Align Maleylacetoacetate isomerase; MAAI; EC 5.2.1.2 (uncharacterized)
to candidate WP_012756561.1 RLEG_RS04470 glutathione S-transferase family protein
Query= curated2:P57109 (212 letters) >NCBI__GCF_000023185.1:WP_012756561.1 Length = 206 Score = 62.4 bits (150), Expect = 6e-15 Identities = 50/164 (30%), Positives = 77/164 (46%), Gaps = 9/164 (5%) Query: 6 YYRSTSSYRVRIALALKGLDYQSLPVNLIRDGGEHRQPAYLALNPQGRVPALQVDEGELL 65 Y T + IAL GL ++ ++L RDG E R P YL +NP+GRVPAL D G +L Sbjct: 6 YAPGTCALASLIALEESGLAFEVKKISL-RDG-EQRSPDYLKINPKGRVPALVTDYG-VL 62 Query: 66 IQSPAIIEYLEERYPQPALLS-SDPLRRARERGVAALVGCDIHPLHNASVLNLLRQWGHD 124 ++PAI+ Y+ + P L DP AR + + + +H H +W + Sbjct: 63 TETPAILAYIAQSAPAAKLAPLDDPFEFARLQSFNSYICSTVHVNHAHRPRG--SRWADE 120 Query: 125 E---EQVRQWIGHWVGQGLAAVEQLIGDQGWCFGDRPGLADVYL 165 E ++ + + +EQ + + W G+ LAD YL Sbjct: 121 PAAIEAMKAKVPQNMVDCFTLIEQTMFEGPWVMGEAYSLADPYL 164 Lambda K H 0.321 0.138 0.434 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: 142 Number of extensions: 8 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: 212 Length of database: 206 Length adjustment: 21 Effective length of query: 191 Effective length of database: 185 Effective search space: 35335 Effective search space used: 35335 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 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