Align butyryl-CoA dehydrogenase; EC 1.3.99.2 (characterized)
to candidate WP_068170917.1 HTA01S_RS11035 isovaleryl-CoA dehydrogenase
Query= CharProtDB::CH_091785 (379 letters) >NCBI__GCF_001592305.1:WP_068170917.1 Length = 393 Score = 286 bits (731), Expect = 9e-82 Identities = 149/385 (38%), Positives = 241/385 (62%), Gaps = 9/385 (2%) Query: 1 MDFNLTREQELVRQMVREFAENEVKPIAAEIDETERFPMENVKKMGQYGMMGIPFSKEYG 60 ++F L + + +R VREFA+ E+ P AAEID++++FPM+ +KMG+ G++GI ++YG Sbjct: 7 LNFQLGEDIDALRDAVREFAQAEIAPRAAEIDKSDQFPMDCWRKMGELGVLGITVPEQYG 66 Query: 61 GAGGDVLSYIIAVEELSKVCGTTGVILSAHTSLCASLINEHGTEEQKQKYLVPLAKGEKI 120 GA L++++A+EE+S+ + G+ AH++LC + IN +G + QK KYL L GE + Sbjct: 67 GANMGYLAHMVAMEEISRASASVGLSYGAHSNLCVNQINRNGNDAQKAKYLPKLISGEHV 126 Query: 121 GAYGLTEPNAGTDSGAQQTVAVLEGDHYVINGSKIFITNGGVADTFVIFAMTDRTKGTKG 180 GA ++EP AG+D + + A +G +Y++NG+K++ITNG ADT V++A ++ G +G Sbjct: 127 GALAMSEPGAGSDVISMKLKAEDKGGYYLLNGNKMWITNGPDADTLVVYAKSEPEMGARG 186 Query: 181 ISAFIIEKGFKGFSIGKVEQKLGIRASSTTELVFEDMIVPVENMIGKEGKGFPIAMKTLD 240 ++AF+IEKG GFSI + KLG+R S T ELVF+++ VP +N++G G + M LD Sbjct: 187 VTAFLIEKGMPGFSIAQKLDKLGMRGSHTGELVFQNVEVPAQNILGGLNMGAKVLMSGLD 246 Query: 241 GGRIGIAAQALGIAEGAFNEARAYMKERKQFGRSLDKFQGLAWMMADMDVAIESARYLVY 300 R + LGI + + Y+ +RKQFG+S+ +FQ + +ADM +++AR Y Sbjct: 247 YERAVLTGGPLGIMQSVMDNVIPYIHDRKQFGQSIGEFQLIQGKVADMYTVLQAARSFAY 306 Query: 301 KAAYLKQAGLPYTVDAARAKLHAANVAMDVTTKA-------VQLFGGYGYTKDYPVERMM 353 A K L T + + A+V + KA VQ++GG GY +YP+ R+ Sbjct: 307 TVA--KNLDLLGTEHVRQVRKDCASVILWTAEKATWMAGEGVQIYGGNGYINEYPLGRLW 364 Query: 354 RDAKITEIYEGTSEVQKLVISGKIF 378 RDAK+ EI GTSE+++++I ++F Sbjct: 365 RDAKLYEIGAGTSEIRRMLIGRELF 389 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: 396 Number of extensions: 17 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: 393 Length adjustment: 30 Effective length of query: 349 Effective length of database: 363 Effective search space: 126687 Effective search space used: 126687 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