Align 3-hydroxyisobutyrate dehydrogenase; HIBADH; EC 1.1.1.31 (characterized)
to candidate Dsui_3436 Dsui_3436 beta-hydroxyacid dehydrogenase, 3-hydroxyisobutyrate dehydrogenase
Query= SwissProt::P28811 (298 letters) >FitnessBrowser__PS:Dsui_3436 Length = 296 Score = 188 bits (478), Expect = 1e-52 Identities = 112/295 (37%), Positives = 170/295 (57%), Gaps = 11/295 (3%) Query: 4 IAFLGLGNMGGPMAANLLKAGHRVNVFDLQPKAVLGLVEQGAQGADSALQCCEGAEVVIS 63 + F+GLG MG PMA +LL AG+ + V+ +P + L E GA A + + AE+V + Sbjct: 11 VGFIGLGVMGRPMAGHLLDAGYPLTVWGRRPASTAPLAEMGAAVAATPAEVGRRAEIVFT 70 Query: 64 MLPAGQHVESLYLGDDGLLARVAGKPLLIDCSTIAPETARKVAEAAAAKGLTLLDAPVSG 123 ++ +G V+S+ LG+ GL+ +A +++D STIAP AR++A A AA+G+ LDAPVSG Sbjct: 71 VVTSGSDVKSVVLGEAGLIEGLAPGCVVVDMSTIAPGDAREIAAALAARGIHFLDAPVSG 130 Query: 124 GVGGARAGTLSFIVGGPAEGFARARPVLENMGRNIFHAGDHGAGQVAKICNNMLLGILMA 183 G GA TL+ + GG A R +P+L +G+ + H GD+GAGQVAK CN M++ + Sbjct: 131 GEQGAIHATLAIMAGGDAAVLERVKPLLLRLGKTVVHIGDNGAGQVAKACNQMIMVAAIQ 190 Query: 184 GTAEALALGVKNGLDPAVLSEVMKQSSGGNWALNLYNPWPGVMPQAPASNGYAGGFQVRL 243 AEA+ L +G+D + L E + S G+ L VM + A +A G + RL Sbjct: 191 ACAEAMHLAAASGVDTSRLREALLGGSAGSRVLE-------VMGERMAERDFAAGIEARL 243 Query: 244 MNKDLGLALANAQAVQASTPLGA-LARNLFSLHAQADAEHEGLDFSSIQKLYRGK 297 +KD G+ LA A A+ A P+ A + + L +L Q + D SS+ ++ GK Sbjct: 244 HHKDFGILLAEAHALGAPLPVAAQVGQQLNALMGQGMGKD---DTSSLLRVLEGK 295 Lambda K H 0.317 0.135 0.395 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: 254 Number of extensions: 13 Number of successful extensions: 1 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: 298 Length of database: 296 Length adjustment: 26 Effective length of query: 272 Effective length of database: 270 Effective search space: 73440 Effective search space used: 73440 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