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_050655238.1 C1M55_RS19770 pyruvate dehydrogenase (acetyl-transferring) E1 component subunit alpha
Query= SwissProt::P9WIS3 (367 letters) >NCBI__GCF_002893965.1:WP_050655238.1 Length = 362 Score = 290 bits (743), Expect = 3e-83 Identities = 160/348 (45%), Positives = 207/348 (59%), Gaps = 4/348 (1%) Query: 19 PVQLVGPDGTPTAERRYHR---DLPEETLRWLYEMMVVTRELDTEFVNLQRQGELALYTP 75 PVQL+ P+G + R D+ + L LY +VV+R +DTE V LQRQGE+ L+ P Sbjct: 8 PVQLIQPNGARVCRPEFDRLITDIGPDELLSLYRDLVVSRRIDTEAVALQRQGEIGLWAP 67 Query: 76 CRGQEAAQVGAAACLRKTDWLFPQYRELGVYLVRGIPPGHVGVAWRGTWHGGLQFTTKCC 135 GQEAAQVG+A L D+ F YRE V RG+PP + WRG H G Sbjct: 68 MLGQEAAQVGSARALAPGDFAFTSYREHAVAYCRGVPPELLTTMWRGISHSGWDPEQFSV 127 Query: 136 APMSVPIGTQTLHAVGAAMAAQRLDEDSVTVAFLGDGATSEGDVHEALNFAAVFTTPCVF 195 ++ +G+Q LHA G A+ A + T+A+ GDGATS+GD+ EA+ FAA F VF Sbjct: 128 TNPAIVVGSQGLHATGYALGAHLDGAEIATIAYFGDGATSQGDIAEAMGFAASFRVGVVF 187 Query: 196 YVQNNQWAISMPVSRQTAAPSIAHKAIGYGMPGIRVDGNDVLACYAVMAEAAARARAGDG 255 + QNNQWAIS PVS Q+ P I+H+AIGYG+P IRVDGNDVLA AV A RAR G G Sbjct: 188 FCQNNQWAISEPVSLQSRTP-ISHRAIGYGIPAIRVDGNDVLAVLAVTRSALNRAREGSG 246 Query: 256 PTLIEAVTYRLGPHTTADDPTRYRSQEEVDRWATLDPIPRYRTYLQDQGLWSQRLEEQVT 315 PT IEA+T R+GPHTT+DDP+RYR+ ++ W + DP+ R R L + L + + Sbjct: 247 PTFIEAITCRMGPHTTSDDPSRYRTDTDMSEWRSRDPLERMRLLLGRRDLLGENELSTIA 306 Query: 316 ARAKHVRSELRDAVFDAPDFDVDEVFTTVYAEITPGLQAQREQLRAEL 363 A A V + LR A D +F VYAE P + A+RE+ RA L Sbjct: 307 AAADDVAAGLRRATIALADPPPSALFDHVYAEAHPLIDAEREEHRAHL 354 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: 371 Number of extensions: 15 Number of successful extensions: 3 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: 362 Length adjustment: 29 Effective length of query: 338 Effective length of database: 333 Effective search space: 112554 Effective search space used: 112554 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