Align Maleylacetoacetate isomerase; MAAI; EC 5.2.1.2 (uncharacterized)
to candidate AZOBR_RS07405 AZOBR_RS07405 glutathione S-transferase
Query= curated2:Q9X4F7 (213 letters) >FitnessBrowser__azobra:AZOBR_RS07405 Length = 202 Score = 68.2 bits (165), Expect = 1e-16 Identities = 61/193 (31%), Positives = 84/193 (43%), Gaps = 6/193 (3%) Query: 7 LYDYWRSSASYRVRIALNLCGEAYRSVPVDLLAKAHRAPEHLARNPQGLVPVLDI-DGER 65 LYD S Y+ R+ L+ G Y + +D+ R PE LARNP G +P L + DG Sbjct: 4 LYDNLSSGNGYKCRLLLHKLGIPYERIELDIDRAETRTPEFLARNPNGRIPTLQLEDGSH 63 Query: 66 LTQSLAIIEYLAETRDGTGLLPAHPIDRQRVRALSYAVAMDIHPVCNLGVVARVMAGAGD 125 L +S AI+ YLAE GT LP + R RV + P N+ V + + Sbjct: 64 LPESNAILWYLAE---GTPYLPDNREGRARVLQWMFFEQYSHEP--NIATVRFWITHHVE 118 Query: 126 GEAARREWMQKFIGEGLAAFERMLDHPATGAFCHGDRPTMADLCLVPQVYNARRWDVDLA 185 R+ + G A M H A F GDR ++AD+ L + A DL+ Sbjct: 119 MTEERKLGLVTKRRLGHDALGVMDGHLAERRFFVGDRFSVADIALYAYTHVAEEGGFDLS 178 Query: 186 ACPLLVAIDRRCA 198 P + A R A Sbjct: 179 GYPAVRAWMERVA 191 Lambda K H 0.324 0.138 0.433 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: 105 Number of extensions: 6 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: 213 Length of database: 202 Length adjustment: 21 Effective length of query: 192 Effective length of database: 181 Effective search space: 34752 Effective search space used: 34752 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.0 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.6 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