Align Methionine synthase component, methyltransferase domain (EC:2.1.1.13) (characterized)
to candidate WP_015943058.1 DHAF_RS04225 homocysteine S-methyltransferase
Query= reanno::Phaeo:GFF1321 (338 letters) >NCBI__GCF_000021925.1:WP_015943058.1 Length = 285 Score = 142 bits (359), Expect = 8e-39 Identities = 93/288 (32%), Positives = 147/288 (51%), Gaps = 11/288 (3%) Query: 8 LLETKDALLADGATGTNLFNMGLQSGDAPELWNVDEPKKITALYQGAVDAGSDLFLTNTF 67 +L+ ++ DGA GT L L G PE+ N+ P+ I +++ + AGS++ TNTF Sbjct: 2 ILDKDSYVIFDGAMGTMLQKYDLAPGQPPEVLNITRPEVIEEVHRKYIKAGSNIITTNTF 61 Query: 68 GGTAARLKLHDAHRRVRELNVAGAELGRNVADRSERKIAVAGSVGPTGEIMQPVGELSHA 127 G A KL+ V E+ + + R A ++ VA VGPTGE+++P+G+LS Sbjct: 62 G--AIETKLNGTGYSVEEVVQSAIAIARRAAGKN----LVALDVGPTGELIEPLGDLSFE 115 Query: 128 LAVEMFHEQAEALK-EGGVDVLWLETISAPEEYRAAAEAFK-LADMPWCGTMSFDTAGRT 185 +++ Q +A G VD++ +ET E AA A K + +P T +F GRT Sbjct: 116 EVYDLYACQIKAAALTGNVDLVLIETFFDLTEAHAAIRAAKDHSSLPVICTFTFQQKGRT 175 Query: 186 MMGVTSADMAQLVEEFDPAPLAFGANCGTGASDILRTVLGFAAQGTTRPIISKGNAGIPK 245 +MG + +EE+ A G NC G ++L +++ T PI+ + NAG+PK Sbjct: 176 LMGKDIKTVVTSLEEYGVD--AVGVNCSLGPGEML-SIVETMVSSTQLPILVQPNAGLPK 232 Query: 246 YVDGHIHYDGTPTLMGEYAAMARDCGAKIIGGCCGTMPDHLRAMREAL 293 + YD P Y + + G K GGCCGT P+ + A++E+L Sbjct: 233 LIGDRTVYDVEPEEFARYIQVMANLGVKWFGGCCGTTPEFISAIKESL 280 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: 268 Number of extensions: 21 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: 285 Length adjustment: 27 Effective length of query: 311 Effective length of database: 258 Effective search space: 80238 Effective search space used: 80238 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: 48 (23.1 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