Align alcohol dehydrogenase (EC 1.1.1.1) (characterized)
to candidate 208042 DVU2545 alcohol dehydrogenase, iron-containing
Query= BRENDA::P0DJA2 (383 letters) >MicrobesOnline__882:208042 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:
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