Align 2-(1,2-epoxy-1,2-dihydrophenyl)acetyl-CoA isomerase (EC 5.3.3.18) (characterized)
to candidate 3607639 Dshi_1048 Enoyl-CoA hydratase/isomerase (RefSeq)
Query= BRENDA::P77467 (262 letters) >FitnessBrowser__Dino:3607639 Length = 265 Score = 110 bits (275), Expect = 3e-29 Identities = 86/259 (33%), Positives = 124/259 (47%), Gaps = 14/259 (5%) Query: 10 EKGVMTLTLNRPERLNSFNDEMHAQLAECLKQVERDDTIRCLLLTGAG-RGFCAGQDLND 68 E V +TLN P+RLN+ M L + ++ D R ++L GAG R FCAG D+++ Sbjct: 15 EGPVARITLNNPDRLNAMRLAMWQGLGDLAVELAASDA-RVVVLRGAGDRAFCAGADISE 73 Query: 69 RNVDPTGPAPDLGMSVERFYNPLVRR----LAKLPKPVICAVNGVAAGAGATLALGGDIV 124 P A G++ YN V R LA LP PV+ A+ G G G +A+ D+ Sbjct: 74 F---PQVRATPEGVAA---YNRTVARALEGLAALPMPVLAAIRGHCIGGGLEIAVRCDLR 127 Query: 125 IAARSAKFVMAFSKLGLIPDCGGTWLLPRVAGRARAMGLALLGNQLSAEQAHEWGMIWQV 184 +A+ +A+ +KLGL L R+AG A A L + A +A WG++ + Sbjct: 128 LASETARIAFTPAKLGLAIGADEVAALARIAGPAAAAELLYTAQPVDAARAERWGLVNRR 187 Query: 185 VDDETLADTAQQLARHLATQPTFGLGLIKQAINSAETNTLDTQLDLERD-YQRLAGRSAD 243 V ++ L D A LAR +A L +K + +A D D + SAD Sbjct: 188 VPEDMLMDEADALARTIAANAPLTLRAVKAGL-AAFARPGDAAAASHADALVKTCFDSAD 246 Query: 244 YREGVSAFLAKRSPQFTGK 262 YREG AF KR P+F G+ Sbjct: 247 YREGQRAFAEKRRPEFKGQ 265 Lambda K H 0.321 0.136 0.403 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: 132 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: 262 Length of database: 265 Length adjustment: 25 Effective length of query: 237 Effective length of database: 240 Effective search space: 56880 Effective search space used: 56880 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: 47 (22.7 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