Align Methionine synthase component, methyltransferase domain (EC:2.1.1.13) (characterized)
to candidate 3607665 Dshi_1074 homocysteine S-methyltransferase (RefSeq)
Query= reanno::Phaeo:GFF1321 (338 letters) >FitnessBrowser__Dino:3607665 Length = 341 Score = 457 bits (1175), Expect = e-133 Identities = 231/333 (69%), Positives = 261/333 (78%), Gaps = 3/333 (0%) Query: 6 TTLLETKDALLADGATGTNLFNMGLQSGDAPELWNVDEPKKITALYQGAVDAGSDLFLTN 65 T LL + LL DGATGT LFNMGL SGDAPELWN D P +I ALYQGAVDAGSDLFLTN Sbjct: 7 TPLLAERGILLTDGATGTTLFNMGLSSGDAPELWNTDHPDRIAALYQGAVDAGSDLFLTN 66 Query: 66 TFGGTAARLKLHDAHRRVRELNVAGAELGRNVADRSERKIAVAGSVGPTGEIMQPVGELS 125 +FGG A+RLKLH A RVRELN AE+GR VAD+++RK+ VAGS+GPTGEIM P+G L+ Sbjct: 67 SFGGNASRLKLHAAQDRVRELNRLAAEIGRGVADKADRKVLVAGSMGPTGEIMAPMGPLT 126 Query: 126 HALAVEMFHEQAEALKEGGVDVLWLETISAPEEYRAAAEAFKLADMPWCGTMSFDTAGRT 185 H +AVEMFHEQAE LKEGG D+LW+ETISAPEEY AAAEA ADMPWCGTMSFDTAGRT Sbjct: 127 HDIAVEMFHEQAEGLKEGGADILWVETISAPEEYAAAAEAAARADMPWCGTMSFDTAGRT 186 Query: 186 MMGVTSADMAQLVEEFDPAPLAFGANCGTGASDILRTVLGFAAQGTTRPIISKGNAGIPK 245 MMG TSA MA++VE+ P+AFGANCG GASD+LRTVLGFAA GT RPII+KGNAGIPK Sbjct: 187 MMGTTSATMARMVEKLAHPPVAFGANCGVGASDLLRTVLGFAAAGTERPIIAKGNAGIPK 246 Query: 246 YVDGHIHYDGTPTLMGEYAAMARDCGAKIIGGCCGTMPDHLRAMREALDTRPRG-EQLTL 304 YVDGHIHYDGTP LM +YA +AR GA +IGGCCGT +HLR MR ALD + +L Sbjct: 247 YVDGHIHYDGTPDLMAQYAILARASGASVIGGCCGTTFEHLRHMRAALDASAADMPRPSL 306 Query: 305 ERIVEVLGPFTSDSDGT--GEDTAPDRRSRRGR 335 + I E LG F+S +DGT G DR RR R Sbjct: 307 DEITEALGGFSSAADGTEAGGPKPADRPRRRRR 339 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: 481 Number of extensions: 18 Number of successful extensions: 2 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: 341 Length adjustment: 28 Effective length of query: 310 Effective length of database: 313 Effective search space: 97030 Effective search space used: 97030 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 09 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