Align butanoyl-CoA dehydrogenase (NAD+, ferredoxin) (subunit 3/3) (EC 1.3.1.109); short-chain acyl-CoA dehydrogenase (EC 1.3.8.1) (characterized)
to candidate CCNA_00436 CCNA_00436 acyl-CoA dehydrogenase, short-chain specific
Query= BRENDA::Q18AQ1 (378 letters) >FitnessBrowser__Caulo:CCNA_00436 Length = 382 Score = 291 bits (744), Expect = 3e-83 Identities = 152/379 (40%), Positives = 231/379 (60%), Gaps = 1/379 (0%) Query: 1 MDLNSKKYQMLKELYVSFAENEVKPLATELDEEERFPYETVEKMAKAGMMGIPYPKEYGG 60 M L+ + + L + F ++P+ ++ E + P + +E+M G+ G+ P+E+GG Sbjct: 1 MALDLETREQLIDTVARFVAERLRPIEAQVAENDAVPDDVIEEMKGLGLFGLTIPEEFGG 60 Query: 61 EGGDTVGYIMAVEELSRVCGTTGVILSAHTSLGSWPIYQYGNEEQKQKFLRPLASGEKLG 120 G + EL R + + +GS + +GN+EQK K+L +ASG + Sbjct: 61 LGLTMEEEALVAIELGRASPAFRSVFGTNVGIGSQGLVMFGNDEQKAKWLPGIASGAVIT 120 Query: 121 AFGLTEPNAGTDASGQQTTAVLDGDEYILNGSKIFITNAIAGDIYVVMAMTDK-SKGNKG 179 +F LTEP AG+D++ QT A DGD+YILNGSK +ITNA ++ VMA T+ +KG G Sbjct: 121 SFALTEPEAGSDSAAVQTRATRDGDDYILNGSKRYITNAGKASLFTVMARTNPDAKGGAG 180 Query: 180 ISAFIVEKGTPGFSFGVKEKKMGIRGSATSELIFEDCRIPKENLLGKEGQGFKIAMSTLD 239 +SAF+V + PG + G EKKMG +G+ ++ F++ R+P N LG EG+GFK+AM LD Sbjct: 181 VSAFLVPRDLPGLTVGKPEKKMGQQGAHIHDVTFDNVRVPAWNRLGAEGEGFKVAMQVLD 240 Query: 240 GGRIGIAAQALGLAQGALDETVKYVKERVQFGRPLSKFQNTQFQLADMEVKVQAARHLVY 299 GR+ IAA +G+A+ + + V Y ER QFG+P++ FQ Q +AD + + AA+ LV Sbjct: 241 RGRLHIAAVCVGVAERLIADCVAYASERKQFGQPIASFQLIQAMIADSKTEALAAKALVL 300 Query: 300 QAAINKDLGKPYGVEAAMAKLFAAETAMEVTTKAVQLHGGYGYTRDYPVERMMRDAKITE 359 + A +D G +EAA +KLFA+E V +AVQ+ GG GY DY +ER+ RD +I Sbjct: 301 ETARKRDAGVNVTLEAASSKLFASEMVGRVADRAVQVFGGAGYVADYGIERLYRDVRIFR 360 Query: 360 IYEGTSEVQRMVISGKLLK 378 IYEGTS+VQ+++I+ + LK Sbjct: 361 IYEGTSQVQQLIIARETLK 379 Lambda K H 0.315 0.133 0.373 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: 331 Number of extensions: 18 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: 378 Length of database: 382 Length adjustment: 30 Effective length of query: 348 Effective length of database: 352 Effective search space: 122496 Effective search space used: 122496 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: 42 (22.0 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