Align Glyoxylate reductase; EC 1.1.1.26 (characterized)
to candidate 200048 SO0862 D-3-phosphoglycerate dehydrogenase (NCBI ptt file)
Query= SwissProt::Q9C4M5 (331 letters) >FitnessBrowser__MR1:200048 Length = 409 Score = 156 bits (395), Expect = 7e-43 Identities = 103/328 (31%), Positives = 164/328 (50%), Gaps = 18/328 (5%) Query: 2 KPKVFITRQIPENGIKMIEK--FYEIELWKDPKAPPRGVLLEKVREVDALVTLVTDKVDK 59 K K+ + + ++ + + E+ + IE K L E +++ + ++ Sbjct: 10 KIKILLLEGVHQSAVDVFERAGYTNIEYHKASLGDE--ALHESIKDAHFIGIRSRTQLSA 67 Query: 60 ELLENAPKLKIIAQYAVGYDNIDIEEATKRGIYVTNTPGVLTDATADLAFALLLAVARRI 119 ++L+ A KL I + +G + +D+ A GI V N P T + A+L ++ + R I Sbjct: 68 DVLKRAEKLIAIGCFCIGTNQVDLATAESLGIPVFNAPFSNTRSVAELVLGEIIMLMRGI 127 Query: 120 VEADAFVRSGEWKKSEVGWHPLMFLGYGLKGKTLGIVGFGRIGQALAKRAKGFGMKIIYY 179 E +A G W K+ G Y ++GKTLG++G+G IG L A+ GM+++++ Sbjct: 128 PERNAIAHRGGWMKTAAG-------SYEVRGKTLGVIGYGHIGTQLGILAETLGMRVVFF 180 Query: 180 SRTRKPEAEEEIGAEYVDFETLLKESDFISLHVPLTKETYHMIGEKELKLMKPNAILINT 239 K + E LL ++D +SLHVP T +T MI E M+ +I IN Sbjct: 181 DIEDKLPLGN--AQQIHSMEQLLAQADVVSLHVPETPQTKDMISTAEFAAMRKGSIFINA 238 Query: 240 SRGAVVDTNALIKALKEGWIAGAGLDVFEEEPYYNEELF-----KLKNVVLAPHIGSATH 294 SRG VVD +AL ALKE +AGA +DVF EP N++ F L NV+L PH+G +T Sbjct: 239 SRGTVVDIDALTVALKERHLAGAAIDVFPVEPQSNDDEFISPLRGLDNVLLTPHVGGSTA 298 Query: 295 EAREGMAELVAKNLIAFAKGEIPPNLVN 322 EA+E + VA L ++ + VN Sbjct: 299 EAQENIGIEVAGKLAKYSDNGSTVSAVN 326 Lambda K H 0.317 0.137 0.392 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: 280 Number of extensions: 18 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: 331 Length of database: 409 Length adjustment: 30 Effective length of query: 301 Effective length of database: 379 Effective search space: 114079 Effective search space used: 114079 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 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