Align Maleylacetoacetate isomerase (EC 5.2.1.2) (characterized)
to candidate 203766 SO4697 glutathione S-transferase (NCBI ptt file)
Query= reanno::pseudo3_N2E3:AO353_15560 (211 letters) >FitnessBrowser__MR1:203766 Length = 215 Score = 50.1 bits (118), Expect = 3e-11 Identities = 58/181 (32%), Positives = 81/181 (44%), Gaps = 10/181 (5%) Query: 1 MELFTYYRSTSSFRVRIALALKGLEYQALPINLIAPQGGEHQQPAYLHINPQGRVPALRT 60 MELF + S S +V IAL K + +L P + Q Y P G++P L+T Sbjct: 1 MELFYHPLSRYSQKVLIALYEKQANFYPRITDLRDPLARKAFQQFY----PSGKLPLLKT 56 Query: 61 DEGELLIQSPAIIEYLEERYPQ-VPLLSKDLARRAHERGVAALIGCDI-HPLHNVSVLNQ 118 EG+LL +S IIEYL+ + LL + R R LI DI +PL + L Sbjct: 57 QEGQLLPESSIIIEYLDTHFQNGTELLPAEAERNLAVRLFDRLIDFDINNPLFQLEKLKY 116 Query: 119 LRQLGHDEPQVVHWIGHWITQGLAAVEHLIGDEGYCFGNAPGLADVYLIPQL-YAAERFN 177 + GH E ++ Q HL + C G++ LAD LIP L Y+ N Sbjct: 117 TPE-GH-EFEIKQLEKQMFAQFQRLDSHLRQNHWVC-GDSFTLADCALIPCLSYSFAHLN 173 Query: 178 I 178 + Sbjct: 174 L 174 Lambda K H 0.322 0.139 0.427 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: 107 Number of extensions: 7 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: 211 Length of database: 215 Length adjustment: 22 Effective length of query: 189 Effective length of database: 193 Effective search space: 36477 Effective search space used: 36477 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