Align butanoyl-CoA dehydrogenase (NAD+, ferredoxin) (subunit 1/3) (EC 1.3.1.109) (characterized)
to candidate WP_086510234.1 BZY95_RS12360 FAD-binding protein
Query= BRENDA::Q18AQ5 (336 letters) >NCBI__GCF_002151265.1:WP_086510234.1 Length = 308 Score = 162 bits (411), Expect = 8e-45 Identities = 113/327 (34%), Positives = 174/327 (53%), Gaps = 25/327 (7%) Query: 3 NVLVVIEQRENVIQTVSLELLGKATEIAKDYDTKVSALLLGSKVEGLIDTLAHY-GADEV 61 ++LV+ E + + + ++ A I D D L+ G V + + A G +V Sbjct: 2 SILVLAEHHDGQLAGATAHVVAAAKAIGGDIDV----LVAGENVGAVAEAAAKLDGVSKV 57 Query: 62 IVVDDEALAVYTTEPYTKAAYEAIKAADPIVVLFGATSIGRDLAPRVSARIHTGLTADCT 121 V D+ A EP A A A VL AT+ G+++ PRV+A ++ Sbjct: 58 RVADNAVYAHQLAEPM--GALLAELADGYSHVLAAATTTGKNVLPRVAALKDVSQLSEIV 115 Query: 122 GLAVAEDTKLLLMTRPAFGGNIMATIVCKDFRPQMSTVRPGVMKKNEPD----ETKEAVI 177 + A+ K RP + GN +AT+ D ++ G E + E+ + V+ Sbjct: 116 EVVDADTFK-----RPIYAGNAIATVQSADSLKVITVRSTGFDAVGEGNSAAIESVDTVV 170 Query: 178 NRFKVEFNDADKLVQVVQVIKEAKKQVKIEDAKILVSAGRGMGGKENLDILYELAEIIGG 237 + F V Q + ++ + ++ AK+++S GRGMG EN +L +A+ +G Sbjct: 171 ENRQSAF--------VKQELAQSDRP-ELAAAKVVISGGRGMGSGENFKLLDGIADKLGA 221 Query: 238 EVSGSRATIDAGWLDKARQVGQTGKTVRPDLYIACGISGAIQHIAGMEDAEFIVAINKNP 297 + SRA +DAG++ QVGQTGK V P+LYIA GISGAIQH+AGM+D++ IVAINK+ Sbjct: 222 AIGASRAAVDAGFVPNDMQVGQTGKIVAPELYIAVGISGAIQHLAGMKDSKVIVAINKDE 281 Query: 298 EAPIFKYADVGIVGDVHKVLPELISQL 324 EAPIF+ AD G+VGD+ ++LPEL S+L Sbjct: 282 EAPIFQVADYGLVGDLFEILPELESKL 308 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: 258 Number of extensions: 11 Number of successful extensions: 1 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: 308 Length adjustment: 28 Effective length of query: 308 Effective length of database: 280 Effective search space: 86240 Effective search space used: 86240 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 Apr 09 2024. 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