Align D-3-phosphoglycerate dehydrogenase (characterized, see rationale)
to candidate WP_038211125.1 Q392_RS19260 D-2-hydroxyacid dehydrogenase family protein
Query= uniprot:Q5JGC4 (304 letters) >NCBI__GCF_000745855.1:WP_038211125.1 Length = 322 Score = 186 bits (472), Expect = 6e-52 Identities = 107/262 (40%), Positives = 156/262 (59%), Gaps = 5/262 (1%) Query: 26 YEEYPDEDRLVELVKDVDAIIV-RSKPKVTRKVIEAAPKLKVIGRAGVGLDNIDLKAAEE 84 Y ++ + + + E + DA+++ R + + R +IE PKL+ + GV IDL+AA E Sbjct: 39 YGDHVEGEAVAERLASYDAVVLMRERTALGRALIERLPKLRAVFTTGVRNLAIDLEAARE 98 Query: 85 RGIKVVNSPGASSRSVAELAIGLIFAVARKIAFADRKMREGVWAKKQCMGIELEGKTIGV 144 RGI V + ASS AELA+GL+ A++R+I DR +R G W + +G L+GKT+G+ Sbjct: 99 RGIVVCGTDSASS--TAELALGLMIALSRQIVAEDRAVRAGRW--QTVVGSSLQGKTLGI 154 Query: 145 VGFGRIGYQVAKIANALGMKVLFYDPYPNEERAKEVGGKFADLETLLKESDVVTLHVPLV 204 VG G++G QVA LGM + + +ERA + + D L +DVV+LH+ L Sbjct: 155 VGLGKLGAQVAGYGRMLGMHTIAWSENLTQERAVGLHCERVDKRALFTRADVVSLHLVLS 214 Query: 205 DATYHLINEERLKLMKPTAILINAARGAVVDTDALVKALQEGWIAGAGLDVFEEEPLPAD 264 + T ++ L MK A+LIN AR +VD DALV AL +G I GA +DVFE EPLP D Sbjct: 215 ERTRGVVGARELSWMKRDALLINTARAGLVDMDALVSALHDGRIGGAAIDVFEREPLPPD 274 Query: 265 HPLTKLDNVVLTPHIGASTVEA 286 P+ K +LTPH+G +T +A Sbjct: 275 APILKAPRTILTPHLGYATRDA 296 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: 252 Number of extensions: 15 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: 304 Length of database: 322 Length adjustment: 27 Effective length of query: 277 Effective length of database: 295 Effective search space: 81715 Effective search space used: 81715 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