LOCUS       CP103359                2745 bp    DNA     circular BCT 31-AUG-2022
DEFINITION  Bacteroides fragilis strain BFG-612 plasmid unnamed3, complete
            sequence.
ACCESSION   CP103359
VERSION     CP103359.1
DBLINK      BioProject: PRJNA646575
            BioSample: SAMN30323488
KEYWORDS    .
SOURCE      Bacteroides fragilis
  ORGANISM  Bacteroides fragilis
            Bacteria; Bacteroidota; Bacteroidia; Bacteroidales; Bacteroidaceae;
            Bacteroides.
REFERENCE   1  (bases 1 to 2745)
  AUTHORS   Tisza,M.J., Smith,D. and Dekker,J.P.
  TITLE     Genome Sequencing of Bacteroides fragilis Group Isolates with
            Nanopore Technology
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 2745)
  AUTHORS   Tisza,M.J., Smith,D. and Dekker,J.P.
  TITLE     Direct Submission
  JOURNAL   Submitted (18-AUG-2022) LCIM, National Institute of Allergy and
            Infectious Diseases, 9000 Rockville Pike, Bethesda, MD 20892, USA
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: Flye v. 2.7
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 146x
            Sequencing Technology             :: Oxford Nanopore GridION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI
            Annotation Date                   :: 08/22/2022 22:15:50
            Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline
            (PGAP)
            Annotation Method :: Best-placed reference protein set; GeneMarkS-2+
            Annotation Software revision      :: 6.2
            Features Annotated :: Gene; CDS; rRNA; tRNA; ncRNA; repeat_region
            Genes (total)                     :: 4,528
            CDSs (total)                      :: 4,435
            Genes (coding)                    :: 2,373
            CDSs (with protein)               :: 2,373
            Genes (RNA)                       :: 93
            rRNAs                             :: 6, 6, 6 (5S, 16S, 23S)
            complete rRNAs                    :: 6, 6, 6 (5S, 16S, 23S)
            tRNAs                             :: 73
            ncRNAs                            :: 2
            Pseudo Genes (total)              :: 2,062
            CDSs (without protein)            :: 2,062
            Pseudo Genes (ambiguous residues) :: 0 of 2,062
            Pseudo Genes (frameshifted)       :: 1,976 of 2,062
            Pseudo Genes (incomplete)         :: 82 of 2,062
            Pseudo Genes (internal stop)      :: 114 of 2,062
            Pseudo Genes (multiple problems)  :: 105 of 2,062
            CRISPR Arrays                     :: 1
            ##Genome-Annotation-Data-END##
            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/
            NCBI analysis of this genome has determined that >30% of the
            predicted CDS features contain frameshifts, which is well above the
            usually observed value of <10%.
FEATURES             Location/Qualifiers
     source          1..2745
                     /organism="Bacteroides fragilis"
                     /mol_type="genomic DNA"
                     /strain="BFG-612"
                     /host="Homo sapiens"
                     /db_xref="taxon:817"
                     /plasmid="unnamed3"
                     /geo_loc_name="USA: Bethesda"
                     /collection_date="2016-11-01"
     gene            1..573
                     /locus_tag="NXW60_22570"
     CDS             1..573
                     /locus_tag="NXW60_22570"
                     /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="plasmid recombination protein"
                     /protein_id="UVV57589.1"
                     /translation="MDYVRPELSHLNESWVGDSISHRLESAKQRYLDTVGQKMQAKAAP
                     IREGVIVIKQETTMQELQQFATVCKERFGIEAFQIHIHKDEGYMNAKQWTPNLHAHVVF
                     DWTQPNGKSVRLSRDDMAELQTIASETLGMERGVSSDRKHLSAMQYKTECAKEQLQGTI
                     KRYIQCIRQTQGRTKPASSASERTTFH"
                     /name="plasmid recombination protein"
     gene            629..1033
                     /locus_tag="NXW60_22575"
     CDS             629..1033
                     /locus_tag="NXW60_22575"
                     /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="UVV57590.1"
                     /translation="MIGKTVNDREKDALKAKVKALEGENEQLSDRLGKAILEKEQNGTK
                     AFKAENDKEYYRQQMDNARTTSNRLRTENQELKTETKELKKELGKMKDLFNSEQLEALR
                     HHFPNISKAMEEGKDLLKQITRSRGFGMGM"
                     /name="hypothetical protein"
     gene            1464..2054
                     /locus_tag="NXW60_22580"
     CDS             1464..2054
                     /locus_tag="NXW60_22580"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_004295513.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology. GO_process:
                     GO:0006260 - DNA replication [Evidence IEA]; GO_process:
                     GO:0006276 - plasmid maintenance [Evidence IEA]"
                     /codon_start=1
                     /transl_table=11
                     /product="replication/maintenance protein RepL"
                     /protein_id="UVV57588.1"
                     /translation="MENKKAVKLTDFQKNEENPFMKQAIEGIENHVVKKYKSNSGGDKR
                     AVVALADTETGEVFKTSFIRQIEVDEEQFTKLYLSNFAAFFDLSQAAIRVFGYFMTCMK
                     PKNDLIIFNRKKCLEYTKYKTDKAVYKGLAELVKAEIIARGPADNLWFINPLIVFNGDR
                     VTFAKTYVRKKTLAAQKKEEAEKRQLSLGFDEQ"
                     /name="replication/maintenance protein RepL"
     Typing          1432..2044
                     /name="rep_cluster_1868"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="98.701"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          2..480
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="99.375"
                     /coverage="92.0"
                     /evalue="2.71e-175"
ORIGIN
        1 ttggactatg ttcgtcccga acttagtcat ttgaatgaaa gctgggttgg agatagcatc
       61 tcccatcggc tggaaagtgc gaaacaaaga tatctcgata cggttgggca gaagatgcag
      121 gctaaagccg cacccatacg agagggagta atagtaatca aacaagaaac caccatgcag
      181 gaactccagc agtttgccac ggtctgcaaa gaacgtttcg gtatcgaagc atttcaaatc
      241 catatacaca aggacgaagg atacatgaac gcaaagcaat ggacacctaa ccttcatgcc
      301 catgtagttt tcgattggac gcagccgaat gggaaaagtg tgcgtttatc gcgtgatgac
      361 atggcagaac tccaaaccat agcatctgaa acactgggca tggaacgtgg cgtttcttct
      421 gaccgcaaac acttatcggc tatgcagtac aagaccgaat gtgcgaaaga acagcttcag
      481 ggaactatca aacgatatat ccagtgcatt agacaaacac aaggacgtac aaaaccagct
      541 tcttcagctt cagaaagaac tacgttccat tgaaacaaag aagaacgtcc aaaaactcat
      601 ttctaaggct tcagagaagt tttacggctt gattggaaaa acagtcaacg atagggaaaa
      661 ggatgcctta aaagccaaag taaaggcttt agagggggaa aatgaacagc tatccgatag
      721 actgggaaag gctatacttg aaaaagagca aaacggcaca aaggcattca aagccgagaa
      781 tgacaaggag tattatagac aacaaatgga caacgcaagg acaaccagta accgattaag
      841 gacggagaac caagaactaa agaccgaaac caaggaattg aaaaaagaac ttggtaagat
      901 gaaagacttg ttcaattccg aacaactgga ggctttaagg catcatttcc caaacatatc
      961 aaaagctatg gaagagggga aagacctact caagcaaatc accagaagca gaggtttcgg
     1021 tatgggtatg taaccccccc ccccccccaa aggggggagc gaccaaacgg cagcctctct
     1081 caatggagtg ttacgtcgtt cggattcgga agaaattttg cagggttcgg aaaacggttg
     1141 tgtgcttatt ctaaaaaaag tttatggtgt ggcgctcgtc gggacgggtg gtcccgcccc
     1201 ttgccgctgg gcgctccccg accgatgatt tttaagtgac tgattttgtg ctgttttggg
     1261 ggtatattaa gaatagaaga aatagaataa gttatacaca atatagggca ttttccatat
     1321 tggaaattct cattttccaa tctagaaaat actgatttcc taatataata ctaaacagga
     1381 aaataatatt tcccttaata ttgtttttat ggaaaataat agtttacttt gtggagaata
     1441 atatttccca aaaacacatc aaaatggaaa ataaaaaagc agttaagtta accgattttc
     1501 aaaagaacga agaaaatcct tttatgaaac aagctataga aggtattgaa aatcatgttg
     1561 ttaaaaagta taagagtaat agtggtggcg ataagagagc cgtagtagct ttagccgaca
     1621 ctgaaactgg agaagtgttt aagacttcgt ttatccgtca aatagaagta gatgaagaac
     1681 aattcactaa attgtatctt tctaactttg ctgcattctt tgacctatca caagcagcta
     1741 ttcgggtttt tggttacttt atgacctgca tgaaacccaa aaatgattta atcatcttca
     1801 atagaaaaaa atgcctagaa tataccaaat acaaaacaga caaagccgtt tataaaggac
     1861 ttgcagaact tgtaaaagct gaaatcatag cccgaggacc agccgataat ctttggttta
     1921 ttaatcctct gatagtattc aatggtgacc gagtgacatt tgctaaaaca tacgttcgga
     1981 aaaagacttt agctgcccaa aagaaagaag aagcagagaa acgacaatta tcacttggct
     2041 ttgatgaaca gtaacactcc attgagtgaa gctgccgttt ggtcgctccc cctttggggg
     2101 cgggggggga tagataaagt tcctctatgt aaagttataa tgggggatga aaggcaaggt
     2161 tcgctaacct taccccgatt gtttatgctt cccagcattc aatctatccc cgtttatggg
     2221 tttctctttc accctacaaa gataacctca tgggggaaaa atgtccaaga atatggggta
     2281 aaaactatca agtcggtaga aaataagtat ctttgaagta catttttagt agaggtactg
     2341 gtatgcctag acgaagcaga taggcaaaaa taaagccgct ggagatgtcg gatgtccgtc
     2401 aattaactcc agcggcttgt attttggtaa ctctcccgta tcggtcggct accgtttggt
     2461 cagcaacaaa ggtagtactt tattgtcgca aatccaaatg ttttcccctt tatttgtgca
     2521 tttacagaac atttgctaac ttcgcaccta tgcagtatgg tgatagcaca ctagcaccct
     2581 aaagggtgcg tgtgtaaggg gacaagcccc tttaaacccc ctgtcagccg gctgtcaccg
     2641 gctgttatcg attgtcacaa aaatgttaac ttatgggagc aacaagtatt catgtacaag
     2701 cagtgaagcc aggggagtga gattcacaac tttagggaaa aagag
//
