LOCUS       NZ_CP141651             4942 bp    DNA     circular CON 17-JAN-2024
DEFINITION  Citrobacter freundii strain NFYY328 plasmid pNFYY328-6, complete
            sequence.
ACCESSION   NZ_CP141651
VERSION     NZ_CP141651.1
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 4942)
  AUTHORS   Chen,J., Li,W. and Li,X.
  TITLE     Whole-genome sequencing of Citrobacter freundii strain NFYY328
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 4942)
  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
            CP141651.1.
            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..4942
                     /organism="Citrobacter freundii"
                     /mol_type="genomic DNA"
                     /strain="NFYY328"
                     /isolation_source="cerebrospinal fluid"
                     /host="Homo sapiens"
                     /db_xref="taxon:546"
                     /plasmid="pNFYY328-6"
                     /geo_loc_name="China: Guangzhou"
                     /lat_lon="23.19 N 113.33 E"
                     /collection_date="2023"
                     /collected_by="Jing Chen"
     gene            join(4827..4942,1..298)
                     /locus_tag="U9I37_RS28420"
                     /old_locus_tag="U9I37_28420"
     CDS             join(4827..4942,1..298)
                     /locus_tag="U9I37_RS28420"
                     /old_locus_tag="U9I37_28420"
                     /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_244637524.1"
                     /translation="MRVIEVQAVIGQSLPGVDPGTISPVIVGLQAFSALQFDVREHKIQ
                     LQPVLVPVLHPQTGVLVAVQTGQQCLLKLIHQTHFLIVREVLFPERQHPGGIGAGKLTT
                     INQLPDTLRLTAQYHRFIPITFFSQQVIHRATA"
                     /name="hypothetical protein"
     gene            complement(312..647)
                     /gene="mobC"
                     /locus_tag="U9I37_RS28425"
                     /old_locus_tag="U9I37_28425"
     CDS             complement(312..647)
                     /gene="mobC"
                     /locus_tag="U9I37_RS28425"
                     /old_locus_tag="U9I37_28425"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_006674374.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="plasmid mobilization relaxosome protein MobC"
                     /protein_id="WP_037427024.1"
                     /translation="MDKRTKEIKIRLTESEHERLLARCDRAHLAEWLRSLGLGEHVLRR
                     RRVPDVDPALLRQVTGIGNNLNQIARKLHGLDSLSAHQQVSLLAVLTSLDRQLSELLET
                     QRDRQDS"
                     /name="mobC"
     gene            complement(970..1443)
                     /locus_tag="U9I37_RS28430"
                     /old_locus_tag="U9I37_28430"
     CDS             complement(970..1443)
                     /locus_tag="U9I37_RS28430"
                     /old_locus_tag="U9I37_28430"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000566735.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_084797509.1"
                     /translation="MKQSTLELDYLGYNFFREFARYEYCLKVTGFRKGTNTRVEADWYK
                     YAGEFVSLIESPSKELNESISYLINNPPKKQVLKDGLLCWSNVLPDHRNKSELVFSLIC
                     RIRNNLFHGGKFNGEWFSPQRSKELIEHALIILRTCGKSHSTVLKAYNGQHDE"
                     /name="hypothetical protein"
     gene            complement(1474..1947)
                     /locus_tag="U9I37_RS28435"
                     /old_locus_tag="U9I37_28435"
     CDS             complement(1474..1947)
                     /locus_tag="U9I37_RS28435"
                     /old_locus_tag="U9I37_28435"
                     /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_104652423.1"
                     /translation="MRLSLVASVFTLYLISLSSSVNAENNIFDMPINIPGSKYIDAAHP
                     TMSEWGSHCDSARNDIKEKGAWGFCNGYLAAVIQYDFFKRQKKCPNFSVGDFVQFATEE
                     SIEYRNKNAKPSTSPSTGKVIPNAYVYENVPAPGQRPAFLVLESIVMEKCNIN"
                     /name="hypothetical protein"
     gene            complement(1947..2870)
                     /locus_tag="U9I37_RS28440"
                     /old_locus_tag="U9I37_28440"
     CDS             complement(1947..2870)
                     /locus_tag="U9I37_RS28440"
                     /old_locus_tag="U9I37_28440"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_003030989.1"
                     /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_098947601.1"
                     /translation="MSNQALDLFNERLPRKPYFTDELQFGVRIAGKERAILAKYIQFNQ
                     PHAMFWLGFDVDRPGAAIDWSDRNAPAPTLTIMNPENGHAHLLYALKTAVRTAPDGKIK
                     PLKYAAAVERALCKKLDADTGYSGLICKNPNHDHWQLAVWQPELYTLDWLADSLDLSAA
                     NDKEILPDYGLGRNCTLFDKTRKWAYRAIRQGWPDYEQWLRACYERANAYNLQFAAPLD
                     ENEVNGIAKSIAKWTKSKFSEETFGAYVSRTHSSEIQSVRGKKSRGGGRPKGRISIASD
                     ASLKPWVNLNISRSKYYRLGMNKRFL"
                     /name="replication initiation protein"
     gene            3152..3391
                     /locus_tag="U9I37_RS28445"
                     /old_locus_tag="U9I37_28445"
     CDS             3152..3391
                     /locus_tag="U9I37_RS28445"
                     /old_locus_tag="U9I37_28445"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001118105.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="type II toxin-antitoxin system CcdA family
                     antitoxin"
                     /protein_id="WP_064179603.1"
                     /translation="MPVSAMRHKKTVSVTIEPALLHQAREAGINLSATLTTALKHQIRE
                     SEAERWKRANRKAIQELNRITDEHGLLSDDHRTF"
                     /name="type II toxin-antitoxin system CcdA family
                     antitoxin"
     gene            3391..3699
                     /locus_tag="U9I37_RS28450"
                     /old_locus_tag="U9I37_28450"
     CDS             3391..3699
                     /locus_tag="U9I37_RS28450"
                     /old_locus_tag="U9I37_28450"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001199743.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="CcdB family protein"
                     /protein_id="WP_037427062.1"
                     /translation="MQFMVYRNNSNNRAYPYLLDVQSDIIDELNTRLVIPLFLLDEVNG
                     RPARRLTPVLNVDGEDFLVMTHEMASVRQSQLGEEVVSVREHRQAIKNALDFLLDGF"
                     /name="CcdB family protein"
     gene            complement(3803..4039)
                     /locus_tag="U9I37_RS28455"
                     /old_locus_tag="U9I37_28455"
     CDS             complement(3803..4039)
                     /locus_tag="U9I37_RS28455"
                     /old_locus_tag="U9I37_28455"
                     /inference="COORDINATES: protein motif:HMM:NF016769.4"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MbeD family mobilization/exclusion protein"
                     /protein_id="WP_037427059.1"
                     /translation="MTETEKLLLSALERLQDDYETRQQAWQASYDSLQTMFTTTSAALM
                     RSDQACQHLSGQVESLRQQVMSLTEAVSRLTRR"
                     /name="MbeD family mobilization/exclusion protein"
     gene            complement(4100..4585)
                     /locus_tag="U9I37_RS28460"
                     /old_locus_tag="U9I37_28460"
     CDS             complement(4100..4585)
                     /locus_tag="U9I37_RS28460"
                     /old_locus_tag="U9I37_28460"
                     /inference="COORDINATES: protein motif:HMM:NF016710.4"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MbeB family mobilization protein"
                     /protein_id="WP_139156959.1"
                     /translation="MSGILDLAKAFEETSKQQAQRTGESVKSEFVKLEQSISEALKSSG
                     KSISDAIHEQNVRQTTLLRRSVTIALIWILFCGVLLIGILSGILWFQGTLIASRLDEMN
                     SYSQQLTDLKAKSGAGVEILTDDTRKNKYYVVLPKSAKGVELYTSKNDKQVVTYTAK"
                     /name="MbeB family mobilization protein"
     gene            4633..4773
                     /locus_tag="U9I37_RS28465"
                     /old_locus_tag="U9I37_28465"
     CDS             4633..4773
                     /locus_tag="U9I37_RS28465"
                     /old_locus_tag="U9I37_28465"
                     /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_182115642.1"
                     /translation="MLRLLFVSRTTVSPPFSSALTTFSRLRIIPCATIVSSESVMACAA
                     F"
                     /name="hypothetical protein"
ORIGIN
        1 tcgggaacac aaaattcagc tccagcctgt ccttgtcccg gtgctccacc cacagacagg
       61 cgtactggtc gccgtccaga ccgggcaaca gtgtctgctc aaactcatcc atcagacgca
      121 ctttctcatc gtcagggagg ttttgttccc ggaacgacaa caccccggag gtataggcgc
      181 gggcaaactc acaaccatca atcagttgcc tgacacgctc aggctcaccg cgcagtacca
      241 ccgctttatc ccgatcacgt tcttttccca gcaggtaatc caccgggcca ctgcctgaac
      301 ccgcaccgcg gctatgaatc ttgacgatca cgctgtgtct ccagaagctc agataactgg
      361 cgatcaaggc tggtcagtac cgccagaaga gaaacctgct gatgggccga aagcgaatcc
      421 agaccatgca gcttacgggc tatctgattg aggttattgc cgatgccggt cacctgacga
      481 agcagtgccg gatcaacgtc aggcacacgc cggcgacgca atacatgttc acccagaccg
      541 agcgaacgta accattcagc gagatgagca cgatcacaac gtgccagcag tcgctcatgt
      601 tcactctcag tcaggcggat ttttatctct ttcgttcgct tgtccatgac actccgctga
      661 gaaaactttc gcacccagag tgcgaatttt cgcagtggat gccaggggtt tcggggggcg
      721 gcgagccccc tgaaccagtc acagaaggaa ccctcgtaga ggggacgctg tgtgtactgg
      781 cttatagtga ttgataagta tgtcagattc tgtgctggct gcaaaaaaaa aagccttctc
      841 tggagaaggc tgttatctga tataggttgt ttttagtctc acagagaaca tctagtggat
      901 tgttcttagc tttagcgata tcagtgatat gatcagcatc agcatcagca tcatattagt
      961 tgattgtatt tattcatcat gctggccatt atatgctttg agcaccgtag aatggctctt
     1021 cccgcaagtc cgaagaataa ttagcgcatg ttcaatgagt tctttacttc gttgaggact
     1081 aaaccattca ccattaaatt tacccccatg gaaaagatta tttctaattc tacaaataag
     1141 agaaaaaaca agctcagact tatttctatg gtcaggcaat acattagacc aacataataa
     1201 accatctttt aaaacttgtt tttttggtgg gttgtttatc aggtatgata ttgactcatt
     1261 taactcttta cttggacttt caatcaatga aacgaattca ccagcatact tataccaatc
     1321 agcttctact ctagtatttg tgcccttacg aaatccggta accttaagac aatattcata
     1381 gcgagcaaat tcacgaaaaa agttatatcc taaataatct agttctaatg tagattgctt
     1441 cataaaaacc tcataaatga aaaaatatgt aatttaattt atattacact tttccattac
     1501 aatagattcc aacacaagaa aagcagggcg ctggcccggg gcagggacat tttcataaac
     1561 ataagcatta ggaataactt taccagtaga aggtgaagtc gatggttttg cattcttatt
     1621 tctgtactct atcgattctt cagtagcaaa ctgaacaaag tctccgacag agaagttagg
     1681 acattttttc tgtcttttga aaaaatcata ttgaataaca gcggctaaat agccattaca
     1741 aaaaccccaa gctccttttt cttttatatc gtttcgtgca ctatcacaat gactacccca
     1801 ttctgacatg gtagggtgcg ctgcatcaat atatttactg ccagggatat taataggcat
     1861 atcaaaaata ttattttcag cattaacgga agaagataag ctgattaaat acagagtaaa
     1921 aacagacgca acaagtgaaa gtctcattat aaaaacctct tattcatccc aagtctataa
     1981 tatttactac ggctaatatt taaatttacc catggtttta aacttgcatc agatgcaata
     2041 gatattcgtc cctttgggcg acctcctcct cggctttttt ttcctctaac tgattgaatc
     2101 tcactagaat gagtacgaga tacataggca ccaaatgttt cctcactaaa ttttgactta
     2161 gtccatttag caatgctctt ggctatacca ttaacctcat tttcatccag aggcgctgca
     2221 aattgcaggt tataagcgtt ggcacgttcg tagcaggctc ttaaccactg ttcataatca
     2281 ggccagccct gacgaatggc gcgataagcc catttacggg ttttatcgaa cagggtgcag
     2341 ttacggccta aaccgtagtc gggtaggatt tctttgtcgt tcgctgcact caggtcaagt
     2401 gagtctgcta accagtcgag cgtgtagagt tccggttgcc acacggcaag ctgccagtgg
     2461 tcatggttcg gatttttgca gattaaccct gaatagccag tgtcagcgtc cagtttttta
     2521 cacagcgcac gctcaaccgc tgccgcatac ttcagcggct taatttttcc gtcaggtgcc
     2581 gtgcgcaccg ctgttttcag cgcatacagt aagtgggcat gtccgttttc cggattcatg
     2641 atggtcagcg ttggcgcagg tgcgttccgg tcgctccagt ctatcgccgc gccggggcgg
     2701 tcaacgtcaa aaccgagcca gaacatcgcg tgtggctggt tgaactggat gtatttcgca
     2761 agaatggcgc gctctttccc ggcaatgcgt actccgaact ggagttcgtc ggtaaaatag
     2821 ggtttgcggg gaagccgctc gttaaaaagg tcgagtgcct ggttactcaa tctcgcctgc
     2881 gcttatggcg ggctgttgtt tcgcacggtt catgtgctag tatccttctt aggttttgtg
     2941 cctgcgccct cgttaatcat gtccttccgc caagtcgagc atgattacgg gggcgtcgtc
     3001 ttttctgccg cttaacgtta cacaccccgc cgtattttgt cacctgtcac cgtcagttat
     3061 tgcctgaagc aacagaccat taccttccgg gtaaaaaacg cgtacactgg caacacgtgc
     3121 tatatacacg tgtaaaaatc aggagatcat catgcccgta tcagcgatgc gccataaaaa
     3181 aaccgtcagt gtgacaatcg agcctgcgct tttgcatcag gcccgcgaag ccgggattaa
     3241 tctgtctgcc acgctcacca ccgccctgaa acatcagatc cgcgagtcag aagcggagcg
     3301 ctggaaacgc gccaaccgca aggcaatcca ggagctcaac cgtattacgg acgagcacgg
     3361 cttactctct gacgatcaca ggacgttctg atgcagttca tggtttaccg caataacagc
     3421 aacaaccggg cttatcccta tctgctcgat gtacagagcg atattatcga cgaactgaat
     3481 acccgcctgg tgatcccgct gtttctgctg gatgaagtga atggacggcc cgcccgccgc
     3541 ctgaccccgg tgctgaatgt ggacggtgag gattttctgg tcatgacaca tgaaatggcc
     3601 agcgttcgcc agtcacagct cggggaagag gtggtgagcg tccgggagca ccggcaggcc
     3661 atcaagaatg cgctggattt tctgctcgac ggtttctgag tttacctttc catcccgtga
     3721 tcgtgtcccc ggctgcgtcc gggggcaaat gagcgcgttt tctgtcgttc ctgtttctgc
     3781 gccagctccc tgtccagtct ggctacctgc gcgtcaagcg gctgacggct tcggttaagc
     3841 tcatgacctg ctgccgcaag ctctccacct gcccgctcaa gtgctgacac gcctggtcgc
     3901 tgcgcatcag cgcggcggaa gtagtggtga acatggtctg caagctgtcg taactggcct
     3961 gccatgcctg ctgtcgtgtc tcgtaatcgt cctgtaagcg ctctaacgca ctcagcagca
     4021 gtttttcggt ctcggtcatg gatttgcttg tccttatcgc taaaaacgcc gtatggcgct
     4081 tctgtggcaa ctgacggggc tatttcgcgg tgtaggtcac gacctgtttg tcgtttttcg
     4141 aggtgtacag ctcgacgccc ttcgcgctct tcggcagcac cacgtaatac ttgttcttcc
     4201 gggtgtcgtc cgtgagtatt tccacccccg cccccgattt cgctttcagg tcggtaagct
     4261 gctggctgta gctgttcatc tcgtccagac gtgaggcgat gagtgtcccc tgaaaccaca
     4321 gtatccccga cagaataccg atcagcagca caccacaaaa caatatccat atcagcgcga
     4381 tcgtgaccga gcgccgcagc agggttgtct gcctgacgtt ctgttcgtgg atagcgtcgc
     4441 tgatgctctt cccgcttgat ttcaaggcct cgctgatgga ttgctcgagc ttcacaaact
     4501 cgctcttcac gctctcccct gtacgctgtg cctgctgctt cgaggtctct tcgaaggctt
     4561 tcgctaaatc taaaatcccg ctcatataac gcccctttta accggatatt tcgtccaccg
     4621 tccgggtcgg caatgctgag actgcttttc gtttcccgca ccaccgtcag cccgccgttt
     4681 tccagcgccc tgaccacatt ctcacggttg cggatcatac cctgtgccac catcgtttcc
     4741 agcgagtccg taatggcctg cgccgccttc tgacggtcgc cgggaaggtc attgcccggt
     4801 gtcagggtgc gtcgtcgggc aggatcatga gggtcatcga ggttcaagcg gtcattggtc
     4861 agagtctgcc aggcgttgac cctgggacga tcagcccggt catagtaggg ttgcaggcgt
     4921 tttccgctct gcaattcgat gt
//
