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 N515DRAFT_0356 N515DRAFT_0356 pyruvate dehydrogenase E1 component alpha subunit
Query= SwissProt::P9WIS3 (367 letters) >FitnessBrowser__Dyella79:N515DRAFT_0356 Length = 361 Score = 217 bits (552), Expect = 5e-61 Identities = 124/314 (39%), Positives = 171/314 (54%), Gaps = 4/314 (1%) Query: 47 LYEMMVVTRELDTEFVNLQRQGELALYTPCRGQEAAQVGAAACLRKTDWLFPQYRELGVY 106 LY++M+ TR D + V LQR G+L Y C G EAA VG + ++ D P YRE G Sbjct: 39 LYKLMMSTRVFDAKSVALQRTGKLGTYASCLGHEAAHVGIGSAMKPEDVFAPSYREYGAQ 98 Query: 107 LVRGIPPGHVGVAWRGTWHGG--LQFTTKCCAPMSVPIGTQTLHAVGAAMAAQRLDEDSV 164 L RG+ P V + W G G + + SVPI TQ LHA G+A+A + +E V Sbjct: 99 LYRGVQPREVYMYWGGDERGNDYQKEPARHDFAWSVPIATQCLHAAGSALAFKIRNEKRV 158 Query: 165 TVAFLGDGATSEGDVHEALNFAAVFTTPCVFYVQNNQWAISMPVSRQTAAPSIAHKAIGY 224 V +GDG +S+GD + A+N P V + NNQWAIS+P Q+ AP++A K I Sbjct: 159 AVCTIGDGGSSKGDFYGAINITGAQNLPMVAVIVNNQWAISVPRKIQSGAPTLAQKGIAA 218 Query: 225 GMPGIRVDGNDVLACYAVMAEAAARARAGDGPTLIEAVTYRLGPHTTADDPTRYRSQEEV 284 G+ I+VDGND++A M +A RAR G G +++E VTYRL HTTADD RYR ++EV Sbjct: 219 GLFSIQVDGNDIIAVRKAMEDALDRARNGQGGSVLELVTYRLSDHTTADDARRYRGEQEV 278 Query: 285 -DRWATLDPIPRYRTYLQDQGLWSQRLEEQVTARAKHVRSELRDAVFDAPDFDVDEVFTT 343 D WA +P+ R R +L + +W EE A +A + V +F Sbjct: 279 KDAWAK-EPMKRLRAWLVAKNVWDDAKEEAWKAECDEWMDNEVNAYLETKTQPVTAMFDY 337 Query: 344 VYAEITPGLQAQRE 357 +AE+ L QR+ Sbjct: 338 TFAEVPADLAKQRD 351 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: 299 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: 361 Length adjustment: 29 Effective length of query: 338 Effective length of database: 332 Effective search space: 112216 Effective search space used: 112216 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 17 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