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 6937192 Sama_1362 isovaleryl-CoA dehydrogenase (RefSeq)
Query= BRENDA::Q18AQ1 (378 letters) >FitnessBrowser__SB2B:6937192 Length = 389 Score = 299 bits (766), Expect = 8e-86 Identities = 159/367 (43%), Positives = 227/367 (61%) Query: 10 MLKELYVSFAENEVKPLATELDEEERFPYETVEKMAKAGMMGIPYPKEYGGEGGDTVGYI 69 ML++ FA+ E+ PLA ++D + FP E K G++G+ +EYGG + ++ Sbjct: 18 MLRDAVYEFAKGEIAPLAEKVDRDNAFPNELWAKFGDMGLLGVTVAEEYGGVNMGYLAHV 77 Query: 70 MAVEELSRVCGTTGVILSAHTSLGSWPIYQYGNEEQKQKFLRPLASGEKLGAFGLTEPNA 129 +A+EE+SR + G+ AH++L IY+ GNE Q+ K+L L SGE +GA ++EPNA Sbjct: 78 VAMEEISRASASIGLSYGAHSNLCVNQIYRNGNEAQRAKYLPKLISGEHIGALAMSEPNA 137 Query: 130 GTDASGQQTTAVLDGDEYILNGSKIFITNAIAGDIYVVMAMTDKSKGNKGISAFIVEKGT 189 G+D + A +GD YILNG+K++ITN YV+ A TD KG GI+AFIVE+G Sbjct: 138 GSDVVSMKLHARKEGDRYILNGNKMWITNGPDAHTYVIYAKTDLDKGPHGITAFIVERGF 197 Query: 190 PGFSFGVKEKKMGIRGSATSELIFEDCRIPKENLLGKEGQGFKIAMSTLDGGRIGIAAQA 249 GFS K K+G+RGS T EL+FEDC +P+EN+LG G K+ MS LD R+ ++ Sbjct: 198 KGFSQAQKLDKLGMRGSNTCELVFEDCEVPEENILGGLNNGVKVLMSGLDYERVVLSGGP 257 Query: 250 LGLAQGALDETVKYVKERVQFGRPLSKFQNTQFQLADMEVKVQAARHLVYQAAINKDLGK 309 LG+ +D V YV ERVQFG+ + +FQ Q +LADM + AA+ VY A D G+ Sbjct: 258 LGIMTACMDIVVPYVHERVQFGKSIGEFQLVQGKLADMYTGMNAAKSYVYNVARACDRGE 317 Query: 310 PYGVEAAMAKLFAAETAMEVTTKAVQLHGGYGYTRDYPVERMMRDAKITEIYEGTSEVQR 369 +AA L+AAE A ++ A+QL GG GY +Y R++RDAK+ EI GTSE++R Sbjct: 318 TTRKDAAGVILYAAELATKMALDAIQLLGGNGYVNEYATGRLLRDAKLYEIGAGTSEIRR 377 Query: 370 MVISGKL 376 M+I +L Sbjct: 378 MLIGREL 384 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: 404 Number of extensions: 14 Number of successful extensions: 1 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: 389 Length adjustment: 30 Effective length of query: 348 Effective length of database: 359 Effective search space: 124932 Effective search space used: 124932 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