Align Glyoxylate reductase; EC 1.1.1.26 (uncharacterized)
to candidate 17613 b3553 putative dehydrogenase (VIMSS)
Query= curated2:B1L765 (332 letters) >FitnessBrowser__Keio:17613 Length = 324 Score = 254 bits (649), Expect = 2e-72 Identities = 143/324 (44%), Positives = 198/324 (61%), Gaps = 3/324 (0%) Query: 1 MKPRVFVTREIPERGLSKIEEHFELDLWKDEAPPSKKVIIERVKDCDALVSLLTDPIDAE 60 MKP V + + +P+ L +++EHF + + +P + + + + L+ + ++A Sbjct: 1 MKPSVILYKALPDDLLQRLQEHFTVHQVANLSPQTVEQNAAIFAEAEGLLGS-NENVNAA 59 Query: 61 VFEAAPKLRIVAQYAVGYDNIDVKEATKRGIYVTNTPGVLTETTADFAFALLMAAARRVV 120 + E PKLR + +VGYDN DV T R I + +TP VLTET AD AL+++ ARRVV Sbjct: 60 LLEKMPKLRATSTISVGYDNFDVDALTARKILLMHTPTVLTETVADTLMALVLSTARRVV 119 Query: 121 EADRYVREGKWKVAWHPMMMLGYDVYGRTLGIVGMGRIGAAVARRAK-GFGMRILYYDSI 179 E V+ G+W + P G DV+ +TLGIVGMGRIG A+A+RA GF M ILY Sbjct: 120 EVAERVKAGEWTASIGPDWY-GTDVHHKTLGIVGMGRIGMALAQRAHFGFNMPILYNARR 178 Query: 180 RREDFEKELGVEYVPLEKLLEESDFVSLHVPLTEETYHMIGEEQLRRMKRTAILVNTSRG 239 ++ E+ Y L+ LL+ESDFV L +PLT+ET+H+ G EQ +MK +AI +N RG Sbjct: 179 HHKEAEERFNARYCDLDTLLQESDFVCLILPLTDETHHLFGAEQFAKMKSSAIFINAGRG 238 Query: 240 KVVDQKALYKALKEGWIAGAGLDVFEQEPIPPDDPLLKLENVVLAPHAASASHETRSRMA 299 VVD+ AL AL++G I AGLDVFEQEP+ D PLL + NVV PH SA+HETR MA Sbjct: 239 PVVDENALIAALQKGEIHAAGLDVFEQEPLSVDSPLLSMANVVAVPHIGSATHETRYGMA 298 Query: 300 EMVAENLIAFKRGEIPPNLVNQEV 323 +NLI +G++ N VN V Sbjct: 299 ACAVDNLIDALQGKVEKNCVNPHV 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: 225 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: 324 Length adjustment: 28 Effective length of query: 304 Effective length of database: 296 Effective search space: 89984 Effective search space used: 89984 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