Align Methionine synthase component, B12 binding and B12-binding cap domains (EC:2.1.1.13) (characterized)
to candidate 207036 DVU1585 vitamin B12-dependent methionine synthase family protein
Query= reanno::Phaeo:GFF1319 (233 letters) >MicrobesOnline__882:207036 Length = 804 Score = 128 bits (321), Expect = 4e-34 Identities = 76/198 (38%), Positives = 115/198 (58%), Gaps = 3/198 (1%) Query: 29 GLKEEIEESVNILLERGWAPYKVLTEALVGGMTIVGADFRDGILFVPEVLLAANAMKGGM 88 G ++ + V L G P+ ++ L+ + VG + F+P+++ +A M+ Sbjct: 608 GDRDGVTAIVESELAAGADPFDLVQTKLIPAINEVGVKYERREYFLPQLIRSAETMQTAF 667 Query: 89 AILKPLLAET-GAPRMGSMVIGTVKGDIHDIGKNLVSMMMEGAGFEVVDIGINNPVENYL 147 L+PLL E GA +++ TV+GDIHDIGKN+VS+M+ GFEVVD+G + E + Sbjct: 668 RRLQPLLEEMRGAEVRPVIIMATVEGDIHDIGKNIVSLMLGNHGFEVVDLGKDVKAETIV 727 Query: 148 EALEEHQPDILGMSALLTTTMPYMKVVIDTMIEQGKRDDYIVLVGGAPLNEEFGKAIGAD 207 +A E H I+G+SAL+TTTM M+ + + +G D V+VGGA + + F AIGAD Sbjct: 728 DAAETHGARIIGLSALMTTTMVRMEDTVKLVRARGL--DVKVIVGGAVVTKAFADAIGAD 785 Query: 208 GYCRDAAVAVEMAKDFVA 225 GY DA AV +AK +A Sbjct: 786 GYSADAVEAVRLAKSLLA 803 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: 431 Number of extensions: 25 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: 804 Length adjustment: 32 Effective length of query: 201 Effective length of database: 772 Effective search space: 155172 Effective search space used: 155172 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