Align shikimate dehydrogenase (NADP+) (EC 1.1.1.25); quinate/shikimate dehydrogenase [NAD(P)+] (EC 1.1.1.282) (characterized)
to candidate YP_001314355.1 Smed_5698 shikimate 5-dehydrogenase
Query= BRENDA::Q88K85 (282 letters) >NCBI__GCF_000017145.1:YP_001314355.1 Length = 299 Score = 285 bits (729), Expect = 8e-82 Identities = 149/275 (54%), Positives = 181/275 (65%) Query: 8 AGLIGRGIQLSRTPALHEHEGDAQALRYLYRLIDADQLQLDDSALPGLLEAAQHTGFTGL 67 AGLIG+GIQ S TPALH EG AQ Y Y L D D + L LL A+ G GL Sbjct: 11 AGLIGKGIQASLTPALHMAEGRAQGFEYFYDLFDLDGVVGSSEPLTNLLAEAEGRGLGGL 70 Query: 68 NITYPFKQAILPLLDELSDEARGIGAVNTVVLKDGKRVGHNTDCLGFAEGLRRGLPDVAR 127 NIT+PFKQ ++ LD LSDEA +GAVNT+VL+ G+R GHNTD GFAE RRGLP Sbjct: 71 NITHPFKQQVIEFLDTLSDEAVALGAVNTIVLRGGRRHGHNTDWWGFAESFRRGLPRADL 130 Query: 128 RQVVQMGAGGAGSAVAHALLGEGVERLVLFEVDATRAQALVDNLNTHFGAERAVLGTDLA 187 VVQ+GAGGAG+A A A+L G L +F+ D +R+ ALV+N+ HF G DL+ Sbjct: 131 TSVVQLGAGGAGAATAFAILRSGAAGLTIFDQDESRSLALVENMQRHFPNAFIKAGADLS 190 Query: 188 TALAEADGLVNTTPVGMAKLPGTPLPVELLHPRLWVAEIIYFPLETELLRAARALGCRTL 247 A+A A GL++ TP GMAK PG P+P +LL LWVAE++YFPL TEL+ A GCRTL Sbjct: 191 GAMATASGLIHATPTGMAKYPGLPVPADLLRFSLWVAEVVYFPLSTELVIEAGRRGCRTL 250 Query: 248 DGSNMAVFQAVKAFELFSGRQADAARMQAHFASFT 282 +G MAVFQAVKAF LF+G + +A RM HF T Sbjct: 251 NGGGMAVFQAVKAFRLFTGVEPNAERMLKHFEEMT 285 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: 9 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: 299 Length adjustment: 26 Effective length of query: 256 Effective length of database: 273 Effective search space: 69888 Effective search space used: 69888 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 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