Align isovaleryl-CoA dehydrogenase (EC 1.3.8.4) (characterized)
to candidate 15814 b1695 putative oxidoreductase (VIMSS)
Query= BRENDA::Q75N94 (430 letters) >FitnessBrowser__Keio:15814 Length = 383 Score = 166 bits (421), Expect = 9e-46 Identities = 123/386 (31%), Positives = 183/386 (47%), Gaps = 13/386 (3%) Query: 46 TEDELLELRERVQEFTRREITEEVAAKTDAQNEFPAEMWKKLGDAGFLGITANEDYGGLG 105 TE++ L L ++E EE D +P E + L D G + E++GG+ Sbjct: 6 TEEQELLLAS-IRELITTNFPEEYFRTCDQNGTYPREFMRALADNGISMLGVPEEFGGIP 64 Query: 106 MGYQAHCIVMEELSRASGSIALSYAAHSQLCVNQLSLNGSPEQKERFLPGLL-SGDKIGA 164 Y + + E+S+ A ++ + C++ + GS EQ + L +GD A Sbjct: 65 ADYVTQMLALMEVSKCG---APAFLITNGQCIHSMRRFGSAEQLRKTAESTLETGDPAYA 121 Query: 165 LAMSEHSAGSDVVSMKTTAKEVDGGYVLNGTKMWITNGPDADFIVVYAKT-EPQKGSKGI 223 LA++E AGSD S TT +G +NG K +IT + +++V A+ +P+ K Sbjct: 122 LALTEPGAGSDNNSATTTYTRKNGKVYINGQKTFITGAKEYPYMLVLARDPQPKDPKKAF 181 Query: 224 TAFVVEKTFDGFSCARKLDKLGMRGSNTGELIFEDVFVPKENVLGEVNRGVKVLMEGLDL 283 T + V+ + G L K+G +T E+ ++V V + +++GE G +M ++ Sbjct: 182 TLWWVDSSKPGIKI-NPLHKIGWHMLSTCEVYLDNVEVEESDMVGEEGMGFLNVMYNFEM 240 Query: 284 ERLVLSAGPLGIMQAALDLVLPYTHVRKQFGTPIAHNQLIQGKLADMYTKLQASRAYTYS 343 ERL+ +A G + A + Y + R FG PI HNQ+IQ KLA M K+ R Sbjct: 241 ERLINAARSTGFAECAFEDAARYANQRIAFGKPIGHNQMIQEKLALMAIKIDNMRNMVLK 300 Query: 344 TARHIDNSASLSEVSIRTQDCAGAILYAAERATECALDAIQLMGGNGYINELPAGRLLRD 403 A D SL RT A A LY A A E DAIQ+MGG GY +E R RD Sbjct: 301 VAWQADQHQSL-----RT-SAALAKLYCARTAMEVIDDAIQIMGGLGYTDEARVSRFWRD 354 Query: 404 AKLYEIGAGTSEIRRMVIGRAFNKEY 429 + IG GT EI V GR K+Y Sbjct: 355 VRCERIGGGTDEIMIYVAGRQILKDY 380 Lambda K H 0.317 0.134 0.380 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: 385 Number of extensions: 16 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: 430 Length of database: 383 Length adjustment: 31 Effective length of query: 399 Effective length of database: 352 Effective search space: 140448 Effective search space used: 140448 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