Align Glyoxylate reductase; EC 1.1.1.26 (uncharacterized)
to candidate WP_011939638.1 GURA_RS14190 D-2-hydroxyacid dehydrogenase
Query= curated2:B1L765 (332 letters) >NCBI__GCF_000016745.1:WP_011939638.1 Length = 330 Score = 177 bits (448), Expect = 4e-49 Identities = 115/296 (38%), Positives = 163/296 (55%), Gaps = 13/296 (4%) Query: 30 DEAPPSKKVIIERVKDCDALVSLLTDPIDAEVFEAAPKLRIVAQYAVGYDNIDVKEATKR 89 D PP K +ER +D + ++ L +DA+ +A PKLR ++ A GY+N+DV A Sbjct: 35 DRTPPELK--LERARDAE-IILLSKVKLDADTLKALPKLRYISLLATGYNNVDVAAAGAL 91 Query: 90 GIYVTNTPGVLTETTADFAFALLMAAARRVVEADRYVREGKW-----KVAWHPMMMLGYD 144 GI V+N P TE+ A FALL+ A V D V+ G+W W ++ + Sbjct: 92 GIPVSNVPAYSTESVAQTTFALLLELAVNVGVHDAAVKAGEWIRCPDHSFWKAPIV---E 148 Query: 145 VYGRTLGIVGMGRIGAAVARRAKGFGMRILYYDSIRREDFEKELGVEYVPLEKLLEESDF 204 + G T+GIVG G IG AVAR A FGMR++ Y +D + V +VPLE+L +D Sbjct: 149 LNGLTIGIVGYGVIGKAVARIAAAFGMRVIAYAPRIPQD-AGPVPVSFVPLEELFAIADV 207 Query: 205 VSLHVPLTEETYHMIGEEQLRRMKRTAILVNTSRGKVVDQKALYKALKEGWIAGAGLDVF 264 V+L+ P T E + L MK A L+N +RG +V++ L AL+ G IAGA LDV Sbjct: 208 VTLNCPQTPENTGFVNSRLLGCMKPGAFLINVARGGLVNEADLAHALRSGQIAGAALDVV 267 Query: 265 EQEPIPPDDPLLKLENVVLAPHAASASHETRSRMAEMVAENLIAFKRGEIPPNLVN 320 EP+ ++PLL N + PH A AS R R+ ++VA N+ +F G P N+VN Sbjct: 268 AHEPMLAENPLLSAPNCIFTPHIAWASLAARRRLMDIVAANVASFLGGS-PINVVN 322 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: 240 Number of extensions: 12 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: 332 Length of database: 330 Length adjustment: 28 Effective length of query: 304 Effective length of database: 302 Effective search space: 91808 Effective search space used: 91808 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: 49 (23.5 bits)
This GapMind analysis is from Apr 09 2024. 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