Align Isovaleryl-CoA dehydrogenase, mitochondrial; IVD; Isovaleryl-CoA dehydrogenase 2; St-IVD2; EC 1.3.8.4 (characterized)
to candidate WP_036834462.1 N784_RS09610 acyl-CoA dehydrogenase
Query= SwissProt::Q9FS87 (412 letters) >NCBI__GCF_000775615.1:WP_036834462.1 Length = 379 Score = 322 bits (825), Expect = 1e-92 Identities = 163/380 (42%), Positives = 247/380 (65%), Gaps = 2/380 (0%) Query: 31 SLLFDDTQKQFKESVAQFAQENIAPHAEKIDRTNYFPQDVNLWKLMGNFNLLGITVPEEY 90 +L F + Q ++ V FA + +AP +++D+ +YFP + L K MG+ L+GI +PE+Y Sbjct: 2 NLQFTEEQHMMRKMVRDFANKEVAPIVQQMDQEDYFP--IELIKQMGDIGLMGIPIPEQY 59 Query: 91 GGLGLGYLYHCIAMEEISRASGSVGLSYGAHTNLCINQLVRNGTHEQKQKYLPKLISGEH 150 GG G+ + + IA+ E+S+ S SVG+ HT++ N ++ GT EQKQKY+PKL SGE Sbjct: 60 GGSGMDFPSYIIAIHELSKVSASVGVILSVHTSVGTNPILYFGTEEQKQKYIPKLASGEF 119 Query: 151 VGALAMSEPNAGSDVVSMKCKADRVEGGYVLNGNKMWCTNGPTAQTLVVYAKTDVTAGSK 210 +GA A++EP AGSD S+K KA R Y+LNG+K++ TNG A T +V+A+TD AG+K Sbjct: 120 LGAFALTEPGAGSDAGSLKMKAVREGEEYILNGSKVFITNGEKADTFIVFARTDSNAGNK 179 Query: 211 GITAFIIEKGMTGFSTAQKLDKLGMRGSDTCELVFENCFVPEENVLGQVGRGVYVLMSGL 270 G+TAFI+E+ +GF +K K+GM GS T L F+NC +P E LG+ G G + M+ L Sbjct: 180 GVTAFIVERNTSGFEIGKKEHKMGMNGSGTVTLNFDNCRIPAEQRLGEEGEGFKIAMANL 239 Query: 271 DLERLVLASGPVGIMQACLDVVLPYVKQREQFGRPIGEFQFVQGKVADMYTSMQSSRSYL 330 ++ R+ +A+ +GI +A L+ + Y K+REQFG+PI Q + K+ADM TS+++++ Sbjct: 240 NVGRIGIAAQSLGIAEAALEHAVGYAKEREQFGKPIARNQGISFKLADMATSVEAAKLLT 299 Query: 331 YSVARECDSGTINTKDCAGVILSAAERATQVALQAIQCLGGNGYVNEYPTGRFLRDAKLY 390 Y A G K+ + ++A++ A VA +AIQ GG GY +YP RF RDAK+ Sbjct: 300 YHAANLRHQGIDCGKEASMAKMTASQAAMNVATEAIQVYGGYGYTEDYPVERFFRDAKVC 359 Query: 391 EIGAGTSEIRRMIIGRELFK 410 EI GT+EI+R++IG+ + K Sbjct: 360 EIYEGTNEIQRVVIGKHVLK 379 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: 384 Number of extensions: 24 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: 412 Length of database: 379 Length adjustment: 31 Effective length of query: 381 Effective length of database: 348 Effective search space: 132588 Effective search space used: 132588 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 24 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