Align Glyoxylate reductase; EC 1.1.1.26 (uncharacterized)
to candidate CCNA_03322 CCNA_03322 D-3-phosphoglycerate dehydrogenase
Query= curated2:B1L765 (332 letters) >FitnessBrowser__Caulo:CCNA_03322 Length = 526 Score = 192 bits (488), Expect = 2e-53 Identities = 108/300 (36%), Positives = 172/300 (57%), Gaps = 11/300 (3%) Query: 35 SKKVIIERVKDCDALVSLLTDPIDAEVFEAAPKLRIVAQYAVGYDNIDVKEATKRGIYVT 94 SK +I + D D + +D +V AA KLR++A+ +G DN+D+ AT +GI V Sbjct: 34 SKDELIAVIGDYDGIAIRSGAKLDKDVIAAANKLRVIARAGIGVDNVDIPAATAKGIVVM 93 Query: 95 NTPGVLTETTADFAFALLMAAARRVVEADRYVREGKWKVAWHPMMMLGYDVYGRTLGIVG 154 NTP + TTA+ A A++ A AR++ AD + GKW+ +G ++Y +TLG++G Sbjct: 94 NTPFGNSITTAEHAIAMMFALARQIPAADVSTQGGKWE----KNRFMGVELYAKTLGLIG 149 Query: 155 MGRIGAAVARRAKGFGMRILYYDSIRREDFEKELGVEYVPLEKLLEESDFVSLHVPLTEE 214 G IG VA RA G M+++ YD + E+GVE V L++LL +D ++LH PLT++ Sbjct: 150 AGNIGGIVADRALGLKMKVVAYDPFLSPERAVEMGVEKVELDELLARADVITLHTPLTDK 209 Query: 215 TYHMIGEEQLRRMKRTAILVNTSRGKVVDQKALYKALKEGWIAGAGLDVFEQEPIPPDDP 274 T +++ E L + K+ ++VN +RG +VD+ AL K L EG + GA DVF EP ++P Sbjct: 210 TRNILSAENLAKTKKGVMIVNCARGGLVDEAALRKLLDEGHVGGAAFDVFTVEP-AKENP 268 Query: 275 LLKLENVVLAPHAASASHETRSRMAEMVAENLI------AFKRGEIPPNLVNQEVVKVRP 328 L + VV PH ++++E + +A VAE + A P++ +E K++P Sbjct: 269 LFGSDKVVATPHLGASTNEAQENVALQVAEQVSDYLLTGAVTNALNSPSITAEEAPKLKP 328 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: 355 Number of extensions: 18 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: 526 Length adjustment: 31 Effective length of query: 301 Effective length of database: 495 Effective search space: 148995 Effective search space used: 148995 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: 50 (23.9 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