Align 2-keto-isovalerate dehydrogenase component α subunit (EC 1.2.4.4) (characterized)
to candidate GFF1392 Psest_1429 Pyruvate/2-oxoglutarate dehydrogenase complex, dehydrogenase (E1) component, eukaryotic type, alpha subunit
Query= metacyc::MONOMER-11683 (330 letters) >FitnessBrowser__psRCH2:GFF1392 Length = 329 Score = 163 bits (412), Expect = 6e-45 Identities = 116/322 (36%), Positives = 161/322 (50%), Gaps = 17/322 (5%) Query: 19 MYRTMLLARKIDERMWLLNRSGKIPFVISCQG-----------QEAAQVGAAFALDREMD 67 MY ML +R ++E + + GK P +G QE VG L+ E D Sbjct: 12 MYEQMLTSRYMEESIERIYMEGKTPVFNMAKGPIPGEMHLSNGQEPCAVGVCAHLEAE-D 70 Query: 68 YVLPYYRDMGVVLAFGMTAKDLMMSGFAKAADPNSGGRQMPGHFGQKKNRIVTGSSPVTT 127 V +R + +A G+ ++M F KA SGGR GH R+ S + Sbjct: 71 IVTATHRPHHIAVAKGVDLNEMMAEIFGKATGL-SGGRG--GHMHLFDGRVNFSCSGIIA 127 Query: 128 Q-VPHAVGIALAGRMEKKDIAAFVTFGEGSSNQGDFHEGANFAAVHKLPVIFMCENNKYA 186 + + AVG AL+ +M+ K A GEG++NQG FHE N AA+ KLPV+F+ E+N + Sbjct: 128 EGMGPAVGAALSRQMQGKPGVAVSFIGEGAANQGAFHETLNLAALWKLPVVFVIEDNAWG 187 Query: 187 ISVPYDKQVACENISDRAIGYGMPGVTVNGNDPLEVYQAVKEARERARRGEGPTLIETIS 246 ISV RA YGMPGV V NDP V++A EA ERAR G GPTLIE + Sbjct: 188 ISVAKASATCIAQHHVRAAAYGMPGVFVENNDPDGVFRAAGEAIERARAGGGPTLIEIET 247 Query: 247 YRLTPHSSDDDDSSYRGREEVEEAKKSDPLLTYQAYLKETGLLSDEIEQTMLDEIMAIVN 306 YRL H D + +YR E + K DP+ Y+ L + G+LS+ + + ++ Sbjct: 248 YRLAGHFMGDGE-TYRPEGEKDGLIKKDPIPGYRQRLIDEGVLSEAQAEDIAARARGRID 306 Query: 307 EATDEAENAPYAAPESALDYVY 328 EA A +PY PE AL+ V+ Sbjct: 307 EAVQFARESPYPRPEEALEKVF 328 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: 245 Number of extensions: 10 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: 330 Length of database: 329 Length adjustment: 28 Effective length of query: 302 Effective length of database: 301 Effective search space: 90902 Effective search space used: 90902 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 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