Align butyryl-CoA dehydrogenase; EC 1.3.99.2 (characterized)
to candidate 201903 SO2768 acyl-CoA dehydrogenase family protein (NCBI ptt file)
Query= CharProtDB::CH_091785 (379 letters) >FitnessBrowser__MR1:201903 Length = 596 Score = 125 bits (314), Expect = 3e-33 Identities = 101/325 (31%), Positives = 157/325 (48%), Gaps = 50/325 (15%) Query: 96 SLINEHGTEEQKQKYLVPLAKGEKIGAYGLTEPNAGTDSGAQQTVAVLEGD-HYVINGSK 154 S I+ HG+E KQKYL L GE G LTE +AGTD +T AV D ++ I G K Sbjct: 135 SAIHAHGSEALKQKYLPKLVSGEWTGTMNLTESHAGTDLALLRTKAVPAADGYFAITGEK 194 Query: 155 IFITNGGVADT-----FVIFAMTDRTKGTKGISAFIIEKGF--KGFSIGK--------VE 199 IFI++G T V+ + D +G KGIS F + K S+G+ +E Sbjct: 195 IFISSGDHPFTDNIVHLVLARLPDAPEGVKGISLFAVPKVLVNSDGSLGQANSLYASGLE 254 Query: 200 QKLGIRASSTTELVFEDMIVPVENMIGKEGKGFPIAMKTLDGGRIGIAAQALGIAEGAFN 259 K+GI +ST +VF+ + ++G+ +G ++ R+G+ Q LG++E A+ Sbjct: 255 HKMGIHGNSTCVMVFDGAL---GELVGEPHQGLRAMFTMMNQARLGVGMQGLGVSEIAYQ 311 Query: 260 EARAYMKERKQFGRSLDKFQG-------------LAWMMADMDVAIESARYLV-YKAAYL 305 A AY K+R Q R++ + + M+ E AR LV +A +L Sbjct: 312 NALAYAKDRLQ-SRAISGAKAPEKAADPILVHGDVRRMLLSQKAFNEGARALVGQQALWL 370 Query: 306 KQAGLPYTVDAARAKLHA--------------ANVAMDVTTKAVQLFGGYGYTKDYPVER 351 +A D A+AK + N + A Q+FGG+GY ++ +E+ Sbjct: 371 DEA--ERHSDPAKAKAASQLAALFTPVVKGFITNRGFNACVDAQQVFGGHGYIHEWGMEQ 428 Query: 352 MMRDAKITEIYEGTSEVQKLVISGK 376 +RD++I IYEGT+ +Q L + G+ Sbjct: 429 FVRDSRIALIYEGTNGIQALDLVGR 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: 488 Number of extensions: 28 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