LOCUS       NZ_CP137174             4942 bp    DNA     circular CON 31-JAN-2024
DEFINITION  Citrobacter freundii strain F3517 plasmid pF3517-3, complete
            sequence.
ACCESSION   NZ_CP137174
VERSION     NZ_CP137174.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN37932926
            Assembly: GCF_036289085.1
KEYWORDS    RefSeq.
SOURCE      Citrobacter freundii
  ORGANISM  Citrobacter freundii
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Citrobacter; Citrobacter freundii complex.
REFERENCE   1  (bases 1 to 4942)
  AUTHORS   Li,X.
  TITLE     Citrobacter freundii F3517 Genome sequencing and assembly
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 4942)
  AUTHORS   Li,X.
  TITLE     Direct Submission
  JOURNAL   Submitted (23-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 01:50:58
            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)                     :: 5,333
            CDSs (total)                      :: 5,212
            Genes (coding)                    :: 5,100
            CDSs (with protein)               :: 5,100
            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)              :: 112
            CDSs (without protein)            :: 112
            Pseudo Genes (ambiguous residues) :: 0 of 112
            Pseudo Genes (frameshifted)       :: 26 of 112
            Pseudo Genes (incomplete)         :: 84 of 112
            Pseudo Genes (internal stop)      :: 18 of 112
            Pseudo Genes (multiple problems)  :: 16 of 112
            Pseudo Genes (short protein)      :: 1 of 112
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP137174.1.
            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="F3517"
                     /isolation_source="throat swab"
                     /host="Homo sapiens"
                     /db_xref="taxon:546"
                     /plasmid="pF3517-3"
                     /geo_loc_name="China: Hangzhou"
                     /lat_lon="29.86 N 121.56 E"
                     /collection_date="2017-10-02"
                     /collected_by="Jayao Yao"
     gene            join(4732..4942,1..263)
                     /locus_tag="R4T09_RS00025"
                     /old_locus_tag="R4T09_00025"
     CDS             join(4732..4942,1..263)
                     /locus_tag="R4T09_RS00025"
                     /old_locus_tag="R4T09_00025"
                     /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            294..767
                     /locus_tag="R4T09_RS00030"
                     /old_locus_tag="R4T09_00030"
     CDS             294..767
                     /locus_tag="R4T09_RS00030"
                     /old_locus_tag="R4T09_00030"
                     /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            1090..1425
                     /gene="mobC"
                     /locus_tag="R4T09_RS00035"
                     /old_locus_tag="R4T09_00035"
     CDS             1090..1425
                     /gene="mobC"
                     /locus_tag="R4T09_RS00035"
                     /old_locus_tag="R4T09_00035"
                     /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            1625..>2077
                     /locus_tag="R4T09_RS00040"
                     /old_locus_tag="R4T09_00040"
                     /pseudo=""
     CDS             1625..>2077
                     /locus_tag="R4T09_RS00040"
                     /old_locus_tag="R4T09_00040"
                     /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            2094..2579
                     /locus_tag="R4T09_RS00045"
                     /old_locus_tag="R4T09_00045"
     CDS             2094..2579
                     /locus_tag="R4T09_RS00045"
                     /old_locus_tag="R4T09_00045"
                     /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            2640..2876
                     /locus_tag="R4T09_RS00050"
                     /old_locus_tag="R4T09_00050"
     CDS             2640..2876
                     /locus_tag="R4T09_RS00050"
                     /old_locus_tag="R4T09_00050"
                     /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(2980..3288)
                     /locus_tag="R4T09_RS00055"
                     /old_locus_tag="R4T09_00055"
     CDS             complement(2980..3288)
                     /locus_tag="R4T09_RS00055"
                     /old_locus_tag="R4T09_00055"
                     /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(3288..3527)
                     /locus_tag="R4T09_RS00060"
                     /old_locus_tag="R4T09_00060"
     CDS             complement(3288..3527)
                     /locus_tag="R4T09_RS00060"
                     /old_locus_tag="R4T09_00060"
                     /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            3809..4732
                     /locus_tag="R4T09_RS00065"
                     /old_locus_tag="R4T09_00065"
     CDS             3809..4732
                     /locus_tag="R4T09_RS00065"
                     /old_locus_tag="R4T09_00065"
                     /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"
ORIGIN
        1 atggctattt agccgctgtt attcaatatg attttttcaa aagacagaaa aaatgtccta
       61 acttctctgt cggagacttt gttcagtttg ctactgaaga atcgatagag tacagaaata
      121 agaatgcaaa accatcgact tcaccttcta ctggtaaagt tattcctaat gcttatgttt
      181 atgaaaatgt ccctgccccg ggccagcgcc ctgcttttct tgtgttggaa tctattgtaa
      241 tggaaaagtg taatataaat taaattacat attttttcat ttatgaggtt tttatgaagc
      301 aatctacatt agaactagat tatttaggat ataacttttt tcgtgaattt gctcgctatg
      361 aatattgtct taaggttacc ggatttcgta agggcacaaa tactagagta gaagctgatt
      421 ggtataagta tgctggtgaa ttcgtttcat tgattgaaag tccaagtaaa gagttaaatg
      481 agtcaatatc atacctgata aacaacccac caaaaaaaca agttttaaaa gatggtttat
      541 tatgttggtc taatgtattg cctgaccata gaaataagtc tgagcttgtt ttttctctta
      601 tttgtagaat tagaaataat cttttccatg ggggtaaatt taatggtgaa tggtttagtc
      661 ctcaacgaag taaagaactc attgaacatg cgctaattat tcttcggact tgcgggaaga
      721 gccattctac ggtgctcaaa gcatataatg gccagcatga tgaataaata caatcaacta
      781 atatgatgct gatgctgatg ctgatcatat cactgatatc gctaaagcta agaacaatcc
      841 actagatgtt ctctgtgaga ctaaaaacaa cctatatcag ataacagcct tctccagaga
      901 aggctttttt ttttgcagcc agcacagaat ctgacatact tatcaatcac tataagccag
      961 tacacacagc gtcccctcta cgagggttcc ttctgtgact ggttcagggg gctcgccgcc
     1021 ccccgaaacc cctggcatcc actgcgaaaa ttcgcactct gggtgcgaaa gttttctcag
     1081 cggagtgtca tggacaagcg aacgaaagag ataaaaatcc gcctgactga gagtgaacat
     1141 gagcgactgc tggcacgttg tgatcgtgct catctcgctg aatggttacg ttcgctcggt
     1201 ctgggtgaac atgtattgcg tcgccggcgt gtgcctgacg ttgatccggc actgcttcgt
     1261 caggtgaccg gcatcggcaa taacctcaat cagatagccc gtaagctgca tggtctggat
     1321 tcgctttcgg cccatcagca ggtttctctt ctggcggtac tgaccagcct tgatcgccag
     1381 ttatctgagc ttctggagac acagcgtgat cgtcaagatt catagccgcg gtgcgggttc
     1441 aggcagtggc ccggtggatt acctgctggg aaaagaacgt gatcgggata aagcggtggt
     1501 actgcgcggt gagcctgagc gtgtcaggca actgattgat ggttgtgagt ttgcccgcgc
     1561 ctatacctcc ggggtgttgt cgttccggga acaaaacctc cctgacgatg agaaagtgcg
     1621 tctgatggat gagtttgagc agacactgtt gcccggtctg gacggcgacc agtacgcctg
     1681 tctgtgggtg gagcaccggg acaaggacag gctggagctg aattttgtgt tcccgaacat
     1741 cgaattgcag agcggaaaac gcctgcaacc ctactatgac cgggctgatc gtcccagggt
     1801 caacgcctgg cagactctga ccaatgaccg cttgaacctc gatgaccctc atgatcctgc
     1861 ccgacgacgc accctgacac cgggcaatga ccttcccggc gaccgtcaga aggcggcgca
     1921 ggccattacg gactcgctgg aaacgatggt ggcacagggt atgatccgca accgtgagaa
     1981 tgtggtcagg gcgctggaaa acggcgggct gacggtggtg cgggaaacga aaagcagtct
     2041 cagcattgcc gacccggacg gtggacgaaa tatccggtta aaaggggcgt tatatgagcg
     2101 ggattttaga tttagcgaaa gccttcgaag agacctcgaa gcagcaggca cagcgtacag
     2161 gggagagcgt gaagagcgag tttgtgaagc tcgagcaatc catcagcgag gccttgaaat
     2221 caagcgggaa gagcatcagc gacgctatcc acgaacagaa cgtcaggcag acaaccctgc
     2281 tgcggcgctc ggtcacgatc gcgctgatat ggatattgtt ttgtggtgtg ctgctgatcg
     2341 gtattctgtc ggggatactg tggtttcagg ggacactcat cgcctcacgt ctggacgaga
     2401 tgaacagcta cagccagcag cttaccgacc tgaaagcgaa atcgggggcg ggggtggaaa
     2461 tactcacgga cgacacccgg aagaacaagt attacgtggt gctgccgaag agcgcgaagg
     2521 gcgtcgagct gtacacctcg aaaaacgaca aacaggtcgt gacctacacc gcgaaatagc
     2581 cccgtcagtt gccacagaag cgccatacgg cgtttttagc gataaggaca agcaaatcca
     2641 tgaccgagac cgaaaaactg ctgctgagtg cgttagagcg cttacaggac gattacgaga
     2701 cacgacagca ggcatggcag gccagttacg acagcttgca gaccatgttc accactactt
     2761 ccgccgcgct gatgcgcagc gaccaggcgt gtcagcactt gagcgggcag gtggagagct
     2821 tgcggcagca ggtcatgagc ttaaccgaag ccgtcagccg cttgacgcgc aggtagccag
     2881 actggacagg gagctggcgc agaaacagga acgacagaaa acgcgctcat ttgcccccgg
     2941 acgcagccgg ggacacgatc acgggatgga aaggtaaact cagaaaccgt cgagcagaaa
     3001 atccagcgca ttcttgatgg cctgccggtg ctcccggacg ctcaccacct cttccccgag
     3061 ctgtgactgg cgaacgctgg ccatttcatg tgtcatgacc agaaaatcct caccgtccac
     3121 attcagcacc ggggtcaggc ggcgggcggg ccgtccattc acttcatcca gcagaaacag
     3181 cgggatcacc aggcgggtat tcagttcgtc gataatatcg ctctgtacat cgagcagata
     3241 gggataagcc cggttgttgc tgttattgcg gtaaaccatg aactgcatca gaacgtcctg
     3301 tgatcgtcag agagtaagcc gtgctcgtcc gtaatacggt tgagctcctg gattgccttg
     3361 cggttggcgc gtttccagcg ctccgcttct gactcgcgga tctgatgttt cagggcggtg
     3421 gtgagcgtgg cagacagatt aatcccggct tcgcgggcct gatgcaaaag cgcaggctcg
     3481 attgtcacac tgacggtttt tttatggcgc atcgctgata cgggcatgat gatctcctga
     3541 tttttacacg tgtatatagc acgtgttgcc agtgtacgcg ttttttaccc ggaaggtaat
     3601 ggtctgttgc ttcaggcaat aactgacggt gacaggtgac aaaatacggc ggggtgtgta
     3661 acgttaagcg gcagaaaaga cgacgccccc gtaatcatgc tcgacttggc ggaaggacat
     3721 gattaacgag ggcgcaggca caaaacctaa gaaggatact agcacatgaa ccgtgcgaaa
     3781 caacagcccg ccataagcgc aggcgagatt gagtaaccag gcactcgacc tttttaacga
     3841 gcggcttccc cgcaaaccct attttaccga cgaactccag ttcggagtac gcattgccgg
     3901 gaaagagcgc gccattcttg cgaaatacat ccagttcaac cagccacacg cgatgttctg
     3961 gctcggtttt gacgttgacc gccccggcgc ggcgatagac tggagcgacc ggaacgcacc
     4021 tgcgccaacg ctgaccatca tgaatccgga aaacggacat gcccacttac tgtatgcgct
     4081 gaaaacagcg gtgcgcacgg cacctgacgg aaaaattaag ccgctgaagt atgcggcagc
     4141 ggttgagcgt gcgctgtgta aaaaactgga cgctgacact ggctattcag ggttaatctg
     4201 caaaaatccg aaccatgacc actggcagct tgccgtgtgg caaccggaac tctacacgct
     4261 cgactggtta gcagactcac ttgacctgag tgcagcgaac gacaaagaaa tcctacccga
     4321 ctacggttta ggccgtaact gcaccctgtt cgataaaacc cgtaaatggg cttatcgcgc
     4381 cattcgtcag ggctggcctg attatgaaca gtggttaaga gcctgctacg aacgtgccaa
     4441 cgcttataac ctgcaatttg cagcgcctct ggatgaaaat gaggttaatg gtatagccaa
     4501 gagcattgct aaatggacta agtcaaaatt tagtgaggaa acatttggtg cctatgtatc
     4561 tcgtactcat tctagtgaga ttcaatcagt tagaggaaaa aaaagccgag gaggaggtcg
     4621 cccaaaggga cgaatatcta ttgcatctga tgcaagttta aaaccatggg taaatttaaa
     4681 tattagccgt agtaaatatt atagacttgg gatgaataag aggtttttat aatgagactt
     4741 tcacttgttg cgtctgtttt tactctgtat ttaatcagct tatcttcttc cgttaatgct
     4801 gaaaataata tttttgatat gcctattaat atccctggca gtaaatatat tgatgcagcg
     4861 caccctacca tgtcagaatg gggtagtcat tgtgatagtg cacgaaacga tataaaagaa
     4921 aaaggagctt ggggtttttg ta
//
