Align phosphoglycerate dehydrogenase (EC 1.1.1.95) (characterized)
to candidate GFF2935 PS417_15020 2-hydroxyacid dehydrogenase
Query= BRENDA::O58256 (333 letters) >FitnessBrowser__WCS417:GFF2935 Length = 317 Score = 144 bits (362), Expect = 4e-39 Identities = 100/293 (34%), Positives = 157/293 (53%), Gaps = 18/293 (6%) Query: 24 DVEIILYPS----GEELKGVIGRFDGIIVSPTTKITREVLENAERLKVISCHSAGYDNID 79 D +IL P+ E +K + ++ + E + +L++I AGY+++D Sbjct: 23 DFHVILAPTPAERAEAIKAHGSQIKAVLTRGPLGLYAEEIAALPQLEIICVIGAGYEHVD 82 Query: 80 LEEATKRGIYVTKVSGLLSEAVAEFTVGLIINLMRKIHYADKFIRRGEWESHAKIWTGFK 139 L+ A+ RGI VT +G+ + +VA+ + L+++L+R I D +RRGEW + Sbjct: 83 LQAASNRGIVVTNGAGVNAPSVADHAMALLLSLVRGIPQTDVAVRRGEWPKVMR------ 136 Query: 140 RIESLYGKKVGILGMGAIGKAIARRLIP-FGVKLYYWSRHRKVNVEKELKARYMDIDELL 198 SL GK++GILG+GA+G IA+R FG+++ Y +R + +V+ A + EL Sbjct: 137 --PSLGGKQLGILGLGAVGLEIAKRASQGFGMEVSYHNRQPRDDVDYTYCATAV---ELA 191 Query: 199 EKSDIVILALPLTRDTYHIINEERVKKL-EGKYLVNIGRGALVDEKAVTEAIKQGKLKGY 257 SD +ILA P T H+I+ + L YLVNIGRG++V + A++Q ++ G Sbjct: 192 RTSDFLILATPGGASTRHLIDRHALDALGPNGYLVNIGRGSVVVTADLVAALEQRRIGGA 251 Query: 258 ATDVFEKEPVREHELFKYEWETVLTPHYAGLALEAQEDVGFRAVENLLKVLRG 310 A DVF+ EP L K TVLT H AGL+ EA D R +NL++ G Sbjct: 252 ALDVFDDEPQVPDALKKLS-NTVLTSHVAGLSPEAAHDTVQRVADNLVEYFAG 303 Lambda K H 0.319 0.139 0.393 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: 232 Number of extensions: 14 Number of successful extensions: 5 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: 333 Length of database: 317 Length adjustment: 28 Effective length of query: 305 Effective length of database: 289 Effective search space: 88145 Effective search space used: 88145 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 48 (23.1 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