Align alcohol dehydrogenase (EC 1.1.1.1) (characterized)
to candidate Echvi_0924 Echvi_0924 Alcohol dehydrogenase, class IV
Query= BRENDA::P0DJA2 (383 letters) >FitnessBrowser__Cola:Echvi_0924 Length = 381 Score = 202 bits (515), Expect = 1e-56 Identities = 118/321 (36%), Positives = 183/321 (57%), Gaps = 4/321 (1%) Query: 60 INSAVYDGVMPNPTVTAVLEGLKILKDNNSDFVISLGGGSPHDCAKAIALVATNGGEVKD 119 + AVYD PT + + LK +KD +D ++ +GGGS D AK +A + + G++ D Sbjct: 60 VEVAVYDA--GEPTFSHYEDFLKQVKDFGADTIVGIGGGSVLDLAKLLAAMQDSTGQLSD 117 Query: 120 YEGIDKSKKPALPLMSINTTAGTASEMTRFCIITDEVRHVKMAIVDRHVTPMVSVNDPLL 179 + GI+ + ++ I TTAGT SE++ I+ DE K I+ + P + DP L Sbjct: 118 FVGINLLESRNTHMVCIPTTAGTGSEVSPNAILLDEATLEKKGIISPFLVPDATYIDPAL 177 Query: 180 MVGMPKGLTAATGMDALTHAFEAYSSTAATPITDACALKAASMIAKNLKTACDNGKDMPA 239 VG+P +TA TG+DAL+H EAY++ + P+ D AL+ ++I +NL A + +DM A Sbjct: 178 TVGLPPKITAETGIDALSHCIEAYTNKFSHPLVDDYALRGIALIGQNLHRAFEVPEDMDA 237 Query: 240 REAMAYAQFLAGMAFNNASLGYVHAMAHQLGGYYNLPHGVCNAVLLPHVLAYNASVVAGR 299 R A+A G+ + VHA+++ LGG Y++PHG+ NAVLLP V+AYN S + Sbjct: 238 RTAVALGSMYGGLCLGPVNTAAVHALSYPLGGKYHVPHGLANAVLLPEVMAYNLSSNIQK 297 Query: 300 LKDVGVAMGLDIANLGDKEGAEATIQAVRDLAASIGIPANLTELGAKKEDVPLLADHALK 359 + + +AMG + N +E A +Q V++L IP +LT LG ++EDVP L A+K Sbjct: 298 HEQIALAMGAEQGN-SPEETASNGVQKVKELVKRCDIPQDLTTLGVQQEDVPELTALAMK 356 Query: 360 DACAL-TNPRQGDQKEVEELF 379 L NPR+ + EE++ Sbjct: 357 VTRLLKNNPREVTFADAEEIY 377 Lambda K H 0.316 0.132 0.373 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: 17 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: 383 Length of database: 381 Length adjustment: 30 Effective length of query: 353 Effective length of database: 351 Effective search space: 123903 Effective search space used: 123903 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 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