LOCUS       NZ_CP137184             5406 bp    DNA     circular CON 31-JAN-2024
DEFINITION  Citrobacter freundii strain F1917 plasmid pF1917-7, complete
            sequence.
ACCESSION   NZ_CP137184
VERSION     NZ_CP137184.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN37933681
            Assembly: GCF_036289145.1
KEYWORDS    RefSeq.
SOURCE      Citrobacter freundii
  ORGANISM  Citrobacter freundii
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Citrobacter; Citrobacter freundii complex.
REFERENCE   1  (bases 1 to 5406)
  AUTHORS   Li,X.
  TITLE     Citrobacter freundii F1917 Genome sequencing and assembly
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 5406)
  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 02:12:19
            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)                     :: 5,708
            CDSs (total)                      :: 5,588
            Genes (coding)                    :: 5,456
            CDSs (with protein)               :: 5,456
            Genes (RNA)                       :: 120
            rRNAs                             :: 9, 8, 8 (5S, 16S, 23S)
            complete rRNAs                    :: 9, 8, 8 (5S, 16S, 23S)
            tRNAs                             :: 83
            ncRNAs                            :: 12
            Pseudo Genes (total)              :: 132
            CDSs (without protein)            :: 132
            Pseudo Genes (ambiguous residues) :: 0 of 132
            Pseudo Genes (frameshifted)       :: 31 of 132
            Pseudo Genes (incomplete)         :: 94 of 132
            Pseudo Genes (internal stop)      :: 25 of 132
            Pseudo Genes (multiple problems)  :: 17 of 132
            Pseudo Genes (short protein)      :: 1 of 132
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP137184.1.
            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..5406
                     /organism="Citrobacter freundii"
                     /mol_type="genomic DNA"
                     /strain="F1917"
                     /isolation_source="urine"
                     /host="Homo sapiens"
                     /db_xref="taxon:546"
                     /plasmid="pF1917-7"
                     /geo_loc_name="China: Hangzhou"
                     /lat_lon="29.86 N 121.56 E"
                     /collection_date="2017-11-22"
                     /collected_by="Jiayao Yao"
     gene            join(5312..5406,1..208)
                     /locus_tag="R4T16_RS25020"
                     /old_locus_tag="R4T16_24995"
     CDS             join(5312..5406,1..208)
                     /locus_tag="R4T16_RS25020"
                     /old_locus_tag="R4T16_24995"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_004020443.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="BrnA antitoxin family protein"
                     /protein_id="WP_166479958.1"
                     /translation="MSMVRYKRSEIPPLTEKRSSELKTLAAEADNHIDYEGIAPLDDAF
                     WKQASRGQFYRPLKTQASVRIDADVMAWLKEPGKGYQTRLNAILREAMLRELHRK"
                     /name="BrnA antitoxin family protein"
     gene            317..1014
                     /locus_tag="R4T16_RS25025"
                     /old_locus_tag="R4T16_25000"
     CDS             join(317..566,566..1014)
                     /locus_tag="R4T16_RS25025"
                     /old_locus_tag="R4T16_25000"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_086558260.1"
                     /ribosomal_slippage=""
                     /GO_function="GO:0004803 - transposase activity [Evidence
                     IEA]"
                     /GO_process="GO:0006313 - DNA transposition [Evidence IEA]"
                     /note="programmed frameshift; Derived by automated
                     computational analysis using gene prediction method:
                     Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="IS1-like element IS1B family transposase"
                     /protein_id="WP_225248593.1"
                     /translation="MASVSISCPSCSATDGVVRNGKSTAGHQRYLCSHCRKTWQLQFTY
                     TASQPGTHQKIIDMAMNGVGCRATARIMGVGLNTIFRHFKKLRPQSVTSRIQPGSDVIV
                     CAEMDEQWGYVGAKSRQRWLFYAYDRLRKTVVAHVFGERTMATLGRLMSLLSPFDVVIW
                     MTDGWPLYESRLKGKLHVISKRYTQRIERHNLNLRQHLARLGWKSLSFSKSVELHDKVI
                     GHYLNIKHYQ"
                     /name="IS1-like element IS1B family transposase"
     gene            1972..2163
                     /locus_tag="R4T16_RS25030"
                     /old_locus_tag="R4T16_25005"
     CDS             1972..2163
                     /locus_tag="R4T16_RS25030"
                     /old_locus_tag="R4T16_25005"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000166328.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="Rop family plasmid primer RNA-binding protein"
                     /protein_id="WP_050074851.1"
                     /translation="MNKEQKTALNMAKFIQGQSLLLLEKLNALDFDTEADLCEKLHEDT
                     EQLYRVLSERLKESEDGY"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            2163..2594
                     /locus_tag="R4T16_RS25035"
                     /old_locus_tag="R4T16_25010"
     CDS             2163..2594
                     /locus_tag="R4T16_RS25035"
                     /old_locus_tag="R4T16_25010"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000135007.1"
                     /GO_function="GO:0003677 - DNA binding [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="excisionase family DNA-binding protein"
                     /protein_id="WP_166479956.1"
                     /translation="MAKVSISEAARLVNVSRPTLYKMLNNGTLTYTSVVKHGKQVKTID
                     TSELIRVFGSLGGVKDDTQNAVSVDGHATAINSDILQDLQHQIALLKTENDGLKGAVNA
                     RDEHISSLRQAMLLLEHKQEQLAPQISSPAHSPWWKFWK"
                     /name="excisionase family DNA-binding protein"
     gene            complement(2600..2758)
                     /locus_tag="R4T16_RS25040"
                     /old_locus_tag="R4T16_25015"
     CDS             complement(2600..2758)
                     /locus_tag="R4T16_RS25040"
                     /old_locus_tag="R4T16_25015"
                     /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_196305342.1"
                     /translation="MRLTGGWVVPARTGNALWKDRFLTLLLTALILLCVSTGGAFLGMW
                     YYGAVMH"
                     /name="hypothetical protein"
     gene            3852..4094
                     /locus_tag="R4T16_RS25045"
                     /old_locus_tag="R4T16_25020"
     CDS             3852..4094
                     /locus_tag="R4T16_RS25045"
                     /old_locus_tag="R4T16_25020"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001408098.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="type II toxin-antitoxin system RelB/DinJ family
                     antitoxin"
                     /protein_id="WP_137399573.1"
                     /translation="MATMNIRIDDDLKARSGAALDALGVTTSEAVRLVLEYVAQNNRLP
                     VQIALLADEDADIIELARARLANPGKRIRVKLDDL"
                     /name="type II toxin-antitoxin system RelB/DinJ family
                     antitoxin"
     gene            4084..4383
                     /locus_tag="R4T16_RS25050"
                     /old_locus_tag="R4T16_25025"
     CDS             4084..4383
                     /locus_tag="R4T16_RS25050"
                     /old_locus_tag="R4T16_25025"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000143805.1"
                     /GO_function="GO:0008657 - DNA topoisomerase type II
                     (double strand cut, ATP-hydrolyzing) inhibitor activity
                     [Evidence IEA]; GO:0042803 - protein homodimerization
                     activity [Evidence IEA]"
                     /GO_process="GO:0030541 - plasmid partitioning [Evidence
                     IEA]; GO:0051290 - protein heterotetramerization [Evidence
                     IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="type II toxin-antitoxin system RelE/ParE family
                     toxin"
                     /protein_id="WP_137399574.1"
                     /translation="MTYDIEFYEEAFDEWHRLDASVRDQFKKKLAKLVEDPHRPANRLR
                     GLEGCYKIKLRAAGVRLVYKVEDGELVILVVAVGKRDKNAVYDTARERLVTIDK"
                     /name="type II toxin-antitoxin system RelE/ParE family
                     toxin"
     gene            complement(4423..4836)
                     /locus_tag="R4T16_RS25055"
                     /old_locus_tag="R4T16_25030"
     CDS             complement(4423..4836)
                     /locus_tag="R4T16_RS25055"
                     /old_locus_tag="R4T16_25030"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_020803328.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_166479957.1"
                     /translation="MEKLDYVSKKTEKSRSFLIRESLERFIDELETEYEKREVKIDMNG
                     SFYELLVDECKTPMELTTGARKVAFTMFSDEGKLYVLNSKGNTRPLDEKPANDFFETFK
                     KTGSTSPITYRDSTFNASYFLAATQELMRRGTI"
                     /name="hypothetical protein"
     gene            5032..5325
                     /locus_tag="R4T16_RS25060"
                     /old_locus_tag="R4T16_25035"
     CDS             5032..5325
                     /locus_tag="R4T16_RS25060"
                     /old_locus_tag="R4T16_25035"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_010849001.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="BrnT family toxin"
                     /protein_id="WP_137399576.1"
                     /translation="MRTELEFEWDSVKAETNYRKHGIRFEEAALVFDDPFHLSAQDRIE
                     NGEFRWQTIGTVKGCVVVLVAHTTRFEDGTEIIRLISARKAEKNERRRYEHG"
                     /name="BrnT family toxin"
ORIGIN
        1 tattgattac gaaggcatcg ctccgctgga tgatgcgttc tggaagcagg catccagagg
       61 tcagttttac cggccgctga aaacccaggc atcagtccgg attgatgctg atgtcatggc
      121 gtggctgaaa gaacccggaa aaggatacca gacaagactc aacgccattc ttcgtgaagc
      181 aatgctgcgg gaattgcatc gtaagtaact tcagacaaca acacggtccc gctatatgcg
      241 ggatttgtta taaccttttt tggtgatgct gccaacttac tgatttagtg tatgatggtg
      301 tttttgaggt gctccagtgg cttctgtttc tatcagctgt ccctcctgtt cagctactga
      361 cggggtggtg cgtaacggca aaagcaccgc cggacatcag cgctatctct gctctcactg
      421 ccgtaaaaca tggcaactgc agttcactta caccgcttct caacccggta cgcaccagaa
      481 aatcattgat atggccatga atggcgttgg atgccgggca accgcccgca ttatgggcgt
      541 tggcctcaac acgattttcc gccatttaaa aaactcaggc cgcagtcggt aacctcgcgc
      601 atacagccgg gcagtgacgt catcgtctgc gcggaaatgg acgaacagtg gggatacgtc
      661 ggggctaaat cgcgccagcg ctggctgttt tacgcgtatg acaggctccg gaagacggtt
      721 gttgcgcacg tattcggtga acgcactatg gcgacgctgg ggcgtcttat gagcctgctg
      781 tcaccctttg acgtggtgat atggatgacg gatggctggc cgctgtatga atcccgcctg
      841 aagggaaagc tgcacgtaat cagcaagcga tatacgcagc gaattgagcg gcataacctg
      901 aatctgaggc agcacctggc acggctggga tggaagtcgc tgtcgttctc aaaatcggtg
      961 gagctgcatg acaaagtcat cgggcattat ctgaacataa aacactatca ataagttgga
     1021 gtcattaccc gcatcctgtt aatactaata atgcaataac acttagaggt attgtacttt
     1081 tcattaaaaa tcctttcatg agaactttta taagataatg attttactaa aaaataattt
     1141 tgttataaca aattattcgc caaagtgtga cactggtctt tgattgcgta gatctcgagg
     1201 atcgcgagag gaatatcttg agatctatct tccgtcgtcg taatctcttc tactgtaaac
     1261 aaaaaaacca cctggggagg tggttttttc gaaggttaag tcagttgggg aactgtttaa
     1321 ccgggtaact ggcttatgag gagcgcagtc accaaaactt gttctttcag tttagcctta
     1381 actggcgcat aaattcaaga ctcaactcct ctaatcagtt accagtggct accgccagtg
     1441 gcgattcgtc gtgtctttcc gggttggatt caagtgttaa gttaccggaa cggacgtggt
     1501 agtcggacta aacggggagt tcgtgcagat agtccagctt ggagcgaacc acctgtcagg
     1561 aacccagttg cacgggaagg aatgagaaaa cgccaccacg gagtctacgg aacggcggaa
     1621 tgcaacgggt aaaccttacg gtgggaacag gagagcgcac gagggagcca tcagggggaa
     1681 acgcctggta tctttaagtc ctgtcgggtt tcgccacttc tgatttgagt accggagatc
     1741 gtctgatttc tgtgaaactc gtcaggaggg cgaagcctat ggaaaaacgc cctggcgggg
     1801 cgtgtccttc tcgtttttgc cctggctttt ggtcacgctt accgtctacg ttatctgtta
     1861 cttagaatcc caccgctcgc cgcagactca tgaccgaacg tagtgagcga atgagcgagg
     1921 aagcggaata tcatcagatc ctgcatttgg tactgccaca cggaggtttt cgtgaacaaa
     1981 gaacaaaaaa ctgcgctgaa tatggccaaa ttcattcagg gtcagtctct gcttttgctg
     2041 gagaagctca atgccctgga tttcgatact gaggctgacc tttgcgagaa gctccatgag
     2101 gatacggaac agctttaccg tgttttgtca gaacgactga aggaatcaga ggatggctac
     2161 taatggcgaa agtctctatc agtgaagctg cgcggcttgt aaatgtcagt cgccctacgc
     2221 tttacaagat gcttaacaat ggaacgctta cttacacctc ggttgtaaag catggaaagc
     2281 aagtaaaaac cattgatacg tctgagctta tacgtgtttt tggttcgctt ggtggtgtaa
     2341 aggacgatac acaaaacgct gtaagtgttg acggtcatgc tacagcgatt aacagtgata
     2401 ttttacaaga tttacagcat cagattgcgt tgttaaagac cgaaaatgac gggcttaaag
     2461 gggcggtgaa tgccagggat gaacatatca gttcacttcg tcaggctatg ttgcttctgg
     2521 agcataaaca ggagcagcta gcaccgcaga tctcttctcc ggcgcactcc ccgtggtgga
     2581 agttctggaa gtagttctgt cagtgcataa ccgccccgta ataccacatc cccaggaatg
     2641 cgccgcccgt actgacgcac agcaggatca gtgcggtgag cagtagcgtc aggaaccggt
     2701 ctttccataa agcattccct gtacgggctg gaacgaccca tccacctgtt aggcgcattt
     2761 gcttttgaat ttggggttcg gtttttgggc acggccgtcg ggcgtaatca tcgggcacag
     2821 ggtgcgcccg atgattacgc ccgatgattt tatcggtgag tggcctcggt gaacgtcctc
     2881 ggtgaatcgc atgcaccgag gacgttcacc gatgaaccgt cttcagggag tcgctaaatc
     2941 cctttaattc tggcgttccg atggcttgct ggacgccgcc atctctacga cacaggatat
     3001 tattccgctg gacgctgcat aacatcctga agggcggcca caccgtctcg ctacgcgcga
     3061 ccaaccccct tacaagccaa tttttacccc tgttttttcc tgtgcgtttc ccgctcataa
     3121 aaaaccagtg gaattgtctg taacgaggtt ggtcgcgcgt cgtccttgag gactagctta
     3181 acggtgtggc gggctttgcc cccaaatccg aagtcgccat tgggatggct tgcctcagta
     3241 ggctgagtca ttcgaattcg gcccccccga aggcatgatc ccctgaacgg gtatcacaaa
     3301 aaacaggtca gacccggttt aacaggagga tggctcgcag tggcgaacca tcccccttcc
     3361 ccaagggtgg ggtcgttaca gcccgtaaag ggttcgcttc gccgctacgc gtccttgact
     3421 ggctttctct cgattctaaa gcagttctaa gtccccttga tctggcggcg gtggcttgct
     3481 catacaagac ttcgtgcgct atggggcttt tacgcgcgaa tttccgcatc tgccttaggt
     3541 aaacccggat aaatccgcat tacggtgttt ctttcacgcc agttcgggca ccaggcagtg
     3601 ccgtgcatag tcatgcatac ggttaaaact tatcaggggc gtttttcggc atttcagcca
     3661 gggataaggc ggtcttttac ggcgaacgcg ccggaaccgc actgagcgcg ttttcgcggt
     3721 gcacgcaatg tggtgttatg gtaaatgagg aggcatgaac aaccccgcct tggctggatt
     3781 ttaattgcct attatacggt tattgcttat atttcgtgta tacaaatgta attacatcga
     3841 gggccgtgta tatggcaact atgaacatcc gcatcgatga cgatttaaag gcacgttctg
     3901 gtgcagcgct tgacgcgtta ggcgttacaa cgtccgaagc cgttcgcctt gtcctggagt
     3961 acgttgcgca gaataaccgc ttgccggtgc agatcgcatt actggcagac gaagacgcag
     4021 acatcatcga actggcgcgc gctcgcctgg ctaacccggg caaacggata cgcgtgaaac
     4081 tcgatgacct atgacattga attttacgaa gaggcttttg acgaatggca ccggctggat
     4141 gccagcgtac gtgaccagtt taaaaagaag ttagcaaaac tggtcgaaga cccgcaccgg
     4201 cccgctaatc ggctgcgtgg gcttgagggc tgttacaaaa tcaagctacg cgccgcaggg
     4261 gtgcgtttag tttataaagt cgaggatggc gagttagtga tcctggtcgt ggctgtcggc
     4321 aaacgggata aaaacgcagt ttacgacacc gcccgcgaac gactagtcac catagacaaa
     4381 tagcccgcga ctgcgggctt tttcattggg tttacactta tgctaaatcg tccctctacg
     4441 catcaactcc tgagttgcgg ctaagaagta ggatgcattg aatgtggaat ctcgatatgt
     4501 gattggtgat gtgcttccag tctttttgaa tgtttcaaaa aaatcattgg ctggtttctc
     4561 atcaagagga cgggtatttc ctttagagtt taatacgtag agttttccct catcactgaa
     4621 catagtgaaa gcaacttttc gcgcaccagt tgttagctcc atcggcgttt tacattcatc
     4681 aaccagtaat tcgtaaaatg aaccattcat gtctattttt acctctcttt tttcatattc
     4741 agtttcgagt tcatcaatga agcgctctag ggattctcga ataagaaacg aacggctttt
     4801 ctctgttttt ttagatacat aatcgagctt ttccatgagt tcttccggga gtgtgactgc
     4861 aatcataatc gcctctaatt ttaacctaat gtttcatcta gtttatatat taaagttttt
     4921 tagtcaagtg tgtttgattg cgtaggttgg cgtagccttg aatttacagt tattttttct
     4981 gctgccctgt ggtattgtct atacttaatt gtatatacaa aagtgtattt catgagaaca
     5041 gagcttgagt ttgaatggga ttcagtcaaa gcggagacga actaccgtaa gcatggaatt
     5101 cgttttgaag aggcagctct ggtatttgat gatccatttc atctgtcggc ccaggaccgt
     5161 atcgagaacg gtgagttcag gtggcagacc ataggtacgg tgaaggggtg tgttgtggtt
     5221 cttgtggcgc atacgacacg gtttgaagat ggtacggaaa taatccggct tatcagtgcg
     5281 cgaaaagcag agaagaatga gaggagacgc tatgagcatg gttagatata aacgcagtga
     5341 aatcccccct ctgacagaga agcgttcatc tgaattgaaa actcttgctg ctgaggctga
     5401 taatca
//
