Align isobutyryl-CoA dehydrogenase (EC 1.3.8.1) (characterized)
to candidate AO356_17045 AO356_17045 acyl-CoA dehydrogenase
Query= reanno::psRCH2:GFF2392 (383 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_17045 Length = 378 Score = 259 bits (661), Expect = 1e-73 Identities = 141/372 (37%), Positives = 211/372 (56%), Gaps = 1/372 (0%) Query: 7 SEDQRMIRDMARDFARREIAPHAQAWEKAGWIDDTLVAQMGELGLLGMVVPEEWGGSYID 66 S + + RD R F +E P+ WEK G +D L + GE G+L +PE +GG D Sbjct: 8 SPEHELFRDSVRTFLEKEAVPYHSQWEKQGHVDRQLWNKAGEAGMLCSHLPEAYGGLDAD 67 Query: 67 YVAYALAVEEISAGDGATGALMSIHNSVGCGPVLNYGSQAQKDEWLTELASGRAIGCFAL 126 ++ + +EEI G TG S+H+ + +L+YGS+A K ++L +L SG + A+ Sbjct: 68 FLYSTVVIEEIGRL-GLTGIGFSLHSDIVAPYILHYGSEALKHKYLPKLVSGEMVTAIAM 126 Query: 127 TEPQAGSEAHNLRTRAELVDGHWVLNGSKQFCSNAKRSKLAIVFAVTDPELGKKGLSAFL 186 TEP AGS+ ++T A L +V+NGSK F +N + L IV A TDP+ G KG S FL Sbjct: 127 TEPGAGSDLQGVKTTAVLDGDEYVINGSKTFITNGFLADLVIVVAKTDPKAGAKGTSLFL 186 Query: 187 VPTDTPGFAVERSEHKMGIRASDTCGVSLSDCRIPEANLLGERGKGLAIALSNLEGGRIG 246 V TPGF + K+G++A DT + D R+P+ NLLG+ G G A + L R+ Sbjct: 187 VEAGTPGFEKGKRLEKVGMKAQDTSELFFQDVRVPKDNLLGQAGMGFAYLMQELPQERLT 246 Query: 247 IGAQALGIARAAFEAALLYARERVQFGKPIAEHQSIANMLADMQTQLNAARLLILHAARL 306 + L A AA + L Y RER FGK IA+ Q+ LA+M T++ R+ + L Sbjct: 247 VAIGGLASAEAALQWTLDYTRERKAFGKTIADFQNTRFKLAEMATEIQIGRVFVDRCLEL 306 Query: 307 KSAGLPCLSEASQAKLFASEMAEKVCSQAVQIHGGYGYLEDYPVERYYRDARITQIYEGS 366 G + A+ AK + +++ KV + VQ+HGGYG++ +YP+ R + DAR+ +IY G+ Sbjct: 307 HLQGKLDVPTAAMAKYWGTDLQCKVLDECVQLHGGYGFMWEYPIARAWADARVQRIYAGT 366 Query: 367 SEIQRLLIAREL 378 +EI + +IAR L Sbjct: 367 NEIMKEIIARSL 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: 15 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 Apr 09 2024. 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