Align shikimate dehydrogenase (NADP+) (EC 1.1.1.25); 3-dehydroquinate dehydratase (EC 4.2.1.10) (characterized)
to candidate SMc02791 SMc02791 shikimate 5-dehydrogenase
Query= BRENDA::A0A5H2X4C4 (538 letters) >FitnessBrowser__Smeli:SMc02791 Length = 286 Score = 124 bits (312), Expect = 4e-33 Identities = 97/282 (34%), Positives = 146/282 (51%), Gaps = 28/282 (9%) Query: 265 IIGKPVGHSKSPLLYNQAFKSAGFDGVFLHLLVDDVA--SFLQTYSS--TDFAGFSCTIP 320 + G PV HS+SPL++ K G G + V A F++ TDF G + TIP Sbjct: 14 VTGYPVKHSRSPLIHGHWLKQFGIRGSYRAHEVTPEAFPDFMRQIKEGRTDFCGGNVTIP 73 Query: 321 HKEAAVKCCDEVDPVAKSIGAVNCIIRRQSDAKLFGYNTDYVGAISAIEDGLRGSQNGNS 380 HKEAA + D D ++ +GA N + + K+ NTD G ++ +++ +G ++ Sbjct: 74 HKEAAFRLADRPDELSAELGAANTLWLE--NGKIRATNTDGRGFVANLDERAKGWDRISA 131 Query: 381 AGASPLNGKLFVVIGAGGAGKALGYGAKEKGARVV-IANRTYDRARELAETIGG--DALS 437 A V++GAGGA +A+ +++G + + + NRT +RARELA+ G A S Sbjct: 132 A----------VILGAGGASRAVIQAIRDRGVKTIHVVNRTPERARELADRFGTAVHAHS 181 Query: 438 LADLENFHPEDGMILANTTSIGMQPKVDETPIPK---HALKHYSLVFDAVYTPKITRLLK 494 +A L G+ + NTTS+GM D P P L ++V D VY P T LL+ Sbjct: 182 MAALPEVVSGAGLFV-NTTSLGM----DGEPAPAIDFSGLAPDAVVTDIVYVPLKTPLLR 236 Query: 495 EAEECGATIVSGLEMFIGQAYGQYERYTGL-PAPKELFRKIM 535 +AEE G IV GL M + QA +E++ GL P E R+I+ Sbjct: 237 QAEEQGFRIVDGLGMLLHQAVPGFEKWFGLRPVVDETLRQII 278 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: 344 Number of extensions: 18 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: 286 Length adjustment: 31 Effective length of query: 507 Effective length of database: 255 Effective search space: 129285 Effective search space used: 129285 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