Align D-3-phosphoglycerate dehydrogenase; PGDH; EC 1.1.1.95 (uncharacterized)
to candidate WP_014027207.1 PYRFU_RS08225 glyoxylate reductase
Query= curated2:O27051 (525 letters) >NCBI__GCF_000223395.1:WP_014027207.1 Length = 323 Score = 219 bits (558), Expect = 1e-61 Identities = 129/280 (46%), Positives = 173/280 (61%), Gaps = 7/280 (2%) Query: 36 ELLDAIKDFDAIVVRSRTKVTREVIEAAPRLKIIARAGVGVDNVDVKAATDRGIMVINAP 95 EL IKD D IVV ++ EVI + +LK+IA + G D+VD++AA +RGI+V N P Sbjct: 43 ELFKRIKDAD-IVVTVSYPISGEVIRKSEKLKMIAVSFTGYDHVDIEAAKERGIVVSNVP 101 Query: 96 ESTSITVAEHSIGLMLALARKIAIADRSVKEGKWEKNRFMGIELNGKTLGIIGMGRIGSQ 155 + +VAE GL++ AR++ ADR ++ G W +G EL GKT+GI+G G IG + Sbjct: 102 GYATDSVAELVFGLVIVAARRVIQADRVMRTGGWRTPELLGTELRGKTIGIVGFGAIGRR 161 Query: 156 VVVRTKAFGMDIMVYD--PY--ISKEAAEEMGVTVTDLETLLRESDIVTIHVPLTPETRH 211 V KAFGMDI+VYD P+ K+ AEE+G L+ L+R+SDIVT+HVPLT ETRH Sbjct: 162 VAELAKAFGMDILVYDRSPWKEEKKKKAEEVGARFVSLDELMRKSDIVTVHVPLTSETRH 221 Query: 212 LISEDEFKLMKDTAFIVNCARGGIIDEDALYRALKDGEIAGAALDVFEEEP-PEGSPLLE 270 +I + +L+K A +VN ARG +I ED L R LK+ + A LDV+ EP P L + Sbjct: 222 MIRYEHLRLLKPGAILVNVARGAVIKEDDLVRFLKERKDVTACLDVYSVEPLPPDHELRK 281 Query: 271 LENVVLTPHIGASTSEAQRDAAIIVANEIKTVFQGGAPRN 310 LENV+LTPHIG T EA + IK F G P+N Sbjct: 282 LENVILTPHIGFYTKEALERRTRVTFENIK-AFIEGRPQN 320 Lambda K H 0.316 0.135 0.366 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: 420 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: 525 Length of database: 323 Length adjustment: 31 Effective length of query: 494 Effective length of database: 292 Effective search space: 144248 Effective search space used: 144248 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