LOCUS       NZ_CP102507             6338 bp    DNA     circular CON 31-MAR-2024
DEFINITION  Citrobacter youngae strain CF10 plasmid pCF10-G, complete sequence.
ACCESSION   NZ_CP102507
VERSION     NZ_CP102507.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN30174882
            Assembly: GCF_024662035.1
KEYWORDS    RefSeq.
SOURCE      Citrobacter youngae
  ORGANISM  Citrobacter youngae
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Citrobacter; Citrobacter freundii complex.
REFERENCE   1  (bases 1 to 6338)
  AUTHORS   Huang,J.
  TITLE     Emergence of tmexCD-toprJ1, blaKPC-2, and blaNDM-1 plasmids
            coexisted in a Clinic Citrobacter freundii strain from sepsis
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 6338)
  AUTHORS   Huang,J.
  TITLE     Direct Submission
  JOURNAL   Submitted (08-AUG-2022) Department of Laboratory Medicine, The First
            Affiliated Hospital of Chongqing Medical University, 1 Youyi Road,
            Yuzhong District, Chongqing 400016, China
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: HGAP v. 3.5.0
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 80.0x
            Sequencing Technology :: Oxford Nanopore MinION; Illumina HiSeq
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_024662035.1-RS_2024_03_31
            Annotation Date                   :: 03/31/2024 07:17:49
            Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline
            (PGAP)
            Annotation Method :: Best-placed reference protein set; GeneMarkS-2+
            Annotation Software revision      :: 6.7
            Features Annotated                :: Gene; CDS; rRNA; tRNA; ncRNA
            Genes (total)                     :: 5,419
            CDSs (total)                      :: 5,300
            Genes (coding)                    :: 5,136
            CDSs (with protein)               :: 5,136
            Genes (RNA)                       :: 119
            rRNAs                             :: 9, 8, 8 (5S, 16S, 23S)
            complete rRNAs                    :: 9, 8, 8 (5S, 16S, 23S)
            tRNAs                             :: 83
            ncRNAs                            :: 11
            Pseudo Genes (total)              :: 164
            CDSs (without protein)            :: 164
            Pseudo Genes (ambiguous residues) :: 0 of 164
            Pseudo Genes (frameshifted)       :: 49 of 164
            Pseudo Genes (incomplete)         :: 128 of 164
            Pseudo Genes (internal stop)      :: 26 of 164
            Pseudo Genes (multiple problems)  :: 32 of 164
            Pseudo Genes (short protein)      :: 1 of 164
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP102507.1.
            Bacteria and source DNA available from Department of Clinical
            Laboratory, The First Affiliated Hospital of Chongqing Medical
            University.
            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..6338
                     /organism="Citrobacter youngae"
                     /mol_type="genomic DNA"
                     /strain="CF10"
                     /host="Homo sapiens"
                     /db_xref="taxon:133448"
                     /plasmid="pCF10-G"
                     /geo_loc_name="China"
                     /collection_date="2021-04-04"
     gene            13..330
                     /locus_tag="NUG39_RS27010"
                     /old_locus_tag="NUG39_27010"
     CDS             13..330
                     /locus_tag="NUG39_RS27010"
                     /old_locus_tag="NUG39_27010"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000718044.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_023224510.1"
                     /translation="MKKIFILSAALIMAGCATKQYPQAANVTGPESSAMDCKAVALEIA
                     KTRSVQQEIEATGEFDGRTVLGFLGDFGIGNGMAKGEARKKAANRLNQLEALKAAKCAD
                     Q"
                     /name="hypothetical protein"
     gene            582..770
                     /locus_tag="NUG39_RS27015"
                     /old_locus_tag="NUG39_27015"
     CDS             582..770
                     /locus_tag="NUG39_RS27015"
                     /old_locus_tag="NUG39_27015"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000165998.1"
                     /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_000165998.1"
                     /translation="MTKQESAALNMAKFIRAQSLLLLEKLDVLDLDDEAADCERMHEQA
                     EALYQKLSARFGIQDGE"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            complement(818..1045)
                     /locus_tag="NUG39_RS27020"
                     /old_locus_tag="NUG39_27020"
     CDS             complement(818..1045)
                     /locus_tag="NUG39_RS27020"
                     /old_locus_tag="NUG39_27020"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001046776.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_206659768.1"
                     /translation="MFGFSPGELMNLCPDERLLFVRMISAMLRRSGGDAGAVMFEAYRH
                     IVSDTNQARRSCMLDLLESVRHDYVHGGYT"
                     /name="hypothetical protein"
     gene            complement(2707..3312)
                     /locus_tag="NUG39_RS27025"
                     /old_locus_tag="NUG39_27025"
     CDS             complement(2707..3312)
                     /locus_tag="NUG39_RS27025"
                     /old_locus_tag="NUG39_27025"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001549957.1"
                     /GO_function="GO:0003677 - DNA binding [Evidence IEA];
                     GO:0000150 - DNA strand exchange activity [Evidence IEA]"
                     /GO_process="GO:0006310 - DNA recombination [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="recombinase family protein"
                     /protein_id="WP_000509966.1"
                     /translation="MGHRAAIYCRVSTADQSCERQEFDLRAFAGRAGYDVVGIFKETGS
                     GTKLDRAERKKVLALAQSRQIDAILVTELSRWGRSTLDLLNTLRELENWKVSVIAMNGM
                     AFDLSSPYGRMLATFLSGIAEFERDLISERVKSGLAVAKARGKRLGRQAGVRPKSDRLL
                     PKVVAMRAEGRSYRWIARELGISKNTVADIVQRHRANA"
                     /name="recombinase family protein"
     gene            3407..6304
                     /locus_tag="NUG39_RS27030"
                     /old_locus_tag="NUG39_27030"
     CDS             3407..6304
                     /locus_tag="NUG39_RS27030"
                     /old_locus_tag="NUG39_27030"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_020326821.1"
                     /GO_function="GO:0004803 - transposase activity [Evidence
                     IEA]"
                     /GO_process="GO:0006313 - DNA transposition [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="Tn3-like element Tn5403 family transposase"
                     /protein_id="WP_001553819.1"
                     /translation="MSRRHIFTERQRAALFDLPTDELSLLKFYTLGDDDLENIRQRRRP
                     ENRIGFALQLCALRYPGRALAPGEMIPREVLSFVGAQLGVPADALLTYATRRQTRQQHM
                     DTLREIYGYKTFTGRGARDLREWTFGQAEDARSNEDLAHRFIVRCRETSTILPAVSTIE
                     RLCADALVAAERRIETRIAENLTADVRDHLDKLLSEMLAGNISRFIWLRNFEVGNNSAA
                     ANRLLDRLEFLRTLNINHSALASIPAHRIARLRRQGERYFTDGLRDITSDRRWAILAVC
                     VVEWEAAIADAIVETHDRIVGKTWREAKRQHDETISGSKATLTDTIRTFTALGASLLEA
                     RSDGTPLEMAVASSVAWDRLAQLVATGTQLSNTLADEPLAYVGQGYHRFRRYAPRMLRC
                     LKLEAAPVAGPLVAAALSIGEMKGVASPERRFLRPSSKWNRHLRAQEKGDTRLWEVAVL
                     FHLRDAFRSGDVWLAHSRRYGDLKQVLVPMIAAQENAKLAVPSNPQDWLADRKARLTIA
                     LKRLARAARNGTIPHGSIEDGTLRIDRLTADVPDGAEALILDLYRRMPSVRITDMLLEV
                     DAALGFTDAFTHLRTGAPCRDRIGLLNVLLAEGLNLGLRKMAEATNTHDYWQLSRLARW
                     HVESEAMNQALAIVVAAQGKLPMSRVWGMGTSASSDGQFFPTARHGEAMNMVNAKYGSV
                     PGLKAYTHVSDQFAPFACQSIPATVSEAPYILDGLLMNEVGRHVREQYADTAGFTDHLF
                     GASSLLGYNLVLRIRDLPSKRLYVFNPDTTPRELRKLVGGKAREDLIVANWPDIFRCAA
                     TMTAGKIRPSQLLRKLASYPRQNNLAVALREVGRIERTLFIIEWILDTDMQRRAQIGLN
                     KGEAHHALKNALRIGRQGEIRDRTTEGQHYRIAGLNLLTAVIIYWNTVHLGHAVTERRN
                     EGLDVPPEFLPHISPLGWAHILLTGEYLWPKEPKA"
                     /name="Tn3-like element Tn5403 family transposase"
     Typing          1707..2227
                     /name="rep_cluster_2358"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="88.868"
                     /coverage="99.0"
                     /evalue="0.0"
ORIGIN
        1 ataaggataa ttttgaaaaa aatattcatc ctatcggcag cgctgatcat ggcaggatgc
       61 gcaacaaagc aatatccaca ggccgcgaac gtcaccggtc cagaatcttc cgcaatggat
      121 tgcaaagcgg tagctctgga aatcgccaaa acgcgcagtg tacaacaaga aattgaggca
      181 accggcgaat ttgacgggcg caccgtatta ggtttcctgg gtgattttgg gataggaaat
      241 ggcatggcaa aaggcgaagc ccgcaaaaaa gcagctaacc ggctaaatca gctggaagcc
      301 ctgaaggctg caaagtgtgc agatcaataa ggtacaaaaa agccctgccg ggcttttttt
      361 gtacctgcca atcagctgga tttaccataa catctgttgc gtgcaccgcc tgagaggctc
      421 tcagggcgtt tctacgacct cacctgcaaa agaacacatc ttaccccctg aaaaccgctc
      481 agaaacgcgc tgatgatttc tgcgtacctg catggctatg cactcaagtg aatgaagtaa
      541 gatttcagtc tgcgatcacc ataaaaccgg gaaaaagccg tatgacaaaa caggaatcag
      601 ccgcactgaa catggcaaaa tttatccggg cgcagtcgct gctgctgctc gaaaaactcg
      661 acgtgctcga tcttgatgac gaggcagccg actgtgagcg aatgcacgaa caggcagaag
      721 cgctttatca gaagctgagc gcacgcttcg gtatacagga cggcgaataa agagacgaaa
      781 agaacgctca cttagacgaa aagcgtatcc agggcaacta tgtatatcca ccgtgtacat
      841 agtcatgcct gacgctttcg agcaggtcga gcatgcagga acgacgagct tgattggtat
      901 cggacacaat atggcgatac gcctcaaaca taacagcacc cgcatcaccg cccgaacggc
      961 gaagcatagc ggaaatcatc cgcacaaaga gcagacgttc atcggggcaa aggttcataa
     1021 gttctcctgg tgaaaaacca aacatgaaag cacccatcta ttaacgtcag ctgtgaacgc
     1081 ttcattagaa gaaaataggt aaacccggga aaaagatcca aacgttaaca tcacaggtaa
     1141 acagaaacgt cgggtcgatc gggaaattct ttcccggacg gcgcggggtt gggcaagccg
     1201 caggcgcgtc agtgctttta gcgggtgtcg gggcgcagcc ctgaaccagt cacgtagcgc
     1261 tagcggagtg tatactggct aaacttcaga gatgccaagg aagggacagg atatgttttg
     1321 tagcaccgcc accacggtgg cgatactcca aaacgcctgg tcagggcaca gccccgacac
     1381 cccagagccg actgtaggtc actggacgaa cgcggcggaa tgatgtcgga tgacgtcatt
     1441 ttgcggcgtt tgccctatcc tgcatcgtat taaaaaatgc agcactggcg cgtacggtgc
     1501 cgaagataag tccggggata ttccgcttcc tcgctcactg actcgctacg ctcggtcgtt
     1561 cggctgcggc gagcggaggg aacggagaca ttaaggcaca ggcaatgaga gaggatcgag
     1621 aggcaaaaga aaaggccgcg gcgttgccgg ttttccatag gctccgcccc cctgacaagc
     1681 atcacgaaat ctgacgctca aatcagtggt ggcgaaaccc gacaggactt aaagatacca
     1741 ggcgtttccc cctggtggct ccctcgtgcg ctctcctgtt cctgcctttc ggtttaccgg
     1801 tgtcattccg ctgttatggc cgcgtttatc tcattccacg cctgacactc agttccggga
     1861 aggcagttcg ctccaagctg gactgtatgc acgaaccccc cgttcagtcc gactgctgcg
     1921 ccttatccgg taactatcgt cttgagtcca acccggaaag acacgacaaa gcgccactgg
     1981 cagcagccac tggtaacagg attagcagag cgagttaatt taggtggtgc tatagagttc
     2041 ttgaagtggt ggcctaacta cggctacact ggaaggacag tatttggtat ctgcgctctg
     2101 ctgaagccag ttaccaggtt aagcagttcc ccaactgact taaccttcga aaaaccacct
     2161 ccccaggtgg ttttttcgtt ttcagagcaa gagattacgc gtagaaaaaa aggaactcaa
     2221 gaagatcctt tctatgctca accaccgcat ggcccatagc cgcgctggcc gttgccggtc
     2281 agctccagaa tcctcgacca atatggggtc gatagagaaa acgggaaata aagcacggta
     2341 agacagcggc aggccatgcc atgcttggtc tttctggaat ggtgtccagt tgaagtacgc
     2401 ctcaaccggg cgtcaggcac cccacctatg ttgcgtcaga ttaggatcgt ttttcgcctt
     2461 ttctgacgat ctgcgctcgg cctctcaggc ttcaacctga cagatcaacc gctagcgtgc
     2521 tttattttcc gaattctgag acgaccccat atggaacctt gcccctccca aaattcaact
     2581 aaaaaaccct catttcctgc cgataaaatg ggtatctctt aactatgcct aaatgataaa
     2641 atgggtatct cttaactatg cctaaataaa taaggggtcg gttccggctg agggcgaaat
     2701 gacaccctaa gcgttagctc tgtgtcgttg cacgatgtca gcgacggtat tcttgctgat
     2761 accgagctcg cgtgcgatcc agcgatagct gcgtccctcg gccctcatcg caaccacctt
     2821 aggcaaaagt cggtctgatt ttggtcgcac tccggcctga cgaccaagcc tcttaccacg
     2881 tgccttcgca acagcaaggc ctgacttgac ccgctcgctg atgagatccc gctcaaactc
     2941 cgcaatgccg gaaagaaacg tcgccagcat tcgtccatac ggcgacgaaa gatcgaacgc
     3001 cattccattc atggctatca cggaaacctt ccagttctcc agttcacgta gcgtattgag
     3061 cagatcgagc gtcgagcgcc cccaccggga aagctcagtg accaggattg catcaatttg
     3121 tctggactgg gcaagcgcca ggactttctt tcgctcggcc cggtcgagtt tagttcctga
     3181 acctgtttcc ttaaatattc ccaccacgtc gtagccggca cggccggcga aggctcgcag
     3241 atcaaattcc tggcgttcac aagactgatc cgctgttgaa acccggcagt aaatggcggc
     3301 acgatgtccc aattgaaccc tcctggattt ttgtatcgga acgccctgat ttatatgggc
     3361 tggctgttgt ccaaaacaga ctatacttca aaagggacga atttgtatgt cacgacgcca
     3421 tattttcacc gaacggcagc gagcagcgct gttcgatctg cccacggacg aactgtcgct
     3481 actgaagttc tacacgctgg gcgatgatga cctggaaaac attaggcagc gccgcagacc
     3541 ggaaaacagg attggctttg ccctgcaact ttgtgcctta cgatatccgg gccgtgcact
     3601 ggctcctggt gagatgatcc cgcgtgaagt cctttccttc gtcggtgctc agcttggagt
     3661 tccggctgat gcgcttctca cttatgccac acggcgccaa acccgtcagc agcacatgga
     3721 cacgctgcgc gaaatttacg gctacaagac cttcacgggc cgtggtgccc gtgatctgcg
     3781 ggagtggact ttcggccagg ccgaagatgc cagatcaaac gaggatcttg ctcatcgttt
     3841 tattgtgcgg tgtcgggaaa cttccaccat tctgcccgca gtatcgacaa tcgagcgctt
     3901 gtgcgcggat gctctggtcg ccgctgagcg gcggattgaa acgcggattg cggaaaattt
     3961 aacagcggat gttcgcgatc acctggacaa acttctgagt gaaatgctcg ccggcaatat
     4021 cagtcgtttc atctggcttc gcaacttcga ggttggtaac aactcggctg ctgctaaccg
     4081 tttgctcgac aggctcgaat ttctgcgtac cctgaatatc aatcatagtg ctttggccag
     4141 catacctgcc catcgcattg cccggctgcg tcggcagggt gaacgctact tcaccgacgg
     4201 tttgcgtgac atcacttcgg accgccgctg ggcgatcctt gccgtctgtg ttgtggagtg
     4261 ggaagcggcg attgctgatg ccatagtcga aacccatgac aggatcgtag gaaaaacctg
     4321 gcgggaagcg aagcgccagc atgacgaaac aatttccggc tctaaagcca cactcacgga
     4381 tacgatccgt accttcaccg cgctgggagc ttcgttgctt gaggcccgca gtgacggaac
     4441 cccgctggag atggctgtcg ccagttcggt tgcatgggac cggcttgctc aactggtagc
     4501 gacagggact caactcagca acacgctagc cgatgagcct cttgcatatg tcgggcaggg
     4561 ataccatcgc tttcgtcgtt atgcgccccg catgttgcgc tgtctgaagc tcgaagccgc
     4621 gccggtcgcc ggaccattgg tagcagcagc tttgtcgatc ggagagatga aaggtgttgc
     4681 atcgccagaa aggcgtttcc tgcggcccag ctccaaatgg aaccgtcatt tacgagctca
     4741 ggaaaaagga gatacccgtc tttgggaagt ggctgtactc tttcacctcc gggatgcttt
     4801 tcgttccgga gatgtctggc tcgctcattc gcgccgctat ggtgacctca agcaggtact
     4861 ggtgccgatg atcgcggcgc aggaaaatgc aaaactggcc gtgccttcca acccacagga
     4921 ttggctggca gacagaaagg cgcgactcac gatcgctctt aagcggctgg cccgggctgc
     4981 ccgtaacggc actattccgc acggtagcat agaagatgga acgttgcgga tcgacaggtt
     5041 gacagcagac gtgccggatg gtgccgaggc actcatactg gatctgtatc gccgaatgcc
     5101 gtccgttcgg attaccgaca tgctgcttga agttgatgca gcccttggtt tcacagatgc
     5161 gtttacccat ctgagaaccg gggctccatg tcgcgaccgg atcggtctgc tcaacgtcct
     5221 gctcgctgaa gggctcaatc tgggcctgcg taagatggcg gaagctacaa acacgcatga
     5281 ttactggcag ctctcacgcc ttgcccgctg gcatgttgaa agcgaagcca tgaaccaggc
     5341 attggcaatt gtggtggccg cgcagggtaa actgccgatg tcacgcgtct gggggatggg
     5401 cacgtcagca tcgagcgatg gtcagttttt cccgacagcg cggcatggcg aagccatgaa
     5461 catggtcaat gccaaatatg gttctgttcc cggcctcaaa gcgtatactc acgtaagcga
     5521 ccagttcgcg ccattcgctt gtcagtcgat cccggcgacc gtgagcgagg caccgtatat
     5581 tctcgatgga ctactgatga acgaggtcgg tcgccatgtt cgcgaacagt atgccgatac
     5641 agcaggattc accgaccatt tgttcggagc cagtagcctg ctcggctaca atctcgttct
     5701 gcgaatcagg gatctgccat cgaagcggtt gtacgtattt aatcccgata cgacccccag
     5761 ggagttacgc aagttggtag gtggaaaagc ccgggaggat cttatcgttg cgaactggcc
     5821 tgatattttc cgttgtgccg cgacgatgac cgctggcaaa atcaggccca gccaactcct
     5881 gcgcaagctc gcttcttacc cacgacaaaa caaccttgca gttgcgcttc gtgaagttgg
     5941 tcgtattgaa cggacccttt tcattattga gtggatcctg gatacggaca tgcagcggcg
     6001 tgctcagatc ggtcttaaca agggagaggc ccaccatgcg ctcaaaaatg cgctccgtat
     6061 cgggaggcag ggggaaattc gcgatcgcac gacagagggg cagcactacc gaatcgctgg
     6121 gctcaattta ttgactgcgg tgatcattta ctggaatacc gtccatcttg gtcatgccgt
     6181 cacggagcgg cggaacgaag ggttggatgt tccccctgaa tttcttcccc acatatcccc
     6241 attgggctgg gcgcacattc tactgactgg cgaatatctt tggcccaagg aaccgaaagc
     6301 ttagggtgtc atttcgccct cagccggaac cgacccca
//
