Align shikimate dehydrogenase (NADP+) (EC 1.1.1.25); quinate/shikimate dehydrogenase [NAD(P)+] (EC 1.1.1.282) (characterized)
to candidate WP_011880899.1 shikimate dehydrogenase
Query= BRENDA::Q88K85 (282 letters) >NCBI__GCF_000016205.1:WP_011880899.1 Length = 284 Score = 322 bits (826), Expect = 4e-93 Identities = 165/280 (58%), Positives = 198/280 (70%) Query: 1 MSQQAILAGLIGRGIQLSRTPALHEHEGDAQALRYLYRLIDADQLQLDDSALPGLLEAAQ 60 MS+ + L GLIG+GI S +PA+HE EG Q Y+YR ID D L ++ ALP LL+AAQ Sbjct: 1 MSRPSFLIGLIGQGIGGSLSPAMHEEEGFRQGYGYVYRRIDLDALGVNADALPQLLDAAQ 60 Query: 61 HTGFTGLNITYPFKQAILPLLDELSDEARGIGAVNTVVLKDGKRVGHNTDCLGFAEGLRR 120 G+ GLNIT+P KQ ++ LD LSD+AR +GAVNTV+ KDGKR+GHNTD GFA RR Sbjct: 61 QMGYNGLNITHPCKQRVIEHLDALSDDARALGAVNTVLFKDGKRIGHNTDWSGFARSFRR 120 Query: 121 GLPDVARRQVVQMGAGGAGSAVAHALLGEGVERLVLFEVDATRAQALVDNLNTHFGAERA 180 GLPD + +VVQ+GAGGAG+AVAHA L G L +F+VD RA AL L F A R Sbjct: 121 GLPDASLARVVQLGAGGAGAAVAHAALQMGAAELTIFDVDGARAIALAGELQQRFPAARV 180 Query: 181 VLGTDLATALAEADGLVNTTPVGMAKLPGTPLPVELLHPRLWVAEIIYFPLETELLRAAR 240 G DLA A+ A GL++ TP GMAK PG PLP ELLH +WVA+I+YFPLETEL+RAAR Sbjct: 181 AAGDDLAAAMRAATGLIHATPTGMAKHPGLPLPAELLHAGMWVADIVYFPLETELIRAAR 240 Query: 241 ALGCRTLDGSNMAVFQAVKAFELFSGRQADAARMQAHFAS 280 A+GC TL G MAV+QAV AFELF+GR D RM HF S Sbjct: 241 AVGCATLPGGGMAVYQAVDAFELFTGRTPDDERMFEHFQS 280 Lambda K H 0.321 0.137 0.395 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: 236 Number of extensions: 11 Number of successful extensions: 1 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: 282 Length of database: 284 Length adjustment: 26 Effective length of query: 256 Effective length of database: 258 Effective search space: 66048 Effective search space used: 66048 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 (21.9 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