Align isobutyryl-CoA dehydrogenase (EC 1.3.8.5) (characterized)
to candidate 3607424 Dshi_0838 acyl-CoA dehydrogenase domain protein (RefSeq)
Query= reanno::pseudo3_N2E3:AO353_25670 (383 letters) >FitnessBrowser__Dino:3607424 Length = 382 Score = 248 bits (633), Expect = 2e-70 Identities = 140/376 (37%), Positives = 215/376 (57%), Gaps = 3/376 (0%) Query: 6 LTEEQVMIRDMARDFARGEIAPHAQAWEKAGWIDDALVAKMGELGLLGMVVPEEWGGTYV 65 +T+E M+ +M R+F E APH + W G +D + + GELGLL VPE +GG Sbjct: 7 MTDEHRMLAEMTRNFITTEWAPHFERWRDQGEMDREIWQQAGELGLLCPSVPEAYGGPGG 66 Query: 66 DYVAYALAVEEISAGD-GATGALMSIHNSVGCGPVLNYGTEEQKQTWLADLASGQAIGCF 124 D+ A + EI+ + A GA IH+ + +L YG+EEQKQ WL + SG+ +G Sbjct: 67 DFGHEAAILIEIARANLSAWGAGHGIHSGIVAHYILAYGSEEQKQKWLPKMVSGEMVGAL 126 Query: 125 CLTEPQAGSEAHNLRTRAELRDGQWVINGAKQFVSNGRRAKLAIVFAVTDPDLGKKGLSA 184 +TEP AGS+ ++TRA + ++G+K F++NG+ A L +V A TDP G KG+S Sbjct: 127 AMTEPGAGSDLQGIKTRAVKDGNGYRLSGSKIFITNGQHANLIVVAAKTDPSAGAKGVSL 186 Query: 185 FLVPTD-TPGFIVDRSEHKMGIRASDTCAVTLNNCTIPEANLLG-ERGKGLAIALSNLEG 242 ++ T+ GF R+ HK+G+ ASDT + +N IP NLLG E GKG ++ L Sbjct: 187 VVLETEGAEGFSRGRNLHKVGMHASDTSELFFDNVAIPPENLLGGEVGKGFYQMMTQLPQ 246 Query: 243 GRIGIAAQALGIARAAFEAALAYARDRVQFDKPIIEHQSVANMLADMHTRLNAARLLILH 302 R+ IAA A+G A E +AYA++R F PI++ Q+ LA+ T+ AR + Sbjct: 247 ERLIIAAGAVGAMEGAVERTVAYAKERQAFGGPILQFQNTRFKLAECQTKTTVARAFLNE 306 Query: 303 AARLRSAGKPCLSEASQAKLFASEMAEKVCSSAIQIHGGYGYLEDYPVERYYRDARITQI 362 GK + +A+ AK + ++ +V +Q+HGGYGY+ +Y + + + DAR+ +I Sbjct: 307 CMAEHLEGKLSVEKAAMAKYWITDTQGEVIDECVQLHGGYGYMAEYDIAQMWSDARVQRI 366 Query: 363 YEGSSEIQRMVIAREL 378 Y G++EI + +I R L Sbjct: 367 YGGTNEIMKELIGRAL 382 Lambda K H 0.319 0.134 0.394 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: 363 Number of extensions: 20 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: 383 Length of database: 382 Length adjustment: 30 Effective length of query: 353 Effective length of database: 352 Effective search space: 124256 Effective search space used: 124256 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