Align shikimate dehydrogenase (NADP+) (EC 1.1.1.25); quinate/shikimate dehydrogenase [NAD(P)+] (EC 1.1.1.282) (characterized)
to candidate WP_051953420.1 Q392_RS13315 shikimate dehydrogenase
Query= BRENDA::Q88JP1 (269 letters) >NCBI__GCF_000745855.1:WP_051953420.1 Length = 275 Score = 170 bits (430), Expect = 3e-47 Identities = 110/252 (43%), Positives = 140/252 (55%), Gaps = 10/252 (3%) Query: 2 IRGSTELVAIVGSPIAQVKSPQNFNTWFNHNNCNLAMLPIDLHEAALDSFADTLRGW--- 58 + G+T + IVG PIAQVKSPQ F ++P + A D AD LRG Sbjct: 14 LSGATRVHFIVGDPIAQVKSPQGVTQAFQARGLQAVVVPAHV---APDDLADWLRGVSLA 70 Query: 59 QNLRGCVVTVPYKQALANRVDGLSERAAALGSINVIRRERDGRLLGDNVDGAGFLGAAHK 118 QN+ G +VTVP+K A A LSE+AA LG++N +RR DGR GD DG G + A Sbjct: 71 QNVDGVIVTVPHKFASAALCATLSEQAAFLGAVNTLRRNADGRWHGDMFDGLGCVQALRA 130 Query: 119 HGFEPAGKRALVIGCGGVGSAIAYALAEAGIASITLCDPSTARMGAVCELLGNGFPGLTV 178 HG +PAG+RAL++G GG G+AIA+AL AG+A + + D AR A+ L G V Sbjct: 131 HGCDPAGRRALLVGAGGAGTAIAHALVLAGVAQLAVHDGDAARRDALVGRLA-GLGRCPV 189 Query: 179 STQFSGLEDFDLVANASPVGMGTRAELPLSAALLATLQPDTLVADVVTSPEITPLLNRAR 238 + + FDLV NASP GM LP+ LA P T VA VVT P +TPL+ AR Sbjct: 190 AAGSADPAGFDLVVNASPAGMREDDPLPVQVEGLA---PGTFVACVVTQPAVTPLIAAAR 246 Query: 239 QVGCRIQTGPEM 250 G TG +M Sbjct: 247 ARGLDTSTGNDM 258 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: 227 Number of extensions: 16 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: 275 Length adjustment: 25 Effective length of query: 244 Effective length of database: 250 Effective search space: 61000 Effective search space used: 61000 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