Align alcohol dehydrogenase (EC 1.1.1.1) (characterized)
to candidate WP_011384506.1 AMB_RS10625 3-oxoacyl-[acyl-carrier-protein] reductase
Query= BRENDA::Q4J9F2 (255 letters) >NCBI__GCF_000009985.1:WP_011384506.1 Length = 245 Score = 118 bits (296), Expect = 1e-31 Identities = 83/253 (32%), Positives = 129/253 (50%), Gaps = 14/253 (5%) Query: 6 LKNKVVIVTGAGSGIGRAIAKKFALNDSIVVAVELLEDRLNQIVQELRGMGKEVLGVKAD 65 L K +VTGA GIG AIAK + V + L+ + EL G+ V + A+ Sbjct: 4 LTGKTALVTGASGGIGGAIAKALHARGATVGLHGTRREALDALAAEL---GERVHVLPAN 60 Query: 66 VSKKKDVEEFVRRTFETYSRIDVLCNNAGIM-DGVTPVAEVSDELWERVLAVNLYSAFYS 124 +S VE+ + +D+L NNAG+ DG+ V + DE W+ VL VNL +AF Sbjct: 61 LSDAAAVEQLAKDAEAAMGSVDILVNNAGLTKDGL--VLRMKDEDWQTVLDVNLTAAFRL 118 Query: 125 SRAVIPIMLKQGKGVIVNTASIAGIRGGFAGAPYTVAKHGLIGLTRSIAAHYGDQGIRAV 184 SRA + +K+ G I+N SI G+ G Y +K G+IG+++++A + I Sbjct: 119 SRAAVKGQMKRRWGRIINITSIVGVTGNPGQVNYAASKAGMIGMSKALAQEVASRNITVN 178 Query: 185 AVLPGTVKTNIGLGSSKPSELGMRTLTKLMS--LSSRLAEPEDIANVIVFLASDEASFVN 242 V PG V S+ L TKL + + R+ ++IA +V+LAS EA++V Sbjct: 179 CVAPGFV------SSAMTDVLSDEQKTKLNAGIPAGRMGTADEIAAAVVYLASAEAAYVT 232 Query: 243 GDAVVVDGGLTVL 255 G + V+GG+ ++ Sbjct: 233 GQTLHVNGGMAMI 245 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: 138 Number of extensions: 8 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: 245 Length adjustment: 24 Effective length of query: 231 Effective length of database: 221 Effective search space: 51051 Effective search space used: 51051 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: 46 (22.3 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