Align Methionine synthase component, B12 binding and B12-binding cap domains (EC:2.1.1.13) (characterized)
to candidate 8499710 DvMF_0476 homocysteine S-methyltransferase (RefSeq)
Query= reanno::Phaeo:GFF1319 (233 letters) >FitnessBrowser__Miya:8499710 Length = 818 Score = 127 bits (319), Expect = 7e-34 Identities = 71/184 (38%), Positives = 113/184 (61%), Gaps = 3/184 (1%) Query: 42 LERGWAPYKVLTEALVGGMTIVGADFRDGILFVPEVLLAANAMKGGMAILKPLL-AETGA 100 L G P+ ++ E L+ G+T VG + F+P+++ +A M+ L+PLL A+ G Sbjct: 634 LSEGADPFSLVQEKLIPGITEVGRRYERREYFLPQLIRSAETMQHAFRKLQPLLEAQRGH 693 Query: 101 PRMGSMVIGTVKGDIHDIGKNLVSMMMEGAGFEVVDIGINNPVENYLEALEEHQPDILGM 160 +++ TV+GDIHDIGKN+V++M+ GF+VVD+G + + +EA E H ++G+ Sbjct: 694 EARPVIIMATVEGDIHDIGKNIVTLMLGNHGFDVVDLGKDVKAADIVEAAERHGARVIGL 753 Query: 161 SALLTTTMPYMKVVIDTMIEQGKRDDYIVLVGGAPLNEEFGKAIGADGYCRDAAVAVEMA 220 SAL+TTTM M+ + + E+G V+VGGA + + +AIGADGY DA AV +A Sbjct: 754 SALMTTTMVRMEDTVRLVRERGL--PVKVMVGGAVVTPAYAEAIGADGYSADAVEAVRVA 811 Query: 221 KDFV 224 K+ + Sbjct: 812 KELL 815 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: 434 Number of extensions: 23 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: 818 Length adjustment: 32 Effective length of query: 201 Effective length of database: 786 Effective search space: 157986 Effective search space used: 157986 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 09 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