Align alcohol dehydrogenase (EC 1.1.1.1) (characterized)
to candidate Echvi_3364 Echvi_3364 Dehydrogenases with different specificities (related to short-chain alcohol dehydrogenases)
Query= BRENDA::Q4J702 (264 letters) >FitnessBrowser__Cola:Echvi_3364 Length = 255 Score = 157 bits (398), Expect = 2e-43 Identities = 87/256 (33%), Positives = 147/256 (57%), Gaps = 2/256 (0%) Query: 1 MDIDRLFSVKGMNAVVLGASSGIGKAIAEMFSEMGGKVVLSDIDEEGLKRLSDSLRSRGH 60 MD+ LFS+ A++ GAS GIG +IAE F+ G KVV+ +E L ++ L +G+ Sbjct: 1 MDLSSLFSLNNKVALITGASKGIGLSIAEFFAAAGAKVVICSRHQEHLDEIAKKLYEKGY 60 Query: 61 EVNHMKCDITDLNQVKKLVNFSLSVYGNVDALYVTPSINVRKS-IENYTYEDFEKVINVN 119 ++ + C++ N++ +LV ++ YG +D L N + T E F+K+++VN Sbjct: 61 DIMGIACNVGRPNELVQLVEKTIEAYGQIDILVNNAGTNPYMGPVHETTLELFDKIMDVN 120 Query: 120 LKGNFMVVKEFLSVMKNNKGGGSVVLFSSIRGTVVEPGQSVYAMTKAGIIQLAKVAAAEY 179 +K F + K L ++ + S++ SSI EP +Y+++K+ + L KV A E+ Sbjct: 121 VKAPFELSKLCLPHLRKSSQA-SIINISSIGALSPEPQLGIYSVSKSALHSLTKVCAKEW 179 Query: 180 GKYNIRVNVIAPGVVDTPLTRQIKSDPEWFKAYTEKTILKRWATPEEIANVALFLAMPAS 239 G+ IRVN I PG++ T ++ + + + ++ +KR EEIA +ALFLA PA+ Sbjct: 180 GQQKIRVNAICPGIIKTNFSKALWGNDQIMDVIMKRLAIKRLGKTEEIAALALFLASPAA 239 Query: 240 SYITGTVIYVDGGWTA 255 SYI+G++ VDGG+T+ Sbjct: 240 SYISGSIFTVDGGFTS 255 Lambda K H 0.317 0.134 0.381 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: 170 Number of extensions: 11 Number of successful extensions: 3 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: 264 Length of database: 255 Length adjustment: 24 Effective length of query: 240 Effective length of database: 231 Effective search space: 55440 Effective search space used: 55440 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: 47 (22.7 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