Align D-3-phosphoglycerate dehydrogenase (characterized, see rationale)
to candidate WP_245610704.1 Q392_RS12045 D-2-hydroxyacid dehydrogenase family protein
Query= uniprot:Q5JGC4 (304 letters) >NCBI__GCF_000745855.1:WP_245610704.1 Length = 321 Score = 195 bits (496), Expect = 1e-54 Identities = 118/286 (41%), Positives = 161/286 (56%), Gaps = 4/286 (1%) Query: 20 AGFEVVYEEYPDEDRLVELVKDVDAIIV-RSKPKVTRKVIEAAPKLKVIGRAGVGLDNID 78 A E ++ ED+ + + D ++ R + T ++E P+L+++ G ID Sbjct: 30 ATVEFFHDHLDTEDKAAQRLVSYDVVVTERERTHFTAALLERLPRLRLLVTTGTHNRYID 89 Query: 79 LKAAEERGIKVVNSPGASSRSVAELAIGLIFAVARKIAFADRKMREGVWAKKQCMGIELE 138 AA GI V + A + ELA+GL+ A+ R+IA + M G W + +G L Sbjct: 90 FAAAGRLGITVCKTE-AILHAAPELAMGLMLALMRRIAVDNTAMHAGGW--QTGLGRSLR 146 Query: 139 GKTIGVVGFGRIGYQVAKIANALGMKVLFYDPYPNEERAKEVGGKFADLETLLKESDVVT 198 GKT+GVVG G G QV +A+A GMK + + P+ + RA G + A E LL SDVV+ Sbjct: 147 GKTLGVVGLGVTGSQVVTLAHAFGMKTVAWSPHMTQARAAAAGTRLASQEELLSGSDVVS 206 Query: 199 LHVPLVDATYHLINEERLKLMKPTAILINAARGAVVDTDALVKALQEGWIAGAGLDVFEE 258 LH+ L D+T LI L LMKPTA L+N +RGA+VD ALV+AL+E IAGAGLDVF E Sbjct: 207 LHMVLADSTRGLIGRRELALMKPTAYLVNTSRGALVDEAALVEALRERRIAGAGLDVFAE 266 Query: 259 EPLPADHPLTKLDNVVLTPHIGASTVEAQMRAGVEVAEKIVEALKG 304 EPLP HPL +DNV+LTPH G T E + E I+ G Sbjct: 267 EPLPDPHPLRAVDNVILTPHTGYVTDEQYALCFGQAVENILAFAAG 312 Lambda K H 0.317 0.136 0.378 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: 212 Number of extensions: 12 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: 304 Length of database: 321 Length adjustment: 27 Effective length of query: 277 Effective length of database: 294 Effective search space: 81438 Effective search space used: 81438 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: 48 (23.1 bits)
This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 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