Align D-3-phosphoglycerate dehydrogenase; PGDH; EC 1.1.1.95 (uncharacterized)
to candidate WP_073039882.1 BUB04_RS12175 D-glycerate dehydrogenase
Query= curated2:O27051 (525 letters) >NCBI__GCF_900129305.1:WP_073039882.1 Length = 332 Score = 216 bits (551), Expect = 8e-61 Identities = 122/318 (38%), Positives = 183/318 (57%), Gaps = 8/318 (2%) Query: 4 MKVLIADSINEKGISELEEVA-EVVVNTTITP---EELLDAIKDFDAIVVRSRTKVTREV 59 MKVL+ + ++ + +L +V + + P EELL ++ + ++ ++ REV Sbjct: 7 MKVLVTAKLPDEAVRKLILAGCDVDGHGEVRPMNREELLARVEGAEGLLCTITDRIDREV 66 Query: 60 IEAAPRLKIIARAGVGVDNVDVKAATDRGIMVINAPESTSITVAEHSIGLMLALARKIAI 119 + AP L++ A GVG D++DV A RGI+V N P+ + A+ + L+LA+AR++ Sbjct: 67 FDKAPGLRVAANYGVGFDHIDVAEAGRRGILVTNTPDVLTDATADLAFALILAVARRVVE 126 Query: 120 ADRSVKEGK---WEKNRFMGIELNGKTLGIIGMGRIGSQVVVRTKAFGMDIM-VYDPYIS 175 DR + G+ W F+G E++GKTLGI+G GRIG V R + F M ++ + Sbjct: 127 GDRRTRSGQFRFWAPLHFLGTEVSGKTLGIVGFGRIGKAVARRARGFDMQVLYTARKPLE 186 Query: 176 KEAAEEMGVTVTDLETLLRESDIVTIHVPLTPETRHLISEDEFKLMKDTAFIVNCARGGI 235 K E +GV LE LL +SD V++HVPLTP+TRHLI E LMK +AF++N ARG + Sbjct: 187 KREEERLGVRFAPLEELLAQSDFVSLHVPLTPQTRHLIGARELSLMKPSAFLINTARGPV 246 Query: 236 IDEDALYRALKDGEIAGAALDVFEEEPPEGSPLLELENVVLTPHIGASTSEAQRDAAIIV 295 +DE AL L+ G I GA LDV+E EP L +L+NVVL PH+G++T E + A + Sbjct: 247 VDEKALVETLRGGGIRGAGLDVYENEPELTPGLADLQNVVLLPHVGSATVETRTRMAEMA 306 Query: 296 ANEIKTVFQGGAPRNVLN 313 + G P + LN Sbjct: 307 VENLLEGLAGRRPPHCLN 324 Lambda K H 0.316 0.135 0.366 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: 365 Number of extensions: 17 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: 525 Length of database: 332 Length adjustment: 31 Effective length of query: 494 Effective length of database: 301 Effective search space: 148694 Effective search space used: 148694 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 10 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