Align butyryl-CoA dehydrogenase; EC 1.3.99.2 (characterized)
to candidate 7025397 Shewana3_2552 acyl-CoA dehydrogenase domain-containing protein (RefSeq)
Query= CharProtDB::CH_091785 (379 letters) >FitnessBrowser__ANA3:7025397 Length = 596 Score = 130 bits (327), Expect = 1e-34 Identities = 112/365 (30%), Positives = 173/365 (47%), Gaps = 57/365 (15%) Query: 59 YGGAGGDVLSYIIAVEELSKVCGTTGVILSAHTSL---CASLINEHGTEEQKQKYLVPLA 115 YGG G + I A E + +T + + + L S I+ HG+E KQKYL L Sbjct: 99 YGGQGLPEVVGIFATEMQT----STNMAFAMYPGLTHGAYSAIHAHGSEALKQKYLAKLV 154 Query: 116 KGEKIGAYGLTEPNAGTDSGAQQTVAVLEGD-HYVINGSKIFITNGGVADT-----FVIF 169 GE G LTE +AGTD +T AV D ++ I G KIFI++G T V+ Sbjct: 155 SGEWTGTMNLTESHAGTDLALLRTKAVPTADGYFAITGEKIFISSGDHQFTDNIVHLVLA 214 Query: 170 AMTDRTKGTKGISAFIIEKGF--KGFSIGK--------VEQKLGIRASSTTELVFEDMIV 219 + D +G KGIS F + K S+G+ +E K+GI +ST +VFE + Sbjct: 215 RLPDAPEGVKGISLFAVPKVLVNSDGSLGEANSLYASGLEHKMGIHGNSTCVMVFEGAL- 273 Query: 220 PVENMIGKEGKGFPIAMKTLDGGRIGIAAQALGIAEGAFNEARAYMKERKQFGRSLDKFQ 279 ++G+ +G ++ R+G+ Q LG++E A+ A AY K+R Q R++ + Sbjct: 274 --GELVGEPHQGLRAMFTMMNQARLGVGMQGLGVSEIAYQSALAYAKDRLQ-SRAISGAK 330 Query: 280 G-------------LAWMMADMDVAIESARYLV-YKAAYLKQAGLPYTVDAARAKLHA-- 323 + M+ E AR LV +A +L +A D A+AK+ A Sbjct: 331 APEKAADPILVHGDVRRMLLSQKAFNEGARALVGQQALWLDEA--ERHSDPAKAKVAAQL 388 Query: 324 ------------ANVAMDVTTKAVQLFGGYGYTKDYPVERMMRDAKITEIYEGTSEVQKL 371 N + A Q+FGG+GY ++ +E+ +RD++I IYEGT+ +Q L Sbjct: 389 AALFTPVVKGFITNRGFNACVDAQQVFGGHGYIHEWGMEQFVRDSRIALIYEGTNGIQAL 448 Query: 372 VISGK 376 + G+ Sbjct: 449 DLVGR 453 Lambda K H 0.317 0.135 0.377 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: 495 Number of extensions: 31 Number of successful extensions: 6 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: 379 Length of database: 596 Length adjustment: 33 Effective length of query: 346 Effective length of database: 563 Effective search space: 194798 Effective search space used: 194798 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: 51 (24.3 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