Align isobutyryl-CoA dehydrogenase (EC 1.3.8.1) (characterized)
to candidate GFF814 PS417_04135 acyl-CoA dehydrogenase
Query= reanno::psRCH2:GFF2392 (383 letters) >FitnessBrowser__WCS417:GFF814 Length = 378 Score = 270 bits (689), Expect = 6e-77 Identities = 148/372 (39%), Positives = 219/372 (58%), Gaps = 1/372 (0%) Query: 7 SEDQRMIRDMARDFARREIAPHAQAWEKAGWIDDTLVAQMGELGLLGMVVPEEWGGSYID 66 S + + R+ R F ++ AP WEK G+ID L + GE G+L +PEE+GG D Sbjct: 8 SPEHELFRESVRTFLEKDAAPFHGHWEKQGYIDRRLWNKAGEAGMLCSHLPEEYGGLGAD 67 Query: 67 YVAYALAVEEISAGDGATGALMSIHNSVGCGPVLNYGSQAQKDEWLTELASGRAIGCFAL 126 ++ A+ +EEIS G TG S+H+ + +L+YGS+A K ++L +L SG + A+ Sbjct: 68 FLYSAVVIEEISRL-GLTGIGFSLHSDIVAPYILHYGSEALKHKYLPKLISGEMVTAIAM 126 Query: 127 TEPQAGSEAHNLRTRAELVDGHWVLNGSKQFCSNAKRSKLAIVFAVTDPELGKKGLSAFL 186 TEP AGS+ ++T A L +V+NGSK F +N ++L IV A TDP+ G KG S FL Sbjct: 127 TEPGAGSDLQGVKTTAVLDGDEYVINGSKTFITNGYLAELVIVVAKTDPKAGAKGTSLFL 186 Query: 187 VPTDTPGFAVERSEHKMGIRASDTCGVSLSDCRIPEANLLGERGKGLAIALSNLEGGRIG 246 V DTPGF + K+G++A DT + D R+P+ NLLG+ G G A + L R+ Sbjct: 187 VEADTPGFDKGKRLEKVGMKAQDTSELFFQDVRVPKENLLGQAGMGFAYLMQELPQERLT 246 Query: 247 IGAQALGIARAAFEAALLYARERVQFGKPIAEHQSIANMLADMQTQLNAARLLILHAARL 306 + AL A AA E L Y RER FGK IA+ Q+ LA+M T++ R+ + L Sbjct: 247 VAIGALSSAEAALEWTLEYTRERKAFGKAIADFQNTRFKLAEMATEIQIGRVFVDKCMAL 306 Query: 307 KSAGLPCLSEASQAKLFASEMAEKVCSQAVQIHGGYGYLEDYPVERYYRDARITQIYEGS 366 G + A+ AK +A+++ KV + VQ+HGGYG++ +YP+ R + DAR+ +IY G+ Sbjct: 307 HLEGKLDVPTAAMAKYWATDLQCKVLDECVQLHGGYGFMWEYPIARAWADARVQRIYAGT 366 Query: 367 SEIQRLLIAREL 378 +EI + +IAR L Sbjct: 367 NEIMKEIIARAL 378 Lambda K H 0.318 0.133 0.390 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: 324 Number of extensions: 16 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: 383 Length of database: 378 Length adjustment: 30 Effective length of query: 353 Effective length of database: 348 Effective search space: 122844 Effective search space used: 122844 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