Align Isovaleryl-CoA dehydrogenase (EC 1.3.8.4) (characterized)
to candidate Ga0059261_3681 Ga0059261_3681 Acyl-CoA dehydrogenases
Query= reanno::psRCH2:GFF1051 (387 letters) >FitnessBrowser__Korea:Ga0059261_3681 Length = 380 Score = 238 bits (606), Expect = 3e-67 Identities = 133/376 (35%), Positives = 210/376 (55%), Gaps = 3/376 (0%) Query: 8 FALGETIDMLREQVQAFVAAEIAPRAEAIDQENLFPADMWRKFGEMGLLGVTVSEEYGGA 67 F L E ++E + F A I P A D++++FP + + E+G + VSEE GG Sbjct: 4 FDLNEDQRAIQEMARKFTADAITPHAAEWDEKHIFPRETVKAAAELGFGAIYVSEESGGI 63 Query: 68 GLGYLAHVVAMEEISRGSASVALSYGAHSNLCVNQINRNGNPEQKARYLPKLISGEHVGA 127 GLG L + ME ++ G + + H N+ I+R G+ K +YLP+L++ + + + Sbjct: 64 GLGRLESALIMEAMAYGCPATSAFISIH-NMASWMIDRFGSQAVKDKYLPRLVTADWLAS 122 Query: 128 LAMSEPNAGSDVVSMKLRAEKRGDRYVLNGSKTWITNGPDANTYVIYAKTDLDKGAHGIT 187 ++EP++GSD ++K A++ GD +++NGSK +I+ + YV +T D G GI+ Sbjct: 123 YCLTEPSSGSDAAALKTTAKRDGDHFIVNGSKQFISGAGENELYVTMVRTGAD-GPKGIS 181 Query: 188 AFIVERDWKGFSRGNKFDKLGMRGSNTCELFFDDVEVPQENVLGAENGGVKVLMSGLDYE 247 +E+D G S G KLG T ++ FD+V VP EN++G E G ++ M GLD Sbjct: 182 CLAIEKDMPGVSFGANERKLGWHAQPTRQVTFDNVRVPVENLVGGEGEGFRIAMMGLDGG 241 Query: 248 RVVLAGGPTGIMQSCLDVVVPYIHDRKQFGQSIGEFQFIQGKVADMYTQLNASRAYLY-A 306 R+ + G Q CLD V Y DRKQFG +I +FQ Q +ADM T+L A+RA LY A Sbjct: 242 RLNIGACSLGGAQRCLDEAVQYTKDRKQFGSAIADFQNTQFMLADMATELEAARALLYLA 301 Query: 307 VAQACDRGETTRKDAAGVILYTAENATQMALQAIQILGGNGYINEFPTGRLLRDAKLYEI 366 A+ K AA + + + + +A+Q+ GG GY+ ++P R RD +++ I Sbjct: 302 AAKVTSNAPDKTKFAAMAKRFATDTGSSVVDRALQLHGGYGYLMDYPIERFWRDLRVHSI 361 Query: 367 GAGTSEIRRMLIGREL 382 GT+++ RM++GREL Sbjct: 362 LEGTNQVMRMIVGREL 377 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: 334 Number of extensions: 11 Number of successful extensions: 4 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