Align butyryl-CoA dehydrogenase; EC 1.3.99.2 (characterized)
to candidate WP_011914286.1 PST_RS16120 isovaleryl-CoA dehydrogenase
Query= CharProtDB::CH_091785 (379 letters) >NCBI__GCF_000013785.1:WP_011914286.1 Length = 387 Score = 293 bits (749), Expect = 7e-84 Identities = 151/378 (39%), Positives = 234/378 (61%) Query: 1 MDFNLTREQELVRQMVREFAENEVKPIAAEIDETERFPMENVKKMGQYGMMGIPFSKEYG 60 ++F L +++R+ V+ F E+ P A ID+ FP + KK G+ G++G+ S+EYG Sbjct: 6 LNFALGETIDMLREQVQAFVAAELAPRAEAIDQDNLFPADMWKKFGEMGLLGVTVSEEYG 65 Query: 61 GAGGDVLSYIIAVEELSKVCGTTGVILSAHTSLCASLINEHGTEEQKQKYLVPLAKGEKI 120 GAG L++++A+EE+S+ + + AH++LC + IN +G EQK +YL L GE + Sbjct: 66 GAGLGYLAHVVAMEEISRGSASVALSYGAHSNLCVNQINRNGNPEQKARYLPKLISGEHV 125 Query: 121 GAYGLTEPNAGTDSGAQQTVAVLEGDHYVINGSKIFITNGGVADTFVIFAMTDRTKGTKG 180 GA ++EPNAG+D + + A GD YV+NGSK +ITNG A+T+VI+A TD KG G Sbjct: 126 GALAMSEPNAGSDVVSMKLRAEKRGDRYVLNGSKTWITNGPDANTYVIYAKTDLDKGPHG 185 Query: 181 ISAFIIEKGFKGFSIGKVEQKLGIRASSTTELVFEDMIVPVENMIGKEGKGFPIAMKTLD 240 I+AFI+E+ +KGFS G KLG+R S+T EL F+D+ VP EN++G E G + M LD Sbjct: 186 ITAFIVERDWKGFSRGNKFDKLGMRGSNTCELFFDDVEVPQENVLGVENGGVKVLMSGLD 245 Query: 241 GGRIGIAAQALGIAEGAFNEARAYMKERKQFGRSLDKFQGLAWMMADMDVAIESARYLVY 300 R+ +A GI + + Y+ +RKQFG+S+ +FQ + +ADM + ++R +Y Sbjct: 246 YERVVLAGGPTGIMQACLDVVVPYIHDRKQFGQSIGEFQFIQGKVADMYTQLNASRAYLY 305 Query: 301 KAAYLKQAGLPYTVDAARAKLHAANVAMDVTTKAVQLFGGYGYTKDYPVERMMRDAKITE 360 A G DAA L+ A A + +A+Q+ GG GY ++P R++RDAK+ E Sbjct: 306 AVAQACDRGETTRKDAAGVILYTAENATQMALQAIQILGGNGYINEFPTGRLLRDAKLYE 365 Query: 361 IYEGTSEVQKLVISGKIF 378 I GTSE+++++I ++F Sbjct: 366 IGAGTSEIRRMLIGRELF 383 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: 360 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: 387 Length adjustment: 30 Effective length of query: 349 Effective length of database: 357 Effective search space: 124593 Effective search space used: 124593 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 Apr 09 2024. 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