Align 2-(1,2-epoxy-1,2-dihydrophenyl)acetyl-CoA isomerase (EC 5.3.3.18) (characterized)
to candidate RR42_RS36495 RR42_RS36495 enoyl-CoA hydratase
Query= BRENDA::P77467 (262 letters) >FitnessBrowser__Cup4G11:RR42_RS36495 Length = 259 Score = 158 bits (400), Expect = 9e-44 Identities = 94/258 (36%), Positives = 144/258 (55%), Gaps = 3/258 (1%) Query: 2 MEFILSHVEKGVMTLTLNRPERLNSFNDEMHAQLAECLKQVERDDTIRCLLLTGAGRGFC 61 ME I V GV TLTL+ P+R N+ N M ++ E + Q+ +D ++R L+LTGAG FC Sbjct: 1 METIRYAVADGVATLTLDFPKRKNALNGTMRREIGEVVHQLRQDTSVRALILTGAGSDFC 60 Query: 62 AGQDLNDRNVDPTGPAPDLGMSVERFYNPLVRRLAKLPKPVICAVNGVAAGAGATLALGG 121 +G D++ + + + G +P + L L +PVI AV+G A GAG +LAL Sbjct: 61 SGGDISSMQGEISA---EQGRQRLAAIHPWLEDLIHLDRPVIAAVDGAAYGAGFSLALVA 117 Query: 122 DIVIAARSAKFVMAFSKLGLIPDCGGTWLLPRVAGRARAMGLALLGNQLSAEQAHEWGMI 181 DI++A A+F + F +LGL+PDCG + LPR+ G RA L +LSA A E G++ Sbjct: 118 DIILATPRARFGLPFLRLGLVPDCGVFYTLPRMIGLQRAKTLMFSMRELSAAAALEQGIV 177 Query: 182 WQVVDDETLADTAQQLARHLATQPTFGLGLIKQAINSAETNTLDTQLDLERDYQRLAGRS 241 ++V E L A LA + L K+A+N++ L + L++E D Q +A + Sbjct: 178 MEIVPPEALQARALALASAFTEASPVAVALTKKALNASLNQDLHSMLEMEADGQGIAFAT 237 Query: 242 ADYREGVSAFLAKRSPQF 259 A +E + FL K+ P++ Sbjct: 238 AYRQEAATRFLEKQPPRY 255 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: 4 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: 259 Length adjustment: 25 Effective length of query: 237 Effective length of database: 234 Effective search space: 55458 Effective search space used: 55458 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