Align D-3-phosphoglycerate dehydrogenase; PGDH; EC 1.1.1.95 (uncharacterized)
to candidate BPHYT_RS11290 BPHYT_RS11290 bifunctional glyoxylate/hydroxypyruvate reductase B
Query= curated2:Q58424 (524 letters) >FitnessBrowser__BFirm:BPHYT_RS11290 Length = 321 Score = 216 bits (550), Expect = 1e-60 Identities = 123/317 (38%), Positives = 179/317 (56%), Gaps = 7/317 (2%) Query: 1 MVKILVTDPLHEDAIKILEEVGEVEVATGLTKEELLEKIKDADVLVVRSGTKVTRDVIEK 60 M KI+ L ED + L++ +V + + +KDAD + S K+T ++E Sbjct: 1 MKKIVAWKSLPEDVLAYLQQHAQVVQVDATQHDAFVAALKDADG-GIGSSVKITPAMLEG 59 Query: 61 AEKLKVIGRAGVGVDNIDVEAATEKGIIVVNAPDASSISVAELTMGLMLAAARNIPQATA 120 A +LK + VG D DV T +GI++ N PD + S A+ L+LA+AR + + Sbjct: 60 ATRLKALSTISVGFDQFDVADLTRRGIVLANTPDVLTESTADTVFSLILASARRVVELAE 119 Query: 121 SLKRGEWDRK---RFKGIELYGKTLGVIGLGRIGQQVVKRAK-AFGMNIIGYDPYIPKEV 176 +K G W G+++ GKTLG++GLGRIG V +RA F M ++ + + Sbjct: 120 WVKAGHWQHSIGPALFGVDVQGKTLGIVGLGRIGGAVARRAALGFNMKVLYTNRSANPQA 179 Query: 177 AESMGVELVDDINELCKRADFITLHVPLTPKTRHIIGREQIALMKKNAIIVNCARGGLID 236 E+ G V+ + EL ADF+ L VPLTP+T+H+IG ++ MKK+AI++N +RG +D Sbjct: 180 EEAYGARRVE-LAELLATADFVCLQVPLTPETKHLIGAAELKSMKKSAILINASRGATVD 238 Query: 237 EKALYEALKEGKIRAAALDVFEEEP-PKDNPLLTLDNVIGTPHQGASTEEAQKAAGTIVA 295 EKAL EAL+ G I A LDVFE EP P D+PLL L NV+ PH G++T E + A A Sbjct: 239 EKALIEALQNGTIHGAGLDVFETEPLPSDSPLLKLANVVALPHIGSATHETRHAMARNAA 298 Query: 296 EQIKKVLRGELAENVVN 312 E + L G L N+VN Sbjct: 299 ENLVAALDGTLTSNIVN 315 Lambda K H 0.316 0.137 0.372 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: 370 Number of extensions: 18 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: 524 Length of database: 321 Length adjustment: 31 Effective length of query: 493 Effective length of database: 290 Effective search space: 142970 Effective search space used: 142970 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 (21.5 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