Align glutathione transferase (EC 2.5.1.18); maleylacetoacetate isomerase (EC 5.2.1.2) (characterized)
to candidate SM_b20005 SM_b20005 glutathione S-transferase
Query= BRENDA::O43708 (216 letters) >FitnessBrowser__Smeli:SM_b20005 Length = 203 Score = 68.6 bits (166), Expect = 8e-17 Identities = 63/196 (32%), Positives = 91/196 (46%), Gaps = 11/196 (5%) Query: 8 LYSYFRSSCSWRVRIALALKGIDYKTVPINLIKDRGQQFSKDFQALNPMKQVPTLKIDGI 67 LY + S + R R+ L+L GI+++ V ++ + +Q DF LN QVP L G Sbjct: 3 LYHHPLSGHAHRARLFLSLLGIEHELVVVDFARREHKQ--ADFLKLNSFGQVPVLDDAGT 60 Query: 68 TIHQSLAIIEYLEEMRPTPRLLPQDPKKRASVRMISDLIAGGIQ--PLQN--LSVLKQVG 123 I S AI+ YL + P LP+D A+V+ + AG I P Q ++V K Sbjct: 61 IISDSNAILVYLAKKTGRPDWLPEDAVGAAAVQRWLSVAAGQIAHGPAQARLINVFKAPY 120 Query: 124 EEMQLTWAQNAITCGFNALEQILQSTAGIYCVGDEVTMADLCLVPQVANAERFKVDLTPY 183 ++ +AI +EQ L+ I D T+AD+ L VA A VDL PY Sbjct: 121 RPEEVIPRSHAILA---LIEQELEGRGWI--AADRPTIADVALYSYVARAPEGDVDLQPY 175 Query: 184 PTISSINKRLLVLEAF 199 P I + R+ L F Sbjct: 176 PEIRAWLARIEALPGF 191 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: 89 Number of extensions: 5 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: 203 Length adjustment: 21 Effective length of query: 195 Effective length of database: 182 Effective search space: 35490 Effective search space used: 35490 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: 45 (21.9 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