Align phosphoglycerate dehydrogenase (EC 1.1.1.95) (characterized)
to candidate WP_022950142.1 H035_RS0116940 2-hydroxyacid dehydrogenase
Query= metacyc::MONOMER-20569 (394 letters) >NCBI__GCF_000421465.1:WP_022950142.1 Length = 339 Score = 121 bits (303), Expect = 3e-32 Identities = 79/240 (32%), Positives = 127/240 (52%), Gaps = 14/240 (5%) Query: 71 AGVNTIDVNAASNHGVLVTNTPGQNNDAVAELAFGHIIACDRCIPQNTMHIKNGEWRKKL 130 AG N +D++A + + + + P + AVAE A ++ +R +P+ ++ G + Sbjct: 77 AGFNNVDLHALARAKLKLVHVPAYSPHAVAEHAAALVLGLNRHLPRAYNRVREGNFSLS- 135 Query: 131 FLNSTGLRDRTLGLVGCGNISHSMIHIAK-GFNMNVAVYSIPFSPEEAKSLGVQYCGTLE 189 L L +T+G++G G I + I K GF V + P+ EE + +GV+Y +L Sbjct: 136 GLEGFNLFGKTVGVIGTGRIGATFARIMKHGFGCRVIAFD-PYINEECREMGVEYL-SLH 193 Query: 190 ELAKIADVVSVHVPYMKETHHLINKQFFDAMKKKAIFINTSRGEIVDTVAMIEAIKEKGI 249 EL ++DV+SVH P +THHLIN + MK+ + INTSRG ++DT+A+IE +K + Sbjct: 194 ELYAVSDVISVHCPLNPKTHHLINGEAVARMKRGVMLINTSRGAVIDTLAVIEGLKSGRV 253 Query: 250 -KVGLDVYENEPAGSFGTFQNNQIAEVV---------TSATCHIGASTQQASERIADETI 299 +G+DVYE E F + I + V T H G T++A IA+ET+ Sbjct: 254 GSLGIDVYEQEGDLFFEDLSDQVIQDDVFERLITFPNVLVTGHQGFFTEEALTAIAEETL 313 Lambda K H 0.319 0.134 0.384 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: 332 Number of extensions: 12 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: 394 Length of database: 339 Length adjustment: 30 Effective length of query: 364 Effective length of database: 309 Effective search space: 112476 Effective search space used: 112476 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 (21.8 bits) S2: 49 (23.5 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