Align alcohol dehydrogenase (EC 1.1.1.1) (characterized)
to candidate AO356_00820 AO356_00820 alcohol dehydrogenase
Query= BRENDA::D4GSN2 (353 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_00820 Length = 346 Score = 261 bits (667), Expect = 2e-74 Identities = 144/354 (40%), Positives = 204/354 (57%), Gaps = 14/354 (3%) Query: 1 MRAAVLREHGEPLDVTEVPDPTCDADGVVVEVEACGICRSDWHSWMGHGEWADDAVPSGQ 60 M+A V +P + V DPT + GVVV+V G+CRSDWH W GH D + Sbjct: 1 MKAVVYEAFSQPPRLMTVEDPTPERHGVVVQVLGTGVCRSDWHGWKGH----DPDIQLPH 56 Query: 61 ILGHEPAGRVVEAGDRVETIREGDRVALPFNLACGSCGYCQTGHGNVCTGDHPHALGFEP 120 + GHE AG V E G V + GDR+ +PF CG+C C +G+ VC F+P Sbjct: 57 VPGHELAGIVAEVGRDVTRWKVGDRITVPFVGGCGACPECNSGNQQVCHSQ------FQP 110 Query: 121 AAQ--GAFAELVHLPSADYNAIQLPEDVLPTDVAALGCRFMTAYNALDARAGLRAGQWVA 178 G+FAE V + AD N + LPE++ A+LGCRF+T++ A+ + + AGQWVA Sbjct: 111 GFTHWGSFAEYVGIHKADLNLVALPENMDFATAASLGCRFVTSFRAVVDQGKVTAGQWVA 170 Query: 179 VHGCGGVGLSTIQVANVLGARVVAVDVRESALDAAADLGADAVVDGS-AEDPVDAIRGLT 237 VHGCGGVGLS + +A+ +GA V+A+D+ + L A LGA A ++ S D +A+ +T Sbjct: 171 VHGCGGVGLSAVMIAHAIGANVIAIDICDDKLKLAQSLGAVATINASRVADVTEAVLEIT 230 Query: 238 DGGAHVSLDALGVAETCRNSVRSVRPRGSHVQVGLTTEAEKGNVSLPTDWMTRHEVSFLG 297 GGAHVSLDALG TC NS+ ++R RG HVQVGL A+ S+P + +E+ G Sbjct: 231 KGGAHVSLDALGHPTTCFNSINNLRRRGRHVQVGLML-ADHSTPSIPMSKVIAYELEICG 289 Query: 298 ARGMPPTNADDLLSLLASDAVDPGSLVTKTVSLDEVPERLAAMTDYDTVGVEVM 351 + GM ++ ++ S + P LV KT+SL++ + L M +DT GV V+ Sbjct: 290 SHGMQAHRYGAMMEMITSGKLAPEKLVGKTISLEQSIDALMNMDRFDTAGVTVV 343 Lambda K H 0.317 0.134 0.412 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: 439 Number of extensions: 23 Number of successful extensions: 5 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: 353 Length of database: 346 Length adjustment: 29 Effective length of query: 324 Effective length of database: 317 Effective search space: 102708 Effective search space used: 102708 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: 49 (23.5 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