Align Isovaleryl-CoA dehydrogenase (EC 1.3.8.4) (characterized)
to candidate SMa1400 SMa1400 acyl-CoA dehydrogenase
Query= reanno::Smeli:SM_b21121 (387 letters) >FitnessBrowser__Smeli:SMa1400 Length = 380 Score = 248 bits (632), Expect = 3e-70 Identities = 149/366 (40%), Positives = 206/366 (56%), Gaps = 2/366 (0%) Query: 17 LRASVRRFASERIAPLADDADRSNAFPMSLWREMGELGLLGITADEAHGGAGLGYLAHCV 76 +R R FA E I P+A+ DR FP L+ EM +LGL GI E GG G L + V Sbjct: 10 VRDMARAFADEVIRPMAESLDREERFPAELYGEMAKLGLFGIGVPEHLGGPGFDTLTYAV 69 Query: 77 AMEEISRASASVGLSYGAHSNLCVNQINRNGKPAQKSRYLPKLISGEHVGALAMSEPGAG 136 MEE+SR ASV G L + R+G Q+ R LP +++ A ++EP AG Sbjct: 70 VMEELSRGYASVADQCGL-VELISTLLVRHGTEGQQ-RMLPDVLNMSAKVAYCITEPEAG 127 Query: 137 SDVVSMKLKADKRGDRYVLNGSKMWITNGPDADVLVVYAKTDPAAGPRGITAFLVEKAFP 196 +DV ++ A++ GD ++LNG K+WI N P ADV V A+TD AG RG++ F+V+ Sbjct: 128 TDVSGIRTTAERDGDGWMLNGGKIWIHNAPVADVGFVLARTDKEAGNRGMSIFIVDLNSA 187 Query: 197 GFSAGQKLDKLGMRGSNTSELIFTDCEVPEENVLGGVGEGVKVLMSGLDYERVVLSAGPL 256 G G K K+G R S L FTD +P +LG G G ++MS LD RV ++A + Sbjct: 188 GVERGPKEHKMGQRASQVGALTFTDVRLPGGALLGQEGRGFHMMMSVLDKGRVGIAALAV 247 Query: 257 GIMAACLDVVVPYLHERKQFGQPIGEFQLMQGKLADMYVTMNAARAYVYAVAAACDRGET 316 GI A L+ V Y RKQFG+ I +FQ +Q LADM + AAR V++ A+ DRG Sbjct: 248 GIAQAGLEAAVDYAGTRKQFGKAISDFQGVQWLLADMAKDIEAARLLVHSAASKIDRGLD 307 Query: 317 ARKDAAGCILYAAEKATAMALEAIQALGGNGYTNDYPAGRLLRDAKLYEIGAGTSEIRRM 376 A K + +A + A +A+Q GG+GY + RL RDAK+ +I GT++I+RM Sbjct: 308 ATKACSIAKCFAGDMAVQRTADAVQVFGGSGYIRGFEVERLYRDAKITQIYEGTNQIQRM 367 Query: 377 LIGREL 382 +I REL Sbjct: 368 IIAREL 373 Lambda K H 0.318 0.135 0.391 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: 318 Number of extensions: 20 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: 387 Length of database: 380 Length adjustment: 30 Effective length of query: 357 Effective length of database: 350 Effective search space: 124950 Effective search space used: 124950 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 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