Align D-3-phosphoglycerate dehydrogenase; PGDH; EC 1.1.1.95 (uncharacterized)
to candidate WP_077277716.1 B1C78_RS03315 3-phosphoglycerate dehydrogenase
Query= curated2:O27051 (525 letters) >NCBI__GCF_002000365.1:WP_077277716.1 Length = 308 Score = 209 bits (531), Expect = 1e-58 Identities = 108/270 (40%), Positives = 166/270 (61%), Gaps = 4/270 (1%) Query: 34 PEELLDAIKDFDAIVVRSRTKVTREVIEAAPRLKIIARAGVGVDNVDVKAATDRGIMVIN 93 P++L + D +A++VR+RT+V +++ AP LK++ R GVG+DN+D +A RG+ VI Sbjct: 34 PDKLAPLLADCEALIVRNRTQVRPDLLGKAPALKVVGRLGVGLDNIDQEACKGRGVQVIP 93 Query: 94 APESTSITVAEHSIGLMLALARKIAIADRSVKEGKWEKNRFM-GIELNGKTLGIIGMGRI 152 A + ++ VAE+ I + L R ++ V G+W + G EL+GKTLG+ G G I Sbjct: 94 ATGANALAVAEYVICTAMMLLRGAYLSSDQVAAGEWPRPALSKGRELSGKTLGLAGFGGI 153 Query: 153 GSQVVVRTKAFGMDIMVYDPYISKEAA--EEMGVTVTDLETLLRESDIVTIHVPLTPETR 210 G + GM + YDPY+ +A +E + D++ LL ESD++++H+PLT ETR Sbjct: 154 GQLTARLARGLGMHTVAYDPYLKPDAPALKETDTRLVDMDGLLAESDVISLHIPLTDETR 213 Query: 211 HLISEDEFKLMKDTAFIVNCARGGIIDEDALYRALKDGEIAGAALDVFEEEP-PEGSPLL 269 +L M+ + ++N ARGGI+DE AL ALK+G +AGAALDVF +EP GSPL Sbjct: 214 NLFDAKRIAAMRKGSVLINSARGGIVDEVALASALKEGHLAGAALDVFNDEPLAAGSPLA 273 Query: 270 ELENVVLTPHIGASTSEAQRDAAIIVANEI 299 ++ N+VLTPHI T E+ + ++A + Sbjct: 274 DIRNLVLTPHIAGVTEESNTRVSRLIAERV 303 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: 343 Number of extensions: 15 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: 308 Length adjustment: 31 Effective length of query: 494 Effective length of database: 277 Effective search space: 136838 Effective search space used: 136838 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