Align butyryl-CoA dehydrogenase; EC 1.3.99.2 (characterized)
to candidate 7024494 Shewana3_1672 isovaleryl-CoA dehydrogenase (RefSeq)
Query= CharProtDB::CH_091785 (379 letters) >lcl|FitnessBrowser__ANA3:7024494 Shewana3_1672 isovaleryl-CoA dehydrogenase (RefSeq) Length = 389 Score = 310 bits (793), Expect = 6e-89 Identities = 159/378 (42%), Positives = 242/378 (64%) Query: 1 MDFNLTREQELVRQMVREFAENEVKPIAAEIDETERFPMENVKKMGQYGMMGIPFSKEYG 60 ++F L E +++R V++FA++E+ PIAA++D FP E +G G++G+ +EYG Sbjct: 8 LNFGLGEEVDMLRDAVQDFAKHEIAPIAAKVDHDNAFPNEIWPVLGGMGLLGVTVPEEYG 67 Query: 61 GAGGDVLSYIIAVEELSKVCGTTGVILSAHTSLCASLINEHGTEEQKQKYLVPLAKGEKI 120 GA L++++A+EE+S+ + G+ AH++LC + IN +G EQK KYL L GE I Sbjct: 68 GANMGYLAHVVAMEEISRASASIGLSYGAHSNLCVNQINRNGNAEQKAKYLPKLVSGEHI 127 Query: 121 GAYGLTEPNAGTDSGAQQTVAVLEGDHYVINGSKIFITNGGVADTFVIFAMTDRTKGTKG 180 GA ++EPNAG+D + + A EGD Y++NG+K++ITNG A+T+VI+A TD TKG G Sbjct: 128 GALAMSEPNAGSDVVSMKLHARKEGDRYILNGNKMWITNGPDANTYVIYAKTDLTKGAHG 187 Query: 181 ISAFIIEKGFKGFSIGKVEQKLGIRASSTTELVFEDMIVPVENMIGKEGKGFPIAMKTLD 240 I+AFI+E+GFKGFS + KLG+R S+T ELVFED+ VP EN++G G + M LD Sbjct: 188 ITAFIVERGFKGFSQAQKLDKLGMRGSNTCELVFEDVEVPEENILGGLNNGVKVLMSGLD 247 Query: 241 GGRIGIAAQALGIAEGAFNEARAYMKERKQFGRSLDKFQGLAWMMADMDVAIESARYLVY 300 R+ ++ LGI + Y+ ER+QFG+S+ +FQ + +ADM + +A+ VY Sbjct: 248 YERVVLSGGPLGIMNACMDIVVPYIHEREQFGKSIGEFQLVQGKLADMYTGMNAAKAYVY 307 Query: 301 KAAYLKQAGLPYTVDAARAKLHAANVAMDVTTKAVQLFGGYGYTKDYPVERMMRDAKITE 360 A G DAA A L++A +A + A+QL GG GY +Y R++RDAK+ E Sbjct: 308 SVAKSCDRGETTRKDAAGAILYSAELATKMALDAIQLLGGNGYVNEYATGRLLRDAKLYE 367 Query: 361 IYEGTSEVQKLVISGKIF 378 I GTSE+++++I ++F Sbjct: 368 IGAGTSEIRRMLIGRELF 385 Lambda K H 0.317 0.135 0.377 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: 12 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: 379 Length of database: 389 Length adjustment: 30 Effective length of query: 349 Effective length of database: 359 Effective search space: 125291 Effective search space used: 125291 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.
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