Align 3-oxoadipate enol-lactonase (EC 3.1.1.24); 4-carboxymuconolactone decarboxylase (EC 4.1.1.44) (characterized)
to candidate Echvi_4304 Echvi_4304 Predicted hydrolases or acyltransferases (alpha/beta hydrolase superfamily)
Query= BRENDA::Q0SH24 (400 letters) >FitnessBrowser__Cola:Echvi_4304 Length = 270 Score = 151 bits (382), Expect = 2e-41 Identities = 88/243 (36%), Positives = 128/243 (52%), Gaps = 2/243 (0%) Query: 15 GAADAPVVVLLGSLGSNRSMWDPQIAALSYECRVVAVDQRGHGESPAPDGPYSVRDLSED 74 G PV+VL S+ ++ +MWD Q+ A R++ D RGHG S +P G YSV L++D Sbjct: 26 GEVTNPVLVLSNSIATDLAMWDGQVEAFCKSYRLLRFDTRGHGLSESPVGDYSVARLAKD 85 Query: 75 VLALLDSLGVDAAHFVGLSMGGAIAQWLGAHAPRRVLSLSLLCTAAKFGEPQAWIERAAA 134 V+ L+D LG++ AHF GLS+GG I QWLG H P R+ L L T+ G W E Sbjct: 86 VIELMDYLGIEKAHFCGLSLGGFIGQWLGVHVPHRLDKLILANTSPYLGPDTIWNENIHL 145 Query: 135 SRTDGPES-LADAVVARWFSEGLAKRDPEFVRHYREMIASTSPEGYAACCDALADWDFTA 193 R S + + WF + + V +R+MI STSP G A A+ D DF Sbjct: 146 LRNGSDMSHFEELFINGWFPKQMINNQKNRVVPFRKMILSTSPIGLAGAYAAVRDADFRK 205 Query: 194 DLSRISAPTLVIAGEEDPSTPPSVMQILADGITEARFEVLSPAAHVANLEQAGAVTALLR 253 + I TL++AGE D T P +++ + I A +VL P H++N+E+ L+ Sbjct: 206 TNALIPNKTLILAGEHDQVTKPEHSKLMHEVIRGATLKVL-PVVHLSNIERINEFERLVL 264 Query: 254 EHI 256 + + Sbjct: 265 QFL 267 Lambda K H 0.318 0.132 0.392 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: 266 Number of extensions: 15 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: 400 Length of database: 270 Length adjustment: 28 Effective length of query: 372 Effective length of database: 242 Effective search space: 90024 Effective search space used: 90024 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: 49 (23.5 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