Align D-3-phosphoglycerate dehydrogenase; PGDH; EC 1.1.1.95 (uncharacterized)
to candidate Echvi_0181 Echvi_0181 Phosphoglycerate dehydrogenase and related dehydrogenases
Query= curated2:Q58424 (524 letters) >FitnessBrowser__Cola:Echvi_0181 Length = 311 Score = 181 bits (458), Expect = 4e-50 Identities = 102/309 (33%), Positives = 175/309 (56%), Gaps = 13/309 (4%) Query: 2 VKILVTDPLHEDAIKILEEVG-EVEVATGLTKEELLEKIKDADVLVVRSGTKVTRDVIEK 60 + IL+ D +H I +LEE G +V + +T+EE+ I D + L++RS T + + ++EK Sbjct: 1 MNILIIDEMHSSIIPLLEEKGFKVNYSPKITREEIEAIIADYEGLIIRSKTPMDKPLLEK 60 Query: 61 AEKLKVIGRAGVGVDNIDVEAATEKGIIVVNAPDASSISVAELTMGLMLAAARNIPQATA 120 A+KLK IGRAG G+D ID++ ++GI + +AP+ + +V E + ++L N+ +A + Sbjct: 61 AKKLKFIGRAGAGLDKIDLDFIQKQGIKLFHAPEGNRDAVGEHAVAMLLMLFNNLKKADS 120 Query: 121 SLKRGEWDRKRFKGIELYGKTLGVIGLGRIGQQVVKRAKAFGMNIIGYDPYIPKEVAESM 180 +++G WDR+ +G EL GKT+G+ G G +G+ +R FG+ ++ YD Y+ K E Sbjct: 121 EVRQGVWDREGNRGEELQGKTVGIFGYGNMGKAFARRLSGFGVKVVAYDKYLDKYSDEYA 180 Query: 181 GVELVDDINELCKRADFITLHVPLTPKTRHIIGREQIALMKKNAIIVNCARGGLIDEKAL 240 D +L ++AD +++HVPLT +TR+ E +A K ++N ARG +I + L Sbjct: 181 AQVTFD---QLQQQADVLSIHVPLTEETRNFFTEEVLAGFSKPFYLINTARGEVISMETL 237 Query: 241 YEALKEGKIRAAALDVFEEE---------PPKDNPLLTLDNVIGTPHQGASTEEAQKAAG 291 AL++G ++ A LDV E E L D+V+ +PH T ++ K Sbjct: 238 NAALEKGILKGALLDVLENEKLHTLNDVQKTAFEKLSVRDDVLFSPHIAGWTFQSYKKIN 297 Query: 292 TIVAEQIKK 300 ++ +I + Sbjct: 298 EVLVSKISE 306 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: 365 Number of extensions: 21 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: 524 Length of database: 311 Length adjustment: 31 Effective length of query: 493 Effective length of database: 280 Effective search space: 138040 Effective search space used: 138040 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 Aug 03 2021. The underlying query database was built on Aug 03 2021.
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