Align butanoyl-CoA dehydrogenase (NAD+, ferredoxin) (subunit 1/3) (EC 1.3.1.109) (characterized)
to candidate 15817 b1698 predicted electron transfer flavoprotein, FAD-binding (NCBI)
Query= BRENDA::Q18AQ5 (336 letters) >FitnessBrowser__Keio:15817 Length = 312 Score = 135 bits (339), Expect = 2e-36 Identities = 86/258 (33%), Positives = 139/258 (53%), Gaps = 8/258 (3%) Query: 70 AVYTTEPYTKAAYEAIKAADPIVVLFGATSIGRDLAPRVSARIHTGLTADCTGLAVAEDT 129 A+ TE Y ++ +K P ++L AT G+ LA R+S +++ L D T + + + Sbjct: 60 ALQRTENYAESIAALLKDKHPAMLLLAATKRGKALAARLSVQLNAALVNDATAVDIVDGH 119 Query: 130 KLLLMTRPAFGGNIMATIVCKDFRP-QMSTVRPGVMKKNEPDETKEAVINRFKVEFNDAD 188 + +GG +A K P + T+ PGV + D + + + Sbjct: 120 --ICAEHRMYGG--LAFAQEKINSPLAIITLAPGVQEPCTSDTSHQCPTETVPYVAPRHE 175 Query: 189 KLVQVVQVIKEAKKQVKIEDAKILVSAGRGMGGKENLDILYELAEIIGGEVSGSRATIDA 248 L + + +A V + AK +V GRG+ +++L +++ELA ++ EV SR + Sbjct: 176 ILCRERRA--KAASSVDLSKAKRVVGVGRGLAAQDDLKMVHELAAVLNAEVGCSRPIAEG 233 Query: 249 -GWLDKARQVGQTGKTVRPDLYIACGISGAIQHIAGMEDAEFIVAINKNPEAPIFKYADV 307 W+++ R +G +G ++ DLY+ GISG IQH+ G A+ IVAINK+ APIF YAD Sbjct: 234 ENWMERERYIGVSGVLLKSDLYLTLGISGQIQHMVGGNGAKVIVAINKDKNAPIFNYADY 293 Query: 308 GIVGDVHKVLPELISQLS 325 G+VGD++KV+P LISQLS Sbjct: 294 GLVGDIYKVVPALISQLS 311 Lambda K H 0.316 0.135 0.371 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: 219 Number of extensions: 7 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: 336 Length of database: 312 Length adjustment: 28 Effective length of query: 308 Effective length of database: 284 Effective search space: 87472 Effective search space used: 87472 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: 48 (23.1 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