Align phosphoglycerate dehydrogenase (EC 1.1.1.95) (characterized)
to candidate WP_042441178.1 TX73_RS16685 2-hydroxyacid dehydrogenase
Query= BRENDA::C3SVM7 (410 letters) >NCBI__GCF_000195775.1:WP_042441178.1 Length = 316 Score = 127 bits (319), Expect = 5e-34 Identities = 90/269 (33%), Positives = 132/269 (49%), Gaps = 22/269 (8%) Query: 65 LTEDVINAAEKLVAIGCFCIGTNQVDLDAAAKRGIPVFNAPFSNTRSVAELVIGELLLLL 124 L + + L A+ C+ G + VDL AAA+RGI V N+P +N +VA+L + LL L+ Sbjct: 56 LGRETFDMLPALGAVVCYGTGYDGVDLKAAAERGIVVGNSPAANASAVADLALALLLALM 115 Query: 125 RGVPEANAKAHRGVWNKLAAGSF-----EARGKKLGIIGYGHIGTQLGILAESLGMYVYF 179 R V A+A G W+ G K+G+ G G IG ++ V + Sbjct: 116 RRVLPADAYVRAGGWSGAKPSPMLKPPRGLTGAKVGVYGIGEIGRKIAARVAGFETEVAY 175 Query: 180 YD-IENKLPLGNATQVQHLSDLLNMSDVVSLHVPENPSTKNMMGAKEISLMKPGSLLINA 238 + + +P V L +L++ DV+ + V P T+ ++ A + + P +++N Sbjct: 176 HSRSRHDVPY---RYVGDLGELVDWCDVLLVAVRAGPDTEKIIDAGMLKRLGPSGVVVNI 232 Query: 239 SRGTVVDIPALCDALASKHLAGAAIDVFPTEPATNSDPFTSPLCEFDNVLLTPHIGGSTQ 298 SRG+V+D AL ALA +AGA +DVF EP L EF NV+LTPHIGG TQ Sbjct: 233 SRGSVIDQAALIAALADGTIAGAGLDVFALEPYA-----PDALAEFPNVVLTPHIGGHTQ 287 Query: 299 EAQE--------NIGLEVAGKLIKYSDNG 319 EA N+ AGK + Y G Sbjct: 288 EAHRAMQDCVIANLAAFFAGKPLPYPVQG 316 Lambda K H 0.318 0.135 0.383 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: 255 Number of extensions: 15 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: 410 Length of database: 316 Length adjustment: 29 Effective length of query: 381 Effective length of database: 287 Effective search space: 109347 Effective search space used: 109347 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 (21.7 bits) S2: 49 (23.5 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