Align 2-(1,2-epoxy-1,2-dihydrophenyl)acetyl-CoA isomerase (EC 5.3.3.18) (characterized)
to candidate GFF1676 PGA1_c16990 putative enoyl-CoA hydratase FadB
Query= BRENDA::P77467 (262 letters) >FitnessBrowser__Phaeo:GFF1676 Length = 258 Score = 201 bits (512), Expect = 1e-56 Identities = 106/258 (41%), Positives = 156/258 (60%), Gaps = 5/258 (1%) Query: 5 ILSHVEKGVMTLTLNRPERLNSFNDEMHAQLAECLKQVERDDTIRCLLLTGAGRGFCAGQ 64 IL +E G+ +TLNRP ++N+ A++ +++ ++ R ++LTG+G FC+GQ Sbjct: 6 ILFSLEDGLAVVTLNRPAKMNALTGLTRAEITHAMQRAGKE--ARAVVLTGSGVSFCSGQ 63 Query: 65 DLNDRNVDPTGPAPDLGMSVERFYNPLVRRLAKLPKPVICAVNGVAAGAGATLALGGDIV 124 DL+D + DL ++ Y P++ + P P I AVNG AAGAGA LAL D+V Sbjct: 64 DLSDA---ASQGKLDLERTLRDEYTPMLEAIYNCPVPTIAAVNGPAAGAGANLALAADVV 120 Query: 125 IAARSAKFVMAFSKLGLIPDCGGTWLLPRVAGRARAMGLALLGNQLSAEQAHEWGMIWQV 184 IA SA F+ AF+++GL+PD GGTW +PR G A+AMG AL +++SA+QA +WGMIW+ Sbjct: 121 IATESAYFMQAFARIGLMPDAGGTWFMPRQMGMAKAMGAALFADKISAKQASDWGMIWEA 180 Query: 185 VDDETLADTAQQLARHLATQPTFGLGLIKQAINSAETNTLDTQLDLERDYQRLAGRSADY 244 + D + A +LA+ PT G IK AI N+L QL E Q G++ D+ Sbjct: 181 IPDAEFDAHWRARAAYLASGPTRAFGAIKTAIRDGYGNSLPEQLSEEAHLQGQCGKTRDF 240 Query: 245 REGVSAFLAKRSPQFTGK 262 EGV+AF+ KR +F G+ Sbjct: 241 MEGVTAFMEKRPAKFEGR 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: 156 Number of extensions: 9 Number of successful extensions: 3 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: 258 Length adjustment: 24 Effective length of query: 238 Effective length of database: 234 Effective search space: 55692 Effective search space used: 55692 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