Align D-3-phosphoglycerate dehydrogenase; PGDH; EC 1.1.1.95 (uncharacterized)
to candidate GFF2783 PGA1_c28260 glyoxylate reductase GyaR
Query= curated2:O27051 (525 letters) >FitnessBrowser__Phaeo:GFF2783 Length = 328 Score = 176 bits (447), Expect = 9e-49 Identities = 114/315 (36%), Positives = 172/315 (54%), Gaps = 9/315 (2%) Query: 3 RMKVLIADSINEKGISELEEVAEVVVNTTITP---EELLDAIKDFDAIVVRSRTKVTREV 59 R+ V++ + E + L E+ +V + TP EL A+KD D +V ++ + Sbjct: 5 RLSVVVTRRLPEPVETRLSELFDVRLREDDTPMSRAELATALKDADVLVPTVTDEIDAGL 64 Query: 60 I-EAAPRLKIIARAGVGVDNVDVKAATDRGIMVINAPESTSITVAEHSIGLMLALARKIA 118 + +A RLK+IA G GVD++DV A RGI+V N P + A+ ++ L++A+ R+I Sbjct: 65 LGQAGDRLKLIANYGAGVDHIDVATARQRGILVSNTPGVLTDDTADMAMALIMAVVRRIP 124 Query: 119 IADRSVKEGKWE---KNRFMGIELNGKTLGIIGMGRIGSQVVVRTKAFGMDIMVYDPY-I 174 +++G W+ +G L G+ LGI+GMG IG V R AFGM + ++ + Sbjct: 125 EGLAVMQKGDWQGWSPTALLGGRLAGRRLGILGMGSIGQAVAKRAAAFGMQVHYHNRRRL 184 Query: 175 SKEAAEEMGVTVTD-LETLLRESDIVTIHVPLTPETRHLISEDEFKLMKDTAFIVNCARG 233 E + T + L+ ++ D+++I+ P TP T HL++ KLMK A IVN +RG Sbjct: 185 RPEIEQRFEATYWESLDQMVARMDVLSINCPSTPSTFHLMNARRLKLMKPDAVIVNTSRG 244 Query: 234 GIIDEDALYRALKDGEIAGAALDVFEEEPPEGSPLLELENVVLTPHIGASTSEAQRDAAI 293 +IDE AL R L+ EIAGA LDV+E L ELENVVL PH+G++T E + + Sbjct: 245 EVIDEHALTRMLRASEIAGAGLDVYEHGTDINPRLRELENVVLLPHMGSATLEGRLEMGE 304 Query: 294 IVANEIKTVFQGGAP 308 V IKT G P Sbjct: 305 KVLLNIKTFEDGHRP 319 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: 396 Number of extensions: 23 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: 525 Length of database: 328 Length adjustment: 31 Effective length of query: 494 Effective length of database: 297 Effective search space: 146718 Effective search space used: 146718 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