Align Maleylacetoacetate isomerase; MAAI; EC 5.2.1.2 (uncharacterized)
to candidate WP_011386296.1 AMB_RS19950 glutathione S-transferase family protein
Query= curated2:P57109 (212 letters) >NCBI__GCF_000009985.1:WP_011386296.1 Length = 223 Score = 64.7 bits (156), Expect = 1e-15 Identities = 66/218 (30%), Positives = 95/218 (43%), Gaps = 18/218 (8%) Query: 3 LYTYYRSTSSYRVRIALALKGLDYQSLPVNLIRDGGEHRQPAYLALNPQGRVPALQVDEG 62 LY + S VRI LA K LD++ I E R+P +LALNP G +P L ++G Sbjct: 4 LYHHPLCPFSRLVRIVLAEKKLDFEPQ----IEKTWE-RRPEFLALNPAGVLPVLVEEDG 58 Query: 63 ELLIQSPAIIEYLEERYPQPALLSSDPLRRARERGVAALVGCDIHP-----LHNASVLNL 117 L + AI+EYLEE + LL ++PL RA R + A G H L V Sbjct: 59 AALADATAIVEYLEETSRETPLLPAEPLARAEVRRLVAWFGQKFHAEVTDHLVGEKVFKR 118 Query: 118 LRQWGH--DEEQVRQWIGHWVGQGLAAVEQLIGDQGWCFGDRPGLADVYLVPQLYAAERF 175 L + D ++R G+ + + L + L G+ G LAD+ Q+ A + Sbjct: 119 LESGRNEPDSRRIRAGFGN-IHRHLDYLGTLTERHGYLAGGAFTLADIAAAAQISAVDYL 177 Query: 176 GVALDAWPRIRRVADLAA---AHPAFRQAHPANQPDTP 210 G W + D A + P+FR + P P Sbjct: 178 GDV--PWDQHAPAKDWYARVKSRPSFRVLLADHLPGLP 213 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: 144 Number of extensions: 10 Number of successful extensions: 1 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: 223 Length adjustment: 22 Effective length of query: 190 Effective length of database: 201 Effective search space: 38190 Effective search space used: 38190 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 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