LOCUS       NZ_CP103370             3773 bp    DNA     circular CON 26-JAN-2024
DEFINITION  Citrobacter freundii strain 140542 plasmid p3_140542, complete
            sequence.
ACCESSION   NZ_CP103370
VERSION     NZ_CP103370.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN30470988
            Assembly: GCF_024800305.1
KEYWORDS    RefSeq.
SOURCE      Citrobacter freundii
  ORGANISM  Citrobacter freundii
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Citrobacter; Citrobacter freundii complex.
REFERENCE   1  (bases 1 to 3773)
  AUTHORS   Wen,H., Wu,S., Liu,L., Feng,Y. and Zong,Z.
  TITLE     The complete genome of Citrobacter freundii strain 140542
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 3773)
  AUTHORS   Wen,H., Wu,S., Liu,L., Feng,Y. and Zong,Z.
  TITLE     Direct Submission
  JOURNAL   Submitted (23-AUG-2022) Center of Infectious Diseases, West China
            Hospital, Sichuan University, Guoxuexiang 37, Chengdu, Sichuan
            610041, China
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: Trycycler v. 0.5.3
            Genome Representation             :: Full
            Expected Final Version            :: No
            Genome Coverage                   :: 150.0x
            Sequencing Technology :: Illumina HiSeq; Oxford Nanopore MinION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 01/24/2024 16:49:42
            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)                     :: 5,674
            CDSs (total)                      :: 5,553
            Genes (coding)                    :: 5,389
            CDSs (with protein)               :: 5,389
            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)              :: 164
            CDSs (without protein)            :: 164
            Pseudo Genes (ambiguous residues) :: 0 of 164
            Pseudo Genes (frameshifted)       :: 37 of 164
            Pseudo Genes (incomplete)         :: 118 of 164
            Pseudo Genes (internal stop)      :: 29 of 164
            Pseudo Genes (multiple problems)  :: 19 of 164
            Pseudo Genes (short protein)      :: 1 of 164
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP103370.1.
            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..3773
                     /organism="Citrobacter freundii"
                     /mol_type="genomic DNA"
                     /strain="140542"
                     /isolation_source="rectal swab"
                     /host="Homo sapiens"
                     /db_xref="taxon:546"
                     /plasmid="p3_140542"
                     /geo_loc_name="China: Chengdu, Sichuan"
                     /collection_date="2020-11-23"
     gene            complement(45..461)
                     /locus_tag="NYE91_RS28295"
                     /old_locus_tag="NYE91_28260"
     CDS             complement(45..461)
                     /locus_tag="NYE91_RS28295"
                     /old_locus_tag="NYE91_28260"
                     /inference="COORDINATES: protein motif:HMM:NF015076.4"
                     /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_258983436.1"
                     /translation="MIIQDNHTIEIFKNQLPVKPYCSNNLENGLSIRNKNKALEMLYLQ
                     ANQPAIQTCLLFDLDEDNASYKFDEVGLPVPTFITKSPESGRCHYGYMLKAGVCKTQHA
                     RLKPLKYAAAIEAGIAGKLASDRGYAGLITKSTA"
                     /name="replication initiation protein"
     gene            741..1046
                     /locus_tag="NYE91_RS28300"
                     /old_locus_tag="NYE91_28265"
     CDS             741..1046
                     /locus_tag="NYE91_RS28300"
                     /old_locus_tag="NYE91_28265"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001722506.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_107334418.1"
                     /translation="MQKSKRKLGFMIGKSNATLPDEATDAAIDDEVTNLFFESLLESAK
                     EAVEIHNGKRPAARRTLHKVNRTTKDTIERSEARTDVFKATDAPDLFKKLKMDRDN"
                     /name="hypothetical protein"
     gene            complement(1260..1511)
                     /locus_tag="NYE91_RS28305"
                     /old_locus_tag="NYE91_28270"
     CDS             complement(1260..1511)
                     /locus_tag="NYE91_RS28305"
                     /old_locus_tag="NYE91_28270"
                     /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_258983438.1"
                     /translation="MSKAKEKIDNRMAYHLQQLAQLRAKKKEELSKEKKAEKAKRASKN
                     ILFGASICKVLGIDYTKIDEYLPSVIGYLDLKKTELKK"
                     /name="hypothetical protein"
     gene            1743..2603
                     /locus_tag="NYE91_RS28310"
                     /old_locus_tag="NYE91_28275"
     CDS             1743..2603
                     /locus_tag="NYE91_RS28310"
                     /old_locus_tag="NYE91_28275"
                     /inference="COORDINATES: protein motif:HMM:NF015354.4"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MobA/MobL family protein"
                     /protein_id="WP_258983439.1"
                     /translation="MAIYSFQCKIVARTKRLNNAVAHAAYINRIDLDNSRDGSKWRYNH
                     RHDDVYKSAVLLPDNANKKFSDPAYLWNEVEKKENRSNSRLARSFIIALPNELTPEQNK
                     NLIEDYIKNHMTSKGMIVNYAIHIDDTNNFHAHLMSTTRELDPNGLEFAKKNVIGRTWN
                     DDDFLEGLRKGWADTANTHLARFDHQVRIDHRTLSAQRDEALEQFDMATTAEAKAEALA
                     KAVSLDRPAIGRIWRSKLNTEEGRALREAQQDRRDVQLVVAEETKKSVLSLPQEIVLNN
                     FTPKK"
                     /name="MobA/MobL family protein"
     gene            2844..3002
                     /locus_tag="NYE91_RS28315"
                     /old_locus_tag="NYE91_28280"
     CDS             2844..3002
                     /locus_tag="NYE91_RS28315"
                     /old_locus_tag="NYE91_28280"
                     /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_258983434.1"
                     /translation="MPNHYNSDYFIDDKSTIIKDEYKDDEYKKLQKFFDDVNKRGVELK
                     NKKRSHT"
                     /name="hypothetical protein"
     gene            complement(3113..3382)
                     /locus_tag="NYE91_RS28320"
                     /old_locus_tag="NYE91_28285"
     CDS             complement(3113..3382)
                     /locus_tag="NYE91_RS28320"
                     /old_locus_tag="NYE91_28285"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001722510.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="HTH domain-containing protein"
                     /protein_id="WP_094929360.1"
                     /translation="MIINGKKVKAKELAEMAGVSRRTVVKYYAMPREAYEDEAAERRKK
                     AYELREKGLKWKDVGKELNTSLHGAVALYKRYLKLDLNQQQQQQ"
                     /name="HTH domain-containing protein"
     gene            complement(3379..3768)
                     /locus_tag="NYE91_RS28325"
                     /old_locus_tag="NYE91_28290"
     CDS             complement(3379..3768)
                     /locus_tag="NYE91_RS28325"
                     /old_locus_tag="NYE91_28290"
                     /inference="COORDINATES: protein motif:HMM:NF020291.4"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="primase C-terminal domain-containing protein"
                     /protein_id="WP_258983435.1"
                     /translation="MADFVELQTPTKEVKSENYGLGRNVNLFEDLRAYAYKRVLKFKQD
                     LNYEAWERDVLNVAEGLNTHCNALNPLQYNEIKATARSVSRWTWKHFDSATFSDIQSNR
                     GKRNLGKTKRTSAKNKIDNVLELFK"
                     /name="primase C-terminal domain-containing protein"
     Typing          complement(6..461)
                     /name="rep_cluster_1451"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="86.768"
                     /coverage="94.0"
                     /evalue="3.76e-141"
     Typing          complement(3424..3773)
                     /name="rep_cluster_1451"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="88.92"
                     /coverage="94.0"
                     /evalue="2.33e-118"
     Typing          1744..2594
                     /name="MOBQ"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="94.014"
                     /coverage="91.0"
                     /evalue="4.53e-177"
ORIGIN
        1 ctaactcata cagatcagca cctgaccaat agggtgacca atgttcatgc agtggatttt
       61 gtaatcagtc cagcatatcc tcgatcagaa gctaactttc cagcaatgcc agcctctatg
      121 gctgctgcat actttaaagg cttcagcctt gcgtgttgtg tcttacaaac accggctttg
      181 agcatatagc cgtagtggca acgtccagac tcaggagatt ttgtgatgaa cgtaggaaca
      241 ggaagcccta cctcatcgaa cttgtaggag gcgttgtcct catcgagatc gaacagtaag
      301 cacgtctgta tagctggctg atttgcttga aggtaaagca tctcaagtgc tttgtttttg
      361 ttcctgatac taagaccatt ttctaaatta ttggaacagt aaggcttcac aggtaattga
      421 tttttaaata tttctatagt atggttatct tgtattatca tttttaagca gtcctttttt
      481 atctggcccc gccttctgta tgtcgccaaa catagagcag aatgcggggt tttttgtttt
      541 tgttatattt ttttcaactc tgtaacggtt ttaaccgatc taaaaagttt gtcaagtggg
      601 agtcttaacc atatcagata acagcccttt aaaggggcag ttttccggca ctactggaaa
      661 cctattccaa caaaccaaca aggccgaagg ctgataaaat agagagtaag atctggctgt
      721 gctggatagg agaacatgag atgcagaaat caaagcgtaa gctggggttt atgattggta
      781 agagcaatgc aaccttgcct gatgaagcaa ctgatgcagc tattgatgac gaagttacca
      841 acctgttttt tgagtctctg cttgagtctg caaaagaagc tgtcgaaatc cacaacggga
      901 aacgtcctgc agctcgtaga acgctgcata aggtaaaccg aactaccaaa gacacgatag
      961 aacgctcaga agcccgtaca gacgttttta aagctactga tgcccctgat ctcttcaaaa
     1021 agctaaaaat ggacagggac aactgaccac ctccaccaaa caaaccacca agttacgaag
     1081 ctggccagct atcccggagg gcagtatata ctatactaat atatactata ctctgttgat
     1141 tttatgacca tttctaactg catagacgcc agcaaacgag caaaagcaag ttttactcgt
     1201 ttctgtcgcc gttatttttc cagctttcta aaagttcatt gcctctatcg gcatacacac
     1261 tatttcttaa gttctgtttt ttttaaatct aaatatccaa taacagaagg caaatattca
     1321 tctattttag tgtaatcaat acctaacact ttacagatag aagcaccaaa caaaatattt
     1381 ttacttgctc tttttgcttt ttctgccttt ttttctttgc tcaactcttc ttttttcttt
     1441 gctcttagtt gtgcaagctg ttgaagatga taagccatcc tattatctat tttctctttt
     1501 gctttactca tatattaagc tcctattatt tattttaata tttattcaat aatatattta
     1561 taaatatttg tcaaaagtat ttttatatgt tatttaataa atataagtaa agcgacattg
     1621 cttattttag tccgagcgaa agcgaggaaa aaataaaaca gcaatgccca cttacacaaa
     1681 ctaaagtttg tagtggtccc tgcggggcta aggtcaaaag caaaaaaata aggtttccat
     1741 ttatggctat atatagtttt caatgtaaga ttgtagcaag aacaaaacgt ttaaataatg
     1801 ctgttgctca tgcagcatat attaaccgta ttgatcttga taatagccgc gatggttcaa
     1861 agtggcgtta taatcatagg catgatgatg tatataaatc tgctgttttg cttccagata
     1921 atgccaacaa aaagttttct gacccagctt atttatggaa cgaagtagag aagaaagaaa
     1981 atagatctaa tagccgtttg gctcgtagtt ttattattgc tttaccaaac gaactaacac
     2041 cggaacaaaa caagaacttg attgaagatt acattaaaaa tcatatgaca tctaaaggta
     2101 tgattgtaaa ctatgccatt catatagatg atacaaacaa ctttcacgct catttgatga
     2161 gcactacaag ggagttagat cctaatggtt tagagttcgc aaaaaagaat gttatcggca
     2221 gaacttggaa tgatgatgat tttcttgaag ggttaaggaa aggctgggca gataccgcta
     2281 atactcattt agcaaggttt gatcatcagg tcaggattga ccatagaacg ctgtcagctc
     2341 aacgtgatga agctcttgag cagttcgata tggctaccac tgcagaggct aaagctgagg
     2401 ctctggctaa ggctgtaagc cttgatagac ctgctattgg taggatttgg cgtagtaagc
     2461 tgaacacgga agagggtaga gctttacgtg aagcacagca agacagaaga gatgtgcagc
     2521 tcgttgttgc tgaagagact aaaaagagtg ttttgtcttt accacaagag atagttttaa
     2581 ataacttcac acctaaaaaa taaaatcaaa atcaaaatca aaaactacta ttgaaaaaac
     2641 acgccccgcc caagaagcag ttttaaaaac tgctgataca ggggagagat aaaagatctc
     2701 aaatatagtt cttttaataa gtttttatta gatattaaga taagatataa caagcatcaa
     2761 aaaaataacg ccactaaaaa gctaaataag aaaatagaca agataataaa gactatagat
     2821 agagaagaga aaaatctaac atcatgccta atcattataa tagtgattat ttcattgatg
     2881 ataaaagtac gattattaaa gatgaataca aagatgatga atataagaag ctacagaagt
     2941 tttttgatga tgtgaataaa agaggtgttg agctaaaaaa taaaaaaaga agccatactt
     3001 aaagctgagc aagaaaataa aaagatgcta tcacaacaac ctaaacacaa cccaaaaaat
     3061 gacgatcaga atgatagaca cattaaatac aaataagcag gccgtaaacc tgctattgtt
     3121 gttgttgttg ttggtttaaa tctaacttca aataacgctt ataaagagct acagcaccat
     3181 gcagagaagt attcaactct ttccctacat ctttccactt caagcctttc tctctcagct
     3241 cataggcttt ttttctacgt tctgctgctt catcttcata ggcttcacgc ggcatagcat
     3301 aatacttaac taccgttctg cgtgatacgc cagccatttc agccagctct ttagctttaa
     3361 ctttcttacc atttataatc atttgaatag ctccaatacg ttatctattt tatttttagc
     3421 actggttctt tttgttttgc ctaagtttct tttacctctg tttgattgta tatctgaaaa
     3481 agtagcacta tcaaaatgct tccaagtcca gcgactaaca gatctcgcag ttgcttttat
     3541 ctcattatat tgtagcggat ttaaagcatt acaatgagta ttgagtcctt cagctacatt
     3601 taaaacatca cgttcccacg cttcatagtt caaatcctgc ttgaacttca atactcgctt
     3661 ataagcataa gctcttaaat cttcaaacaa gttaacattg cgtcccagcc cgtagttctc
     3721 tgatttaact tcctttgttg gtgtttgtaa ctcaacaaaa tcagccaaat aat
//
