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_042451488.1 C1M55_RS23135 thiamine pyrophosphate-dependent dehydrogenase E1 component subunit alpha
Query= SwissProt::P9WIS3 (367 letters) >NCBI__GCF_002893965.1:WP_042451488.1 Length = 307 Score = 115 bits (287), Expect = 2e-30 Identities = 79/241 (32%), Positives = 115/241 (47%), Gaps = 14/241 (5%) Query: 68 GELALYTPCRGQEAAQVGAAACLRKTDWLFPQYRELGVYLVRGIPPGHVGVAWRGT---- 123 G + LY+ GQEA VG L D++ +R G + +G + G Sbjct: 22 GFIHLYS---GQEAIAVGVCENLSDADYIGSTHRGHGHCIAKGCDLNGMMAEIFGKDDGL 78 Query: 124 --WHGGLQFTTKCCAPM---SVPIGTQTLHAVGAAMAAQRLDEDSVTVAFLGDGATSEGD 178 GG M + +G A+GAA++ + L + +F GDG +++G Sbjct: 79 CRGKGGSMHIADLSVGMLGANAIVGGAPSLAIGAALSGKTLRNGVIAASFTGDGGSNQGT 138 Query: 179 VHEALNFAAVFTTPCVFYVQNNQWAISMPVSRQTAAPSIAHKAIGYGMPGIRVDGNDVLA 238 V EA+N A V P VF ++NN + + AP IA +A +GMP ++VDG D A Sbjct: 139 VFEAMNMAVVLDLPIVFVIENNGFGEATGTDYAVGAPDIAARAASFGMPAVKVDGTDFFA 198 Query: 239 CYAVMAEAAARARAGDGPTLIEAVTYRLGPHTTADDPTRYRSQEEVDRW-ATLDPIPRYR 297 Y MAEA+ RAR G GPT IEA +R H D YR+ E+V + T DP+ +R Sbjct: 199 VYDAMAEASERARIGGGPTTIEAAAFRWHGHFEG-DAQLYRTAEQVAQLRETKDPLKNFR 257 Query: 298 T 298 + Sbjct: 258 S 258 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: 250 Number of extensions: 13 Number of successful extensions: 1 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: 307 Length adjustment: 28 Effective length of query: 339 Effective length of database: 279 Effective search space: 94581 Effective search space used: 94581 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