Align 2-keto-isovalerate dehydrogenase component β subunit (EC 1.2.4.4) (characterized)
to candidate Echvi_0200 Echvi_0200 Pyruvate/2-oxoglutarate dehydrogenase complex, dehydrogenase (E1) component, eukaryotic type, beta subunit
Query= metacyc::MONOMER-11684 (327 letters) >FitnessBrowser__Cola:Echvi_0200 Length = 804 Score = 174 bits (442), Expect = 5e-48 Identities = 103/297 (34%), Positives = 162/297 (54%), Gaps = 7/297 (2%) Query: 8 DAINLAMKEEMERDSRVFVLGEDVGRKGGVFKATAGLYEQFGEERVMDTPLAESAIAGVG 67 + + + + D RVF GEDVG+ G V +A AGL E+ GE RV DT + E I G G Sbjct: 475 EVLQACFDQMLSNDPRVFAFGEDVGKIGDVNQAFAGLQEKHGELRVTDTGIREMTIIGQG 534 Query: 68 IGAAMYGMRPIAEMQFADFIMPAVNQIISEAAKIRYRSNNDWSCPIVVRAPYGGGVHGAL 127 IG A+ G+RPIAE+Q+ D+I A+ + + A + YR+ P++VR G + G Sbjct: 535 IGTALRGLRPIAEIQYLDYIYYALMTLTDDLACLHYRTKGGQKAPMIVRT-RGHRLEGVW 593 Query: 128 YHSQSVEAIFANQPGLKIVMPSTPYDAKGLLKAAVRDEDPVLFFEHKRAYRLIKGEVPAD 187 + + AI + GL + +P A G+ +R ++P L E AYR K +P + Sbjct: 594 HSGSPMSAILGSLRGLLVCVPRNMTQAAGMYNTLLRSDEPALMIECLNAYRQ-KELMPTN 652 Query: 188 --DYVLPIGKADVKREGDDITVITYGLCVHFALQAAERLEKDGISAHVVDLRTVYPLDKE 245 ++ +P+G+ +V REG DITV+TYG L AAE+L + G+S V+D++T+ P D + Sbjct: 653 VGEFTVPLGRPEVLREGTDITVVTYGAMCRIVLDAAEQLVEYGVSVEVIDVQTLLPFDVD 712 Query: 246 -AIIEAASKTGKVLLVTEDTKEGSIMSEVAAII-SEHCLFDLDA-PIKRLAGPDIPA 299 I+E+ KT +V+ ED G+ + ++ + + LD+ P+ A P PA Sbjct: 713 HVILESIKKTSRVIFADEDVPGGASAYMMQQVLEKQKAYYQLDSEPVTLSAQPHRPA 769 Lambda K H 0.319 0.136 0.392 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: 559 Number of extensions: 29 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: 327 Length of database: 804 Length adjustment: 34 Effective length of query: 293 Effective length of database: 770 Effective search space: 225610 Effective search space used: 225610 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 (21.8 bits) S2: 52 (24.6 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