Align Shikimate dehydrogenase (NADP(+)); SDH; EC 1.1.1.25 (uncharacterized)
to candidate N515DRAFT_2996 N515DRAFT_2996 3-hydroxyisobutyrate dehydrogenase
Query= curated2:Q5V450 (265 letters) >FitnessBrowser__Dyella79:N515DRAFT_2996 Length = 286 Score = 40.4 bits (93), Expect = 4e-08 Identities = 25/67 (37%), Positives = 35/67 (52%), Gaps = 4/67 (5%) Query: 119 AVVVGAGGAGRAVAFGLADEGLSVRIANRTESKADALADEVPDASGHGLDSLSDLLANAD 178 A VG G G +A L +GL +ANRT++KADALA E+ G L L A + Sbjct: 5 AAFVGLGAMGAPMAGHLKSKGLLHAVANRTQAKADALAREL----GVVAPPLEQLAAQCE 60 Query: 179 ILVNCTS 185 ++ C + Sbjct: 61 VIALCVT 67 Lambda K H 0.314 0.134 0.388 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: 160 Number of extensions: 8 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: 265 Length of database: 286 Length adjustment: 25 Effective length of query: 240 Effective length of database: 261 Effective search space: 62640 Effective search space used: 62640 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: 42 (22.0 bits) S2: 47 (22.7 bits)
This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 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