Align Methionine synthase component, B12 binding and B12-binding cap domains (EC:2.1.1.13) (characterized)
to candidate WP_019557234.1 F612_RS0107950 methionine synthase
Query= reanno::Phaeo:GFF1319 (233 letters) >NCBI__GCF_000381085.1:WP_019557234.1 Length = 1241 Score = 105 bits (261), Expect = 5e-27 Identities = 62/164 (37%), Positives = 98/164 (59%), Gaps = 7/164 (4%) Query: 34 IEESVNILLERGWAPYKVLTEALVGGMTIVGADFRDGILFVPEVLLAANAMKGGMAILKP 93 +E++ LE G AP V+ L+ GM +VG F G +F+P+V+ +A MK +A L P Sbjct: 677 VEDTEEARLELG-APINVIEGPLMDGMNVVGDLFGAGKMFLPQVVKSARVMKRAVAYLDP 735 Query: 94 LLA---ETGAPRMGSMVIGTVKGDIHDIGKNLVSMMMEGAGFEVVDIGINNPVENYLEAL 150 LA TG R G +V+ TVKGD+HDIGKN+V ++++ F+V+D+G+ P E L+ Sbjct: 736 FLAAAKSTGQAR-GKIVMATVKGDVHDIGKNIVGVVLQCNNFDVIDLGVMVPAEKILDTA 794 Query: 151 EEHQPDILGMSALLTTTMPYMKVVIDTMIEQGKRDDYIVLVGGA 194 +++G+S L+T ++ M V M E+G + +L+GGA Sbjct: 795 IAENANVIGLSGLITPSLEEMVNVAKLMKERGM--NLPLLIGGA 836 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: 640 Number of extensions: 36 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 233 Length of database: 1241 Length adjustment: 35 Effective length of query: 198 Effective length of database: 1206 Effective search space: 238788 Effective search space used: 238788 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