Align Methylmalonyl-CoA epimerase; DL-methylmalonyl-CoA racemase; EC 5.1.99.1 (characterized)
to candidate WP_028323007.1 H567_RS0121800 hypothetical protein
Query= SwissProt::O58010 (136 letters) >NCBI__GCF_000422285.1:WP_028323007.1 Length = 141 Score = 89.4 bits (220), Expect = 2e-23 Identities = 48/131 (36%), Positives = 80/131 (61%), Gaps = 5/131 (3%) Query: 6 KRIDHVGIAVKNLEEAIKIWE---GLGFKVEEIEEVPDQKVKVAVIKVGENRIELLEATT 62 ++IDH+ AVK+L++ +I++ GL E + E +K+KVA +GE +E +E+T Sbjct: 4 EKIDHICFAVKDLDDVKRIYQDDFGLTPACEYVAE--SEKIKVARYYIGEVAVEFMESTA 61 Query: 63 EDSPIAKFIEKRGEGIHHLAIRVENIESKLEELKQKGYKLIDEKPRVGAGGAKIAFIHPK 122 D +AKFI+++GEG ++ +V+++ + ELK+K +LID+KPR G HP Sbjct: 62 PDGEVAKFIDRQGEGFFLISYKVDDLPKAMAELKEKNVRLIDDKPRELLGNRYAFVHHPN 121 Query: 123 SVTGVLLELCE 133 + GVL EL + Sbjct: 122 KLHGVLTELLD 132 Lambda K H 0.317 0.138 0.389 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: 68 Number of extensions: 5 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: 136 Length of database: 141 Length adjustment: 15 Effective length of query: 121 Effective length of database: 126 Effective search space: 15246 Effective search space used: 15246 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 42 (20.8 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