LOCUS       NZ_CP154592             4510 bp    DNA     circular CON 09-MAY-2024
DEFINITION  Citrobacter freundii strain NFYY361 plasmid pNFYY361-5, complete
            sequence.
ACCESSION   NZ_CP154592
VERSION     NZ_CP154592.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN41129895
            Assembly: GCF_039554995.1
KEYWORDS    RefSeq.
SOURCE      Citrobacter freundii
  ORGANISM  Citrobacter freundii
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Citrobacter; Citrobacter freundii complex.
REFERENCE   1  (bases 1 to 4510)
  AUTHORS   Chen,J., Li,X. and Rui,Y.
  TITLE     Citrobacter freundii strain NFYY361
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 4510)
  AUTHORS   Chen,J., Li,X. and Rui,Y.
  TITLE     Direct Submission
  JOURNAL   Submitted (30-APR-2024) Laboratory Medicine Center, Nanfang
            Hospital, Southern Medical University, North Guangzhou Avenue,
            Guangzhou 1838th, GuangZhou 510515, China
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: Unicycler v. V0.4.8
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 323.0x
            Sequencing Technology             :: Illumina; PacBio
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_039554995.1-RS_2024_05_08
            Annotation Date                   :: 05/08/2024 13:35:01
            Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline
            (PGAP)
            Annotation Method :: Best-placed reference protein set; GeneMarkS-2+
            Annotation Software revision      :: 6.7
            Features Annotated                :: Gene; CDS; rRNA; tRNA; ncRNA
            Genes (total)                     :: 5,768
            CDSs (total)                      :: 5,648
            Genes (coding)                    :: 5,491
            CDSs (with protein)               :: 5,491
            Genes (RNA)                       :: 120
            rRNAs                             :: 9, 8, 8 (5S, 16S, 23S)
            complete rRNAs                    :: 9, 8, 8 (5S, 16S, 23S)
            tRNAs                             :: 85
            ncRNAs                            :: 10
            Pseudo Genes (total)              :: 157
            CDSs (without protein)            :: 157
            Pseudo Genes (ambiguous residues) :: 0 of 157
            Pseudo Genes (frameshifted)       :: 41 of 157
            Pseudo Genes (incomplete)         :: 109 of 157
            Pseudo Genes (internal stop)      :: 29 of 157
            Pseudo Genes (multiple problems)  :: 22 of 157
            Pseudo Genes (short protein)      :: 1 of 157
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP154592.1.
            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..4510
                     /organism="Citrobacter freundii"
                     /mol_type="genomic DNA"
                     /strain="NFYY361"
                     /isolation_source="rectal swab"
                     /host="Homo sapiens"
                     /db_xref="taxon:546"
                     /plasmid="pNFYY361-5"
                     /geo_loc_name="China: Guangzhou"
                     /lat_lon="23.19 N 113.33 E"
                     /collection_date="2023"
                     /collected_by="Jing Chen"
     gene            1..915
                     /locus_tag="AAIM57_RS28790"
                     /old_locus_tag="AAIM57_28790"
     CDS             1..915
                     /locus_tag="AAIM57_RS28790"
                     /old_locus_tag="AAIM57_28790"
                     /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_128295861.1"
                     /translation="MLLKPTAIRKDGRTYQVFLPYIIDELSERHRKRPAQWFKASLARL
                     QGAPIELQEFCTPKLISGEWDHRTDWISVFDALALLACSPDSYQNDDLIKEIEHETKVE
                     LPVKPGRSKHEAVFGERLNKTLKRISETSGRQFSVITQKHFNGRKYRVDFVVTLEGAPK
                     QYVIEFDEAFHAEKRQRERDLERDRWFRKHEKTLDLIRVEHKHQDNWLKCLEGIGEPRP
                     IEHYYAHCIRVASEIRSKTERVITGESSKAAYDPAKNGCSCLLKHDKRRLKELSAIMVD
                     LNIPFRATDRLFVTRRSPSKYGL"
                     /name="hypothetical protein"
     gene            1570..2172
                     /locus_tag="AAIM57_RS28795"
                     /old_locus_tag="AAIM57_28795"
     CDS             1570..2172
                     /locus_tag="AAIM57_RS28795"
                     /old_locus_tag="AAIM57_28795"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_013716169.1"
                     /GO_function="GO:0003677 - DNA binding [Evidence IEA];
                     GO:0000150 - DNA strand exchange activity [Evidence IEA]"
                     /GO_process="GO:0006310 - DNA recombination [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="recombinase family protein"
                     /protein_id="WP_241657254.1"
                     /translation="MRASTAEQDAARASQSLNTFAEERGLTIAANFIENVSGASLQRPE
                     LFRLLAVAQAGDILLVEQIDRLSRLDADDWERLRGVIQSKGIRIVALDLPTSYLQLQSG
                     NDEFMRSMMNAINGMMLDMLAAIARKDYTDRRRRQAQGIEKAKEMGLYKGRQPDLEKHE
                     HIRTLISQGNSQRKVAKMLGCAVGTVRNALNAEKTMG"
                     /name="recombinase family protein"
     gene            2670..3140
                     /locus_tag="AAIM57_RS28800"
                     /old_locus_tag="AAIM57_28800"
     CDS             2670..3140
                     /locus_tag="AAIM57_RS28800"
                     /old_locus_tag="AAIM57_28800"
                     /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_182347746.1"
                     /translation="MMSEKDSFFKTVNANINAEKAGIEAFKKDVFEFQKGTTWLLDEIQ
                     SWFDGSPITSQKSTARVTEGSDSFEVSTLILKNSGKTLTIAPECLYFWGGRGSLEVSIH
                     NINRSPNTSKFTLHQHDKTSNIDGWVIVSAGNPAQRIEFNQENFFSMIQSFA"
                     /name="hypothetical protein"
     gene            complement(3156..3530)
                     /locus_tag="AAIM57_RS28805"
                     /old_locus_tag="AAIM57_28805"
     CDS             complement(3156..3530)
                     /locus_tag="AAIM57_RS28805"
                     /old_locus_tag="AAIM57_28805"
                     /inference="COORDINATES: protein motif:HMM:NF024139.4"
                     /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_128295858.1"
                     /translation="MASHSVTEAAKLAGVTRRTIYRHIKAGKLSASVTGGDNTVIETSE
                     LLRVYGVLSQPEPEKVSTGSLENQPEYVTLLLAEMSQLREMVSHLSSKVDELQSRLALP
                     APRDQSVLEWVKERRGKRAD"
                     /name="helix-turn-helix domain-containing protein"
     gene            3652..4236
                     /locus_tag="AAIM57_RS28810"
                     /old_locus_tag="AAIM57_28810"
     CDS             3652..4236
                     /locus_tag="AAIM57_RS28810"
                     /old_locus_tag="AAIM57_28810"
                     /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_128295859.1"
                     /translation="MYEYYTRAQQVLDVLERTCEKLQLNRSIKLVSNLRRKGLLAEPSI
                     AYLMDSLRPNEAKRFCEAMAFIEGHFARLKPEDKIFIKTEAPATKGFYMAHLRDHSTII
                     ELARRMMIGERRFTGVDPQLVDVASTLASSPTWCVRVLIPSIDPRKAAIIINKLAALIY
                     RALERVKGKPVPHQYVAQLQRMSYELHQMRS"
                     /name="hypothetical protein"
     gene            complement(4233..4454)
                     /locus_tag="AAIM57_RS28815"
                     /old_locus_tag="AAIM57_28815"
     CDS             complement(4233..4454)
                     /locus_tag="AAIM57_RS28815"
                     /old_locus_tag="AAIM57_28815"
                     /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_128295860.1"
                     /translation="MSISDDIWQDIQFGSLEPFCRDGFFPSPQTFSRVFWEQYVAGGNA
                     GWDDYRPALNELVYRGYLKQSQNGWYVF"
                     /name="hypothetical protein"
ORIGIN
        1 ttgttactca aaccaacggc aataagaaag gatggtcgga catatcaagt attcctgcca
       61 tatatcatcg acgaactttc tgaacgacac cgaaaacggc ccgcccaatg gttcaaggct
      121 tcactagcac gtcttcaggg ggccccaatc gaactgcaag aattctgcac gccaaagctg
      181 atttccggcg agtgggatca ccgtacagac tggatttcgg tatttgacgc tctggcatta
      241 ctcgcttgta gccctgacag ttaccagaac gatgatctca tcaaggaaat cgaacatgaa
      301 accaaagtag aacttccggt taagcccgga agaagcaagc atgaagccgt atttggcgag
      361 cggctcaaca aaacccttaa acgcatttca gaaaccagcg gtaggcaatt cagtgtcatc
      421 acgcagaagc atttcaacgg aagaaagtac cgcgtcgact tcgttgtcac cctcgaggga
      481 gcaccaaaac aatacgtaat tgagtttgat gaggcattcc acgcagagaa gcggcagcga
      541 gaacgggatt tagagcgtga cagatggttt agaaagcatg agaaaaccct agacctcatc
      601 cgagtagagc ataaacacca agacaactgg cttaaatgcc ttgaaggtat cggagaacca
      661 cgcccaatcg agcactatta cgctcactgc atccgagttg ccagcgagat caggtcgaaa
      721 acggagcggg taattacagg agaatcatca aaagcggcct acgatccggc gaaaaatggc
      781 tgttcctgcc tgctaaagca cgataaacgc cgcctgaaag agctatcagc catcatggta
      841 gacctcaaca ttccattcag agcaaccgat cggctgttcg taacccgccg cagccccagt
      901 aaatacgggc tgtaattaca aaagtcacat gaaaagttac aacgaaatgt tgatgctctg
      961 cgattttcgg ggtgttcaaa cgttgtaacc tttgtaaccc acctcaacac acccttatat
     1021 agatatttat ctctttatta attattgact tgccttcagt ttcctagccg atgttctcat
     1081 cattagattt acctacgctt caaccaaact agcaattcca gtcatgatct gaaatctggc
     1141 ctaactcact gcactacatt cagccaaaag cagcatagaa ccaacaaatt catgaaccac
     1201 aggtatcaga atcacatacc aaacgatact cacccataaa tcactcatca gaagcaacca
     1261 gacgacctgt gaggcgatga gtgacatatt cacacccaaa tccacacgca catcatagag
     1321 gctctcaaaa tgcgattcat gaagttattc aggcacgcac tgatggcagc agcaacggct
     1381 ttccttgctg ctatcatcga cgggctatcc ggcactatct gacccgttca ttatgggtat
     1441 acctcagcta taacggcctg acctactcaa aaaccggtac atttagaccc cgccgatgac
     1501 tcaaaatgca ccaccaccat agtgacacac caaaatgaca cataggatga catgaggact
     1561 tacgcttaca tgcgggcatc cacagctgaa caagatgctg cccgtgcatc acaatcactg
     1621 aacaccttcg cggaagaacg cgggttaacc atcgctgcaa acttcatcga gaacgtatcc
     1681 ggtgcatcac tacagcgtcc tgaactgttc cggcttctcg ccgtagctca agcgggtgac
     1741 attctgcttg ttgaacaaat cgaccgcctc agccgtctcg atgctgacga ttgggaacgc
     1801 ctcagaggag taatacagag caagggaatc aggatagtcg ctctggatct gccaaccagc
     1861 tatctgcaac tacaatccgg aaacgatgag ttcatgcgtt cgatgatgaa tgctatcaac
     1921 gggatgatgc tagatatgct cgccgccata gcccgcaagg actacacaga tcgccgtcgt
     1981 cggcaagctc agggcatcga gaaggctaaa gaaatggggc tctacaaagg gcggcaaccc
     2041 gatttagaaa agcatgagca cattcggact ctgatctctc agggaaactc acagagaaag
     2101 gtggctaaga tgctgggctg tgccgtggga acggtaagaa atgcacttaa tgcggagaaa
     2161 acaatgggat gatcaaccct caaatgtaca aaagccccgt gacagaatca cagggcttcg
     2221 gtactctaat tcttgcagat gcctgccagg atcagacttc gacaatccaa tcctagcagg
     2281 gctggctagc tatgtcacta ccagcttaat accattcaac gacattaaac ccacatctgc
     2341 acccttgaaa ctcaggtcta cgccccggac tccggcagga taaacaggca aacggtggga
     2401 acctaaccag cacgggaaag aagctggctc taccccgtct cgctgtacga taacaagcac
     2461 ctgataaagt gagaatcaag gaagtagttg cggtgacgtg taattgccac ggtctggctc
     2521 atcacccaca caatgcagat aaaacagacg accagacgct ggtcgctccg ctcccatttt
     2581 ctggtgtacc caccatgggg gcattaggca tctattgcca tttatttgtc ttcccgtcac
     2641 catagttgga acacaatcag agaggatcaa tgatgtcaga aaaagattcg ttctttaaaa
     2701 ccgtcaacgc gaatataaat gcagagaaag caggaattga ggcgttcaaa aaggatgtat
     2761 ttgaatttca gaaaggcact acatggttgc tcgatgaaat tcaaagctgg tttgatggct
     2821 caccaataac atcacaaaag tccacagccc gggttactga aggtagtgac agctttgaag
     2881 tatcaacatt gatactaaaa aacagcggaa aaacactgac cattgcccct gagtgccttt
     2941 atttctgggg ggggagaggt agcttagagg tatctatcca taacatcaat cgctcaccaa
     3001 atacctctaa attcaccctt caccagcacg acaaaactag caacattgat ggatgggtaa
     3061 tagtttctgc gggaaaccct gctcaacgaa ttgagttcaa ccaagagaac ttcttctcaa
     3121 tgattcaatc gtttgcctga tgcctaaagg gctagttaat cagccctttt tccacgtctc
     3181 tccttcaccc attctaaaac actttggtca cgaggggcag gtagagccaa ccgactctgt
     3241 aactcatcca ccttgcttga aagatgacta accatctccc gaagttgtga catttcagcc
     3301 aataaaagtg tgacatattc aggctgattt tcgagtgatc ccgtggatac cttctcaggt
     3361 tcaggctgtg acaacacgcc atagacacgc agtaattcac tggtttcaat aaccgtattg
     3421 tcaccccccg tcacacttgc ggaaagctta ccagccttga tatgccgata gattgtccgt
     3481 cgtgtgacac cagctaactt tgcagcctca gtgacactgt gactcgccat gtgacaccac
     3541 cagaattaat tgagtgatcg taagtgacag gatcacatga tgtcacacca ctatagcacc
     3601 cgcaaattgc agctaatatc aatgaaccaa taccagataa acggaggtcg aatgtacgag
     3661 tattacacga gggcacaaca agtgctggat gtactggaaa gaacctgtga aaaacttcag
     3721 ttgaacagat caatcaagtt agtttcaaac ctacgcagaa aaggactact ggcagaacca
     3781 tctatcgcct acctgatgga ctcgctacgc ccaaatgaag cgaaacggtt ctgcgaggct
     3841 atggcattca ttgaaggcca ctttgcacga ctaaaacccg aagacaaaat attcataaaa
     3901 acagaagcac cagcaactaa aggcttctac atggcacacc ttcgtgatca ttcaaccatc
     3961 atagagctgg ctcgcagaat gatgattggc gaacgacgct tcactggcgt tgatccacaa
     4021 ctggtcgacg tcgcatcaac ccttgcaagc agccctacat ggtgcgtcag agtgctaatc
     4081 cccagcatcg acccacgaaa agcggcaata atcatcaaca aattggcagc attaatttat
     4141 cgggctctag aacgagtgaa agggaaacca gtgccacatc aatacgtagc ccaacttcag
     4201 cgaatgagct acgaattaca tcaaatgcgg agctaaaaca cgtaccaccc gttctgactt
     4261 tgtttcagat aacctctata gaccagctcg tttaacgctg gtctatagtc atcccatcca
     4321 gcattaccgc cagcaacata ctgctcccag aacactcgtg aaaaggtttg cggcgatggg
     4381 aaaaaaccat cacggcagaa tggttctaac gaaccaaatt gtatatcttg ccaaatatca
     4441 tcactaatac tcataaaatc ctccttaaag ggttgttgta attaaattta tttataaaac
     4501 aggaggcatt
//
