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_037574209.1 BS73_RS19260 alpha-ketoacid dehydrogenase subunit beta
Query= SwissProt::P9WIS1 (348 letters) >NCBI__GCF_000744815.1:WP_037574209.1 Length = 326 Score = 363 bits (933), Expect = e-105 Identities = 187/325 (57%), Positives = 235/325 (72%), Gaps = 2/325 (0%) Query: 22 ITQSLTMVQAINRALYDAMAADERVLVFGEDVAVEGGVFRVTEGLADTFGADRCFDTPLA 81 + + TMV+A+N AL ++ AD + LV GEDV GGVFRVT+GL FG DR DTPLA Sbjct: 1 MAEKYTMVKALNEALRRSLDADPKTLVMGEDVGRLGGVFRVTDGLYKDFGEDRVIDTPLA 60 Query: 82 ESAIIGIAVGLALRGFVPVPEIQFDGFSYPAFDQVVSHLAKYRTRTRGEVDMPVTVRIPS 141 ES I+G A+GL LRG+ PV EIQFDGF YPAFDQ+VS LAK R+ G+V +PVT+RIP Sbjct: 61 ESGIVGTAIGLCLRGYRPVLEIQFDGFVYPAFDQIVSQLAKMHARSLGKVRLPVTIRIPW 120 Query: 142 FGGIGAAEHHSDSTESYWVHTAGLKVVVPSTPGDAYWLLRHAIACPDPVMYLEPKRRYHG 201 GGIGA EHHS+S E+Y+ HTAGLKVV P++P DA+W+LR AIA DPV++LEPKRRY Sbjct: 121 AGGIGAVEHHSESHEAYFAHTAGLKVVAPASPADAHWMLRQAIASDDPVIFLEPKRRYWD 180 Query: 202 RGMVDTSRPEPPIGH-AMVRRSGTDVTVVTYGNLVSTALSSADTAEQQHDWSLEVIDLRS 260 + VD P H A V RSGTD+T++ YG +V L +A A + S+EV+DLRS Sbjct: 181 KAEVDPDGEAPAGLHDARVVRSGTDLTLLAYGPMVKVCLEAA-AAAAEDGRSIEVVDLRS 239 Query: 261 LAPLDFDTIAASIQRTGRCVVMHEGPRSLGYGAGLAARIQEEMFYQLEAPVLRACGFDTP 320 L+P+DFDT+ AS++RTGR VV+HE P LG G+ LAAR+ E FY LEAPVLR GF P Sbjct: 240 LSPVDFDTLEASVRRTGRAVVVHEAPVFLGMGSELAARLTERCFYALEAPVLRVGGFFAP 299 Query: 321 YPPARLEKLWLPGPDRLLDCVERVL 345 YPP+R+E +LP DR+LD V+R + Sbjct: 300 YPPSRVEDTFLPDLDRVLDAVDRAM 324 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: 391 Number of extensions: 15 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: 326 Length adjustment: 28 Effective length of query: 320 Effective length of database: 298 Effective search space: 95360 Effective search space used: 95360 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