Align 2-hydroxy-3-oxopropionate reductase (EC 1.1.1.60) (characterized)
to candidate 16820 b2736 predicted dehydrogenase, with NAD(P)-binding Rossmann-fold domain (NCBI)
Query= BRENDA::Q8ZLV8 (296 letters) >FitnessBrowser__Keio:16820 Length = 302 Score = 172 bits (435), Expect = 1e-47 Identities = 95/280 (33%), Positives = 160/280 (57%), Gaps = 2/280 (0%) Query: 5 VGFIGLGIMGKPMSKNLLKAGYSLVVSDRNPEAIADVIAAGA-ETASTAKAIAEQCDVII 63 VG +GLG MG + + ++AG S +D N A A + AGA + A AE+ D ++ Sbjct: 9 VGIVGLGSMGMGAALSYVRAGLSTWGADLNSNACATLKEAGACGVSDNAATFAEKLDALL 68 Query: 64 TMLPNSPHVKEVALGENGIIEGAKPGTVLIDMSSIAPLASREISDALKAKGVEMLDAPVS 123 ++ N+ VK+V GE G+ + KPGT ++ S+IA ++EI+ AL +EMLDAPVS Sbjct: 69 VLVVNAAQVKQVLFGETGVAQHLKPGTAVMVSSTIASADAQEIATALAGFDLEMLDAPVS 128 Query: 124 GGEPKAIDGTLSVMVGGDKAIFDKYYDLMKAMAGSVVHTG-DIGAGNVTKLANQVIVALN 182 GG KA +G ++VM G F++ +++A+AG V G + G G+ K+ +Q++ ++ Sbjct: 129 GGAVKAANGEMTVMASGSDIAFERLAPVLEAVAGKVYRIGAEPGLGSTVKIIHQLLAGVH 188 Query: 183 IAAMSEALTLATKAGVNPDLVYQAIRGGLAGSTVLDAKAPMVMDRNFKPGFRIDLHIKDL 242 IAA +EA+ LA +AG+ D++Y + S + + + V+D ++ P +D+ +KDL Sbjct: 189 IAAGAEAMALAARAGIPLDVMYDVVTNAAGNSWMFENRMRHVVDGDYTPHSAVDIFVKDL 248 Query: 243 ANALDTSHGVGAQLPLTAAVMEMMQALRADGHGNDDHSAL 282 DT+ + LPL + + M + G+G +D SA+ Sbjct: 249 GLVADTAKALHFPLPLASTALNMFTSASNAGYGKEDDSAV 288 Lambda K H 0.316 0.132 0.367 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: 240 Number of extensions: 14 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: 296 Length of database: 302 Length adjustment: 27 Effective length of query: 269 Effective length of database: 275 Effective search space: 73975 Effective search space used: 73975 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