Align shikimate dehydrogenase (NADP+) (EC 1.1.1.25); quinate/shikimate dehydrogenase [NAD(P)+] (EC 1.1.1.282) (characterized)
to candidate BPHYT_RS30065 BPHYT_RS30065 shikimate dehydrogenase
Query= BRENDA::Q88JP1 (269 letters) >FitnessBrowser__BFirm:BPHYT_RS30065 Length = 282 Score = 147 bits (370), Expect = 3e-40 Identities = 92/262 (35%), Positives = 135/262 (51%), Gaps = 4/262 (1%) Query: 2 IRGSTELVAIVGSPIAQVKSPQNFNTWFNHNNCNLAMLPIDLHEAALDSFADTLRGWQNL 61 + G+T +V IVG PIAQV+SP + ++P + A L +F + +N+ Sbjct: 17 LSGATRVVFIVGDPIAQVRSPSGVTAALRAAGRDALVVPAHVAPADLPAFFAGVTPMRNV 76 Query: 62 RGCVVTVPYKQALANRVDGLSERAAALGSINVIRRERDGRLLGDNVDGAGFLGAAHKHGF 121 G ++TVP+K + L+E+A+ LG++N +RR DG G DG GF+ A G Sbjct: 77 DGVIITVPHKFSAIKYCGSLTEQASFLGAVNTLRRTADGNWHGGMFDGTGFVAALVDAGC 136 Query: 122 EPAGKRALVIGCGGVGSAIAYALAEAGIASITLCDPSTARMGAVCELLGNGFPGLTVSTQ 181 + GK AL++G GG G AI +AL + G+AS+ + D R ++ L G S Sbjct: 137 DLRGKHALLVGAGGAGCAIGHALVQGGVASLDVRDNDAERTASLIGRLNALRQGEVRSAA 196 Query: 182 FS-GLEDFDLVANASPVGMGTRAELPLSAALLATLQPDTLVADVVTSPEITPLLNRARQV 240 S +D+V NASP+GM LPL ++ L T V DVVT P +TPL+ AR Sbjct: 197 ASVDASTYDVVINASPLGMRADDPLPLD---VSRLPATTFVGDVVTKPPLTPLIEAARAR 253 Query: 241 GCRIQTGPEMAFAQLGHLGAFM 262 GC TG +M + AF+ Sbjct: 254 GCPTVTGTQMFGRVCDRMVAFL 275 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: 229 Number of extensions: 13 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: 282 Length adjustment: 25 Effective length of query: 244 Effective length of database: 257 Effective search space: 62708 Effective search space used: 62708 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