Align butanoyl-CoA dehydrogenase (NAD+, ferredoxin) (subunit 1/3) (EC 1.3.1.109) (characterized)
to candidate GFF1797 HP15_1755 electron transfer flavoprotein subunit alpha
Query= BRENDA::Q18AQ5 (336 letters) >FitnessBrowser__Marino:GFF1797 Length = 313 Score = 165 bits (417), Expect = 2e-45 Identities = 112/332 (33%), Positives = 175/332 (52%), Gaps = 34/332 (10%) Query: 3 NVLVVIEQRENVIQTVSLELLGKATEIAKDYDTKVSALLLGSKVEGLIDTLAHYGADEVI 62 ++LV+ E + ++ +L ++ A I D D V+ G+ E + G ++V+ Sbjct: 2 SILVIAEHDNSSLKQATLNVVAAAKAIGGDIDVLVAGENCGAVAEAAVKA---EGVNKVL 58 Query: 63 VVDDEALAVYTTEPYTKAAYEAIKAADPIVVLFGATSIGRDLAPRVSARIHTGLTADCTG 122 V D+ A + E + E K I+ G ++G+D PRV+A + +D Sbjct: 59 VADNAAYGHFLGENLGELVAEVGKGYSHILAAAG--TVGKDFMPRVAALLDVAQVSDIMR 116 Query: 123 LAVAEDTKLLLMTRPAFGGNIMATIVCKDFRPQMSTVRP----------GVMKKNEPDET 172 + +EDT RP + GN +AT+ D ++ TVRP G + D Sbjct: 117 VE-SEDT----FVRPIYAGNAIATVKSSD-SIKVVTVRPTAFDPVAAEGGSASVEQLDVV 170 Query: 173 KEAVINRFKVEFNDADKLVQVVQVIKEAKKQVKIEDAKILVSAGRGMGGKENLDILYELA 232 K+A +++F E ++ K + + A I+VS GRGM +N +L ++A Sbjct: 171 KDAGLSQFVSE-----------ELAKSDRPD--LASAGIVVSGGRGMQNGDNFKMLEQVA 217 Query: 233 EIIGGEVSGSRATIDAGWLDKARQVGQTGKTVRPDLYIACGISGAIQHIAGMEDAEFIVA 292 +++G V SRA +DAG++ QVGQTGK V P LYIA GISGAIQH+AGM D++ IVA Sbjct: 218 DLMGAAVGASRAAVDAGFVPNDMQVGQTGKIVAPQLYIAVGISGAIQHLAGMSDSKVIVA 277 Query: 293 INKNPEAPIFKYADVGIVGDVHKVLPELISQL 324 INK+ EAPIF+ AD G+V D+ + +P+L +L Sbjct: 278 INKDEEAPIFQVADYGLVADLFEAVPQLEEEL 309 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: 277 Number of extensions: 14 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: 313 Length adjustment: 28 Effective length of query: 308 Effective length of database: 285 Effective search space: 87780 Effective search space used: 87780 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