Align glutamate mutase α subunit (EC 5.4.99.1) (characterized)
to candidate 207036 DVU1585 vitamin B12-dependent methionine synthase family protein
Query= metacyc::MONOMER-16253 (151 letters) >MicrobesOnline__882:207036 Length = 804 Score = 47.4 bits (111), Expect = 5e-10 Identities = 29/95 (30%), Positives = 44/95 (46%) Query: 1 MTGKYMPRTVILGVIGSDAHVVGITILEQALSAAGFEVINLGVQTAQDEFVSAAKSHDAE 60 M G + +I+ + D H +G I+ L GFEV++LG + V AA++H A Sbjct: 677 MRGAEVRPVIIMATVEGDIHDIGKNIVSLMLGNHGFEVVDLGKDVKAETIVDAAETHGAR 736 Query: 61 AVLVSSLYGHARQDCEGLHDELDDAGLDVLTYVGG 95 + +S+L E + GLDV VGG Sbjct: 737 IIGLSALMTTTMVRMEDTVKLVRARGLDVKVIVGG 771 Lambda K H 0.316 0.133 0.367 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: 227 Number of extensions: 17 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: 151 Length of database: 804 Length adjustment: 28 Effective length of query: 123 Effective length of database: 776 Effective search space: 95448 Effective search space used: 95448 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: 49 (23.5 bits)
This GapMind analysis is from Sep 17 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