Align 2-keto-isovalerate dehydrogenase component α subunit (EC 1.2.4.4) (characterized)
to candidate Echvi_1221 Echvi_1221 pyruvate dehydrogenase E1 component, alpha subunit
Query= metacyc::MONOMER-11683 (330 letters) >FitnessBrowser__Cola:Echvi_1221 Length = 340 Score = 156 bits (395), Expect = 6e-43 Identities = 107/311 (34%), Positives = 156/311 (50%), Gaps = 6/311 (1%) Query: 20 YRTMLLARKIDERMWLLNRSGKIP-FVISCQGQEAAQVGAAFALDREMDYVLPYYRDMGV 78 Y +MLL R+ +E+ L KI F GQEA GA AL+++ D + YRD Sbjct: 24 YESMLLMRRFEEKAGQLYGQQKIRGFCHLYIGQEACAAGAITALEKD-DKWITAYRDHAH 82 Query: 79 VLAFGMTAKDLMMSGFAKAADPNSG-GRQMPGHFGQKKNRIVTGSSPVTTQVPHAVGIAL 137 L G +M F KA G G M H K+ + G V QVP +GI Sbjct: 83 PLGLGTDPGAVMAELFGKATGTTKGKGGSM--HIFDKERNFMGGHGIVGAQVPMGLGIGF 140 Query: 138 AGRMEKKDIAAFVTFGEGSSNQGDFHEGANFAAVHKLPVIFMCENNKYAISVPYDKQVAC 197 A + + G+G+ QG HE N A ++K+PVIF+ ENN YA+ + Sbjct: 141 AEKYKGTKNLCICHMGDGAVRQGAVHESFNLAMLYKVPVIFVIENNGYAMGTSVKRSSNV 200 Query: 198 ENISDRAIGYGMPGVTVNGNDPLEVYQAVKEARERARRGEGPTLIETISYRLTPHSSDDD 257 +++S Y MP V+G + EV++AV EA ERAR+G+GPTL+E +YR HS D Sbjct: 201 DDLSTLGESYDMPSFAVDGMNVEEVHEAVAEAAERARKGDGPTLLEVRTYRYKGHSM-SD 259 Query: 258 DSSYRGREEVEEAKKSDPLLTYQAYLKETGLLSDEIEQTMLDEIMAIVNEATDEAENAPY 317 YR REEVEE K DP+ + + + +LS++ + + ++ V +A AE +P+ Sbjct: 260 PQKYRTREEVEEYKAKDPIEQVKKTILDNKILSEDDIKEIDAKVKKQVADAVKFAEESPW 319 Query: 318 AAPESALDYVY 328 + A + VY Sbjct: 320 PDGQKAFEDVY 330 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: 268 Number of extensions: 11 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: 340 Length adjustment: 28 Effective length of query: 302 Effective length of database: 312 Effective search space: 94224 Effective search space used: 94224 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 Apr 09 2024. 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