Align 2-(1,2-epoxy-1,2-dihydrophenyl)acetyl-CoA isomerase (EC 5.3.3.18) (characterized)
to candidate Echvi_0069 Echvi_0069 Enoyl-CoA hydratase/carnithine racemase
Query= BRENDA::P77467 (262 letters) >FitnessBrowser__Cola:Echvi_0069 Length = 260 Score = 171 bits (432), Expect = 2e-47 Identities = 87/258 (33%), Positives = 144/258 (55%), Gaps = 4/258 (1%) Query: 3 EFILSHVEKGVMTLTLNRPERLNSFNDEMHAQLAECLKQVERDDTIRCLLLTGAGRGFCA 62 ++I S V + ++RP N+ N E+ +L Q + +T+RC++LTG G FC+ Sbjct: 4 KYIRSSVNNHCQEIAIDRPAVFNALNFEVLEELKAAFDQAAQAETVRCVVLTGGGGAFCS 63 Query: 63 GQDLNDRNVDPTG-PAPDLGMSVERFYNPLVRRLAKLPKPVICAVNGVAAGAGATLALGG 121 GQDL D G P ++ + ++YNPL+ ++ L KP+IC +NG A GAG +LAL Sbjct: 64 GQDLKAVGTDLDGIPFKEI---IRKYYNPLIIQMRNLSKPIICKLNGAAVGAGCSLALAT 120 Query: 122 DIVIAARSAKFVMAFSKLGLIPDCGGTWLLPRVAGRARAMGLALLGNQLSAEQAHEWGMI 181 D++IA++ A F+ +GL+ D G + LP+ G A LA G ++ AE+A G++ Sbjct: 121 DVIIASKEAYLAEMFAHIGLVMDAGSNYFLPKRVGYPLAFELATTGRKVYAEEAERLGLV 180 Query: 182 WQVVDDETLADTAQQLARHLATQPTFGLGLIKQAINSAETNTLDTQLDLERDYQRLAGRS 241 + ++ L +T Q +G+IK+ + + +L+ L++E YQ AG Sbjct: 181 NKAIEHSALDETVAQYVEVYVNASGSAIGMIKEMLRKSNGMSLEEVLEMEAVYQEKAGSH 240 Query: 242 ADYREGVSAFLAKRSPQF 259 D++EGV++FL KR P+F Sbjct: 241 QDFKEGVTSFLEKRKPRF 258 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: 126 Number of extensions: 3 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: 260 Length adjustment: 25 Effective length of query: 237 Effective length of database: 235 Effective search space: 55695 Effective search space used: 55695 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