Align phosphoglycerate dehydrogenase (EC 1.1.1.95) (characterized)
to candidate 6938020 Sama_2153 erythronate-4-phosphate dehydrogenase (RefSeq)
Query= BRENDA::A4VGK3 (468 letters) >FitnessBrowser__SB2B:6938020 Length = 375 Score = 92.0 bits (227), Expect = 3e-23 Identities = 77/260 (29%), Positives = 119/260 (45%), Gaps = 33/260 (12%) Query: 108 EKIADAHFIGIRSRTQLTEEVFDCAKKLIAVGCFCIGTNQVDLNAARERGIAVFNAPYSN 167 E++ADA + +RS TQ+ E + ++L VG IGT+ VD + RGI NAP N Sbjct: 33 EQLADADVLLVRSVTQVNEALLCQNQQLKFVGSATIGTDHVDTAYLKSRGIPFTNAPGCN 92 Query: 168 TRSVAELVLAEAILLLRGIPEKNASCHRGGWIKSAANSFEIRGKKLGIIGYGSIGTQLSV 227 +V E + L + + ++ KK+ +IG G+ GT + Sbjct: 93 ATAVGEYAFIAMLELAQRYRQ------------------PLKDKKVAVIGAGNTGTATAR 134 Query: 228 LAEALGMQVFFYDVVTKLPLGNATQIGSLYELLGMCDIVSLHVPELPS----TQWMIGEK 283 EA G++ D V G+ Q L EL+ D++SLHVP T ++ ++ Sbjct: 135 CLEAYGVEHRLCDPVLAAQ-GDNRQFYELDELIAWADVISLHVPITKGGDHPTWYLFDQQ 193 Query: 284 EIRAMKKGAILINAARGTVVELDHLAAAIKDEHLIGAAIDVFPVEPKSNDEEFESPLRGL 343 + A+K GA L+N RG V++ L + I +DV+ EP SP+ L Sbjct: 194 RLEALKTGAWLLNCCRGEVIDNRALIEVKQRRVDIKLVLDVWEGEP--------SPMLAL 245 Query: 344 DRV--ILTPHIGGSTAEAQA 361 + I TPHI G + E +A Sbjct: 246 VPLVDIATPHIAGYSLEGKA 265 Lambda K H 0.318 0.135 0.385 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: 375 Number of extensions: 20 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: 468 Length of database: 375 Length adjustment: 32 Effective length of query: 436 Effective length of database: 343 Effective search space: 149548 Effective search space used: 149548 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 (21.7 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