Align Glyoxylate reductase; EC 1.1.1.26 (uncharacterized)
to candidate 6938708 Sama_2811 glycerate dehydrogenase (RefSeq)
Query= curated2:Q9YAW4 (335 letters) >FitnessBrowser__SB2B:6938708 Length = 317 Score = 187 bits (475), Expect = 3e-52 Identities = 115/293 (39%), Positives = 167/293 (56%), Gaps = 5/293 (1%) Query: 25 DVEVWDKYQPPPYETLLSKAREADALYTLLTDRIDCDLLSQAPRLRIVAQMAVGFDNIDV 84 D+ +D + P E +LS+A A L T T +D L P L + +A G + +DV Sbjct: 24 DIGPFDVHDRTPKELILSRAAGARFLLTNKTV-LDAATLEAMPSLEYIGVLATGTNVVDV 82 Query: 85 ECATRLGIYVTNTPGVLTEATAEFTWALILAAARRVVEADHFVRWGEWWRLRTGWHPMMM 144 A RLGI VTN PG +A A+ +A +L RV V G+W + Sbjct: 83 AAAKRLGIAVTNVPGYGPDAVAQMGFAHVLHHMSRVSAHHDAVTQGQWSGQADFCFTLGQ 142 Query: 145 LGVELRGKTLGILGMGRIGSRVAEIGKAFGMRIIYHSRSRKREIEKELGAEYRSLEDLLR 204 L L GKTLG++G G I ++A IG AFGM+++ HSRS+ ++ + GA++ +L+ L Sbjct: 143 LE-SLSGKTLGLVGFGDIARQMARIGMAFGMKLLVHSRSKPTDLPE--GAKFVALDTLFA 199 Query: 205 ESDILSIHLPLTDETRHLIGESELKLMKKTAILVNTGRGAIVDTGALVKALREGWIAAAA 264 ESD+LS+H PLTD+TR ++ L LMK+ A+L+NT RG +VD AL AL G + A Sbjct: 200 ESDVLSLHCPLTDDTRDMVNRESLALMKQGALLINTARGGLVDEVALADALNAGRV-RAG 258 Query: 265 LDVFEEEPLNPNHPLTAFKNVVLAPHAASATRETRLRMAMMAAENLVAFAQGK 317 +DV EP PN+PL N+ + PH A AT + R ++ +A ENL AF++G+ Sbjct: 259 VDVLSTEPPAPNNPLLHAANISITPHNAWATVKARQKLLDIAVENLRAFSRGE 311 Lambda K H 0.322 0.136 0.406 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: 253 Number of extensions: 10 Number of successful extensions: 4 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: 335 Length of database: 317 Length adjustment: 28 Effective length of query: 307 Effective length of database: 289 Effective search space: 88723 Effective search space used: 88723 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.9 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