Align Glyoxylate reductase; EC 1.1.1.26 (uncharacterized)
to candidate WP_057508923.1 ABB28_RS12365 phosphoglycerate dehydrogenase
Query= curated2:Q9YAW4 (335 letters) >NCBI__GCF_001431535.1:WP_057508923.1 Length = 414 Score = 154 bits (388), Expect = 5e-42 Identities = 108/328 (32%), Positives = 164/328 (50%), Gaps = 21/328 (6%) Query: 5 RVFVTREVFPEALELLSK--YYDVEVWDKYQPPPYETLLSKAREADALYTLLTDR--IDC 60 RV + V A+++ + Y +E+ K P KAR ADA + R + Sbjct: 14 RVLLLEGVSQTAVDVFTAAGYSQIELHSKALPEDE----LKARIADAHIVGIRSRSQLSA 69 Query: 61 DLLSQAPRLRIVAQMAVGFDNIDVECATRLGIYVTNTPGVLTEATAEFTWALILAAARRV 120 ++L++A R+ V +G + +D++ A GI V N P T + AE A + R + Sbjct: 70 EVLAEAKRVIAVGCFCIGTNQVDLDAAELAGIPVFNAPYSNTRSVAELVIAEAIMLTRGI 129 Query: 121 VEADHFVRWGEWWRLRTGWHPMMMLGVELRGKTLGILGMGRIGSRVAEIGKAFGMRIIYH 180 + + G W + G H E+RGKTLGI+G G IG++V + ++ G+++I+H Sbjct: 130 PQKNAECHRGGWSKSAAGSH-------EVRGKTLGIIGYGHIGTQVGVLAESLGLQVIFH 182 Query: 181 SRSRKREIEKELGAEYRSLEDLLRESDILSIHLPLTDETRHLIGESELKLMKKTAILVNT 240 K + A SL+DLL SDI+++H+P T T+ +IG +EL M++ A ++N Sbjct: 183 DVEAKLALGNARAAV--SLDDLLERSDIITLHVPETPATQWMIGATELAKMRRGAHVINA 240 Query: 241 GRGAIVDTGALVKALREGWIAAAALDVFEEEPLNP----NHPLTAFKNVVLAPHAASATR 296 RG IVD AL AL G I AALDVF EP PLTA NV+L PH +T Sbjct: 241 ARGTIVDIAALDAALGSGHIGGAALDVFPVEPKGNGDVFESPLTAHDNVILTPHVGGSTL 300 Query: 297 ETRLRMAMMAAENLVAFAQGKVPPNLVN 324 E + + + A LV ++ VN Sbjct: 301 EAQDNIGIEVAAKLVRYSDNGSTLTAVN 328 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: 263 Number of extensions: 14 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: 414 Length adjustment: 30 Effective length of query: 305 Effective length of database: 384 Effective search space: 117120 Effective search space used: 117120 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: 49 (23.5 bits)
This GapMind analysis is from Sep 24 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