Align 3-hydroxyisobutyrate dehydrogenase, mitochondrial; HIBADH; EC 1.1.1.31 (characterized)
to candidate AO353_17140 AO353_17140 2-hydroxy-3-oxopropionate reductase
Query= SwissProt::P31937 (336 letters) >FitnessBrowser__pseudo3_N2E3:AO353_17140 Length = 297 Score = 156 bits (394), Expect = 7e-43 Identities = 96/301 (31%), Positives = 156/301 (51%), Gaps = 7/301 (2%) Query: 36 VASKTPVGFIGLGNMGNPMAKNLMKHGYPLIIYDVFPDACKEFQDAGEQVVSSPADVAEK 95 +A+ + F G+G MG PM + L+ GYPL +++ PD C +AG + V++PA++ + Sbjct: 1 MAALPSLAFAGIGLMGLPMCRRLLAAGYPLTVWNRNPDKCAPLVEAGARQVATPAELCQH 60 Query: 96 ADRIITMLPTSINAIEAYSGANGILKKVKKGSLLIDSSTIDPAVSKELAKE-VEKMGAVF 154 AD ++ L + E GA G+ K G LL+D S+++P ++E+A E V + G + Sbjct: 61 ADLVMLCLANTEVVREVVFGAAGVASGAKTGQLLVDFSSLEPTATREMAAELVSRTGMGW 120 Query: 155 MDAPVSGGVGAARSGNLTFMVGGVEDEFAAAQELLGCMGSNVVYCGAVGTGQAAKICNNM 214 +DAPVSGGV A + +L MVGG + + +L +G V + GAVG GQ K CN M Sbjct: 121 VDAPVSGGVAGAEAASLAIMVGGESADVERVRLVLSSLGQRVTHMGAVGAGQVTKACNQM 180 Query: 215 LLAISMIGTAEAMNLGIRLGLDPKLLAKILNMSSGRCWSSDTYNPVPGVMDGVPSANNYQ 274 ++A + + AE + L R G++ LLA+ L S G S P + + + Sbjct: 181 IVACNALVIAEVVALAERSGVEASLLAEAL--SGGFADSKPLQILAPQMAESRFEPIKWH 238 Query: 275 GGFGTTLMAKDLGLAQDSATSTKSPILLGSLAHQIYRMMCAKGYSKKDFSSVFQFLREEE 334 + KDL A + S + LA Q+ R+ +GY +KD +++ RE + Sbjct: 239 ----VRTLLKDLDGAVKFSREQGSATPISGLAAQLMRLHAGQGYLEKDPATLIHLYREPD 294 Query: 335 T 335 + Sbjct: 295 S 295 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: 237 Number of extensions: 12 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: 336 Length of database: 297 Length adjustment: 27 Effective length of query: 309 Effective length of database: 270 Effective search space: 83430 Effective search space used: 83430 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