Align butyryl-CoA dehydrogenase; EC 1.3.99.2 (characterized)
to candidate 14185 b0039 crotonobetaine reductase subunit II, FAD-binding (NCBI)
Query= CharProtDB::CH_091787 (383 letters) >lcl|FitnessBrowser__Keio:14185 b0039 crotonobetaine reductase subunit II, FAD-binding (NCBI) Length = 380 Score = 171 bits (433), Expect = 3e-47 Identities = 114/384 (29%), Positives = 184/384 (47%), Gaps = 8/384 (2%) Query: 1 MDFNLTDIQQDFLKLAHDF-GEKKLAPTVTERDHKGIYDKELIDELLSLGITGAYFEEKY 59 MDFNL D Q+ F+ + + E D +Y + + L +GI E++ Sbjct: 1 MDFNLNDEQELFVAGIRELMASENWEAYFAECDRDSVYPERFVKALADMGIDSLLIPEEH 60 Query: 60 GGSGDDGGDVLSYILAVEELAKYDAGVAITLSATVSLCANPIWQFGTEAQKEKFLVPLVE 119 GG D G L+ + EL + A + N + GT+ Q +K + Sbjct: 61 GGL-DAGFVTLAAVWM--ELGRLGAPTYVLYQLPGGF--NTFLREGTQEQIDKIMAFRGT 115 Query: 120 GTKLGAFGLTEPNAGTDASGQQTIATKNDDGTYTLNGSKIFITNGGAADIYIVFAMTDKS 179 G ++ +TEP AG+D +T T+ + Y LNGSK FIT+ +V A S Sbjct: 116 GKQMWNSAITEPGAGSDVGSLKTTYTRRNGKIY-LNGSKCFITSSAYTPYIVVMARDGAS 174 Query: 180 KGNHGITAFILEDGTPGFTYGKKEDKMGIHTSQTMELVFQDVKVPAENMLGEEGKGFKIA 239 T + ++ PG K E K+G+ E+ F DV++ ++M G EG GF Sbjct: 175 PDKPVYTEWFVDMSKPGIKVTKLE-KLGLRMDSCCEITFDDVELDEKDMFGREGNGFNRV 233 Query: 240 MMTLDGGRIGVAAQALGIAEAALADAVEYSKQRVQFGKPLCKFQSISFKLADMKMQIEAA 299 D R VA G A A DA Y+ QRVQFG+ + +FQ I K A M +++ + Sbjct: 234 KEEFDHERFLVALTNYGTAMCAFEDAARYANQRVQFGEAIGRFQLIQEKFAHMAIKLNSM 293 Query: 300 RNLVYKAACKKQEGKPFTVDAAIAKRVASDVAMRVTTEAVQIFGGYGYSEEYPVARHMRD 359 +N++Y+AA K G + DAA+ K ++ A V A+Q+ GG G + + ++R RD Sbjct: 294 KNMLYEAAWKADNGTITSGDAAMCKYFCANAAFEVVDSAMQVLGGVGIAGNHRISRFWRD 353 Query: 360 AKITQIYEGTNEVQLMVTGGALLR 383 ++ ++ G++E+Q++ G A+L+ Sbjct: 354 LRVDRVSGGSDEMQILTLGRAVLK 377 Lambda K H 0.316 0.135 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: 340 Number of extensions: 12 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: 383 Length of database: 380 Length adjustment: 30 Effective length of query: 353 Effective length of database: 350 Effective search space: 123550 Effective search space used: 123550 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 (21.6 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.
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