Align Methionine synthase component, methyltransferase domain (EC:2.1.1.13) (characterized)
to candidate WP_013841580.1 DESRU_RS07875 5-methyltetrahydrofolate--homocysteine methyltransferase
Query= reanno::Phaeo:GFF1321 (338 letters) >NCBI__GCF_000215085.1:WP_013841580.1 Length = 799 Score = 179 bits (453), Expect = 3e-49 Identities = 107/283 (37%), Positives = 151/283 (53%), Gaps = 6/283 (2%) Query: 12 KDALLADGATGTNLFNMGLQSGDAPELWNVDEPKKITALYQGAVDAGSDLFLTNTFGGTA 71 ++ L+ DGA GT L GL +G PE WNV P+ I ++ + AG+D+ TNTFG Sbjct: 9 REILIVDGAMGTLLQERGLPAGWCPEEWNVSHPEVIKEVHGLYLRAGADIITTNTFGAIP 68 Query: 72 ARLKLHDAHRRVRELNVAGAELGRNVADRSERKIAVAGSVGPTGEIMQPVGELSHALAVE 131 +L+ +D RVRE N+A L R A VAGSVGP G+ +QP+G LS A + Sbjct: 69 LKLEEYDMPDRVREFNLAAGRLAREAA--KPFGAMVAGSVGPLGKFLQPLGTLSFDEAYQ 126 Query: 132 MFHEQAEALKEGGVDVLWLETISAPEEYRAA-AEAFKLADMPWCGTMSFDTAGRTMMGVT 190 F Q AL E VD++ ET E RAA A +P + +FD +GRT G Sbjct: 127 QFLVQCRALVEAEVDLILFETFGDIGEMRAALIAAADAGSVPVVASFTFDESGRTFTGTD 186 Query: 191 SADMAQLVEEFDPAPLAFGANCGTGASDILRTVLGFAAQGTTRPIISKGNAGIPKYVDGH 250 A + E A A G NC G L V+ + T P++ NAG+P+ V+G Sbjct: 187 PETAAVVAERLGVA--AVGVNCSVGPRQ-LEGVVRQLTRSTNLPVLISPNAGMPEIVEGR 243 Query: 251 IHYDGTPTLMGEYAAMARDCGAKIIGGCCGTMPDHLRAMREAL 293 + TP ++ +YAA D GA ++GGCCGT P+H++A+ +A+ Sbjct: 244 TVFRETPEVLADYAARFVDYGASLLGGCCGTTPEHIKAISQAV 286 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: 673 Number of extensions: 36 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: 799 Length adjustment: 35 Effective length of query: 303 Effective length of database: 764 Effective search space: 231492 Effective search space used: 231492 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