Align Isovaleryl-CoA dehydrogenase (EC 1.3.8.4) (characterized)
to candidate Echvi_1473 Echvi_1473 Acyl-CoA dehydrogenases
Query= reanno::Smeli:SM_b21121 (387 letters) >FitnessBrowser__Cola:Echvi_1473 Length = 380 Score = 299 bits (765), Expect = 1e-85 Identities = 160/377 (42%), Positives = 222/377 (58%) Query: 6 LNFALGEEIDALRASVRRFASERIAPLADDADRSNAFPMSLWREMGELGLLGITADEAHG 65 +NF L E + +R F ++ I P + D FP+ L++++GELGL+G+ +G Sbjct: 2 MNFQLTENQSMIAQMIRDFGAKEITPFRKEWDDHQTFPLPLFKKLGELGLMGVLIPSEYG 61 Query: 66 GAGLGYLAHCVAMEEISRASASVGLSYGAHSNLCVNQINRNGKPAQKSRYLPKLISGEHV 125 G+G GYL + A+ E+++ +GLS AH++LC I G QK +YLPKL S E + Sbjct: 62 GSGFGYLEYVTAILELAKLDPGIGLSMAAHNSLCSGHIMLFGSEEQKQKYLPKLASCEFL 121 Query: 126 GALAMSEPGAGSDVVSMKLKADKRGDRYVLNGSKMWITNGPDADVLVVYAKTDPAAGPRG 185 GA ++EP GSD +MK A GD +VLNG+K +IT+G DV VV A+T G Sbjct: 122 GAWGLTEPNTGSDAANMKTTATAEGDYFVLNGAKNFITHGVSGDVAVVIARTGEVGDKHG 181 Query: 186 ITAFLVEKAFPGFSAGQKLDKLGMRGSNTSELIFTDCEVPEENVLGGVGEGVKVLMSGLD 245 +TAF+VEK GF G+K DKLGMR S T+ELIF DC V + +LG VGEG M LD Sbjct: 182 MTAFVVEKGTEGFRGGRKEDKLGMRTSETAELIFEDCRVHKSQILGEVGEGFIQSMKVLD 241 Query: 246 YERVVLSAGPLGIMAACLDVVVPYLHERKQFGQPIGEFQLMQGKLADMYVTMNAARAYVY 305 R+ ++A LGI + + Y ER+QF +PI +Q + KLADM + AA+ + Sbjct: 242 GGRISIAALSLGIAEGAFEAALSYSKERQQFQKPISAYQGISFKLADMATKLEAAKLLTF 301 Query: 306 AVAAACDRGETARKDAAGCILYAAEKATAMALEAIQALGGNGYTNDYPAGRLLRDAKLYE 365 A +RGE +A YA+E A +A EA+Q GG G+T DYP + RD KL Sbjct: 302 KAADLKNRGEYVTLASAQAKYYASEIAVELANEAVQVYGGYGFTKDYPVEKYYRDVKLCT 361 Query: 366 IGAGTSEIRRMLIGREL 382 IG GTSEI++++I REL Sbjct: 362 IGEGTSEIQKIVISREL 378 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: 314 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: 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