LOCUS       NC_004663               4619 bp    DNA     linear   CON 21-AUG-2022
DEFINITION  Bacteroides thetaiotaomicron VPI-5482, complete sequence.
ACCESSION   NC_004663 REGION: 4883107..4887725
VERSION     NC_004663.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN02604314
            Assembly: GCF_000011065.1
KEYWORDS    RefSeq.
SOURCE      Bacteroides thetaiotaomicron VPI-5482
  ORGANISM  Bacteroides thetaiotaomicron VPI-5482
            Bacteria; Bacteroidota; Bacteroidia; Bacteroidales; Bacteroidaceae;
            Bacteroides.
REFERENCE   1  (bases 1 to 4619)
  AUTHORS   Mahowald,M.A., Rey,F.E., Seedorf,H., Turnbaugh,P.J., Fulton,R.S.,
            Wollam,A., Shah,N., Wang,C., Magrini,V., Wilson,R.K.,
            Cantarel,B.L., Coutinho,P.M., Henrissat,B., Crock,L.W., Russell,A.,
            Verberkmoes,N.C., Hettich,R.L. and Gordon,J.I.
  TITLE     Characterizing a model human gut microbiota composed of members of
            its two dominant bacterial phyla
  JOURNAL   Proc Natl Acad Sci U S A 106 (14), 5859-5864 (2009)
   PUBMED   19321416
REFERENCE   2  (bases 1 to 4619)
  AUTHORS   Xu,J., Bjursell,M.K., Himrod,J., Deng,S., Carmichael,L.K.,
            Chiang,H.C., Hooper,L.V. and Gordon,J.I.
  TITLE     A genomic view of the human-Bacteroides thetaiotaomicron symbiosis
  JOURNAL   Science 299 (5615), 2074-2076 (2003)
   PUBMED   12663928
REFERENCE   3  (bases 1 to 4619)
  AUTHORS   Mahowald,M.A. and Gordon,J.I.
  TITLE     Direct Submission
  JOURNAL   Submitted (06-FEB-2009) Center for Genome Science, Washington
            University in St. Louis, 4444 Forest Park Ave., St. Louis, MO
            63108, USA
  REMARK    Protein update by submitter
REFERENCE   4  (bases 1 to 4619)
  AUTHORS   Xu,J., Bjursell,M.K., Himrod,J., Deng,S., Carmichael,L.K.,
            Chiang,H.C., Hooper,L.V. and Gordon,J.I.
  TITLE     Direct Submission
  JOURNAL   Submitted (31-OCT-2002) Department of Molecular Biology and
            Pharmacology, Washington University in St. Louis, 660 S. Euclid,
            St. Louis, MO 63110, USA
COMMENT     REFSEQ INFORMATION: The reference sequence is identical to
            AE015928.1.
            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/
            
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 08/21/2022 09:52:22
            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)                     :: 4,877
            CDSs (total)                      :: 4,790
            Genes (coding)                    :: 4,695
            CDSs (with protein)               :: 4,695
            Genes (RNA)                       :: 87
            rRNAs                             :: 5, 5, 5 (5S, 16S, 23S)
            complete rRNAs                    :: 5, 5, 5 (5S, 16S, 23S)
            tRNAs                             :: 70
            ncRNAs                            :: 2
            Pseudo Genes (total)              :: 95
            CDSs (without protein)            :: 95
            Pseudo Genes (ambiguous residues) :: 0 of 95
            Pseudo Genes (frameshifted)       :: 45 of 95
            Pseudo Genes (incomplete)         :: 49 of 95
            Pseudo Genes (internal stop)      :: 20 of 95
            Pseudo Genes (multiple problems)  :: 15 of 95
            ##Genome-Annotation-Data-END##
            COMPLETENESS: full length.
FEATURES             Location/Qualifiers
     source          1..4619
                     /organism="Bacteroides thetaiotaomicron VPI-5482"
                     /mol_type="genomic DNA"
                     /strain="VPI-5482"
                     /type_material="type strain of Bacteroides
                     thetaiotaomicron"
                     /db_xref="taxon:226186"
     gene            1..1458
                     /gene="rhaB"
                     /locus_tag="BT_RS18975"
                     /old_locus_tag="BT3763"
                     /old_locus_tag="BT_3763"
     CDS             1..1458
                     /gene="rhaB"
                     /locus_tag="BT_RS18975"
                     /old_locus_tag="BT3763"
                     /old_locus_tag="BT_3763"
                     /EC_number="2.7.1.5"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_004304994.1"
                     /GO_function="GO:0008993 - rhamnulokinase activity
                     [Evidence IEA]"
                     /GO_process="GO:0019301 - rhamnose catabolic process
                     [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="rhamnulokinase"
                     /protein_id="WP_011108961.1"
                     /translation="MKQNFFAVDLGATSGRTILGSFIEGGLNLEEINRFPNHLIEVGG
                     HFYWDIYALYRHIIDGLKLVAHRGESIASIGIDTWGVDFVLLGKDGNLLRQPYAYRDP
                     HTVGAPEAFFSRISRSEVYGKTGIQVMNFNSLFQLDTLRRNHDSALEAADKVLFMPDA
                     LSYMLTGKMVTEYTIASTAQLVNAHTQRLEPELLKAVGLQEENFGRFVFPGEKIGTLT
                     EEVQKITGLGAIPVIAVAGHDTGSAVAAVPALDRNFAYLSSGTWSLMGVETDAPVITA
                     ETEALNFTNEGGVEGTIRLLKNICGMWLLERCRLNWGDTSYPELITEADSCEPFRSLI
                     NPDDDCFANPADMEQAIREYCRTTGQPVPEQRGQIVRCIFESLALRYRQVLENLRALS
                     PRPIETLHVIGGGSRNDLLNQFTANAIGIPVVAGPSEATAIGNVMIQAMTVGEATDVA
                     GMRQLISRSIPLKTYHPQDMAAWDAAYIHFKNCVR"
     gene            1518..2774
                     /locus_tag="BT_RS18980"
                     /old_locus_tag="BT3764"
                     /old_locus_tag="BT_3764"
     CDS             1518..2774
                     /locus_tag="BT_RS18980"
                     /old_locus_tag="BT3764"
                     /old_locus_tag="BT_3764"
                     /EC_number="5.3.1.14"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_010536410.1"
                     /GO_function="GO:0008740 - L-rhamnose isomerase activity
                     [Evidence IEA]; GO:0030145 - manganese ion binding
                     [Evidence IEA]"
                     /GO_process="GO:0019299 - rhamnose metabolic process
                     [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="L-rhamnose isomerase"
                     /protein_id="WP_010536410.1"
                     /translation="MKKEEMIQKAYEIAVERYAAVGVDTEKVLKTMQDFHLSLHCWQA
                     DDVTGFEVQAGALSGGIQATGNYPGKARNIDELRADILKAASYIPGTHRLNLHEIYGD
                     FQGKVVDRDQVEPEHFKSWIEWGKEHNMKLDFNSTSFSHPKSGDLSLSNPDEGIRQFW
                     IEHTKRCRAVAEEMGKAQGDPCIMNLWVHDGSKDITVNRMKYRALLKDSLDQIFATEY
                     KNMKDCIESKVFGIGLESYTVGSNDFYIGYGASRNKMVTLDTGHFHPTESVADKVSSL
                     LLYVPELMLHVSRPVRWDSDHVTIMDDPTMELFSEIVRCGALERVHYGLDYFDASINR
                     IGAYVIGSRAAQKCMTRALLEPIAKLREYEANGQGFQRLALLEEEKALPWNAVWDMFC
                     LKNNVPVGEDFIAEIEKYEAEVTSKR"
     gene            2778..3797
                     /gene="rhaT"
                     /locus_tag="BT_RS18985"
                     /old_locus_tag="BT3765"
                     /old_locus_tag="BT_3765"
     CDS             2778..3797
                     /gene="rhaT"
                     /locus_tag="BT_RS18985"
                     /old_locus_tag="BT3765"
                     /old_locus_tag="BT_3765"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_004315661.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="L-rhamnose/proton symporter RhaT"
                     /protein_id="WP_008762702.1"
                     /translation="MDILIGLLIIAIGSFCQSSSYVPIKKVKEWSWESFWLVQGVFAW
                     LVFPFLGSLLGIPAGGSLFDLWGAGGAGMSIFYGVLWGIGGLTFGLSMRYLGVALGQS
                     IALGTCAGFGTLFPAIFAGTNLFEGNGLILLLGVCITLAGIAIIGYAGGLRAQNMSEE
                     EKRAAVKDFALTKGLLVALLAGVMSACFALGLDAGTPIKEAALAGGVDGLYAGLPVIF
                     LVTLGGFMTNAAYCLQQNIANKSVGDYAKGKVWGNNLVFCALAGVLWYMQFFGLEMGK
                     SFLTESPVLLAFSWCILMALNVTFSNVWGIILKEWKGVSAKTITVLICGLVVLIFSLV
                     FPNLF"
     gene            3810..4619
                     /gene="rhaD"
                     /locus_tag="BT_RS18990"
                     /old_locus_tag="BT3766"
                     /old_locus_tag="BT_3766"
     CDS             3810..4619
                     /gene="rhaD"
                     /locus_tag="BT_RS18990"
                     /old_locus_tag="BT3766"
                     /old_locus_tag="BT_3766"
                     /EC_number="4.1.2.19"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_009123928.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="rhamnulose-1-phosphate aldolase"
                     /protein_id="WP_008766960.1"
                     /translation="MKSILENRPALAKEVNKVAEVAGYLWQKGWAERNGGNITVNITE
                     FVDDEIRRMEPISEVKSIGVTLPYLKGCYFYCKGTNKRMRDLARWPMENGSVIRILDD
                     CASYVIIADEAVAPTSELPSHLSVHNDLLSKNSPYKASVHTHPIELIAMTHCEKFLQK
                     DVATNLLWSMIPETKAFCPRGLGIIPYKLPSSVELAEATIKELQDYDVVMWEKHGVFA
                     VDCDAMQAFDQIDVLNKSALIYIAAKNMGFEPDGMSQEQMKEMSVAFNLPK"
ORIGIN      
        1 atgaaacaga acttttttgc agtcgacctg ggcgcaacaa gcggccgtac aatcttaggc
       61 tcttttattg aaggcggatt aaatctggag gagattaatc gttttcctaa ccacttgatc
      121 gaggtgggtg gacatttcta ttgggatatt tatgcattat accgtcacat tatcgacgga
      181 ttgaaattgg tagctcaccg tggcgaatct attgcctcta tcggtataga tacatgggga
      241 gtagatttcg tcctccttgg aaaagatgga aacctgcttc gccagcctta tgcatatcgt
      301 gatccgcata cggtaggagc accggaagcc tttttctctc gtatctctcg tagcgaggta
      361 tatggtaaaa ctggtattca ggtaatgaat tttaattcac ttttccaatt agatactttg
      421 cgtcgcaatc atgacagtgc attggaggca gcagacaaag ttctgtttat gccggatgcg
      481 ttgagctata tgctgaccgg gaagatggta actgaatata ccattgcttc cactgcccaa
      541 ttagtgaatg cacatacgca acgtctggaa ccggagttgc tgaaagcagt cggactgcaa
      601 gaagagaatt tcggtcgttt tgtcttccca ggtgagaaga taggaacatt gactgaagaa
      661 gtgcaaaaga taacaggatt gggggcaatt cctgtgattg cggtggccgg acatgatacc
      721 ggatctgctg tagcagctgt tcccgcactt gatcgtaatt tcgcatattt gagtagcggt
      781 acttggtcgc tgatgggggt ggaaacagat gcaccggtaa tcactgctga aacagaggct
      841 ttgaacttta cgaatgaagg tggcgtagaa ggcacaattc gccttttgaa gaatatttgt
      901 ggaatgtggt tgctggaacg ttgccgtctg aattggggag atacaagcta tccggaatta
      961 ataaccgaag cggattcgtg tgaaccattc cgtagtttaa tcaatccgga tgacgactgt
     1021 tttgcaaatc ctgcggatat ggaacaggcc attcgtgaat attgccggac tactgggcag
     1081 ccggttcctg agcaacgtgg acaaatagta cgttgtatct ttgagagtct ggctttgcgt
     1141 taccgtcagg tgttggaaaa cttgcgtgcg ctttctcctc gtcctatcga aactctgcat
     1201 gtgattggtg gaggtagccg taatgacttg ttgaatcagt ttactgctaa tgctatcggc
     1261 atcccggttg tggcaggacc gtctgaggca acagctatcg gtaatgtcat gattcaggca
     1321 atgacggtgg gagaggcgac ggatgttgcc ggtatgcgtc agttgataag ccgttcaatt
     1381 ccgttgaaga cttatcaccc acaggatatg gcagcttggg atgcggctta tatccatttt
     1441 aaaaactgcg ttcgataaat tccggagaat caaaaaataa tcgacagaat aatattaact
     1501 tttaataata gaatatcatg aaaaaagaag aaatgattca gaaagcgtat gagattgctg
     1561 ttgaacgcta tgcagcagta ggtgtagata ctgaaaaggt actgaaaacc atgcaggact
     1621 tccacttgtc acttcattgc tggcaggctg atgatgtaac gggatttgaa gtgcaggcag
     1681 gtgcactgag cggaggtatt caggcaaccg gtaattatcc gggcaaagct cgcaatattg
     1741 atgaactgcg tgccgacatt ctgaaagccg cttcttatat tccgggtaca caccgtttga
     1801 acctgcacga aatctacggg gattttcaag gtaaagtggt agaccgcgat caggtagagc
     1861 ctgaacattt caagagctgg attgaatggg gtaaagagca taacatgaaa ctcgatttta
     1921 actctacttc cttctcacat ccgaaatctg gtgatttgtc actgtctaat ccggatgagg
     1981 gcatccgtca gttctggatt gagcatacca aacgttgtcg tgccgttgcc gaagaaatgg
     2041 gtaaggcgca gggtgacccg tgtatcatga atctttgggt acatgacgga agcaaggata
     2101 tcactgtaaa ccgcatgaaa tatcgtgcat tgttgaaaga ttctctggat cagatatttg
     2161 ctactgaata taaaaacatg aaagactgta ttgaatcaaa agtattcggt atcggtctgg
     2221 aaagctatac agtaggttcc aatgacttct acatcggtta tggcgcatcc cgtaataaga
     2281 tggtaacttt ggataccggt cacttccatc cgactgaaag tgttgccgac aaagtatctt
     2341 ctcttttgct ttatgtgccc gaattgatgc tgcacgtaag ccgtccggtt cgttgggatt
     2401 ccgaccacgt aaccattatg gatgatccta caatggaact gttcagtgaa attgttcgtt
     2461 gcggtgcgtt ggaacgcgta cactacggtc tcgactattt cgatgcttct atcaaccgta
     2521 tcggtgctta cgttatcggt agccgtgctg ctcagaaatg tatgacacgc gctttgctcg
     2581 aaccgattgc caagctgcgt gaatacgaag ctaacggaca gggattccag cgtctggctc
     2641 tgctcgaaga agagaaagcg cttccatgga atgcagtatg ggatatgttc tgcttgaaga
     2701 acaacgttcc ggtaggcgaa gatttcattg cagaaatcga aaagtacgaa gcggaagtaa
     2761 cttctaaacg ataagtgatg gatattctaa taggcttgtt gattatagcc atcggtagct
     2821 tttgccagtc cagttcctat gtacctatta aaaaggtgaa ggaatggagc tgggaaagct
     2881 tctggttagt acaaggtgtg tttgcctggt tagtgttccc gtttctggga tcactgctgg
     2941 ggatacccgc aggaggcagt ttgttcgact tgtggggagc cggaggtgct ggaatgagca
     3001 tcttttatgg tgtattatgg ggaataggcg gattgacttt cggactctcc atgcgttatc
     3061 tgggtgttgc gcttggacaa agtatcgcat taggtacttg tgccggattc ggaacccttt
     3121 ttcctgccat cttcgccgga accaatctgt tcgaaggtaa cggactgatt cttcttctag
     3181 gagtttgtat tacgctggcg ggtattgcta tcattggtta tgccggtggc ttgcgtgcac
     3241 agaatatgag cgaagaagaa aaacgggctg ccgtaaaaga ctttgcattg acaaaaggtt
     3301 tgctggtagc acttcttgcg ggtgtgatga gtgcctgctt tgctttggga ctggatgccg
     3361 gaactcctat caaggaagct gctttggcag gtggtgtgga tggactttat gcaggtcttc
     3421 ctgttatctt cctcgtgact ttaggcggat tcatgacaaa tgccgcttac tgcctgcagc
     3481 agaatatagc taataagtct gtcggtgact atgccaaagg aaaggtatgg ggtaacaatc
     3541 tcgtcttctg tgcgttggcc ggtgtgctgt ggtatatgca gttcttcgga ttggaaatgg
     3601 gtaagagctt cctcacggaa agtcccgtgt tgctggcttt ctcatggtgt atcctgatgg
     3661 cgctgaacgt aacctttagt aatgtatggg gaatcatcct gaaagagtgg aaaggagtat
     3721 ctgccaaaac aatcacagtg ttgatctgtg gtttggtagt cttgatcttc tcactggtat
     3781 tcccgaactt gttttaataa taaatagata tgaaatcaat tttagaaaat cgtccggcac
     3841 ttgccaaaga agtaaacaag gtagctgaag ttgccggata cttgtggcaa aaaggatggg
     3901 ctgaacgtaa cggtggtaat atcactgtaa atatcacaga gtttgtagac gatgaaatcc
     3961 gtcggatgga accgattagc gaagtaaaat ccattggcgt tacattgcct tatctgaaag
     4021 gatgttactt ttattgcaaa ggaaccaaca aacgcatgcg tgatctggct cgctggccga
     4081 tggaaaatgg ttcggtgatt cgcattttag atgattgcgc cagctatgtg atcattgccg
     4141 acgaagcggt ggcgccgact tcggaactgc cttcccacct gagcgtacac aatgatttgc
     4201 tgagcaagaa ttctccttat aaagcatctg tccatactca cccgatcgaa ctgattgcca
     4261 tgactcattg cgagaagttc cttcagaaag atgtggcaac caatctgtta tggagtatga
     4321 ttcctgaaac gaaggcgttc tgtccgagag gtctgggtat cattccttat aaattgccta
     4381 gttcggtaga gttggcggaa gccactatca aggaattgca ggactatgat gtagtcatgt
     4441 gggaaaaaca cggtgttttt gccgtagact gcgatgctat gcaggctttt gatcagattg
     4501 acgtgctgaa taagtcggcg ctgatctata ttgctgcgaa gaatatgggc ttcgaaccgg
     4561 atggtatgag tcaggaacaa atgaaagaaa tgtccgttgc tttcaatctt cctaaataa
//
