Align isovaleryl-CoA dehydrogenase (EC 1.3.8.4) (characterized)
to candidate SMc01639 SMc01639 acyl-CoA dehydrogenase
Query= BRENDA::P26440 (426 letters) >FitnessBrowser__Smeli:SMc01639 Length = 386 Score = 208 bits (529), Expect = 3e-58 Identities = 124/379 (32%), Positives = 201/379 (53%), Gaps = 9/379 (2%) Query: 45 LSEEQRQLRQTMAKFLQEHLAPKAQEIDRSNEFKNLR--EFWKQLGNLGVLGITAPVQYG 102 L+EEQ+ + T+ F++ + P E++R+ E ++ LG P + G Sbjct: 5 LTEEQQMIVDTVRTFVETEIYPHENEVERTGVVPRELGLEIARKCKELGFFACNFPEEVG 64 Query: 103 GSGLGYLEHVLVMEEISRASGAVGLSYGAHSNLCINQLVRNGNEAQKEKYLPKLISGEYI 162 G+GL +L LV E+ R S + + +G S + + NE Q+E+YL + G+ Sbjct: 65 GAGLDHLTFTLVERELGRGSMGLTVFFGRPSGILMAC-----NEDQRERYLLPAVRGDKF 119 Query: 163 GALAMSEPNAGSDVVSMKLKAEKKGNHYILNGNKFWITNGPDADVLIVYAKTDLAAVPAS 222 ALAM+EP+AGSDV MK A G+ +I+NG K +I++ AD +IV+ T P Sbjct: 120 DALAMTEPDAGSDVRGMKCFARPDGDDWIVNGTKHFISHADIADFVIVFIATGEEQTPRG 179 Query: 223 --RGITAFIVEKGMPGFSTSKKLDKLGMRGSNTCELIFEDCKIPAANILGHENKGVYVLM 280 + IT F+V++G PGF + + + RG C L F+DC++P+A ILG +KG + Sbjct: 180 PKKKITCFLVDRGTPGFEIREGYNSVSHRGYKNCILTFDDCRLPSAQILGEVHKGFDIAN 239 Query: 281 SGLDLERLVLAGGPLGLMQAVLDHTIPYLHVREAFGQKIGHFQLMQGKMADMYTRLMACR 340 L RL +A +G + D+ + Y R+ FG+ I Q + K+ADM T + A Sbjct: 240 DWLYATRLTVAATSVGRARRAFDYALSYAAERKQFGKPISANQGVSFKLADMITEIDAAD 299 Query: 341 QYVYNVAKACDEGHCTAKDCAGVILYSAECATQVALDGIQCFGGNGYINDFPMGRFLRDA 400 + A D+G + ++ A +++ E +V + IQ +GG G ++D P+ RF RDA Sbjct: 300 LLTLSAAWRLDQGLPSNREIASAKVFATEMLARVTDEAIQIYGGMGLMDDLPLARFWRDA 359 Query: 401 KLYEIGAGTSEVRRLVIGR 419 ++ I GTSE++R +I R Sbjct: 360 RVERIWDGTSEIQRHIISR 378 Lambda K H 0.321 0.137 0.410 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: 394 Number of extensions: 17 Number of successful extensions: 3 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: 426 Length of database: 386 Length adjustment: 31 Effective length of query: 395 Effective length of database: 355 Effective search space: 140225 Effective search space used: 140225 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 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