Align Methionine synthase component, methyltransferase domain (EC:2.1.1.13) (characterized)
to candidate WP_013537367.1 THEAM_RS03095 homocysteine S-methyltransferase
Query= reanno::Phaeo:GFF1321 (338 letters) >NCBI__GCF_000185805.1:WP_013537367.1 Length = 841 Score = 178 bits (451), Expect = 5e-49 Identities = 106/278 (38%), Positives = 154/278 (55%), Gaps = 7/278 (2%) Query: 18 DGATGTNLFNMGLQSGDAPELWNVDEPKKITALYQGAVDAGSDLFLTNTFGGTAARLKLH 77 DG GT L G+ APEL NV++P+ + ++ V+AG+D+ TNTFG +L + Sbjct: 16 DGGMGTMLMAKGVDVNFAPELLNVEKPEVLKEIHSEYVEAGADIIETNTFGSNRIKLSHY 75 Query: 78 DAHRRVRELNVAGAELGRNVADRSERKIAVAGSVGPTGEIMQPVGELSHALAVEMFHEQA 137 RV+EL AG +L + A + VA SVGPTG +PVG+ + V++F EQ Sbjct: 76 GLENRVKELTAAGVKLAKEAA---RGRALVALSVGPTGVFAEPVGDYTFDELVDVFKEQI 132 Query: 138 EALKEGGVDVLWLETISAPEEYRAAAEAFK-LADMPWCGTMSFDTAGRTMMGVTSADMAQ 196 EA E G D++ +ET+S +E +AA A + + D+P +M++ GRT++G A Sbjct: 133 EAGAEAGADLVLIETMSDIKEAKAAVFAAREVCDLPVLVSMTYQEDGRTLLGTPPEVAAA 192 Query: 197 LVEEFDPAPLAFGANCGTGASDILRTVLGFAAQGTTRPIISKGNAGIPKYVDGHIHYDGT 256 + E F+ A A GANC G + ++ A TT PII NAG+P +G Y Sbjct: 193 VFEGFNVA--AVGANCSLGPESFVE-IIKRTASVTTTPIIVYANAGLPVLENGKTVYPEP 249 Query: 257 PTLMGEYAAMARDCGAKIIGGCCGTMPDHLRAMREALD 294 P +YA GA IIGGCCGT PDH+RA++ A++ Sbjct: 250 PETFEKYAVEFVKAGANIIGGCCGTTPDHIRAIKRAVE 287 Lambda K H 0.317 0.134 0.397 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: 774 Number of extensions: 44 Number of successful extensions: 4 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: 338 Length of database: 841 Length adjustment: 35 Effective length of query: 303 Effective length of database: 806 Effective search space: 244218 Effective search space used: 244218 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 (21.7 bits) S2: 52 (24.6 bits)
This GapMind analysis is from Apr 10 2024. The underlying query database was built on Apr 09 2024.
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