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 Pf1N1B4_1020 Branched-chain alpha-keto acid dehydrogenase, E1 component, alpha subunit (EC 1.2.4.4)
Query= SwissProt::P9WIS3 (367 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1020 Length = 332 Score = 227 bits (578), Expect = 4e-64 Identities = 136/323 (42%), Positives = 175/323 (54%), Gaps = 6/323 (1%) Query: 47 LYEMMVVTRELDTEFVNLQRQGELALYTPCRGQEAAQVGAAACLRKTDWLFPQYRELGVY 106 LY MV+TR D + V LQR G + Y P GQEA V + + D L P YR+ V Sbjct: 4 LYRQMVLTRLFDQKAVALQRTGRIGTYAPTLGQEAIGVAVGSLMHAEDVLIPYYRDTAVQ 63 Query: 107 LVRGIPPGHVGVAWRGTWHGGLQFTTKCCA---PMSVPIGTQTLHAVGAAMAAQRLDEDS 163 L+RG+ + + W G G F A P+ VPI TQ LHA G A A + E Sbjct: 64 LMRGVRMEEILLYWGGDERGS-DFADPAVAQDFPICVPIATQALHACGVASAFKIRGEHR 122 Query: 164 VTVAFLGDGATSEGDVHEALNFAAVFTTPCVFYVQNNQWAISMPVSRQTAAPSIAHKAIG 223 V V GDG TS+GD EALN A + P VF V NNQWAIS+P Q AP++A KAIG Sbjct: 123 VAVTTCGDGGTSKGDFLEALNVAGAWQLPVVFMVNNNQWAISVPRRIQCGAPTLAQKAIG 182 Query: 224 YGMPGIRVDGNDVLACYAVMAEAAARARAGDGPTLIEAVTYRLGPHTTADDPTRYRSQEE 283 G G +VDGND+LA Y + A R R G GP L+E ++YRLG HTTADD TRYRS +E Sbjct: 183 AGFHGEQVDGNDMLAVYDRVQAALERTRHGKGPVLLECLSYRLGDHTTADDATRYRSADE 242 Query: 284 VDRWATLDPIPRYRTYLQDQGLWSQRLEEQVTARAKHVRSELRDAVFDAPDFDVDE-VFT 342 V + +PI R + ++ QG+W + E+ + + + + D F+A E V Sbjct: 243 VKQAWLEEPIKRLQRFMAGQGVWDEGREQALISECQGLVQRAVDN-FEAAGLQAPESVMD 301 Query: 343 TVYAEITPGLQAQREQLRAELAR 365 VYA+ L QRE +AR Sbjct: 302 HVYAQWPQALAEQREDFLERVAR 324 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: 286 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: 332 Length adjustment: 29 Effective length of query: 338 Effective length of database: 303 Effective search space: 102414 Effective search space used: 102414 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