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_012850714.1 TCUR_RS01610 pyruvate dehydrogenase (acetyl-transferring) E1 component subunit alpha
Query= SwissProt::P9WIS3 (367 letters) >NCBI__GCF_000024385.1:WP_012850714.1 Length = 380 Score = 276 bits (706), Expect = 7e-79 Identities = 156/360 (43%), Positives = 206/360 (57%), Gaps = 6/360 (1%) Query: 9 SGMLMSVDLEPVQLVGPDGTPTAERRYHRDLPEETLRWLYEMMVVTRELDTEFVNLQRQG 68 SG+ + E +QL+ P+G Y +L E +R LY +V+ R +D E V L RQG Sbjct: 12 SGLQQAPPPELIQLLTPEGVRVEHPDYPLELTPEEVRALYRDLVMVRRIDMEAVALTRQG 71 Query: 69 ELALYTPCRGQEAAQVGAAACLRKTDWLFPQYRELGVYLVRGIPPGHVGVAWRGTWHGGL 128 EL L+ GQEAAQVG+ L + D +FP YRE GV RG+ P + +RG +GG Sbjct: 72 ELGLWASLLGQEAAQVGSGRALGERDMVFPTYREHGVAWCRGVDPIRLLSLFRGLSNGGW 131 Query: 129 QFTTKCCAPMSVPIGTQTLHAVGAAMAAQR-----LDEDSVTVAFLGDGATSEGDVHEAL 183 ++ IG+QTLHA G AM QR D+ + +A+ GDGATS+GDV+E+ Sbjct: 132 DPAEHNFHLYTIVIGSQTLHATGYAMGIQRDGVLGTDKAAAAIAYFGDGATSQGDVNESF 191 Query: 184 NFAAVFTTPCVFYVQNNQWAISMPVSRQTAAPSIAHKAIGYGMPGIRVDGNDVLACYAVM 243 FA+VF P VF+ QNNQWAIS P+ +QT P + +A G+G PG+RVDGNDV AC AV Sbjct: 192 VFASVFNAPIVFFCQNNQWAISEPLEKQTRIP-LYRRAQGFGFPGLRVDGNDVFACLAVT 250 Query: 244 AEAAARARAGDGPTLIEAVTYRLGPHTTADDPTRYRSQEEVDRWATLDPIPRYRTYLQDQ 303 A AR+G GPTLIEA TYR+G HTT DDPTRYR + E++ W DPI R + YL Sbjct: 251 RRALEAARSGQGPTLIEAYTYRMGAHTTTDDPTRYRLEAELEAWKLKDPIERVKAYLIKN 310 Query: 304 GLWSQRLEEQVTARAKHVRSELRDAVFDAPDFDVDEVFTTVYAEITPGLQAQREQLRAEL 363 V AK ++LR PD + +F VYAE P + ++ + A L Sbjct: 311 EQADAEFLAGVEEEAKQYAADLRRRCLQLPDPEPGAIFEHVYAEPHPLITEEQREYAAYL 370 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: 399 Number of extensions: 20 Number of successful extensions: 5 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: 380 Length adjustment: 30 Effective length of query: 337 Effective length of database: 350 Effective search space: 117950 Effective search space used: 117950 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