Align Isovaleryl-CoA dehydrogenase, mitochondrial; IVD; Isovaleryl-CoA dehydrogenase 2; St-IVD2; EC 1.3.8.4 (characterized)
to candidate Ga0059261_2164 Ga0059261_2164 Acyl-CoA dehydrogenases
Query= SwissProt::Q9FS87 (412 letters) >FitnessBrowser__Korea:Ga0059261_2164 Length = 394 Score = 216 bits (549), Expect = 1e-60 Identities = 125/381 (32%), Positives = 199/381 (52%), Gaps = 5/381 (1%) Query: 28 FSTSLLFDDTQKQFKESVAQFAQENIAPHAEKIDRTNYFPQDVNLWKLMGNFNLLGITVP 87 F+ D ++ +++ +AQE + P + F +++ MG LLG T+P Sbjct: 13 FALDAQLTDEERMVRDAARAYAQERLLPRVTRAFLDENFDREI--MSEMGQLGLLGPTIP 70 Query: 88 EEYGGLGLGYLYHCIAMEEISRASGSVGLSYGAHTNLCINQLVRNGTHEQKQKYLPKLIS 147 E YGG GLGY+ + + E+ + ++L ++ + GT EQK+KYLPKL+S Sbjct: 71 ETYGGAGLGYVAYGLVAREVEAVDSGYRSAMSVQSSLVMHPINAYGTEEQKRKYLPKLLS 130 Query: 148 GEHVGALAMSEPNAGSDVVSMKCKADRVEGGYVLNGNKMWCTNGPTAQTLVVYAKTDVTA 207 GE VG ++EP+AGSD SM+ +A++++GGY + G+KMW TN P A VV+AK+D Sbjct: 131 GEWVGCFGLTEPDAGSDPGSMRTRAEKIDGGYRITGSKMWITNSPIADVFVVWAKSDAHG 190 Query: 208 GSKGITAFIIEKGMTGFSTAQKLDKLGMRGSDTCELVFENCFVPEENVLGQVGRGVYVLM 267 G GI F++EKGM G S + KL +R S T E+V + V E+ +L +V +G+ Sbjct: 191 G--GIKGFVLEKGMKGLSAPKIEGKLSLRASITGEIVMDGVEVSEDALLPEV-QGLKGPF 247 Query: 268 SGLDLERLVLASGPVGIMQACLDVVLPYVKQREQFGRPIGEFQFVQGKVADMYTSMQSSR 327 L+ R +A G +G +AC Y R+QFGRP+ Q VQ K+A+M T + Sbjct: 248 GCLNRARYGIAWGSMGAAEACFHAARQYTLDRQQFGRPLAATQLVQLKLANMETEIALGL 307 Query: 328 SYLYSVARECDSGTINTKDCAGVILSAAERATQVALQAIQCLGGNGYVNEYPTGRFLRDA 387 R D G + + + + + +A ++A A GGNG E+ R + Sbjct: 308 QAALRAGRMFDQGELAPEAISIIKRNNCGKALEIARVARDMHGGNGISAEFHVMRHAINL 367 Query: 388 KLYEIGAGTSEIRRMIIGREL 408 + GT ++ +I+GR + Sbjct: 368 ETVNTYEGTHDVHGLILGRAI 388 Lambda K H 0.319 0.135 0.396 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: 357 Number of extensions: 14 Number of successful extensions: 3 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: 412 Length of database: 394 Length adjustment: 31 Effective length of query: 381 Effective length of database: 363 Effective search space: 138303 Effective search space used: 138303 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