Align shikimate dehydrogenase (NADP+) (EC 1.1.1.25); 3-dehydroquinate dehydratase (EC 4.2.1.10) (characterized)
to candidate 209045 DVU0115 shikimate 5-dehydrogenase
Query= BRENDA::A0A5H2X4C4 (538 letters) >MicrobesOnline__882:209045 Length = 301 Score = 145 bits (367), Expect = 2e-39 Identities = 98/281 (34%), Positives = 149/281 (53%), Gaps = 22/281 (7%) Query: 261 KVFGIIGKPVGHSKSPLLYNQAFKSAGFDGVFLHLLVDD--VASFLQTYSSTDFAGFSCT 318 +++GI+G P+GH+ SPLL+N F V++ V ASF++ + G S T Sbjct: 35 RLYGIVGHPLGHTLSPLLHNWGFALHSLPAVYMAWPVPPGRFASFMEAVRTLPVHGASVT 94 Query: 319 IPHKEAAVKCCDEVDPVAKSIGAVNCIIRRQSDAKLFGYNTDYVGAISAIEDGLRGSQNG 378 IPHKE A++ CD V A+++GAVN + D + G NTD G ++ + RG + Sbjct: 95 IPHKEEALRLCDRVTDRARAVGAVNTLFLE--DGVVCGENTDVTGFLAPLR--ARGVRID 150 Query: 379 NSAGASPLNGKLFVVIGAGGAGKALGYGAKEKGARVV-IANRTYDRARELAETIGGDALS 437 + +V+GAGGA +A+ G E G R V I+NRT+D+A ELA G D + Sbjct: 151 EA-----------LVLGAGGAARAVLAGLVELGVRRVRISNRTHDKAMELAGAFGADVVP 199 Query: 438 LADLENFHPEDGMILANTTSIGMQ-PKVDETPIPKHALKHYSLVFDAVYTPKITRLLKEA 496 E G+++ NTT GMQ ++ E+P+P+ A + +D VY P TR L +A Sbjct: 200 WD--ERGSAAAGLVV-NTTPCGMQGARMGESPLPEGAFSGRGMAYDLVYNPLTTRFLADA 256 Query: 497 EECGATIVSGLEMFIGQAYGQYERYTGLPAPKELFRKIMSK 537 G GL MF+ Q Q+ +TGL P E R+++++ Sbjct: 257 RAAGWETQDGLGMFVEQGREQFRIWTGLDLPAEGARRLIAE 297 Lambda K H 0.317 0.135 0.385 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: 343 Number of extensions: 15 Number of successful extensions: 4 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: 538 Length of database: 301 Length adjustment: 31 Effective length of query: 507 Effective length of database: 270 Effective search space: 136890 Effective search space used: 136890 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 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