Align Maleylacetoacetate isomerase; MAAI; GSTZ1-1; Glutathione S-transferase zeta 1; EC 5.2.1.2; EC 2.5.1.18 (characterized)
to candidate GFF3215 PGA1_c32680 putative glutathione S-transferase
Query= SwissProt::P57113 (216 letters) >FitnessBrowser__Phaeo:GFF3215 Length = 205 Score = 62.4 bits (150), Expect = 6e-15 Identities = 54/180 (30%), Positives = 84/180 (46%), Gaps = 6/180 (3%) Query: 11 YFRSSCSWRVRIALALKGIDYEIVPINLIKDGGQQFSEEFQTLNPMKQVPALKIDGITIG 70 Y + S V IAL G+DYE PI + +Q + + +NP +VPAL +DG + Sbjct: 6 YAPKTISVAVAIALEEAGLDYE--PIRIDFAAKEQLGDAYAQINPKGRVPALVVDGGILT 63 Query: 71 QSLAILEYLEETRPIPRLLPQDPQKRAIVRMISDLIAS--GIQPLQNLSVLKQVGQENQM 128 ++ A+LEY+ + P L P DP A +R + +AS + L + + + Sbjct: 64 ETGALLEYVADVAPDAGLRPTDPVLLARMREVMFYLASTMHVNHAHKLRGSRWATERSSW 123 Query: 129 PWAQKAITSGFNA-LEKILQS-TAGKYCVGDEVSMADVCLAPQVANAERFKVDLSPYPTI 186 QK + A + I QS G +GD +S+AD L + E VD++ YP I Sbjct: 124 KDMQKMVPQTMAASCDYICQSGLRGPLVLGDALSLADCYLYVVCSWLEGDGVDVADYPKI 183 Lambda K H 0.319 0.135 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: 111 Number of extensions: 3 Number of successful extensions: 3 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: 205 Length adjustment: 21 Effective length of query: 195 Effective length of database: 184 Effective search space: 35880 Effective search space used: 35880 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 (21.8 bits) S2: 45 (21.9 bits)
This GapMind analysis is from Apr 09 2024. 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