Align D-3-phosphoglycerate dehydrogenase; PGDH; EC 1.1.1.95 (uncharacterized)
to candidate CCNA_03838 CCNA_03838 gluconate 2-dehydrogenase/glyoxylate reductase/hydroxypyruvate reductase
Query= curated2:O27051 (525 letters) >FitnessBrowser__Caulo:CCNA_03838 Length = 328 Score = 197 bits (502), Expect = 4e-55 Identities = 123/315 (39%), Positives = 179/315 (56%), Gaps = 9/315 (2%) Query: 3 RMKVLIADSINEKGISELEEVAEVVVNTT---ITPEELLDAIKDFDAIVVRSRTKV-TRE 58 ++KV++ + + + + E+ + +N + +T +EL+DA+ D +V ++ +R Sbjct: 5 KLKVIVTRKLPDPVETRMCELFDTELNVSDKPMTADELVDAMSRADVLVPTITDRIDSRL 64 Query: 59 VIEAAPRLKIIARAGVGVDNVDVKAATDRGIMVINAPESTSITVAEHSIGLMLALARKIA 118 + + RLK+IA G GVDN+DV A RGI+V N P + A+ ++ L++A +R+I Sbjct: 65 LSRSGDRLKLIANFGAGVDNIDVATANARGIIVTNTPGVLTEDTADLTMTLIMAASRRIV 124 Query: 119 IADRSVKEGK---WEKNRFMGIELNGKTLGIIGMGRIGSQVVVRTKAFGMDIMVYDPY-I 174 VK G W MG L GK LGIIGMGRIG V R KAFGM + ++ + Sbjct: 125 EGAEVVKAGGFHGWSPTWMMGRRLWGKRLGIIGMGRIGQAVARRAKAFGMQVHYHNRKPV 184 Query: 175 SKEAAEEMGVTVTD-LETLLRESDIVTIHVPLTPETRHLISEDEFKLMKDTAFIVNCARG 233 S AEE+G T + L+ +L D V+++ P TP T HL+S KL++ A +VN ARG Sbjct: 185 SPRIAEELGCTYWESLDQMLARMDFVSVNCPHTPATYHLLSARRLKLLRPHAVVVNTARG 244 Query: 234 GIIDEDALYRALKDGEIAGAALDVFEEEPPEGSPLLELENVVLTPHIGASTSEAQRDAAI 293 +IDE AL L GEIAGA LDV+E EP LL+L NVVL PH+G++T E + D Sbjct: 245 EVIDEGALANMLAKGEIAGAGLDVYEHEPAINPKLLKLPNVVLLPHMGSATVEGRIDMGE 304 Query: 294 IVANEIKTVFQGGAP 308 V +KT G P Sbjct: 305 KVIVNVKTFMDGHRP 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: 409 Number of extensions: 27 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: 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