Align alcohol dehydrogenase (EC 1.1.1.1) (characterized)
to candidate WP_078716111.1 B5D49_RS02645 iron-containing alcohol dehydrogenase
Query= BRENDA::P0DJA2 (383 letters) >NCBI__GCF_900167125.1:WP_078716111.1 Length = 382 Score = 261 bits (666), Expect = 3e-74 Identities = 140/381 (36%), Positives = 226/381 (59%), Gaps = 1/381 (0%) Query: 1 MASSTFYIPFVNEMGEGSLEKAIKDLNGSGFKNALIVSDAFMNKSGVVKQVADLLKAQGI 60 M++ F P G G++ + ++ G + ++ + ++G ++ V L G+ Sbjct: 1 MSTYIFQTPPRIIFGNGAVAQVGRETARLGSRALIVTGKSSSTRTGSLEAVTASLNEAGV 60 Query: 61 NSAVYDGVMPNPTVTAVLEGLKILKDNNSDFVISLGGGSPHDCAKAIALVATNGGEVKDY 120 + ++ V +P++ V G + ++N D ++ LGGGSP D AK I L+ T+ G+++DY Sbjct: 61 HPVLFAEVESDPSIQTVEAGAALARENQCDVIVGLGGGSPLDAAKGIVLLLTHPGDIRDY 120 Query: 121 EGIDKSKKPALPLMSINTTAGTASEMTRFCIITDEVRHVKMAIVDRHVTPMVSVNDPLLM 180 + P +PL+SI TTAGTASE+TRF +ITD + +KM++ + P V++ DP L Sbjct: 121 TS-QPADGPGMPLISIPTTAGTASEITRFTVITDTEQKIKMSLQGTALIPSVALLDPQLT 179 Query: 181 VGMPKGLTAATGMDALTHAFEAYSSTAATPITDACALKAASMIAKNLKTACDNGKDMPAR 240 V MP+ +TAATGMDALTHA EAY S ATP++D AL+A +I NL A D+ +M AR Sbjct: 180 VTMPQHVTAATGMDALTHAIEAYISKLATPMSDLHALEAIRLIGANLIKAVDSPDNMAAR 239 Query: 241 EAMAYAQFLAGMAFNNASLGYVHAMAHQLGGYYNLPHGVCNAVLLPHVLAYNASVVAGRL 300 EAM Q AG+AF+NAS+ VH+M+ LG + + HG NA+LLP V+ +N S A R Sbjct: 240 EAMLRGQMHAGLAFSNASVALVHSMSRPLGALFGIAHGQANAMLLPVVMDFNRSAAADRY 299 Query: 301 KDVGVAMGLDIANLGDKEGAEATIQAVRDLAASIGIPANLTELGAKKEDVPLLADHALKD 360 + + A+G ++ L ++ A+ T+ +V +L G+ +L+ G +++D+ LA A++ Sbjct: 300 RHIAEALGENVQELSARDAAKTTVLSVEELFEETGLEQHLSAYGVQEKDIARLAKDAMES 359 Query: 361 ACALTNPRQGDQKEVEELFLS 381 A NPR+ D + V ++ S Sbjct: 360 ASTAFNPRKADLESVAAIYHS 380 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: 312 Number of extensions: 12 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: 382 Length adjustment: 30 Effective length of query: 353 Effective length of database: 352 Effective search space: 124256 Effective search space used: 124256 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