Align 2-(1,2-epoxy-1,2-dihydrophenyl)acetyl-CoA isomerase (EC 5.3.3.18) (characterized)
to candidate Ga0059261_2840 Ga0059261_2840 Enoyl-CoA hydratase/carnithine racemase
Query= BRENDA::P77467 (262 letters) >FitnessBrowser__Korea:Ga0059261_2840 Length = 263 Score = 184 bits (466), Expect = 2e-51 Identities = 107/262 (40%), Positives = 147/262 (56%), Gaps = 4/262 (1%) Query: 1 MMEFILSHVEKGVMTLTLNRPERLNSFNDEMHAQLAECLKQVERDDTIRCLLLTGAGRGF 60 M E + + G++ T+NRP R+N+ + + A +++ D R L+LTGAGR F Sbjct: 1 MNELQIDRHDGGIVIATINRPARMNAIDRNLIASFEALFDRLDADREARVLILTGAGRAF 60 Query: 61 CAGQDLNDRNVDPTGPAPDLGMSVERFYNPLVRRLAKLPKPVICAVNGVAAGAGATLALG 120 CAG DL V+ GP L + L+ R+A L +PVI AVNG AAG G L Sbjct: 61 CAGADLKSDFVESAGPEESLASQLR--LARLMERIANLRQPVIAAVNGAAAGGGFAFTLA 118 Query: 121 GDIVIAARSAKFVMAFSKLGLIP-DCGGTWLLPRVAGRARAMGLALLGNQLSAEQAHEWG 179 DI IA RSA F +A ++LGL +CG +WLLPR+ G +RA L L G + AE+A G Sbjct: 119 ADIRIAGRSAHFSIANARLGLSAGECGISWLLPRLIGLSRAFELMLTGRKFDAEEAERIG 178 Query: 180 MIWQVVDDETLADTAQQLARHLATQPTFGLGLIKQAI-NSAETNTLDTQLDLERDYQRLA 238 + + V D+ L DTA + AR +A FG+ + K + + ET ++ + LE Q L Sbjct: 179 YVVRTVADDVLLDTALETARLIAANAPFGVAMTKDVVRRNLETASMQAAIALEARTQLLC 238 Query: 239 GRSADYREGVSAFLAKRSPQFT 260 G S D+RE VSAFL KR P FT Sbjct: 239 GGSGDFREAVSAFLEKRPPDFT 260 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: 159 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: 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 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