Align butanoyl-CoA dehydrogenase (NAD+, ferredoxin) (subunit 3/3) (EC 1.3.1.109); short-chain acyl-CoA dehydrogenase (EC 1.3.8.1) (characterized)
to candidate GFF814 PS417_04135 acyl-CoA dehydrogenase
Query= BRENDA::Q18AQ1 (378 letters) >FitnessBrowser__WCS417:GFF814 Length = 378 Score = 286 bits (732), Expect = 7e-82 Identities = 153/374 (40%), Positives = 226/374 (60%), Gaps = 1/374 (0%) Query: 3 LNSKKYQMLKELYVSFAENEVKPLATELDEEERFPYETVEKMAKAGMMGIPYPKEYGGEG 62 L S ++++ +E +F E + P +++ K +AGM+ P+EYGG G Sbjct: 6 LFSPEHELFRESVRTFLEKDAAPFHGHWEKQGYIDRRLWNKAGEAGMLCSHLPEEYGGLG 65 Query: 63 GDTVGYIMAVEELSRVCGTTGVILSAHTSLGSWPIYQYGNEEQKQKFLRPLASGEKLGAF 122 D + + +EE+SR+ G TG+ S H+ + + I YG+E K K+L L SGE + A Sbjct: 66 ADFLYSAVVIEEISRL-GLTGIGFSLHSDIVAPYILHYGSEALKHKYLPKLISGEMVTAI 124 Query: 123 GLTEPNAGTDASGQQTTAVLDGDEYILNGSKIFITNAIAGDIYVVMAMTDKSKGNKGISA 182 +TEP AG+D G +TTAVLDGDEY++NGSK FITN ++ +V+A TD G KG S Sbjct: 125 AMTEPGAGSDLQGVKTTAVLDGDEYVINGSKTFITNGYLAELVIVVAKTDPKAGAKGTSL 184 Query: 183 FIVEKGTPGFSFGVKEKKMGIRGSATSELIFEDCRIPKENLLGKEGQGFKIAMSTLDGGR 242 F+VE TPGF G + +K+G++ TSEL F+D R+PKENLLG+ G GF M L R Sbjct: 185 FLVEADTPGFDKGKRLEKVGMKAQDTSELFFQDVRVPKENLLGQAGMGFAYLMQELPQER 244 Query: 243 IGIAAQALGLAQGALDETVKYVKERVQFGRPLSKFQNTQFQLADMEVKVQAARHLVYQAA 302 + +A AL A+ AL+ T++Y +ER FG+ ++ FQNT+F+LA+M ++Q R V + Sbjct: 245 LTVAIGALSSAEAALEWTLEYTRERKAFGKAIADFQNTRFKLAEMATEIQIGRVFVDKCM 304 Query: 303 INKDLGKPYGVEAAMAKLFAAETAMEVTTKAVQLHGGYGYTRDYPVERMMRDAKITEIYE 362 GK AAMAK +A + +V + VQLHGGYG+ +YP+ R DA++ IY Sbjct: 305 ALHLEGKLDVPTAAMAKYWATDLQCKVLDECVQLHGGYGFMWEYPIARAWADARVQRIYA 364 Query: 363 GTSEVQRMVISGKL 376 GT+E+ + +I+ L Sbjct: 365 GTNEIMKEIIARAL 378 Lambda K H 0.315 0.133 0.373 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: 367 Number of extensions: 13 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: 378 Length of database: 378 Length adjustment: 30 Effective length of query: 348 Effective length of database: 348 Effective search space: 121104 Effective search space used: 121104 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: 42 (22.0 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