Align Isovaleryl-CoA dehydrogenase (EC 1.3.8.4) (characterized)
to candidate GFF814 PS417_04135 acyl-CoA dehydrogenase
Query= reanno::Smeli:SM_b21121 (387 letters) >FitnessBrowser__WCS417:GFF814 Length = 378 Score = 258 bits (660), Expect = 1e-73 Identities = 150/370 (40%), Positives = 208/370 (56%), Gaps = 1/370 (0%) Query: 13 EIDALRASVRRFASERIAPLADDADRSNAFPMSLWREMGELGLLGITADEAHGGAGLGYL 72 E + R SVR F + AP ++ LW + GE G+L E +GG G +L Sbjct: 10 EHELFRESVRTFLEKDAAPFHGHWEKQGYIDRRLWNKAGEAGMLCSHLPEEYGGLGADFL 69 Query: 73 AHCVAMEEISRASASVGLSYGAHSNLCVNQINRNGKPAQKSRYLPKLISGEHVGALAMSE 132 V +EEISR + G+ + HS++ I G A K +YLPKLISGE V A+AM+E Sbjct: 70 YSAVVIEEISRLGLT-GIGFSLHSDIVAPYILHYGSEALKHKYLPKLISGEMVTAIAMTE 128 Query: 133 PGAGSDVVSMKLKADKRGDRYVLNGSKMWITNGPDADVLVVYAKTDPAAGPRGITAFLVE 192 PGAGSD+ +K A GD YV+NGSK +ITNG A++++V AKTDP AG +G + FLVE Sbjct: 129 PGAGSDLQGVKTTAVLDGDEYVINGSKTFITNGYLAELVIVVAKTDPKAGAKGTSLFLVE 188 Query: 193 KAFPGFSAGQKLDKLGMRGSNTSELIFTDCEVPEENVLGGVGEGVKVLMSGLDYERVVLS 252 PGF G++L+K+GM+ +TSEL F D VP+EN+LG G G LM L ER+ ++ Sbjct: 189 ADTPGFDKGKRLEKVGMKAQDTSELFFQDVRVPKENLLGQAGMGFAYLMQELPQERLTVA 248 Query: 253 AGPLGIMAACLDVVVPYLHERKQFGQPIGEFQLMQGKLADMYVTMNAARAYVYAVAAACD 312 G L A L+ + Y ERK FG+ I +FQ + KLA+M + R +V A Sbjct: 249 IGALSSAEAALEWTLEYTRERKAFGKAIADFQNTRFKLAEMATEIQIGRVFVDKCMALHL 308 Query: 313 RGETARKDAAGCILYAAEKATAMALEAIQALGGNGYTNDYPAGRLLRDAKLYEIGAGTSE 372 G+ AA +A + + E +Q GG G+ +YP R DA++ I AGT+E Sbjct: 309 EGKLDVPTAAMAKYWATDLQCKVLDECVQLHGGYGFMWEYPIARAWADARVQRIYAGTNE 368 Query: 373 IRRMLIGREL 382 I + +I R L Sbjct: 369 IMKEIIARAL 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: 296 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: 387 Length of database: 378 Length adjustment: 30 Effective length of query: 357 Effective length of database: 348 Effective search space: 124236 Effective search space used: 124236 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