Align 3-hydroxyisobutyrate dehydrogenase, mitochondrial; HIBADH; EC 1.1.1.31 (characterized)
to candidate 3609054 Dshi_2443 6-phosphogluconate dehydrogenase NAD-binding (RefSeq)
Query= SwissProt::P31937 (336 letters) >FitnessBrowser__Dino:3609054 Length = 289 Score = 117 bits (292), Expect = 5e-31 Identities = 85/252 (33%), Positives = 127/252 (50%), Gaps = 14/252 (5%) Query: 42 VGFIGLGNMGNPMAKNLMKHGYPLIIYDVFPDA-CKEFQDAGEQVVSSPADVAEKADRII 100 VGFIG+G MG MA L+ G+P+ + A D G + + + D + Sbjct: 6 VGFIGVGMMGAGMAGCLLSAGHPVTLLAHRNRAPLTPLLDRGAREAPDAVTLLDGCDVLF 65 Query: 101 TMLPTSINAIEAYSG-ANGILKKVKKGSLLIDSSTIDPAVSKELAKEVEKMGAVFMDAPV 159 T LP + EA +G A+ +L + G + ID++T P S LA ++ GAVF DAPV Sbjct: 66 TCLPDA----EAVAGLADTLLPHTRPGQIWIDTTTSRPETSATLAHRLDAAGAVFSDAPV 121 Query: 160 SGGVGAARSGNLTFMVGGVEDEFAAAQELLGCMGSNVVYCGAVGTGQAAKICNNMLLAIS 219 +GG A+ G LT +VG +F L+G + + G GTG AAK+ NN++ + Sbjct: 122 TGGPKQAQDGALTSLVGCAAAQFDTIASLVGTYSTAIRRFGDAGTGHAAKLLNNLVTQGT 181 Query: 220 MIGTAEAMNLGIRLGLDPKLLAKILNMSSGRCWSSDTYNPVPGVMDGVPSANNYQGG-FG 278 M+ ++A RLG+DP+ L ++ M +G S VP +DG +Y G F Sbjct: 182 MVLLSDAFQAAGRLGVDPRALYEV--MMTGAARSGTLQKAVPPALDG-----DYTGARFS 234 Query: 279 TTLMAKDLGLAQ 290 + AKDLG A+ Sbjct: 235 ISNAAKDLGYAE 246 Lambda K H 0.318 0.133 0.384 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: 251 Number of extensions: 16 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: 336 Length of database: 289 Length adjustment: 27 Effective length of query: 309 Effective length of database: 262 Effective search space: 80958 Effective search space used: 80958 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 (21.7 bits) S2: 48 (23.1 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