Align butyryl-CoA dehydrogenase; EC 1.3.99.2 (characterized)
to candidate WP_039790199.1 CEJ45_RS12595 isovaleryl-CoA dehydrogenase
Query= CharProtDB::CH_091785 (379 letters) >NCBI__GCF_002213425.1:WP_039790199.1 Length = 394 Score = 293 bits (751), Expect = 4e-84 Identities = 157/384 (40%), Positives = 241/384 (62%), Gaps = 6/384 (1%) Query: 1 MDFNLTREQELVRQMVREFAENEVKPIAAEIDETERFPMENVKKMGQYGMMGIPFSKEYG 60 ++F+ + +R+ V FA+ E+ P AAEID +++FPM+ KK+G G++GI +EYG Sbjct: 7 LNFDHGEDIAALREAVAAFAQTEIAPRAAEIDRSDQFPMDLWKKLGDLGVLGITVGEEYG 66 Query: 61 GAGGDVLSYIIAVEELSKVCGTTGVILSAHTSLCASLINEHGTEEQKQKYLVPLAKGEKI 120 GAG L++IIA+EE+S+ + G+ AH++LC + I +G EEQK+KYL L G+ I Sbjct: 67 GAGLGYLAHIIAMEEISRASASVGLSYGAHSNLCVNQIKRNGNEEQKRKYLPKLISGDFI 126 Query: 121 GAYGLTEPNAGTDSGAQQTVAVLEGDHYVINGSKIFITNGGVADTFVIFAMTDRTKGTKG 180 GA ++EPNAG+D + + A +GD YV+NGSK++ITNG AD V++A TD G +G Sbjct: 127 GALAMSEPNAGSDVVSMKLRADKKGDRYVLNGSKMWITNGPDADVLVVYAKTDLDAGARG 186 Query: 181 ISAFIIEKGFKGFSIGKVEQKLGIRASSTTELVFEDMIVPVENMIGKEGKGFPIAMKTLD 240 ++AF++EKG+KGFS+ + KLG+R S T ELVF+D VP EN++G G+G + M LD Sbjct: 187 MTAFLVEKGYKGFSVAQKLDKLGMRGSHTGELVFQDCEVPEENVLGGVGRGVNVLMSGLD 246 Query: 241 GGRIGIAAQALGIAEGAFNEARAYMKERKQFGRSLDKFQGLAWMMADMDVAIESARYLVY 300 R ++ LGI + + Y+ +RKQFG+++ +FQ + +ADM + + + VY Sbjct: 247 FERSVLSGGPLGIMQACMDVVVPYVHDRKQFGQAIGEFQLMQGKLADMYSTMMACKAYVY 306 Query: 301 KA------AYLKQAGLPYTVDAARAKLHAANVAMDVTTKAVQLFGGYGYTKDYPVERMMR 354 A DAA A L++A A + +A+Q GG GY +YPV R+ R Sbjct: 307 AVGQACDRADSADKVRALRKDAAGAILYSAEKATWMAGEAIQSLGGNGYINEYPVGRLWR 366 Query: 355 DAKITEIYEGTSEVQKLVISGKIF 378 DAK+ EI GTSE+++++I ++F Sbjct: 367 DAKLYEIGAGTSEIRRMLIGRELF 390 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: 403 Number of extensions: 12 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: 394 Length adjustment: 30 Effective length of query: 349 Effective length of database: 364 Effective search space: 127036 Effective search space used: 127036 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 24 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