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_050655903.1 C1M55_RS30495 alpha-ketoacid dehydrogenase subunit beta
Query= SwissProt::P9WIS1 (348 letters) >NCBI__GCF_002893965.1:WP_050655903.1 Length = 334 Score = 357 bits (916), Expect = e-103 Identities = 178/319 (55%), Positives = 228/319 (71%), Gaps = 2/319 (0%) Query: 26 LTMVQAINRALYDAMAADERVLVFGEDVAVEGGVFRVTEGLADTFGADRCFDTPLAESAI 85 LTM QA+N AL D++AAD+ V+VFGEDV GGVFRVT+GL FG DRCFDTPLAES I Sbjct: 4 LTMAQALNTALRDSLAADDNVVVFGEDVGTLGGVFRVTDGLTRDFGDDRCFDTPLAESGI 63 Query: 86 IGIAVGLALRGFVPVPEIQFDGFSYPAFDQVVSHLAKYRTRTRGEVDMPVTVRIPSFGGI 145 IG A+G+A+ GF PV E+QFD F+YPAF+Q+ SH+AK R RT+G + +P+ +R+P GGI Sbjct: 64 IGFAIGMAMAGFRPVVEMQFDAFAYPAFEQIASHVAKIRNRTKGALSIPIVIRVPFAGGI 123 Query: 146 GAAEHHSDSTESYWVHTAGLKVVVPSTPGDAYWLLRHAIACPDPVMYLEPKRRYHGRGMV 205 G EHH DS+E Y+ HT GLKVV PST DAY LLR AI DPV++LEPK+ Y R V Sbjct: 124 GGVEHHCDSSEGYYAHTPGLKVVAPSTVEDAYSLLRSAIEDLDPVIFLEPKKLYFARADV 183 Query: 206 DTSRPEPPIGHAMVRRSGTDVTVVTYGNLVSTALSSADTAEQQHDWSLEVIDLRSLAPLD 265 + + E PIG A+VRR G D T++ YG V AL SA+ A + +EVID+RS+ P D Sbjct: 184 ELTACE-PIGRAVVRRPGRDATLIAYGPSVDVALRSAEAAAAE-GRDIEVIDIRSIVPFD 241 Query: 266 FDTIAASIQRTGRCVVMHEGPRSLGYGAGLAARIQEEMFYQLEAPVLRACGFDTPYPPAR 325 +T+ AS+++TGRC+V+ E G GA +AAR+QE F+ L APVLR GFD PYP + Sbjct: 242 DETVTASVRKTGRCIVIQEAQGFAGVGAEIAARVQERCFHHLHAPVLRVSGFDIPYPAPK 301 Query: 326 LEKLWLPGPDRLLDCVERV 344 LE+ LP DR+LD V+R+ Sbjct: 302 LERHHLPSVDRVLDAVDRL 320 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: 378 Number of extensions: 16 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: 334 Length adjustment: 29 Effective length of query: 319 Effective length of database: 305 Effective search space: 97295 Effective search space used: 97295 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