Align 3-hydroxypropionyl-CoA dehydratase (EC 4.2.1.116) (characterized)
to candidate 6937208 Sama_1378 enoyl-CoA hydratase (RefSeq)
Query= BRENDA::A4YI89 (259 letters) >FitnessBrowser__SB2B:6937208 Length = 257 Score = 167 bits (422), Expect = 3e-46 Identities = 100/250 (40%), Positives = 142/250 (56%), Gaps = 2/250 (0%) Query: 11 EGNLFWITLNRPDKLNALNAKLLEELDRAVSQAESDPEIRVIIITGKG-KAFCAGADITQ 69 EGN +T++ P N + L EL V + + EI +++TG+G K F AGAD+ Sbjct: 9 EGNTAILTISNPPA-NTWTRESLNELKEKVLELNDNNEIYALVLTGEGEKFFSAGADLKL 67 Query: 70 FNQLTPAEAWKFSKKGREIMDKIEALSKPTIAMINGYALGGGLELALACDIRIAAEEAQL 129 F A +K E + + A +IA INGYA+GGGLE+ALACDIRIA +A + Sbjct: 68 FADGDKGNAATMAKAFGEAFETLSAFRGVSIAAINGYAMGGGLEVALACDIRIAEIQAVM 127 Query: 130 GLPEINLGIYPGYGGTQRLTRVIGKGRALEMMMTGDRIPGKDAEKYGLVNRVVPLANLEQ 189 LPE +G+ P GGTQ LT ++G+G A M++ G+RI A GLV VV Sbjct: 128 ALPEATVGLLPCAGGTQNLTALVGEGWAKRMILCGERIDATKALNLGLVEEVVEKGESLS 187 Query: 190 ETRKLAEKIAKKSPISLALIKEVVNRGLDSPLLSGLALESVGWGVVFSTEDKKEGVSAFL 249 LA K+AK+SP ++A+ K+++ G + P L LE + +F TED+ EGV+AFL Sbjct: 188 AAIALAAKVAKQSPSAVAVCKKLIQSGRNMPRTQALPLERELFVGLFDTEDQAEGVNAFL 247 Query: 250 EKREPTFKGK 259 EKR +K + Sbjct: 248 EKRAAQWKNR 257 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: 135 Number of extensions: 5 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: 257 Length adjustment: 24 Effective length of query: 235 Effective length of database: 233 Effective search space: 54755 Effective search space used: 54755 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