Align D-3-phosphoglycerate dehydrogenase; PGDH; EC 1.1.1.95 (uncharacterized)
to candidate GFF2987 HP15_2931 glycerate dehydrogenase
Query= curated2:O27051 (525 letters) >FitnessBrowser__Marino:GFF2987 Length = 320 Score = 189 bits (481), Expect = 1e-52 Identities = 110/279 (39%), Positives = 168/279 (60%), Gaps = 11/279 (3%) Query: 33 TPEELLDAIKDFDAIVVRSRTKVTREVIEAAPRLKIIARAGVGVDNVDVKAATDRGIMVI 92 TP+++L+ I+ FD ++V ++ +TRE +A P LK IA G++N+D AA D GI V+ Sbjct: 43 TPDQILERIRGFDTVLV-NKVVLTREHFDACPELKTIAVVATGLNNIDQAAAKDHGIKVM 101 Query: 93 NAPESTSITVAEHSIGLMLALARKIAIADRSVKEGKWEKNRFMGI------ELNGKTLGI 146 N TVA+H++ LMLALA ++ R V+ G W K+ + EL G+TLGI Sbjct: 102 NVTNYGRSTVAQHTMALMLALATRLLDYTRDVQAGHWGKSDMFCLMDHPIMELEGRTLGI 161 Query: 147 IGMGRIGSQVVVRTKAFGMDIMVYDPYISKEAAEEMGVTVTDLETLLRESDIVTIHVPLT 206 +G G +G V R AFGM +++ +E G + L+ LL ++D+V++H LT Sbjct: 162 VGYGDLGQGVAERAAAFGMKVLL-GARPGQEPGVVDGYSRIPLDELLPQADVVSLHCLLT 220 Query: 207 PETRHLISEDEFKLMKDTAFIVNCARGGIIDEDALYRALKDGEIAGAALDVFEEEPP-EG 265 ETR LI E K+MK + ++N +RGG+++E AL AL+ GEI GA DV EEPP G Sbjct: 221 DETRDLIGARELKMMKPDSLLINTSRGGLVNEQALADALRAGEIGGAGFDVLTEEPPRNG 280 Query: 266 SPLL--ELENVVLTPHIGASTSEAQRDAAIIVANEIKTV 302 +PLL ++ N+++TPH ++ EA++ I A +K+V Sbjct: 281 NPLLADDIPNLIVTPHSAWASREARQRIVGITAVNLKSV 319 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: 364 Number of extensions: 18 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 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