Align phosphoglycerate dehydrogenase (EC 1.1.1.95) (characterized)
to candidate WP_012755652.1 RLEG_RS26505 2-hydroxyacid dehydrogenase
Query= BRENDA::Q9I6H5 (409 letters) >NCBI__GCF_000023185.1:WP_012755652.1 Length = 315 Score = 99.4 bits (246), Expect = 1e-25 Identities = 78/256 (30%), Positives = 118/256 (46%), Gaps = 10/256 (3%) Query: 73 AKKLIAVGCFCIGTNQVDLNAARERGIAVFNAPYSNTRSVAELVLAEAILLLRGIPEKNA 132 A KL A C G +Q+D+ A RGI + N VA++ L + R +PE + Sbjct: 68 ALKLAA--CSSAGYDQMDVEAMTRRGIKLTNTSEVLCDDVADMALLLMLAARRRLPEGDR 125 Query: 133 SCHRGGWIKSAANSF--EIRGKKLGIVGYGSIGTQLSVLAEALGMQVFFYDTVTKLPLGN 190 G W + GKK GIVG G IG ++ EA+G+ V +Y TK + Sbjct: 126 YVRSGDWGQKGMMPLTTSTSGKKAGIVGLGRIGMAIAKRCEAVGLTVGYYGR-TKKDGND 184 Query: 191 AVQIGSLHELLGMSDIVSLHVPELPSTQWMIGEKEIRAMKKGGILINAARGTVVELDHLA 250 + +L +DI+ + P PST+ +I + A+ G IN ARGTVV+ L Sbjct: 185 FAYFDTPAKLADWADILIVATPGGPSTEGLISADVLNALGPTGSFINIARGTVVDEPALI 244 Query: 251 AAIKDEHLIGAAIDVFPVEPKSNDEEFASPLRGLDRVILTPHIGGSTAEAQANIGLEVAE 310 A+++ + A IDV+ EP + D FA+ LD V+L PH T E + + + Sbjct: 245 KALQERRIASAGIDVYLNEP-NPDPRFAA----LDNVVLYPHHASGTEETRDRMAQLTVD 299 Query: 311 KLVKYSDNGTSVSSVN 326 L + ++ VN Sbjct: 300 NLAAFFAGRPLLTPVN 315 Lambda K H 0.317 0.135 0.381 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: 218 Number of extensions: 9 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: 409 Length of database: 315 Length adjustment: 29 Effective length of query: 380 Effective length of database: 286 Effective search space: 108680 Effective search space used: 108680 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: 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