Align 3-hydroxyisobutyrate dehydrogenase, mitochondrial; HIBADH; EC 1.1.1.31 (characterized)
to candidate PfGW456L13_4603 2-hydroxy-3-oxopropionate reductase (EC 1.1.1.60)
Query= SwissProt::P31937 (336 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4603 Length = 298 Score = 159 bits (402), Expect = 8e-44 Identities = 98/293 (33%), Positives = 159/293 (54%), Gaps = 9/293 (3%) Query: 42 VGFIGLGNMGNPMAKNLMKHGYPLIIYDVFPDACKEFQDAGEQVVSSPADVAEKADRIIT 101 +GF G+G MG PM + L+ GYPL +++ PD CK +AG + V+SPA++ + AD ++ Sbjct: 8 LGFAGIGLMGLPMCRRLLAAGYPLAVWNRNPDKCKPLVEAGARQVASPAELCQYADVVML 67 Query: 102 MLPTSINAIEAYSGANGILKKVKKGSLLIDSSTIDPAVSKELAKEV-EKMGAVFMDAPVS 160 L + E G G+++ KKG LL+D S+++P ++E+A E+ K G ++D PVS Sbjct: 68 CLADTSVVREVVFGPAGVVEGAKKGQLLVDFSSLEPNATREMAAELAAKTGMGWLDTPVS 127 Query: 161 GGVGAARSGNLTFMVGGVEDEFAAAQELLGCMGSNVVYCGAVGTGQAAKICNNMLLAISM 220 GGV A +G+L MVGG + + +L +G V + G VG GQ K CN M++A + Sbjct: 128 GGVVGAEAGSLAIMVGGELQDLERVRPVLLSLGQRVTHMGGVGAGQVTKACNQMIVACNA 187 Query: 221 IGTAEAMNLGIRLGLDPKLLAKILNMSSGRCWSSDTYNPVPGVMDGVPSANNYQG-GFGT 279 + AE + L R G+D L+A+ L + G S P + + N ++ + Sbjct: 188 LVIAEVVALAERSGVDASLIAEAL--AGGFADSKPLQILAPQM-----AQNRFEPVKWHV 240 Query: 280 TLMAKDLGLAQDSATSTKSPILLGSLAHQIYRMMCAKGYSKKDFSSVFQFLRE 332 + KDL A + S + LA Q+ R+ ++G+ +KD S++ Q RE Sbjct: 241 RTLLKDLDTAVKFSREQGSATPISGLAAQLMRLHGSQGFLEKDPSTLVQMYRE 293 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: 250 Number of extensions: 11 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: 298 Length adjustment: 27 Effective length of query: 309 Effective length of database: 271 Effective search space: 83739 Effective search space used: 83739 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