Align 3-hydroxyisobutyrate dehydrogenase; HIBADH; EC 1.1.1.31 (characterized)
to candidate HSERO_RS04805 HSERO_RS04805 3-hydroxyisobutyrate dehydrogenase
Query= SwissProt::P28811 (298 letters) >FitnessBrowser__HerbieS:HSERO_RS04805 Length = 288 Score = 154 bits (389), Expect = 2e-42 Identities = 100/293 (34%), Positives = 146/293 (49%), Gaps = 14/293 (4%) Query: 1 MTDIAFLGLGNMGGPMAANLLKAGHRVNVFDLQPKAVLGLVEQGAQGADSALQCCEGAEV 60 M I +GLGNMG MA +L + G+ V +D Q L +QG DS E+ Sbjct: 1 MKKIGVIGLGNMGRGMAFSLQRGGYEVLGYDAQESTRTALAQQGLHCVDSIAALAPAVEM 60 Query: 61 VISMLPAGQHVESLYLGDDGLLARVAGKPLLIDCSTIAPETARKVAEAAAAKGLTLLDAP 120 V+ LP VE + G+ GLL A +++D +T P + R++A A G+ L+DAP Sbjct: 61 VVLSLPTSDIVEQVVEGEGGLLQHGAPGLVIVDTTTADPNSTRRLAARLQAAGMELVDAP 120 Query: 121 VSGGVGGARAGTLSFIVGGPAEGFARARPVLENMGRNIFHAGDHGAGQVAKICNNMLLGI 180 VSGG GA T+ ++GG AE AR PVL M H G GAG VAK+ NN++ G Sbjct: 121 VSGGPKGAATATMGMVIGGSAETVARIEPVLAVMSAKRVHVGPVGAGHVAKLLNNLVTGT 180 Query: 181 LMAGTAEALALGVKNGLDPAVLSEVMKQSSGGNWALNLYNP-WPGVMPQAPASNGYAGGF 239 + EA + GLD + + + S + + ++ P W + + GF Sbjct: 181 HLLIAGEAARIAAAAGLDARQIFQGLAAGSANSKVIEVFYPTW-------IFNEAFDSGF 233 Query: 240 QVRLMNKDLGLALANAQAVQASTPLGALARNLF--SLHAQADAEHEGLDFSSI 290 ++LM KDL LA+ + +++TPL A L+ S+ ADAE DF+ I Sbjct: 234 TMKLMRKDLRLAMNLIEETRSTTPLAREAGRLWARSVEGLADAE----DFNRI 282 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: 230 Number of extensions: 7 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: 298 Length of database: 288 Length adjustment: 26 Effective length of query: 272 Effective length of database: 262 Effective search space: 71264 Effective search space used: 71264 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