Align Isovaleryl-CoA dehydrogenase (EC 1.3.8.4) (characterized)
to candidate AZOBR_RS22365 AZOBR_RS22365 acyl-CoA dehydrogenase
Query= reanno::Smeli:SM_b21121 (387 letters) >FitnessBrowser__azobra:AZOBR_RS22365 Length = 379 Score = 270 bits (691), Expect = 4e-77 Identities = 153/378 (40%), Positives = 218/378 (57%), Gaps = 3/378 (0%) Query: 6 LNFALGEEIDALRASVRRFASERIAPLADDADRSNAFPMSLWREMGELGLLGITADEAHG 65 ++FAL EE A R + R FA + +AP A D ++ FP+ R+ LG GI E G Sbjct: 1 MDFALSEEQQAFRDTARDFAQQEMAPNAAHWDENSVFPVDTLRQAAALGFAGIYVGEEFG 60 Query: 66 GAGLGYLAHCVAMEEISRASASVGLSYGAHSNLCVNQINRNGKPAQKSRYLPKLISGEHV 125 G+GLG L + EE+S A S H N+ I+R G Q+ R+LPKL + EH Sbjct: 61 GSGLGRLDAALIFEELSAACPSTAAYISIH-NMASWMIDRFGNAEQRERFLPKLTTMEHF 119 Query: 126 GALAMSEPGAGSDVVSMKLKADKRGDRYVLNGSKMWITNGPDADVLVVYAKTDPAAGPRG 185 + ++EPGAGSD S++ +A++ GD YVLNGSK +I+ G +DV V +T GP+G Sbjct: 120 ASYCLTEPGAGSDAASLRTRAERVGDHYVLNGSKAFISGGGTSDVYVCMVRTGEP-GPKG 178 Query: 186 ITAFLVEKAFPGFSAGQKLDKLGMRGSNTSELIFTDCEVPEENVLGGVGEGVKVLMSGLD 245 I+ VEK PG S G++ KLG + TS +IF +C VP N +G GEG ++ M GLD Sbjct: 179 ISCIAVEKGTPGLSFGKQEHKLGWKSQPTSAVIFENCRVPVANRIGEEGEGFRIAMKGLD 238 Query: 246 YERVVLSAGPLGIMAACLDVVVPYLHERKQFGQPIGEFQLMQGKLADMYVTMNAARAYVY 305 R+ ++A +G CL+ V Y ERKQFG+P+ FQ +Q KLADM ++AAR ++ Sbjct: 239 GGRLNIAACSVGGARFCLEQAVAYTTERKQFGKPLNAFQALQFKLADMATELDAARLMLH 298 Query: 306 AVAAACDRGE-TARKDAAGCILYAAEKATAMALEAIQALGGNGYTNDYPAGRLLRDAKLY 364 AA+ D G A A +A + + EA+Q GG GY +YP R+ RD +++ Sbjct: 299 RAAASLDAGSPEATAHCAMAKRFATDAGFQVVNEALQLHGGYGYIKEYPIERIFRDLRVH 358 Query: 365 EIGAGTSEIRRMLIGREL 382 +I GT+EI R++I R L Sbjct: 359 QILEGTNEIMRVIIARHL 376 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: 309 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: 379 Length adjustment: 30 Effective length of query: 357 Effective length of database: 349 Effective search space: 124593 Effective search space used: 124593 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