Align D-3-phosphoglycerate dehydrogenase; EC 1.1.1.95 (characterized, see rationale)
to candidate AO353_04850 AO353_04850 bifunctional glyoxylate/hydroxypyruvate reductase B
Query= uniprot:Q6LWW6 (523 letters) >FitnessBrowser__pseudo3_N2E3:AO353_04850 Length = 324 Score = 179 bits (455), Expect = 1e-49 Identities = 96/270 (35%), Positives = 158/270 (58%), Gaps = 4/270 (1%) Query: 46 VIRSGTTATREIIEASENLKVIARAGVGVDNVDLDAATEKGIVVVNAPDASSISVAELLF 105 +I G R +E + L+V++ VG DN DL E+GI++ N PD + S A+L F Sbjct: 49 LIGVGRKLGRAQLENASKLEVVSSVSVGYDNYDLAYFNERGIMLTNTPDVLTESTADLAF 108 Query: 106 GMMLAAARNIPQATASIKSGKWDRK---SFKGMEIYGKTLGIVGLGRIGQQVAKRAQ-AF 161 +++++AR + + A K+G+W G +++GKTLGIVG+G IG +A+R + F Sbjct: 109 ALLMSSARRVAELDAWTKAGQWQATVGAPLFGCDVHGKTLGIVGMGNIGAAIARRGRLGF 168 Query: 162 GMTIVAYDPYIPEDVASELGIKLLTVDELCTVSDFITLHVPLTPKTKHMIGKEQIALMKS 221 M I+ + ELG + ++D+L +DF+ L VPL+ KT+H+I ++ALMK Sbjct: 169 NMPILYSGNSRKPQLEQELGAQFRSLDQLLAEADFVCLVVPLSDKTRHLISHRELALMKP 228 Query: 222 NMVIMNCARGGLIDEAALYDALNSGKIKAAALDVFEQEPPKESPLLTLNNLIGTPHQGAS 281 + +++N +RG ++DE AL +AL + +I+ A LDV+E+EP ESPL L N + PH G++ Sbjct: 229 SAILVNISRGPVVDEPALIEALQNNRIRGAGLDVYEKEPLAESPLFQLKNAVTLPHIGSA 288 Query: 282 TEEAQLSAGTIVAEQTVKILKGESAENVVN 311 T E + + L G+ +++VN Sbjct: 289 THETREAMAHRALANLRSALLGKRPQDLVN 318 Lambda K H 0.316 0.134 0.364 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: 341 Number of extensions: 16 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: 523 Length of database: 324 Length adjustment: 31 Effective length of query: 492 Effective length of database: 293 Effective search space: 144156 Effective search space used: 144156 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: 50 (23.9 bits)
This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.
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