagaagcg atcatctctt ttcccgttag
     1621 ctggtaacgc tcgccgcagc gtttaactag cgaagtctgt taaaccgagg aagcggaata
     1681 tcactgatgc taaggttttc gcttacacac tgatgttgag gagtttccct tgtcccgtct
     1741 ctaccgtgct gcacttcctg aagattacgt ccataaccct gaaacaggtc tttgggaact
     1801 ttcattcgat cagcgccccg tagcaggaac gcgcgcagct tctcctgaag aaggcgctgc
     1861 tcagtacaat gctgcccgcg aaaagtttaa gtcggctgtg tctgccgtcc gtcagcgtcc
     1921 ggaaccggta ttttctttta ccgaaatgac ggagtgggtt gtggaacatg gcacgccgga
     1981 gcaatgtcag gccgtccgtc ttatgtttga tgcacgtgat aaaaatgagt ttgatattgc
     2041 ggtgcgtgaa ggtctgaaag tgctgccccg gcatctcgat tttgcctact tctttggtcg
     2101 cttttccgat cggatgcgtg tgtctgttcc gctgcgggaa cgactcagtc tgcgtctgtc
     2161 ctgacgttta ctcagcgtaa actctgcgtt ctctgcttcc tgttttactc cctattttga
     2221 cccctatttt tatctattgt gatgcatagg gagcaaaata gaggtcaaaa taggggggct
     2281 ggcgcattgc atgcgccaga aagggacatg attttctgaa cgaaaatcac gccccagggg
     2341 ttgcgccgtg cggcttcacc ctctctgact tctccgcggc tggacgccac tccgtcgcca
     2401 gattcacccg gccccgtccg acgtctccga cgcctgacca cccccttaag acgcttactc
     2461 gtgtaactcg taagctttaa gagggtggtc aggcgcctgc ggcaccgacg ggggggcgta
     2521 gcccccgctg cgcaaatcgt ccgtgggcgg actcggaacg ctggggcgtt ccgttgcttg
     2581 cggctccccc gaaagcacga tcccctggac gggtatcgca aagccttaac ccgcacccgt
     2641 atgttcttcc ggctctcttt ttttgatgcg atgcaggata gggctgacgc cgcaaagtga
     2701 cgtcatctga cgttctcttg ttgagttatc aggacaggaa atgttttgtg gccaccgcca
     2761 ctgcgccgac accacaaaac agcgggacaa gatgtgtctt tggagtaccg ccggcacacc
     2821 aaatcctcct ggtcaggccc cgcccgacac cctgaaaaat ttcgacacgt cgaaatttct
     2881 gcgttctggt tatccacgtt aaatcgcccc ccttacgaaa tctctgccgc gcctggcggc
     2941 ttggccaacg cctcacggcc gcacagtaaa ctgcgccccc gttcaccgtt atcggtgggg
     3001 ttcagcgagc cttttgaccc gttcgcagga ttttagcggc taaaatcgca gtcatgcacc
     3061 tgcgtgcata gccatgcagt cgcgccaaaa tcgtcagggg cgtttttcag ggttatgggc
     3121 ggggaaaggt gccggaaatc cgcaggaggc cgcagaaacg cgctgagggc gtctcagggg
     3181 gtgcggccaa gaggtgttat ggtaaatcag agtaattggc aggctcgctt aaccatgaaa
     3241 agttgaactc ggcggaaatt tcaaattgta gtttttctta cggtatatat gggtttttta
     3301 tggcgtggtt tttttacctg ttctgctact gatggaccca ttgtgtctag gtagtcaaca
     3361 agctttgtta ggtcataaat gttacgacct ccatatcggc tgtcactttt tgatgttggt
     3421 ttcttgtcca agagattggc tttttccaga tcattgatag ctctctgaac tgtccttaca
     3481 g
//
