LOCUS       NZ_CP110902             5651 bp    DNA     circular CON 26-JAN-2024
DEFINITION  Citrobacter freundii strain CF2206 plasmid pCF2206-7, complete
            sequence.
ACCESSION   NZ_CP110902
VERSION     NZ_CP110902.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN31693662
            Assembly: GCF_026240855.1
KEYWORDS    RefSeq.
SOURCE      Citrobacter freundii
  ORGANISM  Citrobacter freundii
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Citrobacter; Citrobacter freundii complex.
REFERENCE   1  (bases 1 to 5651)
  AUTHORS   Li,X.
  TITLE     Sequence characteristics of the clinical Citrobacter freundii-2
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 5651)
  AUTHORS   Li,X.
  TITLE     Direct Submission
  JOURNAL   Submitted (11-NOV-2022) Faculty of Graduate Studies, Hangzhou
            Medical University, Xi hu district, Hangzhou 310000, China
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: Unicycler v. v0.4.8
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 100.0x
            Sequencing Technology             :: Oxford Nanopore
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 01/24/2024 15:46:40
            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)                     :: 5,545
            CDSs (total)                      :: 5,423
            Genes (coding)                    :: 5,294
            CDSs (with protein)               :: 5,294
            Genes (RNA)                       :: 122
            rRNAs                             :: 9, 8, 8 (5S, 16S, 23S)
            complete rRNAs                    :: 9, 8, 8 (5S, 16S, 23S)
            tRNAs                             :: 83
            ncRNAs                            :: 14
            Pseudo Genes (total)              :: 129
            CDSs (without protein)            :: 129
            Pseudo Genes (ambiguous residues) :: 0 of 129
            Pseudo Genes (frameshifted)       :: 33 of 129
            Pseudo Genes (incomplete)         :: 86 of 129
            Pseudo Genes (internal stop)      :: 26 of 129
            Pseudo Genes (multiple problems)  :: 15 of 129
            Pseudo Genes (short protein)      :: 1 of 129
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP110902.1.
            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..5651
                     /organism="Citrobacter freundii"
                     /mol_type="genomic DNA"
                     /strain="CF2206"
                     /isolation_source="urine"
                     /host="Homo sapiens"
                     /db_xref="taxon:546"
                     /plasmid="pCF2206-7"
                     /geo_loc_name="China"
                     /lat_lon="29.86 N 121.56 E"
                     /collection_date="2022-06-23"
                     /collected_by="zhangxiaofan"
     gene            complement(535..1314)
                     /locus_tag="OQY67_RS25605"
                     /old_locus_tag="OQY67_25600"
     CDS             complement(535..1314)
                     /locus_tag="OQY67_RS25605"
                     /old_locus_tag="OQY67_25600"
                     /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            complement(1560..>1859)
                     /locus_tag="OQY67_RS25610"
                     /old_locus_tag="OQY67_25605"
                     /pseudo=""
     CDS             complement(1560..>1859)
                     /locus_tag="OQY67_RS25610"
                     /old_locus_tag="OQY67_25605"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_004821790.1"
                     /note="incomplete; partial in the middle of a contig;
                     missing N-terminus; Derived by automated computational
                     analysis using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="enoyl-CoA hydratase/isomerase family protein"
                     /name="enoyl-CoA hydratase/isomerase family protein"
     gene            1917..2614
                     /locus_tag="OQY67_RS25615"
                     /old_locus_tag="OQY67_25610"
     CDS             join(1917..2166,2166..2614)
                     /locus_tag="OQY67_RS25615"
                     /old_locus_tag="OQY67_25610"
                     /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(3353..3883)
                     /locus_tag="OQY67_RS25620"
                     /old_locus_tag="OQY67_25615"
     CDS             complement(3353..3883)
                     /locus_tag="OQY67_RS25620"
                     /old_locus_tag="OQY67_25615"
                     /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(3886..4821)
                     /locus_tag="OQY67_RS25625"
                     /old_locus_tag="OQY67_25620"
     CDS             complement(3886..4821)
                     /locus_tag="OQY67_RS25625"
                     /old_locus_tag="OQY67_25620"
                     /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            4988..5374
                     /locus_tag="OQY67_RS25630"
                     /old_locus_tag="OQY67_25625"
     CDS             4988..5374
                     /locus_tag="OQY67_RS25630"
                     /old_locus_tag="OQY67_25625"
                     /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(539..1314)
                     /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(3890..4821)
                     /name="MOBQ"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="95.177"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 caccttgact ctcaggtcta cgccccggac tccggcagga taaacaggca agcggtggga
       61 acctgaccag ctcgggaaag aagctggctc tacccggtct cacgttaacc aataacgtac
      121 ctgataaagt gagagtgaag gcagcggttg cggtgaagcg tgattgccaa ggtctggcgc
      181 aacacccaca aaatcgaagc agcatacgaa cggcctgatg ctggtcgctt cgctccccgt
      241 tttctggtgt acccaccacg ggggcattag gctttctttg ccctaatatg ggtttgcgac
      301 tctcaaatcc gggttgtggt gtaacacata tcgccttcac cgaaatgggt aatgatacca
      361 acgtgttgat ttcgtatttt cactgacacc aggatcatcc tgatgttaca aggattgaat
      421 gacaacagat taaaatagtc atcaacaggt tgacagcatt accttttttc acttatttat
      481 ttaaaaatta gcaacttaaa aatacagcta agtattttta gatattgctt ggagttaatt
      541 caattcatca agttttaaaa aataattcct tttgtcaggc atatcgtttt ttaaatgctt
      601 taaaaatatt ttagcagttt cctcagatac atcctctctt aggcaacgtt caacaaaaga
      661 tatatctaca aattcatctg ctaatccagc acgaccaaga tctaaaaagt aaatttcacc
      721 agatttatct ataaaaatat tactatccgt gatatcgcca tgagaaaaaa ccaatctttc
      781 ttcaacacga gtctcattta actcattcca aagacttagg taagttttat ggtctcccca
      841 taattcagcc tcaaaatcat cttgatctat ctcgtcaagg agttggttat caataaaaaa
      901 ttttgactct tttaaccgat gatcaatgct tgaaataaat gggcaatcaa aaatagcaac
      961 tgcatttaac tgattgagtg tttccttata gatagaaagc aattcttgct ctgttaaaaa
     1021 aagcgctgaa attggttttg cattgatcgc tttagtgatc atgaattcaa actgctcatc
     1081 ctgaaaagtc atgatgagtt caggcacctt taatttatca gagagccaac tcatcatttt
     1141 cgcttcacga gagacactgt atgtggtctc tgtatataaa gtgctagatc gcttaagaaa
     1201 aaaagtttca ttatttcgat taaaagaata aacatccgat ggcgactgac caattttatt
     1261 tggctctaaa acgctgtttc caataaattg ttgaataata ttaggcaatt ccatcaagtt
     1321 ttccttttat tcagcattaa aaacctcgca aatgcgaggc ctagtaaata gatgatctta
     1381 attaggttca ctgtagcaaa aatatggctt attgtctata gagggtcaat gcatcaaact
     1441 tttgtcatta cctctcaatt gcataaatag cgctaggctt aaggaaaatg ggttgctgta
     1501 tttctctgtc tcaaatctca agaataagct agagcagaat attagacagc agcaagacct
     1561 caggatgcag acaaatcgcg gagtagttgc tccaaatcct gttcgcccac ttttgtttga
     1621 gcacctgcct gcaagccgcc acgaatgagt ttttcagcag ccggacgcgc aaacagacca
     1681 gcccatgcct tgtgctctcg aaggaagtct tcacttaaat ccgttggtgg gattgctttc
     1741 tttgcagcgg cgatgacccc ttcaggtaaa gctgcaatat ttgtggcgat gcgatgaaca
     1801 aaagcgtcta actcatttgc cggaagcgca cgatttaccc aaccatatcg ttcggctagc
     1861 aggtgatgct gccaacttac tgatttagtg tatgatggtg tttttgaggt gctccagtgg
     1921 cttctgtttc tatcagctgt ccctcctgtt cagctactga cggggtggtg cgtaacggca
     1981 aaagcactgc cggacatcag cgctatctct gctctcactg ccgtaaaaca tggcaactgc
     2041 agttcactta caccgcttct caacccggta cgcaccagaa aatcattgat atggccatga
     2101 atggcgttgg atgccgggca accgcccgca ttatgggcgt tggcctcaac acgattttcc
     2161 gccatttaaa aaactcaggc cgcagtcggt aacctcgcgc atacagccgg gcagtgacgt
     2221 catcgtctgc gcggaaatgg acgaacagtg gggatacgtc ggggctaaat cgcgccagcg
     2281 ctggctgttt tacgcgtatg acaggctccg gaagacggtt gttgcgcacg tattcggtga
     2341 acgcacgatg gcgacgctgg ggcgtcttat gagcctgctg tcaccctttg acgtggtgat
     2401 atggatgacg gatggctggc cgctgtatga atcccgcctg aagggaaagc tgcacgtaat
     2461 cagcaagcga tatacgcagc gaattgagcg gcataacctg aatctgaggc agcacctggc
     2521 acggctggga cggaagtcgc tgtcgttctc aaaatcggtg gagctgcatg acaaagtcat
     2581 cgggcattat ctgaacataa aacactatca gtaagttgga gtcattacca ccgaaatgat
     2641 gtgaagactt catcatttta gcaatcacag gttgccctaa tcacttaacg ctattattgt
     2701 tctattgaag ccttaaccta aacccactca caaaacgtgg attatctggt tagtgattcg
     2761 cagcaacaaa gcgtcccggt tcaaaacgaa tcgtaagacg tagtttccct tgatgtaggg
     2821 cttgccgatg gaacaggcgg cttttttatt ctccggcgtg gggggggatg ctgttgacag
     2881 aaatggaaat aagtaacatc cggaatatta cgcttattgc ccggcgtctt gcctggatta
     2941 atgccaaaag aactcatatc gatataccat cgtttgcaga actgcttttc tccggccaaa
     3001 aagcgctgtt cttcgaacaa tataattatt ttcactcacg acggtacaca acggcaggca
     3061 cgtcaaagcc accggattta ccataacatc cgttgcgtgc accgcctcag aggctctcag
     3121 ggcggtttta agtcctgagc cataaaaacc cccggcttct caccgaaaac cgctcagaat
     3181 cgcataccgt gattttcagc cccatgcata accatgcacc tgactgactg gcgagaactt
     3241 ccggcctgaa ttcaggccgg aagtctcaaa agacgcccca aactcggctg aaaacggtga
     3301 acgggtgcgc aatttattgt gcgaacgtga ggcgttggac aagcgcagcg cgtcagttct
     3361 ttttcttttc cggtttctgt tccgttgtca gcagcttttc aaggtctgcc actttctgat
     3421 agacggcagc agacgcgttg taattgtcct gtagttccgt tttcacaaac cagcttgtgg
     3481 caaatatcag tacgacaaag gcaaccgcaa ccccagcaaa ccacttccag ctgtaacccc
     3541 gcagcgtgtt gtactccgcg atgatgttac tgcggataat ggaaatttcc ttgtccagcg
     3601 cgtccgcatt gattttcatg ttcccgacgg atttttccag acgctgaaaa tcagcgctga
     3661 tacgctcgcc aatcagcccc gcaacatcca ttttctgcac ttcctgccgg acttcatccc
     3721 ttacctgctg tgccacactg tccgatattt cccggtagcc tttcagggtt tcccttgcca
     3781 ccgccagcga atccgccacg gctttctgct gctcttttgc ggcctctttc agatgctccg
     3841 ccgacagcag gagtgtgaga agtttttctt cggtgctcgc catagttacc tgcttatgga
     3901 aaatccgcgt gacagggatt tcacgcgctc tatttcaaca tttccctgtt ttgtgacccg
     3961 tgcagccatc tcccgcccgt actgctgcga gatatcatgc gtcagagatc tgaccagttc
     4021 cttccggttt acctcgatac cgctggcatt catccagcta cggtcgctgt ggtcgatatg
     4081 tttcgcctgt tcaggcacat ccacgactga aaacgtccgg ctgtctttaa tatcctgcct
     4141 ctggctgtcg tccagtcgtc cggctgcttc aaaaccgaga tgctgttccg gtttccggtc
     4201 gataccctgt gttttcagtg accggctatc aataaaaccc tgctcaaagc catatcgttt
     4261 catatgcgcg ttgtgcgtac gctcccagcg ctcccgcagg gctttcagtg cctgtttttg
     4321 ttctgtaggg gttaaattat gccctgagtc cttgcgcgcg ccgccacgcg ccggaaattt
     4381 ggcgttatag cgcctgaaat actgttcggg actgcgctca ataccgtcat tgacgcgctg
     4441 gctcatcatg atatgggcgt gcggctgttc gccgccgtca atgctggctt tcggattgtg
     4501 gatcgcaaac gtccatgcat gtttgtcgcc cgtttcctgc ttcacaaaat cccggacaag
     4561 cgccagccgc tgcgcttcat tcagctcgcg gggtagagcg atctcaattt ccctgtacgt
     4621 tgaaccgttg gcacgttcga acgcatccgc agcctgccag aaatgagcgg gttcatctct
     4681 cgcccattcc ggcatattgc cgtgttcggt gtgctcgaga tcctggcgct ggctgaactt
     4741 atcttcccgc gtaatgtaac tggcatgagc aagggcttta cccttgccgc caaatttcac
     4801 gctgagatga tacgttgcca tgttgtgtca gcccccggca gggcgcactg tttctgcccg
     4861 cagggagaaa catataagtg cgctttagtc taatttaaag aattatgagt aaagataagt
     4921 catgcgactt ctgaccgcaa gttatatact ttccccgtcg gaaatatcgg gatggggaag
     4981 ttaaacgatg cggatcagta acgtcgaatg gcttaaaaag cgcatagcct tcatcagaaa
     5041 gctgggagaa aaaacggcac ggcaacggca gattatcgat ctgctggatg atgaagcttc
     5101 gctcagtgag actgaaagac gactgctcca cgttctggca accgctgaaa aaaacgcgtt
     5161 gcaggaacgg gatgccgcac agaaaaaggc ggttcaggcg cggatttcag ggcagaaaaa
     5221 ccgcagggaa cgcaatcaca gactgtttct ggcggctggt ctgatgattg acgcgggact
     5281 ggttgataca aaaacgggtg agttgaattt tgaccacgaa aaattactga ctgcgctgaa
     5341 acgggtacgc tacgatctgg aaacatcggc gtgaacgtgc attctgcaag gccggagaaa
     5401 tgccgcttcc tcgctcactg actcgcgtcg ctcggtcgtt cggctgcggc gagcggtagg
     5461 gattttcgga taggagcatg aattttcttg ctccagatgt acaaaagccc cgtgacagaa
     5521 tcacggggct tgagtactct aattcttgca gatacctgcc aggatcagac gtcacaatca
     5581 aatcctagca gggctggcta ggaatgtcac taccagctta ataccattca acgacattaa
     5641 acccatatct g
//
