Align 2-(1,2-epoxy-1,2-dihydrophenyl)acetyl-CoA isomerase (EC 5.3.3.18) (characterized)
to candidate AZOBR_RS24105 AZOBR_RS24105 enoyl-CoA hydratase
Query= BRENDA::Q5SLK3 (254 letters) >FitnessBrowser__azobra:AZOBR_RS24105 Length = 256 Score = 142 bits (358), Expect = 7e-39 Identities = 89/248 (35%), Positives = 136/248 (54%), Gaps = 3/248 (1%) Query: 2 VLKERQDGVLVLTLNRPEKLNAITGELLDALYAALKEGEEDREVRALLLTGAG-RAFSAG 60 +L E + V ++TLNRPE LNA + D L A + E VRA++LTGAG RAF AG Sbjct: 5 ILTEVRGPVGIITLNRPEILNAWNAAMRDELVVAFDQFENQDGVRAIILTGAGDRAFGAG 64 Query: 61 QDLTEFGDRKPDY-EAHLRRYNRVVEALSGLEKPLVVAVNGVAAGAGMSLALWGDLRLAA 119 QDL E D E + + R+ + L KPL++A+NGVAAG+ +AL GD R+ Sbjct: 65 QDLNETKTFNADRAEEWVAEWERLYHRMRTLSKPLIIALNGVAAGSAFQVALLGDFRIGH 124 Query: 120 VGASFTTAFVRIGLVPDSGLSFLLPRLVGLAKAQELLLLSPRLSAEEALALGLVHRVVPA 179 G + G+ +G +++ ++GLA+ +L L + AEE+ +GL++R+VP Sbjct: 125 AGVRMGQPEINSGIASTTG-PWIMKEMIGLARTMDLTLSGRLMDAEESHRIGLINRIVPQ 183 Query: 180 EKLMEEALSLAKELAQGPTRAYALTKKLLLETYRLSLTEALALEAVLQGQAGQTQDHEEG 239 +++M E+L+LA+ELA P A L K+ E +ALA +Q +A + + Sbjct: 184 DRVMAESLALAEELAAKPPVAMRLDKQRFREMTEAGFRDALAAGVRIQREAYASGEPARM 243 Query: 240 VRAFREKR 247 + F KR Sbjct: 244 MEEFLAKR 251 Lambda K H 0.318 0.135 0.371 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: 185 Number of extensions: 10 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: 254 Length of database: 256 Length adjustment: 24 Effective length of query: 230 Effective length of database: 232 Effective search space: 53360 Effective search space used: 53360 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 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