Align 3-methyl-2-oxobutanoate dehydrogenase subunit beta; Branched-chain alpha-ketoacid dehydrogenase E1 component subunit beta; BCKADH E1-beta; EC 1.2.4.4 (characterized)
to candidate WP_084704192.1 BS73_RS19370 alpha-ketoacid dehydrogenase subunit beta
Query= SwissProt::P9WIS1 (348 letters) >NCBI__GCF_000744815.1:WP_084704192.1 Length = 373 Score = 341 bits (874), Expect = 2e-98 Identities = 173/320 (54%), Positives = 218/320 (68%), Gaps = 3/320 (0%) Query: 27 TMVQAINRALYDAMAADERVLVFGEDVAVEGGVFRVTEGLADTFGADRCFDTPLAESAII 86 TM QA+NRAL DA+ AD V + GEDV GGVFRVT+GL FG DRC DTPLAE+ I+ Sbjct: 38 TMAQALNRALRDALRADPSVHLLGEDVGALGGVFRVTDGLTAEFGEDRCTDTPLAEAGIV 97 Query: 87 GIAVGLALRGFVPVPEIQFDGFSYPAFDQVVSHLAKYRTRTRGEVDMPVTVRIPSFGGIG 146 G AVG+A+ G PV E+QFD F+YPAF+Q+ SH+AK R RT G + +P+TVRIP GGIG Sbjct: 98 GTAVGMAMYGLRPVVELQFDAFAYPAFEQLASHVAKMRNRTAGRLPLPLTVRIPYGGGIG 157 Query: 147 AAEHHSDSTESYWVHTAGLKVVVPSTPGDAYWLLRHAIACPDPVMYLEPKRRYHGRGMVD 206 EHH DS+E+Y+VHT GL V+ P+T DAY +LR AIA DPV++LEPKR Y + D Sbjct: 158 GVEHHGDSSEAYYVHTPGLHVMAPATVEDAYGMLRAAIASDDPVVFLEPKRLYWSKAEWD 217 Query: 207 TSRP--EPPIGHAMVRRSGTDVTVVTYGNLVSTALSSADTAEQQHDWSLEVIDLRSLAPL 264 P P G A++RR G ++ YG V L +A+ A + W L V+DLRSL P Sbjct: 218 PEAPAATAPPGRAVLRREGRSAVLIAYGPSVPVCLEAAEAA-RADGWDLAVLDLRSLVPF 276 Query: 265 DFDTIAASIQRTGRCVVMHEGPRSLGYGAGLAARIQEEMFYQLEAPVLRACGFDTPYPPA 324 D +T+ A+++RTGR VV+HE G GA +AAR+ E F+ LEAPVLR GFD PYPP Sbjct: 277 DDETVCAAVRRTGRAVVVHESSGFAGVGAEIAARVTERCFHHLEAPVLRVAGFDIPYPPP 336 Query: 325 RLEKLWLPGPDRLLDCVERV 344 LE+ LPG DR+LD V R+ Sbjct: 337 MLERHHLPGVDRILDAVARL 356 Lambda K H 0.321 0.137 0.417 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: 457 Number of extensions: 25 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: 348 Length of database: 373 Length adjustment: 29 Effective length of query: 319 Effective length of database: 344 Effective search space: 109736 Effective search space used: 109736 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 (21.9 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