Align Methionine synthase component, methyltransferase domain (EC:2.1.1.13) (characterized)
to candidate YP_426618.1 Rru_A1531 methionine synthase (B12-dependent)
Query= reanno::Phaeo:GFF1321 (338 letters) >NCBI__GCF_000013085.1:YP_426618.1 Length = 1182 Score = 127 bits (319), Expect = 1e-33 Identities = 94/303 (31%), Positives = 141/303 (46%), Gaps = 20/303 (6%) Query: 15 LLADGATGTNLFNMGLQ-SGD------APELWNVDEPKKITALYQGAVDAGSDLFLTNTF 67 LL DG G+ + M L GD E+ N+ P + ++ AG+D TNTF Sbjct: 13 LLCDGGMGSLVQAMDLSVDGDFMGRENCTEVLNLSRPDVVRDIHTRYFAAGADCVETNTF 72 Query: 68 GGTAARLKLHDAHRRVRELNVAGAELGRNVAD--RSERKIAVAGSVGPTGEIMQPVGELS 125 GG+ L D R RE+N AE+ R A+ R V GS+GP G + +G + Sbjct: 73 GGSTLTLAEFDLADRTREINRRAAEIAREAAESFADGRDRFVLGSIGP-GTKLPSLGHID 131 Query: 126 HALAVEMFHEQAEALKEGGVDVLWLETISAPEEYRAAAEAFKLA------DMPWCGTMSF 179 + + Q E L EGG D + +ET P +++AA A K A D ++ Sbjct: 132 YDTLKDAITVQCEGLIEGGADAILVETCQDPLQFKAAINAAKAARLALGSDTAILLQVTV 191 Query: 180 DTAGRTMMGVTSADMAQLVEEFDPAPLAFGANCGTGASDILRTVLGFAAQGTTRPIISKG 239 +T G ++G A A + L G NC TG ++ V + + I + Sbjct: 192 ETTGTLLVGADIAAAATVAHALGVDSL--GLNCATGPQEMSEHV-RWLKENWPGLISLQP 248 Query: 240 NAGIPKYVDGHIHYDGTPTLMGE-YAAMARDCGAKIIGGCCGTMPDHLRAMREALDTRPR 298 NAG+P+ +DG HY TP + + + R+ G +IGGCCGT PDH+ A+ L+T + Sbjct: 249 NAGLPELLDGKTHYPLTPAELADWHGRFIREDGVNLIGGCCGTTPDHIAAVNAMLETLGQ 308 Query: 299 GEQ 301 G + Sbjct: 309 GRR 311 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: 925 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: 1182 Length adjustment: 37 Effective length of query: 301 Effective length of database: 1145 Effective search space: 344645 Effective search space used: 344645 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: 54 (25.4 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