Align glutathione transferase (EC 2.5.1.18); maleylacetoacetate isomerase (EC 5.2.1.2) (characterized)
to candidate PfGW456L13_1835 Glutathione S-transferase (EC 2.5.1.18)
Query= BRENDA::O43708 (216 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1835 Length = 210 Score = 47.0 bits (110), Expect = 3e-10 Identities = 48/182 (26%), Positives = 76/182 (41%), Gaps = 13/182 (7%) Query: 7 ILYSYFRSSCSWRVRIALALKGIDYKTVPINLIK-DRGQQFSKDFQALNPMKQVPTLKID 65 I+ SS S R +AL L G Y I L + D ++ K +P +VP LK + Sbjct: 6 IIGDKLHSSWSLRGALALDLAGASYTEELIKLNQPDTRERLLKH----SPTGKVPLLKTE 61 Query: 66 GITIHQSLAIIEYLEEMRPTPRLLPQDPKKRASVRMISDLIAGGIQPLQNLSVLKQVGEE 125 TI SLAI EYL E P L P+D RA R + G ++ ++ +G + Sbjct: 62 HGTIADSLAIAEYLAEQFPDANLWPKDTAARAQARSACAQMHSGFFAMRG-NMPFDLGHD 120 Query: 126 MQLTWAQNAITCGFNALE------QILQSTAGIYCVGDEVTMADLCLVPQVANAERFKVD 179 L+ + + ++ + +G Y G +T+AD P ++V Sbjct: 121 AALSPVPADVQADIERMSALWAECRVAATESGPYLFG-RITLADAFFAPIAVRLRTYRVK 179 Query: 180 LT 181 L+ Sbjct: 180 LS 181 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: 94 Number of extensions: 6 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: 216 Length of database: 210 Length adjustment: 22 Effective length of query: 194 Effective length of database: 188 Effective search space: 36472 Effective search space used: 36472 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