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_011604188.1 FRAAL_RS13280 thiamine pyrophosphate-dependent dehydrogenase E1 component subunit alpha
Query= SwissProt::P9WIS3 (367 letters) >NCBI__GCF_000058485.1:WP_011604188.1 Length = 342 Score = 138 bits (347), Expect = 3e-37 Identities = 101/313 (32%), Positives = 148/313 (47%), Gaps = 35/313 (11%) Query: 58 DTEFVNLQRQGELA-LYTPCRGQEAAQVGAAACLRKTDWLFPQYRELGVYLVRGIPPGHV 116 D ++ +L G + +Y RGQE A AA LR+ D++ YR L + +G+P + Sbjct: 38 DEKYRSLMTSGAIGGMYYSPRGQEFAAASVAAHLRRDDYVVTTYRGLHDQIAKGVPLREL 97 Query: 117 GVAWRGTWHG----------------GLQFTTKCCAPMSVPIGTQTLHAVGAAMAAQRLD 160 + G G GL TT +G+ A G A++AQ Sbjct: 98 WAEYLGKAAGTCGGKGGPMHVTAPEYGLMVTTGV-------VGSGLPIANGLALSAQLRG 150 Query: 161 EDSVTVAFLGDGATSEGDVHEALNFAAVFTTPCVFYVQNNQWAISMPVSRQTAAPSIAHK 220 D VTV GDGA++ G HE+LN A+++ P +F QNN++A P+ T+ IA + Sbjct: 151 TDQVTVVNFGDGASNIGAFHESLNLASIWRLPVIFVCQNNRYAEYTPLREGTSVDRIAQR 210 Query: 221 AIGYGMPGIRVDGNDVLACYAVMAEAAARARAGDGPTLIEAVTYRLGPHTTADDPTRYRS 280 A Y +PG+ VDGND + Y A RAR G GPTL+EA+T+R H D Y Sbjct: 211 AAAYSLPGVTVDGNDPIELYNAAGAAIERARTGGGPTLLEAMTFRFCGHIMGDQQV-YMP 269 Query: 281 QEEVDRWATLDPIPRYRTYL-QDQGLWSQRLEEQVTARAKHVRSELRDAVFDAPDFDV-- 337 EE+ DP+ R+R L D G E+++ A + E+ DA A ++ Sbjct: 270 PEELRAAIAADPLVRFRAQLAADVG------EDELAAVERAAADEVADAWEFARTAELPA 323 Query: 338 -DEVFTTVYAEIT 349 + T VYA+ T Sbjct: 324 ASALTTDVYADTT 336 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: 309 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: 342 Length adjustment: 29 Effective length of query: 338 Effective length of database: 313 Effective search space: 105794 Effective search space used: 105794 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