LOCUS       NZ_CP137126             5186 bp    DNA     circular CON 02-NOV-2023
DEFINITION  Citrobacter freundii strain F3021 plasmid pF3021-4, complete
            sequence.
ACCESSION   NZ_CP137126
VERSION     NZ_CP137126.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN37878029
            Assembly: GCF_033160275.1
KEYWORDS    RefSeq.
SOURCE      Citrobacter freundii
  ORGANISM  Citrobacter freundii
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Citrobacter; Citrobacter freundii complex.
REFERENCE   1  (bases 1 to 5186)
  AUTHORS   Li,X.
  TITLE     Citrobacter freundii F3021 Genome sequencing and assembly
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 5186)
  AUTHORS   Li,X.
  TITLE     Direct Submission
  JOURNAL   Submitted (18-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                   :: 11/02/2023 06:23:09
            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)                     :: 5,321
            CDSs (total)                      :: 5,200
            Genes (coding)                    :: 5,055
            CDSs (with protein)               :: 5,055
            Genes (RNA)                       :: 121
            rRNAs                             :: 9, 8, 8 (5S, 16S, 23S)
            complete rRNAs                    :: 9, 8, 8 (5S, 16S, 23S)
            tRNAs                             :: 85
            ncRNAs                            :: 11
            Pseudo Genes (total)              :: 145
            CDSs (without protein)            :: 145
            Pseudo Genes (ambiguous residues) :: 0 of 145
            Pseudo Genes (frameshifted)       :: 47 of 145
            Pseudo Genes (incomplete)         :: 100 of 145
            Pseudo Genes (internal stop)      :: 29 of 145
            Pseudo Genes (multiple problems)  :: 29 of 145
            Pseudo Genes (short protein)      :: 1 of 145
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP137126.1.
            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..5186
                     /organism="Citrobacter freundii"
                     /mol_type="genomic DNA"
                     /strain="F3021"
                     /isolation_source="stool"
                     /host="Homo sapiens"
                     /db_xref="taxon:546"
                     /plasmid="pF3021-4"
                     /geo_loc_name="China: Hangzhou"
                     /lat_lon="29.86 N 121.56 E"
                     /collection_date="2021-11-17"
                     /collected_by="Jiayao Yao"
     gene            complement(505..1284)
                     /locus_tag="R2X28_RS26585"
                     /old_locus_tag="R2X28_26585"
     CDS             complement(505..1284)
                     /locus_tag="R2X28_RS26585"
                     /old_locus_tag="R2X28_26585"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000422636.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="APH(3')-VI family aminoglycoside
                     O-phosphotransferase"
                     /protein_id="WP_109018074.1"
                     /translation="MELPNIIQQFIGNSVLEPNKIGQSPSDVYSFNRNNETFFLKRSST
                     LYTETTYSVSREAKMMSWLSDKLKVPELIMTFQDEQFEFMITKAINAKPISALFLTEQE
                     LLSIYKETLNQLNAVAIFDCPFISSIDHRLKESKFFIDNQLLDEIDQDDFEAELWGDHK
                     TYLSLWNELNETRVEERLVFSHGDITDSNIFIDKSGEIYFLDLGRAGLADEFVDISFVE
                     RCLREDVSEETAKIFLKHLKNDMPDKRNYFLKLDELN"
                     /name="APH(3')-VI family aminoglycoside
                     O-phosphotransferase"
     gene            1422..2119
                     /locus_tag="R2X28_RS26590"
                     /old_locus_tag="R2X28_26590"
     CDS             join(1422..1671,1671..2119)
                     /locus_tag="R2X28_RS26590"
                     /old_locus_tag="R2X28_26590"
                     /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_095033700.1"
                     /translation="MASVSISCPSCSATDGVVRNGKSTAGHQRYLCSHCRKTWQLQFTY
                     TASQPGTHQKIIDMAMNGVGCRATARIMGVGLNTIFRHFKKLRPQSVTSRIQPGSDVIV
                     CAEMDEQWGYVGAKSRQRWLFYAYDRLRKTVVAHVFGERTMATLGRLMSLLSPFDVVIW
                     MTDGWPLYESRLKGKLHVISKRYTQRIERHNLNLRQHLARLGRKSLSFSKSVELHDKVI
                     GHYLNIKHYQ"
                     /name="IS1-like element IS1B family transposase"
     gene            complement(2858..3388)
                     /locus_tag="R2X28_RS26595"
                     /old_locus_tag="R2X28_26595"
     CDS             complement(2858..3388)
                     /locus_tag="R2X28_RS26595"
                     /old_locus_tag="R2X28_26595"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000168766.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_012634455.1"
                     /translation="MASTEEKLLTLLLSAEHLKEAAKEQQKAVADSLAVARETLKGYRE
                     ISDSVAQQVRDEVRQEVQKMDVAGLIGERISADFQRLEKSVGNMKINADALDKEISIIR
                     SNIIAEYNTLRGYSWKWFAGVAVAFVVLIFATSWFVKTELQDNYNASAAVYQKVADLEK
                     LLTTEQKPEKKKN"
                     /name="hypothetical protein"
     gene            complement(3391..4326)
                     /locus_tag="R2X28_RS26600"
                     /old_locus_tag="R2X28_26600"
     CDS             complement(3391..4326)
                     /locus_tag="R2X28_RS26600"
                     /old_locus_tag="R2X28_26600"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_016235474.1"
                     /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_045626452.1"
                     /translation="MATYHLSVKFGGKGKALAHASYITREDKFSQRQDLEHTEHGNMPE
                     WARDEPAHFWQAADAFERANGSTYREIEIALPRELNEAQRLALVRDFVKQETGDKHAWT
                     FAIHNPKASIDGGEQPHAHIMMSQRVNDGIERSPEQYFRRYNAKFPARGGARKDSGHNL
                     TPTEQKQALKALRERWERTHNAHMKRYGFEQGFIDSRSLKTQGIDRKPEQHLGFEAAGR
                     LDDSQRQDIKDSRTFSVVDVPEQAKHIDHSDRSWMNASGIEVNRKELVRSLTHDISQQY
                     GREMAARVTKQGNVEIERVKSLSRGFSISR"
                     /name="MobA/MobL family protein"
     gene            4493..4879
                     /locus_tag="R2X28_RS26605"
                     /old_locus_tag="R2X28_26605"
     CDS             4493..4879
                     /locus_tag="R2X28_RS26605"
                     /old_locus_tag="R2X28_26605"
                     /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_045282373.1"
                     /translation="MRISNVEWLKKRIAFIRKLGEKTARQRQIIDLLDDEASLSETERR
                     LLHVLATAEKNALQERDAAQKKAVQARISGQKNRRERNHRLFLAAGLMIDAGLVDTKTG
                     ELNFDHEKLLTALKRVRYDLETSA"
                     /name="hypothetical protein"
     ARG             complement(509..1284)
                     /name="aph(3')-VIb"
                     /gene="aph(3')-VIb"
                     /gene_name="aminoglycoside O-phosphotransferase
                     APH(3')-VIb"
                     /tool="amrfinderplus"
                     /drug_class="AMINOGLYCOSIDE"
                     /identity="98.07"
                     /coverage="100.0"
     Typing          complement(3395..4326)
                     /name="MOBQ"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="95.177"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 tccggcagga taaacaggca agcggtggga acctgaccag ctcgggaaag aagctggctc
       61 tacccggtct cacgttaacc aataacgtac ctgataaagt gagagtgaag gcagcggttg
      121 cggtgaagcg tgattgccaa ggtctggcgc aacacccaca aaatcgaagc agcatacgaa
      181 cggcctgatg ctggtcgctt cgctccccgt tttctggtgt acccaccacg ggggcattag
      241 gctttctttg ccctaatatg ggtttgcgac tctcaaatcc gggttgtggt gtaacacata
      301 tcgccttcac cgaaatgggt aatgatacca acgtgttgat ttcgtatttt cactgacacc
      361 aggatcatcc tgatgttaca aggattgaat gacaacagat taaaatagtc atcaacaggt
      421 tgacagcatt accttttttc acttatttat ttaaaaatta gcaacttaaa aatacagcta
      481 agtattttta gatattgctt ggagttaatt caattcatca agttttaaaa aataattcct
      541 tttgtcaggc atatcgtttt ttaaatgctt taaaaatatt ttagcagttt cctcagatac
      601 atcctctctt aggcaacgtt caacaaaaga tatatctaca aattcatctg ctaatccagc
      661 acgaccaaga tctaaaaagt aaatttcacc agatttatct ataaaaatat tactatccgt
      721 gatatcgcca tgagaaaaaa ccaatctttc ttcaacacga gtctcattta actcattcca
      781 aagacttagg taagttttat ggtctcccca taattcagcc tcaaaatcat cttgatctat
      841 ctcgtcaagg agttggttat caataaaaaa ttttgactct tttaaccgat gatcaatgct
      901 tgaaataaat gggcaatcaa aaatagcaac tgcatttaac tgattgagtg tttccttata
      961 gatagaaagc aattcttgct ctgttaaaaa aagcgctgaa attggttttg cattgatcgc
     1021 tttagtgatc atgaattcaa actgctcatc ctgaaaagtc atgatgagtt caggcacctt
     1081 taatttatca gagagccaac tcatcatttt cgcttcacga gagacactgt atgtggtctc
     1141 tgtatataaa gtgctagatc gcttaagaaa aaaagtttca ttatttcgat taaaagaata
     1201 aacatccgat ggcgactgac caattttatt tggctctaaa acgctgtttc caataaattg
     1261 ttgaataata ttaggcaatt ccatcaagtt ttccttttat tcagcattaa aaacctcgca
     1321 aatgcgaggc ctagtaaata gatgatctta attaggttca ctgtagggtg atgctgccaa
     1381 cttactgatt tagtgtatga tggtgttttt gaggtgctcc agtggcttct gtttctatca
     1441 gctgtccctc ctgttcagct actgacgggg tggtgcgtaa cggcaaaagc actgccggac
     1501 atcagcgcta tctctgctct cactgccgta aaacatggca actgcagttc acttacaccg
     1561 cttctcaacc cggtacgcac cagaaaatca ttgatatggc catgaatggc gttggatgcc
     1621 gggcaaccgc ccgcattatg ggcgttggcc tcaacacgat tttccgccat ttaaaaaact
     1681 caggccgcag tcggtaacct cgcgcataca gccgggcagt gacgtcatcg tctgcgcgga
     1741 aatggacgaa cagtggggat acgtcggggc taaatcgcgc cagcgctggc tgttttacgc
     1801 gtatgacagg ctccggaaga cggttgttgc gcacgtattc ggtgaacgca ctatggcgac
     1861 gctggggcgt cttatgagcc tgctgtcacc ctttgacgtg gtgatatgga tgacggatgg
     1921 ctggccgctg tatgaatccc gcctgaaggg aaagctgcac gtaatcagca agcgatatac
     1981 gcagcgaatt gagcggcata acctgaatct gaggcagcac ctggcacggc tgggacggaa
     2041 gtcgctgtcg ttctcaaaat cggtggagct gcatgacaaa gtcatcgggc attatctgaa
     2101 cataaaacac tatcagtaag ttggagtcat taccaccgaa atgatgtgaa gacttcatca
     2161 ttttagcaat cacaggttgc cctaatcact taacgctatt attgttctat tgaagcctta
     2221 acctaaaccc actcacaaaa cgtggattat ctggttagtg attcgcagca acaaagcgtc
     2281 ccggttcaaa acgaatcgta agacgtagtt tcccttgatg tagggcttgc cgatggaaca
     2341 ggcggctttt ttattctccg gcgtgggggg ggatgctgtt gacagaaatg gaaataagta
     2401 acatccggaa tattacgctt attgcccggc gtcttgcctg gattaatgcc aaaagaactc
     2461 atatcgatat accatcgttt gcagaactgc ttttctccgg ccaaaaagcg ctgttcttcg
     2521 aacaatataa ttattttcac tcacgacggt acacaacggc aggcacgtca aagccaccgg
     2581 atttaccata acatccgttg cgtgcaccgc ctcagaggct ctcagggcgg ttttaagtcc
     2641 tgagccataa aaacccccgg cttctcaccg aaaaccgctc agaatcgcat accgtgattt
     2701 tcagccccat gcataaccat gcacctgact gactggcgag aacttccggc ctgaattcag
     2761 gccggaagtc tcaaaagacg ccccaaactc ggctgaaaac ggtgaacggg tgcgcaattt
     2821 attgtgcgaa cgtgaggcgt tggacaagcg cagcgcgtca gttctttttc ttttccggtt
     2881 tctgttccgt tgtcagcagc ttttcaaggt ctgccacttt ctgatagacg gcagcagacg
     2941 cgttgtaatt gtcctgtagt tccgttttca caaaccagct tgtggcaaat atcagtacga
     3001 caaaggcaac cgcaacccca gcaaaccact tccagctgta accccgcagc gtgttgtact
     3061 ccgcgatgat gttactgcgg ataatggaaa tttccttgtc cagcgcgtcc gcattgattt
     3121 tcatgttccc gacggatttt tccagacgct gaaaatcagc gctgatacgc tcgccaatca
     3181 gccccgcaac atccattttc tgcacttcct gccggacttc atcccttacc tgctgtgcca
     3241 cactgtccga tatttcccgg tagcctttca gggtttccct tgccaccgcc agcgaatccg
     3301 ccacggcttt ctgctgctct tttgcggcct ctttcagatg ctccgccgac agcaggagtg
     3361 tgagaagttt ttcttcggtg ctcgccatag ttacctgctt atggaaaatc cgcgtgacag
     3421 ggatttcacg cgctctattt caacatttcc ctgttttgtg acccgtgcag ccatctcccg
     3481 cccgtactgc tgcgagatat catgcgtcag agatctgacc agttccttcc ggtttacctc
     3541 gataccgctg gcattcatcc agctacggtc gctgtggtcg atatgtttcg cctgttcagg
     3601 cacatccacg actgaaaacg tccggctgtc tttaatatcc tgcctctggc tgtcgtccag
     3661 tcgtccggct gcttcaaaac cgagatgctg ttccggtttc cggtcgatac cctgtgtttt
     3721 cagtgaccgg ctatcaataa aaccctgctc aaagccatat cgtttcatat gcgcgttgtg
     3781 cgtacgctcc cagcgctccc gcagggcttt cagtgcctgt ttttgttctg taggggttaa
     3841 attatgccct gagtccttgc gcgcgccgcc acgcgccgga aatttggcgt tatagcgcct
     3901 gaaatactgt tcgggactgc gctcaatacc gtcattgacg cgctggctca tcatgatatg
     3961 ggcgtgcggc tgttcgccgc cgtcaatgct ggctttcgga ttgtggatcg caaacgtcca
     4021 tgcatgtttg tcgcccgttt cctgcttcac aaaatcccgg acaagcgcca gccgctgcgc
     4081 ttcattcagc tcgcggggta gagcgatctc aatttccctg tacgttgaac cgttggcacg
     4141 ttcgaacgca tccgcagcct gccagaaatg ggcgggttca tctctcgccc attccggcat
     4201 attgccgtgt tcggtgtgct cgagatcctg gcgctggctg aacttatctt cccgcgtaat
     4261 gtaactggca tgagcaaggg ctttaccctt gccgccaaat ttcacgctga gatgatacgt
     4321 tgccatgttg tgtcagcccc cggcagggcg cactgtttct gcccgcaggg agaaacatat
     4381 aagtgcgctt tactctaatt taaagaatta tgagtaaaga taagtcatgc gacttctgac
     4441 cgcaagttat atactttccc cgtcggaaat atcgggatgg ggaagttaaa cgatgcggat
     4501 cagtaacgtc gaatggctta aaaagcgcat agccttcatc agaaagctgg gagaaaaaac
     4561 ggcacggcaa cggcagatta tcgatctgct ggatgatgaa gcttcgctca gtgagactga
     4621 aagacgactg ctccacgttc tggcaaccgc tgaaaaaaac gcgttgcagg aacgggatgc
     4681 cgcacagaaa aaggcggttc aggcgcggat ttcagggcag aaaaaccgca gggaacgcaa
     4741 tcacagactg tttctggcgg ctggtctgat gattgacgcg ggactggttg atacaaaaac
     4801 gggtgagttg aattttgacc acgaaaaatt actgactgcg ctgaaacggg tacgctacga
     4861 tctggaaaca tcggcgtgaa cgtgcattct gcaaggccgg agaaatgccg cttcctcgct
     4921 cactgactcg cgtcgctcgg tcgttcggct gcggcgagcg gtagggattt tcggatagga
     4981 gcatgaattt tcttgctcca gatgtacaaa agccccgtga cagaatcacg gggcttgagt
     5041 actctaattc ttgcagatac ctgccaggat cagacgtcac aatcaaatcc tagcagggct
     5101 ggctaggaat gtcactacca gcttaatacc attcaacgac attaaaccca tatctgcacc
     5161 ttgactctca ggtctacgcc ccggac
//
