Align butyryl-CoA dehydrogenase; EC 1.3.99.2 (characterized)
to candidate WP_012116241.1 XAUT_RS21625 isovaleryl-CoA dehydrogenase
Query= CharProtDB::CH_091785 (379 letters) >NCBI__GCF_000017645.1:WP_012116241.1 Length = 390 Score = 306 bits (783), Expect = 8e-88 Identities = 157/377 (41%), Positives = 236/377 (62%) Query: 2 DFNLTREQELVRQMVREFAENEVKPIAAEIDETERFPMENVKKMGQYGMMGIPFSKEYGG 61 DF+L +++R VR F++ E+ P AAEID T +FP + K+G G++G+ +EYGG Sbjct: 10 DFDLGETADMLRDTVRSFSDAEIAPRAAEIDRTNQFPRDLWPKLGALGLLGVTAEEEYGG 69 Query: 62 AGGDVLSYIIAVEELSKVCGTTGVILSAHTSLCASLINEHGTEEQKQKYLVPLAKGEKIG 121 +G L ++IA+EE+S+ + G+ AH++LC + I+ +GT EQK KYL L GE +G Sbjct: 70 SGLGYLEHVIAMEEISRASASVGLSYGAHSNLCINQISRNGTAEQKAKYLPKLISGEHVG 129 Query: 122 AYGLTEPNAGTDSGAQQTVAVLEGDHYVINGSKIFITNGGVADTFVIFAMTDRTKGTKGI 181 A ++EP AG+D + +T A +GD Y++NGSK++ITNG +A+T V++A TD G KG+ Sbjct: 130 ALAMSEPGAGSDVVSMRTRADKKGDRYILNGSKMWITNGPIAETLVVYAKTDPAAGPKGM 189 Query: 182 SAFIIEKGFKGFSIGKVEQKLGIRASSTTELVFEDMIVPVENMIGKEGKGFPIAMKTLDG 241 +AF++E+ F GFS + KLG+R S T ELVF+D VP EN++G G+G + M LD Sbjct: 190 TAFLVERDFPGFSTAQKLDKLGMRGSDTGELVFQDCEVPEENVLGAVGRGVNVLMSGLDY 249 Query: 242 GRIGIAAQALGIAEGAFNEARAYMKERKQFGRSLDKFQGLAWMMADMDVAIESARYLVYK 301 R +A GI + + Y+ ERKQFG+ + FQ + +ADM V + + + VY Sbjct: 250 ERAVLAGGPTGIMQACMDIVLPYVHERKQFGQPIGTFQLMQGKIADMYVTMNATKAYVYA 309 Query: 302 AAYLKQAGLPYTVDAARAKLHAANVAMDVTTKAVQLFGGYGYTKDYPVERMMRDAKITEI 361 A G DAA A L+AA A + +A+Q GG GY DYP R++RDAK+ EI Sbjct: 310 VAKACDRGATTREDAAGAILYAAEKATWMALEAIQTLGGNGYINDYPTGRLLRDAKLYEI 369 Query: 362 YEGTSEVQKLVISGKIF 378 GTSE+++++I ++F Sbjct: 370 GAGTSEIRRMLIGRQLF 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: 364 Number of extensions: 10 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: 390 Length adjustment: 30 Effective length of query: 349 Effective length of database: 360 Effective search space: 125640 Effective search space used: 125640 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