Align alcohol dehydrogenase (NADP+) (EC 1.1.1.2); alcohol dehydrogenase [NAD(P)+] (EC 1.1.1.71) (characterized)
to candidate 5207536 Shew_0070 iron-containing alcohol dehydrogenase (RefSeq)
Query= BRENDA::U6CL97 (387 letters) >FitnessBrowser__PV4:5207536 Length = 387 Score = 412 bits (1060), Expect = e-120 Identities = 214/388 (55%), Positives = 267/388 (68%), Gaps = 4/388 (1%) Query: 1 MLNFTLHTPTKILFGEGQIAELGKEIPADARILITYGGGSVKHNGVLDQVYRALEGRNVR 60 MLNF PT+I+FG+ ++AEL K IPA AR+++TYGGGSVK G LD+V AL R V Sbjct: 1 MLNFDYRNPTQIVFGKDRLAELDKLIPAGARVMVTYGGGSVKRFGTLDKVLSALGDRTVV 60 Query: 61 EFSGIEPNPTYETLMKAVEVVRAEKIDFLLAVGGGSVVDGTKFIAAAADYQAAQDP--WH 118 EF GIE NP YETL KA ++ R E IDFLLAVGGGSV+DGTKFIA A ++ D +H Sbjct: 61 EFGGIEANPQYETLAKAAKLAREESIDFLLAVGGGSVMDGTKFIALATRFEGDSDSLLFH 120 Query: 119 ILQTGGAEIDRGVALAAVLTLPATGSESNNGAVITRKSTNDKLAFRSPHTQPLFAVLDPV 178 E D+ + L + TLPATGSE N V++ K P P F++LDP Sbjct: 121 GFAPVPVEADQVLPLGTIATLPATGSEMNAFGVVSYNG--GKFPVNHPSIYPTFSLLDPT 178 Query: 179 VTYTLPARQIANGVVDAFVHTVEQYLTYSVDAKVQDRFAEGLLLTLVEEGPRALAEPENY 238 +T+TLP Q+ANGVVDAFVH +EQY TY VD +VQDR AEG++ TL+E GP L EPENY Sbjct: 179 LTFTLPKIQVANGVVDAFVHVLEQYATYPVDGRVQDRTAEGIMRTLIEIGPITLEEPENY 238 Query: 239 KVRANVMWSATMALNGLIGAGVPQDWSTHMLGHELTALHGLDHAQTLAIVLPAMLAARKS 298 RAN+MWSAT ALNG+IGAGVP DW+THM+GHELTA G+DHAQTLA VLP++ RK Sbjct: 239 NARANLMWSATSALNGMIGAGVPFDWTTHMIGHELTAQFGIDHAQTLAAVLPSVWRVRKI 298 Query: 299 QKRDKLLQYAERVWNLRDGSEDQRIDGAIAATRDFFEKMGVPTRLSDYQLDGSSIPTLVA 358 QK KLLQYAERVW++ +G E R+D AI T FF+++G+ T L DY + I +VA Sbjct: 299 QKHAKLLQYAERVWDITEGDEASRVDLAIDKTEQFFQQLGLKTHLRDYDIAQEQIDDIVA 358 Query: 359 KLSEHGLTALGEHRDITLEESQKIYEAA 386 L HG+TAL E D+ L+ S++I + A Sbjct: 359 ALEAHGMTALSESGDLGLDISREILQLA 386 Lambda K H 0.317 0.134 0.383 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: 438 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: 387 Length of database: 387 Length adjustment: 30 Effective length of query: 357 Effective length of database: 357 Effective search space: 127449 Effective search space used: 127449 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