Align D-3-phosphoglycerate dehydrogenase; PGDH; EC 1.1.1.95; 2-oxoglutarate reductase; EC 1.1.1.399 (uncharacterized)
to candidate 200152 SO0968 D-lactate dehydrogenase (NCBI ptt file)
Query= curated2:O33116 (528 letters) >FitnessBrowser__MR1:200152 Length = 329 Score = 151 bits (382), Expect = 3e-41 Identities = 97/265 (36%), Positives = 137/265 (51%), Gaps = 17/265 (6%) Query: 58 EVLAAAPK--LKIVARAGVGLDNVDVDAATARGVLVVNAPTSNIHSAAEHALALLLAASR 115 EVL K KI+A G +NVD+ AA G+ VVN P + S AEH +AL+L +R Sbjct: 59 EVLVELAKGGTKIIAMRCAGFNNVDLVAAKRLGMQVVNVPAYSPESVAEHTVALMLTLNR 118 Query: 116 QIAEADASLRAHIWKRSSFSGTEIFGKTVGVVGLGRIGQLVAARIAAFGAHVIAYDPYVA 175 +I +A R + G +FGKTVGV+G G+IG + FG VIA+DPY Sbjct: 119 KIHKAYQRTRDANFSLEGLVGFNMFGKTVGVIGTGKIGVATIKVLLGFGCKVIAFDPYPN 178 Query: 176 PARAAQLGIELMSFDDLLARADFISVHLPKTPETAGLIDKEALAKTKPGVIIVNAARGGL 235 PA A L +E D + A +D IS+H P TP+ L++K++ AK KPGV+++N +RGGL Sbjct: 179 PAVEA-LDVEYQDLDTIYATSDIISLHCPLTPDNHHLLNKDSFAKMKPGVMVINTSRGGL 237 Query: 236 VDEVALADAVRSGHVRAAGLDVFATEP-----------CTDSPLFELS---QVVVTPHLG 281 ++ +A++ G + A GLDV+ E D LS V+ T H Sbjct: 238 LNAFDAMEALKLGQIGALGLDVYENEKELFFEDKSNQIIQDDVFRRLSACHNVIFTGHQA 297 Query: 282 ASTAEAQDRAGTDVAESVRLALAGE 306 T EA +V+ LAG+ Sbjct: 298 FLTEEALGAIANTTLSNVQAVLAGK 322 Lambda K H 0.317 0.132 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: 337 Number of extensions: 12 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: 528 Length of database: 329 Length adjustment: 31 Effective length of query: 497 Effective length of database: 298 Effective search space: 148106 Effective search space used: 148106 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