Align D-3-phosphoglycerate dehydrogenase; EC 1.1.1.95 (characterized, see rationale)
to candidate WP_011320918.1 AVA_RS21485 D-2-hydroxyacid dehydrogenase
Query= uniprot:Q6LWW6 (523 letters) >NCBI__GCF_000204075.1:WP_011320918.1 Length = 317 Score = 110 bits (274), Expect = 1e-28 Identities = 78/264 (29%), Positives = 131/264 (49%), Gaps = 7/264 (2%) Query: 52 TATREIIEASENLKVIARAGVGVDNVDLDAATEKGIVVVNAPDASSISVAELLFGMMLAA 111 T +++EA+ ++ GV+++ E I++ N +I ++E + ++L Sbjct: 52 TTLHKVLEAAPGIRWQQTPSAGVNHILTPIFLEHDIILTNGAGVHAIPISEFVLSLILYH 111 Query: 112 ARNIPQATASIKSGKWDRKSFKGMEIYGKTLGIVGLGRIGQQVAKRAQAFGMTIVAYDPY 171 A+ + Q A+ W + E+ T+ I+G G IGQ +A R +AFG IV Sbjct: 112 AKQLRQLQAAHDQRIWRKSWLVLPELAKSTVLILGTGNIGQAIASRLKAFG-AIVWGGRR 170 Query: 172 IPEDVASELGIKLLTVDE---LCTVSDFITLHVPLTPKTKHMIGKEQIALMKSNMVIMNC 228 PE +A+ K+ +E L D++ + PLTP+TK +I +E + + S+ ++N Sbjct: 171 RPEPLANF--DKIFVGNEWHALLPEVDYLVVATPLTPETKALIDEEVLRSLPSHAYLINV 228 Query: 229 ARGGLIDEAALYDALNSGKIKAAALDVFEQEP-PKESPLLTLNNLIGTPHQGASTEEAQL 287 RG ++DE+AL AL G I A LD EP P ES L +L NL TPH A + + Sbjct: 229 GRGAVVDESALTKALTEGWIGGAGLDTVSIEPLPPESHLWSLPNLFITPHTSAISPVLKE 288 Query: 288 SAGTIVAEQTVKILKGESAENVVN 311 T+ + + G+S N+V+ Sbjct: 289 RIATLFLDNLERYRTGQSLRNIVD 312 Lambda K H 0.316 0.134 0.364 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: 303 Number of extensions: 12 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: 523 Length of database: 317 Length adjustment: 31 Effective length of query: 492 Effective length of database: 286 Effective search space: 140712 Effective search space used: 140712 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: 50 (23.9 bits)
This GapMind analysis is from Apr 09 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