LOCUS       NZ_CP054004             2783 bp    DNA     circular CON 23-OCT-2023
DEFINITION  Bacteroides fragilis strain FDAARGOS_763 plasmid unnamed3, complete
            sequence.
ACCESSION   NZ_CP054004
VERSION     NZ_CP054004.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN11056478
            Assembly: GCF_013267555.1
KEYWORDS    RefSeq.
SOURCE      Bacteroides fragilis
  ORGANISM  Bacteroides fragilis
            Bacteria; Bacteroidota; Bacteroidia; Bacteroidales; Bacteroidaceae;
            Bacteroides.
REFERENCE   1  (bases 1 to 2783)
  AUTHORS   Bojja,K., Kessler,A., Tallon,L., Sadzewicz,L., Zhao,X.,
            Vavikolanu,K., Mehta,A., Aluvathingal,J., Nadendla,S., Myers,T.,
            Yan,Y. and Sichtig,H.
  TITLE     FDA dAtabase for Regulatory Grade micrObial Sequences (FDA-ARGOS):
            Supporting development and validation of Infectious Disease Dx tests
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 2783)
  AUTHORS   Bojja,K., Kessler,A., Tallon,L., Sadzewicz,L., Zhao,X.,
            Vavikolanu,K., Mehta,A., Aluvathingal,J., Nadendla,S., Myers,T.,
            Yan,Y. and Sichtig,H.
  TITLE     Direct Submission
  JOURNAL   Submitted (26-MAY-2020) Center for Devices and Radiological Health,
            US Food and Drug Administration, 10903 New Hampshire Avenue, Silver
            Spring, MD 20993-0002, USA
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method :: SMRT v. 2.3.0, HGAP v. 3, SPAdes v. 3.11.1
            Genome Coverage                   :: 695.66x
            Sequencing Technology             :: Pacbio; Illumina
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 10/23/2023 03:09:34
            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)                     :: 4,800
            CDSs (total)                      :: 4,706
            Genes (coding)                    :: 4,638
            CDSs (with protein)               :: 4,638
            Genes (RNA)                       :: 94
            rRNAs                             :: 6, 6, 6 (5S, 16S, 23S)
            complete rRNAs                    :: 6, 6, 6 (5S, 16S, 23S)
            tRNAs                             :: 74
            ncRNAs                            :: 2
            Pseudo Genes (total)              :: 68
            CDSs (without protein)            :: 68
            Pseudo Genes (ambiguous residues) :: 0 of 68
            Pseudo Genes (frameshifted)       :: 26 of 68
            Pseudo Genes (incomplete)         :: 47 of 68
            Pseudo Genes (internal stop)      :: 10 of 68
            Pseudo Genes (multiple problems)  :: 13 of 68
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP054004.1.
            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..2783
                     /organism="Bacteroides fragilis"
                     /mol_type="genomic DNA"
                     /strain="FDAARGOS_763"
                     /isolation_source="transverse colon"
                     /host="Homo sapiens"
                     /culture_collection="FDA:FDAARGOS_763"
                     /db_xref="taxon:817"
                     /plasmid="unnamed3"
                     /geo_loc_name="USA: VA"
                     /collected_by="BEI Resources/American Type and Culture
                     Collection (ATCC)"
     gene            join(1938..2783,1..258)
                     /locus_tag="FOC69_RS23835"
                     /old_locus_tag="FOC69_23835"
     CDS             join(1938..2783,1..258)
                     /locus_tag="FOC69_RS23835"
                     /old_locus_tag="FOC69_23835"
                     /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_005783389.1"
                     /translation="MGATSIHVQAVKPGSEIHNFREKELDYVRPELSHLNESWVGDSIS
                     HRLESAKQRYFDTVGQKMQTKAAPIREGVIVIKQETTMQELQQFAAVCKERFGIEAFQI
                     HIHKDEGYMNAKQWTPNLHAHVVFDWTQPNGKSVRLSRDDMAELQTIASEALGMERGVS
                     SDRKHLSAMQYKTECAKEQLQELSNDISSALDKHKDVQNQLLQLQKELRSIETKKNVQK
                     LISKASEKFYGLIGKTVNDREKDTLKAKIKALEGENEQLSDRLGKAILEKERNGTKVFK
                     AENDKEYYRQQMDNARTTSNRLRTENQELKTETKELKKELGKMKDLFNSEQLEALRHHF
                     PNISKAMEEGKDLLKQITRSRGFGMGM"
                     /name="plasmid recombination protein"
     gene            730..1320
                     /locus_tag="FOC69_RS23840"
                     /old_locus_tag="FOC69_23840"
     CDS             730..1320
                     /locus_tag="FOC69_RS23840"
                     /old_locus_tag="FOC69_23840"
                     /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          731..1310
                     /name="rep_cluster_1868"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="80.479"
                     /coverage="95.0"
                     /evalue="2.71e-121"
     Typing          1939..2783
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="95.745"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 gagaacgaca aggagtatta tagacagcaa atggacaatg caaggacaac cagtaaccga
       61 ctaagaacgg agaaccaaga actaaagacc gaaaccaagg aattgaaaaa agaacttggt
      121 aagatgaaag acttgttcaa ttccgaacaa ctggaggctt taaggcatca tttcccaaac
      181 atatcaaaag ctatggaaga ggggaaagac ctactcaagc aaatcaccag aagcagaggt
      241 ttcggtatgg gtatgtaacc ccccccgccc ccaaaggggg agcgaccaaa cggcagcttc
      301 actcaatgga gtgttacgcc gttcgggttc ggaagaaatt ttgcagggtt cgaaaaacgg
      361 ttgtgtgctt attcgaaaaa aagtttatgg tgtgggcgct cgtcgggacg ggtggtcccg
      421 ccccttgccg ctgggcgctc cccgaccgat gattttttaa gtagttgatt atatgccgtt
      481 tttagggtat aataagaact taagaaatag aataagttaa gtagttgata ctcaatatag
      541 ggtattttcc atattggaaa atcagatttt ccatattaga aagtcactct ttcctattag
      601 atgttaaaaa ggaaaatata ttttgctttt ttattgtatt aatggaaatt taaatattcc
      661 tttgtggaaa atcaaattat actttttcac cgatatatag aaagtcaaat ttgcctaaat
      721 agaatgttta tggaaaataa gaaagtactc aaattaaccg attttcaaaa aaacgaagaa
      781 aaccccttta tgaaacaagc aattgaaggg attgaaaatc acgttgttaa gaaatacaaa
      841 agtagtacgg gaagtgataa aaaagctgta gttgctgttg ctgatacaga tacaggagaa
      901 gtattcaaaa cctcgtttat ccgacaaata gaagtagatg aagagcaatt tgcaaaacta
      961 taccttgcga attttgccgc ttttttcaat ctatcacaat cagctattcg ggttttcggg
     1021 tatattctaa cttgcatgaa gcctaagaat gatatgataa ttttcgatag gcgaaaatgc
     1081 ttagaataca cccaatacaa atcagacaaa gccatataca aaggattggc agagctcgta
     1141 caaagtgaaa tcatagcaag aggtccaaac gaatataatt ggttcattaa tccgttgatt
     1201 gtctttaatg gggatagggt ttcatttaca aaaacatacg ttcggaaaaa gactttagct
     1261 gcccaaaaga aagaagaagc agagaaacga cagttatcac ttggttttga tgaactgtaa
     1321 cactccattg agtgaagctg ccgtttggtc gctccccctt tgggggcggg gggggataga
     1381 taaagttcct ctatgtaaag ttataatggg ggatgaaagg caaggttcgc taaccttacc
     1441 ccgattgttt atgcttccca gcattcaatc tatccccgtt tatgggtttc tctttcaccc
     1501 tacaaagata acctcatggg ggaaaaatgt ccaagaatat ggggtaaaaa ctatcaagtc
     1561 ggtagaaaat aagtatcttt gaagtacatt tttagtagag gtactggtat gcctagacga
     1621 agcagatagg caaaaataaa gccgctgggg atgtcggatg tccgtcaatt aactccagcg
     1681 gcttgtattt tggtaactct cccgtatcgg tcagctaccg tttggtcagc aacaaaggta
     1741 gtactttatt gtcgcaaatc caaatgtttt cccctttatt tgtgcattta caaaacattc
     1801 actaacttcg cacctatgca gtatggtgat agcacactag caccctaaag ggtacgtgtg
     1861 taaggggaca agccccctta accccctgtc agccggctgt caccggctgt tatcgattgt
     1921 cacaaaaatg ttaacttatg ggagcaacaa gtattcatgt acaagcagtg aagccgggga
     1981 gcgagattca caactttagg gaaaaagagt tggactatgt tcgtccggaa cttagtcatt
     2041 tgaatgaaag ctgggttgga gatagcatct cccatcggct ggagagtgcg aaacagagat
     2101 atttcgatac ggttgggcag aagatgcaga ctaaagcagc acccatacgg gagggggtaa
     2161 tagtaatcaa gcaagaaacc accatgcagg aactccagca attcgctgcg gtctgcaagg
     2221 aacgtttcgg tattgaagcg tttcaaatcc atatacacaa ggacgaagga tacatgaacg
     2281 caaagcaatg gacacctaac cttcacgccc atgtagtttt cgattggacg cagccgaacg
     2341 ggaagagtgt gcgtttatcg cgtgatgaca tggcagaact ccaaaccata gcatctgaag
     2401 cactgggcat ggaacgtggt gtttcttctg atcgcaaaca cttatcggct atgcagtaca
     2461 agaccgaatg tgcgaaagaa cagcttcagg aactatccaa cgatatatcc agtgcgttag
     2521 acaagcacaa ggacgtgcaa aaccagcttc ttcagcttca gaaagaacta cgttccattg
     2581 aaacaaagaa aaacgtccaa aaactcattt ctaaggcttc agagaagttt tacggcttga
     2641 tagggaaaac ggttaacgat agggaaaaag ataccttaaa agccaaaata aaggctttag
     2701 agggggaaaa tgaacagcta tccgatagac tgggaaaggc tatacttgaa aaagagcgaa
     2761 acggcacaaa ggtattcaaa gcc
//
