Align 3-hydroxypropionyl-CoA dehydratase (EC 4.2.1.116) (characterized)
to candidate N515DRAFT_0416 N515DRAFT_0416 3-hydroxyacyl-CoA dehydrogenase / enoyl-CoA hydratase / 3-hydroxybutyryl-CoA epimerase
Query= BRENDA::A4YI89 (259 letters) >FitnessBrowser__Dyella79:N515DRAFT_0416 Length = 686 Score = 118 bits (296), Expect = 3e-31 Identities = 70/191 (36%), Positives = 111/191 (58%), Gaps = 4/191 (2%) Query: 11 EGNLFWITLNRPDK-LNALNAKLLEELDRAVSQAESDPEIRVIIITGKGKAFCAGADITQ 69 + + +TL+R + +NAL+ ++L+EL + V + + V+I + K F GADI + Sbjct: 16 DSGIVTLTLDRANSSVNALSREVLDELGQIVERLSIEKPAGVLIHSAKPGGFAVGADIKE 75 Query: 70 FNQLT-PAEAWKFSKKGREIMDKIEALSKPTIAMINGYALGGGLELALACDIRIAA--EE 126 F + + + G+ + + + L PT+A I+G +GGG EL LAC RIAA E+ Sbjct: 76 FVEYARDGTVLQNIENGQRVFESLARLPCPTVAAIHGACMGGGTELVLACRQRIAADDEK 135 Query: 127 AQLGLPEINLGIYPGYGGTQRLTRVIGKGRALEMMMTGDRIPGKDAEKYGLVNRVVPLAN 186 ++GLPE+ LGI+PG+GGT RL R+IG AL +M+TG + + A G+V+R+ P Sbjct: 136 TRIGLPEVMLGIHPGWGGTARLPRLIGALDALPVMLTGKALSARRAAALGVVDRLAPPNE 195 Query: 187 LEQETRKLAEK 197 L E R L + Sbjct: 196 LLAEARALLRR 206 Lambda K H 0.315 0.135 0.382 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: 383 Number of extensions: 21 Number of successful extensions: 2 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: 259 Length of database: 686 Length adjustment: 32 Effective length of query: 227 Effective length of database: 654 Effective search space: 148458 Effective search space used: 148458 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