LOCUS       NZ_AP028868             2784 bp    DNA     circular CON 04-APR-2024
DEFINITION  Dysgonomonas capnocytophagoides strain SMU001 plasmid pDCPSUM001,
            complete sequence.
ACCESSION   NZ_AP028868
VERSION     NZ_AP028868.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMD00639221
            Assembly: GCF_036511535.1
KEYWORDS    RefSeq.
SOURCE      Dysgonomonas capnocytophagoides
  ORGANISM  Dysgonomonas capnocytophagoides
            Bacteria; Bacteroidota; Bacteroidia; Bacteroidales;
            Dysgonomonadaceae; Dysgonomonas.
REFERENCE   1
  AUTHORS   Imai,K., Kodana,M., Omachi,R. and Maeda,T.
  TITLE     A fatal case of peritonitis caused by Dysgonomonas
            capnocytophagoides harboring novel metallo-beta lactamase gene
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 2784)
  AUTHORS   Imai,K., Omachi,R., Kodana,M. and Maeda,T.
  TITLE     Direct Submission
  JOURNAL   Submitted (05-SEP-2023) Contact:Kazuo Imai Saitama Medical
            University Hospital, Department of Clinical Laboratory; Moroyama
            Moro Hongo 38, Iruma, Saitama 350-0495, Japan
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method :: Flye v. 2.9.2; Unicycler v. 0.5.0
            Genome Coverage                   :: 134x
            Sequencing Technology :: Illumina Iseq100; Nanopore Flongle
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_036511535.1-RS_2024_04_03
            Annotation Date                   :: 04/03/2024 23:47:07
            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)                     :: 3,868
            CDSs (total)                      :: 3,803
            Genes (coding)                    :: 3,769
            CDSs (with protein)               :: 3,769
            Genes (RNA)                       :: 65
            rRNAs                             :: 4, 4, 4 (5S, 16S, 23S)
            complete rRNAs                    :: 4, 4, 4 (5S, 16S, 23S)
            tRNAs                             :: 50
            ncRNAs                            :: 3
            Pseudo Genes (total)              :: 34
            CDSs (without protein)            :: 34
            Pseudo Genes (ambiguous residues) :: 0 of 34
            Pseudo Genes (frameshifted)       :: 13 of 34
            Pseudo Genes (incomplete)         :: 21 of 34
            Pseudo Genes (internal stop)      :: 6 of 34
            Pseudo Genes (multiple problems)  :: 6 of 34
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            AP028868.1.
            Annotated by DFAST https://dfast.ddbj.nig.ac.jp/
            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..2784
                     /organism="Dysgonomonas capnocytophagoides"
                     /mol_type="genomic DNA"
                     /strain="SMU001"
                     /isolation_source="blood"
                     /host="Homo sapiens"
                     /db_xref="taxon:45254"
                     /plasmid="pDCPSUM001"
                     /geo_loc_name="Japan:Saitama, Iruma-gun Moroyama"
                     /lat_lon="35.95834716 N 139.30226322 E"
                     /collection_date="2023-05-18"
                     /collected_by="Department of clinical laboratory, Saitama
                     medical university hospital"
     gene            join(1685..2784,1..4)
                     /locus_tag="AABJ51_RS19335"
     CDS             join(1685..2784,1..4)
                     /locus_tag="AABJ51_RS19335"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_004295514.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="plasmid recombination protein"
                     /protein_id="WP_007572070.1"
                     /translation="MGATSIHVQAVKPGSEIHNFREKELDYVRPELSHLNESWVGDSIS
                     HRLESAKQRYFDTVGQKMQTKAAPIREGVIVIKQETTMQELQQFAAVCKERFGIEAFQI
                     HIHKDEGYMNAKQWTPNLHAHVVFDWTQPNGKSVRLSRDDMAELQTIASEALGMERGVS
                     SDRKHLSAMQYKTECAKEQLQELSNDISSALDKHKDVQNQLLQLQKELRSIETKKNVQK
                     LISKASEKFYGLIGKTVNDREKDALKAKIKALEGENEQLSDRLGKAILEKERNGTKVFK
                     AENDKEYYRQQMDNARTTSNRLRTENQELKTETKELKKELGKMKDLFNSEQLEALRHHF
                     PNISKAMEEGKDLLKQITRSRGFGMGM"
                     /name="plasmid recombination protein"
     gene            476..1066
                     /locus_tag="AABJ51_RS19340"
                     /old_locus_tag="DCPSUM001_38050"
     CDS             476..1066
                     /locus_tag="AABJ51_RS19340"
                     /old_locus_tag="DCPSUM001_38050"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_008670455.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_008670455.1"
                     /translation="MENKKVLKLTDFQKNEENPFMKQAIEGIENHVVKKYKSSTGSDKK
                     AVVAVADTDTGEVFKTSFIRQIEVDEEQFAKLYLANFAAFFNLSQSAIRVFGYILTCMK
                     PKNDMIIFDRRKCLEYTQYKSDKAIYKGLAELVQSEIIARGPNEYNWFINPLIVFNGDR
                     VSFTKTYVRKKTLAAQKKEEAEKRQLSLGFDEL"
                     /name="hypothetical protein"
     Typing          477..1056
                     /name="rep_cluster_1868"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="80.479"
                     /coverage="95.0"
                     /evalue="2.71e-121"
     Typing          1686..2782
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="95.902"
                     /coverage="99.0"
                     /evalue="0.0"
ORIGIN
        1 gtaacccccc ccgcccccaa agggggagcg accaaacggc agcttcactc aatggagtgt
       61 tacgccgttc gggttcggaa gaaattttgc agggttcgaa aaacggttgt gtgcttattc
      121 gaaaaaaagt ttatggtgtg ggcgctcgtc gggacgggtg gtcccgcccc ttgccgctgg
      181 gcgctccccg accgatgatt ttttaagtag ttgattatat gccgttttta gggtataata
      241 agaacttaag aaatagaata agttaagtag ttgatactca atatagggta ttttccatat
      301 tggaaaatct gattttccat attagaaagt cactctttcc tattagatgt taaaaaggaa
      361 aatatatttt gcttttttat tgtattaatg gaaatttaaa tattcctttg tggaaaatca
      421 aattatactt tttcaccgat atatagaaag tcaaatttgc ctaaatagaa tgtttatgga
      481 aaataagaaa gtactcaaat taaccgattt tcaaaaaaac gaagaaaacc cctttatgaa
      541 acaagcaatt gaagggattg aaaatcacgt tgttaagaaa tacaaaagta gtacgggaag
      601 tgataaaaaa gctgtagttg ctgttgctga tacagataca ggagaagtat tcaaaacctc
      661 gtttatccga caaatagaag tagatgaaga gcaatttgca aaactatacc ttgcgaattt
      721 tgccgctttt ttcaatctat cacaatcagc tattcgggtt ttcgggtata ttctaacttg
      781 catgaagcct aagaatgata tgataatttt cgataggcga aaatgcttag aatacaccca
      841 atacaaatca gacaaagcca tatacaaagg attggcagag ctcgtacaaa gtgaaatcat
      901 agcaagaggt ccaaacgaat ataattggtt cattaatccg ttgattgtct ttaatgggga
      961 tagggtttca tttacaaaaa catacgttcg gaaaaagact ttagctgccc aaaagaaaga
     1021 agaagcagag aaacgacagt tatcacttgg ttttgacgaa ctgtaacact ccattgagtg
     1081 aagctgccgt ttggtcgctc cccctttggg ggcggggggg ggatagataa agttcctcta
     1141 tgtaaagtta taatggggga tgaaaggcaa ggttcgctaa ccttaccccg attgtttatg
     1201 cttcccagca ttcaatctat ccccgtttat gggtttctct ttcaccctac aaagataacc
     1261 tcatggggga aaaatgtcca agaatatggg gtaaaaacta tcaagtcggt agaaaataag
     1321 tatctttgaa gtacattttt agtagaggta ctggtatgcc tagacgaagc agataggcaa
     1381 aaataaagcc gctggggatg tcggatgtcc gtcaattaac tccagcggct tgtattttgg
     1441 taactctccc gtatcggtca gctaccgttt ggtcagcaac aaaggtagta ctttattgtc
     1501 gcaaatccaa atgttttccc ctttatttgt gcatttacaa aacattcact aacttcgcac
     1561 ctatgcagta tggtgatagc acactagcac cctaaagggt acgtgtgtaa ggggacaagc
     1621 ccccttaacc ccctgtcagc cggctgtcac cggctgttat cgattgtcac aaaaatgtta
     1681 acttatggga gcaacaagta ttcatgtaca agcagtgaag ccggggagcg agattcacaa
     1741 ctttagggaa aaagagttgg actatgttcg tccggaactt agtcatttga atgaaagctg
     1801 ggttggagat agcatctccc atcggctgga gagtgcgaaa cagagatatt tcgatacggt
     1861 tgggcagaag atgcagacta aagcagcacc catacgggag ggggtaatag taatcaagca
     1921 agaaaccacc atgcaggaac tccagcaatt cgctgcggtc tgcaaggaac gtttcggtat
     1981 tgaagcgttt caaatccata tacacaagga cgaaggatac atgaacgcaa agcaatggac
     2041 acctaacctt cacgcccatg tagttttcga ttggacgcag ccgaacggga agagtgtgcg
     2101 tttatcgcgt gatgacatgg cagaactcca aaccatagca tctgaagcac tgggcatgga
     2161 acgtggtgtt tcttctgatc gcaaacactt atcggctatg cagtacaaga ccgaatgtgc
     2221 gaaagaacag cttcaggaac tatccaacga tatatccagt gcgttagaca agcacaagga
     2281 cgtgcaaaac cagcttcttc agcttcagaa agaactacgt tccattgaaa caaagaaaaa
     2341 cgtccaaaaa ctcatttcta aggcttcaga gaagttttac ggcttgatag ggaaaacggt
     2401 taacgatagg gaaaaagatg ccttaaaagc caaaataaag gctttagagg gggaaaatga
     2461 acagctatcc gatagactgg gaaaggctat acttgaaaaa gagcgaaacg gcacaaaggt
     2521 attcaaagcc gagaacgaca aggagtatta tagacagcaa atggacaatg caaggacaac
     2581 cagtaaccga ctaagaacgg agaaccaaga actaaagacc gaaaccaagg aattgaaaaa
     2641 agaacttggt aagatgaaag acttgttcaa ttccgaacaa ctggaggctt taaggcatca
     2701 tttcccaaac atatcaaaag ctatggaaga ggggaaagac ctactcaagc aaatcaccag
     2761 aagcagaggt ttcggcatgg gtat
//
