Align 2-keto-isovalerate dehydrogenase component α subunit (EC 1.2.4.4) (characterized)
to candidate WP_082126407.1 AAV99_RS09615 pyruvate dehydrogenase (acetyl-transferring) E1 component subunit alpha
Query= metacyc::MONOMER-11683 (330 letters) >NCBI__GCF_001013305.1:WP_082126407.1 Length = 368 Score = 156 bits (394), Expect = 9e-43 Identities = 106/314 (33%), Positives = 165/314 (52%), Gaps = 11/314 (3%) Query: 12 TDQEAVDMYRTMLLARKIDERMWLLNRSGKIP-FVISCQGQEAAQVGAAFALDREMDYVL 70 +D++ + Y MLL R+ +E+ L G I F GQEA +G ALD ++D V+ Sbjct: 49 SDEQLLHFYEQMLLIRRFEEKAGQLYGLGLIGGFCHLYIGQEAVAIGLQSALDSDVDSVI 108 Query: 71 PYYRDMGVVLAFGMTAKDLM--MSGFAKAADPNSGGRQMPGHFGQKKNRIVTGSSPVTTQ 128 YRD G +LA+G+ +M ++G A GG H +++ G V Q Sbjct: 109 TGYRDHGHMLAYGIDPNVIMAELTGRAAGISKGKGGSM---HMFSTEHKFYGGHGIVGAQ 165 Query: 129 VPHAVGIALAGRMEKKDIAAFVTFGEGSSNQGDFHEGANFAAVHKLPVIFMCENNKYAIS 188 V G+A+A + FG+G++NQG +E N AA+ KLP++F+ ENN+YA+ Sbjct: 166 VSLGGGLAMAHQYRGDGGLCLAYFGDGAANQGQVYETMNMAALWKLPMVFVVENNQYAMG 225 Query: 189 VPYDKQVACENISDRAIGYGMPGVTVNGNDPLEVYQAVKEARERARRGEGPTLIETISYR 248 ++ A R + +PG+ VNG D LEV QA + A + R G GP L+E +YR Sbjct: 226 TAVNRSSAETEFYRRGTAFRIPGMEVNGMDVLEVRQAAEIAFKYVREGNGPVLMECNTYR 285 Query: 249 LTPHSSDDDDSSYRGREEVEEAKKS-DPLLTYQAYLKETGLLSDEIEQTMLDE-IMAIVN 306 HS D + YR REEV++ +++ DP+ + L GL D+ + +D+ I A+V+ Sbjct: 286 YRGHSM-SDPAKYRTREEVQDQRENHDPIERLKKELNTAGL--DDAKLKEIDKGIRAVVS 342 Query: 307 EATDEAENAPYAAP 320 A D +E++P P Sbjct: 343 AAADFSESSPEPQP 356 Lambda K H 0.316 0.132 0.377 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: 260 Number of extensions: 10 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: 330 Length of database: 368 Length adjustment: 29 Effective length of query: 301 Effective length of database: 339 Effective search space: 102039 Effective search space used: 102039 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 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