Align Maleylacetoacetate isomerase; MAAI; EC 5.2.1.2 (uncharacterized)
to candidate YP_004143517.1 Mesci_4357 glutathione S-transferase
Query= curated2:P57109 (212 letters) >NCBI__GCF_000185905.1:YP_004143517.1 Length = 221 Score = 77.0 bits (188), Expect = 2e-19 Identities = 63/205 (30%), Positives = 93/205 (45%), Gaps = 16/205 (7%) Query: 1 MKLYTYYRSTSSYRVRIALALKGLDYQSLPVNLIRDGGEHRQPA-YLALNPQGRVPALQV 59 MKLY+ S S VR +K +P+ +I P + A++P R+P L Sbjct: 1 MKLYSRPLSPYSSIVRALAYIK-----DVPLKIIAPPPGFPIPEEFRAISPMNRIPVLIT 55 Query: 60 DEGELLIQSPAIIEYLEERYPQPALLSSDPLRRARERGVAALVGCDI-HPLHNASVLNLL 118 GE +++S I EYLEER+P+PALL D RA R A + D+ PL L+ + Sbjct: 56 GSGETIVESVVIAEYLEERFPEPALLPPDSKDRALVRMFARITDLDVLTPLMKLFELHSV 115 Query: 119 RQWGHDEEQVRQWIGHWVGQGLAAVEQLIGDQGWCFGDRPGLADVYLVPQLYAAERFGV- 177 + + E + H GLAA+E + + GD AD +L P + F Sbjct: 116 PKRNNAEIDAQFARLH---HGLAAIEARMAQGPFALGDDISFADAWLTPTRFIFNNFRAM 172 Query: 178 -----ALDAWPRIRRVADLAAAHPA 197 LDA+P+ +A+ HPA Sbjct: 173 TGRHDLLDAYPKFDAYQQIASQHPA 197 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: 134 Number of extensions: 8 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: 212 Length of database: 221 Length adjustment: 22 Effective length of query: 190 Effective length of database: 199 Effective search space: 37810 Effective search space used: 37810 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