Align Methionine synthase component, methyltransferase domain (EC:2.1.1.13) (characterized)
to candidate YP_004142560.1 Mesci_3387 homocysteine S-methyltransferase
Query= reanno::Phaeo:GFF1321 (338 letters) >NCBI__GCF_000185905.1:YP_004142560.1 Length = 345 Score = 337 bits (864), Expect = 3e-97 Identities = 179/336 (53%), Positives = 223/336 (66%), Gaps = 2/336 (0%) Query: 2 TNTFTTLLETKDALLADGATGTNLFNMGLQSGDAPELWNVDEPKKITALYQGAVDAGSDL 61 TN LL K LLADGATGTNLF MGL++G+APEL N P IT+L+Q VDAG+D+ Sbjct: 9 TNPIDALLAEKGVLLADGATGTNLFAMGLEAGEAPELLNETAPDTITSLHQNFVDAGADI 68 Query: 62 FLTNTFGGTAARLKLHDAHRRVRELNVAGAELGRNVADRSERKIAVAGSVGPTGEIMQPV 121 LTN+FGGT RLKLH A RV LN AE+ R VADR+ RK+ VAGSVGPTGE++ P+ Sbjct: 69 ILTNSFGGTRHRLKLHHAQDRVHALNQRAAEIARAVADRAGRKVIVAGSVGPTGELLVPL 128 Query: 122 GELSHALAVEMFHEQAEALKEGGVDVLWLETISAPEEYRAAAEAFKLADMPWCGTMSFDT 181 G +++ AV+ F EQ E LKEGG +V W+ET+SAP+E RAAAEA +P+ T SFDT Sbjct: 129 GAMTYDEAVDAFAEQIEGLKEGGAEVAWIETMSAPDEIRAAAEAAIRVGLPYTYTGSFDT 188 Query: 182 AGRTMMGVTSADMAQLVEEFDPAPLAFGANCGTGASDILRTVLGFAAQGTTRPIISKGNA 241 AGRTMMG+ D+ + + APL GANCG GASDIL ++L +I KGN Sbjct: 189 AGRTMMGLLPRDIHGVTDGLSAAPLGVGANCGVGASDILASLLDMTEAKPEATVIVKGNC 248 Query: 242 GIPKYVDGHIHYDGTPTLMGEYAAMARDCGAKIIGGCCGTMPDHLRAMREALDTRPRGEQ 301 GIP++ IHY GTP LM +Y +A D GAKIIGGCCGT HL AMR+ALD + ++ Sbjct: 249 GIPEFRGTEIHYSGTPELMADYVRLAVDGGAKIIGGCCGTSFQHLAAMRKALDAHTKADR 308 Query: 302 LTLERIVEVLGPFTSDSDGTGEDTAPDRRSRRGRRR 337 T+ IVE +GP + E+TA +RR RRR Sbjct: 309 PTVAAIVERIGPMRNKV--ATENTAETSEARRERRR 342 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: 412 Number of extensions: 16 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: 345 Length adjustment: 29 Effective length of query: 309 Effective length of database: 316 Effective search space: 97644 Effective search space used: 97644 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