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_003942481.1 C1M55_RS30500 pyruvate dehydrogenase (acetyl-transferring) E1 component subunit alpha
Query= SwissProt::P9WIS3 (367 letters) >NCBI__GCF_002893965.1:WP_003942481.1 Length = 375 Score = 283 bits (725), Expect = 4e-81 Identities = 153/345 (44%), Positives = 199/345 (57%) Query: 20 VQLVGPDGTPTAERRYHRDLPEETLRWLYEMMVVTRELDTEFVNLQRQGELALYTPCRGQ 79 VQ + P G T + ++ L +Y M + R D + L +QG LA+Y RGQ Sbjct: 22 VQYLDPAGELTRSEARYAKPSDDRLIAMYRKMFLGRRFDQQATALTKQGRLAVYPSSRGQ 81 Query: 80 EAAQVGAAACLRKTDWLFPQYRELGVYLVRGIPPGHVGVAWRGTWHGGLQFTTKCCAPMS 139 EA Q+ AA L +DWLFP YR+ RG+ P + G WH G AP Sbjct: 82 EACQIAAAMSLEPSDWLFPTYRDSMALAARGVDPVQILSMLAGDWHCGYDPVALRSAPQC 141 Query: 140 VPIGTQTLHAVGAAMAAQRLDEDSVTVAFLGDGATSEGDVHEALNFAAVFTTPCVFYVQN 199 P+ TQ LHA G A R ++V +A GDGATSEGD HEALNFAAVF P +F VQN Sbjct: 142 TPLATQLLHAAGVAYGESRRGLNTVALALCGDGATSEGDFHEALNFAAVFKAPVIFLVQN 201 Query: 200 NQWAISMPVSRQTAAPSIAHKAIGYGMPGIRVDGNDVLACYAVMAEAAARARAGDGPTLI 259 N +AIS+P+SRQ+AAP++AHK +GYG+ +VDGND +A AVM EAA R+G+GP ++ Sbjct: 202 NGFAISVPLSRQSAAPTLAHKGVGYGIGSEQVDGNDPVAMLAVMDEAARFVRSGNGPVIV 261 Query: 260 EAVTYRLGPHTTADDPTRYRSQEEVDRWATLDPIPRYRTYLQDQGLWSQRLEEQVTARAK 319 EA TYR+ HT ADD TRYR EV+ W DP+PR YL+ L E +TA A+ Sbjct: 262 EAHTYRIDAHTNADDATRYRDSAEVEAWLGRDPLPRLEKYLRAHDLIDDAFVESLTAEAE 321 Query: 320 HVRSELRDAVFDAPDFDVDEVFTTVYAEITPGLQAQREQLRAELA 364 + LR + D ++F V+AE TP L+ Q+ QL ELA Sbjct: 322 TAAATLRAGMNVDRPHDPLDLFRYVFAEQTPQLREQQAQLETELA 366 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: 345 Number of extensions: 10 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: 375 Length adjustment: 30 Effective length of query: 337 Effective length of database: 345 Effective search space: 116265 Effective search space used: 116265 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