Align 2-(1,2-epoxy-1,2-dihydrophenyl)acetyl-CoA isomerase (EC 5.3.3.18) (characterized)
to candidate CCNA_01927 CCNA_01927 enoyl-CoA hydratase
Query= BRENDA::P77467 (262 letters) >FitnessBrowser__Caulo:CCNA_01927 Length = 267 Score = 189 bits (481), Expect = 4e-53 Identities = 107/259 (41%), Positives = 158/259 (61%), Gaps = 8/259 (3%) Query: 10 EKGVMTLTLNRPERLNSFNDEMHAQLAECLKQVERDDT-IRCLLLTGAGRGFCAGQDLND 68 + GV T+TL P LN+ + E+ +L + R ++LTG GRGFC+G +L+ Sbjct: 11 QDGVATVTLADPTTLNAASPEVARELHHAFSSIAAGKIEARAVILTGEGRGFCSGANLSG 70 Query: 69 -----RNVDPTGPAPDLGMSVERFYNPLVRRLAKLPKPVICAVNGVAAGAGATLALGGDI 123 R D G PD G ++E YNPL+ L P P++ AVNG AAG G ++AL GD+ Sbjct: 71 GGAAGREADVDGK-PDAGSALETVYNPLMTLLRDFPLPIVTAVNGPAAGVGCSIALMGDL 129 Query: 124 VIAARSAKFVMAFSKLGLIPDCGGTWLLPRVAGRARAMGLALLGNQLSAEQAHEWGMIWQ 183 ++AA SA F+ AF ++GL+PD G T+LLPR+ G+ARAM + LLG+++ A A +WG++ + Sbjct: 130 IVAAESAYFLQAFRRIGLVPDGGSTYLLPRLIGKARAMEMMLLGDKIPAATALQWGLVNR 189 Query: 184 VVDDETLADTAQQLARHLATQPTFGLGLIKQAINSAETNTLDTQLDLERDYQRLAGRSAD 243 V D L TA LA LA P LG+I++ + + + QL ER Q++AG++ D Sbjct: 190 CVPDAELMVTAHALALELAKGPA-ALGVIRKLVWDSLDSDWTGQLHAERKAQKIAGKTED 248 Query: 244 YREGVSAFLAKRSPQFTGK 262 + EGV+AFL KR+ F G+ Sbjct: 249 FIEGVTAFLQKRAAVFKGR 267 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: 156 Number of extensions: 8 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: 262 Length of database: 267 Length adjustment: 25 Effective length of query: 237 Effective length of database: 242 Effective search space: 57354 Effective search space used: 57354 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