Align shikimate dehydrogenase (NADP+) (EC 1.1.1.25); quinate/shikimate dehydrogenase [NAD(P)+] (EC 1.1.1.282) (characterized)
to candidate WP_015934250.1 MNOD_RS38005 shikimate 5-dehydrogenase
Query= BRENDA::Q88JP1 (269 letters) >NCBI__GCF_000022085.1:WP_015934250.1 Length = 277 Score = 165 bits (418), Expect = 9e-46 Identities = 97/263 (36%), Positives = 137/263 (52%), Gaps = 3/263 (1%) Query: 1 MIRGSTELVAIVGSPIAQVKSPQNFNTWFNHNNCNLAMLPIDLHEAALDSFADTLRGWQN 60 MIRG+T L+A +G P K+P +N WF + ++P+ + ++ N Sbjct: 1 MIRGTTTLIAHLGFPTESFKAPMIYNPWFEKTGIDAVVMPMGVRAENYPDVFRSIFRLTN 60 Query: 61 LRGCVVTVPYKQALANRVDGLSERAAALGSINVIRRERDGRLLGDNVDGAGFLGAAHKHG 120 +RG +VT+P+K + +D +S A GS N + DG LLGD DGAGF+ + G Sbjct: 61 IRGALVTMPHKITTVSLLDEVSTTAKIAGSCNAVLLRPDGSLLGDMFDGAGFVRGIQRKG 120 Query: 121 FEPAGKRALVIGCGGVGSAIAYALAEAGIASITLCDPSTARMGAVCELLGNGFPGLTVST 180 + G R LV+G GGVGSAIA +LA AGI I + D + A+ L +P L + T Sbjct: 121 RDLTGARVLVVGSGGVGSAIAASLAAAGIGEIGVYDYNPTAAEALAGRLREHYPALGIRT 180 Query: 181 QFSGLEDFDLVANASPVGMGTRAELPLSAALLATLQPDTLVADVVTSPEITPLLNRARQV 240 FD+V NA+P+GM LP+ +A L P T V +VV E TP L A++ Sbjct: 181 GSDDPTGFDVVVNATPLGMKEGDPLPVD---VARLDPGTFVGEVVMKQEHTPFLEAAQEK 237 Query: 241 GCRIQTGPEMAFAQLGHLGAFMG 263 GC IQ G +M F Q+ F G Sbjct: 238 GCPIQVGTDMLFEQIPAYLEFFG 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: 184 Number of extensions: 8 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: 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 10 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