Align Methionine synthase component, B12 binding and B12-binding cap domains (EC:2.1.1.13) (characterized)
to candidate WP_010960817.1 MCA_RS07615 methionine synthase
Query= reanno::Phaeo:GFF1319 (233 letters) >NCBI__GCF_000008325.1:WP_010960817.1 Length = 1237 Score = 100 bits (250), Expect = 1e-25 Identities = 60/173 (34%), Positives = 95/173 (54%), Gaps = 6/173 (3%) Query: 26 LYDGLKEEIEESVNILLERGWAPYKVLTEALVGGMTIVGADFRDGILFVPEVLLAANAMK 85 L G+ E IE + P V+ L+ GM +VG F G +F+P+V+ +A MK Sbjct: 673 LVKGIDEFIEVDTEEARRQFERPLHVIEGPLMAGMNVVGDLFGAGKMFLPQVVKSARVMK 732 Query: 86 GGMAILKPLL----AETGAPRMGSMVIGTVKGDIHDIGKNLVSMMMEGAGFEVVDIGINN 141 +A L P + A T G +++ TVKGD+HDIGKN+V ++++ GFEV+D+G+ Sbjct: 733 KAVAYLMPYMDAEKAGTEVGTNGKILMATVKGDVHDIGKNIVGVVLQCNGFEVIDLGVMV 792 Query: 142 PVENYLEALEEHQPDILGMSALLTTTMPYMKVVIDTMIEQGKRDDYIVLVGGA 194 P + L+ E DI+G+S L+T ++ M V M G + +++GGA Sbjct: 793 PCDKILQTAREENVDIIGLSGLITPSLDEMVHVAREMERLG--FEIPLMIGGA 843 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: 629 Number of extensions: 38 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: 1237 Length adjustment: 35 Effective length of query: 198 Effective length of database: 1202 Effective search space: 237996 Effective search space used: 237996 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