Align 3-methyl-2-oxobutanoate dehydrogenase (2-methylpropanoyl-transferring) (EC 1.2.4.4) (characterized)
to candidate 3608766 Dshi_2158 Pyruvate dehydrogenase (acetyl-transferring) (RefSeq)
Query= BRENDA::Q72GU1 (367 letters) >FitnessBrowser__Dino:3608766 Length = 331 Score = 154 bits (388), Expect = 4e-42 Identities = 106/318 (33%), Positives = 159/318 (50%), Gaps = 4/318 (1%) Query: 36 EKLRRLYRDMLAARMLDERYTILIRTGKTS-FIAPAAGHEAAQVAIAHAIRPGFDWVFPY 94 E L YR+ML R +E+ L G F G EA V + A G D Sbjct: 15 EDLMSYYREMLLIRRFEEKAGQLYGMGLIGGFCHLYIGQEAVVVGLEAAAEDG-DKRVTS 73 Query: 95 YRDHGLALALGIPLKELFGQMLATKADPNKGRQMPEHPGSKALNFFTVASPIASHVPPAA 154 YRDHG LA G+ K + ++ + +KG+ H SK +F+ + + VP A Sbjct: 74 YRDHGHMLACGMDPKGVMAELTGREGGYSKGKGGSMHMFSKEKHFYGGHGIVGAQVPIGA 133 Query: 155 GAAISMKLLRTGQVAVCTFGDGATSEGDWYAGINFAAVQGAPAVFVCENNFYAISVDYRH 214 G A S K +V FGDGA ++G Y N A + P VFV ENN YA+ Sbjct: 134 GLAFSDKYRGNDRVTFAYFGDGAANQGQVYETYNMAELWMLPVVFVIENNQYAMGTSVAR 193 Query: 215 QTHSPTIADKAHAFGIPGYLVDGMDVLASYYVVKEAVERARRGEGPSLVELRVYRYGPHS 274 T SP++ ++ A+GIPG VDGMDVLA ++AV R G+GP ++E++ YRY HS Sbjct: 194 STKSPSLWERGAAYGIPGEEVDGMDVLAVKAAGEKAVAHCRAGKGPYILEVKTYRYRGHS 253 Query: 275 SADDDSRYRPKEEVAFWR-KKDPIPRFRRFLEARGLWNEEWEEDVREEIRAELERGLKEA 333 + D ++YR +EEV R ++D I R L + +E+ + + +EI+A + + + Sbjct: 254 MS-DPAKYRTREEVQKVREQRDAIEHVREMLLSGNHASEDELKAIDKEIKAVVNEAAEFS 312 Query: 334 EEAGPVPPEWMFADVFAE 351 E+ ++ D++AE Sbjct: 313 RESPEPALSELWTDIYAE 330 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: 317 Number of extensions: 22 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: 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