Align 3-oxoadipate enol-lactonase (EC 3.1.1.24); 4-carboxymuconolactone decarboxylase (EC 4.1.1.44) (characterized)
to candidate Pf6N2E2_667 Dihydrolipoamide acetyltransferase component (E2) of acetoin dehydrogenase complex (EC 2.3.1.-)
Query= BRENDA::Q0SH24 (400 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_667 Length = 370 Score = 75.5 bits (184), Expect = 2e-18 Identities = 79/252 (31%), Positives = 118/252 (46%), Gaps = 31/252 (12%) Query: 15 GAADAPVVVLLGSLGSNRSMWDPQIAALSYECRVVAVDQRGHGESPAPDGPYSVRDLSED 74 G P++++ G G + + W AL+ RV+A+D GHGES + +LS Sbjct: 129 GEGGTPLLLVHG-FGGDLNNWLFNHEALAAGRRVIALDLPGHGESGKVLQRGDLDELSGV 187 Query: 75 VLALLDSLGVDAAHFVGLSMGGAIAQWLGAHAPRRVLSLSLLCTAAKFGE-----PQAWI 129 VLALLD L ++A H VG SMGGA++ APRRV SL+L+ +A E Q ++ Sbjct: 188 VLALLDHLDINAVHLVGHSMGGAVSLNTARLAPRRVRSLTLIGSAGLGSEINGSYLQGFV 247 Query: 130 ERAAASRTDGPESLADAVVARWFSEGLAKRDPEFVRHYREMIASTSPEGYAACCDAL--- 186 E AA+R +L +V + + L R + +M+ EG A L Sbjct: 248 E--AANR----NALKPQLVQLFSNAELVNR-----QMLDDMLKYKRLEGVDAALQQLSSR 296 Query: 187 --ADWDFTADLSRI----SAPTLVIAGEEDPSTPPSVMQILADGITEARFEVLSPAAHVA 240 AD DL + PTLV+ G +D P + + L+ A+ EVL H+ Sbjct: 297 LFADGRQQTDLREVVQAGQVPTLVVWGSDDAIIPVTHSEGLS-----AQVEVLPGQGHMV 351 Query: 241 NLEQAGAVTALL 252 +E A V +L+ Sbjct: 352 QMEAAEQVNSLI 363 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: 313 Number of extensions: 18 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: 370 Length adjustment: 30 Effective length of query: 370 Effective length of database: 340 Effective search space: 125800 Effective search space used: 125800 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: 50 (23.9 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