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_057509084.1 ABB28_RS13325 pyruvate dehydrogenase (acetyl-transferring) E1 component subunit alpha
Query= SwissProt::P9WIS3 (367 letters) >NCBI__GCF_001431535.1:WP_057509084.1 Length = 360 Score = 220 bits (560), Expect = 5e-62 Identities = 127/315 (40%), Positives = 176/315 (55%), Gaps = 9/315 (2%) Query: 47 LYEMMVVTRELDTEFVNLQRQGELALYTPCRGQEAAQVGAAACLRKTDWLFPQYRELGVY 106 L++ M+ R D++ + LQR G+L Y C G EAA VG A + +D P YRE G Sbjct: 39 LFKQMLYVRVFDSKSIALQRTGKLGTYAACLGHEAAHVGIGAAMHPSDVFAPSYREYGAM 98 Query: 107 LVRGIPPGHVGVAW----RGTWHGGLQFTTKCCAPMSVPIGTQTLHAVGAAMAAQRLDED 162 +RG+ P V + W RG +GG P VPI TQ LHA GAA+ + DE Sbjct: 99 FMRGVRPYDVLMYWGGDERGNDYGG---NAAKDFPFCVPISTQCLHAAGAALKFKLNDEK 155 Query: 163 SVTVAFLGDGATSEGDVHEALNFAAVFTTPCVFYVQNNQWAISMPVSRQTAAPSIAHKAI 222 + VA GDG +S+ D + ALN A + P + + NN WAIS+P S QT A ++A K + Sbjct: 156 QIAVAVCGDGGSSKTDFYAALNSAGAYKLPLILCIVNNGWAISVPRSAQTGAETLAQKGL 215 Query: 223 GYGMPGIRVDGNDVLACYAVMAEAAARARAGDGPTLIEAVTYRLGPHTTADDPTRYRSQE 282 G+ ++VDGND++A A M +A R +G+G T++E +TYRL HTTADD RYR Sbjct: 216 AGGLHCLQVDGNDLIAVLAAMEQARERGLSGNGGTVLELMTYRLSDHTTADDARRYRDDA 275 Query: 283 EV-DRWATLDPIPRYRTYLQDQGLWSQRLEEQVTARAKHVRSELRDAVFDAPDFDVDEVF 341 EV D W L+P+ R R YL DQG+WS+ E+ + E + + P V+ +F Sbjct: 276 EVKDAW-LLEPMLRLRKYLTDQGVWSEAEEKAWIEQCGARVDEDVNQYLNTPVQPVEAMF 334 Query: 342 TTVYAEITPGLQAQR 356 +YA+ P L AQR Sbjct: 335 DFLYADPPPDLLAQR 349 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: 301 Number of extensions: 9 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 367 Length of database: 360 Length adjustment: 29 Effective length of query: 338 Effective length of database: 331 Effective search space: 111878 Effective search space used: 111878 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