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_015798258.1 AFER_RS04250 pyruvate dehydrogenase (acetyl-transferring) E1 component subunit alpha
Query= SwissProt::P9WIS3 (367 letters) >NCBI__GCF_000023265.1:WP_015798258.1 Length = 358 Score = 263 bits (671), Expect = 7e-75 Identities = 145/330 (43%), Positives = 192/330 (58%), Gaps = 8/330 (2%) Query: 42 ETLRWLYEMMVVTRELDTEFVNLQRQGELALYTPCRGQEAAQVGAAACLRKTDWLFPQYR 101 + L +Y MV+ R D NLQRQG + Y P +GQEAAQ+GAA L + DWL P YR Sbjct: 32 DRLAEVYRHMVMLRRFDERAWNLQRQGVIGTYAPYKGQEAAQLGAAHGLAEQDWLVPTYR 91 Query: 102 ELGVYLVRGIPPGHVGVAWRGTWHGGLQFTTKCCAPMSVPIGTQTLHAVGAAMAAQRLDE 161 + RG+P H +G GL P V I QTLH VG A + + E Sbjct: 92 DWAASWARGVPLEHGLFFAKGHPRMGLVPEEATVLPAQVVIAAQTLHGVGVAWSLKLRHE 151 Query: 162 DSVTVAFLGDGATSEGDVHEALNFAAVFTTPCVFYVQNNQWAISMPVSRQTAAPSIAHKA 221 V + GDGA S+GD HEA+NFA+VF P VF+ +NN WAIS+P+ RQ + +IA +A Sbjct: 152 PKVALVTFGDGAASQGDTHEAMNFASVFRVPLVFFCENNHWAISVPLERQMHSETIAQRA 211 Query: 222 IGYGMPGIRVDGNDVLACYAVMAEAAARARAGDGPTLIEAVTYRLGPHTTADDPTRYRSQ 281 + YGM G RVDGND +A ++ + A RAR G+GP L+EAVTYRLG HTTADDP++YR Sbjct: 212 VAYGMEGFRVDGNDYVAVVNLVHDLAERARQGEGPFLVEAVTYRLGAHTTADDPSKYRES 271 Query: 282 EEVDRWATLDPIPRYRTYLQDQGLWSQRLEEQVTARAKHVRSELRDAVFD----APDFDV 337 E +RW DPI R LQ +G RL++ A A+ +E + V + A D + Sbjct: 272 AEEERWEAKDPIRRIERLLQREG----RLDDDAIAAAEASAAEAVEGVLERFHSALDDEP 327 Query: 338 DEVFTTVYAEITPGLQAQREQLRAELARTD 367 +F VYAE+TP L AQR++ A + + Sbjct: 328 ATLFDHVYAELTPQLAAQRDRFVARVKEVE 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: 347 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: 358 Length adjustment: 29 Effective length of query: 338 Effective length of database: 329 Effective search space: 111202 Effective search space used: 111202 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 24 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