Align Methionine synthase component, B12 binding and B12-binding cap domains (EC:2.1.1.13) (characterized)
to candidate WP_012101348.1 CKL_RS04800 homocysteine methyltransferase
Query= reanno::Phaeo:GFF1319 (233 letters) >NCBI__GCF_000016505.1:WP_012101348.1 Length = 801 Score = 126 bits (316), Expect = 1e-33 Identities = 72/214 (33%), Positives = 129/214 (60%), Gaps = 9/214 (4%) Query: 11 ADLNDEDLVQQMFDDLYDGLKEEIEESVNILLERGWAPYKVLTEALVGGMTIVGADFRDG 70 AD N +DL Q + D G+++E E LL+ A +++ ++ + VG + Sbjct: 591 ADNNLKDLKQLIID----GIEDEAEAMTTELLKNKKA-LEIVNSYIIPALDEVGKQYELQ 645 Query: 71 ILFVPEVLLAANAMKGGMAILKPLLAETGAPRM--GSMVIGTVKGDIHDIGKNLVSMMME 128 +F+P+++ +A +K I+K + +G + G++V+ TVKGDIHDIGKN+V +++E Sbjct: 646 DIFLPQLIQSAETVKKSFEIIKDNMLSSGQKSLEKGTIVLATVKGDIHDIGKNIVKVLLE 705 Query: 129 GAGFEVVDIGINNPVENYLEALEEHQPDILGMSALLTTTMPYMKVVIDTMIEQGKRDDYI 188 GFEV+D+G + ++N + + ++ ++G+SAL+TTT+ MK I+ + E + Sbjct: 706 NYGFEVIDLGRDVDIDNIVNTIRDNNIKLVGLSALMTTTVASMKKTIEAIRENNL--NCK 763 Query: 189 VLVGGAPLNEEFGKAIGADGYCRDAAVAVEMAKD 222 ++VGGA LN+ + IGAD Y +DA AV++A++ Sbjct: 764 IVVGGAVLNQNYADMIGADYYAKDAREAVKIAEE 797 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: 447 Number of extensions: 26 Number of successful extensions: 3 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: 801 Length adjustment: 32 Effective length of query: 201 Effective length of database: 769 Effective search space: 154569 Effective search space used: 154569 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