Align mannitol 2-dehydrogenase (EC 1.1.1.67) (characterized)
to candidate GFF4244 Psest_4317 zinc-binding alcohol dehydrogenase family protein
Query= BRENDA::Q9WYD4 (317 letters) >FitnessBrowser__psRCH2:GFF4244 Length = 327 Score = 89.4 bits (220), Expect = 1e-22 Identities = 58/154 (37%), Positives = 79/154 (51%), Gaps = 10/154 (6%) Query: 20 PVPGEDQTLVKVLACGICGTDYKIFSGGTNAN-YPVVPGHEIVGVVERSGV----FEKGQ 74 P PG + V+VLACG+C TD + G A P++PGHEIVG V+ G FE GQ Sbjct: 21 PQPGPGELRVRVLACGVCRTDLHVVDGELPAAPLPIIPGHEIVGRVDALGEGVSGFELGQ 80 Query: 75 MVVID-PNRSCGKCDYCRKGMSQFCENLQATGVTEPGGFAEYVLVENSQVYPVRNVPAER 133 V I +CG C YC+ C+ Q TG T PGG+AEYV+ + + + Sbjct: 81 RVGIPWLGHTCGTCSYCQHAEENLCDAPQFTGYTRPGGYAEYVVADARFAFDLGE--QGD 138 Query: 134 AVFAEPLSC--VLEGVKMVKHGFYDRILVVGAGS 165 AV PL C ++ +VK G R+ + G G+ Sbjct: 139 AVALAPLLCAGLIGWRSLVKAGDGKRLGLYGFGA 172 Lambda K H 0.320 0.140 0.409 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: 273 Number of extensions: 10 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: 317 Length of database: 327 Length adjustment: 28 Effective length of query: 289 Effective length of database: 299 Effective search space: 86411 Effective search space used: 86411 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 (21.7 bits) S2: 48 (23.1 bits)
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
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