Align alcohol dehydrogenase (EC 1.1.1.1); long-chain-alcohol dehydrogenase (EC 1.1.1.192) (characterized)
to candidate SM_b20147 SM_b20147 alcohol dehydrogenase
Query= BRENDA::A4IP64 (395 letters) >FitnessBrowser__Smeli:SM_b20147 Length = 368 Score = 194 bits (492), Expect = 5e-54 Identities = 116/322 (36%), Positives = 181/322 (56%), Gaps = 11/322 (3%) Query: 67 DVVP-EPPLETGEKAVAFARDGKFDLVIGVGGGSALDLAKLAAVLAVHDGSVADYLNLTG 125 D +P EP + T E A+ AR+ + DL++G+GGGS +D+AKL AVL S+AD + G Sbjct: 55 DAIPGEPDITTLEAALEAARNARPDLIVGLGGGSVMDVAKLVAVLWDSGQSLAD---VAG 111 Query: 126 TRTLEKKGLPKILIPTTSGTGSEVTNISVLSL--ETTKDVVTHDYLLADVAIVDPQLTVS 183 + + + TT+GTGSE S+++ + +K V +++AD+A++DP+LT S Sbjct: 112 PNRVAGRNTRLAQVATTAGTGSEAGIRSLITDPGKGSKIAVESPHMIADLAVLDPELTYS 171 Query: 184 VPPRVTAATGIDALTHAVEAYVSVNASPTSDGLAVAAIRLISRSLRKAVANGSDKQARID 243 VPP VTAATG+DA+ H VEA+ + A DG A L+ + L +AV +G D +AR Sbjct: 172 VPPAVTAATGVDAMAHCVEAFTNRKAHTMIDGFARMGFNLVGKYLARAVRDGEDTEAREG 231 Query: 244 MANGSYLAGLAFFNAGVAGVHALAYPLGGQFHIAHGESNAVLLPYVMGYIRQSCTKRMAD 303 M SY G+ A HA++YPLG H+ HG +NA++ P+V+ + + S + A+ Sbjct: 232 MMLASYYGGICLGPVNTAAGHAISYPLGTLLHLPHGLANAIIFPHVLAFNQPSAAAKTAE 291 Query: 304 IFNALGGNSSFLSEVEASYRCVEELERFVADVGIPKTLGGFGIPESALESLTKDAVQQKR 363 + +ALG L + + + + F A +GI +L G + L DA +R Sbjct: 292 VADALG-----LGQGLSQRDLLSAAKDFCAGLGIEMSLAVNGAKAADLPRFAADAHAIRR 346 Query: 364 LLARSPLPLLEADIRAIYEAAF 385 L+ +P+ + EAD+ IY AAF Sbjct: 347 LMDNNPVDMSEADVLEIYRAAF 368 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: 335 Number of extensions: 15 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 395 Length of database: 368 Length adjustment: 30 Effective length of query: 365 Effective length of database: 338 Effective search space: 123370 Effective search space used: 123370 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