Align butanoyl-CoA dehydrogenase (NAD+, ferredoxin) (subunit 1/3) (EC 1.3.1.109) (characterized)
to candidate SMc00728 SMc00728 electron transfer flavoprotein alpha-subunit alpha-ETF flavoprotein
Query= BRENDA::Q18AQ5 (336 letters) >FitnessBrowser__Smeli:SMc00728 Length = 309 Score = 161 bits (408), Expect = 2e-44 Identities = 113/326 (34%), Positives = 175/326 (53%), Gaps = 32/326 (9%) Query: 4 VLVVIEQRENVIQTVSLELLGKATEIAKDYDTKVSALLLGSKVEGLIDTLAHY-GADEVI 62 +L++ + + + + + L A +I D V L+ G V+G+ + + G +V+ Sbjct: 3 ILLLADHDNSHLSDQTAKALTAAAKIGGD----VHVLVAGQNVKGIAEQASKLSGVAKVL 58 Query: 63 VVDDEALAVYTTEPYTKAAYEAIKAADPIVVLFGATSIGRDLAPRVSARIHTGLTADCTG 122 V +D +LA EP AA A + V+ ATS+G+++ PRV+A + ++ Sbjct: 59 VAEDASLANNLAEPL--AALIVSLAGNYDTVVAAATSVGKNVMPRVAALLDVAQVSEIIE 116 Query: 123 LAVAEDTKLLLMTRPAFGGNIMATIVCKDFRPQ-MSTVRPGVMKKNE-----PDETKEAV 176 + A+ + RP + GN + T+ + PQ + TVR + P ET A Sbjct: 117 VVSADTYR-----RPIYAGNAIQTVQTSE--PQKVITVRTASFAAAQEGGSAPVETVAAA 169 Query: 177 INR-FKVEFNDADKLVQVVQVIKEAKKQVKIEDAKILVSAGRGMGGKENL-DILYELAEI 234 N +DA + + ++ AKI++S GR +G E +++ +A+ Sbjct: 170 ANPGLSAHVSDA----------LSSSDRPELTSAKIIISGGRALGSSEKFKEVILPVADK 219 Query: 235 IGGEVSGSRATIDAGWLDKARQVGQTGKTVRPDLYIACGISGAIQHIAGMEDAEFIVAIN 294 +G V SRA +DAG+ QVGQTGK V PDLYIACGISGAIQH+AGM+D++ IVAIN Sbjct: 220 LGAAVGASRAAVDAGYAPNDWQVGQTGKVVAPDLYIACGISGAIQHLAGMKDSKVIVAIN 279 Query: 295 KNPEAPIFKYADVGIVGDVHKVLPEL 320 K+ EAPIF+ AD G+V D+ +VLPEL Sbjct: 280 KDEEAPIFQVADYGLVADLFEVLPEL 305 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: 267 Number of extensions: 15 Number of successful extensions: 4 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