Align 3-oxoadipate enol-lactonase (EC 3.1.1.24); 4-carboxymuconolactone decarboxylase (EC 4.1.1.44) (characterized)
to candidate PP_0553 PP_0553 Dihydrolipoyllysine-residue acetyltransferase component of acetoin cleaving system
Query= BRENDA::Q0SH24 (400 letters) >FitnessBrowser__Putida:PP_0553 Length = 368 Score = 82.0 bits (201), Expect = 3e-20 Identities = 89/258 (34%), Positives = 125/258 (48%), Gaps = 35/258 (13%) Query: 15 GAADAPVVVLLGSLGSNRSMWDPQIAALSYECRVVAVDQRGHGESPAPDGPYSVRDLSED 74 G P+V++ G G + + W AL+ E RV+A+D GHGES + +LSE Sbjct: 129 GEGGTPLVLVHG-FGGDLNNWLFNHPALAAERRVIALDLPGHGESAKALQRGDLDELSET 187 Query: 75 VLALLDSLGVDAAHFVGLSMGGAIAQWLGAHAPRRVLSLSLLCTAAKFGEP------QAW 128 VLALLD L + AH G SMGGA++ + AP+RV SLSL+ +A GE Q + Sbjct: 188 VLALLDHLDIAKAHLAGHSMGGAVSLNVARLAPQRVASLSLVASAG-LGEAINGQYLQGF 246 Query: 129 IERA--AASRTDGPESLAD-AVVARWFSEGLAK-RDPEFVRHYREMIASTSPEGYAACCD 184 + A A + + AD A+V R E + K + E V + +A Sbjct: 247 VTAANRNALKPQMVQLFADPALVTRQMLEDMLKFKRLEGVDQALQQLAG----------- 295 Query: 185 ALADWDFTA-DLSRI--SAPTLVIAGEEDPSTPPSVMQILADGITEARFEVLSPAAHVAN 241 ALAD D DL + + P LV+ G +D P S A+G+ EA +VL A H+ Sbjct: 296 ALADGDRQRHDLRGVLGNHPALVVWGGKDAIIPAS----HAEGL-EAEVQVLPEAGHMVQ 350 Query: 242 LEQAGAVT----ALLREH 255 +E A V A LR+H Sbjct: 351 MEAAEQVNQQLLAFLRKH 368 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: 352 Number of extensions: 24 Number of successful extensions: 1 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: 368 Length adjustment: 30 Effective length of query: 370 Effective length of database: 338 Effective search space: 125060 Effective search space used: 125060 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