Align Maleylacetoacetate isomerase; MAAI; EC 5.2.1.2 (uncharacterized)
to candidate WP_011159866.1 TX73_RS22080 glutathione S-transferase family protein
Query= curated2:Q9X4F7 (213 letters) >NCBI__GCF_000195775.1:WP_011159866.1 Length = 217 Score = 84.3 bits (207), Expect = 2e-21 Identities = 63/191 (32%), Positives = 93/191 (48%), Gaps = 6/191 (3%) Query: 7 LYDYWRSSASYRVRIALNLCGEAYRSVPVDLLAKAHRAPEHLARNPQGLVPVLD-IDGER 65 LY RS SY+VR+AL L YR+V VD+L R P+ LA+NP G VP+L+ G Sbjct: 4 LYSMQRSGNSYKVRLALALLDAPYRAVEVDILRGESRTPDFLAKNPSGQVPLLETAPGRY 63 Query: 66 LTQSLAIIEYLAETRDGTGLLPAHPIDRQRVRALSYAVAMDIHPVCNLGVVARVMAGAGD 125 L +S AI+ YLA GT L P +DR + + P N+G + Sbjct: 64 LAESNAILWYLAV---GTSLAPDTRMDRAEALQWMFFEQHALEP--NIGSAYFWLCLVKG 118 Query: 126 GEAARREWMQKFIGEGLAAFERMLDHPATGAFCHGDRPTMADLCLVPQVYNARRWDVDLA 185 G + ++ ++ G AA + M +H T + + T+AD+ L + A + D DL+ Sbjct: 119 GRDLQTHALEDWLERGYAALQVMENHLKTNDYFAAGQLTIADIALYGYTHVADQCDFDLS 178 Query: 186 ACPLLVAIDRR 196 P + A RR Sbjct: 179 TFPAVNAWLRR 189 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: 101 Number of extensions: 7 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: 213 Length of database: 217 Length adjustment: 22 Effective length of query: 191 Effective length of database: 195 Effective search space: 37245 Effective search space used: 37245 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 24 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