Align methylmalonyl-CoA mutase (subunit 1/2) (EC 5.4.99.2) (characterized)
to candidate WP_036136159.1 N800_RS06475 methionine synthase
Query= BRENDA::A4YIE3 (155 letters) >NCBI__GCF_000768355.1:WP_036136159.1 Length = 895 Score = 47.0 bits (110), Expect = 8e-10 Identities = 27/88 (30%), Positives = 49/88 (55%), Gaps = 1/88 (1%) Query: 22 KVVVAKLGLDGHDRGAKVIARALKDAGMEVVYTGLRQTPEQIVRTAIQEDADVIGISILS 81 K+V+A + D HD G ++ L EV+ G+ + I+ A++E+AD++G+S L Sbjct: 418 KIVMATVKGDVHDIGKNIVGVVLACNNFEVIDLGVMVPAQTILDAAVRENADLVGLSGLI 477 Query: 82 GAHLELMPKIVEALKKAGLDDVGLVLGG 109 LE M + +++ GL + L++GG Sbjct: 478 TPSLEEMSHVAREMQRQGL-SMPLMIGG 504 Lambda K H 0.319 0.140 0.382 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: 286 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: 155 Length of database: 895 Length adjustment: 29 Effective length of query: 126 Effective length of database: 866 Effective search space: 109116 Effective search space used: 109116 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 (21.7 bits) S2: 49 (23.5 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