Align Maleylacetoacetate isomerase; MAAI; EC 5.2.1.2 (uncharacterized)
to candidate WP_086511196.1 BZY95_RS17610 glutathione S-transferase
Query= curated2:Q9X4F7 (213 letters) >NCBI__GCF_002151265.1:WP_086511196.1 Length = 204 Score = 74.3 bits (181), Expect = 1e-18 Identities = 69/206 (33%), Positives = 97/206 (47%), Gaps = 18/206 (8%) Query: 7 LYDYWRSSASYRVRIALNLCGEAYRSVPVDLLAKAHRAPEHLARNPQGLVPVLDIDGERL 66 LY + S ++R + L+L G + + VDL A AH+ PE LA N G VPVLD +G + Sbjct: 3 LYHFPLSGHAHRAALFLSLAGVEHELIEVDLAAGAHKQPEFLALNAFGEVPVLDDNGTVI 62 Query: 67 TQSLAIIEYLAETRDGTGLLPAHPIDRQRV-RALSYAVAMDIHPVCNLGVVARVMAGAGD 125 SLAI+ Y+A + LP P D +V R LS A + C AR++ G Sbjct: 63 ADSLAILVYVARKIGPSHWLPTEPADEAQVQRWLSVAAGKIAYGAC----AARLITVFGA 118 Query: 126 GEAARREWMQKFIGEG---LAAFERMLDHPATGAFCHGDRPTMADLCLVPQVYNARRWDV 182 A ++ IG LA E+ L+ +PT+AD+ L V A +V Sbjct: 119 PFRA-----EEVIGRAHATLAVMEQTLE--GQRWIAGTAQPTIADVALYSYVERAPEGNV 171 Query: 183 DLAACPLLVAIDR---RCAGIDAFQR 205 DL++ P + A R R G FQR Sbjct: 172 DLSSYPSVRAWLRQIERLPGFVPFQR 197 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: 114 Number of extensions: 6 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: 204 Length adjustment: 21 Effective length of query: 192 Effective length of database: 183 Effective search space: 35136 Effective search space used: 35136 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