Align shikimate dehydrogenase (NADP+) (EC 1.1.1.25); quinate/shikimate dehydrogenase [NAD(P)+] (EC 1.1.1.282) (characterized)
to candidate WP_038212450.1 Q392_RS22085 shikimate dehydrogenase
Query= BRENDA::Q88JP1 (269 letters) >NCBI__GCF_000745855.1:WP_038212450.1 Length = 306 Score = 127 bits (319), Expect = 3e-34 Identities = 79/260 (30%), Positives = 122/260 (46%), Gaps = 7/260 (2%) Query: 2 IRGSTELVAIVGSPIAQVKSPQNFNTWFNHNNCNLAMLPIDLHEAALDSFADTLRGWQNL 61 I G+T+L I G P+ V+ P+ FN F+ MLP+ + + +N+ Sbjct: 4 IHGNTDLYLIPGDPVTNVRLPRMFNAVFDRCGIAARMLPVQVRARDFAVWLKASFLARNV 63 Query: 62 RGCVVTVPYKQALANRVDGLSERAAALGSINVIRRERDGRLLGDNVDGAGFLGAAHKHGF 121 +G V+ P+K + +DG A GS+NV+RR G L GD DG G +GA + G Sbjct: 64 KGMVIAPPHKPLAVDLLDGCGLFARIAGSVNVVRRTHTGDLEGDLFDGEGIVGALDRFGI 123 Query: 122 EPAGKRALVIGCGGVGSAIAYALAEA----GIASITLCDPSTARMGAVCELLGNGFPGLT 177 G+R L++G G +AI +LAE G I DP+ + V + + F Sbjct: 124 PFRGRRVLILGAGVSAAAIGVSLAEGGGDDGAGHIAFYDPAPGKSAGVAARIDDAFDARV 183 Query: 178 VSTQFSGLEDFDLVANASPVGMGTRAELPLSAALLATLQPDTLVADVVTSPEITPLLNRA 237 V+ + +DLV N + VG+ LP +A ++P + D++ + TPL+ A Sbjct: 184 VAVPSADPAGYDLVINGTSVGLSEGDPLPCD---VARMEPHAALFDILLRNQPTPLVRAA 240 Query: 238 RQVGCRIQTGPEMAFAQLGH 257 R G Q G EM Q+ H Sbjct: 241 RARGLHAQPGFEMLVQQMAH 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: 208 Number of extensions: 13 Number of successful extensions: 4 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: 306 Length adjustment: 26 Effective length of query: 243 Effective length of database: 280 Effective search space: 68040 Effective search space used: 68040 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