Align D-3-phosphoglycerate dehydrogenase; PGDH; EC 1.1.1.95 (uncharacterized)
to candidate WP_028485699.1 B076_RS0101180 2-hydroxyacid dehydrogenase
Query= curated2:Q58424 (524 letters) >NCBI__GCF_000483485.1:WP_028485699.1 Length = 329 Score = 164 bits (414), Expect = 6e-45 Identities = 101/286 (35%), Positives = 161/286 (56%), Gaps = 18/286 (6%) Query: 42 ADVLVVRSGTKVTRDVIEK--AEKLKVIGRAGVGVDNIDVEAATEKGIIVVNAPDASSIS 99 A+V+ V ++ V+++ A K++ G +++D++AA + GI V P S + Sbjct: 44 AEVVSVFVNDRLDEPVLQQLAAGGTKMLALRCAGFNHVDLQAAQQLGIRVARVPAYSPYA 103 Query: 100 VAELTMGLMLAAARNIPQATASLKRGEWDRKRFKGIELYGKTLGVIGLGRIGQQVVKRAK 159 VAE T+GLMLA R + +A ++ G + G ++YGKT+G+IG G+IG+ V K K Sbjct: 104 VAEHTIGLMLALNRKLYRAYNRVREGNFSLNGMLGFDMYGKTVGIIGAGKIGRLVGKMLK 163 Query: 160 AFGMNIIGYDPYIPKEVAESMGVELVDDINELCKRADFITLHVPLTPKTRHIIGREQIAL 219 AFG ++ YDPY V + +G+E V ++E+ +++D I+LH PLTP+T H+I + IA Sbjct: 164 AFGCRVLVYDPY-ECSVCKQLGIEQV-QLDEIWEQSDIISLHCPLTPETDHVINADTIAK 221 Query: 220 MKKNAIIVNCARGGLIDEKALYEALKEGKIRAAALDVFEEEPP---KDNP---------- 266 MK+ +++N RG L+D +AL LK +I LDV+E+E +D+ Sbjct: 222 MKRGVMLINTGRGALMDTEALVNGLKSKQIGYLGLDVYEKEGALFFEDHSCEIIQDDLFE 281 Query: 267 -LLTLDNVIGTPHQGASTEEAQKAAGTIVAEQIKKVLRGELAENVV 311 LLT NV+ T HQ TEEA ++ I+ L E+ +N V Sbjct: 282 RLLTFHNVLITGHQAYFTEEALNHIAETTSDNIRAYLADEIMQNEV 327 Lambda K H 0.316 0.137 0.372 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: 28 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: 524 Length of database: 329 Length adjustment: 31 Effective length of query: 493 Effective length of database: 298 Effective search space: 146914 Effective search space used: 146914 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 (21.5 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