Align butanoyl-CoA dehydrogenase (NAD+, ferredoxin) (subunit 1/3) (EC 1.3.1.109) (characterized)
to candidate Ga0059261_2885 Ga0059261_2885 Electron transfer flavoprotein, alpha subunit
Query= BRENDA::Q18AQ5 (336 letters) >FitnessBrowser__Korea:Ga0059261_2885 Length = 309 Score = 163 bits (412), Expect = 6e-45 Identities = 110/324 (33%), Positives = 172/324 (53%), Gaps = 18/324 (5%) Query: 3 NVLVVIEQRENVIQTVSLELLGKATEIAKDYDTKVSALLLGSKVEGLIDTLAHY-GADEV 61 +VLV +E N ++ +L + T++ V AL+ G +G D A G +V Sbjct: 2 SVLVWVEHDNNSVKDATLAAVTAGTKLGD-----VVALVAGQGAQGAADAAAKIVGVSKV 56 Query: 62 IVVDDEALAVYTTEPYTKAAYEAIKAADPIVVLFGATSIGRDLAPRVSARIHTGLTADCT 121 ++ DD A E E + D V AT+ G+++APRV+A + ++ Sbjct: 57 LLADDAAYGHGLAENVAPLVAELMAGYDAFVA--PATTTGKNIAPRVAALLDVMQISEVL 114 Query: 122 GLAVAEDTKLLLMTRPAFGGNIMATIVCKDFRPQMSTVRPGVMKKNEPDETKEAVINRFK 181 + A+ TRP + GN +AT+ D + ++ TVR +K + +V Sbjct: 115 SVESADT-----FTRPIYAGNAIATVKSADAK-KVLTVRGTAFEKAATEGGSASVE---A 165 Query: 182 VEFNDADKLVQVVQVIKEAKKQVKIEDAKILVSAGRGMGGKENLDILYE-LAEIIGGEVS 240 V L V ++ ++ AK++VS GR +G E L + LA+ +G V Sbjct: 166 VSGKGDSGLSSFVGAEIAKSERPELTSAKVIVSGGRALGSSEQFHGLIDPLADKLGAAVG 225 Query: 241 GSRATIDAGWLDKARQVGQTGKTVRPDLYIACGISGAIQHIAGMEDAEFIVAINKNPEAP 300 SRA +DAG+ QVGQTGK V P++Y+A GISGAIQH+AGM+D++ I+AINK+ +AP Sbjct: 226 ASRAAVDAGYAPNDYQVGQTGKIVAPEVYVAIGISGAIQHLAGMKDSKTIIAINKDEDAP 285 Query: 301 IFKYADVGIVGDVHKVLPELISQL 324 IF+ AD+G+VGD+ K++PEL +L Sbjct: 286 IFQVADLGLVGDLFKIVPELTEKL 309 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: 275 Number of extensions: 20 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: 336 Length of database: 309 Length adjustment: 28 Effective length of query: 308 Effective length of database: 281 Effective search space: 86548 Effective search space used: 86548 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