Align 2-(1,2-epoxy-1,2-dihydrophenyl)acetyl-CoA isomerase (EC 5.3.3.18) (characterized)
to candidate GFF2642 PGA1_c26820 probable enoyl-CoA hydratase PaaG
Query= BRENDA::P77467 (262 letters) >FitnessBrowser__Phaeo:GFF2642 Length = 261 Score = 271 bits (692), Expect = 1e-77 Identities = 143/262 (54%), Positives = 173/262 (66%), Gaps = 1/262 (0%) Query: 1 MMEFILSHVEKGVMTLTLNRPERLNSFNDEMHAQLAECLKQVERDDTIRCLLLTGAGRGF 60 M E +L + +TLNRP+RLNSF +EMH L L + RD R +LLTGAGRGF Sbjct: 1 MSETLLVEDHGTWVEITLNRPDRLNSFTEEMHHALRAAL-EAARDGGARAVLLTGAGRGF 59 Query: 61 CAGQDLNDRNVDPTGPAPDLGMSVERFYNPLVRRLAKLPKPVICAVNGVAAGAGATLALG 120 CAGQDL DR+ PDLG +V FY PLV + L PVICAVNGVAAGAGA LAL Sbjct: 60 CAGQDLGDRDPRKMDGPPDLGHTVRTFYAPLVNLIRALDFPVICAVNGVAAGAGANLALA 119 Query: 121 GDIVIAARSAKFVMAFSKLGLIPDCGGTWLLPRVAGRARAMGLALLGNQLSAEQAHEWGM 180 D+V+AA SAKF+ +FSK+GLIPD GG+W LPR+ G ARA GLAL L A++A +WG+ Sbjct: 120 CDVVLAAESAKFIQSFSKVGLIPDTGGSWHLPRLLGEARAKGLALTAEPLPAKKAEDWGL 179 Query: 181 IWQVVDDETLADTAQQLARHLATQPTFGLGLIKQAINSAETNTLDTQLDLERDYQRLAGR 240 IW+ V DE L A+ +A A PT GLGL KQ I +A TL QL++E D + G Sbjct: 180 IWKAVPDEELMAEARAMAEKFANGPTLGLGLTKQTIQAAAVTTLSDQLEIEADAMKTCGE 239 Query: 241 SADYREGVSAFLAKRSPQFTGK 262 SADY EGV++FL KR P F GK Sbjct: 240 SADYAEGVASFLEKRVPAFKGK 261 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: 172 Number of extensions: 6 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: 261 Length adjustment: 25 Effective length of query: 237 Effective length of database: 236 Effective search space: 55932 Effective search space used: 55932 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 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