Align Methionine synthase component, methyltransferase domain (EC:2.1.1.13) (characterized)
to candidate WP_092057476.1 BQ4888_RS11910 5-methyltetrahydrofolate--homocysteine methyltransferase
Query= reanno::Phaeo:GFF1321 (338 letters) >NCBI__GCF_900111775.1:WP_092057476.1 Length = 799 Score = 197 bits (500), Expect = 1e-54 Identities = 111/286 (38%), Positives = 164/286 (57%), Gaps = 7/286 (2%) Query: 12 KDALLADGATGTNLFNMGLQSGDAPELWNVDEPKKITALYQGAVDAGSDLFLTNTFGGTA 71 + L+ DGA GT L GLQ+G +PE N++ P + +++ +AG+D+ ++NTFGG+ Sbjct: 10 EQVLVLDGAMGTMLQERGLQAGASPEAMNLEAPAVVEGVHRAYAEAGADILVSNTFGGSR 69 Query: 72 ARLKLHDAHRRVRELNVAGAELGRNVADRSERKIAVAGSVGPTGEIMQPVGELSHALAVE 131 ++L + RV E+N AG E+ R A + VA S+GPTG +QPVG+ VE Sbjct: 70 SKLAHYGLEGRVAEINRAGVEIVRRAAGSGQ---FVAASIGPTGRFLQPVGDAGFDEMVE 126 Query: 132 MFHEQAEALKEGGVDVLWLETISAPEEYRAAAEAFK-LADMPWCGTMSFDTAGRTMMGVT 190 +F EQ +A GG D++ +ET E RAA A + + +P M+FD AGRT++G Sbjct: 127 IFGEQVQAFVAGGADLISMETFLDVRELRAAVIACREFSKLPIIAQMTFDDAGRTVLGTP 186 Query: 191 SADMAQLVEEFDPAPLAFGANCGTGASDILRTVLGFAAQGTTRPIISKGNAGIPKYVDGH 250 A ++ + G+NCG G I +L T+RP+I++ NAG+P+ VDG Sbjct: 187 PEAAAVTLDALGADVI--GSNCGLGIDGIY-AILEKMRTVTSRPLIAQANAGLPQLVDGQ 243 Query: 251 IHYDGTPTLMGEYAAMARDCGAKIIGGCCGTMPDHLRAMREALDTR 296 + GTP M Y GA++IGGCCGT P H+RA+R+ALD R Sbjct: 244 TVFPGTPEEMTAYHDRLIALGARVIGGCCGTTPAHIRAIRDALDGR 289 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: 706 Number of extensions: 50 Number of successful extensions: 5 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