Align shikimate dehydrogenase (NADP+) (EC 1.1.1.25); quinate/shikimate dehydrogenase [NAD(P)+] (EC 1.1.1.282) (characterized)
to candidate SM_b20037 SM_b20037 shikimate 5-dehydrogenase
Query= BRENDA::Q88K85 (282 letters) >FitnessBrowser__Smeli:SM_b20037 Length = 286 Score = 307 bits (786), Expect = 2e-88 Identities = 161/279 (57%), Positives = 193/279 (69%) Query: 4 QAILAGLIGRGIQLSRTPALHEHEGDAQALRYLYRLIDADQLQLDDSALPGLLEAAQHTG 63 +++ AGLIG GIQ S TPA+H EG AQ +RY Y LID + L + LP LL A+ G Sbjct: 7 RSLKAGLIGTGIQASLTPAMHMAEGAAQGIRYDYELIDLNLLGASEKDLPRLLADAERRG 66 Query: 64 FTGLNITYPFKQAILPLLDELSDEARGIGAVNTVVLKDGKRVGHNTDCLGFAEGLRRGLP 123 F GLNIT+P KQA++P LDEL+ EAR +GAVNTVVL+ G+R GHNTD GFAEG RRGLP Sbjct: 67 FAGLNITHPCKQAVIPYLDELASEARQLGAVNTVVLRSGRRYGHNTDWWGFAEGFRRGLP 126 Query: 124 DVARRQVVQMGAGGAGSAVAHALLGEGVERLVLFEVDATRAQALVDNLNTHFGAERAVLG 183 D VQ+GAGGAG A A+A L G++RLV+F+ +A RAQAL L+ F G Sbjct: 127 DADLFSAVQLGAGGAGVATAYAALSLGLQRLVVFDREAGRAQALARMLSPLFPRAEVAAG 186 Query: 184 TDLATALAEADGLVNTTPVGMAKLPGTPLPVELLHPRLWVAEIIYFPLETELLRAARALG 243 DL + + A GL++ TP GMAK PG PL ELL LWVAEI+YFPLET LLR AR G Sbjct: 187 NDLPSEMRNAAGLIHATPTGMAKYPGLPLDAELLSRSLWVAEIVYFPLETALLREARRRG 246 Query: 244 CRTLDGSNMAVFQAVKAFELFSGRQADAARMQAHFASFT 282 C+TLDG MAVFQAV AF LF+G + DAARM HF + T Sbjct: 247 CKTLDGGGMAVFQAVGAFRLFTGLEPDAARMLGHFRAMT 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: 246 Number of extensions: 7 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: 286 Length adjustment: 26 Effective length of query: 256 Effective length of database: 260 Effective search space: 66560 Effective search space used: 66560 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 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