Align butanoyl-CoA dehydrogenase (NAD+, ferredoxin) (subunit 1/3) (EC 1.3.1.109) (characterized)
to candidate PfGW456L13_2137 Electron transfer flavoprotein, alpha subunit
Query= BRENDA::Q18AQ5 (336 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2137 Length = 309 Score = 156 bits (395), Expect = 6e-43 Identities = 113/318 (35%), Positives = 167/318 (52%), Gaps = 16/318 (5%) Query: 4 VLVVIEQRENVIQTVSLELLGKATEIAKDYDTKVSALLLGSKVEGLIDTLAHY-GADEVI 62 +LV+ E V+ +L + A +I D + L+ G V + + A G +V+ Sbjct: 3 ILVIAEHDNKVVAPATLNTVAAAAKIGGD----IHVLVAGQGVGAVAEAAAKIAGVSKVL 58 Query: 63 VVDDEALAVYTTEPYTKAAYEAIKAADPIVVLFGATSIGRDLAPRVSARIHTGLTADCTG 122 V D+ A A E E K I L ATS G+++ PRV+A + ++ Sbjct: 59 VADNAAYAHQLPENVAPLVAELGKGYSHI--LAAATSNGKNILPRVAAALDVDQISEIIS 116 Query: 123 LAVAEDTKLLLMTRPAFGGNIMATIVCKDFRPQMSTVRPGVMKKNEPDETKEAVINRFKV 182 + A+ K RP + GN +AT+ + ++ TVR + AV Sbjct: 117 VESADTFK-----RPIYAGNAIATVQ-SNAAVKVITVRATGFDPVAAEGGSAAV--EAVG 168 Query: 183 EFNDADKLVQVVQVIKEAKKQVKIEDAKILVSAGRGMGGKENLDILYELAEIIGGEVSGS 242 +DA V + + ++ + ++ AKI+VS GRGM +N LY LA+ +G V S Sbjct: 169 AAHDAGISSFVGEELAKSDRP-ELTAAKIVVSGGRGMQNGDNFKHLYALADKLGAAVGAS 227 Query: 243 RATIDAGWLDKARQVGQTGKTVRPDLYIACGISGAIQHIAGMEDAEFIVAINKNPEAPIF 302 RA +DAG++ QVGQTGK V P LYIA GISGAIQH+AGM+D++ IVAINK+ EAPIF Sbjct: 228 RAAVDAGFVPNDMQVGQTGKIVAPQLYIAVGISGAIQHLAGMKDSKVIVAINKDEEAPIF 287 Query: 303 KYADVGIVGDVHKVLPEL 320 + AD G+V D+ + +PEL Sbjct: 288 QVADYGLVADLFEAIPEL 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: 257 Number of extensions: 10 Number of successful extensions: 2 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 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