Align shikimate dehydrogenase (NADP+) (EC 1.1.1.25); quinate/shikimate dehydrogenase [NAD(P)+] (EC 1.1.1.282) (characterized)
to candidate YP_004141774.1 Mesci_2588 shikimate dehydrogenase substrate binding domain-containing protein
Query= BRENDA::Q88JP1 (269 letters) >NCBI__GCF_000185905.1:YP_004141774.1 Length = 270 Score = 164 bits (415), Expect = 2e-45 Identities = 90/261 (34%), Positives = 133/261 (50%), Gaps = 3/261 (1%) Query: 4 GSTELVAIVGSPIAQVKSPQNFNTWFNHNNCNLAMLPIDLHEAALDSFADTLRGWQNLRG 63 G E+ ++ P+A KSP FN F + M+P+ ++F + +N+RG Sbjct: 5 GKAEIFVMLAHPVAHAKSPGIFNEIFEQKGLDSLMVPLSCRPEDFEAFWAGITAAENIRG 64 Query: 64 CVVTVPYKQALANRVDGLSERAAALGSINVIRRERDGRLLGDNVDGAGFLGAAHKHGFEP 123 +++VPYK A+ ++ +RAA + S N +RR DG DN DG GF+ G E Sbjct: 65 VIISVPYKVAVYHKCTAAHDRAARVQSANSVRRLPDGSWYADNFDGVGFIDGLKAGGHEI 124 Query: 124 AGKRALVIGCGGVGSAIAYALAEAGIASITLCDPSTARMGAVCELLGNGFPGLTVSTQFS 183 AG+R L +G GG G+++AY LAEAG I L D T R + L+ FP + + Sbjct: 125 AGRRILQVGAGGAGASLAYCLAEAGAEEIRLADIDTGRAEKLAALVAQVFPKCRIQVGEA 184 Query: 184 GLEDFDLVANASPVGMGTRAELPLSAALLATLQPDTLVADVVTSPEITPLLNRARQVGCR 243 + NA+PVGM LPL ++ L PD V D++ P TPLL A+++GCR Sbjct: 185 EPSGMHMAINATPVGMHAGDPLPLD---VSRLTPDMTVVDIIMEPAETPLLKAAKEIGCR 241 Query: 244 IQTGPEMAFAQLGHLGAFMGV 264 IQ G M Q+ + F + Sbjct: 242 IQPGRPMMDFQVRAMSEFFDI 262 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: 212 Number of extensions: 11 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: 270 Length adjustment: 25 Effective length of query: 244 Effective length of database: 245 Effective search space: 59780 Effective search space used: 59780 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