LOCUS       NZ_CP137198             4665 bp    DNA     circular CON 31-JAN-2024
DEFINITION  Citrobacter freundii strain F2021 plasmid pF2021-4, complete
            sequence.
ACCESSION   NZ_CP137198
VERSION     NZ_CP137198.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN37934525
            Assembly: GCF_036289185.1
KEYWORDS    RefSeq.
SOURCE      Citrobacter freundii
  ORGANISM  Citrobacter freundii
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Citrobacter; Citrobacter freundii complex.
REFERENCE   1  (bases 1 to 4665)
  AUTHORS   Li,X.
  TITLE     Citrobacter freundii F2021 Genome sequencing and assembly
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 4665)
  AUTHORS   Li,X.
  TITLE     Direct Submission
  JOURNAL   Submitted (24-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                   :: 01/31/2024 01:58:24
            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)                     :: 5,030
            CDSs (total)                      :: 4,906
            Genes (coding)                    :: 4,809
            CDSs (with protein)               :: 4,809
            Genes (RNA)                       :: 124
            rRNAs                             :: 9, 8, 8 (5S, 16S, 23S)
            complete rRNAs                    :: 9, 8, 8 (5S, 16S, 23S)
            tRNAs                             :: 84
            ncRNAs                            :: 15
            Pseudo Genes (total)              :: 97
            CDSs (without protein)            :: 97
            Pseudo Genes (ambiguous residues) :: 0 of 97
            Pseudo Genes (frameshifted)       :: 28 of 97
            Pseudo Genes (incomplete)         :: 61 of 97
            Pseudo Genes (internal stop)      :: 20 of 97
            Pseudo Genes (multiple problems)  :: 13 of 97
            Pseudo Genes (short protein)      :: 1 of 97
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP137198.1.
            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..4665
                     /organism="Citrobacter freundii"
                     /mol_type="genomic DNA"
                     /strain="F2021"
                     /isolation_source="urine"
                     /host="Homo sapiens"
                     /db_xref="taxon:546"
                     /plasmid="pF2021-4"
                     /geo_loc_name="China: Hangzhou"
                     /lat_lon="29.86 N 121.56 E"
                     /collection_date="2023-03-02"
                     /collected_by="Jiaoyao Yao"
     gene            complement(489..2045)
                     /locus_tag="R4T18_RS25130"
                     /old_locus_tag="R4T18_25125"
     CDS             complement(489..2045)
                     /locus_tag="R4T18_RS25130"
                     /old_locus_tag="R4T18_25125"
                     /EC_number="2.7.7.65"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_015589620.1"
                     /GO_function="GO:0052621 - diguanylate cyclase activity
                     [Evidence IEA]; GO:0046872 - metal ion binding [Evidence
                     IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="sensor domain-containing diguanylate cyclase"
                     /protein_id="WP_032993376.1"
                     /translation="MRIKKPHLRPIVITLSVGGILLTSIFLIAVIMVFQRENIEKDLLY
                     ANSSYAMKMSDVMSGYIEMAQGELAYGAKKIKSTNDIDSLKDEADRLRLQSGMFNSVLV
                     VSNDAVVLATSPESLDLVGTRLNSSASKLAIEEKKPFISSPLKSVTGNLIILLSHPIYD
                     KGGNYIGYVGGSIYLKKHNLFGDVLSRHFFKNNTEISIVSDDGNVIFNNDKSAVDRPMV
                     MSDDLKSKLTASDRGEGAFFSSGHRYLLGYASMKNTAWNVLVYSRADSVTTILIAYAKS
                     VLVLLIIIIIVFSLISYFIASSISLPLEKLAISTNAKDIGASLVYIKAINAWYAEADRL
                     KKALFTYIKVMMERVDFLNEVALKDPLTGVNNRLGFLSKIQNHKRDSGYSVIVIDVDFF
                     KEINDSFGHGVGDEVLVSLAHIINSCCRSEDVVCRFGGEEFVVFLPNTSVVTAKCVAER
                     IRSVIESTVFPNNLRVTISAGVATQDDPLGRIDFLLKNADDALYQAKREGRNKVIVYSA
                     I"
                     /name="sensor domain-containing diguanylate cyclase"
     gene            complement(2391..2606)
                     /locus_tag="R4T18_RS25135"
                     /old_locus_tag="R4T18_25130"
     CDS             complement(2391..2606)
                     /locus_tag="R4T18_RS25135"
                     /old_locus_tag="R4T18_25130"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000137422.1"
                     /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_012565230.1"
                     /translation="MTELEKQLLSALEQLQQDYSKRLDEWESAFAEWRTMSGLMLRENA
                     ALSERVTGLSRQVQSLSEQLRRLSSD"
                     /name="MbeD family mobilization/exclusion protein"
     gene            complement(2610..3095)
                     /locus_tag="R4T18_RS25140"
                     /old_locus_tag="R4T18_25135"
     CDS             complement(2610..3095)
                     /locus_tag="R4T18_RS25140"
                     /old_locus_tag="R4T18_25135"
                     /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_012565228.1"
                     /translation="MNSLLTLAKDLEQKSKAQQQNTGEMLKAAFSEHEKSVKAELNESA
                     KRISAAILDHDRKLSSAMSQRTKGMVRMVSQTWLTIVLVSALLIASSAGILWWQGQQIL
                     DNYTTIREQKSTQAMLSERNSGVQLSTCGEQRRRCVKVNPEAGRFGEDSSWMILAGK"
                     /name="MbeB family mobilization protein"
     gene            complement(<3130..3834)
                     /locus_tag="R4T18_RS25145"
                     /old_locus_tag="R4T18_25140"
                     /pseudo=""
     CDS             complement(<3130..3834)
                     /locus_tag="R4T18_RS25145"
                     /old_locus_tag="R4T18_25140"
                     /inference="COORDINATES: protein motif:HMM:NF015397.4"
                     /note="incomplete; partial in the middle of a contig;
                     missing C-terminus; Derived by automated computational
                     analysis using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="relaxase/mobilization nuclease domain-containing
                     protein"
                     /name="relaxase/mobilization nuclease domain-containing
                     protein"
     gene            complement(3773..4096)
                     /locus_tag="R4T18_RS25150"
                     /old_locus_tag="R4T18_25145"
     CDS             complement(3773..4096)
                     /locus_tag="R4T18_RS25150"
                     /old_locus_tag="R4T18_25145"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000957083.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MobC family plasmid mobilization relaxosome
                     protein"
                     /protein_id="WP_007772081.1"
                     /translation="MLTMWVTEDEHRRLLERCDGRQLAAWMRQTCLDEKPARSGKLPSI
                     SPALLRQLAGMGNNLNQIARRVNAGGGTGHDRVQIVAALMAIDAGLERLRHAVLEKGTD
                     DDR"
                     /name="MobC family plasmid mobilization relaxosome protein"
     Typing          complement(4210..4383)
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="98.857"
                     /coverage="100.0"
                     /evalue="5.54e-83"
     Typing          2..194
                     /name="rep_cluster_2335"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="90.863"
                     /coverage="93.0"
                     /evalue="1.19e-66"
     Typing          4350..4662
                     /name="rep_cluster_2335"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="94.921"
                     /coverage="96.0"
                     /evalue="2.2599999999999998e-136"
     Typing          complement(2288..3783)
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="91.182"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          complement(3780..4096)
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="93.396"
                     /coverage="99.0"
                     /evalue="1.81e-61"
ORIGIN
        1 cgctgttatg gccgcgttta tctcattcca cgcctgacac tcggttccgg gaaggcagtt
       61 cgctccaagc tggactgtat gcacgaaccc cccgttcagc ccgactacca cgttgtcccg
      121 gtaactatca tcttgagtcc aacccggaac agacacgaaa aatcgccagt ggcggtagcc
      181 attagtaaga ggattcacgg agcggagtag tagagtgttc tacagagttc ttgaagtggt
      241 ggcctgactg cggctacact ggaaggacag ttttggtacc tgcgctccgt gaaagccagt
      301 taccttcgga agaaagagtt ggtagctctg aattccggca aacgaaccac cgttggtagc
      361 ggtggttttt ttgtttacag ggtatgagat tacgacgaca tcgaagggat aacaagagga
      421 tccgcttctt gcccactctt cgccacaaaa aaaacgacac actagcgcgt aaagcatcat
      481 caaaaaactc aaatagcgct atatacaatc actttattac gcccctccct tttggcttga
      541 taaagagcat cgtcagcatt tttcagcaaa aaatcgatcc taccaagagg atcatcttgt
      601 gttgccacac cagcagatat ggtgacccgc aagttattag ggaagacagt actttcaata
      661 acactcctaa tacgctccgc aacacactta gctgttacca cagatgtatt cggcaggaaa
      721 acaacaaact cttcgccacc aaaccgacaa acaacatctt cactacggca acaggaatta
      781 ataatatgag ccaaagaaac aagcacctca tctccgaccc catgcccgaa actgtcattt
      841 atctctttaa aaaaatcaac atcaattaca ataactgaat accctgaatc ccgcttatga
      901 ttctgtattt tacttaaaaa ccccaatcta ttgttcacgc cggtaagggg atctttaagc
      961 gccacctcat ttagaaaatc aactctttcc atcattacct taatatacgt aaaaagcgcc
     1021 tttttaagcc tatcagcttc ggcataccaa gcattgatag ctttaatata aactagcgaa
     1081 gctccgatat ctttagcatt ggtagatata gcaagctttt ctaaaggaag tgaaatactg
     1141 gaggcaatga aatatgaaat aagtgaaaac acaataatta ttataattag cagaacaagt
     1201 acacttttag cataagcaat aagaatagta gtcacactgt cagcacgact ataaaccaac
     1261 acattccaag cagtattttt catactagca taaccaagaa gatatctatg ccccgaagaa
     1321 aaaaatgccc cctcacctct atcagacgca gttaactttg atttcaaatc atcagacata
     1381 accataggcc gatcaacagc acttttatcg ttattaaaga tcacattccc atcatcacta
     1441 acaatgctaa tttcagtgtt gttcttgaaa aaatgcctgc tcaaaacatc gccaaataaa
     1501 ttatgttttt ttagatatat agacccaccg acatacccta tgtaattgcc acccttatca
     1561 taaataggat gtgacaacaa aataatcaaa ttcccagtaa ctgattttaa cggtgaagat
     1621 atgaatggtt tcttttcctc aatcgccaat ttgctggcac ttgaattcaa gcgggtacca
     1681 actaaatcaa gagattctgg cgaagtcgcc agaacaacag catcattact aacaacaaga
     1741 actgaattaa acataccaga ctgcaatctt aacctatccg cctcatcttt aagtgagtca
     1801 atatcattag ttgattttat tttttttgct ccatatgcta attcaccttg agccatttca
     1861 atataaccac tcattacatc tgacattttc atagcgtacg atgaattagc ataaagcaaa
     1921 tctttttcta tattttcgcg ctgaaaaacc ataataacgg caatcagaaa aatagaagtt
     1981 aacaaaatcc caccaacgga caaggttatg actatcggac gaaggtgagg ctttttaatt
     2041 ctcataaaaa tacactccat ataataaaaa atgccgcatt taccataaca tcccttatca
     2101 gcaccgcccc ggacgggttc ggaacaaatg cggcgtcagc ccggtaaaac cggcagcaaa
     2161 ctctccgcta aaccgcgcat tctgcgccag ataaatttca cccggctgca tggctatgca
     2221 gtcgggtgaa tggctccggc tttcagcgca gatgtccgcc gaaagccccg ttttatcagg
     2281 ttatcacagt gaagggctgt tatacgtccg ctgtcgctga gatcgctcca gctccagcgc
     2341 tttctgatgc tgcaccacgc gctcctgctc ccggtgcagc tcgacggcat tcagtcgctc
     2401 gacaaccggc gcagctgctc gctcaaactc tgcacctgcc tgctcaagcc cgtgacgcgc
     2461 tcgctcagcg ctgcgttctc ccgtagcata agaccagaca tcgtccgcca ttccgcgaag
     2521 gcgctctccc actcgtccag ccttttcgag tagtcctgct gtagctgctc taatgcgctc
     2581 agcaactgtt tttccagctc cgtcatgtgc tatttccccg ccagtatcat ccagctcgaa
     2641 tcctctccga accgtcccgc ttccgggttc accttcacgc agcggcgtct ctgctcgccg
     2701 caggtcgaga gctgcacgcc gctgttcctc tctgacagca tggcctgcgt gctcttctgc
     2761 tcccggatgg tcgtgtagtt gtcgagtatc tgctgcccct gccaccacag aatgcccgcg
     2821 ctcgaggcga tcagcagcgc ggagaccagg acgatggtca gccacgtctg gctgaccatg
     2881 cgcaccatgc ctttcgtgcg ctggctcatg gctgaggaca gtttccggtc gtggtcgagg
     2941 atggcggcgc tgattctctt cgcgctttcg ttcagttccg cttttacaga tttctcgtgc
     3001 tcgctgaatg cggctttcag catctcgccg gtattctgct gctgcgcttt cgatttctgc
     3061 tctaagtcct tcgccagcgt taaaagactg ttcataaatg gctcccttca gtcggatgtt
     3121 tcgccccccg tccgggtcgg caatgctgat actgcttttt gtggtgcgga ccacctcaaa
     3181 acctgcgctt tccagcgcct cagtgacatc ctgacgggtt ttcagctccc cggatgaggc
     3241 aagagcaagc agaccgcgtg taatcgcttc tgcagcctcc tgcttcgctt taggcagtgc
     3301 agacggtgtg accagtgccc gccggttctc cggtgcgttc gggtcgtgca gccccagtct
     3361 gccgttcacg atggtctgcc aggcatcgat gcgtggacgg tcggcgcgat cgtaatacgg
     3421 ctggagccgt ctgccggtca gcagctccgt gttcgggatc agaaaattca gctcaagccg
     3481 ccccttgtca cgatgctcca cccacaggat gctgtactgg tctttatcaa gtccgggcat
     3541 cagaacccgc tcaaagcttg ccatcagctt ttcccgctgg ccggaaggta aatccgcttc
     3601 cgcaaacgac agtaccccgg aggtgtattt cttaacgtaa ggcgacgcgt caatcagctc
     3661 ccggacttct tccggcttcc cctgcaggac ggtggcgcct tcacgctgcc ggtctttacc
     3721 cagcagatag tccaccggcc cggcgccacc gccgcgaccg cgtggatgaa atttaacgat
     3781 catcgtccgt tcctttctca agaacggcgt gccgcagccg ctcaagtccg gcatcgatgg
     3841 ccatcagcgc cgcaacaatc tgcaccctgt catggccggt accgccgccg gcgttaacac
     3901 ggcgggctat ctggttcagg ttattgccca tgccggcaag ctggcgcagc agcgccggcg
     3961 agattgaggg gagctttccg gaacgtgccg gcttttcgtc caggcaggtc tgccgcatcc
     4021 acgccgccag ctgcctgccg tcacagcgct caagcagccg ccggtgctcg tcctccgtca
     4081 cccacatggt gagcatcttg ttccgtttct ctgacaaacc ggtctcctga taacgccggg
     4141 acgggcggga aaacctttcc cggtcggcac ggggttggac aagccgcagg cgcgtcaggc
     4201 ttttggcggg tttcggggcg cagccctgaa ccagtcacgt agcgctagcg gagtgtatac
     4261 tggcttaata tgttggcacg gatgagggtg tcagtgaagt gcttcatgtg gcaggagaaa
     4321 aaaggcggca ccggcgcgtc agcagaatat gtgatacagg atatattccg cttcctcgct
     4381 cactgactcg ctgcgctcgg tcgttcggct gcggcgagcg gtgccggctt acaggtgggg
     4441 cggaaatttc ctggaagatg ccaggaagga acgtaacagg gaagcgagaa ggccgcggcg
     4501 aagccgtttt tccataggct ccgcccccct gacaagcatc acgaaatctg acgctcaaat
     4561 cagtggtggc gaaacccgac aggacttaaa gataccaggc gtttccccct ggtggctccc
     4621 tcgtgcgctc tcctgttcct gcctttcggt ttaccggtgt cattc
//
