Align 3-hydroxypropionyl-CoA dehydratase (EC 4.2.1.116) (characterized)
to candidate GFF3794 PGA1_262p01980 putative enoyl-CoA hydratase
Query= BRENDA::A4YI89 (259 letters) >FitnessBrowser__Phaeo:GFF3794 Length = 263 Score = 185 bits (469), Expect = 9e-52 Identities = 106/260 (40%), Positives = 159/260 (61%), Gaps = 5/260 (1%) Query: 4 ETIETKKEGNLFWITLNRPDKLNALNAKLLEELDRAVSQAESDPEIRVIIITGKG-KAFC 62 E I ++ G + +TLNRP+KLNALN + L ++ E DP IR II+TG G +AF Sbjct: 3 ELITYERNGAVAVLTLNRPEKLNALNYATNDCLLSLLNAIEIDPSIRAIILTGAGERAFS 62 Query: 63 AGADITQFNQLTPA---EAWK-FSKKGREIMDKIEALSKPTIAMINGYALGGGLELALAC 118 AG DI +F + A EA + F K+G+ + ++EA KP IA +NG A GGG E+ A Sbjct: 63 AGGDIHEFTESVKAGVDEAVRDFCKRGQTMTARLEAFQKPIIAAVNGIAFGGGCEITEAV 122 Query: 119 DIRIAAEEAQLGLPEINLGIYPGYGGTQRLTRVIGKGRALEMMMTGDRIPGKDAEKYGLV 178 + +A+E A PEIN+GI P +GGTQRL R+ G+ RALE+++TGD + A + GLV Sbjct: 123 HLAVASERAMFAKPEINIGIPPTFGGTQRLPRLAGRKRALELLLTGDTFSAQRACEMGLV 182 Query: 179 NRVVPLANLEQETRKLAEKIAKKSPISLALIKEVVNRGLDSPLLSGLALESVGWGVVFST 238 NR+VP L LA++I + SP++ + I V RG+++ + GL +E + + +T Sbjct: 183 NRIVPHDELMPAAFDLADRIIRHSPLAASRIITAVTRGINTTIDEGLLIEREQFARMAAT 242 Query: 239 EDKKEGVSAFLEKREPTFKG 258 +D EG+ A++ +R P + G Sbjct: 243 KDVHEGLGAWIARRTPEYVG 262 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: 148 Number of extensions: 6 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: 259 Length of database: 263 Length adjustment: 25 Effective length of query: 234 Effective length of database: 238 Effective search space: 55692 Effective search space used: 55692 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: 47 (22.7 bits)
This GapMind analysis is from Apr 09 2024. 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