Align 2-hydroxy-3-oxopropionate reductase; EC 1.1.1.60; Tartronate semialdehyde reductase; TSAR (uncharacterized)
to candidate Synpcc7942_1857 Synpcc7942_1857 3-hydroxyacid dehydrogenase
Query= curated2:P77161 (292 letters) >FitnessBrowser__SynE:Synpcc7942_1857 Length = 288 Score = 111 bits (278), Expect = 2e-29 Identities = 90/294 (30%), Positives = 139/294 (47%), Gaps = 12/294 (4%) Query: 1 MKLGFIGLGIMGTPMAINLARAGHQLHV-TTIGPVADELLSLGAVSVETARQVTEASDII 59 M+ G IG G++GT +A L G L V + L++LGA T + ++ Sbjct: 1 MRCGLIGTGLLGTAIAERLLTVGQLLTVWNRTAERSQPLVALGATIAPTPAALLADCEVC 60 Query: 60 FIMVPDTPQVEEVLFGENGCTKASLKGKTIVDMSSISPIETKRFARQVNELGGDYLDAPV 119 +++ D + L E +++ L GKTI+ M +ISP E++ A Q+ GG YL+APV Sbjct: 61 LLLLSDAEAIAATLLTEE--SRSQLVGKTIIQMGTISPAESRAIADQIAAAGGQYLEAPV 118 Query: 120 SGGEIGAREGTLSIMVGGDEAVFERVKPLFELLGKNITLVGGNGDGQTCKVA-NQIIVAL 178 G AR GTL +MVG + AVFE+ + L L +G G T K+A NQ+I +L Sbjct: 119 LGSLPEARNGTLIVMVGAEPAVFEQWRSLLCHLSPEPEWIGPIGTAATLKLALNQLIGSL 178 Query: 179 -NIEAVSEALLFASKAGADPVR--VRQALMGGFASSRILEVHGERMIKRTF-NPGFKIAL 234 + S ALL S +P +RQ+ + + L R++ + NP F Sbjct: 179 TSAFGGSLALLQRSGLAVEPFMAILRQSALYAPTFDKKL----SRLLSHQYDNPNFPTTH 234 Query: 235 HQKDLNLALQSAKALALNLPNTATCQELFNTCAANGGSQLDHSALVQALELMAN 288 KDL L ++A L + + + A G D+SAL +A+ +N Sbjct: 235 LAKDLRLFRETAADLGITTDAVEGVESIVQKAIAQGWGDQDYSALYEAINPDSN 288 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: 202 Number of extensions: 10 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: 288 Length adjustment: 26 Effective length of query: 266 Effective length of database: 262 Effective search space: 69692 Effective search space used: 69692 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