Align butyryl-CoA dehydrogenase; EC 1.3.99.2 (characterized)
to candidate GFF1026 HP15_1005 acyl-CoA dehydrogenase domain protein
Query= CharProtDB::CH_091785 (379 letters) >FitnessBrowser__Marino:GFF1026 Length = 389 Score = 311 bits (797), Expect = 2e-89 Identities = 159/379 (41%), Positives = 248/379 (65%), Gaps = 1/379 (0%) Query: 1 MDFNLTREQELVRQMVREFAENEVKPIAAEIDETERFPMENVKKMGQYGMMGIPFSKEYG 60 ++F L +++R+ + FA +E+ P A EID FPM+ +KMG G++GI S+EYG Sbjct: 8 LNFGLGETLDMLREQINGFAASEIAPRAEEIDRNNEFPMDLWRKMGDMGLLGITVSEEYG 67 Query: 61 GAGGDVLSYIIAVEELSKVCGTTGVILSAHTSLCASLINEHGTEEQKQKYLVPLAKGEKI 120 G+ L+++IA+EE+S+ + G+ AH++LC + I+ +GTEEQKQKYL L GE I Sbjct: 68 GSDMGYLAHVIAMEEISRASASVGLSYGAHSNLCVNQIHRNGTEEQKQKYLPKLVSGEHI 127 Query: 121 GAYGLTEPNAGTDSGAQQTVAVLEGDHYVINGSKIFITNGGVADTFVIFAMTDRTKGTKG 180 GA ++EPNAG+D + + A EGDHY++NG+K++ITNG A+T+VI+A TD + G++G Sbjct: 128 GALAMSEPNAGSDVISMKLTAKDEGDHYLLNGNKMWITNGPDANTYVIYAKTDTSAGSRG 187 Query: 181 ISAFIIEKGFKGFSIGKVEQKLGIRASSTTELVFEDMIVPVENMIGKEGKGFPIAMKTLD 240 ++AFI+E+ GFS + KLG+R S+T ELVF+D VP EN++G G G + M LD Sbjct: 188 VTAFIVERDAPGFSRHQKLDKLGMRGSNTCELVFQDCKVPKENVLGGVGNGAKVLMSGLD 247 Query: 241 GGRIGIAAQALGIAEGAFNEARAYMKERKQFGRSLDKFQGLAWMMADMDVAIESARYLVY 300 R+ ++ LGI + A + Y++ERKQFG+++ +F+ + +ADM + +A+ VY Sbjct: 248 YERLVLSGGPLGIMQAAMDVVVPYIRERKQFGQAIGEFELVQGKVADMYTWMNTAKSYVY 307 Query: 301 KAAYLKQAGLPYT-VDAARAKLHAANVAMDVTTKAVQLFGGYGYTKDYPVERMMRDAKIT 359 A G T DAA A L++A +A + A+QL GG GY +YP R++RDAK+ Sbjct: 308 MVAMSADRGAETTRKDAAGAILYSAEMATKIALDAIQLLGGNGYINEYPTGRLLRDAKLY 367 Query: 360 EIYEGTSEVQKLVISGKIF 378 EI GTSE+++++I +++ Sbjct: 368 EIGAGTSEIRRMLIGRELY 386 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: 413 Number of extensions: 10 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: 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:
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