Align shikimate dehydrogenase (NADP+) (EC 1.1.1.25); quinate/shikimate dehydrogenase [NAD(P)+] (EC 1.1.1.282) (characterized)
to candidate WP_012169981.1 AZC_RS07480 shikimate 5-dehydrogenase
Query= BRENDA::Q88JP1 (269 letters) >NCBI__GCF_000010525.1:WP_012169981.1 Length = 276 Score = 164 bits (414), Expect = 2e-45 Identities = 97/266 (36%), Positives = 132/266 (49%), Gaps = 3/266 (1%) Query: 1 MIRGSTELVAIVGSPIAQVKSPQNFNTWFNHNNCNLAMLPIDLHEAALDSFADTLRGWQN 60 MI G+T+L+ +G P KSP +N +F + ++P+ SF N Sbjct: 1 MISGTTKLIGHIGFPTESFKSPMIYNPYFEREGIDAVVVPMGCEVPDYPSFLKLFFRLSN 60 Query: 61 LRGCVVTVPYKQALANRVDGLSERAAALGSINVIRRERDGRLLGDNVDGAGFLGAAHKHG 120 G ++T+P+K + VD S AA G+ N +RR DGRL GD DG GF+ + G Sbjct: 61 ALGTLITMPHKVTTLSLVDAASPTAAIAGACNAVRRREDGRLEGDLFDGEGFVRGMRRKG 120 Query: 121 FEPAGKRALVIGCGGVGSAIAYALAEAGIASITLCDPSTARMGAVCELLGNGFPGLTVST 180 G ALV+G GGVGSAIA +LA AG+A ITL D + E L +P L V Sbjct: 121 RVIEGTHALVVGAGGVGSAIAASLARAGVARITLFDSHPEAARQLAERLKRHYPALEVEV 180 Query: 181 QFSGLEDFDLVANASPVGMGTRAELPLSAALLATLQPDTLVADVVTSPEITPLLNRARQV 240 + D+V NA+P+GM LP+ +A P V +VV + EITP L R Sbjct: 181 GANDPAGCDIVVNATPLGMRAGDPLPVEVERIA---PSAFVGEVVMTHEITPFLAAVRAR 237 Query: 241 GCRIQTGPEMAFAQLGHLGAFMGVTP 266 GC Q G +M F Q+ F G+ P Sbjct: 238 GCAFQVGTDMLFEQIPAYFEFFGLPP 263 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: 203 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: 276 Length adjustment: 25 Effective length of query: 244 Effective length of database: 251 Effective search space: 61244 Effective search space used: 61244 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