Align alcohol dehydrogenase (EC 1.1.1.1) (characterized)
to candidate 203967 SOA0164 iron-containing alcohol dehydrogenase (NCBI ptt file)
Query= BRENDA::P0DJA2 (383 letters) >FitnessBrowser__MR1:203967 Length = 383 Score = 389 bits (999), Expect = e-113 Identities = 199/381 (52%), Positives = 271/381 (71%), Gaps = 1/381 (0%) Query: 3 SSTFYIPFVNEMGEGSLEKAIKDLNGSGFKNALIVSDAFMNKSGVVKQVADLLKAQGINS 62 S+TFY+P ++ MG+ +++ +L F ALIV+D + +V ++ D L A I Sbjct: 2 STTFYMPPMSLMGQHAIKLLGTELQARNFNKALIVTDKALVDIKLVDKLTDELSAHDIAF 61 Query: 63 AVYDGVMPNPTVTAVLEGLKILKDNNSDFVISLGGGSPHDCAKAIALVATNGGEVKDY-E 121 A++DGV PNPT +++GL +L+ DFVIS GGGS HDCAK IALVA NGG ++DY + Sbjct: 62 AIFDGVKPNPTEKNIVQGLALLEAQKCDFVISFGGGSSHDCAKGIALVAANGGHIRDYSK 121 Query: 122 GIDKSKKPALPLMSINTTAGTASEMTRFCIITDEVRHVKMAIVDRHVTPMVSVNDPLLMV 181 G+ S KP LPL+++NTTAGTA+EMT F I+T+E K IVD+++TP+++VND LMV Sbjct: 122 GVHLSAKPQLPLVTVNTTAGTAAEMTIFAIVTNEEDETKYPIVDKNLTPIIAVNDSELMV 181 Query: 182 GMPKGLTAATGMDALTHAFEAYSSTAATPITDACALKAASMIAKNLKTACDNGKDMPARE 241 MPK LTAATGMDALTHA EAY STAATPITDA A+KA +IA+NLK A DNG+D ARE Sbjct: 182 AMPKFLTAATGMDALTHAVEAYVSTAATPITDASAIKAIELIAQNLKAAVDNGEDREARE 241 Query: 242 AMAYAQFLAGMAFNNASLGYVHAMAHQLGGYYNLPHGVCNAVLLPHVLAYNASVVAGRLK 301 AM Y ++LAGMAF+NASLGYVH+MAHQLGG Y+L HG+CNA+LLP V +N++ R Sbjct: 242 AMQYGEYLAGMAFSNASLGYVHSMAHQLGGVYDLVHGLCNAILLPVVSRFNSAEKVERFA 301 Query: 302 DVGVAMGLDIANLGDKEGAEATIQAVRDLAASIGIPANLTELGAKKEDVPLLADHALKDA 361 +V AMG+D + + AE+ I A+ L+AS+G L++LG K++ + +A +AL DA Sbjct: 302 EVAKAMGVDTVGMTLIDAAESGILAIEKLSASVGTDQKLSDLGVKEDKLEFMAINALNDA 361 Query: 362 CALTNPRQGDQKEVEELFLSA 382 C+LTNPR+ +++ +F A Sbjct: 362 CSLTNPRKATTEDIINIFKKA 382 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: 427 Number of extensions: 16 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: 383 Length of database: 383 Length adjustment: 30 Effective length of query: 353 Effective length of database: 353 Effective search space: 124609 Effective search space used: 124609 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