Align 3-methyl-2-oxobutanoate dehydrogenase subunit alpha; Branched-chain alpha-ketoacid dehydrogenase E1 component subunit alpha; BCKADH E1-alpha; EC 1.2.4.4 (characterized)
to candidate AO353_15575 AO353_15575 pyruvate dehydrogenase (acetyl-transferring) E1 component subunit alpha
Query= SwissProt::P9WIS3 (367 letters) >FitnessBrowser__pseudo3_N2E3:AO353_15575 Length = 365 Score = 242 bits (617), Expect = 1e-68 Identities = 149/354 (42%), Positives = 187/354 (52%), Gaps = 5/354 (1%) Query: 15 VDLEPVQLVGPDGTPTAERRYHRDLPEETLRWLYEMMVVTRELDTEFVNLQRQGELALYT 74 VDL + + PDG +E D L LY MV+TR D + V LQR G + Y Sbjct: 6 VDLPYTRYLSPDGQALSELPAWAD-DFNLLTRLYRQMVLTRLFDQKAVALQRTGRIGTYA 64 Query: 75 PCRGQEAAQVGAAACLRKTDWLFPQYRELGVYLVRGIPPGHVGVAWRGTWHGGLQFTTKC 134 P GQEA V + + D L P YR+ GV L+RG+ + + W G G F Sbjct: 65 PTLGQEAIGVAVGSLMHPEDVLIPYYRDTGVQLMRGVRMEEILLYWGGDERGS-DFAEPA 123 Query: 135 CA---PMSVPIGTQTLHAVGAAMAAQRLDEDSVTVAFLGDGATSEGDVHEALNFAAVFTT 191 P+ VPI TQ LHA G A A + E V V GDGATS+GD EALN A + Sbjct: 124 AVEDFPICVPIATQALHACGVASAFKIRGEHRVAVTTCGDGATSKGDFLEALNVAGAWQL 183 Query: 192 PCVFYVQNNQWAISMPVSRQTAAPSIAHKAIGYGMPGIRVDGNDVLACYAVMAEAAARAR 251 P VF + NNQWAIS+P Q AAP++A KAIG G G +VDGND+LA Y + A RAR Sbjct: 184 PVVFVINNNQWAISVPRRIQCAAPTLAQKAIGAGFHGEQVDGNDILAVYDRVQIALERAR 243 Query: 252 AGDGPTLIEAVTYRLGPHTTADDPTRYRSQEEVDRWATLDPIPRYRTYLQDQGLWSQRLE 311 G GP L+E V+YRLG HTTADD TRYR EEV + +P+ R + YL QG+W + E Sbjct: 244 HGKGPVLLECVSYRLGDHTTADDATRYRPAEEVKQAWLEEPVKRLQRYLAGQGVWDEGRE 303 Query: 312 EQVTARAKHVRSELRDAVFDAPDFDVDEVFTTVYAEITPGLQAQREQLRAELAR 365 + + A + + D A + V VYA+ L QRE L AR Sbjct: 304 QALIAECQALVQGAVDNFDAAGQQSAESVIDHVYAQWPAALAEQREWLLERAAR 357 Lambda K H 0.320 0.134 0.413 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 333 Number of extensions: 10 Number of successful extensions: 2 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 367 Length of database: 365 Length adjustment: 30 Effective length of query: 337 Effective length of database: 335 Effective search space: 112895 Effective search space used: 112895 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 49 (23.5 bits)
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory