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_089299388.1 CHB84_RS00120 pyruvate dehydrogenase (acetyl-transferring) E1 component subunit alpha
Query= SwissProt::P9WIS3 (367 letters) >NCBI__GCF_900188115.1:WP_089299388.1 Length = 411 Score = 275 bits (703), Expect = 2e-78 Identities = 158/364 (43%), Positives = 203/364 (55%), Gaps = 17/364 (4%) Query: 17 LEPVQLVGPDGTPTAERRYH---RDLPEETLRWLYEMMVVTRELDTEFVNLQRQGELALY 73 +E QL+ P+G A + D+ E LR LY MV+ R D E LQRQG+L ++ Sbjct: 40 IELTQLLTPEGERVASPIFDGFVSDIGAEQLRGLYRDMVLVRRADREGNALQRQGQLGIW 99 Query: 74 TPCRGQEAAQVGAAACLRKTDWLFPQYRELGVYLVRGIPPGHVGVAWRGTWHGGLQFTTK 133 P GQEAAQ+G+ LR TD FP YRE GV RG+ + +R T G F Sbjct: 100 VPLLGQEAAQIGSGRALRPTDMAFPSYREHGVAWARGVDLKDIFGIFRCTDQGSWDFQGS 159 Query: 134 CCAPMSVPIGTQTLHAVGAAMAAQ-------------RLDEDSVTVAFLGDGATSEGDVH 180 P ++ IG Q ++AVG AM + D D T+ + GDGATS+GDVH Sbjct: 160 RLHPYTIVIGNQVVNAVGYAMGQKFDGKVGNASHEDTAADSDEATITYFGDGATSQGDVH 219 Query: 181 EALNFAAVFTTPCVFYVQNNQWAISMPVSRQTAAPSIAHKAIGYGMPGIRVDGNDVLACY 240 E +++V+ P VF+ QNNQWAIS P RQ+ P + +A GYG PG+RVDGNDVLAC Sbjct: 220 EGFVWSSVYDAPVVFFCQNNQWAISEPTERQSRLP-LYQRARGYGFPGVRVDGNDVLACL 278 Query: 241 AVMAEAAARARAGDGPTLIEAVTYRLGPHTTADDPTRYRSQEEVDRWATLDPIPRYRTYL 300 AV A R G+GP LIEA TYR+ HTT+DDPTRYR EE++ W DPI R R +L Sbjct: 279 AVTRWALHTCRNGNGPVLIEAFTYRMDAHTTSDDPTRYRLSEELEVWRLKDPIERVRAHL 338 Query: 301 QDQGLWSQRLEEQVTARAKHVRSELRDAVFDAPDFDVDEVFTTVYAEITPGLQAQREQLR 360 Q + V A A ELRD + PD + +F+ VYAE +P L AQR+ Sbjct: 339 TRTEGADQEFFDAVDAEADEFAVELRDYCVNMPDPPPERIFSNVYAEPSPALDAQRDSYL 398 Query: 361 AELA 364 + LA Sbjct: 399 SYLA 402 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: 433 Number of extensions: 19 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: 411 Length adjustment: 30 Effective length of query: 337 Effective length of database: 381 Effective search space: 128397 Effective search space used: 128397 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: 50 (23.9 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