Align short-chain acyl-CoA dehydrogenase monomer (EC 1.3.8.1) (characterized)
to candidate Ga0059261_2164 Ga0059261_2164 Acyl-CoA dehydrogenases
Query= metacyc::MONOMER-17424 (375 letters) >FitnessBrowser__Korea:Ga0059261_2164 Length = 394 Score = 228 bits (580), Expect = 3e-64 Identities = 137/371 (36%), Positives = 198/371 (53%), Gaps = 3/371 (0%) Query: 3 VNDEQQQIADAVRAFAQERLKPFAEQWDKDHRFPKEAIDEMAELGLFGMLVPEQWGGSDT 62 + DE++ + DA RA+AQERL P + D F +E + EM +LGL G +PE +GG+ Sbjct: 19 LTDEERMVRDAARAYAQERLLPRVTRAFLDENFDREIMSEMGQLGLLGPTIPETYGGAGL 78 Query: 63 GYVAYAMALEEIAAGDGACSTIMSVHNSVGCVPILRFGNEQQKEQFLTPLATGAMLGAFA 122 GYVAY + E+ A D + MSV +S+ PI +G E+QK ++L L +G +G F Sbjct: 79 GYVAYGLVAREVEAVDSGYRSAMSVQSSLVMHPINAYGTEEQKRKYLPKLLSGEWVGCFG 138 Query: 123 LTEPQAGSDASSLKTRARLEGDHYVLNGSKQFITSGQNAGVVIVFAVTDPEAGKRGISAF 182 LTEP AGSD S++TRA Y + GSK +IT+ A V +V+A +D G GI F Sbjct: 139 LTEPDAGSDPGSMRTRAEKIDGGYRITGSKMWITNSPIADVFVVWAKSDAHGG--GIKGF 196 Query: 183 IVPTDSPGYQVARVEDKLGQHASDTCQIVFDNVQVPVANRLGAEGEGYKIALANLEGGRI 242 ++ G ++E KL AS T +IV D V+V + L E +G K L R Sbjct: 197 VLEKGMKGLSAPKIEGKLSLRASITGEIVMDGVEVS-EDALLPEVQGLKGPFGCLNRARY 255 Query: 243 GIASQAVGMARAAFEVARDYANERQSFGKPLIEHQAVAFRLADMATKISVARQMVLHAAA 302 GIA ++G A A F AR Y +RQ FG+PL Q V +LA+M T+I++ Q L A Sbjct: 256 GIAWGSMGAAEACFHAARQYTLDRQQFGRPLAATQLVQLKLANMETEIALGLQAALRAGR 315 Query: 303 LRDAGRPALVEASMAKLFASEMAEKVCSDALQTLGGYGYLSDFPLERIYRDVRVCQIYEG 362 + D G A S+ K A ++ A GG G ++F + R ++ YEG Sbjct: 316 MFDQGELAPEAISIIKRNNCGKALEIARVARDMHGGNGISAEFHVMRHAINLETVNTYEG 375 Query: 363 TSDIQRMVIAR 373 T D+ +++ R Sbjct: 376 THDVHGLILGR 386 Lambda K H 0.319 0.134 0.382 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: 348 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: 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