Align D-3-phosphoglycerate dehydrogenase; PGDH; EC 1.1.1.95 (uncharacterized)
to candidate WP_018947336.1 B1A74_RS10245 2-hydroxyacid dehydrogenase
Query= curated2:Q58424 (524 letters) >NCBI__GCF_001995255.1:WP_018947336.1 Length = 335 Score = 117 bits (294), Expect = 5e-31 Identities = 79/238 (33%), Positives = 119/238 (50%), Gaps = 18/238 (7%) Query: 64 LKVIGRAGVGVDNIDVEAATEKGIIVVNAPDASSISVAELTMGLMLAAARNIPQATASLK 123 ++VI G DN+D E A G+ P S ++AE + L++ R+ A + Sbjct: 69 IRVIALRCSGHDNLDHEHAASLGMRAGRVPAYSPSAIAEHAVALLMTLNRHTHFAWQRTR 128 Query: 124 RGEWDRKRFKGIELYGKTLGVIGLGRIGQQVVKRAKAFGMNIIGYDPYIPKEVAESMGVE 183 RG++ G ++ + +GVIG G+IG + + FG + DPY P ++ GV Sbjct: 129 RGDFRLNHLAGFDVAQRNVGVIGTGKIGAIFCRIMQGFGARVRAMDPY-PDPELQAAGVT 187 Query: 184 LVDDINELCKRADFITLHVPLTPKTRHIIGREQIALMKKNAIIVNCARGGLIDEKALYEA 243 D ++ L +D + L PLT RH+I + +A M + AI++N ARG L+D AL A Sbjct: 188 YTD-LDGLLSESDVVCLMCPLTRDNRHLINADTLARMPRGAILINTARGPLVDTDALEAA 246 Query: 244 LKEGKIRAAALDVFEEEPP-------------KDNPLLTL---DNVIGTPHQGASTEE 285 L G++ AAALDV+E+E P D L+ L DNV+ T HQ T E Sbjct: 247 LDSGQLDAAALDVYEDEGPVFFRDWSGTEGGVPDERLVRLTQRDNVLVTGHQAFLTHE 304 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: 330 Number of extensions: 22 Number of successful extensions: 2 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: 335 Length adjustment: 32 Effective length of query: 492 Effective length of database: 303 Effective search space: 149076 Effective search space used: 149076 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