Align shikimate dehydrogenase (NADP+) (EC 1.1.1.25); quinate/shikimate dehydrogenase [NAD(P)+] (EC 1.1.1.282) (characterized)
to candidate WP_050460854.1 AKL27_RS01590 shikimate dehydrogenase
Query= BRENDA::Q88JP1 (269 letters) >NCBI__GCF_001189915.1:WP_050460854.1 Length = 273 Score = 140 bits (354), Expect = 2e-38 Identities = 86/267 (32%), Positives = 133/267 (49%), Gaps = 7/267 (2%) Query: 2 IRGSTELVAIVGSPIAQVKSPQNFNTWFNHNNCNLAMLPIDLHEAALDSFADTLRGWQNL 61 I G+T +VAI+ PI V++PQ FN + M+P ++ F NL Sbjct: 9 ITGNTRVVAIIADPIGHVRTPQAFNALMAQRAADAVMVPFNVKPEHFARFIVAAPLIHNL 68 Query: 62 RGCVVTVPYKQALANRVDGLSERAAALGSINVIR----RERDGRLLGDNVDGAGFLGAAH 117 G VVT+PYK+ + L++ A +G++N++R ++ LLG N DGAGF+G Sbjct: 69 AGLVVTIPYKETILAHCTELTDAAQRMGAVNIVRFGDAQDGSRSLLGGNFDGAGFVGGLL 128 Query: 118 KHGFEPAGKRALVIGCGGVGSAIAYALAEAGIASITLCDPSTARMGAVCELLGNGFPGLT 177 G+ G+R + G GG AIA+ALA GIA++ + + S R + L +P L Sbjct: 129 AQGYAVQGRRVYLAGAGGAAKAIAHALAAEGIAALGIYNRSPERAEQLVRELRQYYPQLD 188 Query: 178 VSTQFSGLEDFDLVANASPVGMGTRAELPLSAALLATLQPDTLVADVVTSPEITPLLNRA 237 + D+ L N++ +G+ + LP + L LVA+VV EITPLL +A Sbjct: 189 AHLAGAAPADYTLAINSTSLGLQSADPLPFAP---DGLPAGALVAEVVMKTEITPLLAKA 245 Query: 238 RQVGCRIQTGPEMAFAQLGHLGAFMGV 264 G + G M Q+ +G F+G+ Sbjct: 246 GACGLAVHFGRHMLEVQIERMGQFLGL 272 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: 165 Number of extensions: 7 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: 273 Length adjustment: 25 Effective length of query: 244 Effective length of database: 248 Effective search space: 60512 Effective search space used: 60512 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