Align Glyoxylate reductase; EC 1.1.1.26 (uncharacterized)
to candidate 3607592 Dshi_1001 D-isomer specific 2-hydroxyacid dehydrogenase NAD-binding (RefSeq)
Query= curated2:B1L765 (332 letters) >FitnessBrowser__Dino:3607592 Length = 316 Score = 147 bits (372), Expect = 3e-40 Identities = 97/310 (31%), Positives = 149/310 (48%), Gaps = 6/310 (1%) Query: 1 MKPRVFVTREIPERGLSKIEEHFELDLWKDEAPPSKKVIIERVKDCDALVSLLTDPIDAE 60 M +V +T I R LS+ ++ ++ E + + V D ++ +D Sbjct: 1 MPHQVVITETIDTRALSRFGPEVDV-IYAPELVEDRAACLVAVARADGVIVRNRTQVDRP 59 Query: 61 VFEAAPKLRIVAQYAVGYDNIDVKEATKRGIYVTNTPGVLTETTADFAFALLMAAARRVV 120 +AA +LR++ G DNID+ RGI V G T + A++ + RR Sbjct: 60 FLDAASRLRVIGLLGTGLDNIDMAACAARGISVHPATGANTRSVAEYVITAALMLTRRAF 119 Query: 121 EADRYVREGKWKVAWHPMMMLGYDVYGRTLGIVGMGRIGAAVARRAKGFGMRILYYDSIR 180 + ++EG W + G ++ GR LG+ G G + AVAR AK M IL +D Sbjct: 120 MSTPEMQEGAWP---RGPLGEGGEIAGRKLGLYGCGAVAQAVARLAKPLSMTILGHDPHL 176 Query: 181 REDFEKELGVEYVPLEKLLEESDFVSLHVPLTEETYHMIGEEQLRRMKRTAILVNTSRGK 240 V V +LL +D +SLH+PLT ET I L MK AIL+NT+ G+ Sbjct: 177 GPGHPLWTEVTRVSDAELLARADVLSLHLPLTPETRGRIDATALTAMKPGAILINTAHGE 236 Query: 241 VVDQKALYKALKEGWIAGAGLDVFEQEPIPPDDP--LLKLENVVLAPHAASASHETRSRM 298 +VD +A+ AL+ G + GA LDVFE EP+ D + N++L PH A + E R+ Sbjct: 237 IVDARAVCDALRRGHLGGAALDVFEPEPLGTQDAARFRGVPNLILTPHVAGVTVEADRRV 296 Query: 299 AEMVAENLIA 308 + + +N+ A Sbjct: 297 SALTVDNVRA 306 Lambda K H 0.319 0.137 0.398 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: 229 Number of extensions: 7 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: 332 Length of database: 316 Length adjustment: 28 Effective length of query: 304 Effective length of database: 288 Effective search space: 87552 Effective search space used: 87552 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 (21.8 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