Align glutathione transferase (EC 2.5.1.18); maleylacetoacetate isomerase (EC 5.2.1.2) (characterized)
to candidate Pf6N2E2_4235 Glutathione S-transferase, unnamed subgroup (EC 2.5.1.18)
Query= BRENDA::O43708 (216 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_4235 Length = 236 Score = 66.2 bits (160), Expect = 5e-16 Identities = 60/193 (31%), Positives = 86/193 (44%), Gaps = 7/193 (3%) Query: 9 YSYFRSSCSWRVRIALALKGIDYKTVPINLIKDRGQQFSKDFQALNPMKQVPTLKIDGIT 68 Y + S S RV++ L+L G+ + V ++L K G+ DF ALN QVP + DG+ Sbjct: 35 YHFPLSGHSHRVQLMLSLLGLPVEEVFVDLAK--GEHKQADFLALNAFGQVPVIDDDGVV 92 Query: 69 IHQSLAIIEYLEEMRPTPRLLPQDPKKRASVRMISDLIAGGIQPLQNLSVLKQV-GEEMQ 127 + S AI+ YL R LP DP A V+ AG I + L V G Sbjct: 93 LADSNAILVYLAHKYGKGRWLPTDPVGAARVQRWLSAAAGPIHAGPATARLITVFGAAYN 152 Query: 128 LTWAQNAITCGFNALEQILQSTAG-IYCVGDEVTMADLCLVPQVANAERFKVDLTPYPTI 186 A++ I N L+ I Q + Y GD T+AD+ +A+A V L Y + Sbjct: 153 ---AEDVIARSHNVLKVIDQELSNRAYLAGDAATVADIAGYSYIAHAPEGNVSLEDYAHV 209 Query: 187 SSINKRLLVLEAF 199 + R+ L F Sbjct: 210 RAWLARIEALPGF 222 Lambda K H 0.321 0.136 0.400 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: 78 Number of extensions: 2 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: 216 Length of database: 236 Length adjustment: 22 Effective length of query: 194 Effective length of database: 214 Effective search space: 41516 Effective search space used: 41516 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.9 bits) S2: 46 (22.3 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