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_017601613.1 D471_RS0127595 pyruvate dehydrogenase (acetyl-transferring) E1 component subunit alpha
Query= SwissProt::P9WIS3 (367 letters) >NCBI__GCF_000341125.1:WP_017601613.1 Length = 361 Score = 300 bits (768), Expect = 4e-86 Identities = 153/318 (48%), Positives = 202/318 (63%) Query: 48 YEMMVVTRELDTEFVNLQRQGELALYTPCRGQEAAQVGAAACLRKTDWLFPQYRELGVYL 107 Y +V+ R ++ + L RQG LA+Y GQEA Q GAA L DWLFP YR+ + Sbjct: 41 YASLVIGRRVNDQAGALVRQGRLAVYPSSHGQEACQTGAALALADGDWLFPTYRDTAAVI 100 Query: 108 VRGIPPGHVGVAWRGTWHGGLQFTTKCCAPMSVPIGTQTLHAVGAAMAAQRLDEDSVTVA 167 RG+ P V +G WH G AP + P+ TQ LHAVG A AA+ ED+V +A Sbjct: 101 ARGVDPVEVLTLLKGDWHAGYDPYAHRVAPQATPLATQLLHAVGVAHAARLRGEDTVVMA 160 Query: 168 FLGDGATSEGDVHEALNFAAVFTTPCVFYVQNNQWAISMPVSRQTAAPSIAHKAIGYGMP 227 GDGATSEGD HEALNFAAVF P VF+VQNN++AIS+P++RQTAAPS+AHK +GYG+P Sbjct: 161 LCGDGATSEGDFHEALNFAAVFRAPVVFFVQNNEYAISVPLARQTAAPSLAHKGVGYGVP 220 Query: 228 GIRVDGNDVLACYAVMAEAAARARAGDGPTLIEAVTYRLGPHTTADDPTRYRSQEEVDRW 287 G RVDGND A +V+ A A AR+GDGP L+EA TYR+ HT ADD +RYRS EEVD W Sbjct: 221 GHRVDGNDAAAVLSVLDRAVASARSGDGPQLVEAHTYRMQAHTNADDASRYRSDEEVDPW 280 Query: 288 ATLDPIPRYRTYLQDQGLWSQRLEEQVTARAKHVRSELRDAVFDAPDFDVDEVFTTVYAE 347 DP+ R +L+ + ++ ++T RA+ V + +R+ + + D + E+F V++ Sbjct: 281 VARDPLLRMEAFLKRKRALTKARRAEITERAEAVAAAMREGLAEDTDPEPSELFAHVFSS 340 Query: 348 ITPGLQAQREQLRAELAR 365 TP L Q L EL+R Sbjct: 341 PTPQLAEQAAFLADELSR 358 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: 350 Number of extensions: 14 Number of successful extensions: 1 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 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