Align 2-keto-isovalerate dehydrogenase component α subunit (EC 1.2.4.4) (characterized)
to candidate Echvi_1750 Echvi_1750 Pyruvate/2-oxoglutarate dehydrogenase complex, dehydrogenase (E1) component, eukaryotic type, beta subunit
Query= metacyc::MONOMER-11683 (330 letters) >FitnessBrowser__Cola:Echvi_1750 Length = 661 Score = 172 bits (437), Expect = 2e-47 Identities = 109/303 (35%), Positives = 165/303 (54%), Gaps = 19/303 (6%) Query: 11 LTDQEAVDMYRTMLLARKIDERMWLLNRSGKIPFVISCQGQEAAQVGAAFALDREMDYVL 70 L+D + + Y +L+ RKI+E+M LL R GKI S GQEA + A A+ RE +++L Sbjct: 12 LSDGDLLHFYEMLLMPRKIEEKMLLLLRQGKISKWFSGWGQEAISIAAVMAM-REDEFLL 70 Query: 71 PYYRDMGVVLAFGMTAKDLMM------SGFAKAADPNSGGRQMPGHFGQKKNRIVTGSSP 124 P +R++GV G+ L SGF K GR HFG + +V S Sbjct: 71 PMHRNLGVFTGRGLPLGKLFAQFQGKYSGFTK-------GRDRSFHFGSVAHHVVGMISH 123 Query: 125 VTTQVPHAVGIALAGRMEKKDIAAFVTFGEGSSNQGDFHEGANFAAVHKLPVIFMCENNK 184 + Q+ A GIALA ++ + A V G+G++++GDFHE N AAV +LPVIF+ E+N Sbjct: 124 LGPQLAVADGIALASKLGGERKATLVFTGDGATSEGDFHEALNVAAVWQLPVIFVVEHNG 183 Query: 185 YAISVPYDKQVACENISDRAIGYGMPGVTVNGNDPLEVYQAVKEARERARRGEGPTLIET 244 Y +S P +Q + D+ GYGM V V+GN+ LE+Y A+ E R P L+E Sbjct: 184 YGLSTPSAEQFRFKQFIDKGPGYGMEAVKVDGNNVLELYHALSGIAEDIRHRPRPFLVEA 243 Query: 245 ISYRLTPHSSDDDDSSYRGREEVEEAKKSDPLLTYQAYLKETGLLSDE----IEQTMLDE 300 ++YR+ H + + Y + EE +K DP+ ++ YL+E G+L IE+ + ++ Sbjct: 244 MTYRMRGH-EESSGTKYVPKAYFEEGEKYDPVRNFEDYLQEIGVLDQSAKGVIEKRLSEQ 302 Query: 301 IMA 303 I A Sbjct: 303 IEA 305 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: 458 Number of extensions: 15 Number of successful extensions: 4 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: 661 Length adjustment: 33 Effective length of query: 297 Effective length of database: 628 Effective search space: 186516 Effective search space used: 186516 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: 51 (24.3 bits)
This GapMind analysis is from Sep 17 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