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_004514777.1 GMET_RS12610 pyruvate dehydrogenase (acetyl-transferring) E1 component subunit alpha
Query= SwissProt::P9WIS3 (367 letters) >NCBI__GCF_000012925.1:WP_004514777.1 Length = 352 Score = 276 bits (705), Expect = 8e-79 Identities = 146/350 (41%), Positives = 205/350 (58%), Gaps = 2/350 (0%) Query: 8 PSGMLMSVDLEPVQLVGPDGTPTAERRYHRDLPEETLRWLYEMMVVTRELDTEFVNLQRQ 67 P +L + ++ ++++ PDGT A+ L + LR +Y ++++TR D + LQR+ Sbjct: 2 PESILATFTVKRLEIIAPDGT--ADEDLVPGLSGDELRRIYYLLLLTRAYDGRALALQRE 59 Query: 68 GELALYTPCRGQEAAQVGAAACLRKTDWLFPQYRELGVYLVRGIPPGHVGVAWRGTWHGG 127 G L Y GQEAAQVG+A + + DW+FP +RE+GV+L G P + W G G Sbjct: 60 GRLGTYPSVLGQEAAQVGSAFAIHERDWVFPSFREMGVHLTLGYPAHQLFQYWGGDERGM 119 Query: 128 LQFTTKCCAPMSVPIGTQTLHAVGAAMAAQRLDEDSVTVAFLGDGATSEGDVHEALNFAA 187 P+SV +GT HA GAA+AA+ + +A+ GDG TS+GD HE N A Sbjct: 120 RTPDGMNIFPISVSVGTHIPHAAGAALAAKLRGDPIAVIAYFGDGGTSKGDFHEGFNLAG 179 Query: 188 VFTTPCVFYVQNNQWAISMPVSRQTAAPSIAHKAIGYGMPGIRVDGNDVLACYAVMAEAA 247 V P VF QNNQWAIS+P+S QTA+ S+A KA+ YG GI+VDGNDVLA Y EA Sbjct: 180 VMGLPTVFICQNNQWAISVPLSAQTASRSLAQKALAYGFDGIQVDGNDVLAVYRATREAL 239 Query: 248 ARARAGDGPTLIEAVTYRLGPHTTADDPTRYRSQEEVDRWATLDPIPRYRTYLQDQGLWS 307 +AR+G GPT IE +TYR+ HTT+DD +RYRS EE+++W DPI RY +L +GLW+ Sbjct: 240 EKARSGGGPTFIECLTYRMSDHTTSDDASRYRSPEEMEQWRERDPILRYERFLAKRGLWN 299 Query: 308 QRLEEQVTARAKHVRSELRDAVFDAPDFDVDEVFTTVYAEITPGLQAQRE 357 + ++ +A E P E+F V E++ L+ QRE Sbjct: 300 EDYAAEMKGKAGGEIDEAVRRYESVPPPAPGEMFNFVSGELSARLRRQRE 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: 330 Number of extensions: 8 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: 352 Length adjustment: 29 Effective length of query: 338 Effective length of database: 323 Effective search space: 109174 Effective search space used: 109174 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