Align Methionine synthase component, methyltransferase domain (EC:2.1.1.13) (characterized)
to candidate WP_044137191.1 TERY_RS05005 methionine synthase
Query= reanno::Phaeo:GFF1321 (338 letters) >NCBI__GCF_000014265.1:WP_044137191.1 Length = 1196 Score = 120 bits (300), Expect = 2e-31 Identities = 89/302 (29%), Positives = 146/302 (48%), Gaps = 22/302 (7%) Query: 12 KDALLADGATGTNLFNMGLQSGD--------APELWNVDEPKKITALYQGAVDAGSDLFL 63 + ++ DGA GT+L L + D E +P + +++ + AG+D+ Sbjct: 14 RPVIVFDGAMGTSLQVQNLTAEDFGGKEYEGCNEYLVHTKPDAVAKVHRDFLAAGADVIE 73 Query: 64 TNTFGGTAARLKLHDAHRRVRELNVAGAELGRNVA---DRSERKIAVAGSVGPTGEIMQP 120 T+TFGGT L +D + LN AEL ++ A E+ VAGS+GP G + Sbjct: 74 TDTFGGTKIVLAEYDLADQAYYLNKTAAELAKSAAAEYSTPEKPRFVAGSIGP-GTKLPT 132 Query: 121 VGELSHALAVEMFHEQAEALKEGGVDVLWLETISAPEEYRAAAEAF-----KLADM-PWC 174 +G + A + F EQAE L +GGVD+ +ET + +AA K D P Sbjct: 133 LGHIDFATLKDSFTEQAEGLFDGGVDLFLVETCQDVLQIKAALNGIEEIFAKKGDRRPIM 192 Query: 175 GTMSFDTAGRTMMGVTSADMAQLVEEFDPAPLAFGANCGTGASDILRTVLGFAAQGTTRP 234 +++ ++ G ++G ++E + L G NC TG D+++ + + ++ + Sbjct: 193 VSVTMESFGTMLVGSEINAALTILEPYSIDIL--GLNCATGP-DLMKEHIRYLSENSPFI 249 Query: 235 IISKGNAGIPKYVDGHIHYDGTPT-LMGEYAAMARDCGAKIIGGCCGTMPDHLRAMREAL 293 + NAG+P+ + G HY TP L D G ++IGGCCGT PDH++A+ E Sbjct: 250 VSCIPNAGLPENIGGQAHYKLTPVELKMALMHFVEDLGVQVIGGCCGTRPDHIKALAEIT 309 Query: 294 DT 295 +T Sbjct: 310 ET 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: 913 Number of extensions: 54 Number of successful extensions: 6 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 338 Length of database: 1196 Length adjustment: 38 Effective length of query: 300 Effective length of database: 1158 Effective search space: 347400 Effective search space used: 347400 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