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 Ac3H11_2359 Butyryl-CoA dehydrogenase (EC 1.3.99.2)
Query= BRENDA::D2RL84 (383 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_2359 Length = 388 Score = 294 bits (753), Expect = 3e-84 Identities = 159/380 (41%), Positives = 237/380 (62%), Gaps = 3/380 (0%) Query: 1 MDFNLTEDQQMIKDMAAEFAEKFLAPTVEERDKAHIWDRKLIDKMGEAGFCGICFPEEYG 60 MDF LTE+Q+ A +FA+ AP D+ I+ ++ I K GE GFCG+ PE G Sbjct: 1 MDFELTEEQRAFAQTARDFAQAEFAPHAAHWDEEGIFPKEAIAKAGELGFCGLYAPEAAG 60 Query: 61 GMGLDVLSYILAVEELSKVDDGTGITLSANVSLCATPIYMFGTEEQKQKYLAPIAEGTHV 120 G+ L L L EE++ VD T ++ + ++ + + T + + + G + Sbjct: 61 GLALPRLDATLVFEEMAAVDPSTTAFITIH-NMATWMLGTWATPAVRDHWGPLLTTGEKL 119 Query: 121 GAFGLTEPSAGTDASAQQTTAVLKGDKYILNGSKIFITNGKEADTYVVFAMT-DKSQGVH 179 ++ LTEP AG+DA++ +T A L G++Y++NG+K FI+ D V+ A T D G Sbjct: 120 ASYCLTEPGAGSDAASLKTRAELVGNEYVINGAKAFISGAGSTDVLVLMARTGDAQSGAS 179 Query: 180 GISAFILEKGMPGFRFGKIEDKMGGHTSITAELIFEDCEVPKENLLGKEGEGFKIAMETL 239 GISAF + PG +GK E KMG ++ T + F++ +P ++LLG+EGEGFKIAM+ L Sbjct: 180 GISAFAVPADAPGISYGKKEQKMGWNSQPTRTISFDNVRIPADHLLGREGEGFKIAMKGL 239 Query: 240 DGGRIGVAAQALGIAEGALAAAVKYSKEREQFGRSISKFQALQFMMADMATKIEAARYLV 299 DGGRI +A ++G A+GAL AA +Y ++R+QFG+ I+ FQALQF +ADMAT++ AAR +V Sbjct: 240 DGGRINIATCSVGAAQGALNAAQQYMQDRKQFGKPIASFQALQFKLADMATELVAARQMV 299 Query: 300 YHAAMLKNEG-KPYSEAAAMAKCFASDVAMEVTTDAVQIFGGYGYTVDYPAERYMRNAKI 358 AA + G + S AMAK FA+D V DA+Q+ GGYGY +YP ER +R+A++ Sbjct: 300 RLAASKLDAGARDASTYCAMAKRFATDAGFTVINDALQLHGGYGYIREYPLERLLRDARV 359 Query: 359 TQIYEGTNQVMRIVTSRALL 378 QI EGTN++MR++ +R +L Sbjct: 360 HQILEGTNEIMRVIIARRML 379 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: 349 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: 383 Length of database: 388 Length adjustment: 30 Effective length of query: 353 Effective length of database: 358 Effective search space: 126374 Effective search space used: 126374 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