LOCUS       NZ_CP143945             2750 bp    DNA     circular CON 08-FEB-2024
DEFINITION  Bacteroides thetaiotaomicron strain DFI.6.40 plasmid unnamed4,
            complete sequence.
ACCESSION   NZ_CP143945
VERSION     NZ_CP143945.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN22167535
            Assembly: GCF_036419675.1
KEYWORDS    RefSeq.
SOURCE      Bacteroides thetaiotaomicron
  ORGANISM  Bacteroides thetaiotaomicron
            Bacteria; Bacteroidota; Bacteroidia; Bacteroidales; Bacteroidaceae;
            Bacteroides.
REFERENCE   1  (bases 1 to 2750)
  AUTHORS   Lin,H., Sundararajan,A. and Pamer,E.G.
  TITLE     17 beneficial commensal bacteria to re-establish healthy gut
            microbiome
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 2750)
  AUTHORS   Lin,H., Sundararajan,A. and Pamer,E.G.
  TITLE     Direct Submission
  JOURNAL   Submitted (22-JAN-2024) Duchossois Family Institute, University of
            Chicago, 900 E 57th St., Chicago, IL 60637, USA
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Date                     :: 14-JUL-2023
            Assembly Method                   :: Unicycler v. v0.5.0
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 100x
            Sequencing Technology :: Oxford Nanopore MinION + Illumina NextSeq
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 02/07/2024 12:25:36
            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)                     :: 5,522
            CDSs (total)                      :: 5,425
            Genes (coding)                    :: 5,354
            CDSs (with protein)               :: 5,354
            Genes (RNA)                       :: 97
            rRNAs                             :: 6, 5, 5 (5S, 16S, 23S)
            complete rRNAs                    :: 6, 5, 5 (5S, 16S, 23S)
            tRNAs                             :: 79
            ncRNAs                            :: 2
            Pseudo Genes (total)              :: 71
            CDSs (without protein)            :: 71
            Pseudo Genes (ambiguous residues) :: 0 of 71
            Pseudo Genes (frameshifted)       :: 24 of 71
            Pseudo Genes (incomplete)         :: 43 of 71
            Pseudo Genes (internal stop)      :: 16 of 71
            Pseudo Genes (multiple problems)  :: 11 of 71
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP143945.1.
            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..2750
                     /organism="Bacteroides thetaiotaomicron"
                     /mol_type="genomic DNA"
                     /strain="DFI.6.40"
                     /isolation_source="fecal sample"
                     /host="Homo sapiens"
                     /db_xref="taxon:818"
                     /plasmid="unnamed4"
                     /geo_loc_name="USA:Chicago"
     gene            64..654
                     /locus_tag="V3C11_RS27605"
                     /old_locus_tag="V3C11_27605"
     CDS             64..654
                     /locus_tag="V3C11_RS27605"
                     /old_locus_tag="V3C11_27605"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_004295513.1"
                     /GO_process="GO:0006260 - DNA replication [Evidence IEA];
                     GO:0006276 - plasmid maintenance [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="replication/maintenance protein RepL"
                     /protein_id="WP_004295513.1"
                     /translation="MENKKAVKLTDFQKNEENPFMKQAIEGIENHVVKKYKSNSGGDKR
                     AVVALADTETGEVFKTSFIRQIEVDEEQFTKLYLSNFAAFFDLSQAAIRVFGYFMTCMK
                     PKNDLIIFNRKKCLEYTKYKTDKAVYKGLAELVKAEIIARGPADNLWFINPLIVFNGDR
                     VTFAKTYVRKKTLAAQKKEEAEKRQLSLGFDEQ"
                     /name="replication/maintenance protein RepL"
     gene            1273..2376
                     /locus_tag="V3C11_RS27610"
                     /old_locus_tag="V3C11_27610"
     CDS             1273..2376
                     /locus_tag="V3C11_RS27610"
                     /old_locus_tag="V3C11_27610"
                     /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_007219893.1"
                     /translation="MGATSIHVQAVKPGSEIHNFREKELDYVRPELSHLNESWVGDSIS
                     HRLESAKQRYLDTVGQKMQAKAAPIREGVIVIKQETTMQELQQFATVCKERFGIEAFQI
                     HIHKDEGYMNAKQWTPNLHAHVVFDWTQPNGKSVRLSRDDMAELQTIASETLGMERGVS
                     SDRKHLSAMQYKTECAKEQLQELSNDISSALDKHKDVQNQLLQLQKELRSIETKKNVQK
                     LISKASEKFYGLIGKTVNDREKDALKAKVKALEGENEQLSDRLGKAILEKEQNGTKAFK
                     AENDKEYYRQQMDNARTTSNRLRTENQELKTETKELKKELGKMKDLFNSEQLEALRHHF
                     PNISKAMEEGKDLLKQITRSRGFGMGM"
                     /name="plasmid recombination protein"
     Typing          32..644
                     /name="rep_cluster_1868"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="98.701"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          1274..2373
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="97.275"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 ttgtttttat ggaaaataat agtttacttt gtggagaata atatttccca aaaacacatc
       61 aaaatggaaa ataaaaaagc agttaagtta accgattttc aaaagaacga agaaaatcct
      121 tttatgaaac aagctataga aggtattgaa aatcatgttg ttaaaaagta taagagtaat
      181 agtggtggcg ataagagagc cgtagtagct ttagccgaca ctgaaactgg agaagtgttt
      241 aagacttcgt ttatccgtca aatagaagta gatgaagaac aattcactaa attgtatctt
      301 tctaactttg ctgcattctt tgacctatca caagcagcta ttcgggtttt tggttacttt
      361 atgacctgca tgaaacccaa aaatgattta atcatcttca atagaaaaaa atgcctagaa
      421 tataccaaat acaaaacaga caaagccgtt tataaaggac ttgcagaact tgtaaaagct
      481 gaaatcatag cccgaggacc agccgataat ctttggttta ttaatcctct gatagtattc
      541 aatggtgacc gagtgacatt tgctaaaaca tacgttcgga aaaagacttt agctgcccaa
      601 aagaaagaag aagcagagaa acgacaatta tcacttggct ttgatgaaca gtaacactcc
      661 attgagtgaa gctgccgttt ggtcgctccc cctttggggg cggggggggg atagataaag
      721 ttcctctatg taaagttata atgggggatg aaaggcaagg ttcgctaacc ttaccccgat
      781 tgtttatgct tcccagcatt caatctatcc ccgtttatgg gtttctcttt caccctacaa
      841 agataacctc atgggggaaa aatgtccaag aatatggggt aaaaactatc aagtcggtag
      901 aaaataagta tctttgaagt acatttttag tagaggtact ggtatgccta gacgaagcag
      961 ataggcaaaa ataaagccgc tggagatgtc ggatgtccgt caattaactc cagcggcttg
     1021 tattttggta actctcccgt atcggtcggc taccgtttgg tcagcaacaa aggtagtact
     1081 ttattgtcgc aaatccaaat gttttcccct ttatttgtgc atttacagaa catttgctaa
     1141 cttcgcacct atgcagtatg gtgatagcac actagcaccc taaagagtgc gtgtgtaagg
     1201 ggacaagccc ccttaacccc ctgtcagccg gctgtcaccg gctgttatcg attgtcacaa
     1261 aaatgttaac ttatgggagc aacaagtatt catgtacaag cagtgaagcc ggggagtgag
     1321 attcacaact ttagggaaaa agagttggac tatgttcgtc ccgaacttag tcatttgaat
     1381 gaaagctggg ttggagatag catctcccat cggctggaaa gtgcgaaaca aagatatctc
     1441 gatacggttg ggcagaagat gcaggctaaa gccgcaccca tacgagaggg agtaatagta
     1501 atcaaacaag aaaccaccat gcaggaactc cagcagtttg ccacggtctg caaagaacgt
     1561 ttcggtatcg aagcatttca aatccatata cacaaggacg aaggatacat gaacgcaaag
     1621 caatggacac ctaaccttca tgcccatgta gttttcgatt ggacgcagcc gaatgggaaa
     1681 agtgtgcgtt tatcgcgtga tgacatggca gaactccaaa ccatagcatc tgaaacactg
     1741 ggcatggaac gtggcgtttc ttctgaccgc aaacacttat cggctatgca gtacaagacc
     1801 gaatgtgcga aagaacagct tcaggaacta tcaaacgata tatccagtgc attagacaaa
     1861 cacaaggacg tacaaaacca gcttcttcag cttcagaaag aactacgttc cattgaaaca
     1921 aagaagaacg tccaaaaact catttctaag gcttcagaga agttttacgg cttgattgga
     1981 aaaacagtca acgataggga aaaggatgcc ttaaaagcca aagtaaaggc tttagagggg
     2041 gaaaatgaac agctatccga tagactggga aaggctatac ttgaaaaaga gcaaaacggc
     2101 acaaaggcat tcaaagccga gaatgacaag gagtattata gacaacaaat ggacaacgca
     2161 aggacaacca gtaaccgatt aaggacggag aaccaagaac taaagaccga aaccaaggaa
     2221 ttgaaaaaag aacttggtaa gatgaaagac ttgttcaatt ccgaacaact ggaggcttta
     2281 aggcatcatt tcccaaacat atcaaaagct atggaagagg ggaaagacct actcaagcaa
     2341 atcaccagaa gcagaggttt cggtatgggt atgtaacccc ccccgccccc aaagggggag
     2401 cgaccaaacg gcagcctctc tcaatggagt gttacgtcgt tcggattcgg aagaaatttt
     2461 gcagggttcg gaaaacggtt gtgtgcttat tctaaaaaaa gtttatggtg tggcgctcgt
     2521 cgggacgggt ggtcccgccc cttgccgctg ggcgctcccc gaccgatgat ttttaagtga
     2581 ctgattttgt gctgttttgg gggtatatta agaatagaag aaatagaata agttaagtac
     2641 ttgatacaca atatagggca ttttccatat tggaaattct cattttccaa tctagaaaat
     2701 actgatttcc taatataata ctaaacagga aaataatatt tcccttaata
//
