Align Methionine synthase component, methyltransferase domain (EC:2.1.1.13) (characterized)
to candidate YP_001327441.1 Smed_1771 methionine synthase I
Query= reanno::Phaeo:GFF1321 (338 letters) >NCBI__GCF_000017145.1:YP_001327441.1 Length = 337 Score = 339 bits (870), Expect = 5e-98 Identities = 175/326 (53%), Positives = 222/326 (68%), Gaps = 1/326 (0%) Query: 8 LLETKDALLADGATGTNLFNMGLQSGDAPELWNVDEPKKITALYQGAVDAGSDLFLTNTF 67 LL K LLADGATGT+LF MGL++G+APE+WN +P+ IT L+Q VDAG+D+ LTN+F Sbjct: 11 LLAQKGVLLADGATGTSLFAMGLEAGEAPEIWNETKPENITKLHQDFVDAGADIILTNSF 70 Query: 68 GGTAARLKLHDAHRRVRELNVAGAELGRNVADRSERKIAVAGSVGPTGEIMQPVGELSHA 127 GGT RLKLH A RV +LN AE+ R VAD++ RK+ AGSVGPTGE++ P+G LS+ Sbjct: 71 GGTRHRLKLHQAEDRVHQLNKRAAEIARAVADKAPRKVITAGSVGPTGELLIPLGALSYE 130 Query: 128 LAVEMFHEQAEALKEGGVDVLWLETISAPEEYRAAAEAFKLADMPWCGTMSFDTAGRTMM 187 AV F EQ E LK GG +V W+ET+S+ +E RAAAEA +P+ T SFDTAG+TMM Sbjct: 131 DAVAAFVEQIEGLKAGGAEVAWIETMSSADEIRAAAEAAVKVGLPYVYTGSFDTAGKTMM 190 Query: 188 GVTSADMAQLVEEFDPAPLAFGANCGTGASDILRTVLGFAAQGTTRPIISKGNAGIPKYV 247 G+ D+ + + P+A GANCG GASDIL ++L A+ I+ KGN GIP++ Sbjct: 191 GLHPKDIHGVAADIGEGPVAVGANCGVGASDILSSLLDMTAESPDATIVVKGNCGIPEFR 250 Query: 248 DGHIHYDGTPTLMGEYAAMARDCGAKIIGGCCGTMPDHLRAMREALDTRPRGEQLTLERI 307 IHY GTP LM EYA +A D GA+IIGGCCGT +HL AMR A+D +GE+ TLE I Sbjct: 251 GSEIHYSGTPPLMAEYARLAMDAGARIIGGCCGTSCNHLAAMRLAIDNHIKGERPTLETI 310 Query: 308 VEVLGPFTSDSDGTGEDTAPDRRSRR 333 VE +GP + S G AP R RR Sbjct: 311 VEKIGPLRNKSANEG-PAAPARERRR 335 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: 408 Number of extensions: 22 Number of successful extensions: 1 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: 337 Length adjustment: 28 Effective length of query: 310 Effective length of database: 309 Effective search space: 95790 Effective search space used: 95790 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: 49 (23.5 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