Align 2-methylbutanoyl-CoA dehydrogenase / butanoyl-CoA dehydrogenase / isobutyryl-CoA dehydrogenase (EC 1.3.8.1; EC 1.3.8.5) (characterized)
to candidate Ga0059261_3681 Ga0059261_3681 Acyl-CoA dehydrogenases
Query= reanno::pseudo3_N2E3:AO353_25680 (375 letters) >FitnessBrowser__Korea:Ga0059261_3681 Length = 380 Score = 291 bits (746), Expect = 2e-83 Identities = 156/372 (41%), Positives = 228/372 (61%), Gaps = 3/372 (0%) Query: 5 DEQLQISDAARQFAQERLKPFAAEWDREHRFPKEAIGEMAELGFFGMLVPEQWGGCDTGY 64 ++Q I + AR+F + + P AAEWD +H FP+E + AELGF + V E+ GG G Sbjct: 8 EDQRAIQEMARKFTADAITPHAAEWDEKHIFPRETVKAAAELGFGAIYVSEESGGIGLGR 67 Query: 65 LAYAMALEEIAAGDGACSTIMSVHNSVGCVPILKFGNDDQKERFLKPLASGAMLGAFALT 124 L A+ +E +A G A S +S+HN + I +FG+ K+++L L + L ++ LT Sbjct: 68 LESALIMEAMAYGCPATSAFISIHNMASWM-IDRFGSQAVKDKYLPRLVTADWLASYCLT 126 Query: 125 EPQAGSDASSLKTRARLNGDHYVLNGCKQFITSGQNAGVVIVFAVTDPSAGKRGISAFIV 184 EP +GSDA++LKT A+ +GDH+++NG KQFI SG + V V + G +GIS + Sbjct: 127 EPSSGSDAAALKTTAKRDGDHFIVNGSKQFI-SGAGENELYVTMVRTGADGPKGISCLAI 185 Query: 185 PTDSPGYKVARVEDKLGQHASDTCQILFEDVQVPVANRLGEEGEGYKIALANLEGGRVGI 244 D PG E KLG HA T Q+ F++V+VPV N +G EGEG++IA+ L+GGR+ I Sbjct: 186 EKDMPGVSFGANERKLGWHAQPTRQVTFDNVRVPVENLVGGEGEGFRIAMMGLDGGRLNI 245 Query: 245 ASQSVGMARAAFEAARDYARERESFGKPIIEHQAVAFRLADMATQIAVARQMVHYAAALR 304 + S+G A+ + A Y ++R+ FG I + Q F LADMAT++ AR +++ AAA Sbjct: 246 GACSLGGAQRCLDEAVQYTKDRKQFGSAIADFQNTQFMLADMATELEAARALLYLAAAKV 305 Query: 305 DSGKPALVE-ASMAKLFASEMAEKVCSTALQTLGGYGYLSDFPLERIYRDVRVCQIYEGT 363 S P + A+MAK FA++ V ALQ GGYGYL D+P+ER +RD+RV I EGT Sbjct: 306 TSNAPDKTKFAAMAKRFATDTGSSVVDRALQLHGGYGYLMDYPIERFWRDLRVHSILEGT 365 Query: 364 SDIQRMVISRNL 375 + + RM++ R L Sbjct: 366 NQVMRMIVGREL 377 Lambda K H 0.319 0.134 0.389 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: 323 Number of extensions: 13 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: 375 Length of database: 380 Length adjustment: 30 Effective length of query: 345 Effective length of database: 350 Effective search space: 120750 Effective search space used: 120750 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