Align tartronate semialdehyde reductase 2 (characterized)
to candidate Dsui_3438 Dsui_3438 beta-hydroxyacid dehydrogenase, 3-hydroxyisobutyrate dehydrogenase
Query= ecocyc::G6278-MONOMER (292 letters) >FitnessBrowser__PS:Dsui_3438 Length = 299 Score = 246 bits (628), Expect = 4e-70 Identities = 131/292 (44%), Positives = 179/292 (61%), Gaps = 5/292 (1%) Query: 1 MKLGFIGLGIMGTPMAINLARAGHQLHVTTIGPVA-DELLSLGAVSVETARQVTEASDII 59 M++GFIGLGIMG PMA+NL + GH +HV P + LL GAV + V +++ Sbjct: 1 MEIGFIGLGIMGRPMALNLLKGGHGVHVWARRPESMAPLLEAGAVGCSSPAAVAGQVEVV 60 Query: 60 FIMVPDTPQVEEVLFGENGCTK----ASLKGKTIVDMSSISPIETKRFARQVNELGGDYL 115 MV D P V +V+ G +G A G VDMS+I+P + A ++ G D++ Sbjct: 61 ISMVADAPDVAQVMLGPDGVAAGAEGAGKHGLVAVDMSTIAPAAARDLAARLQARGVDFV 120 Query: 116 DAPVSGGEIGAREGTLSIMVGGDEAVFERVKPLFELLGKNITLVGGNGDGQTCKVANQII 175 DAPVSGGE+GA G+LSIM GG F + P F LG+N+ VG G GQ K NQI+ Sbjct: 121 DAPVSGGEVGAIAGSLSIMAGGSAEAFAKALPAFLCLGQNVVHVGAAGAGQVAKACNQIV 180 Query: 176 VALNIEAVSEALLFASKAGADPVRVRQALMGGFASSRILEVHGERMIKRTFNPGFKIALH 235 + + AV+EA FA +AG DP +VR+AL+GGFA SRILE HG+RM++R F PGFK +H Sbjct: 181 TGMGVLAVAEAFNFARQAGVDPAKVREALLGGFAYSRILENHGQRMLERNFKPGFKSWMH 240 Query: 236 QKDLNLALQSAKALALNLPNTATCQELFNTCAANGGSQLDHSALVQALELMA 287 QKDLN+ +QSA L L LP A ++FN +G + D A+++ LE ++ Sbjct: 241 QKDLNIVMQSAHELGLCLPGAAATAQMFNAMVGSGLEEEDSVAVLKLLERLS 292 Lambda K H 0.318 0.135 0.376 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: 239 Number of extensions: 5 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: 292 Length of database: 299 Length adjustment: 26 Effective length of query: 266 Effective length of database: 273 Effective search space: 72618 Effective search space used: 72618 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