Align 3-methyl-2-oxobutanoate dehydrogenase (2-methylpropanoyl-transferring) (EC 1.2.4.4) (characterized)
to candidate GFF2282 PGA1_c23140 acetoin:2,6-dichlorophenolindophenol oxidoreductase subunit alpha
Query= BRENDA::Q72GU1 (367 letters) >FitnessBrowser__Phaeo:GFF2282 Length = 331 Score = 154 bits (388), Expect = 4e-42 Identities = 101/310 (32%), Positives = 159/310 (51%), Gaps = 6/310 (1%) Query: 36 EKLRRLYRDMLAARMLDERYTILIRTGKTSFIAPA-AGHEAAQVAIAHAIRPGFDWVFPY 94 E R+YR M+ R ++ L + K + +G EA V I A++ D + Sbjct: 9 EDYLRMYRQMVRIRSFEDNANQLYLSAKMPGLTHMYSGEEAVAVGICEALKVT-DKITST 67 Query: 95 YRDHGLALALGIPLKELFGQMLATKADPNKGRQMPEHPGSKALNFFTVASPIASHVPPAA 154 +R HG +A G KE+F ++L + +G+ H ++ + + + A Sbjct: 68 HRGHGHCVAKGADFKEMFCELLGKEEGYCRGKGGSMHIADQSNGNLGANAIVGGSMGIAT 127 Query: 155 GAAISMKLLRTGQVAVCTFGDGATSEGDWYAGINFAAVQGAPAVFVCENNFYAISVDYRH 214 G+A + KLL V VC FGDGAT++G Y +N AA+ P ++ CENN Y+ Sbjct: 128 GSAFTAKLLGKDDVTVCFFGDGATAQGLMYEVMNMAALWNLPVIYACENNGYS-EYTKTE 186 Query: 215 QTHSPTIADKAHAFGIPGYLVDGMDVLASYYVVKEAVERARRGEGPSLVELRVYRYGPHS 274 + + +I +A AFGI + VDG DVLA + ++ V RAR+GEGP +E YRY H Sbjct: 187 EIAAGSITARAEAFGIEAHQVDGQDVLAVNELTQKLVARARKGEGPFFMEFMTYRYHGHH 246 Query: 275 SAD-DDSRYRPKEEVAFWRK-KDPIPRFRRFLEARGLWNEEWEEDVREEIRAELERGLKE 332 D + YR KEE W++ +DPI +FR +L +G+ +E+ E + E++ + E + Sbjct: 247 VGDINREYYRSKEEEKDWKENRDPIIKFRGWLVEQGIASEDEIEAMNAEVKKDAEEAVAY 306 Query: 333 AEEAGPVPPE 342 A EA P P + Sbjct: 307 A-EAAPYPDQ 315 Lambda K H 0.320 0.138 0.426 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: 302 Number of extensions: 14 Number of successful extensions: 3 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: 331 Length adjustment: 29 Effective length of query: 338 Effective length of database: 302 Effective search space: 102076 Effective search space used: 102076 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