Align Isovaleryl-CoA dehydrogenase, mitochondrial; IVD; Isovaleryl-CoA dehydrogenase 2; St-IVD2; EC 1.3.8.4 (characterized)
to candidate WP_110205192.1 DNK54_RS01550 acyl-CoA dehydrogenase
Query= SwissProt::Q9FS87 (412 letters) >NCBI__GCF_003194585.1:WP_110205192.1 Length = 383 Score = 264 bits (675), Expect = 3e-75 Identities = 138/377 (36%), Positives = 220/377 (58%), Gaps = 3/377 (0%) Query: 33 LFDDTQKQFKESVAQFAQENIAPHAEKIDRTNYFPQDVNLWKLMGNFNLLGITVPEEYGG 92 L+ D + F+ +VA F + + P+ E+ + +DV W G LLG+ PEEYGG Sbjct: 5 LYTDDHEAFRGTVAAFVEREVVPNLERWEEERIIDRDV--WLAAGKQGLLGLAAPEEYGG 62 Query: 93 LGLGYLYHCIAMEEISRASG-SVGLSYGAHTNLCINQLVRNGTHEQKQKYLPKLISGEHV 151 G Y + + +EE ++ S+ S+ ++ I + GT EQKQ++LP++I+GE + Sbjct: 63 AGGDYRFRNVILEEFAKVHATSLASSFSLQDDIAIPYIAEIGTEEQKQRWLPRMIAGELI 122 Query: 152 GALAMSEPNAGSDVVSMKCKADRVEGGYVLNGNKMWCTNGPTAQTLVVYAKTDVTAGSKG 211 GA+AM+EP GSD+ +K A +V GG+V+NG K + TNG A ++ A+TD G +G Sbjct: 123 GAIAMTEPGTGSDLQGIKTSARQVPGGWVINGAKTFITNGINADLVITVARTDPAGGPRG 182 Query: 212 ITAFIIEKGMTGFSTAQKLDKLGMRGSDTCELVFENCFVPEENVLGQVGRGVYVLMSGLD 271 T F++E+ M GFS +KL K+G+ DT ELV+E+ FVP+ VLG++G G L + L Sbjct: 183 FTLFVVEREMEGFSRGRKLKKVGLHAQDTAELVYEDVFVPDAGVLGEIGGGFGQLKNMLP 242 Query: 272 LERLVLASGPVGIMQACLDVVLPYVKQREQFGRPIGEFQFVQGKVADMYTSMQSSRSYLY 331 LERL +A+ V + +A L + Y K R+ FG+ I +FQ Q ++A+M T + +R Y+ Sbjct: 243 LERLSIAAHAVAVAEAVLADTITYTKDRKAFGQRIADFQNTQFELAEMQTIVHVARVYVD 302 Query: 332 SVARECDSGTINTKDCAGVILSAAERATQVALQAIQCLGGNGYVNEYPTGRFLRDAKLYE 391 + G + D A A++ V + +Q GG G++ EYP GR +DA++ Sbjct: 303 QAILAFNLGELTDVDAAQAKWWASDLQNDVIDRCLQLHGGYGFMLEYPVGRAYQDARIQR 362 Query: 392 IGAGTSEIRRMIIGREL 408 I G +E+ ++IIGR++ Sbjct: 363 IFGGANEVMKLIIGRKI 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: 355 Number of extensions: 11 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: 383 Length adjustment: 31 Effective length of query: 381 Effective length of database: 352 Effective search space: 134112 Effective search space used: 134112 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