Align butanoyl-CoA dehydrogenase (NAD+, ferredoxin) (subunit 1/3) (EC 1.3.1.109); short-chain acyl-CoA dehydrogenase (subunit 1/2) (EC 1.3.8.1) (characterized)
to candidate 3608348 Dshi_1750 acyl-CoA dehydrogenase domain protein (RefSeq)
Query= BRENDA::D2RL84 (383 letters) >FitnessBrowser__Dino:3608348 Length = 381 Score = 275 bits (704), Expect = 1e-78 Identities = 156/383 (40%), Positives = 225/383 (58%), Gaps = 3/383 (0%) Query: 1 MDFNLTEDQQMIKDMAAEFAEKFLAPTVEERDKAHIWDRKLIDKMGEAGFCGICFPEEYG 60 MDF L+E+Q I DMA +F + +AP +K + L ++ GF G+ EE G Sbjct: 1 MDFALSEEQSAIFDMARDFGAENIAPHALAWEKDGTIPKTLWPELAALGFGGLYVTEESG 60 Query: 61 GMGLDVLSYILAVEELSKVDDGTGITLSANVSLCATPIYMFGTEEQKQKYLAPIAEGTHV 120 G GL L L E LS LS + ++CA + FG+++ K ++L P V Sbjct: 61 GSGLSRLDATLVFEALSMACPSVAAFLSIH-NMCAAMLDKFGSDDVKARFLPPALTMETV 119 Query: 121 GAFGLTEPSAGTDASAQQTTAVLKGDKYILNGSKIFITNGKEADTYVVFAMTDKSQGVHG 180 ++ LTEP +G+DA+A +T A + Y L G+K FI+ G +D Y+V A T + G G Sbjct: 120 FSYCLTEPGSGSDAAALKTRAERTNEGYRLTGTKAFISGGGYSDAYIVMARTGED-GPRG 178 Query: 181 ISAFILEKGMPGFRFGKIEDKMGGHTSITAELIFEDCEVPKENLLGKEGEGFKIAMETLD 240 IS+ I+E G PG FG +EDKMG T ++ +DC VP NLLG+EG GF+ AM LD Sbjct: 179 ISSLIVEDGAPGLSFGGLEDKMGWRAQPTRQVQLDDCAVPAANLLGEEGAGFRYAMMGLD 238 Query: 241 GGRIGVAAQALGIAEGALAAAVKYSKEREQFGRSISKFQALQFMMADMATKIEAARYLVY 300 GGR+ +AA +LG A+ AL A V Y ER FG+ I +FQALQF +AD +++AAR + Sbjct: 239 GGRLNIAACSLGAAQAALDATVAYMGERRAFGKPIDQFQALQFRLADAEIELQAARVFLR 298 Query: 301 HAAMLKNEGKPYSEA-AAMAKCFASDVAMEVTTDAVQIFGGYGYTVDYPAERYMRNAKIT 359 AA ++G P + AMAK F ++ V +Q+ GGYGY DY E+ +R+ ++ Sbjct: 299 QAAWKLDQGAPDATTHCAMAKKFVTEAGSRVADQCLQLHGGYGYLADYGIEKLVRDLRVH 358 Query: 360 QIYEGTNQVMRIVTSRALLRDKK 382 QI EGTN++MR++T+RALL ++ Sbjct: 359 QILEGTNEIMRLLTARALLAARR 381 Lambda K H 0.318 0.134 0.379 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: 380 Number of extensions: 20 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: 383 Length of database: 381 Length adjustment: 30 Effective length of query: 353 Effective length of database: 351 Effective search space: 123903 Effective search space used: 123903 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 (21.7 bits) S2: 50 (23.9 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