Align isovaleryl-coenzyme A dehydrogenase; EC 1.3.99.10 (characterized)
to candidate Dsui_3369 Dsui_3369 acyl-CoA dehydrogenase
Query= CharProtDB::CH_122627 (430 letters) >FitnessBrowser__PS:Dsui_3369 Length = 394 Score = 189 bits (480), Expect = 1e-52 Identities = 128/376 (34%), Positives = 194/376 (51%), Gaps = 16/376 (4%) Query: 52 ELRESVQEFTSR--ISTVVAARTDAQNEFPAEMWKKLGNAGFLGVTADEEYGGLGMGYQA 109 ++R++ ++++ + +V A Q + PA ++++LG G LG T D YG G Y + Sbjct: 22 QVRDTARQYSQDRLLPRIVQAFRHEQTD-PA-IFRELGELGLLGATLDG-YGCAGASYVS 78 Query: 110 HCVVMEEISRASGSIALSYAAHSQLCVNQLSLNGTPEQKARFLPGLLSGEKIGALAMSEH 169 + ++ EI R + S L + + G+ K R LP + +GE IG ++E Sbjct: 79 YGLLAREIERVDSGYRSMVSVQSSLAMYPIHAFGSEALKERLLPKMATGELIGCFGLTEP 138 Query: 170 SAGSDVVSMKTSAKEVDGGWVLNGTKMWITNGPDADYIVVYAKTEPEKGSKGITAFVVEK 229 + GSD SM++ A+ V GGW L G KMWITN P AD VV+AK ++ I FV+EK Sbjct: 139 NHGSDPGSMESRAEAVPGGWELTGAKMWITNSPIADVFVVWAKDGQDEDGGEIRGFVLEK 198 Query: 230 TFKGFSCARKLDKLGMRGSNTGELIFEDVFVPRENLLGEVNRGVKVLMEGLDLERLVLSA 289 KG S K+G+R S TGE++ + VFVP ENLL +V +G+K L+ R ++ Sbjct: 199 GMKGLSAPVIQGKMGLRASVTGEIVMDKVFVPEENLLPKV-KGLKGPFACLNQARYGIAW 257 Query: 290 GPLGIMQAALDLVLPYTHVRKQFGAPIAHNQLIQGKLADMHTKLAASRAYTYATARHID- 348 G LG +A YT R QFG P+A NQL+Q KLADM T++A R D Sbjct: 258 GALGAAEACWHAARQYTLDRPQFGRPLAANQLVQKKLADMQTEIALGLQGCLRLGRLKDE 317 Query: 349 -SHASLGSAAIRTQDCAGAILYAAERATECALDAIQLMGGNGYINEIPAGRLLRDAKLYE 407 A ++ ++ C +A E A A + GGNG +E R + + ++ Sbjct: 318 GKDAPEMTSLLKRNSCG--------KALEIARTARDMHGGNGISDEFHVVRHMLNLEVVN 369 Query: 408 IGAGTSEIRRMVIGRA 423 GT +I +++GRA Sbjct: 370 TYEGTHDIHALILGRA 385 Lambda K H 0.319 0.134 0.389 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: 365 Number of extensions: 19 Number of successful extensions: 3 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: 394 Length adjustment: 31 Effective length of query: 399 Effective length of database: 363 Effective search space: 144837 Effective search space used: 144837 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 (21.7 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