Align phosphogluconate dehydrogenase (NAD+-dependent, decarboxylating) (EC 1.1.1.343) (characterized)
to candidate RR42_RS24030 RR42_RS24030 3-hydroxyisobutyrate dehydrogenase
Query= BRENDA::D4GST8 (299 letters) >FitnessBrowser__Cup4G11:RR42_RS24030 Length = 298 Score = 60.5 bits (145), Expect = 5e-14 Identities = 58/187 (31%), Positives = 81/187 (43%), Gaps = 27/187 (14%) Query: 1 MQLGVIGLGRMGRIVVDRVLDAGHEVVAFDLSAEAVAAAADAGAEPADSVADLVDRLGDD 60 M++ IGLG MG + +L AGH + FDL A AVAAA AGA A S + R D Sbjct: 1 MEIAFIGLGNMGAPMAANLLKAGHALTVFDLDANAVAAALLAGATSAGSPREAAARA--D 58 Query: 61 KRIWLMVPAGDAVDATLDDLDPHLDGDDVVVDGGN--------SHFEESVRRAEACSAA- 111 I ++ A L G+D V+ G S + + R A +AA Sbjct: 59 LVITMLPAAAHVRQVYL--------GEDGVLAGARPGVPMVDCSTIDPATVRTVAEAAAS 110 Query: 112 ----YLDCGTSGGPAGAELG-FSLMVGGPQWAYDELTPVFDAVATGPDGHGHMGDSGSGH 166 + D SGG GA+ G + MVG Q ++ + PV A+ G G+G Sbjct: 111 QDSPFADAPVSGGTGGAQAGTLTFMVGADQPLFERIRPVLLAMGRNV---VPCGAPGTGQ 167 Query: 167 YVKMVHN 173 K+ +N Sbjct: 168 VAKICNN 174 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: 176 Number of extensions: 11 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: 298 Length adjustment: 27 Effective length of query: 272 Effective length of database: 271 Effective search space: 73712 Effective search space used: 73712 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