Align 2-(1,2-epoxy-1,2-dihydrophenyl)acetyl-CoA isomerase (EC 5.3.3.18) (characterized)
to candidate Ac3H11_4989 Enoyl-CoA hydratase (EC 4.2.1.17)
Query= BRENDA::Q5SLK3 (254 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_4989 Length = 266 Score = 161 bits (407), Expect = 1e-44 Identities = 101/254 (39%), Positives = 139/254 (54%), Gaps = 1/254 (0%) Query: 2 VLKERQDGVLVLTLNRPEKLNAITGELLDALYAALKEGEEDREVRALLLTGAGRAFSAGQ 61 +L ER+ + L NRPE LNAI + +A AA++ D VRA++L G GR F AG Sbjct: 13 LLLEREGAIATLRFNRPEALNAIDVPMANAFLAAVQTVAADPAVRAVVLCGNGRGFMAGG 72 Query: 62 DLTEF-GDRKPDYEAHLRRYNRVVEALSGLEKPLVVAVNGVAAGAGMSLALWGDLRLAAV 120 DL D L N + L+ + P+V V+GVAAGAG+SL L D +AA Sbjct: 73 DLATLRADPVQSAIDILTPLNAALLLLAQMNAPVVAQVHGVAAGAGLSLLLMADYVIAAE 132 Query: 121 GASFTTAFVRIGLVPDSGLSFLLPRLVGLAKAQELLLLSPRLSAEEALALGLVHRVVPAE 180 G A++ +G D G S+ LPR+VG+ +A E+ LL +A++AL LGLV+RVVPA Sbjct: 133 GTRLNLAYINLGTSCDVGASWALPRIVGVRQALEIALLGDAFTADDALRLGLVNRVVPAA 192 Query: 181 KLMEEALSLAKELAQGPTRAYALTKKLLLETYRLSLTEALALEAVLQGQAGQTQDHEEGV 240 +L +LA+ LA GPT AY K+L+ + +L E LA E T+D GV Sbjct: 193 ELDSATAALAQRLASGPTLAYGAMKRLMRASMDHTLPEQLAAEKDAFVHCAGTEDFRAGV 252 Query: 241 RAFREKRPPRFQGR 254 AF ++ F GR Sbjct: 253 EAFHLRQSASFAGR 266 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: 153 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: 254 Length of database: 266 Length adjustment: 24 Effective length of query: 230 Effective length of database: 242 Effective search space: 55660 Effective search space used: 55660 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