Align D-3-phosphoglycerate dehydrogenase; EC 1.1.1.95 (characterized, see rationale)
to candidate WP_042119753.1 RHE_RS23565 2-hydroxyacid dehydrogenase
Query= uniprot:Q6LWW6 (523 letters) >NCBI__GCF_000092045.1:WP_042119753.1 Length = 313 Score = 152 bits (384), Expect = 2e-41 Identities = 93/275 (33%), Positives = 150/275 (54%), Gaps = 5/275 (1%) Query: 33 EELKLKI-KDVDALVIRSGTTATREIIEASENLKVIARAGVGVDNVDLDAATEKGIVVVN 91 +EL K+ ++ A+ R A+ E+++ L++++ GVG D +DL A GI V N Sbjct: 36 QELISKVGSNIRAIATRGELGASAELMKQLPKLEIVSCYGVGTDAIDLSYARANGIRVTN 95 Query: 92 APDASSISVAELLFGMMLAAARNIPQATASIKSGKWDRKSFKGME-IYGKTLGIVGLGRI 150 PD + VA++ G++L+ AR IPQA +++G+W + + + GK +GIVG+GRI Sbjct: 96 TPDVLTEDVADIAIGLLLSTARQIPQADVFVRTGQWGKIPMPLVRRVSGKKVGIVGMGRI 155 Query: 151 GQQVAKRAQAFGMTIVAYDPYIPEDVASELGIKLLTVDELCTVSDFITLHVPLTPKTKHM 210 G+ +AKRA AFG I + +DVA L+ L +DF+ + VP T + Sbjct: 156 GKAIAKRAAAFGCDISYFARNRDQDVAHGYEANLVA---LANWADFLIVIVPGGAATMKI 212 Query: 211 IGKEQIALMKSNMVIMNCARGGLIDEAALYDALNSGKIKAAALDVFEQEPPKESPLLTLN 270 I E + + +++N +RG +DE AL AL + I+AA LDVF EP + LTL Sbjct: 213 INAEVLEALGPEGMLINVSRGTTVDEEALIAALQNRTIQAAGLDVFLNEPKIDERFLTLP 272 Query: 271 NLIGTPHQGASTEEAQLSAGTIVAEQTVKILKGES 305 N++ PH G+ T E + + G +V + G++ Sbjct: 273 NVVLQPHHGSGTIETRKAMGQLVRDNLAAHFAGQA 307 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: 329 Number of extensions: 20 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: 313 Length adjustment: 31 Effective length of query: 492 Effective length of database: 282 Effective search space: 138744 Effective search space used: 138744 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 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