Align shikimate dehydrogenase (NADP+) (EC 1.1.1.25); 3-dehydroquinate dehydratase (EC 4.2.1.10) (characterized)
to candidate WP_015738681.1 ADEG_RS03355 shikimate dehydrogenase
Query= BRENDA::A0A5H2X4C4 (538 letters) >NCBI__GCF_000024605.1:WP_015738681.1 Length = 297 Score = 144 bits (363), Expect = 4e-39 Identities = 95/296 (32%), Positives = 158/296 (53%), Gaps = 27/296 (9%) Query: 256 IGPDTKVFGIIGKPVGHSKSPLLYNQAFKSAGFDGVFLHLLV--DDVASFLQTYSSTDFA 313 I +T++ GI G P+ H+ SP ++N AF++ + +++ V +++A + + A Sbjct: 3 IDGNTRIVGIFGDPIAHTLSPHMHNAAFRALNLNYIYVPFWVRREELAEATAAIRALNLA 62 Query: 314 GFSCTIPHKEAAVKCCDEVDPVAKSIGAVNCIIRRQSDAKLFGYNTDYVGAISAIEDGLR 373 G + T+PHKEA + DE++ A IGAVN ++ + KL+G NTD G ++A+++ Sbjct: 63 GVNVTVPHKEAIIPYLDELEEEACLIGAVNTVVNQ--GGKLWGSNTDASGFLAALQE--- 117 Query: 374 GSQNGNSAGASPLNGKLFVVIGAGGAGKALGYG-AKEKGARVVIANRTYDRARELAET-- 430 G +P K+ V+GAGGA +A+G A+ + + NRT+DRA ELA Sbjct: 118 -------EGFAPAKKKV-AVLGAGGAARAVGVALARSQVEEITFFNRTFDRAAELAAYLE 169 Query: 431 ----IGGDALSLADLENFHPEDGM----ILANTTSIGMQPKVDETP-IPKHALKHYSLVF 481 + AL ++ +F + + ++ TTS+GM P+ E P + + A + LV Sbjct: 170 ERTGVRARALPWEEMGSFRGIEFLQAADLIVQTTSLGMHPREGEMPPVAEEAFRPGQLVI 229 Query: 482 DAVYTPKITRLLKEAEECGATIVSGLEMFIGQAYGQYERYTGLPAPKELFRKIMSK 537 D VY P TR L A++ GA SGL M + Q + +TG+PAP E+ R + + Sbjct: 230 DLVYRPLKTRFLSLAQKRGAKTASGLGMLLYQGALAFSLWTGVPAPLEVMRAALEE 285 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: 291 Number of extensions: 14 Number of successful extensions: 6 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: 297 Length adjustment: 31 Effective length of query: 507 Effective length of database: 266 Effective search space: 134862 Effective search space used: 134862 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 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