Align Probable maleylacetoacetate isomerase; MAAI; EC 5.2.1.2 (uncharacterized)
to candidate WP_019867502.1 METMI_RS0117000 hypothetical protein
Query= curated2:Q9KSB2 (215 letters) >NCBI__GCF_000384075.1:WP_019867502.1 Length = 201 Score = 77.0 bits (188), Expect = 2e-19 Identities = 61/203 (30%), Positives = 100/203 (49%), Gaps = 15/203 (7%) Query: 4 LILYGYWRSSAAYRVRIALNIKQLVYESRAVHLSREGGEQHH--AEFHRLNPSELIPVLI 61 L LY + S A+++R+ L++ L YE AV+ G E+ H AEF +NP +PVL+ Sbjct: 2 LKLYEFAVSGNAHKIRLMLSLLGLEYEGIAVN----GSEKQHKSAEFLAMNPFGQVPVLL 57 Query: 62 DGELCLNQSLAIIEYLDETYPAPRLIPERGAERYQVKALALDIAADI-HPINNLRILQYL 120 DG+LCL S AI+ YL Y +P+ A QV A A ++ + LR+ Sbjct: 58 DGDLCLRDSNAILVYLARQYGDAHWLPDEPAAMAQVMAWLATAANELAWGPSRLRVHYQF 117 Query: 121 TAKLGVADEEKNRWYRHWIDKGFQGLEEKLRHTAGEYCVGNRLSLVDVCLVPQVYNAERF 180 ++ VA E + H + LE +L + ++ L++ D+ + P + A Sbjct: 118 GREINVA--ESGQITTHLL----HVLESQLAES--DWLALGHLTIADIAIYPYIALAPEG 169 Query: 181 DLDMSRYPTLQQIAARLRALPAF 203 +D+S YP + R++ALP + Sbjct: 170 KIDLSVYPAIIAWQRRIQALPGY 192 Lambda K H 0.322 0.137 0.416 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: 108 Number of extensions: 6 Number of successful extensions: 2 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: 215 Length of database: 201 Length adjustment: 21 Effective length of query: 194 Effective length of database: 180 Effective search space: 34920 Effective search space used: 34920 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