Align butanoyl-CoA dehydrogenase (NAD+, ferredoxin) (subunit 1/3) (EC 1.3.1.109) (characterized)
to candidate Ac3H11_3189 Electron transfer flavoprotein, alpha subunit
Query= BRENDA::Q18AQ5 (336 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_3189 Length = 310 Score = 153 bits (387), Expect = 5e-42 Identities = 116/323 (35%), Positives = 164/323 (50%), Gaps = 15/323 (4%) Query: 3 NVLVVIEQRENVIQTVSLELLGKATEIAKDYDTKVSALLLGSKVEGLIDTLAHYGADEVI 62 +VLV+ E I+ +L + A D V+ G+ G +VI Sbjct: 2 SVLVIAEHDNASIKGATLNTVTAAVACGGDVHVLVAGHNAGAAAAAAGQIA---GVSKVI 58 Query: 63 VVDDEALAVYTTEPYTKAAYEAIKAADPIVVLFGATSIGRDLAPRVSARIHTGLTADCTG 122 D LA E AA A + +LF AT+ G+++APRV+A++ +D T Sbjct: 59 HADAAGLAHGLAE--NVAAQVLAIAGNYSHILFPATASGKNIAPRVAAKLDVAQISDITK 116 Query: 123 LAVAEDTKLLLMTRPAFGGNIMATIVCKDFRPQMSTVRPGVMKKNEPDETKEAVINRFKV 182 + V+ DT RP + GN +AT+ D ++ TVR AV Sbjct: 117 V-VSADT----FERPIYAGNAIATVQSAD-AVKVVTVRTTGFDAAAATGGSAAVETAAAT 170 Query: 183 EFNDADKLVQVVQVIKEAKKQVKIEDAKILVSAGRGMGGKENLD-ILYELAEIIGGEVSG 241 DA K + I + + ++ AKI+VS GR +G KE D ++ LA+ +G + Sbjct: 171 A--DAGKSSYLGSEIAKNDRP-ELTAAKIIVSGGRALGSKEKFDEVITPLADKLGAAIGA 227 Query: 242 SRATIDAGWLDKARQVGQTGKTVRPDLYIACGISGAIQHIAGMEDAEFIVAINKNPEAPI 301 SRA +DAG+ QVGQTGK V P LYIA GISGAIQH+AGM+D++ IVAINK+PEAPI Sbjct: 228 SRAAVDAGYAPNDLQVGQTGKIVAPQLYIAAGISGAIQHLAGMKDSKVIVAINKDPEAPI 287 Query: 302 FKYADVGIVGDVHKVLPELISQL 324 F AD G+ D+ +PEL+ L Sbjct: 288 FSVADYGLEADLFTAVPELVKAL 310 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: 261 Number of extensions: 18 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: 310 Length adjustment: 28 Effective length of query: 308 Effective length of database: 282 Effective search space: 86856 Effective search space used: 86856 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