Align 2-(1,2-epoxy-1,2-dihydrophenyl)acetyl-CoA isomerase (EC 5.3.3.18) (characterized)
to candidate SM_b21633 SM_b21633 enoyl-CoA hydratase
Query= BRENDA::P77467 (262 letters) >FitnessBrowser__Smeli:SM_b21633 Length = 263 Score = 306 bits (783), Expect = 4e-88 Identities = 154/259 (59%), Positives = 190/259 (73%), Gaps = 3/259 (1%) Query: 5 ILSHVEKGVMTLTLNRPERLNSFNDEMHAQLAECLKQVERDDTIRCLLLTGAGRGFCAGQ 64 +LS +E GV+ LTLNRP++LN+FN+EMH L ++ DD +R ++LTGAGRGF AGQ Sbjct: 7 VLSALEAGVLRLTLNRPDKLNAFNEEMHLALRAGFERARSDDDVRAVMLTGAGRGFSAGQ 66 Query: 65 DLNDRNVDPT-GPAPDLGMSVERFYNPLVRRLAKLPKPVICAVNGVAAGAGATLALGGDI 123 DL DR DP G APDLG ++E FYNPL+R + L KPV+CAVNGVAAGAGA +A DI Sbjct: 67 DLGDR--DPRKGGAPDLGRTIETFYNPLLRLIRSLEKPVVCAVNGVAAGAGANIAFACDI 124 Query: 124 VIAARSAKFVMAFSKLGLIPDCGGTWLLPRVAGRARAMGLALLGNQLSAEQAHEWGMIWQ 183 +AARSA+F+ AF+K+GL+PD GGTW LPR+ G ARA LA+ L AE A WG+IW+ Sbjct: 125 TLAARSARFIQAFAKIGLVPDSGGTWSLPRLVGEARAKALAMTAEPLDAETAASWGLIWR 184 Query: 184 VVDDETLADTAQQLARHLATQPTFGLGLIKQAINSAETNTLDTQLDLERDYQRLAGRSAD 243 VDD L D A LA LA PT GLGL K+AI +A T++ D QLDLERD QR AGRSAD Sbjct: 185 AVDDAALMDEASALAVRLAAGPTRGLGLTKRAIQAAATHSFDEQLDLERDLQREAGRSAD 244 Query: 244 YREGVSAFLAKRSPQFTGK 262 Y EGV+AFL KR+P+F G+ Sbjct: 245 YAEGVTAFLDKRNPEFRGR 263 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: 207 Number of extensions: 7 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: 262 Length of database: 263 Length adjustment: 25 Effective length of query: 237 Effective length of database: 238 Effective search space: 56406 Effective search space used: 56406 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