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 PP_3492 PP_3492 short-chain acyl-CoA dehydrogenase
Query= BRENDA::Q18AQ1 (378 letters) >FitnessBrowser__Putida:PP_3492 Length = 383 Score = 342 bits (877), Expect = 1e-98 Identities = 173/372 (46%), Positives = 250/372 (67%) Query: 5 SKKYQMLKELYVSFAENEVKPLATELDEEERFPYETVEKMAKAGMMGIPYPKEYGGEGGD 64 S++ M++++ FA E+ P A ++ V KM + G++G+ P+++GG D Sbjct: 7 SEEQIMIRDMARDFARGEIAPHAQAWEKAGWIDDGVVRKMGELGLLGMVVPEDFGGSYTD 66 Query: 65 TVGYIMAVEELSRVCGTTGVILSAHTSLGSWPIYQYGNEEQKQKFLRPLASGEKLGAFGL 124 V Y +AVEE+S CG TG ++S H S+G P+ YG EQ+Q++L LASGE +G F L Sbjct: 67 YVAYALAVEEISAGCGATGAMMSIHNSVGCGPLLAYGTAEQQQQWLPRLASGEVIGCFCL 126 Query: 125 TEPNAGTDASGQQTTAVLDGDEYILNGSKIFITNAIAGDIYVVMAMTDKSKGNKGISAFI 184 TEP AG++A +T A L ++++NG+K F++NA + +V A+TD G KG+SAF+ Sbjct: 127 TEPQAGSEAHNLRTRAELVDGQWVINGAKQFVSNARRAGLAIVFAVTDPELGKKGLSAFL 186 Query: 185 VEKGTPGFSFGVKEKKMGIRGSATSELIFEDCRIPKENLLGKEGQGFKIAMSTLDGGRIG 244 V PGF E KMGIR S T + F++CRIP N+LG+ G+G IA+S L+GGRIG Sbjct: 187 VPTDNPGFKVDRSEHKMGIRASDTCAVTFDNCRIPAANILGERGKGLAIALSNLEGGRIG 246 Query: 245 IAAQALGLAQGALDETVKYVKERVQFGRPLSKFQNTQFQLADMEVKVQAARHLVYQAAIN 304 IAAQALG+A+ A + + Y ++R+QFG+P+++ Q+ LADM+V+V AAR L+ AA Sbjct: 247 IAAQALGIARAAFEAALVYSRDRIQFGKPINEHQSIANLLADMQVQVNAARLLILHAARL 306 Query: 305 KDLGKPYGVEAAMAKLFAAETAMEVTTKAVQLHGGYGYTRDYPVERMMRDAKITEIYEGT 364 + GKP EA+ AKLFA+E A V + A+Q+HGGYGY DYPVER RDA+IT+IYEG+ Sbjct: 307 RSAGKPCLSEASQAKLFASEMAERVCSMAIQVHGGYGYLEDYPVERYYRDARITQIYEGS 366 Query: 365 SEVQRMVISGKL 376 SE+QRM+I+ +L Sbjct: 367 SEIQRMLIAREL 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: 333 Number of extensions: 9 Number of successful extensions: 1 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: 383 Length adjustment: 30 Effective length of query: 348 Effective length of database: 353 Effective search space: 122844 Effective search space used: 122844 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