Align glutaryl-CoA dehydrogenase (ETF) (EC 1.3.8.6) (characterized)
to candidate CA265_RS22715 CA265_RS22715 acyl-CoA dehydrogenase
Query= BRENDA::Q3JP94 (395 letters) >FitnessBrowser__Pedo557:CA265_RS22715 Length = 379 Score = 232 bits (591), Expect = 2e-65 Identities = 136/372 (36%), Positives = 209/372 (56%), Gaps = 2/372 (0%) Query: 17 QLADDERMVRDAAHAYAQGKLAPRVTEAFRHETTDAAIFREMGEIGLLGPTIPEQYGGPG 76 +L++++ M+R AA +AQ +L P V E H+ A +++GE+G LG + E+Y G G Sbjct: 4 ELSEEQLMIRQAARDFAQQELKPGVIERDEHQKFPAEQVKKLGELGFLGMMVSEKYNGSG 63 Query: 77 LDYVSYGLIAREVERVDSGYRSMMSVQSSLVMVPIFEFGSDAQKEKYLPKLATGEWIGCF 136 LD +SY L+ E+ ++D+ ++SV +SLV + +GS+AQKEKYL LA GE IG F Sbjct: 64 LDAISYVLVMEELSKIDASASVVVSVNNSLVCYGLEAYGSEAQKEKYLKPLAAGEKIGAF 123 Query: 137 GLTEPNHGSDPGSMVTRARKVPGGYSLSGSKMWITNSPIADVFVVWAKLDEDGRDE-IRG 195 L+EP GSD S T A Y L+G+K WITN A ++V A+ + R + I Sbjct: 124 CLSEPEAGSDATSQRTTAEDKGDYYLLNGTKNWITNGSTASTYLVIAQTHPELRHKGINA 183 Query: 196 FILEKGCKGLSAPAIHGKVGLRASITGEIVLDEAFVPEEN-ILPHVKGLRGPFTCLNSAR 254 FI+EKG +G + K+G+R S T ++ ++ VP+EN I G + L R Sbjct: 184 FIVEKGMEGFTVGPKENKLGIRGSDTHSLMFNDVKVPKENRIGEDGFGFKFAMKTLEGGR 243 Query: 255 YGIAWGALGAAESCWHIARQYVLDRKQFGRPLAANQLIQKKLADMQTEITLGLQGVLRLG 314 GIA ALG A+ + +A QY +RK FG+P++ +Q I KLADM T+I V + Sbjct: 244 IGIAAQALGIAQGAFELATQYAKERKSFGKPISEHQAIAFKLADMATQIEAARLLVYKAA 303 Query: 315 RMKDEGTAAVEITSIMKRNSCGKALDIARLARDMLGGNGISDEFGVARHLVNLEVVNTYE 374 +KD+G + S+ K + A+D+ A + GG G E+ V R + + ++ YE Sbjct: 304 WLKDQGLPYTQAGSMAKLYASKVAMDVTIEAVQVHGGYGFVKEYHVERLMRDAKITQIYE 363 Query: 375 GTHDIHALILGR 386 GT +I +++ R Sbjct: 364 GTSEIQKMVISR 375 Lambda K H 0.320 0.138 0.414 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: 341 Number of extensions: 18 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: 395 Length of database: 379 Length adjustment: 30 Effective length of query: 365 Effective length of database: 349 Effective search space: 127385 Effective search space used: 127385 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 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