Align phosphogluconate dehydrogenase (NAD+-dependent, decarboxylating) (EC 1.1.1.343) (characterized)
to candidate Ga0059261_3686 Ga0059261_3686 3-hydroxyisobutyrate dehydrogenase (EC 1.1.1.31)
Query= BRENDA::D4GST8 (299 letters) >FitnessBrowser__Korea:Ga0059261_3686 Length = 295 Score = 68.9 bits (167), Expect = 1e-16 Identities = 63/196 (32%), Positives = 94/196 (47%), Gaps = 12/196 (6%) Query: 2 QLGVIGLGRMGRIVVDRVLDAGHEVVAFDLSAEAVAAAADAGAEPADSVADLVDRLGDDK 61 ++G IGLG MG + + AGH+V AFDLSA+A+ A AG P +S A + + Sbjct: 3 RVGFIGLGNMGGGMAANLAKAGHDVRAFDLSADALERAKAAGCLPVESAAAAAE---GAE 59 Query: 62 RIWLMVPAGDAVDATLDD-LDPHLDGDDVVVDGGNSHFEESVRRAEACSA---AYLDCGT 117 + M+PAG V+ +D + D +++D + R A+A A A +D Sbjct: 60 AVITMLPAGKHVEQVYEDSVFGAADTGAILIDCSTIDVATARRVADAAQAKGLAAVDAPV 119 Query: 118 SGGPAGAELG-FSLMVGGPQWAYDELTPVFDAVATGPDGHGHMGDSGSGHYVKMVHNGVE 176 SGG A A G + MVGG A++ A+ H G +G+G K+ +N + Sbjct: 120 SGGIAAAAGGTLTFMVGGDAAAFERAEVFLAAMGKAVI---HAGGNGAGQASKICNNMLL 176 Query: 177 YALMQAYGEGFELLAE 192 A M A E LLA+ Sbjct: 177 GATMVATCEAL-LLAQ 191 Lambda K H 0.317 0.137 0.413 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: 203 Number of extensions: 7 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: 299 Length of database: 295 Length adjustment: 26 Effective length of query: 273 Effective length of database: 269 Effective search space: 73437 Effective search space used: 73437 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 (21.6 bits) S2: 48 (23.1 bits)
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 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