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_011781240.1 MVAN_RS20475 alpha-ketoacid dehydrogenase subunit beta
Query= SwissProt::P9WIS1 (348 letters) >NCBI__GCF_000015305.1:WP_011781240.1 Length = 351 Score = 500 bits (1287), Expect = e-146 Identities = 252/356 (70%), Positives = 294/356 (82%), Gaps = 13/356 (3%) Query: 1 MTQIADRP-------ARPDET-LAVAVSDITQSLTMVQAINRALYDAMAADERVLVFGED 52 MTQ+ +RP A P T +AV V+ I ++M QAINRAL+DAM D+RVLVFGED Sbjct: 1 MTQLIERPFGFDDDAAEPQRTPVAVPVAPIAP-ISMAQAINRALHDAMRVDDRVLVFGED 59 Query: 53 VAVEGGVFRVTEGLADTFGADRCFDTPLAESAIIGIAVGLALRGFVPVPEIQFDGFSYPA 112 VA GGVFRVTEGLA+T+G RCFDTPLAESAIIGIAVG+A+RG VPVPEIQFDGF+ PA Sbjct: 60 VATLGGVFRVTEGLAETYGEQRCFDTPLAESAIIGIAVGMAIRGLVPVPEIQFDGFAAPA 119 Query: 113 FDQVVSHLAKYRTRTRGEVDMPVTVRIPSFGGIGAAEHHSDSTESYWVHTAGLKVVVPST 172 FDQ+VSHLAKYR RTRG+VDMPVTVRIPSFGGIGA EHHS+STE+YW+HTAGLKVV PST Sbjct: 120 FDQMVSHLAKYRMRTRGDVDMPVTVRIPSFGGIGAVEHHSESTETYWLHTAGLKVVTPST 179 Query: 173 PGDAYWLLRHAIACPDPVMYLEPKRRYHGRGMVDTSRPEPPIGHAMVRRSGTDVTVVTYG 232 P DAYWLLR+AIA DPV++LEPKRRY + +VDT P PIG A +RR+G DVTV+TYG Sbjct: 180 PTDAYWLLRYAIASRDPVIFLEPKRRYWAKEVVDTGNPADPIGRAAIRRAGDDVTVLTYG 239 Query: 233 NLVSTALSSADTAEQQHDWSLEVIDLRSLAPLDFDTIAASIQRTGRCVVMHEGPRSLGYG 292 LV+TAL++A+ + LEV+DLRSL PLDFDT+AAS+++TGR VVMHEG R++G+G Sbjct: 240 PLVATALNAAELSPH----GLEVVDLRSLNPLDFDTVAASVRKTGRAVVMHEGARTVGFG 295 Query: 293 AGLAARIQEEMFYQLEAPVLRACGFDTPYPPARLEKLWLPGPDRLLDCVERVLRQP 348 A LAARI EE FY LEAPVLRA GFDTPYPPARLEKLWLPG DRLLDCV++ + QP Sbjct: 296 AELAARISEECFYDLEAPVLRATGFDTPYPPARLEKLWLPGVDRLLDCVDKAMGQP 351 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: 515 Number of extensions: 25 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: 351 Length adjustment: 29 Effective length of query: 319 Effective length of database: 322 Effective search space: 102718 Effective search space used: 102718 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