Align shikimate dehydrogenase (NADP+) (EC 1.1.1.25); quinate/shikimate dehydrogenase [NAD(P)+] (EC 1.1.1.282) (characterized)
to candidate N515DRAFT_3412 N515DRAFT_3412 shikimate dehydrogenase
Query= BRENDA::Q88GF6 (273 letters) >FitnessBrowser__Dyella79:N515DRAFT_3412 Length = 271 Score = 342 bits (878), Expect = 4e-99 Identities = 175/265 (66%), Positives = 202/265 (76%), Gaps = 1/265 (0%) Query: 6 SRDTVLCISLAGRPGTFGVRFHNHLYQQLGLDFYYKAMRTDDLPAAVAGIRALGIRGCGV 65 SRDT LC+SL+GRPG FG RF N+LY+ LGLD+ YKA T DLPAA+ GIRALGIRGC V Sbjct: 6 SRDTQLCMSLSGRPGNFGTRFQNYLYEALGLDYVYKAFTTRDLPAAIGGIRALGIRGCAV 65 Query: 66 SMPYKEACMALVDEIDPSAAAIESVNTLVNCNGHLKAYNTDYLAVRQLLAQHQVDPGTAF 125 SMP+KEACM LVD ID SA AIESVNT+VN +GHL+AYNTDY+AV +L+ QH+V P T Sbjct: 66 SMPFKEACMPLVDSIDASAQAIESVNTIVNDDGHLRAYNTDYIAVARLIEQHRVAPETTL 125 Query: 126 ALRGSGGMAKAVASALRDAGFAEGIIVARNEQAGRQLADVCGYRWVPEPGDICPPMLVNV 185 ALRGSGGMAKAVA ALRD GF G I+ARNE GR LA CGY W P+ D+ +L+NV Sbjct: 126 ALRGSGGMAKAVACALRDKGFRRGHIIARNETTGRALAQTCGYAWAPDMRDVEAQLLINV 185 Query: 186 TPIGMAGGLEAEELAFPEHAIAAAERVFDVVAMPAQTPLIRRAQALGKPVITGLEVIALQ 245 TP+GM G EAE LAF E + A VFDVVA+P +TPLIR A+A GK VITG EVI LQ Sbjct: 186 TPLGMEGP-EAESLAFTEAEVERASVVFDVVALPPETPLIRLARARGKQVITGAEVIVLQ 244 Query: 246 ALEQFVLYTGVRPTREQVDAAVAYA 270 A+EQFVLYTGVRP + A A+A Sbjct: 245 AVEQFVLYTGVRPEDALIAEAAAHA 269 Lambda K H 0.322 0.136 0.406 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: 288 Number of extensions: 7 Number of successful extensions: 2 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: 273 Length of database: 271 Length adjustment: 25 Effective length of query: 248 Effective length of database: 246 Effective search space: 61008 Effective search space used: 61008 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 (21.9 bits) S2: 47 (22.7 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