Align D-3-phosphoglycerate dehydrogenase; PGDH; EC 1.1.1.95 (uncharacterized)
to candidate GFF932 PS417_04730 bifunctional glyoxylate/hydroxypyruvate reductase B
Query= curated2:O27051 (525 letters) >FitnessBrowser__WCS417:GFF932 Length = 324 Score = 184 bits (468), Expect = 3e-51 Identities = 104/268 (38%), Positives = 162/268 (60%), Gaps = 6/268 (2%) Query: 54 KVTREVIEAAPRLKIIARAGVGVDNVDVKAATDRGIMVINAPESTSITVAEHSIGLMLAL 113 K+ RE ++ A +L++++ VG DN DV +RGIM+ N P+ + + A+ + L+++ Sbjct: 55 KLGREQLQGASKLEVVSSVSVGYDNYDVAYFNERGIMLTNTPDVLTESTADLAFALLMSS 114 Query: 114 ARKIAIADRSVKEGKWEKN---RFMGIELNGKTLGIIGMGRIGSQVVVRTK-AFGMDIMV 169 AR++A D K G+W+ + G +++GKTLGI+GMG IG+ V R + F M I+ Sbjct: 115 ARRVAELDAWTKAGQWKASVGAPLFGCDVHGKTLGIVGMGNIGAAVARRGRLGFNMPIL- 173 Query: 170 YDPYISKEAAE-EMGVTVTDLETLLRESDIVTIHVPLTPETRHLISEDEFKLMKDTAFIV 228 Y K A E E+G L+ LL E+D V + VPL+ +TRHLIS E LMK +A ++ Sbjct: 174 YSGNSRKPALEQELGAQFRSLDELLAEADFVCLVVPLSDKTRHLISTRELGLMKSSAILI 233 Query: 229 NCARGGIIDEDALYRALKDGEIAGAALDVFEEEPPEGSPLLELENVVLTPHIGASTSEAQ 288 N +RG ++DE AL AL++ I GA LDV+E+EP SPL +L N V PHIG++T E + Sbjct: 234 NISRGPVVDEPALIDALQNQTIRGAGLDVYEQEPLAESPLFQLSNAVTLPHIGSATHETR 293 Query: 289 RDAAIIVANEIKTVFQGGAPRNVLNMPV 316 A + +++ G P++++N V Sbjct: 294 EAMANRALDNLRSALLGQRPQDLVNPQV 321 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: 356 Number of extensions: 21 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: 324 Length adjustment: 31 Effective length of query: 494 Effective length of database: 293 Effective search space: 144742 Effective search space used: 144742 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 Aug 03 2021. The underlying query database was built on Aug 03 2021.
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