Align Isovaleryl-CoA dehydrogenase, mitochondrial; IVD; Isovaleryl-CoA dehydrogenase 2; St-IVD2; EC 1.3.8.4 (characterized)
to candidate 3607424 Dshi_0838 acyl-CoA dehydrogenase domain protein (RefSeq)
Query= SwissProt::Q9FS87 (412 letters) >FitnessBrowser__Dino:3607424 Length = 382 Score = 252 bits (643), Expect = 2e-71 Identities = 144/383 (37%), Positives = 223/383 (58%), Gaps = 5/383 (1%) Query: 29 STSLLFDDTQKQFKESVAQFAQENIAPHAEKIDRTNYFPQDVNLWKLMGNFNLLGITVPE 88 S++ D + E F APH E+ + D +W+ G LL +VPE Sbjct: 2 SSTTWMTDEHRMLAEMTRNFITTEWAPHFERW--RDQGEMDREIWQQAGELGLLCPSVPE 59 Query: 89 EYGGLGLGYLYHCIAMEEISRASGSV-GLSYGAHTNLCINQLVRNGTHEQKQKYLPKLIS 147 YGG G + + + EI+RA+ S G +G H+ + + ++ G+ EQKQK+LPK++S Sbjct: 60 AYGGPGGDFGHEAAILIEIARANLSAWGAGHGIHSGIVAHYILAYGSEEQKQKWLPKMVS 119 Query: 148 GEHVGALAMSEPNAGSDVVSMKCKADRVEGGYVLNGNKMWCTNGPTAQTLVVYAKTDVTA 207 GE VGALAM+EP AGSD+ +K +A + GY L+G+K++ TNG A +VV AKTD +A Sbjct: 120 GEMVGALAMTEPGAGSDLQGIKTRAVKDGNGYRLSGSKIFITNGQHANLIVVAAKTDPSA 179 Query: 208 GSKGITAFIIE-KGMTGFSTAQKLDKLGMRGSDTCELVFENCFVPEENVL-GQVGRGVYV 265 G+KG++ ++E +G GFS + L K+GM SDT EL F+N +P EN+L G+VG+G Y Sbjct: 180 GAKGVSLVVLETEGAEGFSRGRNLHKVGMHASDTSELFFDNVAIPPENLLGGEVGKGFYQ 239 Query: 266 LMSGLDLERLVLASGPVGIMQACLDVVLPYVKQREQFGRPIGEFQFVQGKVADMYTSMQS 325 +M+ L ERL++A+G VG M+ ++ + Y K+R+ FG PI +FQ + K+A+ T Sbjct: 240 MMTQLPQERLIIAAGAVGAMEGAVERTVAYAKERQAFGGPILQFQNTRFKLAECQTKTTV 299 Query: 326 SRSYLYSVARECDSGTINTKDCAGVILSAAERATQVALQAIQCLGGNGYVNEYPTGRFLR 385 +R++L E G ++ + A + +V + +Q GG GY+ EY + Sbjct: 300 ARAFLNECMAEHLEGKLSVEKAAMAKYWITDTQGEVIDECVQLHGGYGYMAEYDIAQMWS 359 Query: 386 DAKLYEIGAGTSEIRRMIIGREL 408 DA++ I GT+EI + +IGR L Sbjct: 360 DARVQRIYGGTNEIMKELIGRAL 382 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: 385 Number of extensions: 21 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: 412 Length of database: 382 Length adjustment: 31 Effective length of query: 381 Effective length of database: 351 Effective search space: 133731 Effective search space used: 133731 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