Align acyl-CoA dehydrogenase subunit (EC 1.3.8.4; EC 1.3.8.5) (characterized)
to candidate Ac3H11_2359 Butyryl-CoA dehydrogenase (EC 1.3.99.2)
Query= metacyc::MONOMER-11693 (386 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_2359 Length = 388 Score = 245 bits (625), Expect = 2e-69 Identities = 147/386 (38%), Positives = 218/386 (56%), Gaps = 12/386 (3%) Query: 1 MDHRLTPELEELRRTVEEFAHDVVAPKIGDFYERHEFPYEIVREMGRMGLFGLPFPEEYG 60 MD LT E +T +FA AP + E FP E + + G +G GL PE G Sbjct: 1 MDFELTEEQRAFAQTARDFAQAEFAPHAAHWDEEGIFPKEAIAKAGELGFCGLYAPEAAG 60 Query: 61 GMGGDYLALGIALEELARVDSSVAITLEAGVSLGAMPIHLFGTDAQKA---EWLPRLCSG 117 G+ L + EE+A VD S A +++ M + GT A A W P L +G Sbjct: 61 GLALPRLDATLVFEEMAAVDPSTT----AFITIHNMATWMLGTWATPAVRDHWGPLLTTG 116 Query: 118 EILGAFGLTEPDGGSDAGATRTTARLDESTNEWVINGTKCFITNSGTDITGLVTVTAVTG 177 E L ++ LTEP GSDA + +T A L NE+VING K FI+ +G+ T ++ + A TG Sbjct: 117 EKLASYCLTEPGAGSDAASLKTRAEL--VGNEYVINGAKAFISGAGS--TDVLVLMARTG 172 Query: 178 RKPDGKPLISSIIVPSGTPGFTVAAPYSKVGWNASDTRELSFADVRVPAANLLGEQGRGY 237 G IS+ VP+ PG + K+GWN+ TR +SF +VR+PA +LLG +G G+ Sbjct: 173 DAQSGASGISAFAVPADAPGISYGKKEQKMGWNSQPTRTISFDNVRIPADHLLGREGEGF 232 Query: 238 AQFLRILDEGRIAISALATGLAQGCVDESVKYAGERHAFGRNIGAYQAIQFKIADMEMKA 297 ++ LD GRI I+ + G AQG ++ + +Y +R FG+ I ++QA+QFK+ADM + Sbjct: 233 KIAMKGLDGGRINIATCSVGAAQGALNAAQQYMQDRKQFGKPIASFQALQFKLADMATEL 292 Query: 298 HMARVGWRDAASRLVAG-EPFKKEAAIAKLYSSTVAVDNAREATQIHGGYGFMNEYPVAR 356 AR R AAS+L AG A+AK +++ +A Q+HGGYG++ EYP+ R Sbjct: 293 VAARQMVRLAASKLDAGARDASTYCAMAKRFATDAGFTVINDALQLHGGYGYIREYPLER 352 Query: 357 MWRDSKILEIGEGTSEVQRMLIAREL 382 + RD+++ +I EGT+E+ R++IAR + Sbjct: 353 LLRDARVHQILEGTNEIMRVIIARRM 378 Lambda K H 0.318 0.136 0.402 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: 19 Number of successful extensions: 5 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: 386 Length of database: 388 Length adjustment: 30 Effective length of query: 356 Effective length of database: 358 Effective search space: 127448 Effective search space used: 127448 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