Align Isovaleryl-CoA dehydrogenase (EC 1.3.8.4) (characterized)
to candidate WP_010628345.1 BZY95_RS09135 acyl-CoA dehydrogenase
Query= reanno::Smeli:SM_b21121 (387 letters) >NCBI__GCF_002151265.1:WP_010628345.1 Length = 389 Score = 216 bits (549), Expect = 1e-60 Identities = 131/382 (34%), Positives = 206/382 (53%), Gaps = 3/382 (0%) Query: 6 LNFALGEEIDALRASVRRFASERIAPLADDADRSNAFPMSLWREMGELGLLGITADEAHG 65 + F+L ++ AL + F+ +A A + D ++ FP+ + R GE G LGI E G Sbjct: 1 MEFSLTDDQRALVQAAADFSQAELADHAAEWDATSHFPVDVIRRAGEAGFLGIYIPEERG 60 Query: 66 GAGLGYLAHCVAMEEISRASASVGLSYGAHSNLCVNQINRNGKPAQKSRYLPKLISGEHV 125 G GL L + E++S+ + H N+ + G + ++ +LISGE + Sbjct: 61 GLGLSRLDASLIFEQLSQGCIATTAYLTIH-NMVAWMVASWGSDELRETWVERLISGECL 119 Query: 126 GALAMSEPGAGSDVVSMKLKADKRGDRYVLNGSKMWITNGPDADVLVVYAKTD-PAAGPR 184 G ++EPG+GSD S++ KA + GD YV++GSKM+I+ D+LVV A+T P +G Sbjct: 120 GCYCLTEPGSGSDAASLRTKAVREGDEYVISGSKMFISGAGANDMLVVMARTGAPDSGAG 179 Query: 185 GITAFLVEKAFPGFSAGQKLDKLGMRGSNTSELIFTDCEVPEENVLGGVGEGVKVLMSGL 244 G++A LV G G+ +K+G + T + F VP N+LG G+G K+ M GL Sbjct: 180 GVSAILVPADAAGIEYGKNEEKMGWKSQPTRLISFDGVRVPVGNLLGEEGQGFKLAMKGL 239 Query: 245 DYERVVLSAGPLGIMAACLDVVVPYLHERKQFGQPIGEFQLMQGKLADMYVTMNAARAYV 304 D R+ +++ LG L + YL ERKQFG+ + FQ +Q KLADM + AAR V Sbjct: 240 DGGRLNIASCSLGAAQHALTLARNYLQERKQFGRELAHFQALQFKLADMATELTAARLMV 299 Query: 305 YAVAAACDRGE-TARKDAAGCILYAAEKATAMALEAIQALGGNGYTNDYPAGRLLRDAKL 363 A D+G+ A A +A + + EA+Q GG GY ++P R++RD ++ Sbjct: 300 RHAAWRLDQGDPEATAYCAMAKRFATDMGFNVCNEALQLHGGYGYLREFPLERMVRDTRV 359 Query: 364 YEIGAGTSEIRRMLIGRELFAE 385 ++I GT+EI R+++ R L + Sbjct: 360 HQILEGTNEIMRVIVARRLLTD 381 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: 296 Number of extensions: 14 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: 389 Length adjustment: 30 Effective length of query: 357 Effective length of database: 359 Effective search space: 128163 Effective search space used: 128163 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 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