Align alcohol dehydrogenase (EC 1.1.1.1) (characterized)
to candidate 208042 DVU2545 alcohol dehydrogenase, iron-containing
Query= BRENDA::P0DJA2 (383 letters) >lcl|MicrobesOnline__882:208042 DVU2545 alcohol dehydrogenase, iron-containing Length = 386 Score = 268 bits (686), Expect = 1e-76 Identities = 149/368 (40%), Positives = 210/368 (57%) Query: 15 GEGSLEKAIKDLNGSGFKNALIVSDAFMNKSGVVKQVADLLKAQGINSAVYDGVMPNPTV 74 G G+ A + ++ G L+V+D + ++G V L A GI AV+ + PNP Sbjct: 18 GNGAARLAGRYVHNLGGTRCLVVTDPGVMRNGHADTVIGSLTAYGIAHAVFQDISPNPRD 77 Query: 75 TAVLEGLKILKDNNSDFVISLGGGSPHDCAKAIALVATNGGEVKDYEGIDKSKKPALPLM 134 V G++ D ++++GGGSP DCAK I +VA+NGG + YEG+D KP PL+ Sbjct: 78 VEVQRGVEAYHREGCDAIVAVGGGSPIDCAKGIGIVASNGGSISLYEGVDAIPKPMPPLV 137 Query: 135 SINTTAGTASEMTRFCIITDEVRHVKMAIVDRHVTPMVSVNDPLLMVGMPKGLTAATGMD 194 + TTAG+A+++++F IITD R VK+AIV + VS+ DP M + LTAATG+D Sbjct: 138 CVPTTAGSAADVSQFAIITDTTRMVKIAIVSKAAVADVSLIDPSTTKSMSRDLTAATGID 197 Query: 195 ALTHAFEAYSSTAATPITDACALKAASMIAKNLKTACDNGKDMPAREAMAYAQFLAGMAF 254 LTHA EA++S A+ PITD AL+A S++ +L +G D ARE MA A AG+AF Sbjct: 198 TLTHAIEAFASNASGPITDMFALEAISLVNTHLPQVLADGDDDTAREGMALACLNAGLAF 257 Query: 255 NNASLGYVHAMAHQLGGYYNLPHGVCNAVLLPHVLAYNASVVAGRLKDVGVAMGLDIANL 314 +NA LG VHAMAH LGG +LPHG CNA+LLP V+ N R V A+G+D+ Sbjct: 258 SNAILGAVHAMAHSLGGLLDLPHGECNAILLPFVVRRNFDAAPVRYARVANALGIDVGGT 317 Query: 315 GDKEGAEATIQAVRDLAASIGIPANLTELGAKKEDVPLLADHALKDACALTNPRQGDQKE 374 +A + L + G L+ G +E + LA A++D C TNP D + Sbjct: 318 PATAIRDALFDRLMTLRTAAGFTRGLSAFGVTREQIGRLARLAVEDPCLATNPEALDIAD 377 Query: 375 VEELFLSA 382 +E L+ A Sbjct: 378 IESLYAEA 385 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: 400 Number of extensions: 7 Number of successful extensions: 1 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: 386 Length adjustment: 30 Effective length of query: 353 Effective length of database: 356 Effective search space: 125668 Effective search space used: 125668 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 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.
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