Align 2-keto-isovalerate dehydrogenase component α subunit (EC 1.2.4.4) (characterized)
to candidate AZOBR_RS04795 AZOBR_RS04795 acetoin:2 6-dichlorophenolindophenol oxidoreductase subunit alpha
Query= metacyc::MONOMER-11683 (330 letters) >FitnessBrowser__azobra:AZOBR_RS04795 Length = 327 Score = 141 bits (356), Expect = 2e-38 Identities = 102/321 (31%), Positives = 154/321 (47%), Gaps = 7/321 (2%) Query: 11 LTDQEAVDMYRTMLLARKIDERMWLLNRSGKIP-FVISCQGQEAAQVGAAFALDREMDYV 69 L + + YRTM R+ +ER+ + G IP FV G+EA G L+ + D + Sbjct: 8 LDKADLLQAYRTMRTIREFEERLHIDFAKGDIPGFVHLYAGEEACATGIMMHLN-DNDRI 66 Query: 70 LPYYRDMGVVLAFGMTAKDLMMSGFAKAADPNSG-GRQMPGHFGQKKNRIVTGSSPVTTQ 128 +R G +A G+ ++M + ++ G G M H ++ + + Sbjct: 67 ASTHRGHGHCIAKGVDVHEMMAEIYGRSTGACRGKGGSM--HIADLSKGMMGANGILGAG 124 Query: 129 VPHAVGIALAGRMEKKDIAAFVTFGEGSSNQGDFHEGANFAAVHKLPVIFMCENNKYAIS 188 P G ALA + G+G+SNQG F E N AAV LPV+F+ ENN YA S Sbjct: 125 APLICGAALAAKFRGDGGVGITFVGDGASNQGTFLESMNLAAVWNLPVVFVVENNGYAES 184 Query: 189 VPYDKQVACENISDRAIGYGMPGVTVNGNDPLEVYQAVKEARERARRGEGPTLIETISYR 248 + V+C++ DRA G+G+PGVTV+G D V++A E RAR G GP L+E R Sbjct: 185 TAMEWAVSCDSYIDRATGFGLPGVTVDGTDFFAVHEAAGEIIRRAREGGGPALLECNMVR 244 Query: 249 LTPHSSDDDDSSYRGREEVEEAKKS-DPLLTYQAYLKETGLLSDEIEQTMLDEIMAIVNE 307 H + D +YR + EVE + + D + L ETG ++ + + E+ A++ + Sbjct: 245 FYGH-FEGDAQTYRAKGEVETLRANRDCIKLLAQRLTETGTVAPAELEAIDREVNALIED 303 Query: 308 ATDEAENAPYAAPESALDYVY 328 A A+ AP L VY Sbjct: 304 AVRCAKAAPLPVAADLLKDVY 324 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: 257 Number of extensions: 14 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: 327 Length adjustment: 28 Effective length of query: 302 Effective length of database: 299 Effective search space: 90298 Effective search space used: 90298 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