Align 3-keto-5-aminohexanoate cleavage enzyme (EC 2.3.1.247) (characterized)
to candidate GFF5130 PS417_26280 NADPH:quinone reductase
Query= BRENDA::Q8RHX2 (272 letters) >FitnessBrowser__WCS417:GFF5130 Length = 295 Score = 181 bits (459), Expect = 2e-50 Identities = 113/297 (38%), Positives = 167/297 (56%), Gaps = 29/297 (9%) Query: 1 MMEKLIITAAICGAEVTKEHNPAVPYTVEEIAREAESAYKAGASIIHLHVREDD-GTPTQ 59 M +IIT A+ GA T +P VP T ++IA A A KAGA+++H HVR+ + G ++ Sbjct: 1 MNHDVIITCALTGAGDTTSRSPHVPVTPKQIAAAAVEAAKAGATVVHCHVRDPETGKFSR 60 Query: 60 DKERFRKCIEAIREKCPDVIIQ---------------------PSTGGAVGMTDLERLQP 98 D +R+ +E IRE D+I+ P+T +T L ++ Sbjct: 61 DVALYREVMERIREADIDIIVNLTAGMGGDLEIGGGENPMAFGPNTDLVGPLTRLAHVE- 119 Query: 99 TELHPEMATLDCGTCNFG-GDEIFVNTENTIKNFGKILIERGVKPEIEVFDKGMIDYAIR 157 EL PE+ TLDCGT NFG GD I+V+T ++ K + E GVK E+E+FD G + +A + Sbjct: 120 -ELLPEICTLDCGTLNFGDGDTIYVSTPAQLRAGAKRIQELGVKAELEIFDTGHLWFAKQ 178 Query: 158 YQKQGFIQKPMHFDFVLGVQMSASARDLVF--MSESIPEGSTWTVAGVGRHQFQMAALAI 215 K+G + P+ F LG+ A A M +++P + W G+GR Q MAA A+ Sbjct: 179 MIKEGLLDDPL-FQLCLGIPWGAPADTTTMKAMVDNLPADAVWAGFGIGRMQMPMAAQAV 237 Query: 216 VMGGHVRVGFEDNVYIDKGILAKSNGELVERVVRLAKELGREIATPDEARQILSLKK 272 ++GG+VRVG EDN+++DKG+LA +NG+LVER + LG + TP E R + L K Sbjct: 238 LLGGNVRVGLEDNLWLDKGVLA-TNGQLVERASEILSRLGARVMTPAEGRVKMGLTK 293 Lambda K H 0.319 0.137 0.394 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: 226 Number of extensions: 15 Number of successful extensions: 6 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: 272 Length of database: 295 Length adjustment: 26 Effective length of query: 246 Effective length of database: 269 Effective search space: 66174 Effective search space used: 66174 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 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