Align Isovaleryl-CoA dehydrogenase (EC 1.3.8.4) (characterized)
to candidate 3608348 Dshi_1750 acyl-CoA dehydrogenase domain protein (RefSeq)
Query= reanno::Smeli:SM_b21121 (387 letters) >FitnessBrowser__Dino:3608348 Length = 381 Score = 239 bits (609), Expect = 1e-67 Identities = 139/380 (36%), Positives = 210/380 (55%), Gaps = 3/380 (0%) Query: 6 LNFALGEEIDALRASVRRFASERIAPLADDADRSNAFPMSLWREMGELGLLGITADEAHG 65 ++FAL EE A+ R F +E IAP A ++ P +LW E+ LG G+ E G Sbjct: 1 MDFALSEEQSAIFDMARDFGAENIAPHALAWEKDGTIPKTLWPELAALGFGGLYVTEESG 60 Query: 66 GAGLGYLAHCVAMEEISRASASVGLSYGAHSNLCVNQINRNGKPAQKSRYLPKLISGEHV 125 G+GL L + E +S A SV H N+C +++ G K+R+LP ++ E V Sbjct: 61 GSGLSRLDATLVFEALSMACPSVAAFLSIH-NMCAAMLDKFGSDDVKARFLPPALTMETV 119 Query: 126 GALAMSEPGAGSDVVSMKLKADKRGDRYVLNGSKMWITNGPDADVLVVYAKTDPAAGPRG 185 + ++EPG+GSD ++K +A++ + Y L G+K +I+ G +D +V A+T GPRG Sbjct: 120 FSYCLTEPGSGSDAAALKTRAERTNEGYRLTGTKAFISGGGYSDAYIVMARTGED-GPRG 178 Query: 186 ITAFLVEKAFPGFSAGQKLDKLGMRGSNTSELIFTDCEVPEENVLGGVGEGVKVLMSGLD 245 I++ +VE PG S G DK+G R T ++ DC VP N+LG G G + M GLD Sbjct: 179 ISSLIVEDGAPGLSFGGLEDKMGWRAQPTRQVQLDDCAVPAANLLGEEGAGFRYAMMGLD 238 Query: 246 YERVVLSAGPLGIMAACLDVVVPYLHERKQFGQPIGEFQLMQGKLADMYVTMNAARAYVY 305 R+ ++A LG A LD V Y+ ER+ FG+PI +FQ +Q +LAD + + AAR ++ Sbjct: 239 GGRLNIAACSLGAAQAALDATVAYMGERRAFGKPIDQFQALQFRLADAEIELQAARVFLR 298 Query: 306 AVAAACDRG-ETARKDAAGCILYAAEKATAMALEAIQALGGNGYTNDYPAGRLLRDAKLY 364 A D+G A A + E + +A + +Q GG GY DY +L+RD +++ Sbjct: 299 QAAWKLDQGAPDATTHCAMAKKFVTEAGSRVADQCLQLHGGYGYLADYGIEKLVRDLRVH 358 Query: 365 EIGAGTSEIRRMLIGRELFA 384 +I GT+EI R+L R L A Sbjct: 359 QILEGTNEIMRLLTARALLA 378 Lambda K H 0.318 0.135 0.391 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: 284 Number of extensions: 9 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: 387 Length of database: 381 Length adjustment: 30 Effective length of query: 357 Effective length of database: 351 Effective search space: 125307 Effective search space used: 125307 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 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