Align Methionine synthase component, methyltransferase domain (EC:2.1.1.13) (characterized)
to candidate WP_014449805.1 LFE_RS08455 5-methyltetrahydrofolate--homocysteine methyltransferase
Query= reanno::Phaeo:GFF1321 (338 letters) >NCBI__GCF_000284315.1:WP_014449805.1 Length = 828 Score = 163 bits (412), Expect = 2e-44 Identities = 99/284 (34%), Positives = 156/284 (54%), Gaps = 9/284 (3%) Query: 13 DALLADGATGTNLFNMGLQSGDAPELWNVDEPKKITALYQGAVDAGSDLFLTNTFGGTAA 72 + LL DG+ G L + GL +G AP+LWN+++P++I A++ V+AGSD+ LTNTFG + Sbjct: 11 EVLLLDGSMGALLQSRGLPAGYAPDLWNIEKPQEIQAVHTEYVNAGSDIILTNTFGASRL 70 Query: 73 RLKLHDAHRRVRELNVAGAELGRNVADRSERKIAVAGSVGPTGEIMQPVGELSHALAVEM 132 RL ++A R+RE+N +L + S K VAG +GP+G + P G+L A+ + Sbjct: 71 RLSEYNAQDRIREINFQAVDLAQRA---SRGKAYVAGDIGPSGTTIAPFGDLPFDDAIAI 127 Query: 133 FHEQAEALKEGGVDVLWLETISAPEEYRAAAEAFKLAD---MPWCGTMSFDTAGRTMMGV 189 F+EQA+ L E G D++ +ET+ +E RAA + A +P M+F+ G T G Sbjct: 128 FYEQAKLLLEAGADLIAIETMFDIQEMRAALIGVREATNGRIPLMALMTFNMDGITDSGS 187 Query: 190 TSADMAQLVEEFDPAPLAFGANCGTGASDILRTVLGFAAQGTTRPIISKGNAGIPKYVDG 249 A ++E F G NC G + + V+ Q T I + NAG+P + +G Sbjct: 188 DPETAASVLEGFGVD--IMGLNCSVG-PEAMVPVVSRLGQTTDTFIAVEPNAGLPVHRNG 244 Query: 250 HIHYDGTPTLMGEYAAMARDCGAKIIGGCCGTMPDHLRAMREAL 293 Y + ++A + GA IIGGCCGT P+++R + + + Sbjct: 245 ETLYLTGAEEVAKFAPSFVEAGANIIGGCCGTTPEYIRILAKTV 288 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: 712 Number of extensions: 39 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: 828 Length adjustment: 35 Effective length of query: 303 Effective length of database: 793 Effective search space: 240279 Effective search space used: 240279 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