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_2164 Ga0059261_2164 Acyl-CoA dehydrogenases
Query= reanno::pseudo3_N2E3:AO353_25680 (375 letters) >FitnessBrowser__Korea:Ga0059261_2164 Length = 394 Score = 219 bits (558), Expect = 1e-61 Identities = 132/370 (35%), Positives = 194/370 (52%), Gaps = 3/370 (0%) Query: 4 TDEQLQISDAARQFAQERLKPFAAEWDREHRFPKEAIGEMAELGFFGMLVPEQWGGCDTG 63 TDE+ + DAAR +AQERL P + F +E + EM +LG G +PE +GG G Sbjct: 20 TDEERMVRDAARAYAQERLLPRVTRAFLDENFDREIMSEMGQLGLLGPTIPETYGGAGLG 79 Query: 64 YLAYAMALEEIAAGDGACSTIMSVHNSVGCVPILKFGNDDQKERFLKPLASGAMLGAFAL 123 Y+AY + E+ A D + MSV +S+ PI +G ++QK ++L L SG +G F L Sbjct: 80 YVAYGLVAREVEAVDSGYRSAMSVQSSLVMHPINAYGTEEQKRKYLPKLLSGEWVGCFGL 139 Query: 124 TEPQAGSDASSLKTRARLNGDHYVLNGCKQFITSGQNAGVVIVFAVTDPSAGKRGISAFI 183 TEP AGSD S++TRA Y + G K +IT+ A V +V+A +D G GI F+ Sbjct: 140 TEPDAGSDPGSMRTRAEKIDGGYRITGSKMWITNSPIADVFVVWAKSDAHGG--GIKGFV 197 Query: 184 VPTDSPGYKVARVEDKLGQHASDTCQILFEDVQVPVANRLGEEGEGYKIALANLEGGRVG 243 + G ++E KL AS T +I+ + V+V + L E +G K L R G Sbjct: 198 LEKGMKGLSAPKIEGKLSLRASITGEIVMDGVEVS-EDALLPEVQGLKGPFGCLNRARYG 256 Query: 244 IASQSVGMARAAFEAARDYARERESFGKPIIEHQAVAFRLADMATQIAVARQMVHYAAAL 303 IA S+G A A F AAR Y +R+ FG+P+ Q V +LA+M T+IA+ Q A + Sbjct: 257 IAWGSMGAAEACFHAARQYTLDRQQFGRPLAATQLVQLKLANMETEIALGLQAALRAGRM 316 Query: 304 RDSGKPALVEASMAKLFASEMAEKVCSTALQTLGGYGYLSDFPLERIYRDVRVCQIYEGT 363 D G+ A S+ K A ++ A GG G ++F + R ++ YEGT Sbjct: 317 FDQGELAPEAISIIKRNNCGKALEIARVARDMHGGNGISAEFHVMRHAINLETVNTYEGT 376 Query: 364 SDIQRMVISR 373 D+ +++ R Sbjct: 377 HDVHGLILGR 386 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: 342 Number of extensions: 12 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: 375 Length of database: 394 Length adjustment: 30 Effective length of query: 345 Effective length of database: 364 Effective search space: 125580 Effective search space used: 125580 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