Align Methionine synthase component, methyltransferase domain (EC:2.1.1.13) (characterized)
to candidate WP_011337253.1 RSPH17029_RS04065 betaine--homocysteine S-methyltransferase
Query= reanno::Phaeo:GFF1321 (338 letters) >NCBI__GCF_000015985.1:WP_011337253.1 Length = 335 Score = 467 bits (1201), Expect = e-136 Identities = 230/335 (68%), Positives = 269/335 (80%), Gaps = 1/335 (0%) Query: 1 MTNTFTTLLETKDALLADGATGTNLFNMGLQSGDAPELWNVDEPKKITALYQGAVDAGSD 60 MT+ + LL T+D L+ADGATGTNLFNMGL SG+ PELW VD P I +LY+ AV+AGSD Sbjct: 1 MTDALSRLLRTRDWLMADGATGTNLFNMGLSSGEPPELWTVDRPDNIRSLYRAAVEAGSD 60 Query: 61 LFLTNTFGGTAARLKLHDAHRRVRELNVAGAELGRNVADRSERKIAVAGSVGPTGEIMQP 120 +FLTN+FGG AARLKLH+A RV ELN AELGR VAD + R + VAGS+GPTGEI +P Sbjct: 61 IFLTNSFGGNAARLKLHEAQGRVGELNRIAAELGREVADAAGRPVVVAGSMGPTGEIFEP 120 Query: 121 VGELSHALAVEMFHEQAEALKEGGVDVLWLETISAPEEYRAAAEAFKLADMPWCGTMSFD 180 +G L+H +AVE+FHEQAEALK GG DVLW+ETISA EE++AAAEA +LA MPWCGTMSFD Sbjct: 121 MGTLTHRMAVEIFHEQAEALKAGGADVLWVETISAAEEFKAAAEAARLAGMPWCGTMSFD 180 Query: 181 TAGRTMMGVTSADMAQLVEEFDPAPLAFGANCGTGASDILRTVLGFAAQGTTRPIISKGN 240 TAGRTMMG+T+A + LV + PLAFGANCG GASD+LRTVLGFAAQG PII+KGN Sbjct: 181 TAGRTMMGITAAALVDLVTKLPNPPLAFGANCGVGASDLLRTVLGFAAQGIEVPIIAKGN 240 Query: 241 AGIPKYVDGHIHYDGTPTLMGEYAAMARDCGAKIIGGCCGTMPDHLRAMREALDTRPRGE 300 AGIPKY DGHIHYDGTP LM EYA +ARD GA+IIGGCCGTMP+HL+AMR AL+ RPRG Sbjct: 241 AGIPKYHDGHIHYDGTPELMAEYAVLARDAGARIIGGCCGTMPEHLKAMRAALEGRPRGP 300 Query: 301 QLTLERIVEVLGPFTSDSDGTGEDTAPDRRSRRGR 335 + +LE I E LG F+S SDG+ +D P R RR R Sbjct: 301 RPSLETISETLGGFSSASDGS-DDAGPTRERRRRR 334 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: 446 Number of extensions: 14 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: 335 Length adjustment: 28 Effective length of query: 310 Effective length of database: 307 Effective search space: 95170 Effective search space used: 95170 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 16 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