Align phosphoglycerate dehydrogenase (EC 1.1.1.95) (characterized)
to candidate WP_038213769.1 Q392_RS24070 2-hydroxyacid dehydrogenase
Query= BRENDA::A4VGK3 (468 letters) >NCBI__GCF_000745855.1:WP_038213769.1 Length = 312 Score = 124 bits (312), Expect = 3e-33 Identities = 83/258 (32%), Positives = 130/258 (50%), Gaps = 11/258 (4%) Query: 124 LTEEVFDCAKKLIAVGCFCIGTNQVDLNAARERGIAVFNAPYSNTRSVAELVLAEAILLL 183 LTEE L C +G + + A R RGIA N +N VA+ I + Sbjct: 58 LTEEELAAMPALELACCMGVGYEGLPMQALRARGIATANGAGTNDDCVADHAFGLIIGAV 117 Query: 184 RGIPEKNASCHRGGWIKSAANSFEIRGKKLGIIGYGSIGTQLSVLAEALGMQVFFYDVVT 243 RG + C G W +S A + GKKLGI+G G IG +++ A M V +++ Sbjct: 118 RGFHALDRQCREGVWRESIAQPPNVSGKKLGILGLGGIGRKIAKRAAGFEMPVGYHN--- 174 Query: 244 KLPLGNATQ--IGSLYELLGMCDIVSLHVPELPSTQWMIGEKEIRAMKKGAILINAARGT 301 + P+ +A S L CD++ VP P+TQ ++G + + A+ L+N RG+ Sbjct: 175 RRPVEDAPHRYFDSPIALARWCDVLVCAVPGGPATQHLVGAEVLDALGPQGWLVNIGRGS 234 Query: 302 VVELDHLAAAIKDEHLIGAAIDVFPVEPKSNDEEFESPLRGLDRVILTPHIGGSTAEA-Q 360 VV+ D LAAA+++ + GA +DV+ EP+ + L GLD +++TPH+ G + EA Q Sbjct: 235 VVDTDALAAALREHRIAGAGLDVYESEPRPPQQ-----LIGLDNLLITPHVAGWSPEATQ 289 Query: 361 ANIGLEVAEKLVKYSDNG 378 A++ +A +S G Sbjct: 290 ASVDRFMANAEGHFSGRG 307 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: 344 Number of extensions: 20 Number of successful extensions: 3 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: 312 Length adjustment: 30 Effective length of query: 438 Effective length of database: 282 Effective search space: 123516 Effective search space used: 123516 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 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