Align Methionine synthase component, B12 binding and B12-binding cap domains (EC:2.1.1.13) (characterized)
to candidate WP_092057476.1 BQ4888_RS11910 5-methyltetrahydrofolate--homocysteine methyltransferase
Query= reanno::Phaeo:GFF1319 (233 letters) >NCBI__GCF_900111775.1:WP_092057476.1 Length = 799 Score = 144 bits (363), Expect = 5e-39 Identities = 79/199 (39%), Positives = 119/199 (59%), Gaps = 2/199 (1%) Query: 28 DGLKEEIEESVNILLERGWAPYKVLTEALVGGMTIVGADFRDGILFVPEVLLAANAMKGG 87 +G K+ I V L G +P ++ E L+ G+ VG F +F+P+V+L+A M+ Sbjct: 603 EGDKDGIVALVERALGEGLSPLQISNEGLLSGLEEVGRRFGRNQIFLPQVMLSAETMQAA 662 Query: 88 MAILKPLLAETGAPRMGSMVIGTVKGDIHDIGKNLVSMMMEGAGFEVVDIGINNPVENYL 147 A LK L A +G +++ TV+GDIHDIGKN+V ++E GFEV+D+G N P L Sbjct: 663 FARLKQELRGDAAQSLGKILMATVEGDIHDIGKNIVCTLLENHGFEVIDLGKNVPAARIL 722 Query: 148 EALEEHQPDILGMSALLTTTMPYMKVVIDTMIEQGKRDDYIVLVGGAPLNEEFGKAIGAD 207 +A ++HQ D +G+SAL+TTT+ M+VV+ + G + +VGGA + +++ AIGAD Sbjct: 723 DAAQKHQVDAVGLSALMTTTLQQMEVVLGQLRAAGIK--VFTMVGGAVVTQDYADAIGAD 780 Query: 208 GYCRDAAVAVEMAKDFVAR 226 Y DA AV K +AR Sbjct: 781 LYAADALEAVAKVKALLAR 799 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: 442 Number of extensions: 26 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: 799 Length adjustment: 32 Effective length of query: 201 Effective length of database: 767 Effective search space: 154167 Effective search space used: 154167 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