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 WP_205630629.1 AU252_RS03450 pyruvate dehydrogenase (acetyl-transferring) E1 component subunit alpha
Query= SwissProt::P9WIS3 (367 letters) >NCBI__GCF_001484605.1:WP_205630629.1 Length = 369 Score = 290 bits (743), Expect = 3e-83 Identities = 164/355 (46%), Positives = 209/355 (58%), Gaps = 4/355 (1%) Query: 13 MSVDLEPVQLVGPDGTPTAERRYH---RDLPEETLRWLYEMMVVTRELDTEFVNLQRQGE 69 MS D +QLV P G + + +D+ +E L LYE + V R +D E LQRQGE Sbjct: 1 MSTDRNLIQLVTPAGERISHPEFDPWVKDIGDEQLCSLYEDLTVIRRIDVEATALQRQGE 60 Query: 70 LALYTPCRGQEAAQVGAAACLRKTDWLFPQYRELGVYLVRGIPPGHVGVAWRGTWHGGLQ 129 L L+ P GQEAAQVG+ LR D++F YRE GV RG+ + WRGT G Sbjct: 61 LGLWPPLLGQEAAQVGSGRALRDDDFVFSSYRENGVAYCRGVDLTDITRVWRGTASSGWD 120 Query: 130 FTTKCCAPMSVPIGTQTLHAVGAAMAAQRLDEDSVTVAFLGDGATSEGDVHEALNFAAVF 189 + A + IG QTLHA G AM Q DSV V + GDGATSEGDV+EA+ FAA F Sbjct: 121 PYSVNMATPQIIIGAQTLHATGYAMGIQNDGADSVAVTYFGDGATSEGDVNEAMVFAASF 180 Query: 190 TTPCVFYVQNNQWAISMPVSRQTAAPSIAHKAIGYGMPGIRVDGNDVLACYAVMAEAAAR 249 P VF+ NN WAIS PV Q+ IA +A G+G+P +RVDGNDVLA A A R Sbjct: 181 QAPVVFFCSNNHWAISEPVRLQSHI-QIADRATGFGIPSLRVDGNDVLAVMAATRVALDR 239 Query: 250 ARAGDGPTLIEAVTYRLGPHTTADDPTRYRSQEEVDRWATLDPIPRYRTYLQDQGLWSQR 309 AR G GPT IEAVTYR+GPHTTADDPTRYR E++ WA DPI R + L+ +GL + + Sbjct: 240 ARHGGGPTFIEAVTYRMGPHTTADDPTRYRDANELEDWAAKDPILRIKALLERKGLLTDQ 299 Query: 310 LEEQVTARAKHVRSELRDAVFDAPDFDVDEVFTTVYAEITPGLQAQREQLRAELA 364 +++ V +A+ V E+R PD + ++F VY+E L Q++ LA Sbjct: 300 VQQHVHDKAESVAREIRSGCIGMPDPEPMDIFKHVYSEPNSWLDRQQDHYARYLA 354 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: 358 Number of extensions: 14 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: 369 Length adjustment: 30 Effective length of query: 337 Effective length of database: 339 Effective search space: 114243 Effective search space used: 114243 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 Apr 09 2024. 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