Align shikimate dehydrogenase (NADP+) (EC 1.1.1.25); 3-dehydroquinate dehydratase (EC 4.2.1.10) (characterized)
to candidate SM_b20037 SM_b20037 shikimate 5-dehydrogenase
Query= BRENDA::Q6PUG0 (521 letters) >FitnessBrowser__Smeli:SM_b20037 Length = 286 Score = 92.0 bits (227), Expect = 2e-23 Identities = 75/219 (34%), Positives = 109/219 (49%), Gaps = 23/219 (10%) Query: 292 FAGFSVGIPYKEAVVSFCDEVDPLAKSIGAVNTIIQRPCDGKLIGYNTDCEASITAIEDA 351 FAG ++ P K+AV+ + DE+ A+ +GAVNT++ R G+ G+NTD Sbjct: 67 FAGLNITHPCKQAVIPYLDELASEARQLGAVNTVVLR--SGRRYGHNTDWWGFAEGFR-- 122 Query: 352 LKVNGLTNGAAFLPSPLAGKLFVLVGAGGAGRALAFGAKSRRAE-IVIFDIDFDRAKALA 410 GL + F V +GAGGAG A A+ A S + +V+FD + RA+ALA Sbjct: 123 ---RGLPDADLFSA--------VQLGAGGAGVATAYAALSLGLQRLVVFDREAGRAQALA 171 Query: 411 AAVS-----GEALPFENLASFQPEKGAILANATPIGMHPNKDRIPVSEASLKDYVVVFDA 465 +S E +L S + A L +ATP GM +P+ L + V + Sbjct: 172 RMLSPLFPRAEVAAGNDLPS-EMRNAAGLIHATPTGM-AKYPGLPLDAELLSRSLWVAEI 229 Query: 466 VYTPRKTTLLKDAEAAGAITVSGVEMFLRQAIGQFHLFT 504 VY P +T LL++A G T+ G M + QA+G F LFT Sbjct: 230 VYFPLETALLREARRRGCKTLDGGGMAVFQAVGAFRLFT 268 Lambda K H 0.320 0.138 0.405 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: 261 Number of extensions: 17 Number of successful extensions: 3 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: 521 Length of database: 286 Length adjustment: 30 Effective length of query: 491 Effective length of database: 256 Effective search space: 125696 Effective search space used: 125696 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: 50 (23.9 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