Align Phosphoglycerate dehydrogenase (EC 1.1.1.95) (characterized)
to candidate HSERO_RS05655 HSERO_RS05655 D-2-hydroxyacid dehydrogenase
Query= reanno::SB2B:6938941 (308 letters) >FitnessBrowser__HerbieS:HSERO_RS05655 Length = 308 Score = 115 bits (288), Expect = 1e-30 Identities = 66/214 (30%), Positives = 106/214 (49%) Query: 95 MSEYLFGYLLARQREHDLYKSQQQQKLWLPGSYKTLQGSELLLLGTGSIAKHLAQTAKHF 154 M +Y+ +L R+ +Y QQ+ ++W + + +LG G + + + Q Sbjct: 95 MVQYVTHAVLGLHRDSRVYARQQRDQVWRAHRVRPASACRVGVLGLGMLGRAVLQQLHGL 154 Query: 155 GMKVAGINRSAKATEGFDEVATLEALPTLMARADAIASILPSTEATRGILNENILARMKP 214 G AG +RSA +G D + L +AR D + ++P TE TRG+L ++ A++ Sbjct: 155 GFPCAGWSRSAHQMDGIDCYSGSAGLRAFLARTDVLVCLVPLTEETRGLLCRDLFAQLPR 214 Query: 215 DAVLFNLGRGDVLDLDALERQLRQHPQQQAVLDVFNQEPLPEDHPIWGLGNVIVTPHIAA 274 A L N+GRG L D L L AVLDV EPLP HP W ++++TPHIA+ Sbjct: 215 GAALINVGRGGHLVEDDLLAALNDGQLSAAVLDVCEVEPLPPGHPFWTHPDIVLTPHIAS 274 Query: 275 PSFPEQVAEIFSSNYHKFLLGETLSHRVNFERGY 308 + P+ + N ++ G L ++ +RGY Sbjct: 275 MTQPDGAVDAVLENLRRYREGLPLLGLIDRQRGY 308 Lambda K H 0.320 0.137 0.404 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: 238 Number of extensions: 15 Number of successful extensions: 1 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: 308 Length of database: 308 Length adjustment: 27 Effective length of query: 281 Effective length of database: 281 Effective search space: 78961 Effective search space used: 78961 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: 48 (23.1 bits)
This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 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