Align Maleylacetoacetate isomerase; MAAI; EC 5.2.1.2 (uncharacterized)
to candidate WP_012334543.1 M446_RS23200 glutathione S-transferase
Query= curated2:P57109 (212 letters) >NCBI__GCF_000019365.1:WP_012334543.1 Length = 211 Score = 56.6 bits (135), Expect = 3e-13 Identities = 63/205 (30%), Positives = 91/205 (44%), Gaps = 22/205 (10%) Query: 5 TYYRS--TSSYRVRIALALKGLDYQSLPVNLIRDGGEHRQPAYLALNPQGRVPALQVDEG 62 T Y S T S + L G Y +N+ GE+RQPAYLA+NP G+VPA++ G Sbjct: 7 TLYHSPNTRSSSALLLLEELGAPYDLQVLNM--KAGENRQPAYLAVNPMGKVPAIR-HRG 63 Query: 63 ELLIQSPAIIEYLEERYPQPALLSS--DPLRRARERGVAALVGCDIHPLHNASVLNLLRQ 120 L+ + A+ YL + +P+ L + DPLR R + G P +V++ R Sbjct: 64 ALVTEQVAVFLYLADAFPEAGLAPAIGDPLRGPYLRWM-VYYGSSFEP----AVVDKARG 118 Query: 121 WGHDEEQVRQWIGHWVGQ-GLAAVEQLIGDQGWCFGDRPGLADVYLVPQLYAAERFGVAL 179 D E VR + + + LA V + + G+R AD+ L FG Sbjct: 119 LASD-ESVRAMLPYGSYEAALAVVNDQLRQGPYLLGERFTAADILWGAALTWTTMFGFVP 177 Query: 180 DAWPRIRRVADLAAAHPAFRQAHPA 204 + P I AA+ A QA PA Sbjct: 178 ET-PEI-------AAYVARHQARPA 194 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: 163 Number of extensions: 11 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: 211 Length adjustment: 21 Effective length of query: 191 Effective length of database: 190 Effective search space: 36290 Effective search space used: 36290 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