Align D-3-phosphoglycerate dehydrogenase; PGDH; EC 1.1.1.95 (uncharacterized)
to candidate WP_049769571.1 DHAF_RS10215 glyoxylate reductase
Query= curated2:O27051 (525 letters) >NCBI__GCF_000021925.1:WP_049769571.1 Length = 332 Score = 221 bits (562), Expect = 4e-62 Identities = 116/277 (41%), Positives = 173/277 (62%), Gaps = 8/277 (2%) Query: 42 KDFDAIVVRSRT------KVTREVIEAAPRLKIIARAGVGVDNVDVKAATDRGIMVINAP 95 +DF A++ + KV E +EAAP LK+I + G GVD++D+KAA RGI V NAP Sbjct: 55 EDFKAVLAEAHVWVVGINKVYAEDLEAAPNLKLIIKHGTGVDSIDLKAAAARGITVANAP 114 Query: 96 ESTSITVAEHSIGLMLALARKIAIADRSVKEGKWEKNRFMGIELNGKTLGIIGMGRIGSQ 155 + + +VA+ + G ML+LAR+I AD+ ++G W MG ++ GKTLG++G+G+IG Sbjct: 115 GTNANSVADLAFGFMLSLARQIVSADKRTRDGFW--GTVMGKDVYGKTLGVLGLGQIGKG 172 Query: 156 VVVRTKAFGMDIMVYDPYISKEAAEEMGVTVTDLETLLRESDIVTIHVPLTPETRHLISE 215 V+ R F M+I+ YD + +E V LE ++ E+D +++H+PL T+++I Sbjct: 173 VIRRASGFDMNILGYDLVHHSQFEKEYRVRAATLEEIMSEADYISVHLPLLESTKNIIDR 232 Query: 216 DEFKLMKDTAFIVNCARGGIIDEDALYRALKDGEIAGAALDVFEEEPPEGSPLLELENVV 275 + M+ TAF++N +RGG++DE ALY LK+ IAGAALDVF EPP SP EL+NV+ Sbjct: 233 SLLEKMRPTAFLINTSRGGVVDETALYDLLKEKRIAGAALDVFATEPPRQSPFFELDNVI 292 Query: 276 LTPHIGASTSEAQRDAAIIVANEIKTVFQGGAPRNVL 312 + PH+GA T A + I+A I V G P +V+ Sbjct: 293 VAPHMGAYTEGAMGAVSEILAESIVRVLAGKEPLSVI 329 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: 373 Number of extensions: 16 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: 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