Align Maleylacetoacetate isomerase; MAAI; EC 5.2.1.2 (uncharacterized)
to candidate WP_011842692.1 RSPH17029_RS19405 glutathione S-transferase N-terminal domain-containing protein
Query= curated2:Q9X4F7 (213 letters) >NCBI__GCF_000015985.1:WP_011842692.1 Length = 232 Score = 46.6 bits (109), Expect = 4e-10 Identities = 60/192 (31%), Positives = 86/192 (44%), Gaps = 15/192 (7%) Query: 28 EAYRSVPVDLLAK-AHRAPEHLARNPQGLVPVLDIDGERLTQSLAIIEYLAETRDGTGLL 86 EA V+LL + A PEHLAR P G VPVL +DG + +S A + +AE + LL Sbjct: 33 EAELPYEVELLPQGAQETPEHLARQPFGQVPVLTLDGRSMFESGACVWRIAERSE--RLL 90 Query: 87 PAHPIDRQRVRALSYAVAMDIH-PVCNLGVVARV-----MAGAGDGEAAR--REWMQKFI 138 P P R + A + P+ +G++ G D EA R + + Sbjct: 91 PRDPGLRDSCLSWVIAALNTLEPPIMMMGMLWFFERWPDTFGLEDREAPGKVRGPARGML 150 Query: 139 GEGLAAFERMLDHPATGAFCHGDRPTMADLCLVPQVYNARRWDVDLAACPLLVAIDRRCA 198 + LA F R L T GD T+ADL L + A + D+ L A P + A R + Sbjct: 151 DKRLAQFGRALAGRET---IVGDGFTVADLMLTCVLLPAAQMDL-LGAHPEVKAYYDRHS 206 Query: 199 GIDAFQRAHPDR 210 F++A D+ Sbjct: 207 ARPGFRKAQADQ 218 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: 130 Number of extensions: 5 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: 213 Length of database: 232 Length adjustment: 22 Effective length of query: 191 Effective length of database: 210 Effective search space: 40110 Effective search space used: 40110 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 Apr 10 2024. 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