Align butanoyl-CoA dehydrogenase (NAD+, ferredoxin) (subunit 1/3) (EC 1.3.1.109) (characterized)
to candidate Ac3H11_2705 Electron transfer flavoprotein, alpha subunit
Query= BRENDA::Q18AQ5 (336 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_2705 Length = 311 Score = 150 bits (378), Expect = 5e-41 Identities = 115/331 (34%), Positives = 163/331 (49%), Gaps = 29/331 (8%) Query: 3 NVLVVIEQRENVIQTVSLELLGKATEIAKDYDTKVSALLLGSKVEGLIDTLAHYGADEVI 62 +VLV+ E I+ +L + A D V+ G+ G +VI Sbjct: 2 SVLVIAEHDNASIKGATLNTVAAAAACGGDVHVLVAGHNAGAAAAAAAQIA---GVAKVI 58 Query: 63 VVDDEALAVYTTEPYTKAAYEAIKAADPIVVLFGATSIGRDLAPRVSARIHTGLTADCTG 122 D L E AA A + +LF AT+ G+++APRV+A++ +D T Sbjct: 59 HADAAGLEHGLAE--NVAAQVLAIAGNYSHILFPATAGGKNVAPRVAAKLDVAQISDITK 116 Query: 123 LAVAEDTKLLLMTRPAFGGNIMATIVCKDFRPQMSTVRPG-----VMKKNEPDETKEAVI 177 + V DT RP + GN +AT+ D ++ G + P E AV Sbjct: 117 V-VGADT----FERPIYAGNAIATVQSGDAVKVITVRTTGFDAAPATGGSAPVEAAAAVA 171 Query: 178 NRFKVEFNDADKLVQVVQVIKEAKKQVKIE--DAKILVSAGRGMGGKENL-DILYELAEI 234 + K F V +E K + E AKI+VS GR +G E +++ LA+ Sbjct: 172 DAGKSSF-----------VGREVTKNDRPELTAAKIIVSGGRALGSAEKFTEVMTPLADK 220 Query: 235 IGGEVSGSRATIDAGWLDKARQVGQTGKTVRPDLYIACGISGAIQHIAGMEDAEFIVAIN 294 +G + SRA +DAG+ QVGQTGK V P LYIA GISGAIQH+AGM+D++ IVAIN Sbjct: 221 LGAAIGASRAAVDAGYAPNDLQVGQTGKIVAPQLYIAAGISGAIQHLAGMKDSKVIVAIN 280 Query: 295 KNPEAPIFKYADVGIVGDVHKVLPELISQLS 325 K+PEAPIF AD G+ D+ +PEL+ +S Sbjct: 281 KDPEAPIFSVADYGLEADLFTAVPELVKAIS 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: 257 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: 311 Length adjustment: 28 Effective length of query: 308 Effective length of database: 283 Effective search space: 87164 Effective search space used: 87164 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