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_011604377.1 FRAAL_RS14120 pyruvate dehydrogenase E1 subunit alpha
Query= SwissProt::P9WIS3 (367 letters) >NCBI__GCF_000058485.1:WP_011604377.1 Length = 396 Score = 276 bits (707), Expect = 5e-79 Identities = 164/367 (44%), Positives = 208/367 (56%), Gaps = 16/367 (4%) Query: 4 GSRRPSGMLMSVDLEPVQLVGPDGTPTAERRYHRDLPEETLRWLYEMMVVTRELDTEFVN 63 G RR L+ D EPV+++G TP A R E R LY +V+ R + + Sbjct: 20 GPRRDPAPLLP-DPEPVRILG---TPAA-----RTFDAEVQRELYRRIVLGRRFNQQATT 70 Query: 64 LQRQGELALYTPCRGQEAAQVGAAACLRKTDWLFPQYRELGVYLVRGIPPGHVGVAWRGT 123 L RQG LA+Y GQEA QV AA LR DWLFP YR+ + RG+ P RG Sbjct: 71 LTRQGRLAVYPASTGQEACQVTAAMVLRDVDWLFPSYRDTLAVVARGVRPLDALTLMRGH 130 Query: 124 WHGGLQFTTKCCAPMSVPIGTQTLHAVGAAMAAQ-------RLDEDSVTVAFLGDGATSE 176 H G + AP+S P+ TQ HAVG A AA+ E+ V +A +GDG TSE Sbjct: 131 AHSGYDPYSHRIAPLSTPLATQAPHAVGLAHAARLRAATDPAAAENLVALALVGDGGTSE 190 Query: 177 GDVHEALNFAAVFTTPCVFYVQNNQWAISMPVSRQTAAPSIAHKAIGYGMPGIRVDGNDV 236 GD HEALNFA V P VF VQNN +AIS+P++ Q+AAPS+AHKA+GYG+ G VDGND Sbjct: 191 GDFHEALNFAGVLGAPVVFLVQNNGYAISVPLASQSAAPSLAHKAVGYGIAGRLVDGNDA 250 Query: 237 LACYAVMAEAAARARAGDGPTLIEAVTYRLGPHTTADDPTRYRSQEEVDRWATLDPIPRY 296 LA ++V++ A AR+G GP L+EAVTYRL HT ADD TRYRS EVD W DP+ Sbjct: 251 LAMHSVLSAAVDHARSGRGPVLVEAVTYRLDAHTNADDATRYRSAAEVDAWRARDPLTLL 310 Query: 297 RTYLQDQGLWSQRLEEQVTARAKHVRSELRDAVFDAPDFDVDEVFTTVYAEITPGLQAQR 356 +L+ GL A+ + E+R + PD D D +F VYA+ T L+ Q Sbjct: 311 EGHLRAAGLLDDAGVAAAAQAAEDLAVEIRAQFDNPPDPDPDSLFAHVYAQPTSQLREQA 370 Query: 357 EQLRAEL 363 +L A L Sbjct: 371 AELAARL 377 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: 384 Number of extensions: 16 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: 396 Length adjustment: 30 Effective length of query: 337 Effective length of database: 366 Effective search space: 123342 Effective search space used: 123342 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