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 3607424 Dshi_0838 acyl-CoA dehydrogenase domain protein (RefSeq)
Query= BRENDA::Q18AQ1 (378 letters) >FitnessBrowser__Dino:3607424 Length = 382 Score = 253 bits (645), Expect = 8e-72 Identities = 150/373 (40%), Positives = 216/373 (57%), Gaps = 3/373 (0%) Query: 7 KYQMLKELYVSFAENEVKPLATELDEEERFPYETVEKMAKAGMMGIPYPKEYGGEGGDTV 66 +++ML E+ +F E P ++ E ++ + G++ P+ YGG GGD Sbjct: 10 EHRMLAEMTRNFITTEWAPHFERWRDQGEMDREIWQQAGELGLLCPSVPEAYGGPGGDFG 69 Query: 67 GYIMAVEELSRV-CGTTGVILSAHTSLGSWPIYQYGNEEQKQKFLRPLASGEKLGAFGLT 125 + E++R G H+ + + I YG+EEQKQK+L + SGE +GA +T Sbjct: 70 HEAAILIEIARANLSAWGAGHGIHSGIVAHYILAYGSEEQKQKWLPKMVSGEMVGALAMT 129 Query: 126 EPNAGTDASGQQTTAVLDGDEYILNGSKIFITNAIAGDIYVVMAMTDKSKGNKGISAFIV 185 EP AG+D G +T AV DG+ Y L+GSKIFITN ++ VV A TD S G KG+S ++ Sbjct: 130 EPGAGSDLQGIKTRAVKDGNGYRLSGSKIFITNGQHANLIVVAAKTDPSAGAKGVSLVVL 189 Query: 186 E-KGTPGFSFGVKEKKMGIRGSATSELIFEDCRIPKENLLGKE-GQGFKIAMSTLDGGRI 243 E +G GFS G K+G+ S TSEL F++ IP ENLLG E G+GF M+ L R+ Sbjct: 190 ETEGAEGFSRGRNLHKVGMHASDTSELFFDNVAIPPENLLGGEVGKGFYQMMTQLPQERL 249 Query: 244 GIAAQALGLAQGALDETVKYVKERVQFGRPLSKFQNTQFQLADMEVKVQAARHLVYQAAI 303 IAA A+G +GA++ TV Y KER FG P+ +FQNT+F+LA+ + K AR + + Sbjct: 250 IIAAGAVGAMEGAVERTVAYAKERQAFGGPILQFQNTRFKLAECQTKTTVARAFLNECMA 309 Query: 304 NKDLGKPYGVEAAMAKLFAAETAMEVTTKAVQLHGGYGYTRDYPVERMMRDAKITEIYEG 363 GK +AAMAK + +T EV + VQLHGGYGY +Y + +M DA++ IY G Sbjct: 310 EHLEGKLSVEKAAMAKYWITDTQGEVIDECVQLHGGYGYMAEYDIAQMWSDARVQRIYGG 369 Query: 364 TSEVQRMVISGKL 376 T+E+ + +I L Sbjct: 370 TNEIMKELIGRAL 382 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: 364 Number of extensions: 18 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: 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