Align shikimate dehydrogenase (NADP+) (EC 1.1.1.25); quinate/shikimate dehydrogenase [NAD(P)+] (EC 1.1.1.282) (characterized)
to candidate H281DRAFT_03216 H281DRAFT_03216 shikimate dehydrogenase (EC 1.1.1.25)
Query= BRENDA::Q88K85 (282 letters) >FitnessBrowser__Burk376:H281DRAFT_03216 Length = 300 Score = 330 bits (845), Expect = 3e-95 Identities = 166/279 (59%), Positives = 199/279 (71%) Query: 2 SQQAILAGLIGRGIQLSRTPALHEHEGDAQALRYLYRLIDADQLQLDDSALPGLLEAAQH 61 S + L GLIG GI S +PA+HE EG L Y+YR ID + L+LD +ALP LL AA+ Sbjct: 18 SANSYLVGLIGSGIGGSLSPAMHEEEGSKLGLHYVYRRIDLEALKLDVAALPDLLVAAER 77 Query: 62 TGFTGLNITYPFKQAILPLLDELSDEARGIGAVNTVVLKDGKRVGHNTDCLGFAEGLRRG 121 G+ GLNITYP KQA++PLLDELSD+AR +GAVNTV+ KDGKR+GHNTD GFA RRG Sbjct: 78 MGYNGLNITYPCKQAVIPLLDELSDDARALGAVNTVLFKDGKRIGHNTDWSGFARAFRRG 137 Query: 122 LPDVARRQVVQMGAGGAGSAVAHALLGEGVERLVLFEVDATRAQALVDNLNTHFGAERAV 181 LPDVA +VVQ+GAGGAG+AVAHA L G + L LF+VDA RA +L L F Sbjct: 138 LPDVALDRVVQLGAGGAGAAVAHAALAMGTQTLTLFDVDAARAASLAAELQKRFADRTVT 197 Query: 182 LGTDLATALAEADGLVNTTPVGMAKLPGTPLPVELLHPRLWVAEIIYFPLETELLRAARA 241 GT L LA A+GL++ TP GMAKLPG PLP ELLH LWVA+I+YFP+ T LL+AA A Sbjct: 198 AGTSLGETLAAANGLIHATPTGMAKLPGLPLPAELLHSGLWVADIVYFPIRTALLQAAEA 257 Query: 242 LGCRTLDGSNMAVFQAVKAFELFSGRQADAARMQAHFAS 280 LGCRTL G MAV+QAV A +F+G + DA R+ HF S Sbjct: 258 LGCRTLSGGGMAVYQAVDAMRIFTGLEPDAERVYTHFQS 296 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: 218 Number of extensions: 6 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: 300 Length adjustment: 26 Effective length of query: 256 Effective length of database: 274 Effective search space: 70144 Effective search space used: 70144 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: 48 (23.1 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