Align Glyoxylate reductase; EC 1.1.1.26 (uncharacterized)
to candidate 351103 BT1575 putative dehydrogenase (NCBI ptt file)
Query= curated2:B1L765 (332 letters) >FitnessBrowser__Btheta:351103 Length = 333 Score = 153 bits (387), Expect = 5e-42 Identities = 96/305 (31%), Positives = 157/305 (51%), Gaps = 22/305 (7%) Query: 20 EEHFELDLWKDEAPPSKKVIIERVKDCDALVSLLTDPIDAEVFEA--APKLRIVAQYAVG 77 E FE +K + ++ + V DA+ + D DAEV A A ++++A G Sbjct: 24 EFRFEFRYYKGHLNKNNVLLTQGV---DAVCIFVNDTADAEVIHAMAANGVKLLALRCAG 80 Query: 78 YDNIDVKEATKRGIYVTNTPGVLTETTADFAFALLMAAARRVVEADRYVREGKWKVAWHP 137 ++N+D+ A GI V P A++ AL+++ R++ A ++G + + H Sbjct: 81 FNNVDLNAAATAGITVVRVPAYSPYAVAEYTVALMLSLNRKIPRASWRTKDGNFSL--HG 138 Query: 138 MMMLGYDVYGRTLGIVGMGRIGAAVARRAKGFGMRILYYDSIRREDFEKELGVEYVPLEK 197 +M G+D++G+T GI+G G+I + KGFGM IL YD +F +E + Y L++ Sbjct: 139 LM--GFDMHGKTAGIIGTGKIAKILIHILKGFGMNILAYDLYPDYNFAREEQIVYTSLDE 196 Query: 198 LLEESDFVSLHVPLTEETYHMIGEEQLRRMKRTAILVNTSRGKVVDQKALYKALKEGWIA 257 L SD +SLH PLTE T ++I + + +MK +++NT RG+++ AL + LK I Sbjct: 197 LYHSSDIISLHCPLTEATKYLINDYSISKMKDGVMIINTGRGQLIHTNALIEGLKNKKIG 256 Query: 258 GAGLDVFEQEP----------IPPDDPLLKL---ENVVLAPHAASASHETRSRMAEMVAE 304 AGLDV+E+E I DD L +L NV++ H A + E +A + Sbjct: 257 SAGLDVYEEESEYFYEDQSDRIIDDDVLARLLSFNNVIVTSHQAFFTREAMGNIAMTTLQ 316 Query: 305 NLIAF 309 N+ F Sbjct: 317 NIKDF 321 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: 221 Number of extensions: 9 Number of successful extensions: 2 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: 333 Length adjustment: 28 Effective length of query: 304 Effective length of database: 305 Effective search space: 92720 Effective search space used: 92720 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 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