Align glutaryl-CoA dehydrogenase (ETF) (EC 1.3.8.6) (characterized)
to candidate Ac3H11_4557 Crotonobetainyl-CoA dehydrogenase (EC 1.3.99.-)
Query= BRENDA::Q3JP94 (395 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_4557 Length = 411 Score = 118 bits (296), Expect = 3e-31 Identities = 115/379 (30%), Positives = 161/379 (42%), Gaps = 23/379 (6%) Query: 27 DAAHAYAQGKLAPRVTEAFRHETTDAAIFRE----MGEIGLLGPTIPEQYGG--PGLDYV 80 DA A A+G L P ET D A R+ +G G L +P +GG P LD Sbjct: 34 DAHRALAEG-LVPWAAAQEVDETDDRAACRDWVKRLGAGGWLRYCVPAAHGGALPALDSR 92 Query: 81 SYGLIAREVERVDSGYRSMMSVQSSLVMVPIFEFGSDAQKEKYLPKLATGEWIGCFGLTE 140 + L+ RE S L I GS AQ+ YL +A GE I F L+E Sbjct: 93 ALVLL-RETLAYHSPLADFAFAMQGLGSGAITLAGSPAQQAHYLQGVARGELIAAFALSE 151 Query: 141 PNHGSDPGSMVT--------RARKVPGGYSLSGSKMWITNSPIADVFVVWAKLDEDGRDE 192 P GSD G+M T R YSL+G+K WI+N IAD + V+AK D G Sbjct: 152 PEAGSDVGAMKTIAENAYLSRGNGPKDSYSLTGTKTWISNGGIADFYCVFAKTDPAGGTR 211 Query: 193 -IRGFILEKGCKGLSAPA-IHGKVGLRASITGEIVLDEAFVPEENILPHVK-GLRGPFTC 249 I FI++ GL A IH + + D+ VP +L G + Sbjct: 212 GISAFIVDANTPGLDASRHIH---VMAPHPLATLQFDQCTVPATALLGEENGGFKLAMRT 268 Query: 250 LNSARYGIAWGALGAAESCWHIARQYVLDRKQFGRPLAANQLIQKKLADMQTEITLGLQG 309 L+ R +A ALG A A + R+ FG+ LA QL Q K+ +M + Sbjct: 269 LDIFRASVAAAALGMARRALAEAVHHARQRRMFGQTLADFQLTQAKIGEMAALVDSAALL 328 Query: 310 VLRLGRMKDEGTAAVEITSIM-KRNSCGKALDIARLARDMLGGNGISDEFGVARHLVNLE 368 R ++D G A V + M K + A + +A + GG G+ V ++ Sbjct: 329 TYRAAWLRDTGQARVTAEAAMAKMTATENAQRVIDMALQLHGGRGVEVGSKVESLYRDIR 388 Query: 369 VVNTYEGTHDIHALILGRA 387 + YEG ++ LI+G+A Sbjct: 389 SLRIYEGATEVQQLIIGKA 407 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: 329 Number of extensions: 21 Number of successful extensions: 4 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: 411 Length adjustment: 31 Effective length of query: 364 Effective length of database: 380 Effective search space: 138320 Effective search space used: 138320 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