Align Methionine synthase component, methyltransferase domain (EC:2.1.1.13) (characterized)
to candidate WP_077243567.1 B1A74_RS01430 methionine synthase
Query= reanno::Phaeo:GFF1321 (338 letters) >NCBI__GCF_001995255.1:WP_077243567.1 Length = 1263 Score = 112 bits (279), Expect = 7e-29 Identities = 94/285 (32%), Positives = 138/285 (48%), Gaps = 33/285 (11%) Query: 37 ELWNVDEPKKITALYQGAVDAGSDLFLTNTFGGTAARLKLHDAHRR--VRELNVAGAELG 94 +L ++ P I ++ ++AG+D+ NTF GT R+ + D H V ELN A+L Sbjct: 54 DLLSLTRPDIIEQIHNDYLEAGADIIEANTFNGT--RIAMADYHMEDLVPELNRESAKLA 111 Query: 95 RNVADRSERKIA-----VAGSVGPTGEIMQPVGELSHALA--------VEMFHEQAEALK 141 R AD K VAG +GPT +++ A V + E AEAL Sbjct: 112 RKAADAWTAKTPDKPRFVAGILGPTNRTASISPDVNDPGARNVDFDTLVAAYKEAAEALI 171 Query: 142 EGGVDVLWLETISAPEEYRAAAEAFKLA------DMPWC--GTMSFDTAGRTMMGVTSAD 193 EGGVD+L +ET+ +AA A K D+P GT++ D +GRT+ G T+ Sbjct: 172 EGGVDLLLIETVFDTLNAKAAIFAVKTLEDELGKDLPIMISGTIT-DASGRTLSGQTTEA 230 Query: 194 MAQLVEEFDPAPLAFGANCGTGASDILRTVLGFAAQGTTRPIISKGNAGIPKYVDGHIHY 253 V +P ++ G NC GA ++ + V + T + + NAG+P Y Sbjct: 231 FWNSVRHANP--VSIGLNCALGAKEMRQYVEELSRIADTH-VSAHPNAGLPNEFGD---Y 284 Query: 254 DGTPTLMG-EYAAMARDCGAKIIGGCCGTMPDHLRAMREALDTRP 297 D +P M + A IIGGCCGT+P+H+RAMREA++ P Sbjct: 285 DESPEQMAADVGPWAEQGMLNIIGGCCGTLPEHIRAMREAVEKFP 329 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: 974 Number of extensions: 57 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: 1263 Length adjustment: 38 Effective length of query: 300 Effective length of database: 1225 Effective search space: 367500 Effective search space used: 367500 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 Jul 25 2024. The underlying query database was built on Jul 25 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