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_083536329.1 ACG33_RS01280 hypothetical protein
Query= SwissProt::P9WIS3 (367 letters) >NCBI__GCF_001579945.1:WP_083536329.1 Length = 330 Score = 144 bits (362), Expect = 4e-39 Identities = 102/297 (34%), Positives = 141/297 (47%), Gaps = 18/297 (6%) Query: 47 LYEMMVVTRELDTEFVNLQRQGELA-LYTPCRGQEAAQVGAAACLRKTDWLFPQYRELGV 105 +Y M + + L QG ++ +Y RG E +VGA L K D+LF +R G Sbjct: 24 IYRYMYAAERWEATLLRLIEQGVVSGIYHAGRGHEGTEVGAVFALDKNDYLFYDHRGCGH 83 Query: 106 YLVRGIPPGHVGVAWRGTWHGGLQFT----TKCCAP------MSVPIGTQTLHAVGAAMA 155 + +G + + G G + C P S +G L A GAA++ Sbjct: 84 LIAKGADMTSLYGDFLGNELGSTRGLGAGIVHVCDPDLGIMGQSGTLGRGQLLATGAALS 143 Query: 156 AQRLDEDSVTVAFLGDGATSEGDVHEALNFAAVFTTPCVFYVQNNQWAISMPVSRQTAAP 215 A+ V + F GDG+++ G HEA N A + P VF VQNN WA+S+P+ TA Sbjct: 144 AKLRGTTQVAMHFFGDGSSNLGTFHEACNVAGAWKLPVVFIVQNNGWAVSVPIEYSTAGG 203 Query: 216 SIAHKAIGYGMPGIRVDGNDVLACYAVMAEAAARARAGDGPTLIEAVTYRLGPHTTADDP 275 IA +A Y MPG+ VDG D A Y + A RAR G+GPTLIEA R+ H DP Sbjct: 204 GIARRADAYAMPGLVVDGTDAFAVYETTSMAVERARRGEGPTLIEAKLVRMRGHFEG-DP 262 Query: 276 TRYRSQEEVDRWATLDPIPRYRTYLQDQGLWSQRLEEQVTARAKHVRSELRDAVFDA 332 YR + D A DP+ R R L D+ + E Q+T V+ ++ AV A Sbjct: 263 DHYRPK---DADARKDPLVRTRQRLLDEKVAD---EAQLTQLESTVKESVQAAVESA 313 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: 259 Number of extensions: 11 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: 330 Length adjustment: 29 Effective length of query: 338 Effective length of database: 301 Effective search space: 101738 Effective search space used: 101738 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