Align shikimate dehydrogenase (NADP+) (EC 1.1.1.25); quinate/shikimate dehydrogenase [NAD(P)+] (EC 1.1.1.282) (characterized)
to candidate RR42_RS32445 RR42_RS32445 shikimate dehydrogenase
Query= BRENDA::Q88JP1 (269 letters) >FitnessBrowser__Cup4G11:RR42_RS32445 Length = 277 Score = 165 bits (417), Expect = 1e-45 Identities = 100/266 (37%), Positives = 137/266 (51%), Gaps = 9/266 (3%) Query: 1 MIRGSTELVAIVGSPIAQVKSPQNFNTWFNHNNCNLAMLPIDLHEAALDSFADTLRGW-- 58 MI G T L+A +G P K+P +N WF N ++P+ L + FAD LR Sbjct: 1 MIDGKTTLIAHIGYPTESFKAPMIYNPWFAQRGINAVVVPMGLKA---EHFADGLRTLFR 57 Query: 59 -QNLRGCVVTVPYKQALANRVDGLSERAAALGSINVIRRERDGRLLGDNVDGAGFLGAAH 117 NLRG ++T+P+K + VD L+ A G+ N + DG LLGD DGAGF+ Sbjct: 58 LTNLRGALITMPHKVSTMELVDALTPTARIAGACNAVLLRDDGTLLGDQFDGAGFVRGIQ 117 Query: 118 KHGFEPAGKRALVIGCGGVGSAIAYALAEAGIASITLCDPSTARMGAVCELLGNGFPGLT 177 + G + G LV GCGGVGSAIA +LA AG+A + L D A A+ L +P L Sbjct: 118 RKGCQLEGASVLVSGCGGVGSAIAASLAGAGVARLGLFDARDASAQALAARLQAHYPQLQ 177 Query: 178 VSTQFSGLEDFDLVANASPVGMGTRAELPLSAALLATLQPDTLVADVVTSPEITPLLNRA 237 V T + + LV NA+P+GM LP ++ + P V +VV E TPLL A Sbjct: 178 VGTGSNDPAGYQLVVNATPLGMNEDDPLPFD---VSRIDPQAWVGEVVMKTEYTPLLRAA 234 Query: 238 RQVGCRIQTGPEMAFAQLGHLGAFMG 263 + GC++Q G +M F + F G Sbjct: 235 LERGCQVQVGTDMLFEMIPAYLEFFG 260 Lambda K H 0.320 0.137 0.407 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: 202 Number of extensions: 10 Number of successful extensions: 2 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: 269 Length of database: 277 Length adjustment: 25 Effective length of query: 244 Effective length of database: 252 Effective search space: 61488 Effective search space used: 61488 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: 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