LOCUS       NZ_CP141652             3576 bp    DNA     circular CON 17-JAN-2024
DEFINITION  Citrobacter freundii strain NFYY328 plasmid pNFYY328-7, complete
            sequence.
ACCESSION   NZ_CP141652
VERSION     NZ_CP141652.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN38983828
            Assembly: GCF_035620115.1
KEYWORDS    RefSeq.
SOURCE      Citrobacter freundii
  ORGANISM  Citrobacter freundii
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Citrobacter; Citrobacter freundii complex.
REFERENCE   1  (bases 1 to 3576)
  AUTHORS   Chen,J., Li,W. and Li,X.
  TITLE     Whole-genome sequencing of Citrobacter freundii strain NFYY328
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 3576)
  AUTHORS   Chen,J., Li,W. and Li,X.
  TITLE     Direct Submission
  JOURNAL   Submitted (20-DEC-2023) Zhuhai hospital, Jinan University, 79
            Kangning Road, Zhuhai, Guangdong 519000, China
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method :: Hifiasm v. version 0.13-r308; Canu v. version 1.7
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 72.77x
            Sequencing Technology             :: Illumina; PacBio
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 01/13/2024 23:32:11
            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)                     :: 5,701
            CDSs (total)                      :: 5,580
            Genes (coding)                    :: 5,410
            CDSs (with protein)               :: 5,410
            Genes (RNA)                       :: 121
            rRNAs                             :: 9, 8, 8 (5S, 16S, 23S)
            complete rRNAs                    :: 9, 8, 8 (5S, 16S, 23S)
            tRNAs                             :: 84
            ncRNAs                            :: 12
            Pseudo Genes (total)              :: 170
            CDSs (without protein)            :: 170
            Pseudo Genes (ambiguous residues) :: 0 of 170
            Pseudo Genes (frameshifted)       :: 48 of 170
            Pseudo Genes (incomplete)         :: 133 of 170
            Pseudo Genes (internal stop)      :: 25 of 170
            Pseudo Genes (multiple problems)  :: 34 of 170
            Pseudo Genes (short protein)      :: 1 of 170
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP141652.1.
            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..3576
                     /organism="Citrobacter freundii"
                     /mol_type="genomic DNA"
                     /strain="NFYY328"
                     /isolation_source="cerebrospinal fluid"
                     /host="Homo sapiens"
                     /db_xref="taxon:546"
                     /plasmid="pNFYY328-7"
                     /geo_loc_name="China: Guangzhou"
                     /lat_lon="23.19 N 113.33 E"
                     /collection_date="2023"
                     /collected_by="Jing Chen"
     gene            1045..1983
                     /locus_tag="U9I37_RS28470"
                     /old_locus_tag="U9I37_28470"
     CDS             1045..1983
                     /locus_tag="U9I37_RS28470"
                     /old_locus_tag="U9I37_28470"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_013185833.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_200002678.1"
                     /translation="MSVLDFLSSGGMASIGGDLSEEEQKHTNEIVKLFAKKLREYARTL
                     QIPASNIKINKCSFLFVAKDDFSYHFVFADKPGGGNNLVYRNLSEYRQLELQSIVHQVR
                     IDVGDVVWAFSCPVSLSGEELDTYINKLSIEYIQSEIQSSKDNNDGRISEEAMNVPEIA
                     SGLEKFRKDYPKGKKTAFIIMQFGSTAAHVKLVDAIKKELSKHNIIALRADDKEYMDDL
                     FSNIKTYMYGCDFGIAIFERITEDNFNPNVSLEVGYMMGMGKQVLLLKDKTLSSLHTDL
                     AGKLYKPFDVFDIESSLSTHIGKWLSDKGFL"
                     /name="hypothetical protein"
     gene            complement(2293..2424)
                     /locus_tag="U9I37_RS28475"
                     /old_locus_tag="U9I37_28475"
     CDS             complement(2293..2424)
                     /locus_tag="U9I37_RS28475"
                     /old_locus_tag="U9I37_28475"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001422066.1"
                     /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_072052181.1"
                     /translation="MHEPPVQSNRCALSGNYRLESNPKRHDKTPLAAATGNGMYKIN"
                     /name="replication initiation protein"
     gene            2842..3030
                     /locus_tag="U9I37_RS28480"
                     /old_locus_tag="U9I37_28480"
     CDS             2842..3030
                     /locus_tag="U9I37_RS28480"
                     /old_locus_tag="U9I37_28480"
                     /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_044703047.1"
                     /translation="MTKQQKTALNMAKFIQAQSLFLLGNLNEQDLDTEAGLCEKLHEDA
                     ELLFRTLDIRLDDFQED"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            3033..3464
                     /locus_tag="U9I37_RS28485"
                     /old_locus_tag="U9I37_28485"
     CDS             3033..3464
                     /locus_tag="U9I37_RS28485"
                     /old_locus_tag="U9I37_28485"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000135004.1"
                     /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_044703046.1"
                     /translation="MARVSISEAARLVSVSRPTIYKLLKSGELSYTSVVKHGKPVKTID
                     TAELIRLFGALDVVSGDKSDTVKFDGVTTSVNSDFLHSLQHQVALLQAENTGLKDAVNA
                     RDEHISSLRQAMQLLEHKQSTSDPQNVPAKSWWQFWKSH"
                     /name="helix-turn-helix domain-containing protein"
     Typing          complement(2317..2661)
                     /name="rep_cluster_2373"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="94.509"
                     /coverage="80.0"
                     /evalue="2.99e-149"
ORIGIN
        1 tgatggctga taaaggccaa aaaatcgtgt cacaccccac gcagtataca cggctaatgc
       61 cggaagcctt tgctgacaag gcttccgggg gtataccacc ccttgtatga aatggtatac
      121 ccgcatctgt ttttatgcgg ttaaagccag ttctggcaag acctgtaggg ggtataccag
      181 gtggtaactg gcttggtata cctgaaaagc tgctctgagg gcttcagtgc cacacaggat
      241 aagggattgc acttggtata ccctttttct gtttgtgtgg tgcgatatca gtatctctcc
      301 ctgcgcggtg ttatagataa aagacctgtc atggatgcgc cccgacaccc tgccagcgcc
      361 tcacgacccc gcaataaatt gcgtgcccgt tcaccgcttt ctttagccag tctgtgccag
      421 actgttatct gaatggctta ctagtgtgga ggtaaaaagg tgaaagaatg gtttgcgacc
      481 cttatcgatg acctgaaatt tctgggggcg gagtttaaga gagagttttc ggatctggag
      541 atcaggccga tgacggctca ggagaaccga cggagacatg atgagatgca ccgttcttcc
      601 gtggccggga agttagcacg gggcgctttg caaatcaggg acgggaaact gaccccctat
      661 ggtatgggac ggaacaaata ggcttcatca atcccggatt cccgggctag taaaccggga
      721 aaaatctccc ttttagcggc tgttttccgt caaatcacgc accatgcagc cgggagcata
      781 gttattcacc ctctcaggat tcatctgtgg cgttctgagc gttttccccc gggtaaactg
      841 tacaaaacga cgcactcacc ccaaaagcgc tcagagtgcg tctgagcgat gcgcgtaatg
      901 agtgcttatg ttaaatagat ggcagtagac tcaaggtggg ttgtatcatt atcaagtgaa
      961 taggtgatgt taccattaag tagtggttag gttttgggat gtccgggcca agcgttcttt
     1021 agaattggaa aaaggaaatt aactatgtct gttttggatt ttttatcttc cggtgggatg
     1081 gctagtattg gtggagatct gtctgaagaa gaacaaaaac atactaatga aatagttaaa
     1141 ttatttgcca aaaaattgag agagtatgct aggacattac aaattccagc atccaatatc
     1201 aaaataaata aatgttcatt tttgtttgtc gcaaaagacg atttttctta tcatttcgtg
     1261 tttgctgata aacctggtgg cggtaataat ttagtatata gaaacttatc tgaatataga
     1321 cagcttgaac ttcaaagtat cgtccatcag gttcggattg atgttggtga tgttgtttgg
     1381 gcgttctctt gcccagtctc tctctccggg gaagaacttg atacatatat taataaactc
     1441 tctattgaat atattcagtc tgaaattcaa agtagtaaag ataacaatga tggtagaatt
     1501 tcagaagagg ctatgaatgt ccctgaaata gcttctggcc ttgaaaaatt cagaaaagac
     1561 tatccaaaag ggaaaaaaac agcatttatc atcatgcagt ttggtagcac ggcagcgcac
     1621 gtaaagcttg ttgatgcaat aaagaaagag ttgtctaaac acaacataat agctttaagg
     1681 gctgatgata aagagtatat ggatgatctc ttttcaaata tcaaaacata tatgtatggg
     1741 tgcgatttcg gtattgctat ttttgagagg attacagaag ataattttaa ccctaatgtt
     1801 tcattggaag ttggatatat gatgggaatg gggaagcagg ttttactttt aaaggataag
     1861 actctaagtt cattacatac agacttagca ggtaaacttt ataagccatt tgatgttttc
     1921 gatattgagt catccctcag cactcatatt gggaaatggc tatcagacaa gggattttta
     1981 tagtttccgg aacaagtacc gtatgtgcgg tacttgtttg acatcgttag ttatcgaatg
     2041 gggttatgcg aaaatcatgg tcaaatttga gacttgacgc gtttgattga tgagatcttc
     2101 ttgagatcct tcgtctctcg tcgtagtctc ttgttccaga aacgaaaaaa ccgactgggg
     2161 agtcggtttt ttcgagggtt cagcaagttg gggaacttct gaaccgtggt aacagggtgt
     2221 acaagaccgc tgaaaccgta atctgtcctt tcagtttagc cgtagtttag ctcggacttc
     2281 aagaactctc attcagttaa tcttgtacat cccattacca gtggccgctg ccagtggcgt
     2341 tttgtcgtgt cttttcgggt tggactcaag acgatagtta ccggataagg cgcagcggtt
     2401 ggactgaacg gggggttcgt gcatacagtc cagcttggag cgaactgcct acccggaact
     2461 gagtgtcagg cgtggaatga gagaaccgcg gccataacag cggaatgaca ccggtaaacc
     2521 gaaaggcagg aacaggagag cgcacgaggg agccaccagg gggaaacgcc tggtatcttt
     2581 aaagtcctgt cgggtttcgc caccactgat ttgagcgtca aattttgtga tgcttgtcag
     2641 gggggcgaag cctatggaaa aacgccctgg tcgggcatgg ctttatcgtt cttgttctgg
     2701 cttttcgtta cgcttaccgt ctacgttatt tgtctcttag gaagatgcgt ccgctcgccg
     2761 cagataagtg accgagcgta gcgagcgaac ggtcgaggaa gcggaaaaga accggatatc
     2821 atttggagca ctgacactgt gatgacgaaa caacagaaaa cggcactgaa tatggcgaaa
     2881 ttcattcagg cgcaatccct gttcttgctg ggtaatctca atgaacagga tctcgatact
     2941 gaagccggct tgtgcgaaaa attgcatgag gatgcggaac tgctttttcg tactctggat
     3001 attcgtctgg atgattttca agaggattag taatggctcg cgtatccatt agtgaagctg
     3061 cacgtcttgt cagtgtcagt cgcccgacta tttacaagct gcttaaatct ggtgagctta
     3121 gctacacctc cgttgtaaag catggaaaac ccgttaaaac cattgataca gctgagctta
     3181 ttcgtctttt tggtgctctt gatgttgtca gtggtgataa aagtgacact gtaaaatttg
     3241 acggtgtcac tacgtcggtt aacagtgatt ttttacattc tttacagcat caagtggcgc
     3301 ttttacaggc ggagaatacc gggcttaaag atgcagtgaa tgcacgggat gagcatataa
     3361 gttcacttcg tcaggccatg caacttctgg agcataaaca gagtacttct gacccgcaga
     3421 atgttcctgc aaagtcctgg tggcagttct ggaaatccca ttgagtcatt atcaatcatg
     3481 cattccggtc atagcgttcg gccagccacc aggctatcac cggatatgga tgtttatact
     3541 ttctcatctg accgctttac ccgcatgttt gatttc
//
