Align methylmalonyl-CoA epimerase (EC 5.1.99.1) (characterized)
to candidate WP_036834967.1 N784_RS11140 VOC family protein
Query= metacyc::MONOMER-17285 (139 letters) >NCBI__GCF_000775615.1:WP_036834967.1 Length = 142 Score = 79.3 bits (194), Expect = 2e-20 Identities = 46/128 (35%), Positives = 72/128 (56%), Gaps = 4/128 (3%) Query: 5 IDHIGLVVADLDAAIDFYRTAYDVTEWERI--ELPERHALIGVARFGDVLIELIAPTSDQ 62 +DHIG+ V DL +IDFY T +R E + I + EL+APT++ Sbjct: 5 LDHIGVAVRDLQGSIDFYERVLGATLVDRYRSEAEGVESEIAIMDIQGARTELLAPTNNT 64 Query: 63 AS-FARFLREKGPGMHHIAYRVDDIYAALATLQARGLPLIDREPRPGIHDTLVAFVHPKA 121 S ARFL++KG G+HH+AY+VDD+ ALA L+ +G+ + R H + +++P A Sbjct: 65 TSPIARFLKQKGKGVHHVAYQVDDLDEALAQLERQGVRTLPHTLRTNKHGRRLIYLNP-A 123 Query: 122 GGQGVLVE 129 +G ++E Sbjct: 124 DTEGTIIE 131 Lambda K H 0.326 0.142 0.432 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: 4 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: 139 Length of database: 142 Length adjustment: 15 Effective length of query: 124 Effective length of database: 127 Effective search space: 15748 Effective search space used: 15748 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: 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