Align isobutyryl-CoA dehydrogenase (EC 1.3.8.5) (characterized)
to candidate Pf6N2E2_5333 Butyryl-CoA dehydrogenase (EC 1.3.99.2)
Query= reanno::WCS417:GFF2713 (383 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5333 Length = 378 Score = 255 bits (652), Expect = 1e-72 Identities = 140/373 (37%), Positives = 207/373 (55%), Gaps = 1/373 (0%) Query: 6 YTEEQVMIRDMARDFARGEIAPYAQAWEKAGWIDDALVAKMGELGLLGMVVPEEWGGTYV 65 ++ E + RD R F E PY WEK G +D L K GE G+L +PE +GG Sbjct: 7 FSPEHELFRDSVRTFLEKEAVPYHSQWEKQGHVDRQLWNKAGEAGMLCSHLPEAYGGLDA 66 Query: 66 DYVAYALAVEEISAGDGATGALMSIHNSVGCGPILNYGTESQKQTWLADLASGQAIGCFC 125 D++ + +EEI G TG S+H+ + IL+YG+E+ K +L L SG+ + Sbjct: 67 DFLYSTVVIEEIGRL-GLTGIGFSLHSDIVAPYILHYGSEALKHKYLPKLVSGEMVTAIA 125 Query: 126 LTEPQAGSEAHNLRTRAELRDGHWVITGAKQFVSNGKRAKLAIVFAITDPELGKKGISAF 185 +TEP AGS+ ++T A L +VI G+K F++NG A L IV A TDP+ G KG S F Sbjct: 126 MTEPGAGSDLQGVKTTAVLDGDEYVINGSKTFITNGFLADLVIVVAKTDPKAGAKGTSLF 185 Query: 186 LVPTATPGFVVDRTEHKMGIRASDTCAVTLNQCTVPEANLLGERGKGLAIALSNLEGGRI 245 LV T GF + K+G++A DT + VP+ NLLG+ G G A + L R+ Sbjct: 186 LVEAGTLGFEKGKRLEKVGMKAQDTSELFFQDVRVPKENLLGQAGMGFAYLMQELPQERL 245 Query: 246 GIAAQALGIARAAFEAALAYARDRVQFDKAIIEHQSVANLLADMQTQLNAARLLILHAAR 305 +A L A AA + L Y R+R F K+I + Q+ LA+M T++ R+ + Sbjct: 246 TVAIGGLASAEAALQWTLDYTRERKAFGKSIADFQNTRFKLAEMATEIQIGRVFVDRCLE 305 Query: 306 LRSAGKPCLSEASQAKLFASEMAEKVCSSAMQIHGGYGYLEDYPVERYYRDARITQIYEG 365 L GK + A+ AK + +++ KV +Q+HGGYG++ +YP+ R + DAR+ +IY G Sbjct: 306 LHLQGKLDVPTAAMAKYWGTDLQCKVLDECVQLHGGYGFMWEYPIARAWADARVQRIYAG 365 Query: 366 TSEIQRMVIAREL 378 T+EI + +IAR L Sbjct: 366 TNEIMKEIIARSL 378 Lambda K H 0.319 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: 318 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 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 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