Align acyl-CoA dehydrogenase subunit (EC 1.3.8.4; EC 1.3.8.5) (characterized)
to candidate Ac3H11_2996 Butyryl-CoA dehydrogenase (EC 1.3.99.2)
Query= metacyc::MONOMER-11693 (386 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_2996 Length = 376 Score = 256 bits (653), Expect = 1e-72 Identities = 151/383 (39%), Positives = 226/383 (59%), Gaps = 15/383 (3%) Query: 5 LTPELEELRRTVEEFAHDVVAPKIGDFYERHEFPYEIVREMGRMGLFGLPFPEEYGGMGG 64 LT + E +R V +FA + P + + H FP + + + +G +G+ PEE+GG Sbjct: 3 LTQDQEMIRDAVRDFAQTELWPHAARWDKEHHFPKDAHQGLAALGAYGICVPEEFGGANL 62 Query: 65 DYLALGIALEELARVDSSVAITLEAGVSLGAMPIHL----FGTDAQKAEWLPRLCSGEIL 120 DYL L + LEE+A D + +S+ P++ +G QK +WL L GE+L Sbjct: 63 DYLTLALVLEEIAAGDGGTS----TAISVTNCPVNAILMRYGNAQQKRDWLTPLARGEML 118 Query: 121 GAFGLTEPDGGSDAGATRTTARLDESTNEWVINGTKCFITNSGTDITGLVTVTAVTGRKP 180 GAF LTEP GSDA A RTTA + +E+VING K FIT+ G V + K Sbjct: 119 GAFCLTEPHVGSDASALRTTAV--KQGDEYVINGVKQFITSGKN---GQVAIVIAVTDKG 173 Query: 181 DGKPLISSIIVPSGTPGFTVAAPYSKVGWNASDTRELSFADVRVPAANLLGEQGRGYAQF 240 GK +S+ +VP+ PG+ VA K+G ++SDT +++F + R+PA NL+G +G GY Sbjct: 174 AGKKGMSAFLVPTNNPGYVVARLEDKLGQHSSDTAQINFDNCRIPAENLIGAEGEGYKIA 233 Query: 241 LRILDEGRIAISALATGLAQGCVDESVKYAGERHAFGRNIGAYQAIQFKIADMEMKAHMA 300 L L+ GRI I+A + G+A+ D ++ Y+ ER +FG I +QA+ F++AD + A Sbjct: 234 LGALEGGRIGIAAQSVGMARSAFDAALAYSKERESFGTAIFNHQAVGFRLADCATQIEAA 293 Query: 301 R-VGWRDAASRLVAGEPFKKEAAIAKLYSSTVAVDNAREATQIHGGYGFMNEYPVARMWR 359 R + W AA R AG+P KEAA+AKL++S +A A Q GGYG +N++PV R++R Sbjct: 294 RQLIWHAAALR-DAGKPCLKEAAMAKLFASEMAERVCSAAIQTLGGYGVVNDFPVERIYR 352 Query: 360 DSKILEIGEGTSEVQRMLIAREL 382 D ++ +I EGTS+VQ+++I R L Sbjct: 353 DVRVCQIYEGTSDVQKIIIQRAL 375 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: 398 Number of extensions: 16 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: 386 Length of database: 376 Length adjustment: 30 Effective length of query: 356 Effective length of database: 346 Effective search space: 123176 Effective search space used: 123176 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