Align 2-oxoisovalerate dehydrogenase subunit alpha; Branched-chain alpha-keto acid dehydrogenase E1 component alpha chain; BCKDH E1-alpha; EC 1.2.4.4 (characterized)
to candidate BPHYT_RS29360 BPHYT_RS29360 acetoin:2,6-dichlorophenolindophenol oxidoreductase subunit alpha
Query= SwissProt::Q5SLR4 (367 letters) >FitnessBrowser__BFirm:BPHYT_RS29360 Length = 327 Score = 156 bits (394), Expect = 8e-43 Identities = 98/323 (30%), Positives = 160/323 (49%), Gaps = 2/323 (0%) Query: 32 DLEGEKLRRLYRDMLAARMLDERYTILIRTGKT-SFIAPAAGHEAAQVAIAHAIRPGFDW 90 +L E L + YR M R +ER + TG+ F+ AG EA+ V + D+ Sbjct: 6 ELSKEDLLKAYRMMRTIREFEERLHVEFATGEIPGFVHLYAGEEASAVGTMLHLNDA-DY 64 Query: 91 VFPYYRDHGLALALGIPLKELLGQMLATKADPNKGRQMPEHPGSKALNFFTVASPIASHV 150 V +R HG +A G+ ++ ++ ++ K G+ H + + + Sbjct: 65 VATTHRGHGHCIAKGVDVRGMMAEIYGRKTGVCHGKGGSMHIADLSKGMLGANGIVGAGG 124 Query: 151 PPAAGAAISMKLLRTGQVAVCTFGDGATSEGDWYAGINFAAVQGAPAVFIAENNFYAISV 210 P GAA++ K ++G V VC FGDGA+++G + +N A+V PA+F+AENN YA + Sbjct: 125 PLICGAALAAKYKKSGGVGVCFFGDGASNQGVIFESLNLASVWRLPAIFVAENNGYAEAT 184 Query: 211 DYRHQTHSPTIADKAHAFGIPGYLVDGMDVLASYYVVKEAVERARRGEGPSLVELRVYRY 270 + IAD+A FG+PG +VDG D A + + EA+ERAR+G GP+LVE++ RY Sbjct: 185 SSTWSVATDNIADRASGFGMPGVIVDGFDFFAVHEALGEAIERARQGGGPTLVEVKFSRY 244 Query: 271 GPHSSADDDSRYRPKEEVAFWRKKDPIPRFRRFLEARGLWNEEWEEDVREEIRAELERGL 330 H D + P E +KD + RF + + + + V E+++ ++ + Sbjct: 245 FGHFEGDAQTYRAPGEVQKLRDEKDCLKRFEERVVRAEMLSVDQLRGVDAEVKSLIDSAV 304 Query: 331 KEAEEAGPVPPEWMFEDVFAEKP 353 EA+ A E + DV+ P Sbjct: 305 TEAKAAPLPTAEDLLSDVYVSYP 327 Lambda K H 0.320 0.137 0.421 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: 272 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: 327 Length adjustment: 29 Effective length of query: 338 Effective length of database: 298 Effective search space: 100724 Effective search space used: 100724 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 17 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