Align Isovaleryl-CoA dehydrogenase, mitochondrial; IVD; Isovaleryl-CoA dehydrogenase 2; St-IVD2; EC 1.3.8.4 (characterized)
to candidate WP_041929725.1 MPE_RS16000 acyl-CoA dehydrogenase
Query= SwissProt::Q9FS87 (412 letters) >NCBI__GCF_000015725.1:WP_041929725.1 Length = 391 Score = 208 bits (529), Expect = 3e-58 Identities = 121/373 (32%), Positives = 193/373 (51%), Gaps = 7/373 (1%) Query: 36 DTQKQFKESVAQFAQENIAPHAEKIDRTNYFPQDVNLWKLMGNFNLLGITVPEEYGGLGL 95 + ++ +++ + ++ +AP ++ + D +++ MG LLG T+PE YGG GL Sbjct: 19 EDERAVRDAAQAYCRDRLAPRV--LEAFRHEKTDPAIFREMGELGLLGATLPEAYGGAGL 76 Query: 96 GYLYHCIAMEEISRASGSVGLSYGAHTNLCINQLVRNGTHEQKQKYLPKLISGEHVGALA 155 ++ + + E+ R ++L + + GT QKQKYLPKL GE +G Sbjct: 77 NHVCYGLVAREVERVDSGYRSMMSVQSSLVMVPIHAFGTEAQKQKYLPKLARGEWIGCFG 136 Query: 156 MSEPNAGSDVVSMKCKADRVEGGYVLNGNKMWCTNGPTAQTLVVYAKTDVTAGSKGITAF 215 ++EPN GSD S+ +A V+GGYVL+G KMW TN P A VV+AK D I F Sbjct: 137 LTEPNHGSDPGSLATRARAVQGGYVLSGAKMWITNSPIADVFVVWAKDD----GGQIRGF 192 Query: 216 IIEKGMTGFSTAQKLDKLGMRGSDTCELVFENCFVPEENVLGQVGRGVYVLMSGLDLERL 275 I++KGM G K+G+R S T E+V + F PEEN +V RG+ + L+ R Sbjct: 193 ILDKGMKGLEAPAVHGKVGLRASLTGEIVMDEVFCPEENAFPEV-RGLKGPFTCLNSARY 251 Query: 276 VLASGPVGIMQACLDVVLPYVKQREQFGRPIGEFQFVQGKVADMYTSMQSSRSYLYSVAR 335 +A G +G + C YV R QFGRP+ Q +Q K+ADM T + + R Sbjct: 252 GIAWGALGAAEDCFHRARQYVLDRPQFGRPLAANQLIQKKLADMQTEITLGLQGCLRLGR 311 Query: 336 ECDSGTINTKDCAGVILSAAERATQVALQAIQCLGGNGYVNEYPTGRFLRDAKLYEIGAG 395 D GT + + + ++ ++ ++A A +GGNG +E+ R L + ++ G Sbjct: 312 MKDEGTAAVEITSIMKRNSCGKSLEIARMARDMMGGNGISDEFGVARHLVNLEVVNTYEG 371 Query: 396 TSEIRRMIIGREL 408 T ++ +I+GR + Sbjct: 372 THDVHALILGRAI 384 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: 346 Number of extensions: 22 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: 391 Length adjustment: 31 Effective length of query: 381 Effective length of database: 360 Effective search space: 137160 Effective search space used: 137160 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