LOCUS       NZ_CP117478             4942 bp    DNA     circular CON 20-OCT-2023
DEFINITION  Citrobacter freundii strain BC73 plasmid pCFBC3, complete sequence.
ACCESSION   NZ_CP117478
VERSION     NZ_CP117478.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN33169384
            Assembly: GCF_032818495.1
KEYWORDS    RefSeq.
SOURCE      Citrobacter freundii
  ORGANISM  Citrobacter freundii
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Citrobacter; Citrobacter freundii complex.
REFERENCE   1  (bases 1 to 4942)
  AUTHORS   Liu,N.
  TITLE     Characterization of NDM-1-, IMP-4-and SHV-12-producing Citrobacter
            freundii isolate in China
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 4942)
  AUTHORS   Liu,N.
  TITLE     Direct Submission
  JOURNAL   Submitted (07-FEB-2023) Center for Translational Medicine Research,
            the Fifth Clinical Medical College of Henan University of Chinese
            Medicine, 33 Huanghe Road, Zhengzhou, Henan 450000, China
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: unicycer v. September-2022
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 200.0x
            Sequencing Technology             :: Oxford Nanopore MinION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 10/20/2023 13:29:59
            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)                     :: 5,238
            CDSs (total)                      :: 5,117
            Genes (coding)                    :: 4,970
            CDSs (with protein)               :: 4,970
            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)              :: 147
            CDSs (without protein)            :: 147
            Pseudo Genes (ambiguous residues) :: 0 of 147
            Pseudo Genes (frameshifted)       :: 41 of 147
            Pseudo Genes (incomplete)         :: 112 of 147
            Pseudo Genes (internal stop)      :: 23 of 147
            Pseudo Genes (multiple problems)  :: 26 of 147
            Pseudo Genes (short protein)      :: 1 of 147
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP117478.1.
            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="BC73"
                     /isolation_source="urine"
                     /host="Homo sapiens"
                     /db_xref="taxon:546"
                     /plasmid="pCFBC3"
                     /geo_loc_name="China: Henan"
                     /lat_lon="34.75 N 113.62 E"
                     /collection_date="2022-12"
                     /collected_by="NA LIU"
     gene            complement(join(4368..4942,1..349))
                     /locus_tag="PSC61_RS26150"
                     /old_locus_tag="PSC61_26130"
     CDS             complement(join(4368..4942,1..349))
                     /locus_tag="PSC61_RS26150"
                     /old_locus_tag="PSC61_26130"
                     /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            631..870
                     /locus_tag="PSC61_RS26155"
                     /old_locus_tag="PSC61_26135"
     CDS             631..870
                     /locus_tag="PSC61_RS26155"
                     /old_locus_tag="PSC61_26135"
                     /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            870..1178
                     /locus_tag="PSC61_RS26160"
                     /old_locus_tag="PSC61_26140"
     CDS             870..1178
                     /locus_tag="PSC61_RS26160"
                     /old_locus_tag="PSC61_26140"
                     /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(1282..1518)
                     /locus_tag="PSC61_RS26165"
                     /old_locus_tag="PSC61_26145"
     CDS             complement(1282..1518)
                     /locus_tag="PSC61_RS26165"
                     /old_locus_tag="PSC61_26145"
                     /inference="COORDINATES: protein motif:HMM:NF016769.3"
                     /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(1579..2064)
                     /locus_tag="PSC61_RS26170"
                     /old_locus_tag="PSC61_26150"
     CDS             complement(1579..2064)
                     /locus_tag="PSC61_RS26170"
                     /old_locus_tag="PSC61_26150"
                     /inference="COORDINATES: protein motif:HMM:NF016710.3"
                     /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            complement(<2096..2533)
                     /locus_tag="PSC61_RS26175"
                     /old_locus_tag="PSC61_26155"
                     /pseudo=""
     CDS             complement(<2096..2533)
                     /locus_tag="PSC61_RS26175"
                     /old_locus_tag="PSC61_26155"
                     /inference="COORDINATES: protein motif:HMM:NF015397.3"
                     /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(2733..3068)
                     /gene="mobC"
                     /locus_tag="PSC61_RS26180"
                     /old_locus_tag="PSC61_26160"
     CDS             complement(2733..3068)
                     /gene="mobC"
                     /locus_tag="PSC61_RS26180"
                     /old_locus_tag="PSC61_26160"
                     /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(3391..3864)
                     /locus_tag="PSC61_RS26185"
                     /old_locus_tag="PSC61_26165"
     CDS             complement(3391..3864)
                     /locus_tag="PSC61_RS26185"
                     /old_locus_tag="PSC61_26165"
                     /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(3895..4368)
                     /locus_tag="PSC61_RS26190"
                     /old_locus_tag="PSC61_26170"
     CDS             complement(3895..4368)
                     /locus_tag="PSC61_RS26190"
                     /old_locus_tag="PSC61_26170"
                     /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"
ORIGIN
        1 acagcgcacg ctcaaccgct gccgcatact tcagcggctt aatttttccg tcaggtgccg
       61 tgcgcaccgc tgttttcagc gcatacagta agtgggcatg tccgttttcc ggattcatga
      121 tggtcagcgt tggcgcaggt gcgttccggt cgctccagtc tatcgccgcg ccggggcggt
      181 caacgtcaaa accgagccag aacatcgcgt gtggctggtt gaactggatg tatttcgcaa
      241 gaatggcgcg ctctttcccg gcaatgcgta ctccgaactg gagttcgtcg gtaaaatagg
      301 gtttgcgggg aagccgctcg ttaaaaaggt cgagtgcctg gttactcaat ctcgcctgcg
      361 cttatggcgg gctgttgttt cgcacggttc atgtgctagt atccttctta ggttttgtgc
      421 ctgcgccctc gttaatcatg tccttccgcc aagtcgagca tgattacggg ggcgtcgtct
      481 tttctgccgc ttaacgttac acaccccgcc gtattttgtc acctgtcacc gtcagttatt
      541 gcctgaagca acagaccatt accttccggg taaaaaacgc gtacactggc aacacgtgct
      601 atatacacgt gtaaaaatca ggagatcatc atgcccgtat cagcgatgcg ccataaaaaa
      661 accgtcagtg tgacaatcga gcctgcgctt ttgcatcagg cccgcgaagc cgggattaat
      721 ctgtctgcca cgctcaccac cgccctgaaa catcagatcc gcgagtcaga agcggagcgc
      781 tggaaacgcg ccaaccgcaa ggcaatccag gagctcaacc gtattacgga cgagcacggc
      841 ttactctctg acgatcacag gacgttctga tgcagttcat ggtttaccgc aataacagca
      901 acaaccgggc ttatccctat ctgctcgatg tacagagcga tattatcgac gaactgaata
      961 cccgcctggt gatcccgctg tttctgctgg atgaagtgaa tggacggccc gcccgccgcc
     1021 tgaccccggt gctgaatgtg gacggtgagg attttctggt catgacacat gaaatggcca
     1081 gcgttcgcca gtcacagctc ggggaagagg tggtgagcgt ccgggagcac cggcaggcca
     1141 tcaagaatgc gctggatttt ctgctcgacg gtttctgagt ttacctttcc atcccgtgat
     1201 cgtgtccccg gctgcgtccg ggggcaaatg agcgcgtttt ctgtcgttcc tgtttctgcg
     1261 ccagctccct gtccagtctg gctacctgcg cgtcaagcgg ctgacggctt cggttaagct
     1321 catgacctgc tgccgcaagc tctccacctg cccgctcaag tgctgacacg cctggtcgct
     1381 gcgcatcagc gcggcggaag tagtggtgaa catggtctgc aagctgtcgt aactggcctg
     1441 ccatgcctgc tgtcgtgtct cgtaatcgtc ctgtaagcgc tctaacgcac tcagcagcag
     1501 tttttcggtc tcggtcatgg atttgcttgt ccttatcgct aaaaacgccg tatggcgctt
     1561 ctgtggcaac tgacggggct atttcgcggt gtaggtcacg acctgtttgt cgtttttcga
     1621 ggtgtacagc tcgacgccct tcgcgctctt cggcagcacc acgtaatact tgttcttccg
     1681 ggtgtcgtcc gtgagtattt ccacccccgc ccccgatttc gctttcaggt cggtaagctg
     1741 ctggctgtag ctgttcatct cgtccagacg tgaggcgatg agtgtcccct gaaaccacag
     1801 tatccccgac agaataccga tcagcagcac accacaaaac aatatccata tcagcgcgat
     1861 cgtgaccgag cgccgcagca gggttgtctg cctgacgttc tgttcgtgga tagcgtcgct
     1921 gatgctcttc ccgcttgatt tcaaggcctc gctgatggat tgctcgagct tcacaaactc
     1981 gctcttcacg ctctcccctg tacgctgtgc ctgctgcttc gaggtctctt cgaaggcttt
     2041 cgctaaatct aaaatcccgc tcatataacg ccccttttaa ccggatattt cgtccaccgt
     2101 ccgggtcggc aatgctgaga ctgcttttcg tttcccgcac caccgtcagc ccgccgtttt
     2161 ccagcgccct gaccacattc tcacggttgc ggatcatacc ctgtgccacc atcgtttcca
     2221 gcgagtccgt aatggcctgc gccgccttct gacggtcgcc gggaaggtca ttgcccggtg
     2281 tcagggtgcg tcgtcgggca ggatcatgag ggtcatcgag gttcaagcgg tcattggtca
     2341 gagtctgcca ggcgttgacc ctgggacgat cagcccggtc atagtagggt tgcaggcgtt
     2401 ttccgctctg caattcgatg ttcgggaaca caaaattcag ctccagcctg tccttgtccc
     2461 ggtgctccac ccacagacag gcgtactggt cgccgtccag accgggcaac agtgtctgct
     2521 caaactcatc catcagacgc actttctcat cgtcagggag gttttgttcc cggaacgaca
     2581 acaccccgga ggtataggcg cgggcaaact cacaaccatc aatcagttgc ctgacacgct
     2641 caggctcacc gcgcagtacc accgctttat cccgatcacg ttcttttccc agcaggtaat
     2701 ccaccgggcc actgcctgaa cccgcaccgc ggctatgaat cttgacgatc acgctgtgtc
     2761 tccagaagct cagataactg gcgatcaagg ctggtcagta ccgccagaag agaaacctgc
     2821 tgatgggccg aaagcgaatc cagaccatgc agcttacggg ctatctgatt gaggttattg
     2881 ccgatgccgg tcacctgacg aagcagtgcc ggatcaacgt caggcacacg ccggcgacgc
     2941 aatacatgtt cacccagacc gagcgaacgt aaccattcag cgagatgagc acgatcacaa
     3001 cgtgccagca gtcgctcatg ttcactctca gtcaggcgga tttttatctc tttcgttcgc
     3061 ttgtccatga cactccgctg agaaaacttt cgcacccaga gtgcgaattt tcgcagtgga
     3121 tgccaggggt ttcggggggc ggcgagcccc ctgaaccagt cacagaagga accctcgtag
     3181 aggggacgct gtgtgtactg gcttatagtg attgataagt atgtcagatt ctgtgctggc
     3241 tgcaaaaaaa aaagccttct ctggagaagg ctgttatctg atataggttg tttttagtct
     3301 cacagagaac atctagtgga ttgttcttag ctttagcgat atcagtgata tgatcagcat
     3361 cagcatcagc atcatattag ttgattgtat ttattcatca tgctggccat tatatgcttt
     3421 gagcaccgta gaatggctct tcccgcaagt ccgaagaata attagcgcat gttcaatgag
     3481 ttctttactt cgttgaggac taaaccattc accattaaat ttacccccat ggaaaagatt
     3541 atttctaatt ctacaaataa gagaaaaaac aagctcagac ttatttctat ggtcaggcaa
     3601 tacattagac caacataata aaccatcttt taaaacttgt ttttttggtg ggttgtttat
     3661 caggtatgat attgactcat ttaactcttt acttggactt tcaatcaatg aaacgaattc
     3721 accagcatac ttataccaat cagcttctac tctagtattt gtgcccttac gaaatccggt
     3781 aaccttaaga caatattcat agcgagcaaa ttcacgaaaa aagttatatc ctaaataatc
     3841 tagttctaat gtagattgct tcataaaaac ctcataaatg aaaaaatatg taatttaatt
     3901 tatattacac ttttccatta caatagattc caacacaaga aaagcagggc gctggcccgg
     3961 ggcagggaca ttttcataaa cataagcatt aggaataact ttaccagtag aaggtgaagt
     4021 cgatggtttt gcattcttat ttctgtactc tatcgattct tcagtagcaa actgaacaaa
     4081 gtctccgaca gagaagttag gacatttttt ctgtcttttg aaaaaatcat attgaataac
     4141 agcggctaaa tagccattac aaaaacccca agctcctttt tcttttatat cgtttcgtgc
     4201 actatcacaa tgactacccc attctgacat ggtagggtgc gctgcatcaa tatatttact
     4261 gccagggata ttaataggca tatcaaaaat attattttca gcattaacgg aagaagataa
     4321 gctgattaaa tacagagtaa aaacagacgc aacaagtgaa agtctcatta taaaaacctc
     4381 ttattcatcc caagtctata atatttacta cggctaatat ttaaatttac ccatggtttt
     4441 aaacttgcat cagatgcaat agatattcgt ccctttgggc gacctcctcc tcggcttttt
     4501 tttcctctaa ctgattgaat ctcactagaa tgagtacgag atacataggc accaaatgtt
     4561 tcctcactaa attttgactt agtccattta gcaatgctct tggctatacc attaacctca
     4621 ttttcatcca gaggcgctgc aaattgcagg ttataagcgt tggcacgttc gtagcaggct
     4681 cttaaccact gttcataatc aggccagccc tgacgaatgg cgcgataagc ccatttacgg
     4741 gttttatcga acagggtgca gttacggcct aaaccgtagt cgggtaggat ttctttgtcg
     4801 ttcgctgcac tcaggtcaag tgagtctgct aaccagtcga gcgtgtagag ttccggttgc
     4861 cacacggcaa gctgccagtg gtcatggttc ggatttttgc agattaaccc tgaatagcca
     4921 gtgtcagcgt ccagtttttt ac
//
