Align alcohol dehydrogenase (EC 1.1.1.1); long-chain-alcohol dehydrogenase (EC 1.1.1.192) (characterized)
to candidate H281DRAFT_05508 H281DRAFT_05508 Alcohol dehydrogenase, class IV
Query= BRENDA::A4IP64 (395 letters) >FitnessBrowser__Burk376:H281DRAFT_05508 Length = 383 Score = 223 bits (567), Expect = 9e-63 Identities = 138/359 (38%), Positives = 202/359 (56%), Gaps = 6/359 (1%) Query: 29 LGAKHILVITDPMLVKIGLVDQVTSPLRQEGYSVHVYTDVVPEPPLETGEKAVAFARDGK 88 LG +L+++D + GL++ + LR G +V + DV +P T + A AR Sbjct: 29 LGVNSVLLVSDRGVKNAGLLEAPMAHLRTSGIAVECFFDVEADPSAATVQAAAQLARSSG 88 Query: 89 FDLVIGVGGGSALDLAKLAAVLAVHDGSVADYLNLTGTRTLEKKGLPKILIPTTSGTGSE 148 D V+ +GGGS +D+AKLAA+LA S D ++ G E L +L+PTT+GTGSE Sbjct: 89 VDCVVAIGGGSPMDVAKLAALLAK---SGVDLEDIYGIHKTEGPRLRLVLVPTTAGTGSE 145 Query: 149 VTNISVLSLET-TKDVVTHDYLLADVAIVDPQLTVSVPPRVTAATGIDALTHAVEAYVSV 207 T IS+++ K V LL D+A++D +LT+ +P V+AATGIDA+ HA+EAY S Sbjct: 146 ATPISIVTTGAGEKKGVVCPVLLPDIAVLDAELTIGLPKHVSAATGIDAMVHAIEAYTSR 205 Query: 208 NA-SPTSDGLAVAAIRLISRSLRKAVANGSDKQARIDMANGSYLAGLAFFNAGVAGVHAL 266 + +P SD LA A+RL+ L + A G D + R M G+ LAG+AF NA VA VHAL Sbjct: 206 SLKNPLSDCLAREALRLLGPHLERVCAQGHDVETRQAMLLGANLAGMAFANAPVAAVHAL 265 Query: 267 AYPLGGQFHIAHGESNAVLLPYVMGYIRQSCTKRMADIFNALGGNSSFLSEVEASYRCVE 326 AYP+G +FH+ HG SN+++LP V+ + S A++ + L N + S E + + Sbjct: 266 AYPIGARFHVPHGLSNSLMLPAVLRFNMTSAESLYAELASLLVPN-AIGSPEELTRALLA 324 Query: 327 ELERFVADVGIPKTLGGFGIPESALESLTKDAVQQKRLLARSPLPLLEADIRAIYEAAF 385 L +G+P L GI L L DA++Q RLL +P + D A+Y+ F Sbjct: 325 YLTELPVKLGLPVRLRDVGITAEDLPDLAIDAMKQSRLLVNNPREVGYDDALAMYQEVF 383 Lambda K H 0.318 0.135 0.381 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: 371 Number of extensions: 19 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: 395 Length of database: 383 Length adjustment: 30 Effective length of query: 365 Effective length of database: 353 Effective search space: 128845 Effective search space used: 128845 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 (21.7 bits) S2: 50 (23.9 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