LOCUS       CP103358                5563 bp    DNA     circular BCT 31-AUG-2022
DEFINITION  Bacteroides fragilis strain BFG-612 plasmid unnamed2, complete
            sequence.
ACCESSION   CP103358
VERSION     CP103358.1
DBLINK      BioProject: PRJNA646575
            BioSample: SAMN30323488
KEYWORDS    .
SOURCE      Bacteroides fragilis
  ORGANISM  Bacteroides fragilis
            Bacteria; Bacteroidota; Bacteroidia; Bacteroidales; Bacteroidaceae;
            Bacteroides.
REFERENCE   1  (bases 1 to 5563)
  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  JOURNAL   Unpublished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 5563)
  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..5563
                     /organism="Bacteroides fragilis"
                     /mol_type="genomic DNA"
                     /strain="BFG-612"
                     /host="Homo sapiens"
                     /db_xref="taxon:817"
                     /plasmid="unnamed2"
                     /geo_loc_name="USA: Bethesda"
                     /collection_date="2016-11-01"
     gene            1..462
                     /locus_tag="NXW60_22535"
     CDS             1..462
                     /locus_tag="NXW60_22535"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_005812785.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="UVV57583.1"
                     /translation="MNRIIHISLLISTVSLFLISNTGCVEKQGYYNHGEESIISLICDI
                     TWAGKKTTDENGSVWQGTYKFNKNGTYTRTNIEIDKQGNKKEANIYGQWSFGDPSFSTI
                     YFGGEHYWDIDELTKNKFSFYDRSGKFGDPFMNREYIELTPYQENNTTN"
                     /name="hypothetical protein"
     gene            complement(466..1368)
                     /locus_tag="NXW60_22540"
     CDS             complement(466..1368)
                     /locus_tag="NXW60_22540"
                     /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="protein rep"
                     /protein_id="UVV57584.1"
                     /translation="MKAYMDAHVCSNVYTVQGGKAHSHYCHRAFCPICQRIQTAQNVKK
                     FLPVMKYLASEGREFYFVTLTLQNCVTDDARVLRDFMRRCNRMWADGIRTKHKFRSLGI
                     SGVIKKECTYHVVKKDLFSFHYHFHIIVDSLEAAKYVVAQWKKLHGSTVADARFQKYKK
                     IEDFENAAIEVFKYASKASVSKSKGRDGKKKIQINYKALDMIYTAMHGMQRMSSFGQFR
                     TMIGDEALNDFRDEDLVLNIEGLNVEDGCYTWYMSVKDKVADWYNMETGEALCCYKVTR
                     KDELLQDIYLDEDIFPNSG"
                     /name="protein rep"
     gene            complement(2011..2409)
                     /locus_tag="NXW60_22545"
     CDS             complement(2011..2409)
                     /locus_tag="NXW60_22545"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_005799260.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="exo-poly-alpha-D-galacturonosidase"
                     /protein_id="UVV57585.1"
                     /translation="MKPTDYIEWDNLKDIPFFLCQVVEDREKQDLDIYYLGKRVLHDYD
                     HVGHYLRTAVILFRRVKSRTADWVNLRNLWTLRNCVRENYNHGIGMNDLIFGENFDGDN
                     LDTLTPLTKKRFDFLCKRIKELDPYATI"
                     /name="exo-poly-alpha-D-galacturonosidase"
     gene            complement(2446..2766)
                     /locus_tag="NXW60_22550"
     CDS             complement(2446..2766)
                     /locus_tag="NXW60_22550"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_005799262.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="type II toxin-antitoxin system PemK/MazF family
                     toxin"
                     /protein_id="UVV57586.1"
                     /translation="MVEQYEVYWVELDPTRGGEMAKTRPCVVVTPSDLNMYLTTVVIVP
                     ITSTIRNYPYRVLCSVAGREGEIATDQIRTVDKSRLKRKIGDLNFSEIKRLREVFQQMF
                     CE"
                     /name="type II toxin-antitoxin system PemK/MazF family
                     toxin"
     gene            complement(2760..2948)
                     /locus_tag="NXW60_22555"
     CDS             complement(2760..2948)
                     /locus_tag="NXW60_22555"
                     /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="AbrB/MazE/SpoVT family DNA-binding
                     domain-containing protein"
                     /protein_id="UVV57587.1"
                     /translation="MKQLRLSLKSAVSISLDGNNIVIKAQPRRGWAEAAKRAHENGDDE
                     LLIPDVFEDEKFEDWTW"
                     /name="AbrB/MazE/SpoVT family DNA-binding domain-containing
                     protein"
     gene            3380..4630
                     /locus_tag="NXW60_22560"
     CDS             3380..4630
                     /locus_tag="NXW60_22560"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_005799237.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="UVV57581.1"
                     /translation="MAKTCIRVEACNIGSSERHNLRSKELDYIRPELTHRNEQWVECSI
                     AEVHRDITEKYKEATGQGLQKKATPIREGVIVISEETTIQQLQDLAEKLEERFGVHAFQ
                     IYTHKDEGANVWDGKEEAWKPNYHAHMIFDWTDGHTGKTVKLNRHDMAEMQTITAECLN
                     MERGVSSDKKHLSAMQYKNKMETEKAEQLQKDIEQLNRAYTAGTEKITTVQKELSTAQK
                     ELNSMKTDIHINEAKEAAAKAGKTVFNAVTSVFNVGEVKRQAKEIETLKKENYNLSFKN
                     QNLEGQLRTNNIEMRRVQETTDRQIKAEASKLKPITNLFPEMENAQENIEELQTMGIQN
                     KDIRQLLIGKEIYYTGNLYDKDKRKSYQVKNVKIDISKSQNGITTIWLNNIHFKNFLKE
                     LWNTLQKTLDNGNWLHR"
                     /name="hypothetical protein"
     gene            complement(4864..5472)
                     /locus_tag="NXW60_22565"
     CDS             complement(4864..5472)
                     /locus_tag="NXW60_22565"
                     /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="UVV57582.1"
                     /translation="MKKVMFMFISLLTVLGVCSCNDNEVIEPVVSDSVSDMEVLSRFVD
                     VNEITNEYYFNENKKTRALSYVTGSDWQDLEKVSPLSIEKYKNNLQVLNAQVASAISNP
                     NTAYVVFSVNGKTLVKKVKEDANFDFSVFRDVVTETRAVLPSLSINGGSQSTTGVFYDS
                     SRTLKMQVDLNASIQNNYYFFEVLNPNAKPSPDDNITTP"
                     /name="hypothetical protein"
     Typing          complement(467..1514)
                     /name="rep_cluster_870"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="99.714"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          3381..4627
                     /name="MOBV"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 atgaatagaa taatacatat ctctttactt atttcaacag tatcactttt tcttatttca
       61 aacaccggat gtgttgaaaa acaaggatac tacaaccatg gagaagaaag cataatctca
      121 ttaatttgtg atattacatg ggctggtaaa aaaacaacag acgaaaacgg cagtgtctgg
      181 caaggtacat acaaattcaa taaaaacgga acatataccc gtacaaatat agaaatcgac
      241 aaacaaggaa ataaaaaaga agccaatatc tacggacaat ggtcattcgg tgatccaagt
      301 ttcagtacca tttattttgg tggagaacat tactgggaca tagacgagct aactaaaaac
      361 aaattttcct tctatgacag aagtggaaaa tttggcgatc ctttcatgaa tagagaatac
      421 atagaactca caccatacca agaaaacaat acaacaaact aacaactacc cactattagg
      481 aaaaatatcc tcatctaaat aaatatcctg caaaagttca tccttccggg tgaccttata
      541 acaacacaat gcctccccag tttccatatt ataccaatca gccaccttat ctttcacaga
      601 catataccaa gtataacaac catcttcaac attcaatccc tcaatattaa gaaccaaatc
      661 ctcatctcta aaatcattca acgcttcatc tccgatcatg gtgcggaact gtccgaaact
      721 actcatgcgc tgcatcccat gcatggcagt ataaatcata tccaaagcct tataatttat
      781 ctgaatcttt tttttaccgt cacgaccttt cgattttgag acagaagcct ttgaagcata
      841 cttaaaaacc tctatcgctg cattttcaaa atcctctatc ttcttatatt tctgaaaacg
      901 ggcatcagca accgtactac catgcaattt cttccattgg gctactacat attttgcagc
      961 ttccaatgaa tcaacaataa tatgaaaatg ataatggaac gaaaacaaat ccttttttac
     1021 tacatgatag gtacactcct tcttaatcac ccccgaaata ccaagtgaac gaaacttgtg
     1081 tttcgtcctt ataccatcag cccacatccg gttacatcta cgcatgaaat ctcgcaatac
     1141 ccttgcatca tcggttacac aattttgcaa ggtaagcgtc acaaaataaa actctctgcc
     1201 ttccgaagcc aaatacttca taaccggaag gaacttcttt acattttgtg ccgtttgaat
     1261 acgctgacag ataggacaaa aagcccgatg acaataatgg gaatgcgcct tacctccctg
     1321 cacagtataa acatttgaac acacatgggc atccatatat gctttcatca gcttactatc
     1381 cggattcttt tccgaaagtt ttcgagtaaa attatgggat atgattttta ctttagcctt
     1441 tttttaagac tatcagaacc gttttttaac ggactttctt tgcagttggt tatatttgtt
     1501 ctatctttgc acatatgaaa ttttgatgtg gctttcgttt ggtatccgcc ccgccaagaa
     1561 cgaacacaaa cgattgctaa ttcttaaaat acaaagcccg ttggttactg ccttcgggct
     1621 ttcgtttttt ctcagcccaa aagtaggtaa ttcattccaa accgccaaac atcattcaaa
     1681 aaacctacat ataacaagtc aaaaagcatt taccacgaaa ctttctagtt tatctagtat
     1741 gggggctcgc ccccattccc ccggctgcgc aattctgaca caaatacact actaaatcca
     1801 caacagacaa agatacttcc ggaaaaaaaa actatctttg ccgtacacaa agacaaccct
     1861 tgccgagcga tacgggagag ttgcaaaaaa aacaccggag tgaattgacg gatatccgac
     1921 atctccggtg gtattttttc ctttatcccc cctcccgtcc cccaaagggg gagcacacaa
     1981 agacaagccc tgccttcact caatggagtg ttaaatagtt gcatatgggt caagttcctt
     2041 aatccgctta cacaaaaaat caaagcgttt ctttgtaagt ggtgtaagcg tatcgagatt
     2101 atctccatcg aaattctccc caaaaataag gtcgttcatt cctatgccgt gattgtagtt
     2161 ctcacgcaca cagttgcgca gcgtccaaag gttacgcagg tttacccagt ctgctgtgcg
     2221 gctctttacc ctgcggaaca agataacggc agtccgcaaa tagtgcccca catggtcgta
     2281 atcgtgcaag acacgtttgc ccaaatagta aatatccaaa tcttgttttt ctctgtcctc
     2341 gactacttga cagaggaaga atggaatatc cttcaggtta tcccattcga tgtagtcagt
     2401 tggtttcata atgtcttatt tgcatttttc tttccgtact ttccattatt cacagaacat
     2461 ttgctgaaat acttcacgta acctttttat ctcactgaaa ttcaaatctc caatctttct
     2521 tttcagccgg cttttatcca ccgtgcgaat ttgatcagtg gctatctctc cttcacgccc
     2581 ggctacagaa cacagaaccc ggtaaggata atttcttatc gttgaggtta tcggaacaat
     2641 gactactgtt gtaaggtaca tattcaaatc tgaaggagtg acaactacac atggccgtgt
     2701 ctttgccatt tcacccccac gggtagggtc taactctacc caatacactt catactgttc
     2761 taccatgtcc aatcctcaaa cttttcatcc tcaaacacat cggggataag caactcatca
     2821 tccccattct catgggcacg tttggcagct tccgcccatc cccgacgtgg ttgtgccttt
     2881 atcacaatat tgttcccgtc caaagaaatg ctcacagccg atttcaagga caaacgcaac
     2941 tgtttcaacc aatctgaata atattcgtta ccataatgtt ataactttat aattgattat
     3001 cacgatacaa atatatgtaa agttataaca ataacaaaag gaaaaacaac ttttttccat
     3061 tttcaccgag aaccctgtca atggctgcac tcgtcgggag tgttggtgca cccccttgcc
     3121 gtgcagcgct ccccgaccga tgatttttta ttgtgccttg tgtccttttc ccttttgtcc
     3181 ggcttctgtt cccaagcaca tccggaacac atggcagagc gcttgcaaat cccgtccgga
     3241 aggcttacct ttgcaaaagg ttatagcaca ctataacccc taaaggggtt gtgtgcgagg
     3301 ggtgtcccct cgaccccgtg cgatgtgacg tttcacgcca catcttctaa acagacatac
     3361 acacctaaaa cctaaagata tggcaaagac atgtatcaga gtggaagcct gcaatatagg
     3421 cagctcggaa cgtcacaact taagaagcaa ggagctcgac tacatccgtc cggaactcac
     3481 acaccgcaac gaacagtggg tagaatgttc cattgccgaa gtacatcggg acataacgga
     3541 aaaatacaag gaagccaccg gacaaggatt acagaagaaa gctaccccaa tccgggaagg
     3601 ggtaatagta atcagcgagg aaaccacaat ccagcagctt caagacttgg ccgaaaaact
     3661 ggaagaacgc tttggagtgc acgccttcca aatctacacc cataaggatg aaggcgcaaa
     3721 cgtatgggac ggaaaggaag aagcatggaa accgaactat catgcgcaca tgatctttga
     3781 ctggacggac ggccatacag gaaaaactgt aaagctgaac agacacgaca tggcggagat
     3841 gcagactata acagcagagt gtctcaacat ggaacgtgga gtttcttcag acaagaaaca
     3901 cttgtcggcc atgcaataca aaaacaaaat ggaaacagag aaagctgaac aacttcaaaa
     3961 agacatcgag caactaaaca gggcatacac tgccggaacc gagaaaatca ccacagtcca
     4021 aaaggaactt agtacggcac aaaaagagct aaacagcatg aaaaccgaca tacacatcaa
     4081 cgaagccaaa gaagctgccg caaaagccgg aaaaaccgta tttaatgccg ttacaagcgt
     4141 ctttaatgta ggggaagtaa aacgacaagc caaagaaatt gaaaccctca aaaaagaaaa
     4201 ttataacctc tcattcaaga atcaaaattt agaaggacaa ttaagaacca acaacatcga
     4261 gatgcgaagg gtacaggaaa caaccgacag acagataaag gcagaagcat ccaaactaaa
     4321 acccataacc aacctttttc cggaaatgga aaatgcacag gaaaatatag aggaactcca
     4381 aactatggga atacaaaata aagatatccg acaacttctt attggaaagg aaatatacta
     4441 cactggaaac ctttacgata aagacaagag aaaatcatac caagttaaaa acgtgaaaat
     4501 agatatctcc aaaagtcaga atggtattac tacaatttgg ctaaataaca tccactttaa
     4561 aaactttctt aaagaacttt ggaatacact acaaaagact ttagataacg gtaactggct
     4621 acaccgatag aaagacacta atttgaattg cacttctctt ttttgagaag tgcaattcaa
     4681 attaaatccc gttcattttt taacgactaa aggtgcaatt agctataaaa ccaaaagaag
     4741 gagtagtacc ttttccttta aactcccatt taaaaccttg accaaggtac atttgcatcc
     4801 caatacgaag tccaagtgaa agtgttactc cataacggtc cagttccact aaaagcaaca
     4861 ctttcagggt gtcgttatat tatcatccgg acttggttta gcattaggat ttaatacttc
     4921 aaagaaataa taattattct gtattgaagc attcaaatca acttgcatct ttaaagtacg
     4981 actggaatcg taaaaaactc cggtagtgct ttgagaacct ccattaatac tcaaagaagg
     5041 gagaacagcc ctcgtttccg ttacaacatc cctaaatact gaaaaatcaa aattagcatc
     5101 ctccttcacc tttttaacca aagtctttcc atttacagaa aaaacaacat aagcggtatt
     5161 aggatttgaa atagcacttg ccacttgagc atttaaaacc tgcaggttat tcttatattt
     5221 ctcaatactc aaaggactaa ctttttctaa atcctgccaa tccgaacctg ttacataaga
     5281 caacgccctc gttttcttat tctcattgaa atagtattca tttgtaatct catttacatc
     5341 aacaaaacga gataagacct ccatatcaga tacagaatca ctaaccacag gttctattac
     5401 ttcattatca ttacacgaac aaacacccaa aacagtcagt agactgatga acataaacat
     5461 tacttttttc ataaatcctc cttttttaaa gttaataaat aaaggtttcg cccaaaaata
     5521 taaaatttct cctatttttg cattgaatat taaatattta act
//
