Align D-3-phosphoglycerate dehydrogenase; PGDH; EC 1.1.1.95 (uncharacterized)
to candidate WP_058932805.1 AU252_RS07215 hydroxyacid dehydrogenase
Query= curated2:O27051 (525 letters) >NCBI__GCF_001484605.1:WP_058932805.1 Length = 320 Score = 191 bits (484), Expect = 4e-53 Identities = 100/260 (38%), Positives = 159/260 (61%), Gaps = 4/260 (1%) Query: 47 IVVRSRTKVTREVIEAAPRLKIIARAGVGVDNVDVKAATDRGIMVINAPESTSITVAEHS 106 I +R RT R V+E P LK++ G+ +DV AAT+ GI V P S + E + Sbjct: 55 IAMRERTPFPRTVLERLPGLKLLVTTGMANAAIDVAAATELGITVCGTPGSPT-AAPELT 113 Query: 107 IGLMLALARKIAIADRSVKEGKWEKNRFMGIELNGKTLGIIGMGRIGSQVVVRTKAFGMD 166 L+LA+AR + + S++ G W+ + +G+EL+GKTLG++G+G+IG ++ +AFGM+ Sbjct: 114 WALLLAIARNLPSEENSLRAGTWQTS--VGMELSGKTLGVVGLGKIGRRIAAYGQAFGME 171 Query: 167 IMVYDPYISKEAAEEMGVTVTDLETLLRESDIVTIHVPLTPETRHLISEDEFKLMKDTAF 226 ++ + ++ EAA E GV E L SD+V++H+ L+P + ++ E E +L+ Sbjct: 172 VLAWSQNLTDEAAAEAGVQKVSKEDLFENSDVVSLHLRLSPRSEDIVGEQELRLLGPEGI 231 Query: 227 IVNCARGGIIDEDALYRALKDGEIAGAALDVFEEEP-PEGSPLLELENVVLTPHIGASTS 285 +VN +RG ++++DAL RAL +G I GAALDVF++EP P G PLL N VL+PH+G T+ Sbjct: 232 LVNTSRGPLVNQDALVRALNEGWIRGAALDVFDQEPLPAGHPLLSAPNTVLSPHLGYVTA 291 Query: 286 EAQRDAAIIVANEIKTVFQG 305 E+ R ++K +G Sbjct: 292 ESYRQFYGGAFEDVKAWLEG 311 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: 338 Number of extensions: 13 Number of successful extensions: 4 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: 320 Length adjustment: 31 Effective length of query: 494 Effective length of database: 289 Effective search space: 142766 Effective search space used: 142766 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