Align alcohol dehydrogenase (EC 1.1.1.1) (characterized)
to candidate WP_089216568.1 CHB69_RS13650 SDR family oxidoreductase
Query= BRENDA::Q4J9F2 (255 letters) >NCBI__GCF_900188185.1:WP_089216568.1 Length = 267 Score = 141 bits (356), Expect = 1e-38 Identities = 88/255 (34%), Positives = 138/255 (54%), Gaps = 11/255 (4%) Query: 5 SLKNKVVIVTGAGSGIGRAIAKKFALNDSIVVAVELLEDRLNQIVQELRGMGKEVLGVKA 64 +L K+ I+TGAGSGIGRA A +FA + +V + ++ ++ G EV+ ++ Sbjct: 3 ALDGKIAIITGAGSGIGRASALRFAAEGARLVIGDKTA-AVHDTAAAVKDAGGEVVALEI 61 Query: 65 DVSKKKDVEEFVRRTFETYSRIDVLCNNAGIMDGVTPVAEVSDELWERVLAVNLYSAFYS 124 D + DV + V TY +D+ NAGI+ + + +++ E W L VNL Sbjct: 62 DAGVEADVAKLVAAAQGTYGGLDIAFANAGIIGDMGGIFDITPEGWAETLRVNLIGPALM 121 Query: 125 SRAVIPIMLKQGKG-VIVNTASIAGIRGGFAGAPYTVAKHGLIGLTRSIAAHYGDQGIRA 183 + M+ QG+G IV TAS+AG+ G A Y+ +K G+I L ++ A +R Sbjct: 122 VKHAGRAMVDQGRGGAIVLTASVAGLNSGAGPAAYSASKAGVINLAKTAAQQMTTANVRV 181 Query: 184 VAVLPGTVKTNIGLGSSKPS-----ELGMRTLTKLMSLSSRLAEPEDIANVIVFLASDEA 238 A+ PG +T G ++P+ E G+ ++ R +PE++ANV +FLASD+A Sbjct: 182 NAICPGLTET----GMTRPTFDYAKEKGVTHKIGQLNPLKRAGQPEELANVALFLASDQA 237 Query: 239 SFVNGDAVVVDGGLT 253 S+VNG A+ VDGGLT Sbjct: 238 SYVNGQAIAVDGGLT 252 Lambda K H 0.318 0.135 0.369 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: 195 Number of extensions: 11 Number of successful extensions: 4 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: 255 Length of database: 267 Length adjustment: 25 Effective length of query: 230 Effective length of database: 242 Effective search space: 55660 Effective search space used: 55660 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: 47 (22.7 bits)
This GapMind analysis is from Sep 24 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