Align Methionine synthase component, methyltransferase domain (EC:2.1.1.13) (characterized)
to candidate WP_078718028.1 B5D49_RS12400 methionine synthase
Query= reanno::Phaeo:GFF1321 (338 letters) >NCBI__GCF_900167125.1:WP_078718028.1 Length = 806 Score = 125 bits (315), Expect = 3e-33 Identities = 90/287 (31%), Positives = 139/287 (48%), Gaps = 12/287 (4%) Query: 5 FTTLLETKDALLADGATGTNLFNMGLQSGDAPELWNVDEPKKITALYQGAVDAGSDLFLT 64 F LL+ DG GT L GL G +PEL+ + P + +++ + AG+ + T Sbjct: 4 FRKLLKDDQVRFFDGGYGTLLQQRGLPPGMSPELFGLKSPDAVLQVHRDYLAAGAQVLTT 63 Query: 65 NTFGGTAARLKLHDAHRRVRELNVAGAELGRNVADRSERKIAVAGSVGPTGEIMQPVGEL 124 NTFGG+ +L V +LN A L R A + VA S+GPTG +P+GEL Sbjct: 64 NTFGGSRFKL---GPDADVYDLNKAMCTLARKAAGDN---AFVAASIGPTGHFCEPLGEL 117 Query: 125 SHALAVEMFHEQAEALKEGGVDVLWLETISAPEEYRAAAEAFK-LADMPWCGTMSFDTAG 183 + V+ + EQ + +GG D++ ET E RA A + + D+P +M+F+ A Sbjct: 118 TFRELVQAYKEQIQGCVDGGADLILGETHFDLAEARAVVIATREVCDLPVAVSMTFEGA- 176 Query: 184 RTMMGVTSADMAQLVEEFDPAPLAFGANCGTGASDILRTVLGFAAQGTTRPIISKGNAGI 243 ++ G T ++ +A NC G I V + +T P+ NAG+ Sbjct: 177 NSLTGTTPLHFIDTMQNMGVDMVA--TNCSAGPEQIADVVRAMLPRLST-PLYVAANAGL 233 Query: 244 PKY-VDGHIHYDGTPTLMGEYAAMARDCGAKIIGGCCGTMPDHLRAM 289 P+ +G+ + P + + D GAK +GGCCGT PDH+RA+ Sbjct: 234 PELDENGNTVFRLGPDDFAKQSTRFFDMGAKFVGGCCGTGPDHIRAL 280 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: 728 Number of extensions: 43 Number of successful extensions: 4 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: 806 Length adjustment: 35 Effective length of query: 303 Effective length of database: 771 Effective search space: 233613 Effective search space used: 233613 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