Align isovaleryl-CoA dehydrogenase subunit (EC 1.3.8.4) (characterized)
to candidate Dsui_0975 Dsui_0975 acyl-CoA dehydrogenase
Query= metacyc::MONOMER-16063 (387 letters) >FitnessBrowser__PS:Dsui_0975 Length = 390 Score = 577 bits (1486), Expect = e-169 Identities = 287/389 (73%), Positives = 327/389 (84%), Gaps = 3/389 (0%) Query: 1 MTYPSLNFALGETIDMLRDQVRGFVAAELQPRAAQIDQDNQFPMDMWRKFGEMGLLGITV 60 M PSL+F GETI+MLRD VR F A E+ PRAAQID+DN+FP D+W+KFG++GLLG+T Sbjct: 1 MHIPSLDFGHGETIEMLRDTVRAFAAKEIAPRAAQIDRDNEFPADLWQKFGDLGLLGMTA 60 Query: 61 DEEYGGSALGYLAHAVVMEEISRASASVALSYGAHSNLCVNQIKRNGNAEQKARYLPALV 120 +EEYGG+A+GYLAH V MEEISRASASV LSYGAHSNLCVNQI+RNG A QKA+YLP L+ Sbjct: 61 EEEYGGTAMGYLAHIVAMEEISRASASVGLSYGAHSNLCVNQIRRNGTAAQKAKYLPGLI 120 Query: 121 SGEHIGALAMSEPNAGSDVVSMKLRADRVGDRFVLNGSKMWITNGPDAHTYVIYAKTDAD 180 SG +GALAMSEPNAGSDVVSMKL+A++ GDR+VLNGSKMWITNG DA T V+YAKTD + Sbjct: 121 SGTQVGALAMSEPNAGSDVVSMKLKAEKKGDRYVLNGSKMWITNGGDADTLVVYAKTDLN 180 Query: 181 KGAHGITAFIVERDWKGFSRGPKLDKLGMRGSNTCELIFQDVEVPEENVLGAVNGGVKVL 240 GA G+TAFIVE+ +KGFS G LDKLGMRGSNT L F D EVPEENVLG V G KVL Sbjct: 181 AGAKGMTAFIVEKGFKGFSHGTHLDKLGMRGSNTFPLFFDDCEVPEENVLGGVGNGAKVL 240 Query: 241 MSGLDYERVVLSGGPVGIMQACMDVVVPYIHDRRQFGQSIGEFQLVQGKVADMYTALNAS 300 MSGLDYER VL GGP+GIM ACMDVV+PY+H+R QFG +IGEFQL+QGK+ADMY+ A+ Sbjct: 241 MSGLDYERAVLCGGPLGIMAACMDVVLPYLHEREQFGTAIGEFQLMQGKLADMYSTWQAT 300 Query: 301 RAYLYAVAAACDRGE---TTRKDAAGVILYSAERATQMALDAIQILGGNGYINEFPTGRL 357 RAY+YAV ACDR + + RKDAAG ILYSAE+AT MA DAIQ LGG GY NE+PTGRL Sbjct: 301 RAYVYAVGQACDRADHARSLRKDAAGAILYSAEKATWMAGDAIQTLGGVGYTNEYPTGRL 360 Query: 358 LRDAKLYEIGAGTSEIRRMLIGRELFNET 386 RDAKLYEIGAGTSEIRRMLIGRELF ET Sbjct: 361 WRDAKLYEIGAGTSEIRRMLIGRELFAET 389 Lambda K H 0.319 0.136 0.395 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: 528 Number of extensions: 15 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: 390 Length adjustment: 30 Effective length of query: 357 Effective length of database: 360 Effective search space: 128520 Effective search space used: 128520 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 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