Align butanoyl-CoA dehydrogenase (NAD+, ferredoxin) (subunit 1/3) (EC 1.3.1.109) (characterized)
to candidate CA265_RS08865 CA265_RS08865 electron transfer flavoprotein subunit alpha
Query= BRENDA::Q18AQ5 (336 letters) >FitnessBrowser__Pedo557:CA265_RS08865 Length = 322 Score = 179 bits (455), Expect = 6e-50 Identities = 111/326 (34%), Positives = 170/326 (52%), Gaps = 6/326 (1%) Query: 3 NVLVVIEQRENVIQTVSLELLGKATEIAKDYDTKVSALLLGSKVEGLIDTLAHYGADEVI 62 +VLV +EQ E + E + A IA T+++A+ +G + + L YGA +V+ Sbjct: 2 SVLVYVEQAEGKFKKSVFEAVSYAKAIADQQSTQLTAISIGDVADSELKELGKYGASKVL 61 Query: 63 VVDDEALAVYTTEPYTKAAYEAIKAADPIVVLFGATSIGRDLAPRVSARIHTGLTADCTG 122 V + L + + Y A + +V+ + G+ LAPR++ ++ GL Sbjct: 62 NVSSDQLKTFVNQAYASVIAAAAEKEGADIVVLSNSFSGKGLAPRIAVKLKAGLADGAVE 121 Query: 123 LAVAEDTKLLLMTRPAFGGNIMATIVCKDFRPQMSTVRPGVMKKNEPDETKEAVINRFKV 182 L + D K + + AF G A ++ + P E +A I F Sbjct: 122 LP-SNDGKFSVK-KTAFSGKAFAITELTSAN-KVIALNPNAFGVKE--NATDAAIEVFTA 176 Query: 183 EFNDADKLVQVVQVIKEAKKQVKIEDAKILVSAGRGMGGKENLDILYELAEIIGGEVSGS 242 + +D L V++ I A +V + DA+++VSAGRG+ G EN ++ ELA ++G + S Sbjct: 177 DVKQSD-LGTVIKEIVRATDKVSLPDAELVVSAGRGLKGPENWGMIEELAGLLGAATACS 235 Query: 243 RATIDAGWLDKARQVGQTGKTVRPDLYIACGISGAIQHIAGMEDAEFIVAINKNPEAPIF 302 + DA W + VGQTG + P+LYIA GISGAIQH+AG+ ++ IV INK+PEAP F Sbjct: 236 KPVSDADWRPHSEHVGQTGIAISPNLYIAIGISGAIQHLAGVSSSKVIVVINKDPEAPFF 295 Query: 303 KYADVGIVGDVHKVLPELISQLSVAK 328 K AD GIVGD +V+P+LI L K Sbjct: 296 KVADYGIVGDAFEVVPKLIEALKAHK 321 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: 245 Number of extensions: 9 Number of successful extensions: 2 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: 322 Length adjustment: 28 Effective length of query: 308 Effective length of database: 294 Effective search space: 90552 Effective search space used: 90552 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: 49 (23.5 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