Align shikimate dehydrogenase (NADP+) (EC 1.1.1.25); 3-dehydroquinate dehydratase (EC 4.2.1.10) (characterized)
to candidate WP_011841953.1 RSPH17029_RS14595 shikimate dehydrogenase
Query= BRENDA::Q6PUG0 (521 letters) >NCBI__GCF_000015985.1:WP_011841953.1 Length = 279 Score = 103 bits (258), Expect = 6e-27 Identities = 94/283 (33%), Positives = 130/283 (45%), Gaps = 21/283 (7%) Query: 244 GLISKPVGHSKGPILHNPTFRHVGYNGIYVPMFVD--DLKEFFRVYSSPDFAGFSVGIPY 301 G+I P+ HS+ P LH + G G Y+PM V DL++ F G +V IP+ Sbjct: 11 GVIGSPIAHSRSPALHGYWLKRYGLKGHYIPMDVAQADLRDVLAAMPRMGFVGCNVTIPH 70 Query: 302 KEAVVSFCDEVDPLAKSIGAVNTIIQRPCDGKLIGYNTDCEASITAIEDALKVNGLTNGA 361 KE+V+ D V A IGA NT+I R DGK+ NTD N N Sbjct: 71 KESVIGLADIVTDRAALIGAANTLIFRK-DGKIYADNTD--------GTGFTANLRQNAP 121 Query: 362 AFLPSPLAGKLFVLVGAGGAGRA-LAFGAKSRRAEIVIFDIDFDRAKALAAAVSGEALPF 420 A+ P V+ GAGGA RA +A + EI + + RA AL + + Sbjct: 122 AWQPQSGPA---VVWGAGGAARAVIAALIEVGVPEIRLANRSRARADALRSDFGAKVHVH 178 Query: 421 ENL-ASFQPEKGAILANATPIGMHPNKD-RIPVSEASLKDYVVVFDAVYTPRKTTLLKDA 478 + + A E + N T +GM + R+P+ +L VV D VY P +T LL +A Sbjct: 179 DWVQAGNILEDAMTVVNTTSLGMVGKPEFRVPLD--ALNPKAVVTDLVYAPLRTRLLVEA 236 Query: 479 EAAGAITVSGVEMFLRQAIGQFHLF--TRTKAPEEFMRDIVMA 519 EAAG TV G+ M L QA F + R + EE ++ A Sbjct: 237 EAAGCRTVDGLGMLLHQAAPGFERWFGVRPEVDEETRAAVLAA 279 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: 315 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: 279 Length adjustment: 30 Effective length of query: 491 Effective length of database: 249 Effective search space: 122259 Effective search space used: 122259 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 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