Align Methionine synthase component, B12 binding and B12-binding cap domains (EC:2.1.1.13) (characterized)
to candidate WP_028583363.1 G494_RS0103145 5-methyltetrahydrofolate--homocysteine methyltransferase
Query= reanno::Phaeo:GFF1319 (233 letters) >NCBI__GCF_000429965.1:WP_028583363.1 Length = 816 Score = 107 bits (266), Expect = 9e-28 Identities = 66/209 (31%), Positives = 111/209 (53%), Gaps = 9/209 (4%) Query: 20 QQMFDDLYDGLKEEIEESVNILLERGWAPYKVLTEALVGGMTIVGADFRDGILFVPEVLL 79 +Q+F + +G K+E+ + + +L+ER +AP ++ + LV M VG F G + +P VL Sbjct: 318 EQLFLQVVNGNKDEVGDVLPVLMER-FAPLDIINQILVPAMRHVGELFGKGEILLPFVLQ 376 Query: 80 AANAMKGGMAILKPLLAETGAPRMGSMVIGTVKGDIHDIGKNLVSMMMEGAGFEVVDIGI 139 +A MK ++ L+P + +++ TV+GD+HDIGKNLV +++ G+ V +IGI Sbjct: 377 SAEVMKRAVSFLEPFMERIEDEHTTRILLATVQGDVHDIGKNLVDIILSNNGYTVYNIGI 436 Query: 140 NNPVENYLEALEEHQPDILGMSALLTTTMPYMKVVIDTMIEQGKRDDYIVLVGGAPLNEE 199 E +E E +PD++G+S LL + M+ + E G D +L+GGA L + Sbjct: 437 KVGAETIIEKARELKPDLIGLSGLLVKSAIVMQESMAQYREAGL--DIPILLGGAALTPK 494 Query: 200 FGKAI------GADGYCRDAAVAVEMAKD 222 F G YC DA + ++ Sbjct: 495 FVAESCVPNYGGPVVYCSDAFAGLRAVRE 523 Lambda K H 0.318 0.138 0.390 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: 390 Number of extensions: 18 Number of successful extensions: 2 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: 233 Length of database: 816 Length adjustment: 32 Effective length of query: 201 Effective length of database: 784 Effective search space: 157584 Effective search space used: 157584 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: 51 (24.3 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