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_037568597.1 BS73_RS01200 alpha-ketoacid dehydrogenase subunit beta
Query= SwissProt::P9WIS1 (348 letters) >NCBI__GCF_000744815.1:WP_037568597.1 Length = 347 Score = 318 bits (814), Expect = 2e-91 Identities = 167/328 (50%), Positives = 219/328 (66%), Gaps = 6/328 (1%) Query: 23 TQSLTMVQAINRALYDAMAADERVLVFGEDVAVEGGVFRVTEGLADTFGADRCFDTPLAE 82 T LTM QAINRAL + + D R LV GEDV GGVFRVT+GL FG R DTPLAE Sbjct: 19 TTGLTMQQAINRALAELLEEDPRTLVLGEDVGRLGGVFRVTDGLQQRFGRRRVMDTPLAE 78 Query: 83 SAIIGIAVGLALRGFVPVPEIQFDGFSYPAFDQVVSHLAKYRTRTRGEVDMPVTVRIPSF 142 SAI+G++VGLA+ G+ P+PE+QFDGF+YPA DQ+V+ LA+ R R+RG + MPVT+R+PS+ Sbjct: 79 SAIVGMSVGLAMAGWKPIPELQFDGFAYPAIDQIVNQLARMRYRSRGALPMPVTLRVPSY 138 Query: 143 GGIGAAEHHSDSTESYWVHTAGLKVVVPSTPGDAYWLLRHAIACPDPVMYLEPKRRYHGR 202 GGI A EHH +S E+ + H GLKVV PSTPG+AY LL+ A+ PDPV+++EPK RY R Sbjct: 139 GGIQAPEHHGESLEAVFAHVPGLKVVSPSTPGEAYRLLKTAVRDPDPVVFMEPKSRYWDR 198 Query: 203 GMVDTSRPEPPIG-----HAMVRRSGTDVTVVTYGNLVSTALSSADTAEQQHDWSLEVID 257 G VD++ G + R G T+VT+G +V L A+ A LEV+D Sbjct: 199 GPVDSAAGAAEDGPEDEPRLRIARPGRHATLVTWGAMVRRCLQVAELAAAD-GVDLEVVD 257 Query: 258 LRSLAPLDFDTIAASIQRTGRCVVMHEGPRSLGYGAGLAARIQEEMFYQLEAPVLRACGF 317 LR L P+D D +AA+++RT R VV+HE PR+ G GA ++A + E F L +PV R G+ Sbjct: 258 LRWLKPVDADGLAAAVRRTRRAVVVHEAPRTAGLGAEISALLMERCFADLRSPVRRVTGY 317 Query: 318 DTPYPPARLEKLWLPGPDRLLDCVERVL 345 D P P LE+ +LP DR+L V+ VL Sbjct: 318 DVPTPAGPLEEHYLPDADRILLAVQNVL 345 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: 396 Number of extensions: 12 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: 348 Length of database: 347 Length adjustment: 29 Effective length of query: 319 Effective length of database: 318 Effective search space: 101442 Effective search space used: 101442 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