LOCUS       NZ_CP102508             5411 bp    DNA     circular CON 31-MAR-2024
DEFINITION  Citrobacter youngae strain CF10 plasmid pCF10-H, complete sequence.
ACCESSION   NZ_CP102508
VERSION     NZ_CP102508.1
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 5411)
  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  JOURNAL   Unpublished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 5411)
  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
            CP102508.1.
            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..5411
                     /organism="Citrobacter youngae"
                     /mol_type="genomic DNA"
                     /strain="CF10"
                     /host="Homo sapiens"
                     /db_xref="taxon:133448"
                     /plasmid="pCF10-H"
                     /geo_loc_name="China"
                     /collection_date="2021-04-04"
     gene            949..1272
                     /locus_tag="NUG39_RS27035"
                     /old_locus_tag="NUG39_27035"
     CDS             949..1272
                     /locus_tag="NUG39_RS27035"
                     /old_locus_tag="NUG39_27035"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000957083.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MobC family plasmid mobilization relaxosome
                     protein"
                     /protein_id="WP_000957084.1"
                     /translation="MLTMWVTEDEHRRLLERCDGRQLAAWMRQICLDEKPARSGKLPSL
                     SPALLRQLAGMGNNLNQIARRVNAGGGTGHDRVQIVAALMAIDAGLERLRHAVLEKGTD
                     DDR"
                     /name="MobC family plasmid mobilization relaxosome protein"
     gene            1481..>1915
                     /locus_tag="NUG39_RS27040"
                     /old_locus_tag="NUG39_27040"
                     /pseudo=""
     CDS             1481..>1915
                     /locus_tag="NUG39_RS27040"
                     /old_locus_tag="NUG39_27040"
                     /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            1950..2441
                     /locus_tag="NUG39_RS27045"
                     /old_locus_tag="NUG39_27045"
     CDS             1950..2441
                     /locus_tag="NUG39_RS27045"
                     /old_locus_tag="NUG39_27045"
                     /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_142991550.1"
                     /translation="MSSLLTLAKDLEQQSKAQQQSTGEMLKAAFSEHEQSVRAELSASA
                     RRISDAILAHEQSMSEAMEKNRRSVLRTAGRTWLTILMVSALLSGTSGSILWWQGQQIT
                     DNYTHLRQQEDTLAKMTARTWGVRYQESSDGRRFLILPPGIQTEAIPYDGTTWIRLKQE
                     "
                     /name="MbeB family mobilization protein"
     gene            2448..2663
                     /locus_tag="NUG39_RS27050"
                     /old_locus_tag="NUG39_27050"
     CDS             2448..2663
                     /locus_tag="NUG39_RS27050"
                     /old_locus_tag="NUG39_27050"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000137422.1"
                     /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_000137422.1"
                     /translation="MTELEKQLLSALEQLQQDYSQRLDEWESAFAEWRSMCGLMQRENA
                     VLNERVSDLSTQVLSLSEQLRRLSGN"
                     /name="MbeD family mobilization/exclusion protein"
     gene            complement(4196..4489)
                     /locus_tag="NUG39_RS27055"
                     /old_locus_tag="NUG39_27055"
     CDS             complement(4196..4489)
                     /locus_tag="NUG39_RS27055"
                     /old_locus_tag="NUG39_27055"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000609270.1"
                     /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="HigA family addiction module antitoxin"
                     /protein_id="WP_000609279.1"
                     /translation="MINLYDPVHPGEFIREMFMEPFEIPAAELADKLEVSQSALSRLLN
                     GKTDLSYEMALRLSKVIGRSAESWVNMQAQYSLSKSRKTLSETLEHLHPMFP"
                     /name="HigA family addiction module antitoxin"
     gene            4827..5108
                     /locus_tag="NUG39_RS27060"
                     /old_locus_tag="NUG39_27060"
     CDS             4827..5108
                     /locus_tag="NUG39_RS27060"
                     /old_locus_tag="NUG39_27060"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000594459.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="type II toxin-antitoxin system RelE/ParE family
                     toxin"
                     /protein_id="WP_000594459.1"
                     /translation="MIKNIKHKGLRSFAENGNTAGIQPHLAKKLRMILTTLSTATCLQD
                     IVDVRALGCHPLKGERKGEFSVEVNGNWRVVFKVEEPNVLDVDLEDYH"
                     /name="type II toxin-antitoxin system RelE/ParE family
                     toxin"
     Typing          663..836
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="98.857"
                     /coverage="100.0"
                     /evalue="5.54e-83"
     Typing          complement(152..739)
                     /name="rep_cluster_2335"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="91.54"
                     /coverage="97.0"
                     /evalue="0.0"
     Typing          1263..2755
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="95.8"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 gtatcttatg ttcgaaacga aaaaaccgcc tggggaggcg gttttttcga gggttcagta
       61 agttggggaa cttctgaacc gtggtaacag ggtgtacaag accgctgaaa ccaaattctg
      121 tccttccagt ttagcctcag tatggctctg acttcaagaa ctctgcatca gtaatctctt
      181 gtacaccctc ttaccaatgg ccgcagccag tggcgttttg ttgtgtcttt ccgggttgga
      241 ctcaagtcga tagttaccgg ataagacgct gcggtcggac tgaacggggg gttcgtgcat
      301 acagtccagc ttggagcgaa ctgccttccc ggaactgagt gtcaggcgtg gaatgagata
      361 aacgcggcca taacagcgga gtgacaccgg taaaccgaaa ggcaggaaca ggagagcgca
      421 cgagggagcc accaggggga aacgcctggt atctttatag tcctgtcggg tttcgccacc
      481 actgatttga gcgtcagatt tcgtgatgct tgtcaggggg gcggagccta tggaaaaacg
      541 gctttgccgt ggccttctcg cttccctgtt aagcttcttc ctagcatcct ccaggaaatt
      601 tccgccccgt tcgtaagcca tttccgctcg ccgcagccga acgaccgagc gcagcgagtc
      661 agtgagcgag gaagcggaat atatcctgta tcacatattc tgctgacgca ccggtgccgc
      721 cttttttctc ctgccacatg aagcacttca ctgacaccct catccgtgcc aacatagtaa
      781 gccagtatac actccgctag cgctacgtga ctggttcagg gctgcgcccc gaaacccgcc
      841 aaaagcctga cgcgcctgcg gtttgtccaa ccccgcgccg accgggaaag gctttcccgc
      901 ccgtcccggc gttatcagga ggccggtttg tcagagaaac ggagcaagat gctcaccatg
      961 tgggtgacgg aggacgagca ccggcggctg ctcgagcgct gtgacggcag gcagctggcg
     1021 gcgtggatga ggcagatctg cctggacgaa aagccggcac gttcaggaaa gctcccctca
     1081 ctctcgccgg cgctgctgcg ccagcttgcc ggcatgggca ataacctgaa ccagatagcc
     1141 cgccgtgtta acgccggcgg cggcaccggc catgacaggg tacagattgt ggcggcgctg
     1201 atggccatcg atgccggcct tgagcggctg cggcacgccg ttcttgagaa aggaacggac
     1261 gatgatcgtt aaatttcatc cgcgcggccg cggcggtggc gccgggccgg tggactatct
     1321 gctgggtaaa gaccggcagc gtgaaggcgc caccgtcctg caggggaagc cggaagaagt
     1381 ccgggagctg attgacgcgt cgccttacgt taagaaatac acctccggcg ttctgtcgtt
     1441 tgcggaggcc gatctgcctc ccggccagcg ggaaaaactg atggccagct tcgagcgggt
     1501 tctgatgccc ggactcgata aagatcagta cagcattctg tgggtggagc acgcggacaa
     1561 ggggcgtctg gagctgaact ttctgatccc caataccgag ctgctgaccg gcaggcggct
     1621 ccagccttac tacgaccgcg ccgaccggcc gcgcatcgat gcctggcaga ctatcgtgaa
     1681 cggcagactg gggctgcacg acccgaacgc gccggaaaac cgccgggcgc tggtcacgcc
     1741 gtccgggctt ccgaaaacga agcaggaggc cgcagaagcc attacccggg gactgctgac
     1801 ccttgcttcg tccggggagc tgaaaagccg tcaggatgtc actgacactc ttgaaggtgc
     1861 aggttttgag gtggtgcgca ccacgaaaag cagtatcagc attgccgatc cggacggggg
     1921 gcgaaacatc cgactgaagg gagccatcta tgagcagtct tttaacgctg gcgaaggact
     1981 tagagcagca atcgaaagcg cagcagcaga gtaccggcga gatgctgaaa gccgcattca
     2041 gcgagcacga gcagtctgtc agagcggaac tgagcgcaag cgcgaggaga atcagcgacg
     2101 ccatcctcgc ccacgagcag agtatgagcg aggcgatgga gaaaaaccgg cggagcgtac
     2161 tgcggactgc cgggcggaca tggctcacca tcctgatggt gtcagcgctg ctgagcggca
     2221 cgagcgggag cattctgtgg tggcaggggc agcagataac cgacaattac acgcatcttc
     2281 gtcagcagga agataccctg gcgaaaatga ccgccaggac gtggggagtg cgctatcagg
     2341 agagcagcga cggccggagg tttcttatcc tgccgccggg gatacaaacc gaagccatcc
     2401 cttacgacgg gacgacatgg atccgcctga aacaggagta gctgaaaatg acagagctgg
     2461 aaaagcagtt gctgagcgca ttagagcagc tacagcagga ctactcgcaa aggctggacg
     2521 aatgggagag cgccttcgcg gaatggcgga gcatgtgtgg gcttatgcaa cgggagaacg
     2581 cggtgctgaa cgagcgcgtg tcggacttga gcacgcaggt gctgagttta agcgagcagc
     2641 tgcgccgctt gtccgggaac tgaatgccat cgagctccgg cagagggaga atgagtatca
     2701 gaaaacactg gagctggagc gccagccgca gaaaacctac cgcgggccga cactttaaac
     2761 catccaggca gctgacaacc cgcacgaaga ggggctctta tttctcccgc taaataggtt
     2821 cgtgatcaaa aaggtcacga cttattcagg agcgggaaat gaagctgtta aatcttattg
     2881 aatcattgct taactgcctg tatctggcgg cggagctgtg ggactggctg gagaagcatt
     2941 tgtcggtttt taaggcattg gcgcggattt tagtgtgact ttaacatcca tgcatctggc
     3001 tgcatgacta tgcaccagtg taatattcag cggctgcgtt tctggtgttt tttcgttatg
     3061 tctgtcgcca ctttctcgcg tctggcaccg gaaacgcagc caaccccgtt tcagcggtgc
     3121 gcccaacgga tgttatggta aataagagcg accgtcccgg tcgctcttga aagagaattc
     3181 ggccttaggt cagttttcgc agatacaatc atgtggactg cggagacatt cttcgcactc
     3241 ctcacatatg cactcatcca gtttttcacc gcactcgtcg caacgtgagc agctacagtg
     3301 ctcatctaaa tttccacaat cgctgcagcg ctcacagacg cagtctgcca gcttctcgtt
     3361 gcagtcatcg cagaagccac aggtacaggc gctggcaggg agggcacaaa catcgcaaat
     3421 cttatccatt ggatccattt tatctcactt ttattttatc agtggctgtg tgcgggcgat
     3481 ttccccagcg cgatagatgt ggatttaagt gccatttttc aatgattaag gcagctaaaa
     3541 aagtggtttt ttagggcttt tcaacgtgac cagcactgac ggggataaat acaggtaagc
     3601 aataatgctc agtcatgaaa aggagaatcc gatggagcaa catacccctg aatacttacg
     3661 acgtacctta gctcataacc gtgccctaat ggacgatatc attagcagtg gcatgtccag
     3721 gtactacaac acggagattg tggatgccgc atgtgaggcg atagaagctg aattgcgacg
     3781 acgaggaatt ttgtaagaga caaagcccgc ttatgcgggc tttgtcgtta ctggcgcttc
     3841 tgttactcag tgttgtctgg ggttcggtag atctgtagcc agtacctgcc aggtgcgctc
     3901 gttggtggtg cgaactcatt atcgcgaatg gtgcagtatc gtccatattt gcgggtaaca
     3961 gtatgagtgt ttgtgttgat gtcacattct tggaatgagc caccatcacg acctattttg
     4021 ccatgtggtc ctacataaat tgccattttg ttctcctttt tagagccttg tatgggcatc
     4081 ttattggtgt tcaaacaaca atcatttcaa gatctaagaa ctgaactaaa aatcaaacta
     4141 aaggtaggta tgcggggggt tttacggcaa aaagcccgca cgagcgggct tttacttatg
     4201 gaaacatcgg atgaaggtgt tctagcgtct cggataaagt cttacgactt ttcgagaggc
     4261 tgtactgagc ctgcatatta acccacgact ctgcagagcg gcctataact ttagatagtc
     4321 gaagagccat ctcataacta agatcagttt ttccattgag caatctactt aatgcagatt
     4381 gtgatacttc aagcttatca gctaactctg cggcaggtat ttcgaacggt tccatgaaca
     4441 tttccctgat gaattcaccg gggtgtacag gatcgtaaag atttatcatg ccttcctcta
     4501 ttggttttgt atttgattac acaaaacatt ttgtttcttt cgcgttgcgc attgcacaat
     4561 acgcaagtgt ctgttattga caaaaaaagc agtaagcttt aggatgctcg gtggagcaga
     4621 aagctaccgc tgatatggtg tctttaccga ctttttcaag gcgccatatt gtacggttag
     4681 cgctcttgga agtcaaacga ggtaatcgac ctcagagaca aagttacgtc aattatttta
     4741 ataatgcaag gggttcaaat ggacgctgtc aaattgtttt ctgtttatag agatagatat
     4801 cgacgaaaat tttatggaga tgattgatga taaaaaacat aaagcataaa gggcttcgga
     4861 gttttgctga aaacggtaac accgccggaa ttcagcctca cttagcgaaa aaacttcgca
     4921 tgatattgac tacgctaagc accgcaacat gtcttcaaga tattgtggat gtaagggcgc
     4981 tggggtgtca ccccctaaaa ggtgaacgta aaggtgagtt ttccgtagag gttaacggaa
     5041 actggagggt ggttttcaag gtggaagaac caaacgtctt agacgttgat cttgaagatt
     5101 accattagta atcaataagt aagttactaa tccatcctag tggcaatatg gatggattag
     5161 ggactttatt caaaaataag tacctctgga ggatttatga gagcctttat gattttgttg
     5221 ttccctttgc tttgtgtagt cattgctggg gttcttgctg ttcgtggcct agatgggtgg
     5281 ggatggttcc tgtttgcagc tgttttgtgt actggtgttg atacggtgca gaaacatgtc
     5341 tctaacaaga ataattctgt aagcgattga ggctttcagg gttcttcctt gactgattaa
     5401 atcgacaaag c
//
