Align Methionine synthase component, methyltransferase domain (EC:2.1.1.13) (characterized)
to candidate WP_011735322.1 PPRO_RS07025 5-methyltetrahydrofolate--homocysteine methyltransferase
Query= reanno::Phaeo:GFF1321 (338 letters) >NCBI__GCF_000015045.1:WP_011735322.1 Length = 806 Score = 178 bits (451), Expect = 5e-49 Identities = 107/284 (37%), Positives = 159/284 (55%), Gaps = 8/284 (2%) Query: 15 LLADGATGTNLFNMGLQSGDAPELWNVDEPKKITALYQGAVDAGSDLFLTNTFGGTAARL 74 L+ DGA GT L GL+ G +PE N+ P + ++++ ++AG+D+ +TN+FGG+ +L Sbjct: 13 LILDGAMGTMLQERGLRPGQSPEELNLTMPDVVASVHREYIEAGADIIITNSFGGSRFKL 72 Query: 75 KLHDAHRRVRELNVAGAELGRNVADRSERKIAVAGSVGPTGEIMQPVGELSHALAVEMFH 134 R+ E+N E+ R A + V GS+GPTG+ ++P+GE+S E F Sbjct: 73 AHFGLEGRLAEINARAVEIARGEA---RGRAYVGGSMGPTGQFVEPLGEVSFDRMKESFR 129 Query: 135 EQAEALKEGGVDVLWLETISAPEEYRAAAEAFKLAD--MPWCGTMSFDTAGRTMMGVTSA 192 EQAEAL GVD++ LET +E RAA A + +P M+FD GR+++G T Sbjct: 130 EQAEALVSAGVDLISLETFLDIKECRAAVIAIREVSPTIPIIAMMTFDDNGRSVLG-TPP 188 Query: 193 DMAQLVEEFDPAPLAFGANCGTGASDILRTVLGFAAQGTTRPIISKGNAGIPKYVDGHIH 252 + A + + G+NCG G I +L + T+ P+IS+ NAG+P DG Sbjct: 189 EAAAITLAAAGVDIV-GSNCGLGVEGI-HDILVRMRRVTSLPLISQANAGLPILKDGITV 246 Query: 253 YDGTPTLMGEYAAMARDCGAKIIGGCCGTMPDHLRAMREALDTR 296 + GTP M +Y G ++IGGCCGT P H+RAM+EAL R Sbjct: 247 FPGTPREMTDYHDRLISLGVRVIGGCCGTTPAHIRAMKEALAGR 290 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: 670 Number of extensions: 32 Number of successful extensions: 3 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: 806 Length adjustment: 35 Effective length of query: 303 Effective length of database: 771 Effective search space: 233613 Effective search space used: 233613 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