Align Putative branched-chain alpha keto acid dehydrogenase E1 subunit beta (characterized, see rationale)
to candidate Echvi_1750 Echvi_1750 Pyruvate/2-oxoglutarate dehydrogenase complex, dehydrogenase (E1) component, eukaryotic type, beta subunit
Query= uniprot:G1UHX5 (328 letters) >FitnessBrowser__Cola:Echvi_1750 Length = 661 Score = 202 bits (515), Expect = 1e-56 Identities = 120/312 (38%), Positives = 180/312 (57%), Gaps = 11/312 (3%) Query: 2 SEITMAKALNTALRDALRDDPRTILFGEDIGALGGVFRITDGLAAEFGDERCFDTPLAES 61 +E + A++ LR ++R +L G+DIG GG F++T G +EFG ER +TPL ES Sbjct: 343 TEKRLVDAISDGLRLSMRQFSNLVLMGQDIGEYGGAFKVTAGFLSEFGAERVRNTPLCES 402 Query: 62 AILGTAVGMAMYGYRPVVEMQFDAFAYPAFEQLVSHVAKLRNRTRGAIGLPLTIRIPYGG 121 AI+G A+G+++ G++ VVEMQF F F Q+V+++AK+ R + IR+P G Sbjct: 403 AIIGAALGLSVKGFKSVVEMQFADFVSCGFNQIVNNLAKV--HYRWGQHADVVIRMPTGA 460 Query: 122 GIGGVEHHSDSSEIYYMATPGLTVVTPATAADAYSLLRRSIASPDPVVFLEPKRLYWRKE 181 G+G HS S+E ++ TPGL ++ P++ DA LL +I P+P +F E K LY + Sbjct: 461 GVGAGPFHSQSNEAWFFHTPGLKILYPSSPQDAKGLLAAAIEDPNPCLFFEHKALY--RS 518 Query: 182 ALGLPVD---TGPLGSAVIRRHGTHATLIAYGPAVTTALEAAEAAAEHGWDLEVIDLRTL 238 +G D T +G A + + G AT++ YG V A E+ ++++DLRTL Sbjct: 519 VIGQVPDEYYTVEIGKAHLVKEGDQATVVTYGMGVHWAKRVMESLDVR---VDLLDLRTL 575 Query: 239 MPLDDATVCASVRRTGRAVVVHEAHGFAGPGAEIAARITERCFYHLEAPVRRVTGFDVPY 298 +P D V SV++T + +++HE G GAEIAA I+E CF L+APV R D P Sbjct: 576 LPWDKEAVEKSVKKTNKVMILHEDCLTGGIGAEIAAWISEHCFECLDAPVMREGSLDTPV 635 Query: 299 P-PPLLERHYLP 309 P LE ++LP Sbjct: 636 PFAANLEENFLP 647 Lambda K H 0.322 0.138 0.418 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: 487 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: 328 Length of database: 661 Length adjustment: 33 Effective length of query: 295 Effective length of database: 628 Effective search space: 185260 Effective search space used: 185260 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: 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