Align Isovaleryl-CoA dehydrogenase (EC 1.3.8.4) (characterized)
to candidate WP_086509502.1 BZY95_RS08430 acyl-CoA dehydrogenase family protein
Query= reanno::Smeli:SM_b21121 (387 letters) >NCBI__GCF_002151265.1:WP_086509502.1 Length = 385 Score = 279 bits (714), Expect = 8e-80 Identities = 150/368 (40%), Positives = 221/368 (60%), Gaps = 1/368 (0%) Query: 20 SVRRFASERIAPLADDADRSNAFPMSLWREMGELGLLGITADEAHGGAGLGYLAHCVAME 79 ++RRF + +AP + + + P SLW+++GE GLLGI EA GG+G + +A+E Sbjct: 15 TIRRFLEQEVAPHYEAWEEAGEMPRSLWQQLGEAGLLGIDLPEALGGSGADFAIVQLALE 74 Query: 80 EISRAS-ASVGLSYGAHSNLCVNQINRNGKPAQKSRYLPKLISGEHVGALAMSEPGAGSD 138 EISR + +Y H+N+ + + G PAQ+ R+LP + SGE +GA+AM+EPGAGSD Sbjct: 75 EISRQGFGGLASAYNIHANIVMPYLLHIGTPAQRERWLPAMASGETIGAIAMTEPGAGSD 134 Query: 139 VVSMKLKADKRGDRYVLNGSKMWITNGPDADVLVVYAKTDPAAGPRGITAFLVEKAFPGF 198 + +MK +A + + L+GSK++ITNG AD+++V AKTDPAAG RG++ FLV+ GF Sbjct: 135 LAAMKTRASRTESGWRLDGSKLFITNGQIADLVIVCAKTDPAAGARGVSLFLVDTTLAGF 194 Query: 199 SAGQKLDKLGMRGSNTSELIFTDCEVPEENVLGGVGEGVKVLMSGLDYERVVLSAGPLGI 258 S GQ + K+G S+T+EL F D +PEE +LG G G LM L ER+ ++A LG Sbjct: 195 SRGQPIKKIGQHASDTAELFFDDLRLPEEALLGEAGAGFAYLMQELPRERLGVAAQALGA 254 Query: 259 MAACLDVVVPYLHERKQFGQPIGEFQLMQGKLADMYVTMNAARAYVYAVAAACDRGETAR 318 M L + + Y+ ER+ FG+ +GEFQ + LA++ ++ RAY A +GE Sbjct: 255 MEGALALTLDYVRERRAFGRAVGEFQNTRFTLAEVRAQIDMGRAYFEQCVAKYRQGEMNG 314 Query: 319 KDAAGCILYAAEKATAMALEAIQALGGNGYTNDYPAGRLLRDAKLYEIGAGTSEIRRMLI 378 DAA L +E +Q GG GYT +YP R DA++ + AGTSEI + +I Sbjct: 315 TDAAILKLQLSEMQCRTIDACLQLFGGYGYTREYPISRFYLDARVQTLYAGTSEIMKEVI 374 Query: 379 GRELFAET 386 R L ++ Sbjct: 375 ARSLLGKS 382 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: 317 Number of extensions: 12 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: 387 Length of database: 385 Length adjustment: 30 Effective length of query: 357 Effective length of database: 355 Effective search space: 126735 Effective search space used: 126735 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 Apr 09 2024. 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